Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007135.1 Corchorus capsularis cultivar CVL-1 contig07156, 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: 42982
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:6045 original size:16 final size:16
Alignment explanation
Indices: 6024--6056 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6014 TTCAGAAAGC
6024 AGAAAAGCTCTGAAGT
1 AGAAAAGCTCTGAAGT
6040 AGAAAAGCTCTGAAGT
1 AGAAAAGCTCTGAAGT
6056 A
1 A
6057 TTTTCCGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.18
Consensus pattern (16 bp):
AGAAAAGCTCTGAAGT
Found at i:6207 original size:41 final size:41
Alignment explanation
Indices: 6150--6391 Score: 290
Period size: 41 Copynumber: 5.9 Consensus size: 41
6140 TTTTCGTTTG
**
6150 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
6191 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * *
6232 TTCAAGAACAAGTCATCGAGATCCTTGAATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* *
6276 TTCAAGATCAAGTCGTCAAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * * * *
6317 TTCAAGGTCAAATCGTCAAGACCCTTGAATTAAATTATTAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
6358 TTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGATCAAGTCA-TCGAGACCCTTGAATTAAAT
6392 CAAATCAAGT
Statistics
Matches: 179, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
40 15 0.08
41 124 0.69
42 4 0.02
43 2 0.01
44 34 0.19
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:6309 original size:85 final size:82
Alignment explanation
Indices: 6160--6391 Score: 279
Period size: 85 Copynumber: 2.8 Consensus size: 82
6150 TTCAAGATTG
* ** *
6160 AGTCATCGAGACCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGACCCTTGAATTAAA
1 AGTCATCGAGACCCTTGAATGAAATTATCAATTCAAGATCAAGTCATCAAGACCCTTGAATTAAA
6225 TTATCAATTCAAGAACA
66 TTATCAATTCAAGAACA
* *
6242 AGTCATCGAGATCCTTGAATCGAATTATTATCAATTCAAGATCAAGTCGTCAAGACCCTTGAATT
1 AGTCATCGAGACCCTTGAAT-GAA--ATTATCAATTCAAGATCAAGTCATCAAGACCCTTGAATT
**
6307 AAATTATCAATTCAAGGTCA
63 AAATTATCAATTCAAGAACA
* * * * * * *
6327 AATCGTCAAGACCCTTGAATTAAATTATTAATTCAAGACCAAGTCATTC--GACCCTTGAATCAA
1 AGTCATCGAGACCCTTGAATGAAATTATCAATTCAAGATCAAGTCA-TCAAGACCCTTGAATTAA
6390 AT
65 AT
6392 CAAATCAAGT
Statistics
Matches: 129, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
81 15 0.12
82 39 0.30
83 4 0.03
84 2 0.02
85 69 0.53
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (82 bp):
AGTCATCGAGACCCTTGAATGAAATTATCAATTCAAGATCAAGTCATCAAGACCCTTGAATTAAA
TTATCAATTCAAGAACA
Found at i:9131 original size:41 final size:41
Alignment explanation
Indices: 9074--9292 Score: 276
Period size: 41 Copynumber: 5.3 Consensus size: 41
9064 TTTTCGTTTG
**
9074 TTCAAGATTGAGTCATCGAGATCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGATCCTTGAATTAAATTATCAA
