Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014711.1 Corchorus olitorius cultivar O-4 contig14744, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9537
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:2479 original size:969 final size:966
Alignment explanation
Indices: 105--7877 Score: 6707
Period size: 969 Copynumber: 8.0 Consensus size: 966
95 AATCTTGTAT
* *** * ** * * *
105 TAACCATCATGGTTTTAAACTAAAAACGCATTACGGGCCCCGGTTCAGTTTCACATGATTTTTGG
1 TAACCATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCCCGCTTCAGTTTCGCATGATTTTTGG
* * * *
170 CGTAAAGTCTTCTTGAAATATCTATATTCAT-TGAACCAAATCTCAGCCACAATT-GATTAAAGG
66 CGTAAAGACTTCTTGAAATATCTATATTCATCT-AACCAAATCCCAG-CAAAATTGGATTTAAGG
* * *
233 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAATTTAAA-GCGAAAAAAAAAT
129 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA-ATAAATTCG--GAAAAAA-
* * * *
297 TCGAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATATTTGTGGCGTTAAATTATG---TTTT
190 TGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATGTTATTTT
* * *
359 TCAGAGTATTGTGGCAAAAATTTCTAAAAAAATAAAATTTCAGGTCAGTTTTTAGCCGAAATCAT
255 TCAGAGTATTGTGGCAAAAAATTCT-GAAAAA-AAAA-TTCAGGTCAGTTTTTAGCCGAAATCGT
* * * * * *
424 GTACTAACCATAACGATGTTT-GGCTAAAAACGCGTTTCGGGGCACCGGTTCAGTTTCGCATGAT
317 GTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGC-CCCGCTCAGTTTTGCATGAT
* * * * * * *
488 TTTTGGC-GTAAAGACTTCATGAAATATCTATATTCATCGAACCAAATCCCAACTACAGTGGATT
381 TTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATT
* * * * * *
552 TAAGGAATTGTTTTTACGAGCCTCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGAAAAG
445 GAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAATTCGG--AA-
* * * * *
617 AAATGGAAAAACGATATTAGAACCGTGGAAAACCCTTCAATTTTTTTGGCATTAAATTATATATT
507 AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGCATTGAATTATTTA-T
* * * **
682 TTTTCAGAGTATTATGGCAAAAAATTCAGAAATAAAAAAAATTCGGGTCAGTTTTTTG-------
571 TTTTCTGAGTATTGTGGCAAAGAATT--G-AGGAAAAAAAATTCGGGTCAGTTTTTTGCAAAATT
* * * * * * *
740 --A--CG--A----A-A-AA--ATCACGGTTTTTGAGTTAAAAACGCATTTTTTGGTCCTGGCTC
633 TTAGCCGAAATTGTATATAACCATCACGGTTTTTG-GCTAAAAACGC-GTTCTGGGCCCCGGTTC
* * * * *
791 AGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATACCTATATTCATCTAACCAAATCTCA
696 AGTTTCGCATGATTTTTGGC-GTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCA
* ** * *
855 GCGA-AATTGAATTTGAGGATTTATTTTTACGA-CATCTAAATCTTGTTTCGATTTAATTATAAA
760 GCCACAATTG-ATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAA
* * *
918 TAAATTCG-AAAAAAATGGATAAACGATATTAGAAGCATGGAAAACCCTTCAATTATTTTTTTTG
824 TAAATTCGAAAAAAAAAGGAAAAACGATATTAGAAGCGT-GAAAACCCTTCAA-TA--TTTTTTG
* ** * *
982 CATTGAATTATATATATATTTCCTGAGTATTTTGGCAAAGAATTGTGGAAACATTTTTTGGGTCA
885 CATTGAATTATATAT-T-TTT-CTGAGTATTGTGGCAAAGAATT-CAGAAA-AATTTTCGGGTCA
* * * *
1047 GCTTTT-TGCAAAAT--TTAAGC
945 GTTTTTATCCGAAATCGTTTA-C
* * * * * * *
1067 AGAAAATCGTCACGGTTTTTGGCTAAAAACACGTTCTGGGGCCTCGATTCAGTTTCGAATGATTT
1 ---TAACCATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCC-CGCTTCAGTTTCGCATGATTT
* * * * * * *
1132 TTGGTGTAAAAACTTCTTGAAATATCTATATTCATCGAACCAAATCCCCGCCACAGTGGATTTAA
62 TTGGCGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCCCAGCAAAATTGGATTTAA
