Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019418.1 Corchorus olitorius cultivar O-4 contig19451, 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: 76097
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:705 original size:51 final size:51
Alignment explanation
Indices: 629--759 Score: 199
Period size: 51 Copynumber: 2.6 Consensus size: 51
619 CAGAGATTGA
* * *
629 GTGAGTGTAAAAGATTTGTAAATAAATAAGACGCATCCGTCCCTGAATCGG
1 GTGAGTGTAAAAGATTTGTAAATAAATAAGAAGCACCCGCCCCTGAATCGG
* *
680 GTGAGTATAAAAGATTTGTAAATAAATAAGAAGCACCCGCCCCTGGATCGG
1 GTGAGTGTAAAAGATTTGTAAATAAATAAGAAGCACCCGCCCCTGAATCGG
* *
731 GTGAGTGTAAAAGGTTAGTAAATAAATAA
1 GTGAGTGTAAAAGATTTGTAAATAAATAA
760 AAAATTATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 72 1.00
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (51 bp):
GTGAGTGTAAAAGATTTGTAAATAAATAAGAAGCACCCGCCCCTGAATCGG
Found at i:5620 original size:19 final size:19
Alignment explanation
Indices: 5596--5633 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5586 TAACCACTGA
5596 GTGTCCCCTTGGGGATTAT
1 GTGTCCCCTTGGGGATTAT
5615 GTGTCCCCTTGGGGATTAT
1 GTGTCCCCTTGGGGATTAT
5634 ACTACTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.32, T:0.37
Consensus pattern (19 bp):
GTGTCCCCTTGGGGATTAT
Found at i:8173 original size:15 final size:15
Alignment explanation
Indices: 8150--8180 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8140 TTGGAGGAGC
8150 CGTCATCATCTTCAT
1 CGTCATCATCTTCAT
*
8165 CGTCGTCATCTTCAT
1 CGTCATCATCTTCAT
8180 C
1 C
8181 AGAGATCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.10, T:0.39
Consensus pattern (15 bp):
CGTCATCATCTTCAT
Found at i:31615 original size:30 final size:30
Alignment explanation
Indices: 31571--31660 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
31561 ATCATGTAGC
*
31571 GGTGTACGAGTCTTCCTTTGCGTTTGTAAT
1 GGTGTACGAGTCTTCCTTTACGTTTGTAAT
* * **
31601 GGTGTATGAATCTTCCTTTACGTTTACAAT
1 GGTGTACGAGTCTTCCTTTACGTTTGTAAT
* *
31631 GATGTACGAGTCTTCCATTACGTTTGTAAT
1 GGTGTACGAGTCTTCCTTTACGTTTGTAAT
31661 CCCAATCTTA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (30 bp):
GGTGTACGAGTCTTCCTTTACGTTTGTAAT
Found at i:35322 original size:25 final size:26
Alignment explanation
Indices: 35268--35322 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
35258 AATTATTATT
* *
35268 ATATTTTAATAATGGCATAGTTAAAT
1 ATATTTTAATAATGACATAGTTAAAA
*
35294 ATATTTTAATAATGACA-ATTTAAAA
1 ATATTTTAATAATGACATAGTTAAAA
35319 ATAT
1 ATAT
35323 ATTTGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (26 bp):
ATATTTTAATAATGACATAGTTAAAA
Found at i:35466 original size:97 final size:97
Alignment explanation
Indices: 35268--35447 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 97
35258 AATTATTATT
* * *
35268 ATATTTTAATAATGGCATAGTTAAATATATTTTAATAATGACAATTTAAAAATATATTTGAAAAA
1 ATATTTTAATAATGACATAATTAAATATATTTTAATAATGACAATTTAAAAATACATTTGAAAAA
* * **
35333 AATAGTACAATTGGAAAAAAATACATAAAATT
66 AATAGTACAATCGGAAAAAAATAAATAAAACC
* *