** *
9115 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGATCCTTGAATTAAATTATCAA
* *
9156 TTCAAGAACAAGTCATCGAGATCCTTGAATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGATCCTTGAAT-TAA--ATTATCAA
* *
9200 TTCAAGATCAAGTCGTCAAGATCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGATCCTTGAATTAAATTATCAA
* * * * *
9241 TTCAAGGTCAAATCGTCAAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGATCCTTGAATTAAATTATCAA
*
9282 TTCAAGGTCAA
1 TTCAAGATCAA
9293 ATCTAACCAT
Statistics
Matches: 162, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
41 123 0.76
42 2 0.01
43 2 0.01
44 35 0.22
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGATCCTTGAATTAAATTATCAA
Found at i:9238 original size:85 final size:82
Alignment explanation
Indices: 9084--9292 Score: 265
Period size: 85 Copynumber: 2.5 Consensus size: 82
9074 TTCAAGATTG
* ** *
9084 AGTCATCGAGATCCTTGAATTAAATTATCAATTCAAGATTGAGTCATCGAGACCCTTGAATTAAA
1 AGTCATCGAGATCCTTGAATGAAATTATCAATTCAAGATCAAGTCATCAAGACCCTTGAATTAAA
9149 TTATCAATTCAAGAACA
66 TTATCAATTCAAGAACA
* *
9166 AGTCATCGAGATCCTTGAATCGAATTATTATCAATTCAAGATCAAGTCGTCAAGATCCTTGAATT
1 AGTCATCGAGATCCTTGAAT-GAA--ATTATCAATTCAAGATCAAGTCATCAAGACCCTTGAATT
**
9231 AAATTATCAATTCAAGGTCA
63 AAATTATCAATTCAAGAACA
* * * * * *
9251 AATCGTCAAGACCCTTGAATTAAATTATCAATTCAAGGTCAA
1 AGTCATCGAGATCCTTGAATGAAATTATCAATTCAAGATCAA
9293 ATCTAACCAT
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
82 38 0.35
83 2 0.02
84 2 0.02
85 68 0.62
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (82 bp):
AGTCATCGAGATCCTTGAATGAAATTATCAATTCAAGATCAAGTCATCAAGACCCTTGAATTAAA
TTATCAATTCAAGAACA
Found at i:9619 original size:12 final size:12
Alignment explanation
Indices: 9602--9639 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
9592 AAACCCTTAG
9602 GAAAAACTAGAA
1 GAAAAACTAGAA
9614 GAAAAACTAG-A
1 GAAAAACTAGAA
*
9625 G-AAAAGTAGAA
1 GAAAAACTAGAA
9636 GAAA
1 GAAA
9640 TGAAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 7 0.30
11 4 0.17
12 12 0.52
ACGTcount: A:0.66, C:0.05, G:0.21, T:0.08
Consensus pattern (12 bp):
GAAAAACTAGAA
Found at i:20158 original size:932 final size:933
Alignment explanation
Indices: 18342--21868 Score: 5380
Period size: 932 Copynumber: 3.8 Consensus size: 933
18332 CAATGTTTAA
* * * * *
18342 CTCTTTATTCAACCCTTCAACATCAACTTGCCTGAAAGCCTTCCTTTGCAACCTCGACAATGGAT
1 CTCTATATTCAACCCTTCAACATCAACTTGCCTGAAAGCCTGCCTCTGCAACCTCTACAATGGCT
*
18407 GTTAATTTTGTCCCATTGACAACCAA-TCAGCGTATTATGATTAATCTGATTATGGCTGTTGTCC
66 GTTAATTTTGTCCCATTGACAA-CAAGTCAGCGTATTAGGATTAATCTGATTATGGCTGTTGTCC
* * **
18471 TTGGTGTATACCACGTTTTGTGGTATTTCAACATTAAAAACAAACTGAAGACTGACAAC-ACCCC
130 TTGGTGT-TACCACGTTTTGTGGTATTTCAACATTAAAGACAAGCTGAAGACTGACAACTATACC
* **
18535 AAGTTTTGCACCTACATGGATTGGATTATAGTATA-ACCTTACGTCTTCAATGTTATTTGCTTCT
