Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008943.1 Corchorus capsularis cultivar CVL-1 contig08964, 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: 79210
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4289 original size:19 final size:18
Alignment explanation
Indices: 4265--4300 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4255 TGAAGATTTC
4265 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
4284 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
4301 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:7572 original size:16 final size:16
Alignment explanation
Indices: 7551--7591 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
7541 AATAAATTAA
7551 AATCAAACTTATATCC
1 AATCAAACTTATATCC
7567 AATCAAACTTATATCC
1 AATCAAACTTATATCC
*
7583 AACCAAACT
1 AATCAAACT
7592 ATTACGCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (16 bp):
AATCAAACTTATATCC
Found at i:9520 original size:27 final size:27
Alignment explanation
Indices: 9469--9520 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
9459 ATGATTTAGG
*
9469 GGTTACTAACTCCCTTTTTTCTTTTGA
1 GGTTACTAACACCCTTTTTTCTTTTGA
*
9496 GGTTACTAACACTCTTATTTT-TTTT
1 GGTTACTAACACCCTT-TTTTCTTTT
9521 CAGATGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (27 bp):
GGTTACTAACACCCTTTTTTCTTTTGA
Found at i:10140 original size:6 final size:6
Alignment explanation
Indices: 10121--10250 Score: 68
Period size: 6 Copynumber: 19.2 Consensus size: 6
10111 GGCAATTGGG
10121 CGGGTT CGGG-- CGGGTT CGGGTT CGGGTACTT CGGGTT CGGGTATTTT
1 CGGGTT CGGGTT CGGGTT CGGGTT CGGG---TT CGGGTT CGGG----TT
10168 CGGGTT CGGGTATTTT CGGGTT CGGGTTTTT CGGGTT CGGGTATTTT CGGGTT
1 CGGGTT CGGG----TT CGGGTT CGGG---TT CGGGTT CGGG----TT CGGGTT
*
10221 CGGGTT CGGG-T CCGGTT CGGGTT CGGGTT C
1 CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT C
10251 ACTTTCGATA
Statistics
Matches: 101, Mismatches: 2, Indels: 42
0.70 0.01 0.29
Matches are distributed among these distances:
4 4 0.04
5 4 0.04
6 63 0.62
9 12 0.12
10 18 0.18
ACGTcount: A:0.03, C:0.17, G:0.43, T:0.37
Consensus pattern (6 bp):
CGGGTT
Found at i:10159 original size:31 final size:32
Alignment explanation
Indices: 10121--10242 Score: 124
Period size: 31 Copynumber: 3.8 Consensus size: 32
10111 GGCAATTGGG
*
10121 CGGGTTCGGGCGGGTTCGGGTTCGGGTA-CTT
1 CGGGTTCGGGCGGGTTCGGGTTCGGGTATTTT
****
10152 CGGGTTCGGGTATTTTCGGGTTCGGGTATTTT
1 CGGGTTCGGGCGGGTTCGGGTTCGGGTATTTT
***
10184 CGGGTTCGGG-TTTTTCGGGTTCGGGTATTTT
1 CGGGTTCGGGCGGGTTCGGGTTCGGGTATTTT
*
10215 CGGGTTCGGGTTCGGG-TCCGGTTCGGGT
1 CGGGTTCGGG--CGGGTTCGGGTTCGGGT
10243 TCGGGTTCAC
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
31 54 0.70
32 12 0.16
33 11 0.14
ACGTcount: A:0.03, C:0.16, G:0.43, T:0.37
Consensus pattern (32 bp):
CGGGTTCGGGCGGGTTCGGGTTCGGGTATTTT
Found at i:10171 original size:16 final size:16
Alignment explanation
Indices: 10135--10225 Score: 159
Period size: 16 Copynumber: 5.8 Consensus size: 16
10125 TTCGGGCGGG
*
10135 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGGGTATT
10150 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
10166 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
10182 TTCGGGTTCGGGT-TT
1 TTCGGGTTCGGGTATT
10197 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
10213 TTCGGGTTCGGGT
1 TTCGGGTTCGGGT
10226 TCGGGTCCGG
Statistics
Matches: 73, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
15 29 0.40
16 44 0.60
ACGTcount: A:0.04, C:0.14, G:0.40, T:0.42
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:10190 original size:47 final size:47
Alignment explanation
Indices: 10135--10225 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
10125 TTCGGGCGGG