* * * * * *
1197 GGATTTGTTTTTTCGAGCATCCGAATTTTGTTTCGATTTAATAAGAAATAAGTTCGGAAAAGAAA
127 GGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAA-AAT
* ** * * * * *
1262 GAGAAAAACGATCTTAGAATTGTGAAAACCCCTTCAATCTTTTTGGCATTGAATTATATATTTTT
191 G-GAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATGT-TATTT
* **
1327 TTCAGAGTATTGTGGCAAAAAATTC--AAAAAAAAATTCGGGTCAG-TTTTATGTTGAAATCGTG
254 TTCAGAGTATTGTGGCAAAAAATTCTGAAAAAAAAATTCAGGTCAGTTTTTA-GCCGAAATCGTG
* *** *
1389 TA-TAAACCATCACGGTTTTTGGGCTAAAAACGCATTTCGGTGGCAGAGCTCAGTTTTGCACGAT
318 TACT-AACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGG-GGCCCCGCTCAGTTTTGCATGAT
* * *
1453 TTTTGGCAGAATGACTCCTTGAAA-ATCTATTTTCATCTAACCAAATTTCAGCCACATTGGATTG
381 TTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTG
* * * *
1517 AAAGATTTGTTTTTACAAGCAACTGAATCTTGTTTCGATTTAACTATAAATAAATTCGGGAAAAT
446 AAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAATTCGGAAAAAT
* *
1582 GGAAAAACGATATAAGAAGCGTG-AAAACCCTTCAATTTTTTTTGCGTTGAATTATTTATTTTTC
511 GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGCATTGAATTATTTATTTTTC
* *
1646 TGAGTATTGTGGGAAAGAATTTAGGAAAAAAAATTCTGGGTCAGTTTTTTGCAAAATTTTAGCCG
576 TGAGTATTGTGGCAAAGAATTGAGGAAAAAAAATTC-GGGTCAGTTTTTTGCAAAATTTTAGCCG
* *
1711 AAATTGTATACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCTGGGCCGCGGTTCAGTTTCG
640 AAATTGTATA-TAACCATCACGGTTTTTGGCTAAAAACGCGTT-CTGGGCCCCGGTTCAGTTTCG
* * * * *
1776 CATGATTTTTGGTGTGAAGACTTCTTGAAATAACTATATTCATCGAACAAAATCCC-GACCACAT
703 CATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAG-CCACAA
*
1840 TTGA-TAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCG
767 TTGATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCG
* * * * * * *
1904 AAAAAAAAAAGAAAAATGATATTATAAGCGTGAAAATCCTTTAATATTTTTGGCATTGAATTGTA
832 AAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAACCCTTCAATATTTTTTGCATTGAATTATA
* *
1969 TATTTTTCTGAGT-TCTGTGGCAAAAAATTCAGAACAAATTTTCGGGTCTGTTTTTATCCGAAAT
897 TATTTTTCTGAGTAT-TGTGGCAAAGAATTCAGAA-AAATTTTCGGGTCAGTTTTTATCCGAAAT
2033 CGTTTAC
960 CGTTTAC
* * * *
2040 TAACCATCACGGTTTTTGGGTTAAAAACGCGTTTTGGGGTCCCGACTT-AATTTTGTATGATTTT
1 TAACCATCACGGTTTTT-GGCTAAAAACGCGTTTTGGGG-CCCG-CTTCAGTTTCGCATGATTTT
* * * *
2104 TGGCAG-ATAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCAAAATTGGACTTAA
63 TGGC-GTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCCCAGCAAAATTGGATTTAA
2168 GGATTT-TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATG
127 GGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATG
*
2232 GAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATGTTATTTTTC
192 GAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATGTTATTTTTC
* *
2297 AGAGTATTGTGGCAAAAAATTCTGAAAAAAAAATTCAGTTAAGTTTTTAGCCGAAATCGTGTACT
257 AGAGTATTGTGGCAAAAAATTCTGAAAAAAAAATTCAGGTCAGTTTTTAGCCGAAATCGTGTACT
* *
2362 AACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCGTTCAGTTTTGCATGACTTTTGG
322 AACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCGCTCAGTTTTGCATGATTTTTGG
* * *
2427 CAGAAAGACTCCGTGAAATATCTATATTCGTCTAACCAAATCTCAGCCACATTGAATT-AAAGGA
387 CAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTGAAA-GA
* * * * *