194 AAGTTTTGCACCTACATGGATTGGACTATA--ATAGA----A-G--TTCGGTGTTATTTGCTTCT
* * * *
18599 TCAAAAATCTACTTTTG-CAAACAACAGAGCTATGGCCTCTGCAAACGGAGAGCTTGATAATGAT
250 TCAAAAATCTACTTTTGCCAAACGACAGAGCTATGGCCTCTGCAAACGAAGAGCTCGATAGTGAT
** * * * *
18663 GTCAATAAATGTTTAACAGCTCTAGCTTTTACAATTAATTTGGTCTGTATCTCAGGTGTGCCACA
315 GTCAATAAATGTTTGGCAGCTATAGCTTTTACCATTAATTTTGTCTGCATCTCAGGTGTGCCACA
* * *
18728 TTACATCTCTGTAATAATTCTGACTATTCTAGGATTCATAGGCTACCTCTCCCACACAATTACAG
380 TTACATCTCTGCAGTAATTCTGACTATTCTAGGATTCATAGGCTACCTCTCCCACACAATTACCG
* * *
18793 CTAAACATTTTGCATTACTACATTTCA-TAGGAGTAGAAGAGCCTATAAAATTGAAGACAAAATT
445 CTAAGCATTTTGCATTACTACATTTCATTAGGAGTAGAAGACCCTATAAAATTGAAGACAAAATC
*
18857 CAGGTAAATGACTCTGATATCTTTGTCATTGTTAATCACAGTGACTATACAGAATTGATAGAGGT
510 CAGGTAAATGACTCTGATATCTTTGTCATTGTTATTCACAGTGACTATACAGAATTGATAGAGGT
* * *
18922 AAGCTTAAAAGGCAAAAACGTTACCCCTTTACAGAAGCCAAGTGTAGACATTTCAAACTCAACTT
575 AAGATTAAAAGCCAAAAACGTTACCCCTCTACAGAAGCCAAGTGTAGACATTTCAAACTCAACTT
* *
18987 TTAGAGTTTAAGATAAAAGTGGGACTTAGACTGATGATAACGAGGAGATTGCAAAGCTTGCTAAA
640 TTAGAGTTTAAGATAAAAGTGAGACTTAGACTGATGATAACGAGGAGATTACAAAGCTTGCTAAA
* *
19052 ATGGTATGTGATATCCTCCATCATCAACTCTCTTTTTCTCTGTCTCTCTCACTCTCCATACGTGA
705 ATGGTATGTGATATCCTCCACCATCAACTCTCCTTTTCTCTGTCTCTCTCACTCTCCATACGTGA
*
19117 TATCGAAAATACAATTTGCATCACTATATCCTTCTAGGATTTCAATTAGGTTGTCCTTTTGAACC
770 TATCGAAAATACAATTTGCATCACTATATCCTTCTAGGATTTTAATTAGGTTGTCCTTTTGAACC
*
19182 TATATCTTGGAATCCCTAGTCAACTGGGTTGGGTTTCCTTAACATGAATTTATTCTCTAACAGAC
835 TATATCTTGGGATCCCTAGTCAACTGGGTTGGGTTTCCTTAACATGAATTTATTCTCTAACAGAC
19247 TTGAGTCTCATTCCCTTAGCCAACTTCTCAACTAT
900 TTGAGTC-CATTCCCTTAGCCAACTTCTCAACTAT
19282 CTCTATATTCAACCCTTCAACATCAACTTGCCTGAAAGCCTGCCTCTGCAACCTCTACAATGGCT
1 CTCTATATTCAACCCTTCAACATCAACTTGCCTGAAAGCCTGCCTCTGCAACCTCTACAATGGCT
* *
19347 GTTAATTTTGTCCCATTGACAACAAGTCAACGTATTAGCATTAATCTGATTATGGCTGTTGTCCT
66 GTTAATTTTGTCCCATTGACAACAAGTCAGCGTATTAGGATTAATCTGATTATGGCTGTTGTCCT
* * *
19412 TGGTGTTACCACATTTTGTGGTATTTCAACATTAAAGACAAGCTGAAGAATGACAACTATACCGA
131 TGGTGTTACCACGTTTTGTGGTATTTCAACATTAAAGACAAGCTGAAGACTGACAACTATACCAA
* *
19477 GTTTTGCACCTACATGGATTGAACTATAGTAGAAG-T-GGTGTTATTTGCTTCTTCAAAAATCTA
196 GTTTTGCACCTACATGGATTGGACTATAATAGAAGTTCGGTGTTATTTGCTTCTTCAAAAATCTA
** * *
19540 CTTTTGCCAAACGATGGAGCTATGGCCCCTGCAAACGAAGAGGTCGATAGTGATGTCAATAAATG
261 CTTTTGCCAAACGACAGAGCTATGGCCTCTGCAAACGAAGAGCTCGATAGTGATGTCAATAAATG
* * * *
19605 TTTGGCAACTATAGCTTTTACCATTAATTTTGTCTACATCTTAGGCT-TGCCACATTACTTCTCT
326 TTTGGCAGCTATAGCTTTTACCATTAATTTTGTCTGCATCTCAGG-TGTGCCACATTACATCTCT
* * *
19669 ACAGTAATTCTGACTATTCTAGGATTCATAGGCTACCTATCCCACACAATTACCGCTAAGGATTT
390 GCAGTAATTCTGACTATTCTAGGATTCATAGGCTACCTCTCCCACACAATTACCGCTAAGCATTT
*
19734 TGCATTACTACATTTCATTAGGAGTATAAGACCCTATAAAATTGAAGACAAAATCCAGGTAAATG
