Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011089.1 Corchorus capsularis cultivar CVL-1 contig11110, 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: 38232
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:13116 original size:655 final size:647
Alignment explanation
Indices: 11589--14669 Score: 3050
Period size: 655 Copynumber: 4.7 Consensus size: 647
11579 TTGTTTCATA
* * * *
11589 TTTTT-TGAATTAATTTCTAATTAAATCGAAATAAGATTTAAATACTCGTAAAAATAAATCCTTA
1 TTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGA-TTAAATGCTCGTAAAAACAAATCCTTA
* * * * **
11653 AATCCAATATGTCTCAGACTTTGATTAGATAAATA-ACGATATTTCAAGGAGTCTCAATGCCAAA
65 AATCCAATGTGGCTGAGA-TTTGGTTAGATAAATATA-GATATTTCAAGGAGTCTTTATGCCAAA
* ** * * * * *
11717 AACCATGCAAAACAGAACCGTGGTCCT-GGAAGGCGTTTTTAGCCAAAAACTGTGATGGTTAGTA
128 AACCATGCAAAACTGAGTCGAGG-CCTCGAAACGTGTTTTTAGCCAAAAACCGTGAT-G---GTA
* * * * * * *
11781 TATGATTTCGGCTAAGAACTGACCAGAAAAGTTTTTTCTCAATTTTTTGCCATAATACT-AAAAT
188 CACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAA-
* * * * *
11845 ATATATATATATAATTCAACGCCAAAAAGATTGACGGGCTCTTAACGTTTCTAATATCGTTTTTC
252 A-A-A-ATATATAATTTAACGCCAAAAAGATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTC
* * * *
11910 CATTTTTTTT-CGAATTGATTTCTAACTAAATCGAAACAAGATTAAGATGATCGTAAAAACAAAT
314 C-TTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * * * * * * **
11974 ACTTAAATCCAATGTAGCCGGGATTTGGTTAGATAAATATAGATATTTCAAGAAGTCTTTACACC
378 CCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCC
* * * *
12039 AAAAATCATCCAAAACTGAGCCGGGCCCCAAAACGCGTTTTTAGCCATAAACCGTGATGGTTAGT
443 AAAAATCATGCAAAACTGAGCGGGGCTCCAGAACGCGTTTTTAGCCA-AAACCGTGATGGTTAGT
* * *** *
12104 ACACACGATTTCGGCTAAGATTTTGTAAAAACTGATCCG-ATTTTTTTTTCTCAATTTTTT-CCA
507 --ACACGATTTCGGCTAAAATTTTGCAAAAACTGATCCGAAAAGTTTTTCCTCAATTTTTTCCCA
* * * * *
12167 TAATACT-A-AAAAATATATATAATTTCAAAGCCAAAAAAATTGACGGACTTTTT-ACGTTTCTA
570 CAATACTCAGAAAAA-ATATATAA-TTCAACGCC-AAAAAATTGAAGG-GTTTTTCACGCTTCTA
* * *
12229 ATATCATTTTTCTTTTT
631 ATATCGTTTTCCTTTAT
* *
12246 TTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTC-TAAAAACAAATCCTT
1 TTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGA-TTAAATGC-TCGTAAAAACAAATCCTT
* * * * * *
12309 ATATCCAATTTGGCTGAGATTTGGTTCGATAAATATAGATATTTCGAGAAGTTTTTATGCCAAAA
64 AAATCCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAA
* * * * ** * * *
12374 ATCATGCAAAACTGAGGC-AGGGCCTTGGAACACGTTTTTACACCTAAAACTGTGATGGTTATTA
129 ACCATGCAAAACTGAGTCGA-GGCCTCGAAACGTGTTTTTA-GCCAAAAACCGTGATGG----TA
* * * ***** * *
12438 CATGATTTCAGCTAAACACTGACCCGAAAAAAAAAATTCTAAAATTTTTGCCACAATACTCAGAA
188 CACGATTTCGGCTAAAAACTGACCCG-AAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAA
* ** * *
12503 AAAATATATAATTTAATGTAAAAAAAATTGACGGGTTTTTCACGTTTCTAATATCGTTTTTCCTT
252 AAAATATATAATTTAACGCCAAAAAGATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCTT
