Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014048.1 Corchorus capsularis cultivar CVL-1 contig14069, 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: 27274
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5180 original size:19 final size:20
Alignment explanation
Indices: 5153--5190 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5143 TACTATTATT
5153 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
5173 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
5191 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:5413 original size:22 final size:22
Alignment explanation
Indices: 5388--5529 Score: 180
Period size: 22 Copynumber: 6.5 Consensus size: 22
5378 TAGTTATTAT
*
5388 AATTTCATAGTGTGCTTACCAA
1 AATTTCATAGTGTGGTTACCAA
* *
5410 AATTCCATA-TG-GAAGTTATCAA
1 AATTTCATAGTGTG--GTTACCAA
*
5432 AATTTAATAGTGTGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
**
5454 AATTTCATAGCATGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
5476 AATTTCATAGTGTGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
**
5498 AATTTCATAGCATGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
5520 AATTTCATAG
1 AATTTCATAG
5530 GATCAGATTA
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 97 0.94
23 2 0.02
24 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTACCAA
Found at i:5427 original size:44 final size:44
Alignment explanation
Indices: 5354--5529 Score: 203
Period size: 44 Copynumber: 4.0 Consensus size: 44
5344 CTTGTCTCTA
* * * * *
5354 TGTGGTTATCAAAATTTCACAAG-TTAGTTATTATAATTTCATAG
1 TGTGGTTACCAAAATTTCA-TAGCATAGTTATCAAAATTTCATAG
* * * *
5398 TGTGCTTACCAAAATTCCATATGGA-AGTTATCAAAATTTAATAG
1 TGTGGTTACCAAAATTTCATA-GCATAGTTATCAAAATTTCATAG
* *
5442 TGTGGTTACCAAAATTTCATAGCATGGTTACCAAAATTTCATAG
1 TGTGGTTACCAAAATTTCATAGCATAGTTATCAAAATTTCATAG
* *
5486 TGTGGTTACCAAAATTTCATAGCATGGTTACCAAAATTTCATAG
1 TGTGGTTACCAAAATTTCATAGCATAGTTATCAAAATTTCATAG
5530 GATCAGATTA
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
43 3 0.03
44 112 0.97
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (44 bp):
TGTGGTTACCAAAATTTCATAGCATAGTTATCAAAATTTCATAG
Found at i:5686 original size:22 final size:22
Alignment explanation
Indices: 5661--5721 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
5651 TTTATAGTGT
*
5661 GGTTAACAAAATTTCATTAGGA
1 GGTTAACAAAATTTCATGAGGA
* *
5683 GGTT-ACTAATATTTCATGGGGA
1 GGTTAAC-AAAATTTCATGAGGA
*
5705 GGTTATCAAAATTTCAT
1 GGTTAACAAAATTTCAT
5722 ATGAAGGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 29 0.91
23 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (22 bp):
GGTTAACAAAATTTCATGAGGA
Found at i:5729 original size:22 final size:21
Alignment explanation
Indices: 5661--5732 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
5651 TTTATAGTGT
*
5661 GGTTAACAAAATTTCATTAGGA
1 GGTTATCAAAATTTCATT-GGA
* *
5683 GGTTA-CTAATATTTCATGGGGA
1 GGTTATC-AAAATTTCAT-TGGA
*
5705 GGTTATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCAT-TGGA
5727 GGTTAT
1 GGTTAT
5733 AGAAGTCTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
21 1 0.02
22 39 0.95