35365 ATATTTTAATAATGACATAATTAAA-ATATTTTAATAATGGCAATTTAGAAATACATTTGAAAAA
1 ATATTTTAATAATGACATAATTAAATATATTTTAATAATGACAATTTAAAAATACATTTGAAAAA
* *
35429 AATGGGTATAATCGGAAAA
66 AAT-AGTACAATCGGAAAA
35448 CATAAAGTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 39 0.53
97 35 0.47
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.34
Consensus pattern (97 bp):
ATATTTTAATAATGACATAATTAAATATATTTTAATAATGACAATTTAAAAATACATTTGAAAAA
AATAGTACAATCGGAAAAAAATAAATAAAACC
Found at i:41956 original size:24 final size:24
Alignment explanation
Indices: 41910--41956 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
41900 ATATCCACCC
* *
41910 CATTAATAGAACCATCGACAAAAG
1 CATTAACAGAACCATCAACAAAAG
* *
41934 CATTAACAGAGCCATCAATAAAA
1 CATTAACAGAACCATCAACAAAA
41957 AAAGGGTCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.51, C:0.21, G:0.11, T:0.17
Consensus pattern (24 bp):
CATTAACAGAACCATCAACAAAAG
Found at i:48531 original size:46 final size:46
Alignment explanation
Indices: 48464--48556 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
48454 TGTCATGATG
48464 ATGACTTGATAATTTCAATAGGTCATGATACCTCCACAATTGACTC
1 ATGACTTGATAATTTCAATAGGTCATGATACCTCCACAATTGACTC
*
48510 ATGACTTGATAGTTTCAATAGGTCATGATACCTCCACAATTGACTC
1 ATGACTTGATAATTTCAATAGGTCATGATACCTCCACAATTGACTC
48556 A
1 A
48557 AAGTCGCCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (46 bp):
ATGACTTGATAATTTCAATAGGTCATGATACCTCCACAATTGACTC
Found at i:55573 original size:333 final size:328
Alignment explanation
Indices: 54954--56597 Score: 1757
Period size: 331 Copynumber: 5.0 Consensus size: 328
54944 CAAAATTTTG
* * *
54954 TTTCATATTTTTTTGAATTAATTTCTAATTAAAGCGAAACAAGATTCAGATGCTCATAAAAACAA
1 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
** * * *
55019 ATCCTTAAATTTAACGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCTTGGCA
66 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA-ATATTTCAAGGAGTCTTGGCA
* * * * * * *
55084 CAAAAAATCCTGCAAAACTGAGCCGGGCCCCGAAATGCGGTTTTAGCCAAAACCCGTGATGGTTA
130 CCAAAAATCATGCAAAACTAAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * * * * * * *
55149 GTACATGATTTCGGCTAAAATTTTTGTAAATATTGACCCGAAAGACTTTTCCTCGATTTCT-GGT
195 GTACACGATTTCGGCTAAAA-TTTTGCAAAAATTGACTCGAAAGATTTTTCCTCAATTTTTAGCT
* * *
55213 AAAAATACTCATAAAAAATATATAATTCAATGTCAAAAGGATTGGAGTACTTTTCACGCTTTTAA
259 -AAAATACTCATAAAAAATATATAATTCAACGTCAAAAAGATTGAAG-ACTTTTCACGCTTTTAA
55278 TATCGTT
322 TATCGTT
* * * * *
55285 TTTCATTATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAAATTCAGATACACATAAAAAC
1 TTTCA-TA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* * * * *
55350 AAATTCTTAAATCCAATGTGTCTGAGATTTGATTAGATAAATATGAATATCTCAAGGAGTCTTGA
64 AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT-AATATTTCAAGGAGTCTTGG
* * * ** *
55415 CGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCAGAACGCTTTTTTAGCCAAAAACTATGATGA
128 CACCAAAAATCATGCAAAACTAAGCC-GGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGG
* * * * * *