* *
12568 TTTTTTCCGAATTAATTTCTAATTAGATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTT
317 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* ** * *
12633 AAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATAATTCAAAAATTCTTTGTGCCAAAA
382 AAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAA
* * * * ***
12698 ATCATGTAAAATTGAGACGGGGCTCCAGAACTCGTTTTTAGGCAAGAATTATGATGGTTAGTACA
447 ATCATGCAAAACTGAG-CGGGGCTCCAGAACGCGTTTTTAGCCAA-AACCGTGATGGTTAGTACA
*
12763 CGATTTCGGCTAAAATTTTGCAAAAACTGA-CATGAAAAGTTTTTCCTCAATTTTTTTCCCACAA
510 CGATTTCGGCTAAAATTTTGCAAAAACTGATC-CGAAAAGTTTTTCCTCAA-TTTTTTCCCACAA
* * * * **
12827 TAGTCTGAAAAAATATATAACTCAACTCCAAAAAAAAATTGAAGGGTTTTTCAAACTTCTAATAT
573 TACTCAGAAAAAATATATAATTCAACGCC---AAAAAATTGAAGGGTTTTTCACGCTTCTAATAT
12892 CGTTTTCCTTTAT
635 CGTTTTCCTTTAT
*
12905 TTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATATAAATGCTCGTAAAAACAAATCTTTA
1 TTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGAT-TAAATGCTCGTAAAAACAAATCCTTA
* * * * *
12970 AATCCAATGTGGTTGAAATTTGCTTAGATGAATATAGATATTTCAAGGAGTCTATATGCCAAAAA
65 AATCCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAA
* *
13035 CCATGCAAAACTGTGTCGAGACCTCGAAACGTGTTTTTAGCCAAAAACCGTGATGGTACACGATT
130 CCATGCAAAACTGAGTCGAGGCCTCGAAACGTGTTTTTAGCCAAAAACCGTGATGGTACACGATT
*
13100 TCGGCTAAAAACTGACCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACTC-GTAAAAGAATA
195 TCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAG-AAAA-AATA
* * * *
13164 TATAATTTAACTCCAAAAAGATTGAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCATTTTTTT
258 TATAATTTAACGCCAAAAAGATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTT
* * * * * * * **
13229 CCGAATCAAATTCTAATTAAATCGAAATAAGATTTAAATGCTCGTAAACACAAATCGTTAAATTG
323 CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* * ** * * * *
13294 AATTTGGCTGGGATTTTATTCGATAAATATAGATATTTTAAGGAGTCTTAACGCCAAAAATCATG
388 AATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATG
* * * * *
13359 CAAAACAGAGCCGGGG-TCCCGGAACGCGTTTTTAGCCTTAAACTGTGAT-G--AGTAAACGATT
453 CAAAACTGAG-CGGGGCT-CCAGAACGCGTTTTTAGCC-AAAACCGTGATGGTTAGTACACGATT
* * * **
13420 TCGGCTAAAAATTTGCGAAAACTGATCCGAGAAA-TTTTACCTCAA-TGCTTCGCCACAATACTC
515 TCGGCTAAAATTTTGCAAAAACTGATCCGA-AAAGTTTTTCCTCAATTTTTTC-CCACAATACTC
* *
13483 AGAAAAAATTTATAATTCAATGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG--TT--
578 AGAAAAAATATATAATTCAACGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCC
13544 TTT-T
643 TTTAT
* * * * *
13548 TTTTCCATGAATTTGTTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAATAAATCCTT
1 TTTTTC-TGAATTTATTTCTAATTAAATCGAAACAAGATT-AAATGCTCGTAAAAACAAATCCTT
* * * * * *
13613 AAATCTAACT-TGGATGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTTTTTATACCAAA
64 AAATCCAA-TGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAA
* * * * *