455 TGCATTACTACATTTCATTAGGAGTAGAAGACCCTATAAAATTGAAGACAAAATCCAGGTAAATG
* * *
19799 ACTCTGATATCTTTGTCATTGTTATTCACAGTGACTATACA-AATTTGATAGTGGTAAGCTAAAA
520 ACTCTGATATCTTTGTCATTGTTATTCACAGTGACTATACAGAA-TTGATAGAGGTAAGATTAAA
* * * *
19863 AGGCAATAACGTTATCCCTTTACAGAAGCCAAGTGTAGACATTTCAAACTCAACTTTTAGAGTTT
584 AGCCAAAAACGTTACCCCTCTACAGAAGCCAAGTGTAGACATTTCAAACTCAACTTTTAGAGTTT
* * *
19928 AAGATAAAAGTGGGTCTTAGACTGATGATAACGGGGAGATTACAAAGCTTGCTAAAATGGTATGT
649 AAGATAAAAGTGAGACTTAGACTGATGATAACGAGGAGATTACAAAGCTTGCTAAAATGGTATGT
19993 GATATCCTCCACCATCAACTCTCCTTTTCTCTGTCTCTCTCACTCTCCATACGTGATATCGAAAA
714 GATATCCTCCACCATCAACTCTCCTTTTCTCTGTCTCTCTCACTCTCCATACGTGATATCGAAAA
* *
20058 TACAATTTGCATAACTATATCCTTTTAGGATTTTAATTAGGTTGTCCTTTTGAACCTATATCTTG
779 TACAATTTGCATCACTATATCCTTCTAGGATTTTAATTAGGTTGTCCTTTTGAACCTATATCTTG
20123 GGATCCCTAGTCAACTGGGTTGGGTTTCCTTAACATGAATTTATTCTCTAACAGACTTGAGTCCC
844 GGATCCCTAGTCAACTGGGTTGGGTTTCCTTAACATGAATTTATTCTCTAACAGACTTGAGT-CC
20188 ATTCCCTTAGCCAACTTCTCAACTAT
908 ATTCCCTTAGCCAACTTCTCAACTAT
20214 CTCTATATTCAACCCTTCAACATCAACTTGCCTGAAAGCCTGCCTCTGCAACCTCTACAATGGCT
1 CTCTATATTCAACCCTTCAACATCAACTTGCCTGAAAGCCTGCCTCTGCAACCTCTACAATGGCT
20279 GTTAATTTTGTCCCATTGACAACAAGTCAGCGTATTAGGATTAATCTGATTATGGCTGTTGTCCT
66 GTTAATTTTGTCCCATTGACAACAAGTCAGCGTATTAGGATTAATCTGATTATGGCTGTTGTCCT
*
20344 TGGTGTTACCACGTTTTGTGGTATTTCAACATTAAAGACAAGCTGAAGACTGACAACTATACCGA
131 TGGTGTTACCACGTTTTGTGGTATTTCAACATTAAAGACAAGCTGAAGACTGACAACTATACCAA
* *
20409 GTTTTGCACCTACATGGATTGTACTACAATAGAAG-T-GGTGTTATTTGCTTCTTCAAAAATCTA
196 GTTTTGCACCTACATGGATTGGACTATAATAGAAGTTCGGTGTTATTTGCTTCTTCAAAAATCTA
** * * * *
20472 CTTTTGCCAAACGATGGAGCTATTGCCTTTGCAAACGGAGAGGTCGATAGTGATGTCAATAAATG
261 CTTTTGCCAAACGACAGAGCTATGGCCTCTGCAAACGAAGAGCTCGATAGTGATGTCAATAAATG
20537 TTTGGCAGCTATAGCTTTTACCATTAATTTTGTCTGCATCTCAGGCT-TGCCACATTACATCTCT
326 TTTGGCAGCTATAGCTTTTACCATTAATTTTGTCTGCATCTCAGG-TGTGCCACATTACATCTCT
* *
20601 GCAGTAATTCTGACTATTCTAGGATTCATAGGCTACCTCTCCCATACAATTACCACTAAGCATTT
390 GCAGTAATTCTGACTATTCTAGGATTCATAGGCTACCTCTCCCACACAATTACCGCTAAGCATTT
* * *
20666 TGCATTGCTACATTTCATTAGGAGTAGAAGACCCTATAAAATTAAAGATAAAATCCAGGTAAATG
455 TGCATTACTACATTTCATTAGGAGTAGAAGACCCTATAAAATTGAAGACAAAATCCAGGTAAATG
*
20731 ACTCTGATATATTTGTCATTGTTATTCACAGTGACTATACAGAATTGATAGAGGTAAGATTAAAA
520 ACTCTGATATCTTTGTCATTGTTATTCACAGTGACTATACAGAATTGATAGAGGTAAGATTAAAA
* *
20796 GCCAAAAACGTTACCCCTCGACAGAAGCCAAGTGTAGTCATTTCAAACTCAACTTTTAGAGTTTA
585 GCCAAAAACGTTACCCCTCTACAGAAGCCAAGTGTAGACATTTCAAACTCAACTTTTAGAGTTTA
* * * *
20861 TGATATAAAAGTGAGACTTAGACTGATGATAATGAGGAGATTACAAAGCTTGCCAAAATGGTAAG
650 --AGATAAAAGTGAGACTTAGACTGATGATAACGAGGAGATTACAAAGCTTGCTAAAATGGTATG
*
20926 TGATATCCTCCACCATC-A-TCAT-C----ATC--TCTCTCT--CTCTCCATACGTGATATCGAA
