Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014985.1 Corchorus olitorius cultivar O-4 contig15018, 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: 39816
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:187 original size:32 final size:32
Alignment explanation
Indices: 151--260 Score: 118
Period size: 32 Copynumber: 3.3 Consensus size: 32
141 TTGATTATTG
151 GGGACTTTGGATTCTGTTTTTGCTTGGAAGTT
1 GGGACTTTGGATTCTGTTTTTGCTTGGAAGTT
* *
183 GGGACTTTGGAATT-T-TTTGTAGCTTTTGATTA-TT
1 GGGACTTTGG-ATTCTGTTT-TTGC-TTGGA--AGTT
217 GGGGACTTTGGATTCTGTTTTTGCTTGGAAGTT
1 -GGGACTTTGGATTCTGTTTTTGCTTGGAAGTT
*
250 AGGACTTTGGA
1 GGGACTTTGGA
261 AGTTTTTGCT
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
31 3 0.05
32 25 0.39
33 9 0.14
34 9 0.14
35 15 0.23
36 3 0.05
ACGTcount: A:0.15, C:0.08, G:0.30, T:0.46
Consensus pattern (32 bp):
GGGACTTTGGATTCTGTTTTTGCTTGGAAGTT
Found at i:199 original size:29 final size:29
Alignment explanation
Indices: 167--270 Score: 75
Period size: 35 Copynumber: 3.3 Consensus size: 29
157 TTGGATTCTG
167 TTTTTGCTTGGAAGTTGGGACTTTGGAATT
1 TTTTTGCTTGGAAGTTGGGACTTTGGAA-T
* *
197 TTTTGTAGCTTTTGATTA-TTGGGGACTTTGGATTCT
1 TTTT-T-GC-TTGGA--AGTT-GGGACTTTGGA--AT
* *
233 GTTTTTGCTTGGAAGTTAGGACTTTGGAAG
1 -TTTTTGCTTGGAAGTTGGGACTTTGGAAT
263 TTTTTGCT
1 TTTTTGCT
271 GGTTCTGTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 21
0.68 0.07 0.25
Matches are distributed among these distances:
29 8 0.14
30 4 0.07
31 1 0.02
32 13 0.22
33 6 0.10
34 6 0.10
35 14 0.24
36 2 0.03
37 4 0.07
ACGTcount: A:0.15, C:0.08, G:0.28, T:0.49
Consensus pattern (29 bp):
TTTTTGCTTGGAAGTTGGGACTTTGGAAT
Found at i:236 original size:67 final size:67
Alignment explanation
Indices: 128--268 Score: 264
Period size: 67 Copynumber: 2.1 Consensus size: 67
118 ACCTATGATC
*
128 TTTTTTGTAGCTTTTGATTATTGGGGACTTTGGATTCTGTTTTTGCTTGGAAGTTGGGACTTTGG
1 TTTTTTGTAGCTTTTGATTATTGGGGACTTTGGATTCTGTTTTTGCTTGGAAGTTAGGACTTTGG
193 AA
66 AA
195 TTTTTTGTAGCTTTTGATTATTGGGGACTTTGGATTCTGTTTTTGCTTGGAAGTTAGGACTTTGG
1 TTTTTTGTAGCTTTTGATTATTGGGGACTTTGGATTCTGTTTTTGCTTGGAAGTTAGGACTTTGG
260 AA
66 AA
*
262 GTTTTTG
1 TTTTTTG
269 CTGGTTCTGT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 72 1.00
ACGTcount: A:0.15, C:0.07, G:0.28, T:0.50
Consensus pattern (67 bp):
TTTTTTGTAGCTTTTGATTATTGGGGACTTTGGATTCTGTTTTTGCTTGGAAGTTAGGACTTTGG
AA
Found at i:473 original size:14 final size:14
Alignment explanation
Indices: 454--480 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
444 AAAAGTTTTG
454 GTATGCTCTGCTTC
1 GTATGCTCTGCTTC
468 GTATGCTCTGCTT
1 GTATGCTCTGCTT
481 TGCAAAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.26, G:0.22, T:0.44
Consensus pattern (14 bp):
GTATGCTCTGCTTC
Found at i:11027 original size:38 final size:38
Alignment explanation
Indices: 10984--11062 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
10974 TCCATGACTC
10984 CATCAGTAGATGCAATTTCTCCGCAATCTTTGACTGAA
1 CATCAGTAGATGCAATTTCTCCGCAATCTTTGACTGAA
*
11022 CATCAGTGGATGCAATTTCTCCGCAATCTTTGACTGAA
1 CATCAGTAGATGCAATTTCTCCGCAATCTTTGACTGAA
