Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009517.1 Corchorus capsularis cultivar CVL-1 contig09538, 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: 82241
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:1435 original size:167 final size:167
Alignment explanation
Indices: 1170--1477 Score: 483
Period size: 167 Copynumber: 1.8 Consensus size: 167
1160 TACTTTAAAC
* * *
1170 AAACAACAAAGATCAACAAGTTCAAAAGTTCCAAAAACAGGTCAACATCGCAGGACACTTATGAA
1 AAACAACAAAGATCAACAAGTTCAAAAGTTCCAAAAACAGGTCAAAATCACAGAACACTTATGAA
* * * *
1235 AACTAGATAGACAGTGAGCGAAGTTACTTCCAGATCACTCAAAGCAAGAAGGGCTTTCGTTTTCA
66 AACTAGATAGACAGTAAGCAAAGTTACTTCCAGATCACTCAAAACAAGAAGGGCTTTCGTTTACA
*
1300 TTCAAATTAAGCGTGGATATCACTAATCTTATACTTT
131 TTCAAACTAAGCGTGGATATCACTAATCTTATACTTT
* **
1337 AAACAACAAAGATCAACAAGTTTAAAAG-TCCAAAAAACAGGTCAAAATCACTTAACACTTATGA
1 AAACAACAAAGATCAACAAGTTCAAAAGTTCC-AAAAACAGGTCAAAATCACAGAACACTTATGA
* *
1401 AAACTAGATAGACAGTAAGCAAAGTTATTTCCAGATCACTCAAAATAAGAAGGGCTTTCGTTTAC
65 AAACTAGATAGACAGTAAGCAAAGTTACTTCCAGATCACTCAAAACAAGAAGGGCTTTCGTTTAC
1466 ATTCAAACTAAG
130 ATTCAAACTAAG
1478 TGTAAATATC
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
166 3 0.02
167 124 0.98
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (167 bp):
AAACAACAAAGATCAACAAGTTCAAAAGTTCCAAAAACAGGTCAAAATCACAGAACACTTATGAA
AACTAGATAGACAGTAAGCAAAGTTACTTCCAGATCACTCAAAACAAGAAGGGCTTTCGTTTACA
TTCAAACTAAGCGTGGATATCACTAATCTTATACTTT
Found at i:3553 original size:3 final size:3
Alignment explanation
Indices: 3547--3571 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3537 AATCAATTTA
3547 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
3572 ACAGTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:4417 original size:4 final size:4
Alignment explanation
Indices: 4408--4435 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4398 CAATAAAATA
4408 ACAG ACAG ACAG ACAG ACAG ACAG ACAG
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG
4436 GTGAGACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.25, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:6741 original size:18 final size:18
Alignment explanation
Indices: 6718--6754 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6708 CAGTACATCG
* *
6718 AAGGAATCCTAGTTACAA
1 AAGGAATCCAAGATACAA
6736 AAGGAATCCAAGATACAA
1 AAGGAATCCAAGATACAA
6754 A
1 A
6755 GACAGTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (18 bp):
AAGGAATCCAAGATACAA
Found at i:11036 original size:18 final size:18
Alignment explanation
Indices: 11013--11059 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
11003 ATGGGTGCGA
*
11013 TTGAGGCTGGGCCTGTGT
1 TTGAGGCTGGGCCTGGGT
**
11031 TTGAGGCTGCACCTGGGT
1 TTGAGGCTGGGCCTGGGT
*
11049 TTGAGGTTGGG
1 TTGAGGCTGGG
11060 GTTGTGCCTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.15, G:0.45, T:0.32
Consensus pattern (18 bp):
TTGAGGCTGGGCCTGGGT
Found at i:13963 original size:31 final size:31
Alignment explanation
Indices: 13925--13986 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
13915 TATGTTAGAC
**
13925 AAATAAGGATGTAATAGACATTTCAAAAGTT
1 AAATAAGGATACAATAGACATTTCAAAAGTT
* **
13956 AAATAAGGGTACAATAGGTATTTCAAAAGTT
1 AAATAAGGATACAATAGACATTTCAAAAGTT
13987 TTACAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (31 bp):
