Resequencing analysis for Gene: IRF7


There are 3 sections to this alignment:
  - resequencing alignment (unspliced, by construction)
  - Our alignments (spliced for coding sequence)
  - Alignments of ref. [2] (spliced for coding sequence)

Note that:
  - these alignments should be taken in context with whole protein alignment. Spliced alignments may be interrupted by splicing events.
  - Putative signal of positive selection is shown in blue.

                    .... ....|1... ....|2... ....|3... ....|4... ....|5... ....|6... ....|7... ....|8... ....|9... ....|10.. ....|11.. ....|12.. ....|13.. ....|14.. ....|
reseq__G0_humanF95  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_humanF83  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_humanF71  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_humanF59  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_humanF47  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_humanF35  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_humanF23  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_humanF11  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_chimpF95  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_chimpF83  TGATCCGAGAAGCAGTGTGTGATATAGTCACTGCACATAAATCTGAGTCAAGCGATCCTCCCCTCAGCGTCCGAGAAACGTGAAGTACAGGAAGTACCCACACCCTGGGAACGTTTCAAAAAAATTAGAAAAAAGAGATAAGGCTCCCAT
reseq__G0_chimpF59  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_chimpF47  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_chimpF35  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_chimpF23  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_chimpF11  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq_G0_chimpF71_r ------------------------------------------------------------------------------------------------------------------------------------------------------
human_dna_us        ------------------------------------------------------------------------------------------------------------------------------------------------------
chimp_dna           ------------------------------------------------------------------------------------------------------------------------------------------------------
macaque_dna         ------------------------------------------------------------------------------------------------------------------------------------------------------
hg18_gibbs          ------------------------------------------------------------------------------------------------------------------------------------------------------
panTro2_gibbs       ------------------------------------------------------------------------------------------------------------------------------------------------------
rheMac2_gibbs       ------------------------------------------------------------------------------------------------------------------------------------------------------

                    15.. ....|16.. ....|17.. ....|18.. ....|19.. ....|20.. ....|21.. ....|22.. ....|23.. ....|24.. ....|25.. ....|26.. ....|27.. ....|28.. ....|29.. ....|
reseq__G0_humanF95  ----------------------------------------------------------------------------------------------------------------------------------------TGGTACAGCAATAC
reseq__G0_humanF83  --------------------------------------------------------------------------------------------------------------TCGACATGAAGATTCC-------CACGGAGGTGACTCTTT
reseq__G0_humanF71  ---------------------------------------------------------------------CCGAAGCCCAGGAGAAG--GTAAGGGGGGAGCCT-CGCCCGCCTGCCCGAATTCCCCC----AGCTTGGAACAACACATTC
reseq__G0_humanF59  ----------------------------------------------------------------------TCAAGCCCAGGTAGAGAGGAAAGCGTGGAGCCACGCGCTGCATGCCCGAATTCCCCC---AGCTCGTGTAACGGAATCAG
reseq__G0_humanF47  ----------------------------------------------------------------------TCGACCCCACTAGAGG--TAAGGGGGCGAGCCAGCGC----GAGGCCGAAATCCCC--CAGCTCGTACAAC-ACCTCCCC
reseq__G0_humanF35  -------------------------------------------------------------------GTTCGAAGGCCAG-TAGA-GGACAGGGGGGAACCAGCAAGAATTCCGG--GAATTCCACC----AGTATCGAAAAAGAACATC
reseq__G0_humanF23  --------------------------------------------------------------------TTCGAAGCCCAGCCAGAG-GTAAGGTGTGGAGCCA-CGGCGCGCGGCCCGAAATCCCCA------GCTTGAAGTAGGCAT-C
reseq__G0_humanF11  ------------------------------------------------------------------------------------------------------------------------------------------------------
reseq__G0_chimpF95  ---------------------------------CGTGGTGAACCTGGGCTTCGCGAAACGGTAGAGAACGTCAAGCCCATGTGGAT--CCATCCGGGGCGGTAACGGCGAGCCGGACAGAAATCCA-------TCTCGGAACAGTAATAG
reseq__G0_chimpF83  ATGTAGCCAGTCCAGTCGAGCTTGTGGGCATCAAGTGATTCACCTTGGCCTCCCCAAAGGCTGAGATTTCTGAAGCCCAGGCAGAT--GGTATCGGGGGGGGCCAGGCGTGCGGTGCCGAATTTCCC---CCCCCCCCATCAAGCAATTG
reseq__G0_chimpF59  --------------------------------------------------------------------TTCGAAGCCCAGGTAGAG--GTATAGGTGGGAGCCACGCGCGCGGGCCCGAATTCCCAC---CAGCTTTTAGAAGGGACTCC
reseq__G0_chimpF47  -------------------------------------------------------------------------------------------------------------------------------------ACCTGTTTCACACCCTC
reseq__G0_chimpF35  --------------------------------------------------------------------TTCGAAGCCCAGGTAGATGGAAAGGGGGGGAGCCACGGCGCGCCTGCCCGAATTCCCCC----AGC-TCTAAGAAGGATACC
reseq__G0_chimpF23  -------------------------------------------------------------------TTATCAAGCCCAGCCGAGG--TAAGAGGGGGGGCCAGGGCCTGTGGGCCCGAATTTCCCTCCAACTCCCCAGACTGTGGCTGA
reseq__G0_chimpF11  ----------------------------------------------------------------------------------------------------------TGAAGATAGAGGAAGGGGAGAGGGGGGAATTAGGTGATGTAGGA
reseq_G0_chimpF71_r ---------------------------------CGTGGTGAACCTGGGCTTCGCGAAACGGTAGAGAACGTCAAGCCCATGTGGAT--CCATCCGGGGCGGTAACGGCGAGCCGGACAGAAATCCA-------TCTCGGAACAGTAATAG
# Our alignments (spliced for proteins)
human_dna_us        ---------------------------------------------------------------------------------------------------------------------------------------------------TCC
chimp_dna           ---------------------------------------------------------------------------------------------------------------------------------------------------TCC
macaque_dna         ---------------------------------------------------------------------------------------------------------------------------------------------------TCC
# Ref.[2] alignments (spliced for proteins)
hg18_gibbs          ---------------------------------------------------------------------------------------------------------------------------------------------------TCC
panTro2_gibbs       ---------------------------------------------------------------------------------------------------------------------------------------------------TCC
rheMac2_gibbs       ---------------------------------------------------------------------------------------------------------------------------------------------------TCC