11060 CAT
1 CAT
11063 TTTCAGTAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (38 bp):
CATCAGTAGATGCAATTTCTCCGCAATCTTTGACTGAA
Found at i:13719 original size:41 final size:41
Alignment explanation
Indices: 13656--13736 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
13646 ATCCTTAGGG
*
13656 TTTAAATTTTGACGCTTAACTACTGTTAAGAATTTGATAAA
1 TTTAAATTTTGACACTTAACTACTGTTAAGAATTTGATAAA
*
13697 TTTAAATTTTGACACTTGACTACTGTTAAGAATTTGATAA
1 TTTAAATTTTGACACTTAACTACTGTTAAGAATTTGATAA
13737 CGGAAACTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (41 bp):
TTTAAATTTTGACACTTAACTACTGTTAAGAATTTGATAAA
Found at i:14332 original size:22 final size:22
Alignment explanation
Indices: 14182--14679 Score: 176
Period size: 22 Copynumber: 22.5 Consensus size: 22
14172 GACAATCAAC
*
14182 CAAAATTACATA-GGACGGTTAT
1 CAAAATTTCATAGGGA-GGTTAT
* * * * *
14204 CAAAATTTAATAGTGTGCTTAC
1 CAAAATTTCATAGGGAGGTTAT
* * * *
14226 CGAAATTTCATATGAAGATTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
14248 CAAAACTTCATAGTGTA-GTTAT
1 CAAAATTTCATAG-GGAGGTTAT
* * * *
14270 CAAAATTTCATAAGAATGTTAC
1 CAAAATTTCATAGGGAGGTTAT
* ***
14292 CAAATTTTCATAAAAAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
14314 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAGGGAGGTTAT
* * **
14336 C-AAATTTCATACGAAAATTAT
1 CAAAATTTCATAGGGAGGTTAT
* * * * *
14357 CGAAATTTTATAGTGTGGTTAC
1 CAAAATTTCATAGGGAGGTTAT
14379 CAAAATTTCATAGGGAGGGAATTTAT
1 CAAAATTTCATAGGGA-GG---TTAT
**
14405 CAAAA-TT--T--GG-TCTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * * * *
14421 TAAAATCTCCTAGGGACGTTAA
1 CAAAATTTCATAGGGAGGTTAT
*
14443 CAAAATTTCATAGGAAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
14465 GAAAATTTTAT-GGAGAGGTTAT
1 CAAAATTTCATAGG-GAGGTTAT
* * * *
14487 CAAAATTACACAGAGAGGATAT
1 CAAAATTTCATAGGGAGGTTAT
* *
14509 CACAGTTTCATTCTCATAAGGAGGTTAT
1 CA-A----AATT-TCATAGGGAGGTTAT
** *
14537 CAAAATTTTCATACTGAAGTTA-
1 CAAAA-TTTCATAGGGAGGTTAT
* * * * *
14559 C-CAATTTTATAGTGTGATTAT
1 CAAAATTTCATAGGGAGGTTAT
* **
14580 CAAAATTTCACACTGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
14602 CAAAATTTCATAGTGTGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
14624 CAAAATTTCACA-GTATGGTTAT
1 CAAAATTTCATAGGGA-GGTTAT
* *
14646 CAAATTTTCATAGGAAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
**
14668 TGAAATTTCATA
1 CAAAATTTCATA
14680 ATCATGTTAT
Statistics
Matches: 340, Mismatches: 109, Indels: 54
0.68 0.22 0.11
Matches are distributed among these distances:
16 8 0.02
17 1 0.00
19 1 0.00
20 11 0.03
21 26 0.08
22 243 0.71
23 22 0.06
24 2 0.01
25 2 0.01
26 8 0.02
27 4 0.01
28 12 0.04
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGGTTAT
Found at i:14665 original size:66 final size:67
Alignment explanation
Indices: 14595--14719 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 67
14585 TTTCACACTG
* *
14595 AGGTTATCAAAATTTCATAGT-GTGGTTATCAAAATTTCACAGTATGGTTATCAA-ATTTTCATA
1 AGGTTATCAAAATTTCATAATCAT-GTTATCAAAATTTCACAGTATGGTTATCAATATTTTCATA
14658 GGA
65 GGA
** * * * *
14661 AGGTTATTGAAATTTCATAATCATGTTATTAAATTTTCACATTGTGGTTATCAATATTT
