Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008751.1 Corchorus capsularis cultivar CVL-1 contig08772, 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: 41439
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:263 original size:21 final size:21
Alignment explanation
Indices: 239--283 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
229 AAAAAAACGT
239 CAAAAATGGGGCGGTGA-TTAG
1 CAAAAATGGGGCGGT-ATTTAG
260 CAAAAATGGGGCGGTATTTAG
1 CAAAAATGGGGCGGTATTTAG
281 CAA
1 CAA
284 TCCAGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.36, C:0.11, G:0.33, T:0.20
Consensus pattern (21 bp):
CAAAAATGGGGCGGTATTTAG
Found at i:520 original size:7 final size:7
Alignment explanation
Indices: 508--536 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
498 GTAGGATGTT
508 TTTAGGG
1 TTTAGGG
515 TTTAGGG
1 TTTAGGG
522 TTTAGGG
1 TTTAGGG
529 TTTAGGG
1 TTTAGGG
536 T
1 T
537 ATTCATGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:7260 original size:32 final size:32
Alignment explanation
Indices: 7190--7270 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
7180 ATTTTCAGGA
7190 TCGGGTTGAATTTGGGTCTAGTTAATTTAAGT
1 TCGGGTTGAATTTGGGTCTAGTTAATTTAAGT
* **
7222 TTGGGTTGAATTTGGGTC-AGGTTAATTTGGGT
1 TCGGGTTGAATTTGGGTCTA-GTTAATTTAAGT
* *
7254 TCGGGTTCAGTTTGGGT
1 TCGGGTTGAATTTGGGT
7271 TTTGGCCAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 1 0.02
32 41 0.98
ACGTcount: A:0.16, C:0.06, G:0.35, T:0.43
Consensus pattern (32 bp):
TCGGGTTGAATTTGGGTCTAGTTAATTTAAGT
Found at i:7428 original size:16 final size:16
Alignment explanation
Indices: 7407--7502 Score: 93
Period size: 16 Copynumber: 6.0 Consensus size: 16
7397 TTTTCATAAA
*
7407 TTTTCGGATTCGGGTT
1 TTTTCGGGTTCGGGTT
* * *
7423 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTT
*
7439 TTTTCGGGTTCGGATT
1 TTTTCGGGTTCGGGTT
* * *
7455 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTT
*
7471 TTTTCGGGTTCAGGTT
1 TTTTCGGGTTCGGGTT
* *
7487 TTTTTGGGTTCAGGTT
1 TTTTCGGGTTCGGGTT
7503 CAGGCGGGTT
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 63 1.00
ACGTcount: A:0.06, C:0.11, G:0.31, T:0.51
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTT
Found at i:7451 original size:32 final size:32
Alignment explanation
Indices: 7407--7496 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
7397 TTTTCATAAA
*
7407 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
*
7439 TTTTCGGGTTCGGATTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
* *
7471 TTTTCGGGTTCAGGTTTTTTTGGGTT
1 TTTTCGGGTTCGGGTTTTTTCGGGTT
7497 CAGGTTCAGG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.06, C:0.11, G:0.31, T:0.52
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
Found at i:7592 original size:16 final size:15
Alignment explanation
Indices: 7566--7595 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
7556 CGGGTTCATG
7566 TTTTCGGTCGGGTTT
1 TTTTCGGTCGGGTTT
7581 TTTTCAGGTCGGGTT
1 TTTTC-GGTCGGGTT
7596 CACTTTGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.13, G:0.33, T:0.50
Consensus pattern (15 bp):