55480 TTATTACACGATTTCGGCTAAATTTTTGTAAAAATTGATTAGAAA-ATTATTTCCTCAATTTTTG
192 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATT-TTTCCTCAATTTTTA
* *
55544 GCTAAAATACTTATAAAAAATATATAATTCAACG-CTAAAAAGATTGAAGAGCTTTTGACG-TTT
256 GCTAAAATACTCATAAAAAATATATAATTCAACGTC-AAAAAGATTGAAGA-CTTTTCACGCTTT
55607 CTAATATCGTT
319 -TAATATCGTT
** *
55618 TTTCATATTTTTCCAAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
1 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
*
55683 ATCCTTAAATCTAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCA
66 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATA-ATATTTCAAGGAGTCTTGGCA
* *** * * **
55748 CCAAAAGTCATGCAAAACTAAGCCCAACCCCGGAGCGCGGTTTTAGCTGAAAACCGTGATGGTTA
130 CCAAAAATCATGCAAAACTAAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * * *
55813 GTACATGATTTCGGCTAAAATTTTACAAAAATTGACTCGAAAGATTTTTCC-CTGATTTCTAG-T
195 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATTTTTCCTC-AATTTTTAGCT
* * * * *
55876 GAAAATACTCATAAAAAATTTATATTTCAACGTCAAAAAAATTGAAAGCCTCTTTCATGCTTTTA
259 -AAAATACTCATAAAAAATATATAATTCAACGTCAAAAAGATTG-AAGACT-TTTCACGCTTTTA
*
55941 ATATCATT
321 ATATCGTT
* *
55949 TTTCATATTTTTCTGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTCAAAACAA
1 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * *
56014 ATCCTTAAATTCAATGTGGATGAGATTTGATAAGATGAATATAAATATTTCAAGGCA-TCTCGAC
66 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT-AATATTTCAAGG-AGTCTTGGC
* * * * * *
56078 ACAAAAAATCATGCAAAACTGAGTCGGGTCCCGGATCGCGTTTTTAGCCGAAAACCGTGATGGTT
129 ACCAAAAATCATGCAAAACTAAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTT
* * *
56143 AGTACACGATTTGGGCTAAAATTTTGCAAAAATTGACCCGAAAGA-TTTTCCTGTCAAATTTT-G
194 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATTTTTCC--TCAATTTTTAG
* * * *
56206 CATAAAATA-T-AT-----ACA-AT--TT-AACGCCAAAAATATTGGAGGACTTTTCACGCTTTT
257 C-TAAAATACTCATAAAAAATATATAATTCAACGTCAAAAAGATT-GAAGACTTTTCACGCTTTT
56260 AATATCGTT
320 AATATCGTT
** *
56269 TTTCATATTTTTCTGAAGCAATTTCTAGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
1 TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * * * * * * *
56334 ATTCTTCAATCCAATGTAGCTGACATTAGATTAAATGAATATGGATATCTCAAAGAGTATTGGCA
66 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT-AATATTTCAAGGAGTCTTGGCA
* * * * *
56399 CCAAAAATCATGCAAAACTTAGTCGGGGCCCCGGAACGCGTTTTTAG-TAAAAAACGATGATGAT
130 CCAAAAATCATGCAAAACTAAG-CCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCG-TGATGGT
* * * * *
56463 TATTACACGATTTCGACTAGAATTTTGCAAAAAATGACTCGAAAG-TTATTTCCTCAATTTTTAT
193 TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATT-TTTCCTCAATTTTTAG
* * * * ** ** * *
56527 CCACAATACTCATAAAGATTATATAATTCAACACCAAAAAGATTGAATGGTTTTTCATGCTTCTA
257 CTAAAATACTCATAAAAAATATATAATTCAACGTCAAAAAGATTGAA-GACTTTTCACGCTTTTA
56592 ATATCG
321 ATATCG
56598 AAACATGATT
Statistics
Matches: 1094, Mismatches: 176, Indels: 86
0.81 0.13 0.06
Matches are distributed among these distances:
319 1 0.00
320 165 0.15
321 85 0.08
322 10 0.01
