Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010566.1 Corchorus capsularis cultivar CVL-1 contig10587, 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: 31551
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:594 original size:318 final size:315
Alignment explanation
Indices: 1--783 Score: 984
Period size: 318 Copynumber: 2.5 Consensus size: 315
* *
1 AATATATTTTGCGAAAAAATGAGAAATAATTTTTCGAGTCAG-TTTTAGCCAAAATTGTCTATTA
1 AATATATTTTTCGAAAAAATGAGAAATAA-TTTTCGAGTCAGTTTTTAGCC-AAATTGTGTATTA
* * * *
65 ACCATCACGGTTCTTCGCTAAAAACCCGTTCCGGGGTCTCAGCTCAGTTTTGCATGTTTTTTTGC
64 ACCATCACGGTT-TTCGC-AAAAACGCGTTCTGGGGTCTCAGCTCAGTTTAGCATGATTTTTTGC
* * *
130 AGTAAGACTCATTGAAATATTTAAATTCATCAAACCAAATCTCAGCCACGTTGGATTTAAGGATT
127 AGAAAGACTCATTGAAATATTTAAATTCATCAAACCAAATCTCAGACACATTGGATTTAAGGATT
* * * * * *
195 TTTTTTTACGTACATCTAAATCTTGTTACGATTTAACTAAAAATAAATTCGAAATAATTACAAAA
192 TATTTTTACGTACATATAAATCTTATTACGATTTAACTAAAAATAAATTCAAAAAAAATACAAAA
*
260 ACAATATTACAAGCGGGAAAATCCCGTCAATTTTTTTTCGCATT-AAAT-TATATTTTTTT
257 ACAATATTACAAGCGGGAAAATCCCGTCAA--TTTTTTCGCATTGAAATATATATTTTTTC
* * *
319 AATATATTTTTCGAAATATTGAGAAATAATTTTACGAGTCAGTTTTTAGCCAAATTTATGTATTA
1 AATATATTTTTCGAAAAAATGAGAAATAATTTT-CGAGTCAGTTTTTAGCCAAA-TTGTGTATTA
*
384 ACCATCACGGTTGTTCGCAAAAACGCATTCTGGGGTCTCAGCTCAGTTTAGCATGATTTTTTGCA
64 ACCATCACGGTT-TTCGCAAAAACGCGTTCTGGGGTCTCAGCTCAGTTTAGCATGATTTTTTGCA
*
449 GAAAGACTCATTGAAAT-TTCTAAATTCATCAAACCAAATCTTAGACACATTGGATTTAAGGATT
128 GAAAGACTCATTGAAATATT-TAAATTCATCAAACCAAATCTCAGACACATTGGATTTAAGGATT
* * * * **
513 TATTTTTACGTGCATATAAATTTTATTTCGATTTAATTAAAAATAAATTCAAAAAAAATGGAAAA
192 TATTTTTACGTACATATAAATCTTATTACGATTTAACTAAAAATAAATTCAAAAAAAATACAAAA
** * *
578 ATGATATTAGAAGCGGGAAAATCCCGTCAATTTTTTGGCATTGAAATATATATTTTTTC
257 ACAATATTACAAGCGGGAAAATCCCGTCAATTTTTTCGCATTGAAATATATATTTTTTC
* * * *
637 AGA-ATAATTTTTGCGAAAAACTGAGAAATAATTTTCGGGTTAGTTTTTAGCCGAAATCGTGTAT
1 A-ATAT-ATTTTT-CGAAAAAATGAGAAATAATTTTCGAGTCAGTTTTTAGCC-AAATTGTGTAT
* * * * * * * *
701 TAACTATCACGGTTTTCGGCTAAAACGTGTT-TTGGGACCCGGCTCAGTTTAGCATAATTTTTTG
62 TAACCATCACGGTTTTC-GCAAAAACGCGTTCTGGGGTCTCAGCTCAGTTTAGCATGATTTTTTG
* *
765 CAGAAAGATTCCTTGAAAT
126 CAGAAAGACTCATTGAAAT
784 GGGTCCGGCT
Statistics
Matches: 405, Mismatches: 49, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
316 11 0.03
317 10 0.02
318 277 0.68
319 84 0.21
320 23 0.06
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (315 bp):
AATATATTTTTCGAAAAAATGAGAAATAATTTTCGAGTCAGTTTTTAGCCAAATTGTGTATTAAC
CATCACGGTTTTCGCAAAAACGCGTTCTGGGGTCTCAGCTCAGTTTAGCATGATTTTTTGCAGAA
AGACTCATTGAAATATTTAAATTCATCAAACCAAATCTCAGACACATTGGATTTAAGGATTTATT
TTTACGTACATATAAATCTTATTACGATTTAACTAAAAATAAATTCAAAAAAAATACAAAAACAA
TATTACAAGCGGGAAAATCCCGTCAATTTTTTCGCATTGAAATATATATTTTTTC
Found at i:3968 original size:188 final size:188