                    30.. ....|31.. ....|32.. ....|33.. ....|34.. ....|35.. ....|36.. ....|37.. ....|38.. ....|39.. ....|40.. ....|41.. ....|42.. ....|43.. ....|44.. ....|
reseq__G0_humanF95  CAGCACCAGCGACAACGACGACGGCTTGCACCAGTCTGTGCGGGGTTCCCCATCTTCGACTTCAGAGTCTTCTTCCAAGGTCAGTGAGGCCCTTGCCTGGGGGGCTGTCTCCAGGGGTCCTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_humanF83  CCAGCCCATCCAGCAGCAGCGGAAGGGGCACCCGCCTGTGTGGGT--CCCCATCTTCGACTTCAGAGTCTTCTTCCAAGGTCAGTGAGGCCCTTGCCTGGGGGGCTGTCTCCAGGGGTCCTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_humanF71  CAGCACCACTCACAACAGGGGTAGCAAGCATCCC---ATATGTGATTCCCCATCTTCGACTTCAGAGTCTTCTTCCAAGGTCAGTGAGGCCCTTGCCTGGGGGGCTGTCTCCAGGGGTCGTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_humanF59  CGCAAGCACAGGCAGGGGAGAGCAAGGGGACCAG-----GAGTGATTCCCCATCTTCGACTTCAGAGTCTTCTTCCAAGGTCAGTGAGGCCCTTGCCTGGGGGGCTGTCTCCAGGGGTCCTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_humanF47  CACCACCGCCAGCA----GGAGGGGGAGGGACAG---GGAGTGGGT-CCCCATCTTCGACTTCAGAGTCTTCTTCGGAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGGTCGTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_humanF35  CCCATCCAGCGACCAGTGGTGGCCAGCGCCCC-C---GCTGATGCCTCCCCATCTTCGACTTCAGAGTCTTCTTCCGAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGGTCGTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_humanF23  CACCACCACCAGGCAGGTGTAGGCAAGGAGGA-----GGAGGTAGGTCCCCATCTTCGACTTCAGAGTCTTCTTCCAAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGGTCGTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_humanF11  ---------------------------------------------TTCCCCATCTTCGACTTCAGAGTCTTCTTCCAAGGTCAGTGAGGCCCTTGCCTGGGGGGCTGTCTCCAGGGGTCGTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_chimpF95  CAGCTCCACTGACAGAGAGGACGGCGCGCACCACCCTGTTCGGGGT-CCCCATCTTCGACTTCAGAGTCTTCTTCGGAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGGTCCTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_chimpF83  CACAACCACAGACACAGAGATCGGCAAGCTCCCC---AGATGAATT-CCCCATCTTCGACTTCAGAGTCTTCTTCGGAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGGTCCTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_chimpF59  CCGAACCCGCAGGCAGGTGGTAGCAAGGAACGAG-----GATGATTTCCCCATCTTCGACTTCAGAGTCTTCTTCGGAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGGTCCTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_chimpF47  CACGCGCACAGACACAGAGGGGGGGGGGCACCAGA--GGGCAATGTCCCCCATCTTCGACTTCAGAGTCTTCTTCGGAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGGTCCTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_chimpF35  CCGACCCCGCAGGCAGGTGCTCCCAAGGCCCCGT---GGTGATGT-TCCCCATCTTCGACTTCAGAGTCTTCTTCGGAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGGTCCTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_chimpF23  CACCGCCACCGGCACAGAGGAGGCGGGGAGCCAG---GGTTGATGT-CCCCATCTTCGACTTCAGAGTCTTCTTCGGAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGGTCCTTGGGAGCACCTGCCTGCCAGGTACTCAGC
reseq__G0_chimpF11  GAGTGGAAAAGAGGAGGGAGATAGTAGGAAGGAGA--AAATGATTGTCCCCATCTTCGACTTCAGAGTCTTCTTCGGAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGG---------------------------------
reseq_G0_chimpF71_r CAGCTCCACTGACAGAGAGGACGGCGCGCACCACCCTGTTCGGGGT-CCCCATCTTCGACTTCAGAGTCTTCTTCGGAGGTCAGTGAGGCCCCTGCCTGGGGGGCTGTCTCCAGGGGTCCTTGGGAGCACCTGCCTGCCAGGTACTCAGC
# Our alignments (spliced for proteins)
human_dna_us        GCCAGCCCCTCCACCCCAGCCTGCCTGCTGCCTCGGAACTGTGACACCCCCATCTTCGACTTCAGAGTCTTCTTCCAAGG----------------------------------------------------------------------
chimp_dna           GCCAGCCCCTCCACCCCAGCCTGCCTGCTGCCTCGGAACTGTGACACCCCCATCTTCGACTTCAGAGTCTTCTTCGGAGG----------------------------------------------------------------------
macaque_dna         GCCAGCCCCTCCACCCCAGCCTGCCTGCTGCCTCGGAACTGCGACACCCCCATCTTTGACTTCAGAGTCTTCTTCCAAGG----------------------------------------------------------------------
# Ref.[2] alignments (spliced for proteins)
hg18_gibbs          GCCAGCCCCTCCACCCCAGCCTGCCTGCTGCCTCGGAACTGTGACACCCCCATCTTCGACTTCAGAGTCTTCTTCCAA------------------------------------------------------------------------
panTro2_gibbs       GCCAGCCCCTCCACCCCAGCCTGCCTGCTGCCTCGGAACTGTGACACCCCCATCTTCGACTTCAGAGTCTTCTTCGGA------------------------------------------------------------------------
rheMac2_gibbs       GCCAGCCCCTCCACCCCAGCCTGCCTGCTGCCTCGGAACTGCGACACCCCCATCTTTGACTTCAGAGTCTTCTTCCAA------------------------------------------------------------------------

