Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021750.1 Corchorus olitorius cultivar O-4 contig21783, 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: 24873
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:5495 original size:17 final size:17
Alignment explanation
Indices: 5473--5512 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5463 AGATTACCAT
*
5473 TGATCTT-GCATCACTGG
1 TGATCTTAG-ATCACTAG
5490 TGATCTTAGATCACTAG
1 TGATCTTAGATCACTAG
5507 TGATCT
1 TGATCT
5513 GGGGGGTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (17 bp):
TGATCTTAGATCACTAG
Found at i:9132 original size:16 final size:16
Alignment explanation
Indices: 9113--9151 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
9103 CCCGAATCCG
9113 CCCGAACCCGA-AATTA
1 CCCGAACCCGATAA-TA
*
9129 CCCGAGCCCGATAATA
1 CCCGAACCCGATAATA
9145 CCCGAAC
1 CCCGAAC
9152 TCGAGGCAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.33, C:0.41, G:0.15, T:0.10
Consensus pattern (16 bp):
CCCGAACCCGATAATA
Found at i:9383 original size:2 final size:2
Alignment explanation
Indices: 9376--9415 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
9366 AAACTACTAA
*
9376 AT AT AT AT A- AT -T AG AT AT -T 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 AT AT AT
9415 A
1 A
9416 GACAAGCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12460 original size:33 final size:31
Alignment explanation
Indices: 12387--12527 Score: 120
Period size: 33 Copynumber: 4.3 Consensus size: 31
12377 GCTATGATCA
** *
12387 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
12419 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
12452 ACCTAAAACAGATTTAGTATCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
** * * *
12485 ACTCAAATTAGGTTTAGTATCATCACTAACAAC
1 AC-CAAAACAGATTT-GTTTCATCACAAACAAC
*
12518 ATCTAAAACA
1 A-CCAAAACA
12528 CTCTTTGCAA
Statistics
Matches: 92, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
32 7 0.08
33 78 0.85
34 7 0.08
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:13966 original size:20 final size:19
Alignment explanation
Indices: 13928--13966 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
13918 CTGGTCGAAA
13928 TTTTTTATTTTTTCTGATT
1 TTTTTTATTTTTTCTGATT
13947 TTTTTTGATATTTTTC-GATT
1 TTTTTT-AT-TTTTTCTGATT
13967 AAACTACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (19 bp):
TTTTTTATTTTTTCTGATT
Found at i:14104 original size:26 final size:23
Alignment explanation
Indices: 14074--14120 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
14064 CTTGAAAATT
14074 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
14100 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
14121 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:14930 original size:15 final size:15
Alignment explanation
Indices: 14909--14945 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
14899 TTTAAAAATC
14909 ACAATTAAAAAGAAA
1 ACAATTAAAAAGAAA
*
14924 GCAATTAAAAAGAAA
1 ACAATTAAAAAGAAA
14939 ACAATTA
1 ACAATTA
14946 TACTAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (15 bp):
ACAATTAAAAAGAAA
Found at i:17303 original size:12 final size:12
Alignment explanation
Indices: 17286--17313 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17276 GTACGTTTAT
17286 ACGACACGAAAC
1 ACGACACGAAAC
17298 ACGACACGAAAC
1 ACGACACGAAAC
17310 ACGA
1 ACGA
17314 ATTGCCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.32, G:0.18, T:0.00
Consensus pattern (12 bp):
ACGACACGAAAC
Found at i:17560 original size:22 final size:22
Alignment explanation
Indices: 17535--17576 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
17525 TAGAGATAGA
17535 AAAAGATCA-AAAA-AAAAAGAG
1 AAAA-ATCAGAAAATAAAAAGAG
17556 AAAAATCAGAAAATAAAAAGA
1 AAAAATCAGAAAATAAAAAGA
17577 TGCAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (22 bp):
AAAAATCAGAAAATAAAAAGAG
Found at i:19092 original size:15 final size:15
Alignment explanation
Indices: 19069--19112 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
19059 ATAAAAATTA
19069 AATAT-TTTTATTTT
1 AATATATTTTATTTT
19083 AATATATTTTATTTT
1 AATATATTTTATTTT
* * *
19098 ATTAAAATTTATTTT
1 AATATATTTTATTTT
19113 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATATATTTTATTTT
Found at i:20239 original size:15 final size:14
Alignment explanation
Indices: 20214--20242 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20204 ATAAATTTCA
20214 ATAAAATAAAATAT
1 ATAAAATAAAATAT
20228 ATAAAATAAAA-AT
1 ATAAAATAAAATAT
20241 AT
1 AT
20243 TTAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAAATAAAATAT
Found at i:21453 original size:48 final size:47
Alignment explanation
Indices: 21378--21521 Score: 159
Period size: 49 Copynumber: 3.0 Consensus size: 47
21368 GAGCGTGCCA
* * * * *
21378 ATCAATTTTATCCAAAAATTGATAAAAAGTGCGA-TGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG
21425 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG
* * *
21474 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGT-AAAGTAAAAG
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
21520 AT
1 AT
21522 TGCTTGGAGT
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
46 10 0.12
47 14 0.17
48 18 0.21
49 41 0.49
50 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Found at i:22786 original size:9 final size:9
Alignment explanation
Indices: 22768--22796 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
22758 TTAATTCATT
22768 TAATTT-CA
1 TAATTTCCA
22776 TAATTTCCA
1 TAATTTCCA
22785 TAATTTCCA
1 TAATTTCCA
22794 TAA
1 TAA
22797 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:23331 original size:12 final size:12
Alignment explanation
Indices: 23316--23341 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23306 ATGATAGCAA
23316 AAATTTCTAACT
1 AAATTTCTAACT
23328 AAATTTCTAACT
1 AAATTTCTAACT
23340 AA
1 AA
23342 TAAACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATTTCTAACT
Found at i:23732 original size:31 final size:31
Alignment explanation
Indices: 23663--23734 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
23653 GTCTACCATC
*
23663 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
**
23694 TAATAATTTGTTTAATTTAATG-C-TTAATTT
1 TTTTAATTTGTTTAATTTAA-GACTTTAATTT
23724 GTTTTAATTTG
1 -TTTTAATTTG
23735 CAATAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 6 0.18
31 27 0.79
32 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:24213 original size:43 final size:44
Alignment explanation
Indices: 24164--24263 Score: 141
Period size: 45 Copynumber: 2.3 Consensus size: 44
24154 ATTCGCGTAT
* *
24164 ATAAAGCAAATAATTCTA-CTCCATCTCTAGGTAATTCATCAAA
1 ATAAAGCTAATAATTCTATCTCCATCTCTAGATAATTCATCAAA
*
24207 ATAAAGCTAA-AATTTTATTCCTCCATCTCTAGATAATTCATCAAA
1 ATAAAGCTAATAATTCTA-T-CTCCATCTCTAGATAATTCATCAAA
24252 ATAAAGCTAATA
1 ATAAAGCTAATA
24264 TTAATTGTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
42 6 0.12
43 9 0.18
45 34 0.68
46 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (44 bp):
ATAAAGCTAATAATTCTATCTCCATCTCTAGATAATTCATCAAA
Found at i:24813 original size:175 final size:177
Alignment explanation
Indices: 24510--24873 Score: 556
Period size: 175 Copynumber: 2.1 Consensus size: 177
24500 TGTGCTTTTG
* * * *
24510 GAAATGTGGAAATATACTAAATATAAGCAACTAATTATAGAAACCTCAATAAAAAGAAAGTCGAA
1 GAAAAGTGAAAATATACTAAACATAAACAACTAA-TATAGAAACCTCAATAAAAAGAAAGTCGAA
**** * *
24575 TGATAAATAAAATTTTTTTTTGTGAAATTAAAGAGGAATATGAAAATGTTAAATTTAAGTATCAA
65 TGATAAATAAAAAAACTTTTTGTGAAATAAAAGAGGAATAAGAAAATGTTAAATTTAAGTATCAA
*
24640 ATAATATAATCAACAAATAAATCTAGATTTACCTCAAA-ATGTTGCGGT
130 ATAATATAATCAACAAATAAATCCAGATTTACCTCAAATA-GTTGCGGT
*
24688 GAAAAGTGAAAATATACTAAACATAAACAACT-A-ATAGAAACCTCAATAAAAAGGAAGTCGAAT
1 GAAAAGTGAAAATATACTAAACATAAACAACTAATATAGAAACCTCAATAAAAAGAAAGTCGAAT
*
24751 GATAAA-AAAAGAAACTTTTTGTGAAATAAAAGAGGAATAAGAAAATGTTAAATTTAAGTATCAC
66 GATAAATAAAA-AAACTTTTTGTGAAATAAAAGAGGAATAAGAAAATGTTAAATTTAAGTATCAA
24815 ATAATATAATCAACAAATAAATCCAGATTTACCTCAAATAGTTGCGGT
130 ATAATATAATCAACAAATAAATCCAGATTTACCTCAAATAGTTGCGGT
24863 GAAAAGTGAAA
1 GAAAAGTGAAA
Statistics
Matches: 171, Mismatches: 13, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
174 4 0.02
175 137 0.80
176 1 0.01
177 1 0.01
178 28 0.16
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (177 bp):
GAAAAGTGAAAATATACTAAACATAAACAACTAATATAGAAACCTCAATAAAAAGAAAGTCGAAT
GATAAATAAAAAAACTTTTTGTGAAATAAAAGAGGAATAAGAAAATGTTAAATTTAAGTATCAAA
TAATATAATCAACAAATAAATCCAGATTTACCTCAAATAGTTGCGGT
Done.