Alignment explanation
Indices: 3643--4014 Score: 593
Period size: 188 Copynumber: 2.0 Consensus size: 188
3633 GGCTCTGCCA
*
3643 ATAGGTCTGTTTTCTATAATTCATGTCCCATAATCTCGTTAGCTACACTGACTACTGCATTGATT
1 ATAGGTCTGTTTCCTATAATTCATGTCCCATAATCTCGTTAGCTACACTGACTACTGCATTGATT
* *
3708 AGCTATTTATGAAGTGTCATTGCATTTTGAATAGCCATTTGTCACTGTAGATCGTTCGAATTTGG
66 AGCTATTTATGAAGTGTCATTCCATTTTGAATAGCCATTTGTCACTATAGATCGTTCGAATTTGG
* * * *
3773 AATTGTGGTTTAGAGGCTTGATTTACTTCTAAATTCGATCATTGCAGGAAATGACAAT
131 AATTGTGGTTAAGAGGCTTCAGTTAATTCTAAATTCGATCATTGCAGGAAATGACAAT
* * * * *
3831 ATAGTTCTGTTTCCTATAATTCATGTCCCATATTCTTGTTAGCTACATTGATTACTGCATTGATT
1 ATAGGTCTGTTTCCTATAATTCATGTCCCATAATCTCGTTAGCTACACTGACTACTGCATTGATT
**
3896 AGCTATTTATGAAGTGTCATTCCATTTTGAATAGCCATTTGTCACTATAGATTTTTCGAATTT-G
66 AGCTATTTATGAAGTGTCATTCCATTTTGAATAGCCATTTGTCACTATAGATCGTTCGAATTTGG
*
3960 ACATTGTGGTTAAGAGGCTTCAGTTAATTCTAAATTTGATCATTGCAGGAAATGA
131 A-ATTGTGGTTAAGAGGCTTCAGTTAATTCTAAATTCGATCATTGCAGGAAATGA
4015 AGTAGGAGGT
Statistics
Matches: 168, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
187 2 0.01
188 166 0.99
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (188 bp):
ATAGGTCTGTTTCCTATAATTCATGTCCCATAATCTCGTTAGCTACACTGACTACTGCATTGATT
AGCTATTTATGAAGTGTCATTCCATTTTGAATAGCCATTTGTCACTATAGATCGTTCGAATTTGG
AATTGTGGTTAAGAGGCTTCAGTTAATTCTAAATTCGATCATTGCAGGAAATGACAAT
Found at i:7501 original size:5 final size:5
Alignment explanation
Indices: 7457--7500 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
7447 GAATTATCAC
*
7457 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAT ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
7501 TGATCACAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:14450 original size:331 final size:331
Alignment explanation
Indices: 13118--14962 Score: 1965
Period size: 331 Copynumber: 5.6 Consensus size: 331
13108 CTTTGTTACC
* * * * * * * *
13118 AAAAATCGTGATAGTTAATACACGATTTCGGTTAAAATTTTGTAAAAATTTACCCTAAAGAATTT
1 AAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGTAAAAATTGACCCGAGA-AATTT
* *** * * *
13183 -TCCTAAATTTTTAACCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAAAG
65 CTCCTCAATTTTCGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGG
* * * ** * **
13247 TTTTTCACGCTTTTAATATCG-GTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATTAAAACA
130 TTTCTCACGCTTCTAATATCGTTTTTTTTTCTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * * **
13311 TGATTCAGATGCTCATAAAAACAAATCATTAAGTACAATGCAGTTGAGATTTGGTTAGATGGATA
195 TGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGTTGAGATTTGGTTAGATGGATA
* * * * * *
13376 TATATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAGCAGAGTCGGGACCCC-GAAGTGCG
259 TAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAA-CGCG
**
13440 TTTTTAGAAAA