324 2 0.00
325 1 0.00
327 1 0.00
328 2 0.00
329 2 0.00
330 127 0.12
331 400 0.37
332 26 0.02
333 220 0.20
334 52 0.05
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (328 bp):
TTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAATATTTCAAGGAGTCTTGGCAC
CAAAAATCATGCAAAACTAAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
TACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGATTTTTCCTCAATTTTTAGCTAA
AATACTCATAAAAAATATATAATTCAACGTCAAAAAGATTGAAGACTTTTCACGCTTTTAATATC
GTT
Found at i:58256 original size:653 final size:657
Alignment explanation
Indices: 56624--58629 Score: 1601
Period size: 653 Copynumber: 3.1 Consensus size: 657
56614 CTTGTTTTAC
* * * * * *
56624 AAATCCTTAAATCTAATGTGGCTGAGATTTTG-TTAGAT-AAGTATAGATATTTCAAGGAGTCTC
1 AAATTCTTAAATCCAATGTGGCTGAGA-TTTGATTAGATGAA-TATGGAAATCTCAAGGAGTCTT
* * * * * *** ** **
56687 GGTG-CAAATTATCATGCAACACTGAACCGGGACCCTGGAACGCGTTTTTAGTAAAAAACCGTGA
64 GGCGCCAAA-AATCATGCAAAACTGAGCCGGGCCCCCAAAACGCGTTTTTAGCCAAAAACAATGA
* * * * * * * * * * *
56751 TTTCGACTAACGTACACGATTTTGCCTAATATTTTGTAAAAATTTACCCGAAATATTTTTCCTCA
128 --T-GA-TTA-TTACACGATTTCGGCTAAAATATTGCAAAAATTGACCAGAAAAATATTTCCTCA
* * * * * *** *
56816 ATTTTT-GTCTAAAATACTCATAAAATATATATAATTCAACTCTAAAAAGATTGGAGAAATTTTC
188 ATTTTTAGGC-AAAATACTCATAAAA-AAATATAATTCAACGCCAAAAAGATTGAAGGGCTTGTC
* * * ** * * *
56880 TCGCTTTTAATATCGCTTTTCATA-TTTTTCTGAATTAATATCTAATAAAATCGAAAGAAGATTC
251 ACGCTTTCAATATCGTTTTTCATATTTTTTCCAAATTAATATCTAATTAAATCGAAACAAGATTT
* * *
56944 AGATGCTCGTAAAAATAAATCCTTAAATGCAATGTGGCT--GA---GATT----TAATATAGATA
316 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGACAAATATAGATA
** * * *** * **
57000 TTTTGAGGAGTCTC-GATGCCAAAAATCATGCAAAACTGAGTTAGGGCCCCAAAATGCGTTTTTA
381 TTTCAAGGAGTCTCGGA-GCAAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACACG-TTTT-
*** * * * * * * *
57064 ATAATAAAAAAAACGTGATGGCTAGTACACGATTTCGGCTAAAATTTTACAAGAAATT-AC-CAG
443 -T-A-GCCAAAAACCTG-TTG-AAGTACATGATTTCAGCTAAAACTTTGC-A-AAATTGACACA-
* * * ** * * * * * *
57127 AAAAATATTCTCTTAATTTTTAGCCACAATACTCATAAATAATATGTAATTCAACGGCAAAAATA
500 AACAAT-TTCTCCTAATTTTTGGATAAAACAATCACAAA-AATATATAATTCAAC-ACAAAAA-A
*** * * * * **
57192 -ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATT
561 GATTGAAGAACTTTTCACGCTTTTAACATCGTATTTCATA-TTTTTTCTAAATTAATTTCTAA-T
* * * *
57256 AAAAT-GAAACATGATTCAGATGTTTGT------
624 GAAATCGAAACAAGATTCAGATGCTCGTAAAAAA
* * * * * * * * *
57283 -AA-----AAA--CAA--TGGTTGGGATTTGGTTAGATTAATATAGATATTTTAAGGAGTCTCGG
1 AAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATGGAAATCTCAAGGAGTCTTGG
* * * * * * * **
57338 TGCAAAAAATCATTCAAAATTGAACCAGG-CCTCGGAACGCGTTTTTAGCCAAAAACAATGATGA
66 CGCCAAAAATCATGCAAAACTGAGCCGGGCCCCCAAAACGCGTTTTTAGCCAAAAACAATGATGA
* * * *
57402 TTATTACACGATTTCGGGTAACATATTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAG
131 TTATTACACGATTTCGGCTAAAATATTGCAAAAATTGACCAGAAAAATATTTCCTCAATTTTTAG
* * *
57467 TCATAATACTCATAAAAAAATATAATTCAACGCCAAAAAGATTGAAGGGCTTGTCACGCTTTTAA