2491 TTTGTTTTTACGAGCTTCTAAATCTTGTTTCGATTTAATAACAAATAAATTTAGGGAAAAAATGG
451 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAA-TT-CGG-AAAAATGG
* * * * *
2556 -AAAACGATATTAGAAGCATGAAAAACCATTTCAAATTTTTTTGCATTAAATTA-TAATTTTT-T
513 AAAAACGATATTAGAAGCGTGAAAAACC-CTTCAATTTTTTTTGCATTGAATTATTTATTTTTCT
* **** * * * *
2618 TAGTATTGTGGCAAAGAATTGAGGAAAATTTTTTCGCGTAAG-TTTTTGAAAAATTTTAGCCAAA
577 GAGTATTGTGGCAAAGAATTGAGGAAAAAAAATTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAA
* * *
2682 ATCTTGTAT-TAACCATCACGGCTTTTT-ACTAAAAACGCATTAC-GGGCCCCGGTTCAGTTTCA
642 A--TTGTATATAACCATCACGG-TTTTTGGCTAAAAACGCGTT-CTGGGCCCCGGTTCAGTTTCG
* * *
2744 CATGATTTTTGGCGTAAAGTCTTCTTGAAATATCTATATTCATTGAACCAAATCCTAGCCACAAT
703 CATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAGCCACAAT
* ***
2809 TGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT--TCTTAAA-TCGA
768 TGATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCG-
* * * * * * *
2871 AACAAAAAAATCGAAAAATGATATTAGAAGCGTAAAAAACCCTTCAATATTTGTGGCGTT-AAAT
832 AA-AAAAAAA-GGAAAAACGATATTAGAAGCGT-GAAAACCCTTCAATATTTTTTGCATTGAATT
* * * * *
2935 -TATGTTTTTCAGAGTATTGTGGCAAA-AATTTCTGAAAAAATAAAATTTCAGGTCAGTTTTTAG
894 ATATATTTTTCTGAGTATTGTGGCAAAGAA-TTCAG-AAAAAT----TTTCGGGTCAGTTTTTAT
*
2998 CCGAAATCGTGTAC
953 CCGAAATCGTTTAC
* * * * * * *
3012 TAACAATAATGGTGTTTGGGCTAAAAACGCGTTTCGGGGCACCGGTTCAGTTTTGCATGATTTTT
1 TAACCATCACGGT-TTTTGGCTAAAAACGCGTTTTGGGGC-CCGCTTCAGTTTCGCATGATTTTT
* * * * *
3077 GGCGTAAAGACTTCATGAAATATCTATATTCATCGAACCAAATCCCAGCTACAGTGGATTTAAGG
64 GGCGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCCCAGCAAAATTGGATTTAAGG
* * * * *
3142 AATTGTTTTTATGAGGC-TCTGAATCTTATTTCGATCTAATTAGAAATAAATTTGGAAAAGAAAT
129 ATTTGTTTTTACGA-GCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG-AAA-AAAT
* * * * * *
3206 GGAAAAACGATCTTAGAACCGTGGAAAACCCTTCAATTTTTTTGGCATTGAATTAT-ATATTTTT
191 GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATGTTA-TTTT
* * * * *
3270 TCGGAGTATTATGGCAAAAAATTC-G-------------GGTCCGTTTTTTGTCGAAATCGTGTA
255 TCAGAGTATTGTGGCAAAAAATTCTGAAAAAAAAATTCAGGTCAGTTTTTAGCCGAAATCGTGTA
* * * ** **
3321 -TATACCATCACGGTTTTTGGGTTAAAAACGCATTTTGTGGTTCTGGCTCAGTTTTGCATGATTT
320 CTA-ACCATCACGGTTTTTGGGCTAAAAACGCGTTTCG-GGGCCCCGCTCAGTTTTGCATGATTT
* * *
3385 TTGGCAGAAAGACTCCTTGAAATACCTATATTCATCTAACCAAATCTCAGCCAAATTGAATTTG-
383 TTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA-TTGA
* * * * * * * *
3449 AGGATTTATTTTTGCGAACATCTAAATCTTGTTTCGATTTAATTTTAATTAAATTCGAAAAAAAT
447 AAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAATTCG-GAAAAAT
* *
3514 GGAAAAACGATATTAGAAGCATGGAAAACCCTTCAAGTATTTTTTTTGCATTGAATTATATATAT
511 GGAAAAACGATATTAGAAGCGTGAAAAACCCTTC-A--ATTTTTTTTGCATTGAATTAT-T-TAT
* * * *** * * *
3579 ATTTCCTGAGTATTTTGGCAAAGAATTGAGGAAACATTTTTTGGGTCAGCTTTTTGCAAAATTTA
571 -TTTTCTGAGTATTGTGGCAAAGAATTGAGGAAAAAAAATTCGGGTCAGTTTTTTGCAAAATTTT
* * * * *
3644 AGCCG-AA----A-AT---CGTCACGGTTTTAGGCTAAAAACACGTTATGGGGCCTCGGTTCAGT
635 AGCCGAAATTGTATATAACCATCACGGTTTTTGGCTAAAAACGCGTTCT-GGGCCCCGGTTCAGT
* * * *
3700 TTCGCATGAGTTTTGGCGTAAAAACTTCTTGAAATATCTATATTCATCAAACCAAATCCCTGCCA
699 TTCGCATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAGCCA
* * * * ** *
3765 CAGTGGATTTAAGGATTTGTTTTTCCGAGCATCCGAATTTTGTTTCGATTTAATTAGAAATAAAT