AAATAAGGATACAATAGACATTTCAAAAGTT
Found at i:15251 original size:40 final size:39
Alignment explanation
Indices: 15157--15307 Score: 216
Period size: 39 Copynumber: 3.9 Consensus size: 39
15147 GGCTGTGCAT
* *
15157 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGATAAC
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
*
15196 AGTGGACCTGTGCCTCAGGGGGTTAAACTGATTGGTAAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGT-AAG
15236 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
* * * *
15275 AGTGCACCCATGCCTCAAGGGATT-AACTG-TTGG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGG
15308 CTAGATTCGA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
37 4 0.04
38 5 0.05
39 57 0.55
40 37 0.36
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (39 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
Found at i:15289 original size:79 final size:77
Alignment explanation
Indices: 15157--15307 Score: 221
Period size: 79 Copynumber: 1.9 Consensus size: 77
15147 GGCTGTGCAT
* ** * *
15157 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGATAACAGTGGACCTGTGCCTCAGGGGGTTAA
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGATAACAGTGCACCCATGCCTCAAGGGATT-A
15222 ACTGATTGGTAAAG
65 ACTG-TTGGTAAAG
* *
15236 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAGAGTGCACCCATGCCTCAAGGGATTAA
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGATAACAGTGCACCCATGCCTCAAGGGATTAA
15301 CTGTTGG
66 CTGTTGG
15308 CTAGATTCGA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
77 4 0.06
78 5 0.08
79 56 0.86
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (77 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGATAACAGTGCACCCATGCCTCAAGGGATTAA
CTGTTGGTAAAG
Found at i:15348 original size:6 final size:6
Alignment explanation
Indices: 15337--15374 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
15327 TGTTAACGGA
*
15337 TGATTG TGATTG TGATTG TGATTG TAATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG
15375 GTGCAGCCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:17716 original size:123 final size:123
Alignment explanation
Indices: 17567--17819 Score: 301
Period size: 123 Copynumber: 2.1 Consensus size: 123
17557 ATACTAATTT
* * * * * *
17567 GGTTAATAAATTTTAAATTTAAGTTAAAATATAATTCGATCGATTGACCGATATATTTCAGTTCG
1 GGTTCATAAATTTAAAATTTAAGTTAAAATATAATTCGATCAACTAACCGAAATATTTCAGTTCG
* *
17632 GTTAATGTTCAAAATAAGATACTTCGGA-TCTGTTAATGATTTACAAAAAATAGTGTTC
66 GTTAATGTTCAAAATAAGATACTTC-GATTCGGTTAACGATTTACAAAAAATAGTGTTC
* * * * * *
17690 GGTTCATAAATTTAAAATTTATGTTAAAATATCATTCGGTTAACTAATCGAAATATTTCGGTTCG
1 GGTTCATAAATTTAAAATTTAAGTTAAAATATAATTCGATCAACTAACCGAAATATTTCAGTTCG
* ** * * *
17755 GTTGATGTTCGGAATAGGATACTTCGATTCGGTTAACGTTTTACAAAAAATAGTTTTC
66 GTTAATGTTCAAAATAAGATACTTCGATTCGGTTAACGATTTACAAAAAATAGTGTTC
*
17813 GATTCAT
1 GGTTCAT
17820 TTGGTTAACA
Statistics
Matches: 108, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
122 2 0.02
123 106 0.98
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (123 bp):
GGTTCATAAATTTAAAATTTAAGTTAAAATATAATTCGATCAACTAACCGAAATATTTCAGTTCG
GTTAATGTTCAAAATAAGATACTTCGATTCGGTTAACGATTTACAAAAAATAGTGTTC
Found at i:18139 original size:32 final size:33
Alignment explanation