1 AGGTTATCAAAATTTCATAATCATGTTATCAAAATTTCACAGTATGGTTATCAATATTT
14720 CTAGGTTGGA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
66 44 0.90
67 5 0.10
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (67 bp):
AGGTTATCAAAATTTCATAATCATGTTATCAAAATTTCACAGTATGGTTATCAATATTTTCATAG
GA
Found at i:14666 original size:44 final size:45
Alignment explanation
Indices: 14561--14720 Score: 141
Period size: 44 Copynumber: 3.6 Consensus size: 45
14551 TGAAGTTACC
* * * *
14561 AATTTT-ATAGTGTGATTATCAAAATTTCACACTGA-GGTTATCA
1 AATTTTCATAGTGAGGTTATCAAAATTTCACAATCATGGTTATCA
* * *
14604 AAATTTCATAGTGTGGTTATCAAAATTTCACAGT-ATGGTTATCA
1 AATTTTCATAGTGAGGTTATCAAAATTTCACAATCATGGTTATCA
** * *
14648 AATTTTCATAG-GAAGGTTATTGAAATTTCATAATCAT-GTTATTA
1 AATTTTCATAGTG-AGGTTATCAAAATTTCACAATCATGGTTATCA
* * * *
14692 AATTTTCACATTGTGGTTATCAATATTTC
1 AATTTTCATAGTGAGGTTATCAAAATTTC
14721 TAGGTTGGAG
Statistics
Matches: 96, Mismatches: 16, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
43 7 0.07
44 86 0.90
45 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.42
Consensus pattern (45 bp):
AATTTTCATAGTGAGGTTATCAAAATTTCACAATCATGGTTATCA
Found at i:18397 original size:21 final size:21
Alignment explanation
Indices: 18385--18430 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
18375 ACTATATCAA
18385 CCTTTTTAGAAACGTTATAAG
1 CCTTTTTAGAAACGTTATAAG
* **
18406 CCTTTTTAGTAATATTATAAG
1 CCTTTTTAGAAACGTTATAAG
18427 CCTT
1 CCTT
18431 ATTTTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
CCTTTTTAGAAACGTTATAAG
Found at i:19348 original size:132 final size:132
Alignment explanation
Indices: 19203--19479 Score: 527
Period size: 132 Copynumber: 2.1 Consensus size: 132
19193 ACTGTGTATT
19203 ATAAATTTGATAGTCTTCATTGTTATAAAATTGATACTTAATTAATTCACAATGAAAATTTATTG
1 ATAAA-TTGATAGTCTTCATTGTTATAAAATTGATACTTAATTAATTCACAATGAAAATTTATTG
19268 AATACTTTTGTGGTTCAGGTATAGTGTTTTTGATAAAATATATAACTTTTATTTAGTAACTAACT
65 AATACTTTTGTGGTTCAGGTATAGTGTTTTTGATAAAATATATAACTTTTATTTAGTAACTAACT
19333 ACC
130 ACC
*
19336 GTAAATTGATAGTCTTCATTGTTATAAAATTGATACTTAATTAATTCACAATGAAAATTTATTGA
1 ATAAATTGATAGTCTTCATTGTTATAAAATTGATACTTAATTAATTCACAATGAAAATTTATTGA
19401 ATACTTTTGTGGTTCAGGTATAGTGTTTTTGATAAAATATATAACTTTTATTTAGTAACTAACTA
66 ATACTTTTGTGGTTCAGGTATAGTGTTTTTGATAAAATATATAACTTTTATTTAGTAACTAACTA
19466 CC
131 CC
19468 ATAAATTAGATA
1 ATAAATT-GATA
19480 ACTTATGTTA
Statistics
Matches: 141, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
132 133 0.94
133 8 0.06
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (132 bp):
ATAAATTGATAGTCTTCATTGTTATAAAATTGATACTTAATTAATTCACAATGAAAATTTATTGA
ATACTTTTGTGGTTCAGGTATAGTGTTTTTGATAAAATATATAACTTTTATTTAGTAACTAACTA
CC
Found at i:19799 original size:24 final size:24
Alignment explanation
Indices: 19763--19808 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
19753 AATTATTAGA
*
19763 TAAATATAATTTTTAAATTTTTTT
1 TAAATATAATTTTGAAATTTTTTT
*
19787 TAAATA-AACTTTTGGAATTTTT
1 TAAATATAA-TTTTGAAATTTTT
19809 CAAAACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TAAATATAATTTTGAAATTTTTTT