764 CAATTGATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAAT
* * * * * * *
3830 TCGGAAAAGAAGGGGAAAACGATCTTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGCGTTGAAT
829 TCGAAAAAAAAAGGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAATATTTTTTGCATTGAAT
* * *
3895 TATTTATTTTTCTGAGTATTGTGGGAAAGAATTGAAGAAAAAAAATTTT-GGGTCAGTTTTTTGC
893 TATATATTTTTCTGAGTATTGTGGCAAAGAATT-CAG---AAAAATTTTCGGGTCAG-TTTTT--
* *
3959 AAAATTTTAGCCGAAATTGTATAC
951 ---A---T--CCGAAATCGTTTAC
* *
3983 TAACCATCACGATTTTTGGCTAAAAACGCGTTCCT-GGG-CCGCTGTTCAGTTTCGCATGATTTT
1 TAACCATCACGGTTTTTGGCTAAAAACGCGTT-TTGGGGCCCGC--TTCAGTTTCGCATGATTTT
* * * * * * * * *
4046 TGGTGTAAAGACTTCGTGAAACATCTATATTCATCAAACAAAATCCC-GACCACATTTGATTAAA
63 TGGCGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCCCAG-CAAAATTGGATTTAA
**
4110 GGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAA
127 GGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATG
* * * * *
4175 GAAAAATGATATTATAAGCGTG-AAAATCCTTCAATCTTTTTGGCATTGAA-T-TGTATATTTTT
192 GAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATGT-TATTTTT
* * * * ** * * * *
4237 CTGAGTACTGTGGCAAAAAATTCAG-AACAAATTTTCGGGTCAGTTTTTATCCGAAACCGTTTAC
256 CAGAGTATTGTGGCAAAAAATTCTGAAAAAAAAATTCAGGTCAGTTTTTAGCCGAAATCGTGTAC
* * *
4301 TAACCATCACGGTTTTTGGGCTAAAAACGCGTTTTGGGGTCCCGACTTAGTTTTGCATGATTTTT
321 TAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCG-CTCAGTTTTGCATGATTTTT
* * * *
4366 GGCAGATAA-ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCAAAATTGGATTTAAG
385 GGCAGA-AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTGAAA
*
4430 GATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAATTCGGAAAAATGGA
449 GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAATTCGGAAAAATGGA
* * * * *
4495 GAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATGTTATTTTTCAG
514 AAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGCATTGAATTAT-TTATTTTTCTG
* ** ******* ** *** * **
4560 AGTATTGTGGCAAAAAATT-CTGAAAAAAAA-AAAAAAAAAATTCAGGTAAGTTTTTAGCCGAAA
578 AGTATTGTGGCAAAGAATTGAGGAAAAAAAATTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
* * * * * *
4623 TCGTGTACTAACCATCACGGTTTTTGGGCTAAAAGCGTGTT-TCGGGCCCCCGTTCAGTTTTGCA
643 TTGTATA-TAACCATCACGGTTTTT-GGCTAAAAACGCGTTCT-GGGCCCCGGTTCAGTTTCGCA
* * * * * * *
4687 TGAATTTTGGTAG-AAAGACTTCGTGAAATATCTATATTCGTCTATCCAAATCTCAGCCAC-ATT
705 TGATTTTTGG-CGTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAGCCACAATT
* * * * *
4750 GAATTAAAGGATTTGTTTTTACGAGCTTCTAAATCTTGTTTCGATTTAATAATAGATAAATT-TA
769 G-ATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGA
** * * * * *
4814 GGGAAAAAAGGGAAAACGATATTAGAAGCCTGAAAAACCATTTCAAATTTTTTTTGCATTAAATT
833 -AAAAAAAAGGAAAAACGATATTAGAAGCGTG-AAAACC-CTTC-AATATTTTTTGCATTGAATT
* * * * *
4879 ATA-ATTTTTTTTAGTATTGTGGCAAAGAATTGAGGAAAAATTTTTCGCGTAAGTTTTTGCAAAA
894 ATATATTTTTCTGAGTATTGTGGCAAAGAATTCA-GAAAAA-TTTTCGGGTCAGTTTTT-----A
* *
4943 TTTTAACCAAAATC-TTGTAT
952 ---T--CCGAAATCGTT-TAC
* * ** * * *
4963 TAACCATCACGGTTATTT-ACTAAAAACGCATTACGGGCCCCGGTTCAGTTTCACATGATTTTTG
1 TAACCATCACGGTT-TTTGGCTAAAAACGCGTTTTGGGGCCCGCTTCAGTTTCGCATGATTTTTG
* * *
5027 GCGTAAAGTCTTCTTGAAATATCTATATTCAT-TGAACCAAATCCCAGCCACAATT-GATTAAAG