13677 AATCATGCAAAACTGAATCG-GTGCCCCGAAAC-TCGTTTTTAGCGGGAAAAAAAAACGTGATGA
128 AACCATGCAAAACTGAGTCGAG-GCCTCGAAACGT-GTTTTTAGC-----CAAAAACCGTGATG-
* * * *
13740 TTAGTTCACGATTTTGGCTAAAAATTGACTCGAAAATTTTTTTCTCAATTTTTTGCCACAATACT
185 ---GTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACT
* * ** * * * *
13805 CA-AAAAATGTATATAATTTAAAGTAAAAAATG-TTGATGGACTTTTT-ACATTTCTAATATTGT
247 CAGAAAAA-ATATATAATTTAACGCCAAAAA-GATTGAAGG-GTTTTTCACGTTTCTAATATCGT
* *
13867 TTTTCTTTTTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
309 TTTTCCTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* *
13932 AAATCCTTATATCCAATTTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT-
374 AAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTA
* * * ** *
13996 TCGCCAAAAATCTTGCAAAATTGAGTCGGAGCTCTGGAACGCGTTTTTAGCCCAAGACCGTGATG
439 T-GCCAAAAATCATGCAAAACTGAG-CGGGGCTCCAGAACGCGTTTTTAG-CCAAAACCGTGATG
* * * * * *
14061 GTTAGTACACTATTTCAGCTAAAATTTTGCAAAAACTGA-CTTGAAAAGTTTTTTTCTTAATATT
501 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGATC-CGAAAAG-TTTTTCCTCAATTTT
*
14125 TTGCCACAATACTCAGAAAAAATATATAATTCAACGCC-------T--AGGGTTTTTCACGCTTC
564 TTCCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAATTGAAGGGTTTTTCACGCTTC
*
14181 TAATATCATTTTTCC---AT
629 TAATATC-GTTTTCCTTTAT
** * * *
14198 TTTTTCCAAATTTATTTCTAATTAAATTGAAATAAGATTCAAATACTCGTAAAAACAAATCCTTA
1 TTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATT-AAATGCTCGTAAAAACAAATCCTTA
* *
14263 AATCCAATGTGGCTGAGATTTGGTTAGATAAATATTGATATTTCAAGGAGTCTTTCTGCCAAAAA
65 AATCCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAA
*
14328 CCATGCAAAACTGAGTCGAGGCC-CTGAAATGCGT-TTTTTAGCCAAAAACCGTGATGGTTAGTA
130 CCATGCAAAACTGAGTCGAGGCCTC-GAAA--CGTGTTTTTAGCCAAAAACCGTGATGG-TA-CA
* * *
14391 CCTGATTTTCGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTTACCACAATACTCATAA
190 -C-GA-TTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAA
* *
14456 AAAATATATAATTTAACGCCAAAAAGATTGAAGGATTTTTCACGCATT-TAATATCGTTTTTCC-
252 AAAATATATAATTTAACGCCAAAAAGATTGAAGGGTTTTTCACG-TTTCTAATATCGTTTTTCCT
* * *
14519 --TTTTTCCGGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGT-AAAACAAATCT
316 TTTTTTTCC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* * *
14581 TTAAAT-CAAGTGTGGCT-AGGATTTGGTTCGATGCATATAGATATTTAAAGGAGTCTTTATACC
380 TTAAATCCAA-TGTGGCTGA-GATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCC
*
14644 AAAAATCATGCAAAACTTAGTCGGGG
443 AAAAATCATGCAAAACTGAG-CGGGG
14670 TTAAAAACTG
Statistics
Matches: 2014, Mismatches: 322, Indels: 190
0.80 0.13 0.08
Matches are distributed among these distances:
641 1 0.00
642 5 0.00
643 98 0.05
644 185 0.09
645 21 0.01
646 92 0.05
647 31 0.02
648 35 0.02
649 141 0.07
650 21 0.01
651 31 0.02
652 243 0.12
653 75 0.04
654 76 0.04
655 446 0.22
656 150 0.07
657 124 0.06
658 41 0.02
659 64 0.03
660 133 0.07