323 TTTTTAG--CT
* * * *
13451 AAAAACTGTGATGGTTAGTACACGATTTC-GTTTAAAATTTTGCAAAAATTGACACGA-AACATT
1 AAAAACCGTGATGGTTAGTACACGATTTCAG-CTAAAATTTTGTAAAAATTGACCCGAGAA-ATT
* * * * * *
13514 TCTCCTCAATTTCCGGCCACCATATTCATAAAAAATACATAA--CAACATCAAAAAGATTGAAGG
64 TCTCCTCAATTTTCGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAG
* *
13577 GTTTCTCACGCTTCTAATATTGTTTTTTTTTCTATTTTTCCGAATTAATTTCTAATTAAATCAAA
129 GTTTCTCACGCTTCTAATATCGTTTTTTTTTC--TTTTTCCGAATTAATTTCTAATTAAATCGAA
* * ** * *
13642 AC-TGGATTAAGATGCTTGTAAAAA-AAATCCTTAAATCCAATGTATTTGAGATTTCGTTAGATA
192 ACAT-GATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGTTGAGATTTGGTTAGATG
* * * * *
13705 AATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAAACTGAACCGGGGCCGCGGAAC
255 GATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAAC
*
13770 GCGTTTTTAGCC
320 GCGTTTTTAGCT
* * * *
13782 ACAAACCGTGATAGTTAGTACACCGATTTCAGCTAAAATTTTGTAAAAGTTGACCCGATTG-AGT
1 AAAAACCGTGATGGTTAGTACA-CGATTTCAGCTAAAATTTTGTAAAAATTGACCCGA--GAAAT
* * *
13846 TT-TCCTCATTTTTTGGCCACGATACTCAT-AAAAATATATAATTTAACACCAAAAAGATTGAAA
63 TTCTCCTCAATTTTCGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAA
* * * * * *
13909 GGATCCTCACGCTTCTAATATCATTTTTCCTAT-TTTTTCCGAATTAA-TTCTTAATTGAATCGA
128 GGTTTCTCACGCTTCTAATATCGTTTTT-TTTTCTTTTTCCGAATTAATTTC-TAATTAAATCGA
* * *
13972 AACATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTAAGATTTGGTTAGATG
191 AACATGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGTTGAGATTTGGTTAGATG
* * * ** * *
14037 GATATAGATATTTCAATGAAACTTGGCGCCAAAAATCGTGCAAAACTGAGTCTTGGCTCCGAAAC
255 GATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAAC
* *
14102 GCGTTTCTAGTT
320 GCGTTTTTAGCT
* *
14114 AAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAGATTGACCCGAGAAATTTC
1 AAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGTAAAAATTGACCCGAGAAATTTC
* * * * * * ** * *
14179 TTCTAAATTTCCGGCCACCATATTCATAAAAAGTATATAATTCAACGTCAAAAAGATTGAAGGGC
66 TCCTCAATTTTCGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGT
*
14244 TTCTCACGCTTCTAATATTGTTTTTTTTTCTATTTTCCGAATTAATTTCTAATTAAATCGAAACC
131 TTCTCACGCTTCTAATATCGTTTTTTTTTCT-TTTTCCGAATTAATTTCTAATTAAATCGAAA-C
* * * **
14309 A-GATTGAGATGCTCGTAAAAACAAATCCTGAAATCTAATGTGGTTGAGATTTCGTTAGATAAAT
194 ATGATTCAGATGCTCGTAAAAACAAATCCTTAAATC-AATGTGGTTGAGATTTGGTTAGATGGAT
*
14373 ATAGATATTTCAATGAGTCTTGGCGCC-AAAAT-ATGCAAAACTGAGCCGGGGCCCCGGAACGCG
258 ATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCG
14436 TTTTTAGCT
323 TTTTTAGCT
* * *
14445 AAAAACCGTGATAGG-TAGTACATGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGAATT
1 AAAAACCGTGAT-GGTTAGTACACGATTTCAGCTAAAATTTTGTAAAAATTGACCCGAGA-AATT
* * * *
14509 T-TCCTCTATTTTGGGCCACGATAATCATAAAAAATATATAATTCAACACCAAAAATATTGAAAG
64 TCTCCTCAATTTTCGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAG
* * ** * *
14573 GCTAT-TCACGCTTATAATATCGTTTTTCCNATT-TTTTT-CGAATTAATTCCTAATTCAATCGA
129 G-TTTCTCACGCTTCTAATATCGTTTTT--TTTTCTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * *
14635 AACATGATTCATATGCTCGTAAAAACGAATCCTTAAATGCAATGTGGGTAAGATTTGGTTAGATG
191 AACATGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGTTGAGATTTGGTTAGATG
* *
14700 GATATAGAT-TTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGCCGGGGCTCCGGAAC
255 GATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAAC
14764 GCGTTTTTAG-T
320 GCGTTTTTAGCT
* * * * *
14775 CAAAAACCGTGATGATTAGTACACGATTTCAACTAAAATTTTGTAAAAATTTATCTGAGAAATTT
1 -AAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGTAAAAATTGACCCGAGAAATTT
* * * * * * *
14840 CTCCTCAATTTTGGGCCACGATACTAATAAAAAATATATAACTCAACGCAAAAAAGAATGAAGGG
65 CTCCTCAATTTTCGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGG
* * * * **** * *
14905 TTTGTTACGCTTGTAATATTGCTTTTCCAATCTTTTACCAAATTAATTTCTAATTAAA
130 TTTCTCACGCTTCTAATATCG-TTTTTTTTTCTTTTTCCGAATTAATTTCTAATTAAA
14963 AAAAGTATAT
Statistics
Matches: 1260, Mismatches: 209, Indels: 87
0.81 0.13 0.06
Matches are distributed among these distances:
329 22 0.02
330 105 0.08
331 482 0.38
332 268 0.21
333 323 0.26
334 60 0.05
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (331 bp):
AAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGTAAAAATTGACCCGAGAAATTTC
TCCTCAATTTTCGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGT
TTCTCACGCTTCTAATATCGTTTTTTTTTCTTTTTCCGAATTAATTTCTAATTAAATCGAAACAT
GATTCAGATGCTCGTAAAAACAAATCCTTAAATCAATGTGGTTGAGATTTGGTTAGATGGATATA
GATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTT
TTAGCT
Found at i:14617 original size:663 final size:661
Alignment explanation
Indices: 13116--14962 Score: 2474
Period size: 665 Copynumber: 2.8 Consensus size: 661
13106 TCCTTTGTTA
* * * * *
13116 CCAAAAATCGTGATAGTTAATACACGATTTCGGTTAAAATTTTGTAAAAATTTACCCTAAAGAAT
1 CCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGAAT
* ** * *
13181 TTTCCTAAATTTTTAACCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAAA
66 TTTCCT-CATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAAG
* * * * **
13246 GTTTTTCACGCTTTTAATATCGGTTTTCCTA-TTTTTCCGAATTAATT-TCTAATTAAATTAAAA
130 GATATTCACGCTTATAATATCGTTTTTCCTATTTTTTCCGAATTAATTCT-TAATTAAATCGAAA
* * * * ** * *
13309 CATGATTCAGATGCTCATAAAAACAAATCATTAAGTACAATGCAGTTGAGATTTGGTTAGATGGA
194 CATGATTCATATGCTCGTAAAAACAAATCCTTAAATACAATGTGGGTAAGATTTGGTTAGATGGA
* * * * * **
13374 TATATATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAGCAGAGTCGGGACCCCGAAGTGC
259 TATAGATATTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGTCGGG-CTCCGAAACGC
* * *
13439 GTTTTTAGAAAAAAAAACTGTGATGGTTAGTACACGATTTC-GTTTAAAATTTTGCAAAAATTGA