65 GCGTAAAGACTTCTTGAAATATCTATATTCATCT-AACCAAATCCCAG-CAAAATTGGATTTAAG
* * *
5090 GATTTGTTTTTACAAGCATCTGAATCTTGTTTCGA--T-A-TCG----AAA-----AAAAAATCG
128 GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGG
* * * * *
5142 AAAAATGATATTAGAAACGTGAAAAATCCTTCAATATTTGTGGCGTTAAATTATG---TTTTTCA
193 AAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATGTTATTTTTCA
* *
5204 GAGTATTGTGGCAAAAATTTCTGAAAAAATAAAATTTCAAGTCAGTTTTTAGCCGAAATCGTGTA
258 GAGTATTGTGGCAAAAAATTCTG-AAAAA-AAAA-TTCAGGTCAGTTTTTAGCCGAAATCGTGTA
* * * * ** *
5269 CTAACCATAACGGTGTTTGGGCTAAAAACGCGTTTCGGGGCACCGGTTCAGTTTCACATAATTTT
320 CTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGC-CCCGCTCAGTTTTGCATGATTTT
* * * * * * * *
5334 TGGC-GTAAAGACTTCATGAAATATCTATATTCATCGAATCAAATCCCAGCTACAGTGGATTTAA
384 TGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTGAA
* * * * *
5398 GGAATTGTTTTTACGAGCCTCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGAAAAGAAA
448 AGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAATTCGG--AA-AAA
* * * * *
5463 TGGAAAAACGATCTTAGAACCGTGGAAAACCCTTCAATTTTTTTGGCATTGAATTATATATTTTT
510 TGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGCATTGAATTATTTA-TTTT
* * * * ** * *
5528 TCAGAGTATTATGGCAAAAAATTCATAAAAAAAAAAATTCGAGTCAGTTTTTTGTCGAAA---T-
574 TCTGAGTATTGTGGCAAAGAATT--GAGGAAAAAAAATTCGGGTCAGTTTTTTG-CAAAATTTTA
* * * * * *
5589 --CG----TGTATAT-ACCATCACGGTTTTTGGGTTAAAAACGCATTTTGTGGTCCTGGCTCAGT
636 GCCGAAATTGTATATAACCATCACGGTTTTT-GGCTAAAAACGCGTTCTG-GGCCCCGGTTCAGT
* * * * *
5647 TTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATA-CTTATATTCATCTAAGCAAATCTCAGC
699 TTCGCATGATTTTTGGC-GTAAAGACTTCTTGAAATATC-TATATTCATCGAACCAAATCCCAGC
** * *
5710 CA-AATTGAATTTGAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTATAAATA
762 CACAATTG-ATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATA
* * *
5774 AATTCG-AAAAAAATGGATAAACGATATTAGAAGCATGGAAAACCCTTCAATTATTTTTTTTGCA
826 AATTCGAAAAAAAAAGGAAAAACGATATTAGAAGCGT-GAAAACCCTTCAA-TA--TTTTTTGCA
* *
5838 TTGAATTATATATATATATATATATATATATTTCCTGAGTATTTTGGCAAAGAATTGAGGAAACA
887 TTG------------A-AT-TATATAT-T-TTT-CTGAGTATTGTGGCAAAGAATTCA-GAAA-A
* * * * *
5903 TTTTTCGGGTCAGCTTTT-TGCAAAAT--TTAAGTC
933 ATTTTCGGGTCAGTTTTTATCCGAAATCGTTTA--C
* * * * *
5936 GAA-AATTGTCACGGTTTTTGGCTAAAAACACGTTATGGGGCCTCGGTTCAGTTTCGCATGATTT
1 TAACCA---TCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCC-CGCTTCAGTTTCGCATGATTT
* * * * * *
6000 TTGGCGTAAAAACTTCTTGAAATATCTATATTCATCAAACCAAATCCCTGCCACAGTGGATTTAA
62 TTGGCGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCCCAGCAAAATTGGATTTAA
* * * *
6065 GGATTTGTTTTTCCGAGAATCCGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAGAAA
127 GGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG-AAA-AAA
* * * * * * *
6130 GGGAAAAACGATCTTAGAAGCGTGAAAACCCCTTCAATCTTTTTGGCATTGAATTATATATTTTT
190 TGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATT-AAAT-TATGTTATT
* * *
6195 TTTCCA-AGTATTGTGGCAAAAAATTC-AAAAAAAAAATTCGGGTCAG-TTTTATGTCGAAATCG
253 TTT-CAGAGTATTGTGGCAAAAAATTCTGAAAAAAAAATTCAGGTCAGTTTTTA-GCCGAAATCG
* *** *
6257 TGTA-TAAACCATCACGGTTTTTGGGCTAAAAACGCATTTCGGTGGCAGAGCTCAGTTTTGCACG
316 TGTACT-AACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGG-GGCCCCGCTCAGTTTTGCATG