                    45.. ....|46.. ....|47.. ....|48.. ....|49.. ....|50.. ..
reseq__G0_humanF95  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGGCACGGCAGCGCCGTCCACACT-
reseq__G0_humanF83  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT-CCGGGCACGGCAGG--CGCCCG-----
reseq__G0_humanF71  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGGCACGGCAGCGCC-TCCAATG--
reseq__G0_humanF59  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT-CCGGGCACGGCAGCCCCGTCCCAC---
reseq__G0_humanF47  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGGCACG-CAGCGCCGGCCCACTT-
reseq__G0_humanF35  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGGCACGGCAGC-CCGGCCCAT---
reseq__G0_humanF23  AGAGTCCCCTTCTTCAGAGCTGGTGGAATTCCGGACACGGCCAG-------------
reseq__G0_humanF11  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGCCC--------------------
reseq__G0_chimpF95  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGGCACG-CAGCGCCGCCCAGCG--
reseq__G0_chimpF83  AGAGTCCCCTTCTTCAGAGCTGGTG-AAT--CCGGCACGGCAGCGCCCGCCCATG--
reseq__G0_chimpF59  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGGCACGGCAGCCCCGCCCAGTG--
reseq__G0_chimpF47  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGGCACGGCAGCACCGTCCCGACCC
reseq__G0_chimpF35  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGGCACGGCAGCGCCGGCCCCCTG-
reseq__G0_chimpF23  AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGGCACGTCAGCACCAGCCCACG--
reseq__G0_chimpF11  ---------------------------------------------------------
reseq_G0_chimpF71_r AGAGTCCCCTTCTTCAGAGCTGGTGGAAT--CCGGCACG-CAGCGCCGCCCAGCG--
# Our alignments (spliced for proteins)
human_dna_us        ---------------------------------------------------------
chimp_dna           ---------------------------------------------------------
macaque_dna         ---------------------------------------------------------
# Ref.[2] alignments (spliced for proteins)
hg18_gibbs          ---------------------------------------------------------
panTro2_gibbs       ---------------------------------------------------------
rheMac2_gibbs       ---------------------------------------------------------