23 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATTGGA
Found at i:5956 original size:22 final size:21
Alignment explanation
Indices: 5843--5967 Score: 99
Period size: 22 Copynumber: 5.7 Consensus size: 21
5833 TTATAGTGTT
*
5843 GTTATCAAAATTTCA-AAGCGA
1 GTTATCAAAATTTCATAA-AGA
* * *
5864 GTTTATCAAAATTACATAATGT
1 G-TTATCAAAATTTCATAAAGA
* *
5886 GATTATCAGAATTTCATAGAAGG
1 G-TTATCAAAATTTCATA-AAGA
* * *
5909 GTCAACAAAATTTTATAAAGA
1 GTTATCAAAATTTCATAAAGA
5930 GGTTATCAAAATTTCATAAAGAA
1 -GTTATCAAAATTTCATAAAG-A
*
5953 GTTATCAAATTTTCA
1 GTTATCAAAATTTCA
5968 AAATGTGATT
Statistics
Matches: 82, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
21 4 0.05
22 72 0.88
23 6 0.07
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (21 bp):
GTTATCAAAATTTCATAAAGA
Found at i:6189 original size:22 final size:22
Alignment explanation
Indices: 6079--6305 Score: 133
Period size: 22 Copynumber: 10.3 Consensus size: 22
6069 CGAAGTAATA
* *
6079 AAAATTTCA-GGGAGGA-TATC
1 AAAATTTCATAGGAAGATTATC
** *
6099 AAAATTTCATAGTTTAG-TTTTC
1 AAAATTTCATAG-GAAGATTATC
* * * *
6121 AAATTTTCATAAGAGGGTTATC
1 AAAATTTCATAGGAAGATTATC
* * *
6143 AAAATTTCATAGTATG-TAGATC
1 AAAATTTCATAGGAAGAT-TATC
*
6165 AAAATTTCATAGGAAGATTAAC
1 AAAATTTCATAGGAAGATTATC
* *
6187 AAAATTTCATAATG-AGCTTATC
1 AAAATTTCAT-AGGAAGATTATC
** * *
6209 AAAAAATCATAGGGAGGTTATC
1 AAAATTTCATAGGAAGATTATC
* * *
6231 AAAATTTTATAGGGAGGTTTATC
1 AAAATTTCATA-GGAAGATTATC
**
6254 AAAATTTTTTAGGAAGATTTATC
1 AAAATTTCATAGGAAGA-TTATC
*
6277 AAAATTTCATAGTG-TGATTATC
1 AAAATTTCATAG-GAAGATTATC
6299 AAAATTT
1 AAAATTT
6306 TAGAGTGTGA
Statistics
Matches: 157, Mismatches: 39, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
20 9 0.06
21 5 0.03
22 104 0.66
23 38 0.24
24 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGGAAGATTATC
Found at i:6256 original size:23 final size:23
Alignment explanation
Indices: 6217--6307 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
6207 TCAAAAAATC
6217 ATAGGGAGG-TTATCAAAATTTT
1 ATAGGGAGGTTTATCAAAATTTT
6239 ATAGGGAGGTTTATCAAAATTTT
1 ATAGGGAGGTTTATCAAAATTTT
* * * *
6262 TTAGGAAGATTTATCAAAATTTC
1 ATAGGGAGGTTTATCAAAATTTT
* * *
6285 ATAGTG-TGATTATCAAAATTTT
1 ATAGGGAGGTTTATCAAAATTTT
6307 A
1 A
6308 GAGTGTGATT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 22 0.39
23 35 0.61
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (23 bp):
ATAGGGAGGTTTATCAAAATTTT
Found at i:6312 original size:22 final size:22
Alignment explanation
Indices: 6272--6318 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
6262 TTAGGAAGAT
*
6272 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
*
6294 TTATCAAAATTTTAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
6316 TTA
1 TTA
6319 CTAACAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:6572 original size:22 final size:22
Alignment explanation
Indices: 6406--6579 Score: 68
Period size: 22 Copynumber: 7.8 Consensus size: 22
6396 TCATAGTGTT
*
6406 GGTTATCAAAATTTCATTGGGAA
1 GGTTATCAAAATTTCA-TAGGAA
* *
6429 -GTTATCAAAAATTCATATTG-A
1 GGTTATCAAAATTTCATA-GGAA
* * * *
6450 GCTCT-TCAAAATTCCTTAGGGA
1 GGT-TATCAAAATTTCATAGGAA
* * *