661 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (647 bp):
TTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTAAATGCTCGTAAAAACAAATCCTTAA
ATCCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAAC
CATGCAAAACTGAGTCGAGGCCTCGAAACGTGTTTTTAGCCAAAAACCGTGATGGTACACGATTT
CGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATAT
AATTTAACGCCAAAAAGATTGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTTCCG
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
GTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAA
AACTGAGCGGGGCTCCAGAACGCGTTTTTAGCCAAAACCGTGATGGTTAGTACACGATTTCGGCT
AAAATTTTGCAAAAACTGATCCGAAAAGTTTTTCCTCAATTTTTTCCCACAATACTCAGAAAAAA
TATATAATTCAACGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCTTTAT
Found at i:13178 original size:322 final size:316
Alignment explanation
Indices: 11595--14668 Score: 2376
Period size: 324 Copynumber: 9.5 Consensus size: 316
11585 CATATTTTTT
* * * * *
11595 GAATTAATTTCTAATTAAATCGAAATAAGATTTAAATACTCGTAAAAATAAATCCTTAAATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * * * * ** *
11660 TATGTCTCAGACTTTGATTAGATAAATA-ACGATATTTCAAGGAGTCTCAATGCCAAAAACCATG
66 TGTGGCTGAGA-TTTGGTTCGATGAATATA-GATATTTCAAGGAGTCTTTATGCCAAAAATCATG
* ** * * * * * *
11724 CAAAACAGAACCGTGGTCCT-GGAAGGCGTTTTTAGCCAAAAACTGTGATGGTTAGTATATGATT
129 CAAAACTGAGTCG-GG-CCTCGAAACGTGTTTTTAGCCAAAAACCGTGAT-G-T-GTACACGATT
* * * * **
11788 TCGGCTAAGAACTGACCAGAAAAGTTTTTTCTCAATTTTTTGCCATAATACTAAAATATATATAT
189 TCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCGAA-A-A-A-AT
* * * * * * * *
11853 ATATAATTCAACGCCAAAAAGATTGACGGGCTCTTAACGTTTCTAATATCGTTTTTCCATTTTTT
250 ATATAATTTAACTCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTTCC-TTTTTT
11918 TT-C
313 TTCC
* * * * *
11921 GAATTGATTTCTAACTAAATCGAAACAAGATTAAGATGATCGTAAAAACAAATACTTAAATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * * * * ** *
11986 TGTAGCCGGGATTTGGTTAGATAAATATAGATATTTCAAGAAGTCTTTACACCAAAAATCATCCA
66 TGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCA
* * * * *
12051 AAACTGAGCCGGGCCCCAAAACGCGTTTTTAGCCATAAACCGTGATGGTTAGTACACACGATTTC
131 AAACTGAGTCGGGCCTCGAAACGTGTTTTTAGCCAAAAACCGTGAT-G-T-GT--ACACGATTTC
* ** * *
12116 GGCTAAGATTTTGTAAAAACTGATCCG-ATTTTTTTTTCTCAATTTTTT-CCATAATACT-AAAA
191 GGC----------TAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCGAAA
** * * * * *
12178 AATATATATAATTTCAAAGCCAAAAAAATTGACGGACTTTTT-ACGTTTCTAATATCATTTTTCT
246 AA-ATATATAATTT-AACTCCAAAAAAATTGAAGG-GTTTTTCACGCTTCTAATATC-GTTTTCC
*
12242 TTTTTTTTTC
307 TTTTTTTTCC
* *
12252 GAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTC-TAAAAACAAATCCTTATATCCA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC-TCGTAAAAACAAATCCTTAAATCCA
* * * * *
12316 ATTTGGCTGAGATTTGGTTCGATAAATATAGATATTTCGAGAAGTTTTTATGCCAAAAATCATGC
65 ATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGC
* * * ** * * * * *