TTTTCGGTCGGGTTT
Found at i:14360 original size:7 final size:7
Alignment explanation
Indices: 14348--14388 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
14338 AAATTGTAAC
14348 TAATAAT
1 TAATAAT
14355 TAATAAT
1 TAATAAT
14362 TACATAAT
1 TA-ATAAT
14370 TAATAA-
1 TAATAAT
14376 TAATCAA-
1 TAAT-AAT
14383 TAATAA
1 TAATAA
14389 AAAAAATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 7 0.22
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (7 bp):
TAATAAT
Found at i:14370 original size:28 final size:25
Alignment explanation
Indices: 14329--14386 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
14319 ATTAAATTTC
* *
14329 ATAATTTCAAAATTGTAACTAATAATTA
1 ATAATTACAAAA-T-TAA-TAATAATCA
*
14357 ATAATTACATAATTAATAATAATCA
1 ATAATTACAAAATTAATAATAATCA
14382 ATAAT
1 ATAAT
14387 AAAAAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 13 0.48
26 3 0.11
27 1 0.04
28 10 0.37
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (25 bp):
ATAATTACAAAATTAATAATAATCA
Found at i:14586 original size:13 final size:13
Alignment explanation
Indices: 14570--14594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14560 TCCCTTCATT
14570 TTAGATCTACAAC
1 TTAGATCTACAAC
14583 TTAGATCTACAA
1 TTAGATCTACAA
14595 AATAACAACA
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:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TTAGATCTACAAC
Found at i:20134 original size:51 final size:51
Alignment explanation
Indices: 20074--20171 Score: 196
Period size: 51 Copynumber: 1.9 Consensus size: 51
20064 TTATTCAGTT
20074 TTCAAAATTAATTAAAATTGGTAATCAAGAGCTTTTAAGATTTAAACAGAA
1 TTCAAAATTAATTAAAATTGGTAATCAAGAGCTTTTAAGATTTAAACAGAA
20125 TTCAAAATTAATTAAAATTGGTAATCAAGAGCTTTTAAGATTTAAAC
1 TTCAAAATTAATTAAAATTGGTAATCAAGAGCTTTTAAGATTTAAAC
20172 TGAAGTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (51 bp):
TTCAAAATTAATTAAAATTGGTAATCAAGAGCTTTTAAGATTTAAACAGAA
Found at i:23139 original size:52 final size:52
Alignment explanation
Indices: 23058--23156 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
23048 GATTTTTCCT
*
23058 GCAACAACTTCTGCCCCAAAATTGTACAAGTT-CTGGCCCGAAGTTGTTTTGC
1 GCAACAACTTCTGCCCCAAAATTGAACAAGTTGC-GGCCCGAAGTTGTTTTGC
* * * *
23110 GCAACAACTTCTGTCCCGAAGTTGAACAAGTTGCGGGCCGAAGTTGT
1 GCAACAACTTCTGCCCCAAAATTGAACAAGTTGCGGCCCGAAGTTGT
23157 CCTGCAATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
52 40 0.98
53 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (52 bp):
GCAACAACTTCTGCCCCAAAATTGAACAAGTTGCGGCCCGAAGTTGTTTTGC
Found at i:32274 original size:167 final size:167
Alignment explanation
Indices: 32047--32352 Score: 391
Period size: 167 Copynumber: 1.8 Consensus size: 167
32037 TGCGTGCTTG
* * * *
32047 TGCGCAAAACATCGTTCTTAGGAAAACACTAATTTCATATGCGTTTTTTGCACAACGAGTGCTGA
1 TGCGCAAAACATCATTCTTAGGAAAACACTAATTTCAGATGAGTTTTTTGCACAACGAGTGCTCA
* * * * *
32112 AAGGTCATGTG-TCGGAGTGAGCTAAGCTTGTTGGACATCCCCCACA-CCAAACAAAGCTCTTCT
66 AAGGTCATG-GATCGGAGTAAGATAAGCTTGTTGGAAAGCCCCCA-AGCCAAACAAAGCTCTGCT
32175 CGAAACCCAAATCCTTAACTATGTTGTTTTGCACATTTT