6472 GGTTAACAAAACTTCATAAGAA
1 GGTTATCAAAATTTCATAGGAA
* ** **
6494 AGTTAAAAAAAATTT-ATAAAAA
1 GGTT-ATCAAAATTTCATAGGAA
* * * *
6516 GGTTCTCGAAATTCCATAGTGTAT
1 GGTTATCAAAATTTCATAG-G-AA
** *
6540 TATTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAGGAA
6562 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
6580 ATAGGATCAT
Statistics
Matches: 104, Mismatches: 38, Indels: 19
0.65 0.24 0.12
Matches are distributed among these distances:
21 9 0.09
22 71 0.68
23 10 0.10
24 14 0.13
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGAA
Found at i:6722 original size:2 final size:2
Alignment explanation
Indices: 6715--6745 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6705 AATAAAAGTC
6715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6746 AGCCTTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8126 original size:15 final size:15
Alignment explanation
Indices: 8108--8138 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8098 TTCAAAGCCT
*
8108 TTGATTTCTTAAAAG
1 TTGAATTCTTAAAAG
8123 TTGAATTCTTAAAAG
1 TTGAATTCTTAAAAG
8138 T
1 T
8139 CATAATCGTG
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:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
TTGAATTCTTAAAAG
Found at i:10942 original size:42 final size:44
Alignment explanation
Indices: 10878--10962 Score: 120
Period size: 45 Copynumber: 2.0 Consensus size: 44
10868 TGTTGACACA
*
10878 TACCCCACCTGATAAT-TA-ATTATGTATTCAATATTCAAAACC
1 TACCCCACCTGATAATCAATATTATGTATTCAATATTCAAAACC
* *
10920 TACCTCACCTGATAATCAATTATTATGTATTTAATATTCAAAA
1 TACCCCACCTGATAATCAA-TATTATGTATTCAATATTCAAAA
10963 TTAATATCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 15 0.41
43 1 0.03
45 21 0.57
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (44 bp):
TACCCCACCTGATAATCAATATTATGTATTCAATATTCAAAACC
Found at i:11007 original size:19 final size:19
Alignment explanation
Indices: 10983--11022 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
10973 AGGATGCACA
10983 TATCAAGTATTATATCCTT
1 TATCAAGTATTATATCCTT
11002 TATCAAGTATTATATCCTT
1 TATCAAGTATTATATCCTT
11021 TA
1 TA
11023 ACCTCGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (19 bp):
TATCAAGTATTATATCCTT
Found at i:11323 original size:16 final size:16
Alignment explanation
Indices: 11234--11323 Score: 76
Period size: 16 Copynumber: 5.7 Consensus size: 16
11224 CTCGTGGCCT
*
11234 GAATGACCCGGAACCC
1 GAATGACCCGAAACCC
* *
11250 GAATGATCCGAAACTC
1 GAATGACCCGAAACCC
*
11266 -ATATGACCCGAGACCC
1 GA-ATGACCCGAAACCC
* * ** *
11282 GAATAACCCGGATGCA
1 GAATGACCCGAAACCC
11298 G-ATGACCCGAAACCC
1 GAATGACCCGAAACCC
11313 GAATGACCCGA
1 GAATGACCCGA
11324 GAAAACTACC
Statistics
Matches: 54, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
15 11 0.20
16 42 0.78
17 1 0.02
ACGTcount: A:0.34, C:0.32, G:0.22, T:0.11
Consensus pattern (16 bp):
GAATGACCCGAAACCC
Found at i:19201 original size:46 final size:46
Alignment explanation
Indices: 19119--19277 Score: 203
Period size: 46 Copynumber: 3.4 Consensus size: 46
19109 GAGTGTTTCA
* * * * **
19119 CTTTTGATCACTCTCTACCTTTGTCTTCGGCTTCTTGGCAAGGTTGAT
1 CTTTT-ATCACCCTCTACCTCTG-CATCAGCTTCTTGGCGGGGTTGAT