Indices: 18078--18142 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
18068 TCGGGAGCAA
*
18078 CCTCTTCTTTAAGAAGATCTGGATTTGGTCTAG
1 CCTCTTCTTTAAGAAGATCTGGATCTGGTCTAG
18111 CCTCTTCTTTAAGAA-ATCTGGATCTGGTCTAG
1 CCTCTTCTTTAAGAAGATCTGGATCTGGTCTAG
18143 TTCAATCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (33 bp):
CCTCTTCTTTAAGAAGATCTGGATCTGGTCTAG
Found at i:19306 original size:5 final size:5
Alignment explanation
Indices: 19296--19329 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
19286 TTTGTCATTC
*
19296 TTTTA TTTTA TTTTA TTTTA TTTTT TTTCTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTT
19330 GCATTGCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:30130 original size:26 final size:27
Alignment explanation
Indices: 30100--30156 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 27
30090 GTTTCTACTT
*
30100 TTTTTTTTTAATAATCTGGTTAATTTC
1 TTTTTTTGTAATAATCTGGTTAATTTC
30127 TTTTTTTGGATAATAATCTGGTTAATTTC
1 TTTTTTT-G-TAATAATCTGGTTAATTTC
30156 T
1 T
30157 GTTTGATGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 7 0.26
29 20 0.74
ACGTcount: A:0.23, C:0.07, G:0.11, T:0.60
Consensus pattern (27 bp):
TTTTTTTGTAATAATCTGGTTAATTTC
Found at i:31834 original size:87 final size:87
Alignment explanation
Indices: 31709--31882 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
31699 AAAAAAAACA
31709 TGTCTTGTGTCAGGCTTTGAAATTGCTCAAGTGCTCCCTAGTATCAAAGACACCTTTGACTGACG
1 TGTCTTGTGTCAGGCTTTGAAATTGCTCAAGTGCTCCCTAGTATCAAAGACACCTTTGACTGACG
31774 CTCTTTTGGAAAAGAACTCAGT
66 CTCTTTTGGAAAAGAACTCAGT
31796 TGTCTTGTGTCAGGCTTTGAAATTGCTCAAGTGCTCCCTAGTATCAAAGACACCTTTGACTGACG
1 TGTCTTGTGTCAGGCTTTGAAATTGCTCAAGTGCTCCCTAGTATCAAAGACACCTTTGACTGACG
31861 CTCTTTTGGAAAAGAACTCAGT
66 CTCTTTTGGAAAAGAACTCAGT
31883 GCCTGATCCA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (87 bp):
TGTCTTGTGTCAGGCTTTGAAATTGCTCAAGTGCTCCCTAGTATCAAAGACACCTTTGACTGACG
CTCTTTTGGAAAAGAACTCAGT
Found at i:42196 original size:30 final size:28
Alignment explanation
Indices: 42160--42237 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
42150 CATCAGAAAA
42160 GGGCTTATTTGGCCTTTTTAGAGTGTTCAG
1 GGGCTTATTTGGCCTTTTTAGA--GTTCAG
**
42190 GGGCTTATTTGG-CTGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCT--TTTTAGAGTTCAG
*
42219 GGGCTTATTTGGCCGTTTT
1 GGGCTTATTTGGCCTTTTT
42238 GTGTAAGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
28 2 0.05
29 20 0.50
30 13 0.32
31 5 0.12
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.41
Consensus pattern (28 bp):
GGGCTTATTTGGCCTTTTTAGAGTTCAG
Found at i:46230 original size:5 final size:5
Alignment explanation
Indices: 46215--46266 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
46205 AACATATATG
* * * *
46215 TATTT TGTTT TATTT TGTTT TGTTT TGTTTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT T-ATTT TATTT TATTT TATTT TATTT
46266 T
1 T
46267 TTGTTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
5 37 0.90
6 4 0.10
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:46230 original size:10 final size:10
Alignment explanation
Indices: 46215--46266 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
46205 AACATATATG
46215 TATTTTGTTT
1 TATTTTGTTT
46225 TATTTTGTTT
1 TATTTTGTTT
*
46235 TGTTTTGTTTT
1 TATTTTG-TTT
*
46246 TATTTTATTT
1 TATTTTGTTT
*
46256 TATTTTATTT