323 GTTTTTAG--TAAAAAACCGTGATGGTTAGTACACGATTTCAG-CTAAAATTTTGCAAAAATTGA
* * *
13503 CACGA-AACATTTCTCCTCAATTTCCGGCCACCATATTCATAAAAAATACATAA-CAACATCAAA
385 CCCGAGAA-ATTTCTCCTCAATTTCCGGCCACCATATTCATAAAAAATATATAATCAACGTCAAA
13566 AAGATTGAAGGGTTTCTCACGCTTCTAATATTGTTTTTTTTTCTATTTTTCCGAATTAATTTCTA
449 AAGATTGAAGGGTTTCTCACGCTTCTAATATTGTTTTTTTTTCTA-TTTTCCGAATTAATTTCTA
** * * *
13631 ATTAAATCAAAACTGGATTAAGATGCTTGTAAAAAAAATCCTTAAATCCAATGTATTTGAGATTT
513 ATTAAATCAAAACCAGATTAAGATGCTCGTAAAAAAAATCCTGAAATCCAATGTAGTTGAGATTT
13696 CGTTAGATAAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAAACTGAACCGGGG
578 CGTTAGATAAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAAACTGAACCGGGG
*
13761 CCGCGGAACGCGTTTTTAG
643 CCCCGGAACGCGTTTTTAG
* * * ** *
13780 CCACAAACCGTGATAGTTAGTACACCGATTTCAGCTAAAATTTTGTAAAAGTTGACCCGATTGAG
1 CCAAAAACCGTGATAGTTAGTACA-CGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGAA
* *
13845 TTTTCCTCATTTTTTGGCCACGATACTCAT-AAAAATATATAATTTAACACCAAAAAGATTGAAA
65 TTTTCCTCA-TTTTTGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAA
** * * *
13909 GGATCCTCACGCTTCTAATATCATTTTTCCTATTTTTTCCGAATTAATTCTTAATTGAATCGAAA
129 GGATATTCACGCTTATAATATCGTTTTTCCTATTTTTTCCGAATTAATTCTTAATTAAATCGAAA
*
13974 CATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTAAGATTTGGTTAGATGGA
194 CATGATTCATATGCTCGTAAAAACAAATCCTTAAATACAATGTGGGTAAGATTTGGTTAGATGGA
* *
14039 TATAGATATTTCAATGAAACTTGGCGCCAAAAATCGTGCAAAACTGAGTCTTGGCTCCGAAACGC
259 TATAGATATTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGTC-GGGCTCCGAAACGC
* * *
14104 GTTTCTAGTTAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAGATTGACCC
323 GTTTTTAGTAAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCC
* * *
14169 GAGAAATTTCTTCTAAATTTCCGGCCACCATATTCATAAAAAGTATATAATTCAACGTCAAAAAG
388 GAGAAATTTCTCCTCAATTTCCGGCCACCATATTCATAAAAAATATATAA-TCAACGTCAAAAAG
*
14234 ATTGAAGGGCTTCTCACGCTTCTAATATTGTTTTTTTTTCTATTTTCCGAATTAATTTCTAATTA
452 ATTGAAGGGTTTCTCACGCTTCTAATATTGTTTTTTTTTCTATTTTCCGAATTAATTTCTAATTA
* * * *
14299 AATCGAAACCAGATTGAGATGCTCGTAAAAACAAATCCTGAAATCTAATGTGGTTGAGATTTCGT
517 AATCAAAACCAGATTAAGATGCTCGTAAAAA-AAATCCTGAAATCCAATGTAGTTGAGATTTCGT
* *
14364 TAGATAAATATAGATATTTCAATGAGTCTTGGCGCC-AAAAT-ATGCAAAACTGAGCCGGGGCCC
581 TAGATAAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAAACTGAACCGGGGCCC
14427 CGGAACGCGTTTTTAG
646 CGGAACGCGTTTTTAG
* * *
14443 CTAAAAACCGTGATAGGTAGTACATGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGAAT
1 CCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGAAT
* * *
14508 TTTCCTCTATTTTGGGCCACGATAATCATAAAAAATATATAATTCAACACCAAAAATATTGAAAG
66 TTTCCTC-ATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAAG
* * * * *
14573 GCTATTCACGCTTATAATATCGTTTTTCCNATTTTTTTCGAATTAATTCCTAATTCAATCGAAAC
130 GATATTCACGCTTATAATATCGTTTTTCCTATTTTTTCCGAATTAATTCTTAATTAAATCGAAAC
* *
14638 ATGATTCATATGCTCGTAAAAACGAATCCTTAAATGCAATGTGGGTAAGATTTGGTTAGATGGAT
195 ATGATTCATATGCTCGTAAAAACAAATCCTTAAATACAATGTGGGTAAGATTTGGTTAGATGGAT
* *
14703 ATAGAT-TTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGCCGGGGCTCCGGAACGCG
260 ATAGATATTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGTC-GGGCTCCGAAACGCG
* * * * * * *
14767 TTTTTAGTCAAAAACCGTGATGATTAGTACACGATTTCAACTAAAATTTTGTAAAAATTTATCTG
324 TTTTTAGTAAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCG
** * * *
14832 AGAAATTTCTCCTCAATTTTGGGCCACGATACTAATAAAAAATATATAACTCAACG-CAAAAAAG
389 AGAAATTTCTCCTCAATTTCCGGCCACCATATTCATAAAAAATATATAA-TCAACGTC-AAAAAG
* * * * **** * *
14896 AATGAAGGGTTTGTTACGCTTGTAATATTGCTTTTCCAATCT-TTTACCAAATTAATTTCTAATT
452 ATTGAAGGGTTTCTCACGCTTCTAATATTG-TTTTTTTTTCTATTTTCCGAATTAATTTCTAATT
14960 AAA
516 AAA
14963 AAAAGTATAT
Statistics
Matches: 1041, Mismatches: 128, Indels: 30
0.87 0.11 0.03
Matches are distributed among these distances:
661 1 0.00
662 270 0.26
663 315 0.30
664 135 0.13
665 317 0.30
666 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (661 bp):
CCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGAAT
TTTCCTCATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAAGG
ATATTCACGCTTATAATATCGTTTTTCCTATTTTTTCCGAATTAATTCTTAATTAAATCGAAACA
TGATTCATATGCTCGTAAAAACAAATCCTTAAATACAATGTGGGTAAGATTTGGTTAGATGGATA
TAGATATTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACTGAGTCGGGCTCCGAAACGCGTT
TTTAGTAAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAG
AAATTTCTCCTCAATTTCCGGCCACCATATTCATAAAAAATATATAATCAACGTCAAAAAGATTG
AAGGGTTTCTCACGCTTCTAATATTGTTTTTTTTTCTATTTTCCGAATTAATTTCTAATTAAATC
AAAACCAGATTAAGATGCTCGTAAAAAAAATCCTGAAATCCAATGTAGTTGAGATTTCGTTAGAT
AAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAAACTGAACCGGGGCCCCGGAA
CGCGTTTTTAG
Found at i:15076 original size:27 final size:28
Alignment explanation
Indices: 15018--15083 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
15008 AAAAGTACAC
* **
15018 AAAATTATATTTTAATAATGGTATAGTT
1 AAAAATATATTTTAATAATGACATAGTT
*
15046 -AAAATATATTTTAATAATGACA-ATTT
1 AAAAATATATTTTAATAATGACATAGTT
15072 AAAAATATATTT
1 AAAAATATATTT
15084 GAAAAATAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 3 0.09
27 30 0.91
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (28 bp):
AAAAATATATTTTAATAATGACATAGTT
Found at i:15104 original size:29 final size:27
Alignment explanation
Indices: 15046--15105 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
15036 TGGTATAGTT
* * **
15046 AAAATATATTTTAATAATGACAATTTA
1 AAAATATATTTGAAAAATGACAATCGA
15073 AAAATATATTTGAAAAATAGTACAATCGA
1 AAAATATATTTGAAAAAT-G-ACAATCGA
15102 AAAA
1 AAAA
15106 ATACATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 16 0.59
28 1 0.04
29 10 0.37