12381 AAAACTGAGGCAGGGCCTTGGAACACGTTTTTACACCTAAAACTGTGATGGTTATTACATGATTT
130 AAAACTGAGTC-GGGCCTCGAAACGTGTTTTTA-GCCAAAAACCGTGAT-G-T-GTACACGATTT
* * ***** * *
12446 CAGCTAAACACTGACCCGAAAAAAAAAATTCTAAAATTTTTGCCACAATACTCAGAAAAAATATA
190 CGGCTAAAAACTGACCCG-AAAATTTTTTTCTCAATTTTTTGCCACAATACTC-GAAAAAATATA
** * *
12511 TAATTTAA-TGTAAAAAAAATTGACGGGTTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTTC
253 TAATTTAACT-CCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTTCCTTTTTTTTC
12575 C
316 C
* *
12576 GAATTAATTTCTAATTAGATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* ** * * *
12641 TGTGGCTGAGATTTGGTTCGATGAATATAGATAATTCAAAAATTCTTTGTGCCAAAAATCATGTA
66 TGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCA
* * * * * * ***
12706 AAATTGAGACGGGGCTCCAGAAC-TCGTTTTTAGGCAAGAATTATGATGGTTAGTACACGATTTC
131 AAACTGAGTCGGGCCTCGA-AACGT-GTTTTTAGCCAAAAACCGTGAT-G-T-GTACACGATTTC
** * * * *
12770 GGCTAAAATTTTGCAAAAACTGACATGAAAAGTTTTTCCTCAATTTTTTTCCCACAATAGTCTGA
191 GGC--------T--AAAAACTGACCCGAAAATTTTTTTCTCAA-TTTTTTGCCACAATACTC-GA
* * **
12835 AAAAATATATAACTCAACTCCAAAAAAAAATTGAAGGGTTTTTCAAACTTCTAATATCGTTTTCC
244 AAAAATATATAATTTAACTCC--AAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCC
*
12900 TTTATTTTTTCT
307 -TT-TTTTTTCC
* * *
12912 GAATTTATTTCTAATTAAATCGAAACAAGATAT-AAATGCTCGTAAAAACAAATCTTTAAATCCA
1 GAATTAATTTCTAATTAAATCGAAACAAGAT-TCAGATGCTCGTAAAAACAAATCCTTAAATCCA
* * * * * *
12976 ATGTGGTTGAAATTTGCTTAGATGAATATAGATATTTCAAGGAGTCTATATGCCAAAAACCATGC
65 ATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGC
* *
13041 AAAACTGTGTCGAGACCTCGAAACGTGTTTTTAGCCAAAAACCGTGATG-GTACACGATTTCGGC
130 AAAACTGAGTCG-GGCCTCGAAACGTGTTTTTAGCCAAAAACCGTGATGTGTACACGATTTCGGC
*
13105 TAAAAACTGACCCGAAATTTTTTTTCTCAATTTTTTGCCACAATACTCGTAAAAGAATATATAAT
194 TAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCG-AAAA-AATATATAAT
* * *
13170 TTAACTCCAAAAAGATTGAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCATTTTTTTCC
257 TTAACTCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTTCCTTTTTTTTCC
* * * * * * * **
13231 GAATCAAATTCTAATTAAATCGAAATAAGATTTAAATGCTCGTAAACACAAATCGTTAAATTGAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * ** * * * *
13296 TTTGGCTGGGATTTTATTCGATAAATATAGATATTTTAAGGAGTCTTAACGCCAAAAATCATGCA
66 TGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCA
* * * * ** * * *
13361 AAACAGAGCCGGGGTCC-CGGAACGCGTTTTTAGCCTTAAACTGTGATGAGTAAACGATTTCGGC
131 AAACTGAGTC-GGG-CCTCGAAACGTGTTTTTAGCCAAAAACCGTGATGTGTACACGATTTCGGC
* ** ** *
13425 TAAAAATTTGCGAAAACTGATCCGAGAAA-TTTTACCTCAATGCTTCGCCACAATACTCAGAAAA
194 T----A------AAAACTGACCCGA-AAATTTTTTTCTCAATTTTTTGCCACAATACTC-GAAAA
* *
13489 AATTTATAATTCAA-TGCC-AAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG--TT--TTTT
247 AATATATAATTTAACT-CCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCTTTT
13548 TTTTCC
311 TTTTCC