* * * *
6321 ATTTTTGGTAGAATA-ACTCCTTGAAAAATCTATTTTCATCTAACCAAATTTCAGCCACATTGGA
379 ATTTTTGGCAGAA-AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
* * *
6385 TTGAAAGATTTGTTTTTACAAACATCTGAATCTTGTTTCGATTTAACTATAAATAAATTCGGGAA
443 TTGAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAATTC-GGAA
*
6450 AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGCGTTGAATTATTTATT
507 AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGCATTGAATTATTTATT
* * * *
6515 TTTCTGAGTATTATGGGAAAGAATTGAAGAAAAAAAATTTGTGGGTCAGTTTTTTGCAAAATTTT
572 TTTCTGAGTATTGTGGCAAAGAATTGAGGAAAAAAAA-TT-CGGGTCAGTTTTTTGCAAAATTTT
* * *
6580 AGCCGAAATTGTATACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCTGGGCCGCTGTTCAG
635 AGCCGAAATTGTATA-TAACCATCACGGTTTTTGGCTAAAAACGCGTT-CTGGGCCCCGGTTCAG
* * *
6645 TTTCGCATGATTTTTGGTGTAAAGACTTCTTGAAACATCTATATTCATCGAACAAAATCCC-GAC
698 TTTCGCATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAG-C
*
6709 CACATTTGATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAA
762 CACAATTGATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAA
** * * *
6774 ATTCGGAAAAAAATTGGAAAAATGATATTATAAGCGTGAAAATCCTTCAAT-TTTTTTGGCATTG
827 ATTC-GAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAACCCTTCAATATTTTTT-GCATTG
* * * * *
6838 AATTGTATATTTTTCTGAGTACTGTGGAAAAAAATTCAGAACAAATTTTGGGGTCAGTTTTTATC
890 AATTATATATTTTTCTGAGTATTGTGGCAAAGAATTCAGAA-AAATTTTCGGGTCAGTTTTTATC
6903 CGAAATCGTTTAC
954 CGAAATCGTTTAC
**
6916 TAACCATCACGGTTTTTGGGCTAAAAACGCGTTTTGGGGTCCCGACTT-AGTTTTACATGATTTT
1 TAACCATCACGGTTTTT-GGCTAAAAACGCGTTTTGGGG-CCCG-CTTCAGTTTCGCATGATTTT
* * *
6980 TGGCAG-ATAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCAAAATTGGATTTAA
63 TGGC-GTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCCCAGCAAAATTGGATTTAA
*
7044 GGATTT-TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAATTCGGAAAAAAAA
127 GGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG--AAAAAA
* * * ** *
7108 TGGAGAAACGATATTAGAAGCATGAAAAACCCTTTAAT-TTTTTTTCATTGAATTAT-TTATTTT
190 TGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATGTTA-TTT
* * *** *
7171 TTCTA-AGGATTGTTGG-AAAGAAA---TGAGGAAAATTTTTC-GTTTCAGTTTTTAGCCGAAAT
254 TTC-AGAGTATTG-TGGCAAA-AAATTCTGA-AAAAAAAATTCAG-GTCAGTTTTTAGCCGAAAT
* * * ** *
7230 CGTGTACTAACCATCAAGGTTTTGGGGCTAAAAACGTGTTTCTAGGACCCGACTCAGTTTTGCAT
314 CGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCG-CTCAGTTTTGCAT
* * *
7295 GATATTTGGCAGAAAGACTCCTTAAAATATTTATATTTATGAATTCATCTAA-CAAATTCTCAGC
378 GATTTTTGGCAGAAAGACTCCTT--GA-A---ATATCTAT--ATTCATCTAACCAAA-TCTCAGC
* * *
7359 CACATTGGATT-AAAGCATTTGCTTTTACGAGTATCTGAAAT-TTGTTTCGATTTAATTAGAAAT
434 CACATTGGATTGAAAG-ATTTGTTTTTACGAGCATCTG-AATCTTGTTTCGATTTAATTATAAAT
** * * *
7422 AATTTTTTTATT-AAAAAAATGGAAAAA-GATATTAGAAGCATGAAAAATCCTTC-TTCTTTTTT
497 AA-------ATTCGGAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT-TTTTTT
* * * *** * *
7484 TGCATTGAATTATATATTTTTTATGAGTATTGTTGCAAAGAATTGA-G-AAAACTTTTCAGATCA
554 TGCATTGAATTATTTA-TTTTTCTGAGTATTGTGGCAAAGAATTGAGGAAAAAAAATTCGGGTCA
* * * ** * ** *
7547 -ATTTTT-CCAAATTTTAGCCGAAATCATGTA-CTAAGAATCACGGTTTTTTGCTAAAAATACAT
618 GTTTTTTGCAAAATTTTAGCCGAAAT--TGTATATAACCATCACGGTTTTTGGCTAAAAACGCGT