196 GCAAAATACTCATAAAAAAATATAATTCAACGCCAAAAAGATTGAAGGGCTTGTCACGCTTTCAA
* * *
57532 TATCGTTTTTCATATTTTTTCTAAATTAATATCTAATTAAATTGAAATAAGATTTAGATGCTCGT
261 TATCGTTTTTCATATTTTTTCCAAATTAATATCTAATTAAATCGAAACAAGATTTAGATGCTCGT
* * **
57597 AAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAG
326 AAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGACAAATATAGATATTTCAAGGAG
* * * * * * *
57662 TGTCGGCGCCAAAAATCATGTAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAATCC-
391 TCTCGGAGCAAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACACGTTTTTAGCCAAAAACCT
** *
57726 G-TG-A-TACATGATTTTGGCTAAAACTTTGCAAAAAATT-ACCCGAAA-AATTTTTCTCCT-AT
456 GTTGAAGTACATGATTTCAGCTAAAACTTTGC--AAAATTGACAC-AAACAA--TTTCTCCTAAT
* * * * * *
57785 TTCTT-GATAAAATAATCATAAAATATATATAATTTAACACCAAAAGGATTGGAGAACTTTTCAC
516 TT-TTGGATAAAACAATCACAAAA-ATATATAATTCAACACAAAAAAGATTGAAGAACTTTTCAC
* * *
57849 GCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTT-TAATGAAATCGAAACAAGATTCAG
579 GCTTTTAACATCGTATTTCATATTTTTTCTAAATTAATTTCTAATGAAATCGAAACAAGATTCAG
* *
57912 ATGCTTGTAAAAAC
644 ATGCTCGTAAAAAA
57926 AAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATGGAAATCTCAAGGAGTCTTGG
1 AAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATGGAAATCTCAAGGAGTCTTGG
* ** *
57991 CGCCAAAAATCATGCAAAACTGAGCCGGGCCCCCAAAACGCTTTTTTAGCCAAAAACTGTGATGG
66 CGCCAAAAATCATGCAAAACTGAGCCGGGCCCCCAAAACGCGTTTTTAGCCAAAAACAATGATGA
* * **
58056 TTATTACACGATTTCGGCTAAAATTTTGTAAAAA-TGATTAGAAAAATATTTCCTCAA-TTTTAG
131 TTATTACACGATTTCGGCTAAAATATTGCAAAAATTGACCAGAAAAATATTTCCTCAATTTTTAG
* * *
58119 GCTAAAATACTTATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACG-TTTC
196 GC-AAAATACTCATAAAAAA-ATATAATTCAACGCCAAAAAGATTGAAGGGCTTGTCACGCTTT-
* *
58183 CAATATCGTTTTTCTTA-TTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCT
258 CAATATCGTTTTTCATATTTTTTCCAAATTAATATCTAATTAAATCGAAACAAGATTTAGATGCT
* *
58247 CGTAAAAACAAATGCTTAAATCCAATGTGGCTGAGATTTGATTAGACAAATATAGATATTTCAAG
323 CGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGACAAATATAGATATTTCAAG
* * * * * * *
58312 TAGTCTTGGAGCAAAAAATCATGCAAAATTAAGTCGGGTCTCCGGAACACGTTTTTAGCCAAAAA
388 GAGTCTCGGAGCAAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACACGTTTTTAGCCAAAAA
* *
58377 CCTTGATGGTTTGTAAGTACATGATTTCAGCTAAAATTTTGCAAAATTGACACAAACGATTTCTC
453 CC----T-G-TTG-AAGTACATGATTTCAGCTAAAACTTTGCAAAATTGACACAAACAATTTCTC
* * ** **
58442 CTCAATTTTTGGCTAAAACACTCACAAAAATATATAATTCAACGTAAAAAAGATTGAAGTGCTTT
511 CT-AATTTTTGGATAAAACAATCACAAAAATATATAATTCAACACAAAAAAGATTGAAGAACTTT
* * * * *
58507 TTACGCTTTTAACATCGTATTTCTTATTTTTTCTAAATTAATTTCTCATTAAATCGAAACATGAT
575 TCACGCTTTTAACATCGTATTTCATATTTTTTCTAAATTAATTTCTAATGAAATCGAAACAAGAT
58572 TCAGATGCTCGTAAAAAA
640 TCAGATGCTCGTAAAAAA
* * *
58590 AAATTCTTAAATCCAATGTTGCTGAGATTTGGTTATATGA
1 AAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
58630 TGTAAAATAT
Statistics
Matches: 1108, Mismatches: 177, Indels: 119
0.79 0.13 0.08
Matches are distributed among these distances:
