Given a phylip alignment file, and assuming the reference is in the top line of the alignment, this will calculate the start and stop (both gapped and ungapped) of all other sequences in the alignment relative to the reference
Your phylip file should look something like the following, with the reference sequence in the top row of the file. Names can conform to "relaxed phylip" standards (e.g. longer than 10 characters) as long as they are separated from the associated sequence by a space
11731 1861
AY188350.1 ATGGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTGGAACGCATTGATATCACCGGAGCTTGCTCCACTGATATTAATGAGTCGCGAACGGG-TGA-GTAACGCGTAGGTAACCTGCCTG-ATAG-CGGGGG-ATAACTATTGGAAACGAT-AGCTAA-T-A--CCGC-ATGAGAG-TGTT-TAAC-A-CA-TG-T-TAG---AGACT-TAAAAGAT---ACCATTG--TATCAC---TATCAGATGGACCTGCGTTGTATTAGCTAGTTGGTAGGG-TAGCGG-CCTACCAAGGCACC-GATACATAGCCGA-CCT-GA-GAGGG-TGATCGGCCA-CACTGGG-A-CTG-AGACACGG-CCCA-GA-CTCC-TACGGG-AGGCAGC-AGTAGGG-AATC-TT-CG--G-C-AATGGACGA-AA-G-TC-T-GACCGA-GCAA-CG-CCG-CG-TGA-GT-G-A-A-G-AA-GGT-T-T-T-C-G--G-A-TCG-TAAAG-C-TCT-GTT-G-TA-G-C-G-GA-AG-AA---C-GC-G--TG---TA-AG----A-GTG-G-AA-A-GT-T-T-A-C-AC-AG---T-GAC-GGTACGC-T-A-C-C-A-G-AAA-G-GG-AC-GG--C-T-AAC-TA-CGT-G-C-C-A-G-C-A-G-CC-GC-G-GT-AA-TACGTAGG-TC-C-C-GA--GCGTT-G-TCCGGAT-TT-ATT-GGG-CGT-AAA-GGGAGCGCA-GGCGGTT-T-AGT-AA-GTCT--GAAGTTAAA-GGCAT-TGG--CTCAACC-AA-TG-TA-T-GCTTTGGAAA-CTGTTAGA-C-TTGAGTGCAGAAGGGG-AGAG-TGGAATTCCATGTGTAG-C-GGTGAAATGC-GTA-GATATATGGAGGAACACCGGTGGCGAA-A-GCGGCTCT-CTGGTCTG--TCACTGACGCTG-AGGCTCGAAA-GCG-TGGGT-A-GCGAAC-AGGATTAG-ATACCC-T-GGT-AGTCCA-CGCCGTAAACGATGAGTGCTAGGTGTTAGGTCCTTTCCGGGACTTAGTGCCGCAGCTAACGCAATAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAG-C-GGT-GGAGC-ATGTGG-TTT-AATTCGAAGCAACGCG-AA-GAACCTTACCAGG-TCTTGACAT--CC-CGAT-G-CCCGCT-CT-AG-AGATAGA-G-TTTTAC-----TTCTTGAAC-ATCG-G-A-G-ACAGGTGGTGCATGGTTGTCGTC-AGCTCGTGTC-GTGAGATGTTGGGTTAA-GTCCCGCAACGAGCGC-AACCC-TTAT-TGTT-A-GTTG-CCATC-A--T-T--GA-GTT--GGGCAC-TCTAGCGAGAC-TGCCG--GTAA-TAAA-C-CG-G-AGG-AAGGTGGGG-ATG-ACGTCAAA-TCATCA-TGCCCC-TT-A-TGACCT-GGGCT-ACACACGTGCTACAATGGT-TGGTACAAC-G-AGTCGCAAG-CCGGTGACGGCAA-GC-TAA--TCTC-TGAAA-G-CCA-ATCTC-AGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGTCGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGG-TGAATACGTTCCC-GGGCCTT-GTACACACCGCCC-GTCACACCACGAG-AGTT-TGTA-AC-ACCCAAAGTCGG-TGAGG-TAACCT--TATA---G--GAGCCAGCCGCCTAAGGTGGGA-CAGATGATT-GGG--G-TG-AAG-TCGTAACAAGGTAGC-CGTATCGGAAGGTGCGGCTGGATCA
Ex5155;_(reversed) ----------------------------------------------------------------------------------------------------------GTGCGA-CGGG-TGA-GTAACACGTGGGTAACCTACCTA-TAAG-ACTGGG-ATAACTCCGGGAAACCGG-GGCTAA-T-A--CCGG-ATAATAC-ATGA-AACC-G-CA-TG-G-TTA---TGA---TAGAAGACGGT---TTTG-CTGTCAC---TTATAGATGGACCCGCGGCGTATTAGCTAGTTGGTAAGG-TAACGG-CTTACCAAGGCAAC-GATACGTAGC-GA-CCT-GA-GAGGG-TGATCGGCCG-CACTGGA-A-CTG-AGACACGG-TCCA-GA-CTCC-TACGGG-AGGCAGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex11616;_(reversed) ----------------------------------------------------------------------------------------------------------GTGCGA-CGGG-TGA-GTAACACGTGGGTAACCTACCTA-TAAG-ACTGGG-ATAACTCCGGGAAACCGG-GGCTAA-T-A--CCGG-ATAATAC-ATGA-AACC-G-CA-TG-G-TTT---ATGAT-GAAAGACGGTT---TTGC--TGTCAC---TTATAGATGGACCCGCGGCGTATTAGCTAGTTGGTAAGG-TAACGG-CTTACCAAGGCAAC-GATACGTAGCCGA-CCT-GA-GAGGG-TGATCGGCCA-CACTGGA-A-CTG-AGACACGG-TCCA-GA-CTCC-TACGGG-AGGCAGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex5111; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--T-CTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GACGAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex5898; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex3182; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex7478; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--T-CTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCAGCAT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex10372; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAACACGTGGGTAACCTGCCCT-ATAG-TCTGGG-ATACCTTTTGGAAACAGA-AGCTAA-T-A--CCGG-ATAATAA-CTTT-AGTC-G-CA-TG-ACTAA---AGTTT-GAAAGGCGGCG---AAAG-CTGTCGC---TAAAGGATGGACCTGCGTTGCATTAGCTAGTTGGTAAGG-TAACGG-CTTACCAAGGCGAT-GATGCATAGCCGA-GTT-GA-GAGAC-TGA-CGCCGC-CATGGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex7281;_(reversed) -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAACGCGTAGGTAACCTGCCTG-GTAG-CGGGGG-ATAACTATTGGAAACGAT-AGCTAA-T-A--CCGC-ATAACAG-CAGC-CGAC-A-CA-TG-T-TAG---CTGTT-TGAAAGGAGCA---ATTG--CTTCAC---TACCAGATGGACCTGCGTTGTATTAGCTAGTTGGTGAGG-TAACGG-CTCACCAAGGCAAC-GATACATAGC-GA-CCT-GA-GAGGG-TGATCGGCCA-CACTGGG-A-CTG-AGACACGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex3800; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAACACGTGGGTAACCTACCTA-TAAG-ACTGGA-ATAACTCCGGGAAACCGG-GGCTAA-T-G--CCGG-ATAATAC-ACAG-AACT-G-CA-TG-G-TTC---TGTGA-TGAAAGACGGT---TTTG-CTGTCAC---TTATAGATGGACCCGCGGCGTATTAGCTAGTTGGTAAAG-TAACGG-CTTACCAAGGCAAC-GATACGTAGCCGA-CCT-GA-GAGGG-TGATCGGCCA-CACTGGA-A-CTG-AGACGCGG-TCCA-GA-CTCC-TACG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex638; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex4636; -----------------------------------------------------------------------------------------------------------GGCGCACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex5581; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG-A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex2655; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAACATATTGG-AACATACCGA-GTAG-AGGGGG-ATAACTATCCGAAAGGAT-AGCTAA-T-A--CCGC-ATATACT-ATCA-GTAG-G-AA-AG-C-AGG---GGATC-GCAAGACC------------TTGCGC---TACTTGAGTGGCCAATATCTGATTAGCTAGTTGGTGGGG-TAAGGG-CCTACCAAGGCAAC-GATCAGTAGCGGG-TCT-GA-GAGGA-CGATCCGCCA-CACTGGG-A-CTG-AGACACGG-CCCA-GA-CTCC-TACGGG-AG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex5774; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG-AGGC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex11237; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG-AGGC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex155; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--T-CTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG-AGGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex410; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGTCTGGGAAAC-TGCCCG-ATGG-AGGGGG-ATAACTACTGGAAACGGT-AGCTAA-T-A--CCGC-ATAACGT-CGCA-AGAC-C-AA-AG-A-GGG---GGACC-TTAGGGCCTC------------TTGC---CATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGG-TAAAGG-CTCACCTAGGCGAC-GATCCCTAGCTGG-TCT-GA-GAGGA-TGACCAGCCA-CACTGGA-A-CTG-AGACACGG-TCCA-GA-CTCC-TACGGG-AGGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex451; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGGGTGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG-AGGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex1613; -----