* * *
19167 -TATTTATCGCCCTCTACCTCTGCATTAGCTTCTTGGCGGGGTTAAT
1 CT-TTTATCACCCTCTACCTCTGCATCAGCTTCTTGGCGGGGTTGAT
19213 CTTTTATCACCCTCTACCTCTGCATCAGCTTCTTGGCGGGGTTGAT
1 CTTTTATCACCCTCTACCTCTGCATCAGCTTCTTGGCGGGGTTGAT
19259 CTTTTATCACCCTCTACCT
1 CTTTTATCACCCTCTACCT
19278 TATCACCCTC
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
46 78 0.80
47 16 0.16
48 3 0.03
ACGTcount: A:0.14, C:0.29, G:0.17, T:0.40
Consensus pattern (46 bp):
CTTTTATCACCCTCTACCTCTGCATCAGCTTCTTGGCGGGGTTGAT
Found at i:19280 original size:15 final size:15
Alignment explanation
Indices: 19262--19292 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19252 GGTTGATCTT
19262 TTATCACCCTCTACC
1 TTATCACCCTCTACC
19277 TTATCACCCTCTACC
1 TTATCACCCTCTACC
19292 T
1 T
19293 GCATCAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.45, G:0.00, T:0.35
Consensus pattern (15 bp):
TTATCACCCTCTACC
Found at i:19310 original size:59 final size:61
Alignment explanation
Indices: 19216--19336 Score: 228
Period size: 59 Copynumber: 2.0 Consensus size: 61
19206 GGTTAATCTT
19216 TTATCACCCTCTACCTCTGCATCAGCTTCTTGGCGGGGTTGATCTTTTATCACCCTCTACC
1 TTATCACCCTCTACCTCTGCATCAGCTTCTTGGCGGGGTTGATCTTTTATCACCCTCTACC
19277 TTATCACCCTCTA-C-CTGCATCAGCTTCTTGGCGGGGTTGATCTTTTATCACCCTCTACC
1 TTATCACCCTCTACCTCTGCATCAGCTTCTTGGCGGGGTTGATCTTTTATCACCCTCTACC
19336 T
1 T
19337 CTTGGCGGGC
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 46 0.77
60 1 0.02
61 13 0.22
ACGTcount: A:0.15, C:0.34, G:0.15, T:0.36
Consensus pattern (61 bp):
TTATCACCCTCTACCTCTGCATCAGCTTCTTGGCGGGGTTGATCTTTTATCACCCTCTACC
Found at i:22597 original size:36 final size:36
Alignment explanation
Indices: 22550--22646 Score: 151
Period size: 36 Copynumber: 2.7 Consensus size: 36
22540 ACTTCCATAG
*
22550 GCTTTG-TTGATGGAGAGGAACTTTGCTTCAGATTT
1 GCTTTGCTTGATGGAGAAGAACTTTGCTTCAGATTT
*
22585 GCTTTGCTTGATGGAGAAGAACTTTGCTTCTGATTT
1 GCTTTGCTTGATGGAGAAGAACTTTGCTTCAGATTT
* *
22621 GCTTTGCTTGATGCAAAAGAACTTTG
1 GCTTTGCTTGATGGAGAAGAACTTTG
22647 TCTTGCCTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 6 0.11
36 51 0.89
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (36 bp):
GCTTTGCTTGATGGAGAAGAACTTTGCTTCAGATTT
Found at i:24227 original size:7 final size:7
Alignment explanation
Indices: 24215--24240 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
24205 AGAATTATAT
24215 ATTTAAC
1 ATTTAAC
24222 ATTTAAC
1 ATTTAAC
24229 ATTTAAC
1 ATTTAAC
24236 ATTTA
1 ATTTA
24241 TAATAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTTAAC
Found at i:25001 original size:57 final size:57
Alignment explanation
Indices: 24932--25045 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
24922 AAATTAAGGT
24932 TTACTAAAGCTTCGCTCTACCTTGATTATTCATATGAATACGTTACTCTCTTTTACC
1 TTACTAAAGCTTCGCTCTACCTTGATTATTCATATGAATACGTTACTCTCTTTTACC
*
24989 TTACTAAAGCTTCGCTCTACCTTGATTATTCATATGAATATGTTACTCTCTTTTACC
1 TTACTAAAGCTTCGCTCTACCTTGATTATTCATATGAATACGTTACTCTCTTTTACC
25046 CTATAGAGGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.43
Consensus pattern (57 bp):
TTACTAAAGCTTCGCTCTACCTTGATTATTCATATGAATACGTTACTCTCTTTTACC
Done.