636 5 0.00
637 23 0.02
638 16 0.01
640 39 0.04
641 59 0.05
642 66 0.06
643 139 0.13
644 8 0.01
645 4 0.00
646 2 0.00
647 5 0.00
648 34 0.03
649 59 0.05
650 5 0.00
651 9 0.01
652 63 0.06
653 257 0.23
654 110 0.10
658 2 0.00
659 1 0.00
661 10 0.01
662 61 0.06
663 39 0.04
664 92 0.08
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (657 bp):
AAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATGGAAATCTCAAGGAGTCTTGG
CGCCAAAAATCATGCAAAACTGAGCCGGGCCCCCAAAACGCGTTTTTAGCCAAAAACAATGATGA
TTATTACACGATTTCGGCTAAAATATTGCAAAAATTGACCAGAAAAATATTTCCTCAATTTTTAG
GCAAAATACTCATAAAAAAATATAATTCAACGCCAAAAAGATTGAAGGGCTTGTCACGCTTTCAA
TATCGTTTTTCATATTTTTTCCAAATTAATATCTAATTAAATCGAAACAAGATTTAGATGCTCGT
AAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGACAAATATAGATATTTCAAGGAG
TCTCGGAGCAAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACACGTTTTTAGCCAAAAACCT
GTTGAAGTACATGATTTCAGCTAAAACTTTGCAAAATTGACACAAACAATTTCTCCTAATTTTTG
GATAAAACAATCACAAAAATATATAATTCAACACAAAAAAGATTGAAGAACTTTTCACGCTTTTA
ACATCGTATTTCATATTTTTTCTAAATTAATTTCTAATGAAATCGAAACAAGATTCAGATGCTCG
TAAAAAA
Found at i:58282 original size:330 final size:329
Alignment explanation
Indices: 56594--58629 Score: 1668
Period size: 330 Copynumber: 6.2 Consensus size: 329
56584 TGCTTCTAAT
* * *** * *
56594 ATCGAAACATGATTCAGATGCTTGT-TTTACAAATCCTTAAATCTAATGTGGCTGAGATTTTG-T
1 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGA-TTTGAT
* * * * * *
56657 TAGAT-AAGTATAGATATTTCAAGGAGTCTCGGTG-CAAATTATCATGCAACACTGAACCGGGAC
65 TAGATGAA-TATAGATATTTCAAGGAGTCTTGGCGCCAAA-AATCATGCAAAACTGAGCCGGGCC
* * ** * * * * * * *
56720 CCTGGAACGCGTTTTTAGTAAAAAACCGTGATTTCGACTAACGTACACGATTTTGCCTAATATTT
128 CCCGAAACGCGTTTTTAGCCAAAAA-CTTGA--T-G-GTTA-TTACACGATTTCGGCTAAAATTT
* * * * * * * *
56785 TGTAAAAATTTACCCGAAATATTTTTCCTCAATTTTTGTCTAAAATACTCATAAAATATATATAA
187 TGCAAAAA-TGATCAGAAA-AATTTTCCTCAATTTTAGGCTAAAATACTCATAAAAAATATATAA
* * * *** * * *
56850 TTCAACTCTAAAAAGATTGGAGAAATTTTCTCGCTTTTAATATCGCTTTTCATA-TTTTTCTGAA
250 TTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAA
* *
56914 TTAATATCTAATAAA
315 TTAATTTCTAATTAA
* * * *
56929 ATCGAAAGAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATGCAATGTGGCT--GA---GATT
1 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATT
** * ** **
56989 ---T-AATATAGATATTTTGAGGAGTCTCGATGCCAAAAATCATGCAAAACTGAGTTAGGG-CCC
66 AGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG-CCGGGCCCC
* * *** * * * *
57049 CAAAATGCGTTTTTAATAATAAAAAAAACGTGATGGCTAGTACACGATTTCGGCTAAAATTTTAC
130 CGAAACGCG-TTTT--T-A-GCCAAAAACTTGATGGTTATTACACGATTTCGGCTAAAATTTTGC
* * * * * * * *
57114 AAGAAATTACCAGAAAAATATTCTCTTAATTTTTA-GCCACAATACTCATAAATAATATGTAATT
190 AA-AAATGATCAGAAAAATTTTC-CTCAA-TTTTAGGCTAAAATACTCATAAAAAATATATAATT
* * * * * **
57178 CAACGGCAAAAATAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAA
252 CAACGCCAAAAA-GATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTCTAAA
57243 TTAATTTCTAATTAAA
315 TTAATTTCTAATT-AA
* * * * * *
