Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016516.1 Corchorus capsularis cultivar CVL-1 contig16537, 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: 54721
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:4393 original size:8 final size:8
Alignment explanation
Indices: 4365--4398 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4355 GAATCGGCTA
4365 TGAATTTT
1 TGAATTTT
*
4373 TGAAGTTTC
1 TGAA-TTTT
4382 TGAATTTT
1 TGAATTTT
4390 TGAATTTT
1 TGAATTTT
4398 T
1 T
4399 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:5377 original size:33 final size:33
Alignment explanation
Indices: 5301--5423 Score: 133
Period size: 33 Copynumber: 3.7 Consensus size: 33
5291 TAGACAAAGG
* *
5301 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT
** * *
5334 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
*
5367 GTCGCGTGGCCGG-TGATGGCCGGACGTGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT
5400 GTCGCGTGGCCGGTCTTGTGGCCG
1 GTCGCGTGGCCGG--TTGTGGCCG
5424 ATGTTGCGCG
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
32 3 0.04
33 64 0.85
35 6 0.08
36 2 0.03
ACGTcount: A:0.07, C:0.28, G:0.42, T:0.24
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Found at i:6643 original size:42 final size:42
Alignment explanation
Indices: 6581--6698 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
6571 TTGTAATTAT
*
6581 CCTTTCCTTTCACATGAATGTTACTATAATAAATTCTAA-CC
1 CCTTTCCTTTCACATAAATGTTACTATAATAAATTCTAAGCC
*
6622 CTCTTTCCTTTCACATAAATGTTACTATAACAAATTCTAAGCC
1 C-CTTTCCTTTCACATAAATGTTACTATAATAAATTCTAAGCC
6665 CCTTTCCTTTCACATAAATGTTACTATAATAAAT
1 CCTTTCCTTTCACATAAATGTTACTATAATAAAT
6699 CATATCCCCT
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
41 1 0.01
42 68 0.94
43 3 0.04
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (42 bp):
CCTTTCCTTTCACATAAATGTTACTATAATAAATTCTAAGCC
Found at i:7298 original size:119 final size:118
Alignment explanation
Indices: 7087--7325 Score: 392
Period size: 119 Copynumber: 2.0 Consensus size: 118
7077 GCAATTTTTC
*
7087 TTAGTGTCTCAGTGTTTATTAGTTGGAATAATGAATGATGCAATAAAAATAGTCTATATAATATT
1 TTAGTGTCTAAGTGTTTATTAGTTGGAATAATGAATGATGCAATAAAAATAGTCTATAT-ATATT
7152 TCTCAATCTACAAGGTGATGGGTCATTCAACTCAAAACAAATTTAATTTAATTA
65 TCTCAATCTACAAGGTGATGGGTCATTCAACTCAAAACAAATTTAATTTAATTA
*
7206 TTAGTGTCTAAGTGTTTATAATTAGTTGGAATAATGAATTATGCAATAAAAATAGT-TATAT-TA
1 TTAGTGTCTAAGTG-TT-T-ATTAGTTGGAATAATGAATGATGCAATAAAAATAGTCTATATATA
* *
7269 TTTCTCAATCTACAAGGTGATTGGTCATTCAACTCAAAACAAATTTAATTTAGTTA
63 TTTCTCAATCTACAAGGTGATGGGTCATTCAACTCAAAACAAATTTAATTTAATTA
7325 T
1 T
7326 AATTATAATT
Statistics
Matches: 113, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
119 70 0.62
120 2 0.02
121 6 0.05
122 35 0.31
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (118 bp):
TTAGTGTCTAAGTGTTTATTAGTTGGAATAATGAATGATGCAATAAAAATAGTCTATATATATTT
CTCAATCTACAAGGTGATGGGTCATTCAACTCAAAACAAATTTAATTTAATTA
Found at i:9153 original size:23 final size:24
Alignment explanation
Indices: 9122--9172 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
9112 GCCTCATTAT
9122 TATACTTTTA-TTTTGTTTGGCCG
1 TATACTTTTATTTTTGTTTGGCCG
*
9145 TATAGTTTTATTTTTTGTTTGGCCG
1 TATACTTTTA-TTTTTGTTTGGCCG
9170 TAT
1 TAT
9173 TGTTGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 9 0.36
25 16 0.64
ACGTcount: A:0.14, C:0.10, G:0.18, T:0.59
Consensus pattern (24 bp):
TATACTTTTATTTTTGTTTGGCCG
Found at i:9566 original size:28 final size:28
Alignment explanation
Indices: 9512--9571 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
9502 TGGTGAACGT
* **
9512 AAAAGATTTCTTCCCTTAATGTCAAAAA
1 AAAAGATTTCTTCCCTCAATGAAAAAAA
9540 AAAAGATTTCTTCCC-CAAGTGAAAAAAA
1 AAAAGATTTCTTCCCTCAA-TGAAAAAAA
9568 AAAA
1 AAAA
9572 AGAATCATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.50, C:0.17, G:0.08, T:0.25
Consensus pattern (28 bp):
AAAAGATTTCTTCCCTCAATGAAAAAAA
Found at i:13309 original size:17 final size:17
Alignment explanation
Indices: 13289--13329 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
13279 GGCCTAAAAG
13289 ATTTATGAAGGGTTGAA
1 ATTTATGAAGGGTTGAA
* * *
13306 ATTTAAGAAGTGTTGAT
1 ATTTATGAAGGGTTGAA