713 TGATATCCTCCACCATCAACTC-TCCTTTTCTCTGTCTCTCTCACTCTCCATACGTGATATCGAA
* *
20980 AATACAATTTGCATCACTATATCCTTCTAGTATTTTAATTAGGTTGTCCCTTTGAACCTATATCT
777 AATACAATTTGCATCACTATATCCTTCTAGGATTTTAATTAGGTTGTCCTTTTGAACCTATATCT
* * *
21045 TGGGATCCATAGTCAACTAGGTTGGGTTTCCTTAACATGAATTTATTCTCTAATAGACTTGAGTC
842 TGGGATCCCTAGTCAACTGGGTTGGGTTTCCTTAACATGAATTTATTCTCTAACAGACTTGAGTC
* * * *
21110 CTATTCCCGTAGCTAACTTCTCAAATAA
907 C-ATTCCCTTAGCCAACTTCTCAACTAT
* * * * * *
21138 CTCTCTATTCAACTCTTCAACATCAACTTGCCTGAAAGCCT-TCTCTTG-AACCGCAACAATGGT
1 CTCTATATTCAACCCTTCAACATCAACTTGCCTGAAAGCCTGCCTC-TGCAACCTCTACAATGGC
* * * *
21201 TGTTAATTTTGTCCCATTGACAACTAGTCAGCGTATTAGGATTAATTTGATCATGGCTTTTGTCC
65 TGTTAATTTTGTCCCATTGACAACAAGTCAGCGTATTAGGATTAATCTGATTATGGCTGTTGTCC
* * * * *
21266 TTCGAGTTACCACGTTTTGTGGTATTTCAGCATTAAAGACAAGCTGAAGACTGACAACCATCCCA
130 TTGGTGTTACCACGTTTTGTGGTATTTCAACATTAAAGACAAGCTGAAGACTGACAACTATACCA
* * *
21331 AGTTTTACACCTACATGGATGGGACTATAATGGAAGCTTACGTCTTCAGTGTTATTTGCTTCTTC
195 AGTTTTGCACCTACATGGATTGGACTATAATAGAAG-TT-CG------GTGTTATTTGCTTCTTC
* *
21396 AAAAATCTACTTTTGCCAAACTACAGAGCTATGGCCTCTGCAAACGAAGAGCTCGATACTGATGT
252 AAAAATCTACTTTTGCCAAACGACAGAGCTATGGCCTCTGCAAACGAAGAGCTCGATAGTGATGT
* * *
21461 CAATAAATGTTTGGTAGCTCTAGCTTTTACCATTAATTTTGTCTGCATCTTAGGTGTGCCACATT
317 CAATAAATGTTTGGCAGCTATAGCTTTTACCATTAATTTTGTCTGCATCTCAGGTGTGCCACATT
* *
21526 ACTTCTCTGCAGTAATTCTGACTATTCTAGGATTCATAGGCTACCTCTCCTACACAATTACCGCT
382 ACATCTCTGCAGTAATTCTGACTATTCTAGGATTCATAGGCTACCTCTCCCACACAATTACCGCT
* *
21591 AAGCATTTTGCATTACTACATTTCATTAGGAGTAGAAGACCCTATAAAATTGAAGATAAAATCTA
447 AAGCATTTTGCATTACTACATTTCATTAGGAGTAGAAGACCCTATAAAATTGAAGACAAAATCCA
*
21656 GGTAAATGACTCTGATATCTTTGTCATTGTTA-TCGACAATGACTATACAGAATTGATAGAGGTA
512 GGTAAATGACTCTGATATCTTTGTCATTGTTATTC-ACAGTGACTATACAGAATTGATAGAGGTA
*
21720 AGATTAAAAGCCAAAAACGTTACCGCTCTACAGAAGCCAAGTGTAGACATTTCAAACTCAACTTT
576 AGATTAAAAGCCAAAAACGTTACCCCTCTACAGAAGCCAAGTGTAGACATTTCAAACTCAACTTT
* * * *
21785 TAGAGTTTATGATAAAAGTGAGACTTAGACTGATGATAATGAGGAGATTGCAAAGCTTGTTAAAA
641 TAGAGTTTAAGATAAAAGTGAGACTTAGACTGATGATAACGAGGAGATTACAAAGCTTGCTAAAA
21850 TGGTAAT-TGATATCCTCCA
706 TGGT-ATGTGATATCCTCCA
21869 TCATTATCAT
Statistics
Matches: 2395, Mismatches: 165, Indels: 63
0.91 0.06 0.02
Matches are distributed among these distances:
923 168 0.07
924 206 0.09
925 1 0.00
926 7 0.00
927 1 0.00
928 2 0.00
930 31 0.01
931 247 0.10
932 1058 0.44
933 392 0.16
934 74 0.03
935 1 0.00
938 2 0.00
939 51 0.02
940 154 0.06
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (933 bp):
CTCTATATTCAACCCTTCAACATCAACTTGCCTGAAAGCCTGCCTCTGCAACCTCTACAATGGCT
GTTAATTTTGTCCCATTGACAACAAGTCAGCGTATTAGGATTAATCTGATTATGGCTGTTGTCCT
TGGTGTTACCACGTTTTGTGGTATTTCAACATTAAAGACAAGCTGAAGACTGACAACTATACCAA
GTTTTGCACCTACATGGATTGGACTATAATAGAAGTTCGGTGTTATTTGCTTCTTCAAAAATCTA