* **
7609 TAC-GGGACCCCGGCTCAG-TTCAGCATGATTTTTGGCAAAAAGACTTCTTGAAATATCTATATT
681 T-CTGGG-CCCCGGTTCAGTTTC-GCATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATT
* * * * * * * *
7672 CATCAAACCAAATCACAGCCAAAATGGATTTAAGGATTAGTTTCTACGAGCATCTTAATCTTGTT
743 CATCGAACCAAATCCCAGCCACAATTGATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTGTT
* * * * * * **
7737 TCGATTTAATTAGAAATTAATT-----TAGAAA--AAAAATGATATTAGAAACATGAAAATTTCT
808 TCGATTTAATTAGAAATAAATTCGAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAA-CCCT
* * * * * *
7795 TCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTGTGACAAA-ATATTGAGAAAAAC
872 TCAATATTTTTTGCATTGAATTATATA-TTTTTCTGAGTATTGTGGCAAAGA-ATTCAGAAAAA-
*
7859 CTTTTCGGGACAGTTTTTA
934 -TTTTCGGGTCAGTTTTTA
7878 GCCCCGGCTT
Statistics
Matches: 5568, Mismatches: 904, Indels: 660
0.78 0.13 0.09
Matches are distributed among these distances:
956 12 0.00
957 14 0.00
958 4 0.00
959 41 0.01
960 211 0.04
961 122 0.02
962 151 0.03
963 35 0.01
964 124 0.02
965 231 0.04
966 318 0.06
967 100 0.02
968 273 0.05
969 495 0.09
970 247 0.04
971 213 0.04
972 272 0.05
973 101 0.02
974 51 0.01
975 287 0.05
976 154 0.03
977 55 0.01
978 261 0.05
979 440 0.08
980 106 0.02
981 192 0.03
982 217 0.04
983 100 0.02
984 56 0.01
985 4 0.00
986 5 0.00
987 55 0.01
988 44 0.01
989 37 0.01
990 63 0.01
991 52 0.01
992 167 0.03
993 14 0.00
994 7 0.00
996 30 0.01
997 8 0.00
998 8 0.00
999 132 0.02
1000 34 0.01
1001 25 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (966 bp):
TAACCATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCCCGCTTCAGTTTCGCATGATTTTTGG
CGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCCCAGCAAAATTGGATTTAAGGAT
TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAA
AACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCATTAAATTATGTTATTTTTCAGAG
TATTGTGGCAAAAAATTCTGAAAAAAAAATTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
ATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCGCTCAGTTTTGCATGATTTTTGGCAGA
AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTGAAAGATTTGT
TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATAAATTCGGAAAAATGGAAAAACGA
TATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGCATTGAATTATTTATTTTTCTGAGTATTGT
GGCAAAGAATTGAGGAAAAAAAATTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATTGTATAT
AACCATCACGGTTTTTGGCTAAAAACGCGTTCTGGGCCCCGGTTCAGTTTCGCATGATTTTTGGC
GTAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCCCAGCCACAATTGATTAAAGGATT
TGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAAAGGAAA
AACGATATTAGAAGCGTGAAAACCCTTCAATATTTTTTGCATTGAATTATATATTTTTCTGAGTA
TTGTGGCAAAGAATTCAGAAAAATTTTCGGGTCAGTTTTTATCCGAAATCGTTTAC
Found at i:5849 original size:2 final size:2
Alignment explanation
Indices: 5844--5868 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5834 TGCATTGAAT
5844 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5869 TTCCTGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9506 original size:323 final size:325
Alignment explanation
Indices: 8444--9536 Score: 1262
Period size: 333 Copynumber: 3.3 Consensus size: 325
8434 ACAATCTTAA
* * * **
8444 GCCCCGACTCAGTTTTGCATGATTTTTGG-TGTAAATACTCCTTGATTTATCTATATTCATTGAA