57259 AT-GAAACATGATTCAGATGTTTGT-------AA-----AAA--CAA--TGGTTGGGATTTGGTT
1 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATT
* * * * * * * * * *
57307 AGATTAATATAGATATTTTAAGGAGTCTCGGTGCAAAAAATCATTCAAAATTGAACCAGG-CCTC
66 AGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCC
* * * * * *
57371 GGAACGCGTTTTTAGCCAAAAACAATGATGATTATTACACGATTTCGGGTAACATATTGCAAAAA
131 GAAACGCGTTTTTAGCCAAAAAC-TTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAA
* * * * *
57436 TTGACCCGAAAGATATTTCCTCAATTTTTAGTC-ATAATACTCATAAAAAA-ATATAATTCAACG
195 -TGATCAGAAAAAT-TTTCCTCAA-TTTTAGGCTAAAATACTCATAAAAAATATATAATTCAACG
* *
57499 CCAAAAAGATTGAAGGGCTTGTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATAT
257 CCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTT
57564 CTAATTAA
322 CTAATTAA
* * * * * * *
57572 ATTGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATT
1 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATT
* * * *
57637 AGATGAATATAGATATTTCAAGGAGTGTCGGCGCCAAAAATCATGTAAAACTGAGCCGGGGCCCC
66 AGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCC
* * * * *
57702 GAAACGCGTTTTTAGCCAAAATC-CG-T-G--A-TACATGATTTTGGCTAAAACTTTGCAAAAAA
131 GAAACGCGTTTTTAGCCAAAAACTTGATGGTTATTACACGATTTCGGCTAAAATTTTGC-AAAAA
* * * * * * * * * * *
57761 TTACCCGAAAAATTTTTCTCCTATTTCT-TGATAAAATAATCATAAAATATATATAATTTAACAC
195 TGATCAGAAAAATTTTCCT-CAATTT-TAGGCTAAAATACTCATAAAAAATATATAATTCAACGC
* * ** *
57825 CAAAAGGATTGGAGAACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTT-
258 CAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTTC
*
57888 TAATGAA
323 TAATTAA
*
57895 ATCGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATT
1 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATT
* * *
57960 AGATGAATATGGAAATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCC
66 AGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCC
* * *
58025 AAAACGCTTTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAA
131 GAAACGCGTTTTTAGCCAAAAACT-TGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAA
* *
58090 TGATTAGAAAAATATTTCCTCAATTTTAGGCTAAAATACTTATAAAAAATATATAATTCAACGCC
195 TGATCAGAAAAAT-TTTCCTCAATTTTAGGCTAAAATACTCATAAAAAATATATAATTCAACGCC
* * * *
58155 AAAAAGATTGAAGGGCTTTTGACG-TTTCCAATATCGTTTTTCTTA-TTTTTCCAAATTAATTTC
259 AAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTTCATATTTTTTCTAAATTAATTTC
58218 TAATTAA
323 TAATTAA
* *
58225 ATCGAAACAAGATTTAGATGCTCGTAAAAACAAATGCTTAAATCCAATGTGGCTGAGATTTGATT
1 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATT
** * * * * * * * *
58290 AGACAAATATAGATATTTCAAGTAGTCTTGGAGCAAAAAATCATGCAAAATTAAGTCGGGTCTCC
66 AGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCC
* * * * *
58355 GGAACACGTTTTTAGCCAAAAACCTTGATGGTTTGTAAGTACATGATTTCAGCTAAAATTTTGCA
131 GAAACGCGTTTTTAGCCAAAAA-CTTGATGG--T-T-ATTACACGATTTCGGCTAAAATTTTGCA
* * * * * *
58420 AAATTGA-CACAAACGATTTCTCCTCAATTTTTGGCTAAAACACTCA-CAAAAATATATAATTCA
191 AAAATGATCAGAAA-AATTT-TCCTCAATTTTAGGCTAAAATACTCATAAAAAATATATAATTCA