CTTTTGCCAAACGACAGAGCTATGGCCTCTGCAAACGAAGAGCTCGATAGTGATGTCAATAAATG
TTTGGCAGCTATAGCTTTTACCATTAATTTTGTCTGCATCTCAGGTGTGCCACATTACATCTCTG
CAGTAATTCTGACTATTCTAGGATTCATAGGCTACCTCTCCCACACAATTACCGCTAAGCATTTT
GCATTACTACATTTCATTAGGAGTAGAAGACCCTATAAAATTGAAGACAAAATCCAGGTAAATGA
CTCTGATATCTTTGTCATTGTTATTCACAGTGACTATACAGAATTGATAGAGGTAAGATTAAAAG
CCAAAAACGTTACCCCTCTACAGAAGCCAAGTGTAGACATTTCAAACTCAACTTTTAGAGTTTAA
GATAAAAGTGAGACTTAGACTGATGATAACGAGGAGATTACAAAGCTTGCTAAAATGGTATGTGA
TATCCTCCACCATCAACTCTCCTTTTCTCTGTCTCTCTCACTCTCCATACGTGATATCGAAAATA
CAATTTGCATCACTATATCCTTCTAGGATTTTAATTAGGTTGTCCTTTTGAACCTATATCTTGGG
ATCCCTAGTCAACTGGGTTGGGTTTCCTTAACATGAATTTATTCTCTAACAGACTTGAGTCCATT
CCCTTAGCCAACTTCTCAACTAT
Found at i:26601 original size:20 final size:20
Alignment explanation
Indices: 26573--26611 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
26563 AGGATTAATT
* *
26573 AAAAGAAAGCAAATTAAATA
1 AAAAGAAAGAAAAATAAATA
*
26593 AAAATAAAGAAAAATAAAT
1 AAAAGAAAGAAAAATAAAT
26612 TAAATCTAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAAGAAAGAAAAATAAATA
Found at i:28240 original size:9 final size:9
Alignment explanation
Indices: 28226--28253 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28216 GGAATCATCA
28226 GATGAAGAT
1 GATGAAGAT
28235 GATGAAGAT
1 GATGAAGAT
28244 GATGAAGAT
1 GATGAAGAT
28253 G
1 G
28254 CCTATTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (9 bp):
GATGAAGAT
Found at i:28448 original size:109 final size:109
Alignment explanation
Indices: 28269--28589 Score: 552
Period size: 109 Copynumber: 2.9 Consensus size: 109
28259 TAAACAAAGC
*
28269 AGCTTGTTAGTAAGCCTATGAGTTTTAATTTGGACTTATAAGTAATGATATAAATTAAGGAAAAT
1 AGCTTGTTGGTAAGCCTATGAGTTTTAATTTGGACTTATAAGTAATGATATAAATTAAGGAAAAT
28334 TTCAATTTATGTTTATAAATTATGGTTTTGCAATTAAATGTAGT
66 TTCAATTTATGTTTATAAATTATGGTTTTGCAATTAAATGTAGT
28378 AGCTTGTTGGTAAGCCTATGAGTTTTAATTTGGACTTATAAGTAATGATATAAATTAAGGAAAAT
1 AGCTTGTTGGTAAGCCTATGAGTTTTAATTTGGACTTATAAGTAATGATATAAATTAAGGAAAAT
28443 TTCAATTTATGTTTATAAATTATGGTTTTGCAATTAAATGTAGT
66 TTCAATTTATGTTTATAAATTATGGTTTTGCAATTAAATGTAGT
*
28487 AGCTTGTTGGTAAGCCTATGAGTTTTAATTTGGACTTTTATAATTATTAATGATATAAAATTAAG
1 AGCTTGTTGGTAAGCCTATGAGTTTTAATTTGGAC--TTAT-A--AGTAATGATAT-AAATTAAG
* *
28552 GAAATTTTCAATTTATGTTTATGAATTATGGTTTTGCA
60 GAAAATTTCAATTTATGTTTATAAATTATGGTTTTGCA
28590 TGTGGAAATG
Statistics
Matches: 202, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
109 143 0.71
111 4 0.02
112 1 0.00
114 10 0.05
115 44 0.22
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (109 bp):
AGCTTGTTGGTAAGCCTATGAGTTTTAATTTGGACTTATAAGTAATGATATAAATTAAGGAAAAT
TTCAATTTATGTTTATAAATTATGGTTTTGCAATTAAATGTAGT
Found at i:30337 original size:16 final size:16
Alignment explanation
Indices: 30324--30450 Score: 123
Period size: 16 Copynumber: 7.9 Consensus size: 16