------------------------------------------------------------------------------------------------------GGCG-ACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAGGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG-AGGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex2239;_(reversed) -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAACACGTGGGTAACCTGCCCT-ATAG-TCTGGG-ATACCTTTTGGAAACAGA-AGCTAA-T-A--CCGG-ATAATAA-CTTT-AGTC-G-CA-TG-ACTAA---AGTTT-GAAAGGCGGCG---AAAG-CTGTCGC---TAAAGGATGGACCTGCGTTGCATTAGCTAGTTGGTAAGG-TAACGG-CTTACCAAGGCGAT-GATGCATAGCCGA-GTT-GA-GAGAC-TGATCGGCCA-CATTGGG-A-CTG-AGACACGG-CCCA-AA-CTCC-TACGGG-AGGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex4379; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG-AGGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex8385;_(reversed) -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAACGCGTAGGTAACCTGCCTG-GTAG-CGGGGG-ATAACTATTGGAAACGAT-AGCTAA-T-A--CCGC-ATAACAG-CAGC-CGAC-A-CA-TG-T-TAG---CTGTT-TGAAAGGAGCA---ATTG--CTTCAC---TACCAGATGGACCTGCGTTGTATTAGCTAGTTGGTGAGG-TAACGG-CTCACCAAGGCAAC-GATACATAGCCGA-CCT-GA-GAGGG-TGATCGGCCA-CACTGGG-A-CTG-AGACACGG-CCCA-GA-CTCC-TACGGG-AGGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex777; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG-AGGCAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Ex1924; -----------------------------------------------------------------------------------------------------------GGCGGACGGG-TGA-GTAATGCGTGACTAACCTGCCTT-ACAC-TTCAGT-ATAGCTCCTGGAAACGGG-TGGTAA-T-C--CTGA-ATGTTCC-ACCA-TACC-G-CA-TG-G-TGT---GGTGG-GAAATGGT-------TTT--TTCTGG---TGTGAGATGGGGTCGCGTCCTATCAGCTTGTTGGTGGGG-TGATGG-CCTACCAAGGCTTT-GACGGGTAGCCGG-CCT-GA-GAGGG-CGGTCGGCCA-CATTGGG-A-CTG-AGATACGG-CCCA-GA-CTCC-TACGGG-AGGCAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
To run the code, paste the R script from this repository into your R-console, and then call it by:
summarise_alignment_position(phylip_file)
#e.g.
summarise_alignment_position("/Users/alanaalexander/Downloads/Fun_times_Pangolin_data.txt")
It will output a *.csv file called summarize_alignment_position.txt. Sample name is given in the left-hand column, followed by Gapped start (bp) and Gapped end (bp). These are where each sample start and end relative to the alignment in general. Ungapped start (bp) and ungapped end (bp) give the start and stop purely in terms of the reference sequence after stripping out gaps.
Sample,Gapped start (bp),Gapped end (bp),Ungapped start (bp),Ungapped end (bp)
Ex5155;_(reversed),106,1448,106,1185
Ex11616;_(reversed),106,1448,106,1185
Ex5111;,107,1512,107,1237
Ex5898;,107,1507,107,1233
Ex3182;,107,1496,107,1225
Ex7478;,107,1495,107,1224
Ex10372;,107,1492,107,1222
Ex7281;_(reversed),107,1476,107,1208
Ex3800;,107,1458,107,1192
Ex638;,107,1456,107,1191
Ex4636;,107,1456,107,1191
Ex5581;,107,1454,107,1189
Ex2655;,107,1453,107,1188
Ex5774;,107,1451,107,1187
Ex11237;,107,1451,107,1187
Ex155;,107,1450,107,1187
Ex410;,107,1450,107,1187
Ex451;,107,1450,107,1187
Ex1613;,107,1450,107,1187
Ex2239;_(reversed),107,1450,107,1187
Ex4379;,107,1450,107,1187
Ex8385;_(reversed),107,1450,107,1187
Ex777;,107,1449,107,1186
Ex1924;,107,1449,107,1186
Wrote this as a one-off goof to help out a lab mate. I am no longer actively maintaining this repository, but will respond to issues.
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