1 TATTTTGTTT
46266 T
1 T
46267 TTGTTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 30 0.79
11 8 0.21
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.81
Consensus pattern (10 bp):
TATTTTGTTT
Found at i:46237 original size:15 final size:15
Alignment explanation
Indices: 46215--46266 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
46205 AACATATATG
46215 TATTTTGTTTTATTT
1 TATTTTGTTTTATTT
* *
46230 TGTTTTGTTTTGTTTT
1 TATTTTGTTTT-ATTT
*
46246 TATTTTATTTTATTT
1 TATTTTGTTTTATTT
46261 TATTTT
1 TATTTT
46267 TTGTTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 19 0.61
16 12 0.39
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.81
Consensus pattern (15 bp):
TATTTTGTTTTATTT
Found at i:46276 original size:10 final size:10
Alignment explanation
Indices: 46217--46276 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 10
46207 CATATATGTA
*
46217 TTTTGTTTTA
1 TTTTGTTTTT
*
46227 TTTTGTTTTG
1 TTTTGTTTTT
46237 TTTTGTTTTT
1 TTTTGTTTTT
* *
46247 ATTT-TATTT
1 TTTTGTTTTT
* *
46256 TATT-TTATT
1 TTTTGTTTTT
46265 TTTTGTTTTT
1 TTTTGTTTTT
46275 TT
1 TT
46277 ACGAGGAAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
9 12 0.31
10 27 0.69
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.83
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:46276 original size:15 final size:15
Alignment explanation
Indices: 46215--46277 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
46205 AACATATATG
*
46215 TATTTTGTTTTATTT
1 TATTTTTTTTTATTT
*
46230 TGTTTTGTTTTGT-TTT
1 TATTTT-TTTT-TATTT
*
46246 TATTTTATTTTATTT
1 TATTTTTTTTTATTT
46261 TATTTTTTGTTT-TTT
1 TATTTTTT-TTTATTT
46276 TA
1 TA
46278 CGAGGAAGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 23 0.59
16 14 0.36
17 1 0.03
ACGTcount: A:0.11, C:0.00, G:0.08, T:0.81
Consensus pattern (15 bp):
TATTTTTTTTTATTT
Found at i:48182 original size:21 final size:21
Alignment explanation
Indices: 48156--48195 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48146 TGCTCTTATA
*
48156 TAAAAAATAATTATTATATTC
1 TAAAAAATAATTATAATATTC
*
48177 TAAAAAATATTTATAATAT
1 TAAAAAATAATTATAATAT
48196 GTTATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAAATAATTATAATATTC
Found at i:48286 original size:20 final size:20
Alignment explanation
Indices: 48261--48313 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
48251 CAAATAAAGT
*
48261 TAAATATTATTATTT-TGGAC
1 TAAATATTATTATTTGT-AAC
*
48281 TAAATACTATTGATTTGTAAC
1 TAAATATTATT-ATTTGTAAC
48302 TAAATATTATTA
1 TAAATATTATTA
48314 AAATCTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 11 0.39
21 16 0.57
22 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (20 bp):
TAAATATTATTATTTGTAAC
Found at i:78859 original size:2 final size:2
Alignment explanation
Indices: 78848--78885 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
78838 GAACTTTTAG
78848 TA TA TA -A 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 TA T
78886 TAGTATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:79647 original size:2 final size:2
Alignment explanation
Indices: 79640--79670 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
79630 AGTTGATGGA
79640 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
79671 AAAGGGATAA
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
Done.