30314 TCTCGGGTTT
*
30324 TTCGGGTTTCGGGTTA
1 TTCGGGTTTCGGGTCA
* *
30340 TACGGGTCTCGGGTCA
1 TTCGGGTTTCGGGTCA
* *
30356 CTCGGGTTACGGGTCA
1 TTCGGGTTTCGGGTCA
*
30372 TTCGCGTTTCGGGTCA
1 TTCGGGTTTCGGGTCA
* *
30388 -TCTAGGTTACGGGTCA
1 TTC-GGGTTTCGGGTCA
*
30404 TTCGGGTCTCGGGTCA
1 TTCGGGTTTCGGGTCA
*
30420 -TCTGGGTTGCGGGTCA
1 TTC-GGGTTTCGGGTCA
*
30436 TTCGGGTCTCGGGTC
1 TTCGGGTTTCGGGTC
30451 GGGCGGGTTA
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
15 4 0.05
16 79 0.91
17 4 0.05
ACGTcount: A:0.09, C:0.22, G:0.37, T:0.32
Consensus pattern (16 bp):
TTCGGGTTTCGGGTCA
Found at i:30361 original size:32 final size:32
Alignment explanation
Indices: 30327--30450 Score: 169
Period size: 32 Copynumber: 3.9 Consensus size: 32
30317 CGGGTTTTTC
* * *
30327 GGGTTTCGGGTTATACGGGTCTCGGGTCA-CT
1 GGGTTACGGGTCATTCGGGTCTCGGGTCATCT
* *
30358 CGGGTTACGGGTCATTCGCGTTTCGGGTCATCT
1 -GGGTTACGGGTCATTCGGGTCTCGGGTCATCT
*
30391 AGGTTACGGGTCATTCGGGTCTCGGGTCATCT
1 GGGTTACGGGTCATTCGGGTCTCGGGTCATCT
*
30423 GGGTTGCGGGTCATTCGGGTCTCGGGTC
1 GGGTTACGGGTCATTCGGGTCTCGGGTC
30451 GGGCGGGTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
32 79 0.98
33 2 0.02
ACGTcount: A:0.09, C:0.22, G:0.38, T:0.31
Consensus pattern (32 bp):
GGGTTACGGGTCATTCGGGTCTCGGGTCATCT
Found at i:30381 original size:48 final size:47
Alignment explanation
Indices: 30314--30450 Score: 136
Period size: 48 Copynumber: 2.9 Consensus size: 47
30304 CGGGTTAACT
** *
30314 TCTCGGGTTTTTCGGGTTTCGGGTTATACGGGTCTCGGGTCACTCGGG
1 TCTCGGGTCATTCGGGTTTCGGGTCAT-CGGGTCTCGGGTCACTCGGG
* * *
30362 T-TACGGGTCATTCGCGTTTCGGGTCATCTAGGT-TACGGGTCATTCGGG
1 TCT-CGGGTCATTCGGGTTTCGGGTCATC-GGGTCT-CGGGTCACTCGGG
*
30410 TCTCGGGTCA-TCTGGGTTGCGGGTCATTCGGGTCTCGGGTC
1 TCTCGGGTCATTC-GGGTTTCGGGTCA-TCGGGTCTCGGGTC
30451 GGGCGGGTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
47 5 0.07
48 64 0.88
49 4 0.05
ACGTcount: A:0.08, C:0.22, G:0.36, T:0.34
Consensus pattern (47 bp):
TCTCGGGTCATTCGGGTTTCGGGTCATCGGGTCTCGGGTCACTCGGG
Found at i:31350 original size:45 final size:45
Alignment explanation
Indices: 31299--31385 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
31289 TACCTAAACT
*
31299 CTCCTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTA
1 CTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTA
31344 CTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1 CTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
31386 AATTGTTGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (45 bp):
CTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTA
Found at i:32736 original size:11 final size:11
Alignment explanation
Indices: 32720--32754 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
32710 ACCTCACTGA
32720 TGTTGTTTTGT
1 TGTTGTTTTGT
*
32731 TGTTGTTTTGG