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (27 bp):
AAAATATATTTGAAAAATGACAATCGA
Found at i:15173 original size:92 final size:95
Alignment explanation
Indices: 15005--15181 Score: 270
Period size: 92 Copynumber: 1.9 Consensus size: 95
14995 AAATATATTT
** *
15005 GAAAAAAGTACACAAAATTATATTTTAATAATGGTATAGTTAAAATATATTTTAATAATGACAAT
1 GAAAAAAGTACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAATAATGACAAT
*
15070 TTAAAAATATATTTGAAAAATAGTACAATC
66 TTAAAAATATATTAGAAAAATAGTACAATC
*
15100 GAAAAAA-TACATAAAATTATATTTTAATAATGACATAATT-AAA-ATATTTTAATAATGACAAT
1 GAAAAAAGTACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAATAATGACAAT
**
15162 TTGGAAATATATTAGAAAAA
66 TTAAAAATATATTAGAAAAA
15182 ATGGGGTATA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
92 36 0.48
93 3 0.04
94 29 0.39
95 7 0.09
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (95 bp):
GAAAAAAGTACACAAAATTATATTTTAATAATGACATAATTAAAATATATTTTAATAATGACAAT
TTAAAAATATATTAGAAAAATAGTACAATC
Found at i:15257 original size:14 final size:15
Alignment explanation
Indices: 15231--15264 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
15221 GTACTTTTAT
15231 ATATAGTATAGATAG
1 ATATAGTATAGATAG
15246 ATATAG-ATAGATAG
1 ATATAGTATAGATAG
*
15260 CTATA
1 ATATA
15265 AAGTCATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (15 bp):
ATATAGTATAGATAG
Found at i:16111 original size:1 final size:1
Alignment explanation
Indices: 16107--16131 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
16097 TGCCAAAAAA
16107 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
16132 TTAATGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:16987 original size:39 final size:40
Alignment explanation
Indices: 16933--17014 Score: 139
Period size: 39 Copynumber: 2.0 Consensus size: 40
16923 CCTGTTAGGT
16933 TTTTATTTTTATTTCAATAGTCGC-AAAAAAAAAGATTAA
1 TTTTATTTTTATTTCAATAGTCGCAAAAAAAAAAGATTAA
*
16972 TTTTATTTTTATTTCAGTAGTCGCAAAAAAAAAAAGATTAA
1 TTTTATTTTTATTTCAATAGTCGC-AAAAAAAAAAGATTAA
17013 TT
1 TT
17015 GTAAGAAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 23 0.57
41 17 0.43
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTATTTTTATTTCAATAGTCGCAAAAAAAAAAGATTAA
Found at i:23143 original size:6 final size:6
Alignment explanation
Indices: 23132--23159 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
23122 TGTAACCTGG
23132 GATATT GATATT GATATT GATATT GATA
1 GATATT GATATT GATATT GATATT GATA
23160 GAATTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (6 bp):
GATATT
Found at i:24343 original size:2 final size:2
Alignment explanation
Indices: 24336--24363 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24326 GCAGGTTGCC
24336 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
24364 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.