Found at i:23673 original size:22 final size:22
Alignment explanation
Indices: 23647--23688 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
23637 TTAAACATAT
23647 ATTTTATTTTAGTATGCAATGA
1 ATTTTATTTTAGTATGCAATGA
23669 ATTTTATTTTAGTATGCAAT
1 ATTTTATTTTAGTATGCAAT
23689 TCGTCATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (22 bp):
ATTTTATTTTAGTATGCAATGA
Found at i:23714 original size:41 final size:41
Alignment explanation
Indices: 23669--23750 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
23659 TATGCAATGA
*
23669 ATTTTATTTTAGTATGCAATTCGTCATTGTATAGTTGTCAT
1 ATTTTATTTTAGTATGCAATTCGTCATTGTATAATTGTCAT
* *
23710 ATTTTATTTTAGTATTCAATTGGTCATTGTATAATTGTCAT
1 ATTTTATTTTAGTATGCAATTCGTCATTGTATAATTGTCAT
23751 CAATTATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52
Consensus pattern (41 bp):
ATTTTATTTTAGTATGCAATTCGTCATTGTATAATTGTCAT
Found at i:29267 original size:1 final size:1
Alignment explanation
Indices: 29256--29309 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
29246 TTCTTGTTTG
* * * * * *
29256 TTTTTTGTTTTTTGTTTTTTGTTTTTTTGTTTTTTTGTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29310 CCAATCTCCT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:29274 original size:8 final size:7
Alignment explanation
Indices: 29252--29309 Score: 91
Period size: 7 Copynumber: 8.1 Consensus size: 7
29242 CTTCTTCTTG
29252 TTTGTTT
1 TTTGTTT
29259 TTTGTTT
1 TTTGTTT
29266 TTTGTTT
1 TTTGTTT
29273 TTTGTTTT
1 TTTG-TTT
29281 TTTGTTTT
1 TTTG-TTT
29289 TTTGTTT
1 TTTGTTT
29296 TTTGTTT
1 TTTGTTT
29303 TTT-TTT
1 TTTGTTT
29309 T
1 T
29310 CCAATCTCCT
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 4 0.08
7 31 0.62
8 15 0.30
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTGTTT
Found at i:37399 original size:39 final size:40
Alignment explanation
Indices: 37345--37425 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
37335 ATACCTAAGA
*
37345 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
37384 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
37424 AT
1 AT
37426 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:38032 original size:13 final size:13
Alignment explanation
Indices: 38004--38041 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
37994 ATTTATTCAT
38004 TTATTATTATC-A-
1 TTATTATTA-CAAG
38016 TTATTATTACAAG
1 TTATTATTACAAG
38029 TTATTATTACAAG
1 TTATTATTACAAG
38042 GTAGCACTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.04
12 10 0.42
13 13 0.54
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (13 bp):
TTATTATTACAAG
Found at i:39770 original size:17 final size:18
Alignment explanation
Indices: 39730--39776 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
39720 TTCCTTCAAA
39730 CTTCAAAATTT-TCAATT
1 CTTCAAAATTTCTCAATT
*
39747 CTCTCAAATTTTCTCAATT
1 CT-TCAAAATTTCTCAATT
*
39766 -TTCAAACTTTC
1 CTTCAAAATTTC
39777 AAACCTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
18 9 0.35
19 6 0.23
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (18 bp):
CTTCAAAATTTCTCAATT
Done.