** * * *
13554 ATGAATTTGTTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAATAAATCCTTAAATCT
1 --GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* * * * *
13619 AACT-TGGATGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTTTTTATACCAAAAATCAT
64 AA-TGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCAT
* * * * *
13683 GCAAAACTGAATCGGTGCCCCGAAAC-TCGTTTTTAGCGGGAAAAAAAAACGTGATGATTAGTTC
128 GCAAAACTGAGTCGG-GCCTCGAAACGT-GTTTTTAGC-----CAAAAACCGTGATG--T-GTAC
* * *
13747 ACGATTTTGGCTAAAAATTGACTCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTC-AAAAA
183 ACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCGAAAAA
* * * * ** * *
13811 ATGTATATAATTTAAAGT--AAAAAATGTTGATGGACTTTTT-ACATTTCTAATATTGTTTTTCT
248 A--TATATAATTT-AACTCCAAAAAA-ATTGAAGG-GTTTTTCACGCTTCTAATATCG-TTTTCC
*
13873 TTTTTTTTTC
307 TTTTTTTTCC
*
13883 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* *
13948 TTTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT-TCGCCAAAAATCTTGC
66 TGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAT-GCCAAAAATCATGC
* * * * * *
14012 AAAATTGAGTCGGAG-CTCTGGAACGCGTTTTTAGCCCAAGACCGTGATGGTTAGTACACTATTT
130 AAAACTGAGTCGG-GCCTC-GAAACGTGTTTTTAGCCAAAAACCGTGAT-G-T-GTACACGATTT
* ** * *
14076 CAGCTAAAATTTTGCAAAAACTGACTTGAAAAGTTTTTTTCTTAATATTTTGCCACAATACTCAG
190 CGGC--------T--AAAAACTGACCCGAAAA-TTTTTTTCTCAATTTTTTGCCACAATACTC-G
* * *
14141 AAAAAATATATAATTCAACGCC--------T--AGGGTTTTTCACGCTTCTAATATCATTTTTCC
243 AAAAAATATATAATTTAACTCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATC-GTTTTCC
*
14196 -ATTTTTTCC
307 TTTTTTTTCC
* * * * * *
14205 AAATTTATTTCTAATTAAATTGAAATAAGATTCAAATACTCGTAAAAACAAATCCTTAAATCCAA
1 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * * *
14270 TGTGGCTGAGATTTGGTTAGATAAATATTGATATTTCAAGGAGTCTTTCTGCCAAAAACCATGCA
66 TGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCA
14335 AAACTGAGTCGAGGCC-CTGAAATGCGT-TTTTTAGCCAAAAACCGTGATGGTTAGTAC-CTGAT
131 AAACTGAGTCG-GGCCTC-GAAA--CGTGTTTTTAGCCAAAAACCGTGAT-G-T-GTACAC-GA-
* * *
14397 TTTCGGCTAAAAACTTACCCGAAAATTTTTTTCTCAATTTTTTACCACAATACTCATAAAAAATA
187 TTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTC-GAAAAAATA
* * *
14462 TATAATTTAACGCCAAAAAGATTGAAGGATTTTTCACGCATT-TAATATCGTTTTTCC---TTTT
251 TATAATTTAACTCCAAAAAAATTGAAGGGTTTTTCACGC-TTCTAATATCG-TTTTCCTTTTTTT
14523 TCC
314 TCC
* * *
14526 GGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGT-AAAACAAATCTTTAAAT-CA
1 -GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCA
* * *
14589 AGTGTGGCT-AGGATTTGGTTCGATGCATATAGATATTTAAAGGAGTCTTTATACCAAAAATCAT
65 A-TGTGGCTGA-GATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCAT
*
14653 GCAAAACTTAGTCGGG
128 GCAAAACTGAGTCGGG
14669 GTTAAAAACT
Statistics
Matches: 2229, Mismatches: 377, Indels: 290
0.77 0.13 0.10
Matches are distributed among these distances:
313 49 0.02
314 14 0.01
316 1 0.00
318 1 0.00