1 TGTTGTTTTGT
32742 TGTTGCTTTTGT
1 TGTTG-TTTTGT
32754 T
1 T
32755 ATGTAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.00, C:0.03, G:0.29, T:0.69
Consensus pattern (11 bp):
TGTTGTTTTGT
Found at i:33166 original size:151 final size:151
Alignment explanation
Indices: 32892--33190 Score: 474
Period size: 151 Copynumber: 2.0 Consensus size: 151
32882 TCTATCATCC
* * *
32892 ATGTAGTTTTTCTTTCTCCAACTTGGTGTTGAGTAGTAAATAATTTATTAATTTGGGTCTACTTT
1 ATGTAGTTTTTCTTTCTCCAACTTGGTGTTAAGTAGTAAATAATTTATTAATTCGAGTCTACTTT
* * *
32957 GAATCTTTCTTTTTTGACTTGTGTCTGTAGTAGCTTTGCATGCTGATATAGCCTTGTTTTGGCTG
66 GAATCTTTCTTTTCTGACTTGTGTATCTAGTAGCTTTGCATGCTGATATAGCCTTGTTTTGGCTG
33022 GAATTGTTATATTTGCTTATG
131 GAATTGTTATATTTGCTTATG
* * *
33043 ATGTAGTTTTTCTTTGTCCAACTTGGTGTTAAGTAGTAGATGAA-TTATTAATTCGAGTCTGCTT
1 ATGTAGTTTTTCTTTCTCCAACTTGGTGTTAAGTAGTAAAT-AATTTATTAATTCGAGTCTACTT
* * *
33107 TGAATCTTTCTTTTCTGACTTGTGTATCTAGTAGCTTTGCTTGTTGATATGGCCTTGTTTTGGCT
65 TGAATCTTTCTTTTCTGACTTGTGTATCTAGTAGCTTTGCATGCTGATATAGCCTTGTTTTGGCT
33172 GGAATTGTTATATTTGCTT
130 GGAATTGTTATATTTGCTT
33191 TTGTTTTTCC
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
151 133 0.99
152 2 0.01
ACGTcount: A:0.19, C:0.12, G:0.20, T:0.49
Consensus pattern (151 bp):
ATGTAGTTTTTCTTTCTCCAACTTGGTGTTAAGTAGTAAATAATTTATTAATTCGAGTCTACTTT
GAATCTTTCTTTTCTGACTTGTGTATCTAGTAGCTTTGCATGCTGATATAGCCTTGTTTTGGCTG
GAATTGTTATATTTGCTTATG
Found at i:34110 original size:42 final size:43
Alignment explanation
Indices: 34015--34098 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
34005 GTAATTAATC
* * *
34015 CAAATATTGTTCCTAAAGTTTAGGAATAAGATAAAAGTCATTA
1 CAAACATTGTTCCGAAAATTTAGGAATAAGATAAAAGTCATTA
*
34058 CAAACATTGTTCCGAAAATTT-GGAATGAGATAAAAGTCATT
1 CAAACATTGTTCCGAAAATTTAGGAATAAGATAAAAGTCATT
34099 CCTGACTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 19 0.51
43 18 0.49
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (43 bp):
CAAACATTGTTCCGAAAATTTAGGAATAAGATAAAAGTCATTA
Found at i:42804 original size:80 final size:80
Alignment explanation
Indices: 42659--42818 Score: 187
Period size: 80 Copynumber: 2.0 Consensus size: 80
42649 AGAGTACCAT
* * * * *
42659 CGTTTAGTATTTATAAGTGATGGCTAGCAGTAACTGTTTAAACTAAATACTTCTGCCTTACTTGT
1 CGTTTAGTATTTATAAGTGATGGCCAACAGTAACTATTTAAACTAAATAATTCTGCATTACTTGT
42724 GTTTGAAAA-GAAATA
66 GTTT-AAAAGGAAATA
* * * * * ** *
42739 CGTTTCGTTTTTATAGGTGATGGCCAACATTAGCTATTTAAACTAAATAATTCTTTATTATTTGT
1 CGTTTAGTATTTATAAGTGATGGCCAACAGTAACTATTTAAACTAAATAATTCTGCATTACTTGT
42804 GTTTAAAAGGAAATA
66 GTTTAAAAGGAAATA
42819 GGATTTTGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
79 4 0.06
80 62 0.94
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (80 bp):
CGTTTAGTATTTATAAGTGATGGCCAACAGTAACTATTTAAACTAAATAATTCTGCATTACTTGT
GTTTAAAAGGAAATA
Done.