1 GCCCCGACTCAGTTTTGCATGATTTTTGGCAGCAAAGACTCCTTGAAATATCTATATTCATTGAA
* * *
8508 CCAAATCCCAGCCACATTCGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTT
66 CAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTT
* * * *
8573 AATCAGAAATTAATTCGGAAAAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAATCCTTTAA
131 AATTAGAAATTAATTCGG--AAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA
* *** *
8638 TCTTTTTGGCGTTGAATTATAT-TCTTTTAGGAGTATTGTGGCAAAAATTGAGAAAACAATAATT
194 TCTTTTTGGCGTTGAATTATATATTTTTTCCAAGTATTGTGGCAAAAATTGAGAAAA-AAAAATT
* * *
8702 TCGGG-CTAGTTTTTAGCCGAAATCAAT-TACTAACCATCATGATTTTTGGCTAAAAAAGCGTTT
258 TCGGGTCAAATTTTTAGCCGAAATC-ATGTACTAACCATCACGATTTTTGGCTAAAAAAGCGTTT
*
8765 CAGG
322 CGGG
* * * *
8769 GCCTCGGCTCAGTTTTGCATGATTTTTAGCAG-AATGACTCCTTGAAATATCTATATTCATCT-A
1 GCCCCGACTCAGTTTTGCATGATTTTTGGCAGCAAAGACTCCTTGAAATATCTATATTCAT-TGA
* *
8832 ACAAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATT
65 ACAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATT
* * * *
8897 TAATTATAAATAAATTC--AAAAAAAATGGAAAAACAATATTAGAAGAGTGAAAAACCCTTCAAT
130 TAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT
* * * * * **
8960 TTTTTTTGCATTGAATTTTATATTTTTTTCCAAGTATTGTGGCAAAAAATTGAG-GAAAAACTTT
195 CTTTTTGGCGTTGAATTATATA-TTTTTTCCAAGTATTGTGGC-AAAAATTGAGAAAAAAAAATT
* * * * * *
9024 TCGAGTCATTTTTTGCAAAATTTTAGTCGAAATCATGTACTTAACCATCACAAATTTTGACTAAA
258 TCG-G-------GT-CAAATTTTTAGCCGAAATCATGTAC-TAACCATCACGATTTTTGGCTAAA
* * *
9089 AACGCGTTCCGGA
313 AAAGCGTTTCGGG
** * *
9102 GCCCCGGTTCAATTTTACATGATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATTGAA
1 GCCCCGACTCAGTTTTGCATGATTTTTGGCAGCAAAGACTCCTTGAAATATCTATATTCATTGAA
* *
9166 CAAAATCTTAGCCACATTGGATATAAGGATTT-TTTTTACGAGCATCTAAATCTTGTTTCGATTT
66 CAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTT
* * * *
9230 AATTAGAAATTAATTCGGAAAAAAAA-GGGAAAACGATAATAGAAGCGTGAAAAGCCCATCAATC
131 AATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATC
* ** * *
9294 TTTTTGGTGTTGAATTATATAATTTTTTCTTAGTATTGTGGCAAAATTTGAGAAAAAAAAAATTC
196 TTTTTGGCGTTGAATTATAT-ATTTTTTCCAAGTATTGTGGCAAAAATTGAGAAAAAAAAATTTC
* * *
9359 GGGTC-AATTTTTAGCCGAAATCGTGTACTACCCATCACGCTTTTTGGGCTAAAAAAGCGTTTCG
260 GGGTCAAATTTTTAGCCGAAATCATGTACTAACCATCACGATTTTT-GGCTAAAAAAGCGTTTCG
9423 GG
324 GG
* * *
9425 GCCCCGACTCAGTTTTGTATGATTTTTGGCAG-AAAAACTCCTTGAAATATCTATATTTATCT-A
1 GCCCCGACTCAGTTTTGCATGATTTTTGGCAGCAAAGACTCCTTGAAATATCTATATTCAT-TGA
* * *
9488 ACCAAATCTCAGCCACATTGCATTTAAGGATTTTTTTTTACGAGCATCT
65 ACAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
9537 G
Statistics
Matches: 642, Mismatches: 99, Indels: 55
0.81 0.12 0.07
Matches are distributed among these distances:
321 58 0.09
322 20 0.03
323 136 0.21
324 28 0.04
325 126 0.20
326 2 0.00
331 2 0.00
332 75 0.12
333 186 0.29
334 9 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (325 bp):
GCCCCGACTCAGTTTTGCATGATTTTTGGCAGCAAAGACTCCTTGAAATATCTATATTCATTGAA
CAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTT
AATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATC
TTTTTGGCGTTGAATTATATATTTTTTCCAAGTATTGTGGCAAAAATTGAGAAAAAAAAATTTCG
GGTCAAATTTTTAGCCGAAATCATGTACTAACCATCACGATTTTTGGCTAAAAAAGCGTTTCGGG
Done.