** * * * * *
58483 ACGTAAAAAAGATTGAAGTGCTTTTTACGCTTTTAACATCGTATTTCTTATTTTTTCTAAATTAA
254 ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAA
*
58548 TTTCTCATTAA
319 TTTCTAATTAA
* * * *
58559 ATCGAAACATGATTCAGATGCTCGTAAAAAAAAATTCTTAAATCCAATGTTGCTGAGATTTGGTT
1 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATT
*
58624 ATATGA
66 AGATGA
58630 TGTAAAATAT
Statistics
Matches: 1377, Mismatches: 252, Indels: 145
0.78 0.14 0.08
Matches are distributed among these distances:
313 8 0.01
314 38 0.03
315 40 0.03
316 27 0.02
317 69 0.05
318 8 0.01
320 4 0.00
321 13 0.01
322 46 0.03
323 149 0.11
324 62 0.05
325 65 0.05
326 72 0.05
327 85 0.06
328 23 0.02
329 139 0.10
330 237 0.17
331 34 0.02
332 7 0.01
333 62 0.05
334 145 0.11
335 22 0.02
336 22 0.02
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (329 bp):
ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATT
AGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCC
GAAACGCGTTTTTAGCCAAAAACTTGATGGTTATTACACGATTTCGGCTAAAATTTTGCAAAAAT
GATCAGAAAAATTTTCCTCAATTTTAGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAA
AAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTTCTAA
TTAA
Found at i:58990 original size:15 final size:16
Alignment explanation
Indices: 58972--59001 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
58962 ATAAATAATA
58972 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
58987 ATATTATAATCTAAA
1 ATATTATAATCTAAA
59002 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:61687 original size:12 final size:12
Alignment explanation
Indices: 61670--61701 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
61660 CCACAATACT
61670 AATTATGTTATC
1 AATTATGTTATC
61682 AATTATGTTATC
1 AATTATGTTATC
61694 AATTATGT
1 AATTATGT
61702 AATATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (12 bp):
AATTATGTTATC
Found at i:62965 original size:16 final size:15
Alignment explanation
Indices: 62938--62996 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 15
62928 TGGTAGGGAC
62938 GGGAGGAAGGAAATA
1 GGGAGGAAGGAAATA
62953 GGGAGGAAAGGAAATAA
1 GGGAGG-AAGGAAAT-A
* *
62970 GTAGAGTAAGGAAATTA
1 G-GGAGGAAGGAAA-TA
62987 GGGGAGGAAG
1 -GGGAGGAAG
62997 TTTTATTTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 6 0.17
16 8 0.23
17 16 0.46
18 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.44, T:0.10
Consensus pattern (15 bp):
GGGAGGAAGGAAATA
Found at i:63248 original size:41 final size:41
Alignment explanation
Indices: 63192--63278 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
63182 TTTATAACTA
*
63192 GGGGCTAAACATGGATTTAATTTCA-TACCTTAATTATTAGG
1 GGGGTTAAACATGGATTTAATTT-ATTACCTTAATTATTAGG
* * *
63233 GGGGTTAAACCTGGATTTAATTTATTTCTTTAATTATTAGG
1 GGGGTTAAACATGGATTTAATTTATTACCTTAATTATTAGG
*
63274 AGGGT
1 GGGGT
63279 CAAGTTGAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.03
41 39 0.98
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (41 bp):
GGGGTTAAACATGGATTTAATTTATTACCTTAATTATTAGG
Done.