319 148 0.07
320 59 0.03
321 133 0.06
322 247 0.11
323 185 0.08
324 254 0.11
325 198 0.09
326 83 0.04
327 140 0.06
328 34 0.02
329 24 0.01
330 70 0.03
331 174 0.08
332 63 0.03
333 112 0.05
334 17 0.01
335 59 0.03
336 157 0.07
337 7 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (316 bp):
GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
TGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCA
AAACTGAGTCGGGCCTCGAAACGTGTTTTTAGCCAAAAACCGTGATGTGTACACGATTTCGGCTA
AAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCGAAAAAATATATAATTTAA
CTCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCTTTTTTTTCC
Found at i:15770 original size:52 final size:52
Alignment explanation
Indices: 15645--15761 Score: 200
Period size: 52 Copynumber: 2.2 Consensus size: 52
15635 TGGCTTGGCT
*
15645 TTTGGGTTCAAAATTAGCTCTTGACACAAACCATGATTTATTTGGTATTGCG
1 TTTGGGTTCAAAATTAGCTTTTGACACAAACCATGATTTATTTGGTATTGCG
*
15697 TTTGGGTTCAAAATTAGCTTTTGACACAAACCAT-ATTTTATTTGGTATTGTG
1 TTTGGGTTCAAAATTAGCTTTTGACACAAACCATGA-TTTATTTGGTATTGCG
15749 TTTGGGTTCAAAA
1 TTTGGGTTCAAAA
15762 GCAACTTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 1 0.02
52 61 0.98
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (52 bp):
TTTGGGTTCAAAATTAGCTTTTGACACAAACCATGATTTATTTGGTATTGCG
Found at i:34535 original size:29 final size:30
Alignment explanation
Indices: 34493--34554 Score: 108
Period size: 31 Copynumber: 2.1 Consensus size: 30
34483 TTCCCCTGTT
34493 TTGGTGTAG-TATATATATGGGATTAATGG
1 TTGGTGTAGATATATATATGGGATTAATGG
34522 TTGGTGTAGTATATATATATGGGATTAATGG
1 TTGGTGTAG-ATATATATATGGGATTAATGG
34553 TT
1 TT
34555 TGCTCAGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 9 0.29
31 22 0.71
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (30 bp):
TTGGTGTAGATATATATATGGGATTAATGG
Found at i:35411 original size:17 final size:17
Alignment explanation
Indices: 35389--35422 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
35379 ATGCATGAAC
35389 TATATA-GTATATATATA
1 TATATATGTA-ATATATA
35406 TATATATGTAATATATA
1 TATATATGTAATATATA
35423 GTTTGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TATATATGTAATATATA
Found at i:37769 original size:2 final size:2
Alignment explanation
Indices: 37762--37797 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
37752 TATACACATC
37762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37798 TAAAACTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37856 original size:30 final size:30
Alignment explanation
Indices: 37822--37881 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
37812 TTGGACAAAA
*
37822 GGAAATAAATTAATCACTTTAGGTTGATTG
1 GGAAATAAATTAATCACTTTAGATTGATTG
* * *
37852 GGAAATATATTAATTAGTTTAGATTGATTG
1 GGAAATAAATTAATCACTTTAGATTGATTG
37882 ATTAATTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (30 bp):
GGAAATAAATTAATCACTTTAGATTGATTG
Done.