13323 ATTTATG
1 ATTTATG
13330 GGTGGGAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (17 bp):
ATTTATGAAGGGTTGAA
Found at i:15967 original size:25 final size:25
Alignment explanation
Indices: 15936--15984 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
15926 TCTTAGATAT
15936 AATATATATT-AATAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
15961 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
15985 GACTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:16016 original size:25 final size:24
Alignment explanation
Indices: 15936--16016 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 24
15926 TCTTAGATAT
15936 AATATATATTAATAAATAAAT-AATA
1 AATATAT-TTAA-AAATAAATAAATA
*
15961 AATATATTT-TAAAT-AATAAAT-
1 AATATATTTAAAAATAAATAAATA
* *
15982 AAT-GACTTAAAAATAAATAAATA
1 AATATATTTAAAAATAAATAAATA
*
16005 TTATATATTTAA
1 -AATATATTTAA
16017 TTATTAAACG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 3 0.07
21 10 0.23
22 14 0.33
24 4 0.09
25 12 0.28
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (24 bp):
AATATATTTAAAAATAAATAAATA
Found at i:19438 original size:20 final size:20
Alignment explanation
Indices: 19389--19427 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19379 GGATTGATAG
* *
19389 AATAGTAGAAGGGGGTGAGA
1 AATAGAAGAAGGGGATGAGA
19409 AATAGAAGAAGGGGATGAG
1 AATAGAAGAAGGGGATGAG
19428 GAATTAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.13
Consensus pattern (20 bp):
AATAGAAGAAGGGGATGAGA
Found at i:25189 original size:2 final size:2
Alignment explanation
Indices: 25182--25210 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25172 AGAACTAACT
25182 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25211 TTTGGTACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30324 original size:18 final size:21
Alignment explanation
Indices: 30301--30340 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
30291 GGTGTAAGGC
30301 TTATATAA-TT-T-GGTGTAA
1 TTATATAACTTGTAGGTGTAA
30319 TTATATAACTTGTAGGTGTAA
1 TTATATAACTTGTAGGTGTAA
30340 T
1 T
30341 GAAAAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 1 0.05
21 8 0.42
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (21 bp):
TTATATAACTTGTAGGTGTAA
Found at i:30657 original size:22 final size:22
Alignment explanation
Indices: 30629--30674 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
30619 AAATTAGAGC
*
30629 AGAGAAGCTCACTGCTGGTGGA
1 AGAGAAGCTCACCGCTGGTGGA
*
30651 AGAGAAGCTCACCGGTGGTGGA
1 AGAGAAGCTCACCGCTGGTGGA
30673 AG
1 AG
30675 GAAAAAGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.39, T:0.15
Consensus pattern (22 bp):
AGAGAAGCTCACCGCTGGTGGA
Found at i:36638 original size:41 final size:42
Alignment explanation
Indices: 36562--36704 Score: 121
Period size: 50 Copynumber: 3.2 Consensus size: 42
36552 ATATTTAAGG
* * *
36562 GATAATTATGGTGATTATA-TAACTAGCCATATTATCCTTATAA
1 GATAATTAT-G-GATTATATTTATTAACCATATTATCCTTATAA
36605 -ATAATTATGGATTATATTTATTAACCATATTATCTACATAAATATTAGA
1 GATAATTATGGATTATATTTATTAACCATATTATC--C-T---TA-TA-A
** *
36654 GATAATTATGGATTATATTTATTAGTCATATTATCTTTA-AA
1 GATAATTATGGATTATATTTATTAACCATATTATCCTTATAA
36695 GATAATTATG
1 GATAATTATG
36705 ACAATTATCA
Statistics
Matches: 84, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
40 7 0.08
41 26 0.31
42 9 0.11
43 1 0.01
44 3 0.04
47 3 0.04
48 2 0.02
49 1 0.01
50 32 0.38
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (42 bp):
GATAATTATGGATTATATTTATTAACCATATTATCCTTATAA
Found at i:43343 original size:51 final size:51
Alignment explanation
Indices: 43241--43343 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 51
43231 CGTTCTTCAA
* **
43241 TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCTTTTAGTGT
1 TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCGTACAGTGT
43292 TATTTCCTTGTTTCAATCTTGTCTCCGGACATAAA-AACACT-GTACACGTGT
1 TATTTCCTTGTTTCAATCTTGTCTCCGGACA-AAAGAACACTCGTACA-GTGT
43343 T
1 T
43344 TCTCTCATAC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
50 2 0.04
51 42 0.89
52 3 0.06
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (51 bp):
TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCGTACAGTGT
Found at i:44446 original size:13 final size:13
Alignment explanation
Indices: 44428--44452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44418 TTCGAATTCC
44428 AAATAATATTTAT
1 AAATAATATTTAT
44441 AAATAATATTTA
1 AAATAATATTTA
44453 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:45164 original size:11 final size:11
Alignment explanation
Indices: 45150--45180 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
45140 AATCTACTTA
45150 AATCTTCAGAT
1 AATCTTCAGAT
*
45161 AATCTCCAGAT
1 AATCTTCAGAT
45172 AATCTTCAG
1 AATCTTCAG
45181 TTGAAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (11 bp):
AATCTTCAGAT
Found at i:47234 original size:17 final size:17
Alignment explanation
Indices: 47212--47245 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
47202 CTCGATAAAG
47212 ACCAATACGCTCTTCCA
1 ACCAATACGCTCTTCCA
47229 ACCAATACGCTCTTCCA
1 ACCAATACGCTCTTCCA
47246 GAGTAGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.41, G:0.06, T:0.24
Consensus pattern (17 bp):
ACCAATACGCTCTTCCA
Found at i:49705 original size:40 final size:41
Alignment explanation
Indices: 49639--49830 Score: 248
Period size: 40 Copynumber: 4.7 Consensus size: 41
49629 GTAATTCAAG
* * * **
49639 GTGATAACTTCTGGTGTCAACA-GTAATTATACTTTACCGGA
1 GTGACAACTTCTGGTGTCAA-AGGTAATTTTAATTTACCAAA
*
49680 GTAAC-ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAA
1 GTGACAACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAA
*
49720 GTGACAACTTCTGG-GTCAAAGGTAATTTTAATTTACCAAG
1 GTGACAACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAA
* *
49760 GTGACAACTTCTAGTGTCAGTA-GTAATTTTAATTTACCAAA
1 GTGACAACTTCTGGTGTCA-AAGGTAATTTTAATTTACCAAA
*
49801 GTGACAACTTTTGGTGTCAAAGGTAATTTT
1 GTGACAACTTCTGGTGTCAAAGGTAATTTT
49831 CAATATTATT
Statistics
Matches: 132, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.01
40 72 0.55
41 58 0.44
42 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (41 bp):
GTGACAACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAA
Found at i:50214 original size:24 final size:26
Alignment explanation
Indices: 50184--50236 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
50174 TATAATCTAC
50184 TGAAATCTTCAGAT-A-ATCTTCAGT
1 TGAAATCTTCAGATGATATCTTCAGT
* *
50208 TGAAATCTTCTGATGATATCTTCTGT
1 TGAAATCTTCAGATGATATCTTCAGT
50234 TGA
1 TGA
50237 TAATATTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.52
25 1 0.04
26 11 0.44
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (26 bp):
TGAAATCTTCAGATGATATCTTCAGT
Found at i:50216 original size:13 final size:13
Alignment explanation
Indices: 50184--50230 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
50174 TATAATCTAC
50184 TGAAATCTTCAGA
1 TGAAATCTTCAGA
*
50197 T--AATCTTCAGT
1 TGAAATCTTCAGA
*
50208 TGAAATCTTCTGA
1 TGAAATCTTCAGA
*
50221 TGATATCTTC
1 TGAAATCTTC
50231 TGTTGATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 10 0.36
13 18 0.64
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
TGAAATCTTCAGA
Found at i:50574 original size:48 final size:48
Alignment explanation
Indices: 50503--50598 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
50493 CATAGCTATC
50503 CGGACCGAATAGGCCTATGGTACCCGACTTAACTGGTCGAACGATCCA
1 CGGACCGAATAGGCCTATGGTACCCGACTTAACTGGTCGAACGATCCA
50551 CGGACCGAATAGGCCTATGGTACCCGACTTAACTGGTCGAACGATCCA
1 CGGACCGAATAGGCCTATGGTACCCGACTTAACTGGTCGAACGATCCA
50599 TCCGGTTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (48 bp):
CGGACCGAATAGGCCTATGGTACCCGACTTAACTGGTCGAACGATCCA
Found at i:51348 original size:13 final size:13
Alignment explanation
Indices: 51330--51356 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51320 GGATTTATTC
51330 TACCCGTTCAGCT
1 TACCCGTTCAGCT
51343 TACCCGTTCAGCT
1 TACCCGTTCAGCT
51356 T
1 T
51357 TCATGAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.15, T:0.33
Consensus pattern (13 bp):
TACCCGTTCAGCT
Found at i:52933 original size:2 final size:2
Alignment explanation
Indices: 52926--52962 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
52916 TCTTATGTTT
52926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52963 GCAATTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.