129 CGAAACCCAAATCCTTAACTATGTTGTTTTGCACATTTT
* ** * * *
32214 TGCGCAAAACATCATTCTTAGGAATATGCTCATTTCGGATGAGTTTTTTGCGCAACGAGTGCTCA
1 TGCGCAAAACATCATTCTTAGGAAAACACTAATTTCAGATGAGTTTTTTGCACAACGAGTGCTCA
* * * * *
32279 AATGTCGTGGATCGGAGTAAGATGAGCTTTTTGGAAAGCCCCCAAGCCAAACAAAGTTCTGCTCG
66 AAGGTCATGGATCGGAGTAAGATAAGCTTGTTGGAAAGCCCCCAAGCCAAACAAAGCTCTGCTCG
*
32344 AAGCCCAAA
131 AAACCCAAA
32353 ACTTCAACTT
Statistics
Matches: 116, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
166 2 0.02
167 114 0.98
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (167 bp):
TGCGCAAAACATCATTCTTAGGAAAACACTAATTTCAGATGAGTTTTTTGCACAACGAGTGCTCA
AAGGTCATGGATCGGAGTAAGATAAGCTTGTTGGAAAGCCCCCAAGCCAAACAAAGCTCTGCTCG
AAACCCAAATCCTTAACTATGTTGTTTTGCACATTTT
Found at i:32509 original size:160 final size:161
Alignment explanation
Indices: 31952--32658 Score: 600
Period size: 160 Copynumber: 4.4 Consensus size: 161
31942 ACGCATGGTA
** * * * * **
31952 AAATGTCGTGTGTTAGAGTGAAATGAGCTTTTTAGACAGCCAACATGCCAAACAAAGCTCT-CCT
1 AAATGTCGTGTGTCGGAGTGAGATGAGCTTGTTGGATAGCCCCCATGCCAAACAAAGCTCTCCCT
* * * * * *
32016 CGAAGTCCAAAGCCTCAA-TTTTGCGTGC--TTGTGCGCAAAACATCGTTCTTAGGAAAACACTA
66 CGAAGCCCAAAACCTCAACTTAT-CGTGCATTTGTTCGCAAAACATCGTTCTTAGGAAAACGCTC
* ** * *
32078 ATTTCATATGCGTTTTTTGCACAACGAGTGCTG
130 ATTCCGGATG-GTTTTTTGCGCAACGAGTGCTC
* * * * * * ** *
32111 AAAGGTCATGTGTCGGAGTGAGCTAAGCTTGTTGGACATCCCCCACACCAAACAAAGCTCT-TCT
1 AAATGTCGTGTGTCGGAGTGAGATGAGCTTGTTGGATAGCCCCCATGCCAAACAAAGCTCTCCCT
* * * * * * *
32175 CGAAACCCAAATCCTTAACTATGTTGTTTTGCACATTT-TTGCGCAAAACATCATTCTTAGGAAT
66 CGAAGCCCAAAACCTCAACT-TATCG---TG--CATTTGTT-CGCAAAACATCGTTCTTAGGAAA
* *
32239 ATGCTCATTTCGGATGAGTTTTTTGCGCAACGAGTGCTC
124 ACGCTCATTCCGGATG-GTTTTTTGCGCAACGAGTGCTC
* * * * * *
32278 AAATGTCGTG-GATCGGAGTAAGATGAGCTTTTTGGAAAGCCCCCAAGCCAAACAAAGTTCT-GC
1 AAATGTCGTGTG-TCGGAGTGAGATGAGCTTGTTGGATAGCCCCCATGCCAAACAAAGCTCTCCC
* *
32341 TCGAAGCCCAAAACTTCAACTT-T-GTGCATTTGTTCGCAAAACATCGTTCATAGGAAAACGCTC
65 TCGAAGCCCAAAACCTCAACTTATCGTGCATTTGTTCGCAAAACATCGTTCTTAGGAAAACGCTC
* *
32404 ATTCCGGATGTGTTGTTTTGCACAATC-AGTGTTC
130 ATTCCGGATG-GTT-TTTTGCGCAA-CGAGTGCTC
** * *
32438 AAATGTCGTGTGTCCAAGTGAGATGAGCTTGTTGGATAGCCCCCATGCCAAATAGAGCTCTCCCT
1 AAATGTCGTGTGTCGGAGTGAGATGAGCTTGTTGGATAGCCCCCATGCCAAACAAAGCTCTCCCT
* * *
32503 -GAAGCCCAAAGCCTCAACTTATCGTG--TTTGTGT-ACAAAACATCGTTCTTAGGAAAACACTC
66 CGAAGCCCAAAACCTCAACTTATCGTGCATTTGT-TCGCAAAACATCGTTCTTAGGAAAACGCTC
* *
32564 ATTCCAGATGGTTTTTTGTGCAACGAGTGCTC
130 ATTCCGGATGGTTTTTTGCGCAACGAGTGCTC
* * * * * *
32596 AAATGACATGTGTTGGAGTGGGATGAGCTTGTT-GTTCAACCCCCATGCCAAACAAAGCTCTCC
1 AAATGTCGTGTGTCGGAGTGAGATGAGCTTGTTGGAT-AGCCCCCATGCCAAACAAAGCTCTCC
32659 TCAAAGACTT
Statistics
Matches: 442, Mismatches: 85, Indels: 43
0.78 0.15 0.08
Matches are distributed among these distances:
157 3 0.01
158 64 0.14
159 108 0.24
160 126 0.29
161 10 0.02
162 3 0.01
163 2 0.00
164 1 0.00
165 2 0.00
166 3 0.01
167 120 0.27
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (161 bp):
AAATGTCGTGTGTCGGAGTGAGATGAGCTTGTTGGATAGCCCCCATGCCAAACAAAGCTCTCCCT
CGAAGCCCAAAACCTCAACTTATCGTGCATTTGTTCGCAAAACATCGTTCTTAGGAAAACGCTCA
TTCCGGATGGTTTTTTGCGCAACGAGTGCTC
Found at i:35356 original size:23 final size:24
Alignment explanation
Indices: 35330--35407 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 24
35320 TTCATATTCC
35330 TTCAT-AAATATCTCTATCTTGTT
1 TTCATGAAATATCTCTATCTTGTT
* * **
35353 TTCATGAAAT-TAATC-ATATT-CC
1 TTCATGAAATAT-CTCTATCTTGTT
35375 TTCAT-AAATATCTCTATCTTGTT
1 TTCATGAAATATCTCTATCTTGTT
35398 TTCATGAAAT
1 TTCATGAAAT
35408 TAAAGAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 11
0.68 0.13 0.18
Matches are distributed among these distances:
21 6 0.15
22 10 0.24
23 15 0.37
24 10 0.24
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (24 bp):
TTCATGAAATATCTCTATCTTGTT
Found at i:35371 original size:45 final size:45
Alignment explanation
Indices: 35321--35410 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
35311 TCCTTTCACT
35321 TCATATTCCTTCATAAATATCTCTATCTTGTTTTCATGAAATTAA
1 TCATATTCCTTCATAAATATCTCTATCTTGTTTTCATGAAATTAA
35366 TCATATTCCTTCATAAATATCTCTATCTTGTTTTCATGAAATTAA
1 TCATATTCCTTCATAAATATCTCTATCTTGTTTTCATGAAATTAA
35411 AGAAATTAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.47
Consensus pattern (45 bp):
TCATATTCCTTCATAAATATCTCTATCTTGTTTTCATGAAATTAA
Found at i:36139 original size:9 final size:9
Alignment explanation
Indices: 36125--36182 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
36115 AAGAAAAATG
36125 CAATTATAC
1 CAATTATAC
36134 CAATTATAC
1 CAATTATAC
**
36143 CAAGGA-A-
1 CAATTATAC
36150 -AATTATAC
1 CAATTATAC
36158 CAATTATAC
1 CAATTATAC
**
36167 CAAAAATA-
1 CAATTATAC
36175 CAATTATA
1 CAATTATA
36183 TCAAGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
6 3 0.08
7 1 0.03
8 7 0.18
9 27 0.71
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (9 bp):
CAATTATAC
Found at i:36229 original size:17 final size:17
Alignment explanation
Indices: 36199--36232 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
36189 AAAATTATTC
*
36199 AATACCCTGCTAGTGGT
1 AATACACTGCTAGTGGT
*
36216 AATACACTGTTAGTGGT
1 AATACACTGCTAGTGGT
36233 TCTCCGGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (17 bp):
AATACACTGCTAGTGGT
Found at i:36720 original size:17 final size:16
Alignment explanation
Indices: 36698--36748 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
36688 ATCACCTCCC
36698 AGATCACTAGTGATCTA
1 AGATCACTAGTGATC-A
36715 AGATCACCTA-TGATGCA
1 AGATCA-CTAGTGAT-CA
**
36732 AGATCACCGGTGATCA
1 AGATCACTAGTGATCA
36748 A
1 A
36749 AGATTACATG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 4 0.14
17 21 0.72
18 4 0.14
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (16 bp):
AGATCACTAGTGATCA
Found at i:38640 original size:1 final size:1
Alignment explanation
Indices: 38591--38627 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
38581 ACCTATGAAG
**
38591 AAAAAAAAGTAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38628 GGAGCTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.95, C:0.00, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Done.