10135 TTCGGGTTCGGGTACTTCGGGTTCGGGTATTTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTACTTCGGGTTCGGGTATTTTCGGGTTCGGGTATT
**
10182 TTCGGGTTCGGGTTTTTCGGGTTCGGGTATTTTCGGGTTCGGGT
1 TTCGGGTTCGGGTACTTCGGGTTCGGGTATTTTCGGGTTCGGGT
10226 TCGGGTCCGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.04, C:0.14, G:0.40, T:0.42
Consensus pattern (47 bp):
TTCGGGTTCGGGTACTTCGGGTTCGGGTATTTTCGGGTTCGGGTATT
Found at i:11008 original size:11 final size:12
Alignment explanation
Indices: 10994--11054 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 12
10984 TATTTTGATC
10994 TCGGGTTCGGG-
1 TCGGGTTCGGGT
11005 TCGGGTTCGGGT
1 TCGGGTTCGGGT
11017 TCGGG--CGGGT
1 TCGGGTTCGGGT
*
11027 TCGGATTCAGGTTGT
1 TCGGGTTC-GG--GT
11042 CTCGGGTTCGGGT
1 -TCGGGTTCGGGT
11055 ATTTTCGGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
10 9 0.22
11 11 0.27
12 6 0.15
13 4 0.10
15 4 0.10
16 7 0.17
ACGTcount: A:0.03, C:0.18, G:0.48, T:0.31
Consensus pattern (12 bp):
TCGGGTTCGGGT
Found at i:11016 original size:17 final size:16
Alignment explanation
Indices: 10994--11030 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
10984 TATTTTGATC
10994 TCGGGTTCGGGTCGGGT
1 TCGGGTTCGGG-CGGGT
11011 TCGGGTTCGGGCGGGT
1 TCGGGTTCGGGCGGGT
11027 TCGG
1 TCGG
11031 ATTCAGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.00, C:0.19, G:0.54, T:0.27
Consensus pattern (16 bp):
TCGGGTTCGGGCGGGT
Found at i:11062 original size:16 final size:16
Alignment explanation
Indices: 11043--11087 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
11033 TCAGGTTGTC
*
11043 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTAATT
11059 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGTAATT
* *
11075 TCAGGTTTGGGTA
1 TCGGGTTCGGGTA
11088 CAGGCGGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.11, C:0.11, G:0.38, T:0.40
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:11070 original size:6 final size:6
Alignment explanation
Indices: 10994--11054 Score: 56
Period size: 6 Copynumber: 10.0 Consensus size: 6
10984 TATTTTGATC
*
10994 TCGGGT TCGGG- TCGGGT TCGGGT TCGGG- -CGGGT TCGGAT TCAGGTTGT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TC-GG--GT
11042 CTCGGGT TCGGGT
1 -TCGGGT TCGGGT
11055 ATTTTCGGGT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
4 4 0.09
5 5 0.11
6 28 0.61
7 4 0.09
9 3 0.07
10 2 0.04
ACGTcount: A:0.03, C:0.18, G:0.48, T:0.31
Consensus pattern (6 bp):
TCGGGT
Found at i:19871 original size:2 final size:2
Alignment explanation
Indices: 19864--19927 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
19854 GGTTATACAT
19864 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
19906 CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA
19928 AAGGAGTAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28532 original size:69 final size:68
Alignment explanation
Indices: 28267--28601 Score: 323
Period size: 68 Copynumber: 4.8 Consensus size: 68
28257 CTTTTATTCT
** * * * *
28267 CTTAAATGTGAAAACATGAC-AAGATTGACCCTTTGACCGAAAAGGCAATTTTGGAAAGCAGAGA
1 CTTAAATGCAAAAACATGACGAA-ATTGACCCTTTGACCGAAAGGGTACTTTTGGAAA--ATA-A
** *
28331 ATTTGAA
62 AACTAAA
* * * *
28338 CTTAAATGCAAAAACATATGACAAAATTAACCCTTTGACCGAAAGGGTATTTTTGGAAAGTAAAA
1 CTTAAATGCAAAAAC--ATGACGAAATTGACCCTTTGACCGAAAGGGTACTTTTGGAAAATAAAA
*
28403 ATAAA
64 CTAAA
* * * * * * *
28408 CTCACATGCAAAAATATGACGAAGTTGACCCTTCGACCGAAATGGTACTTCTGGAAAATAAAACT
1 CTTAAATGCAAAAACATGACGAAATTGACCCTTTGACCGAAAGGGTACTTTTGGAAAATAAAACT
28473 AAA
66 AAA
* * * * *
28476 CTTAAATACAAAAACATGACGAAACCTGACCCTTTGACCGAGAGGGTACTTTTGGAAAACAATAC
1 CTTAAATGCAAAAACATGACGAAA-TTGACCCTTTGACCGAAAGGGTACTTTTGGAAAATAAAAC
28541 TAAA
65 TAAA
* * *
28545 CTTAAATGCAAAAA-AGTGATGAAATTGACCTTTTGACCGAAAGGGTATTTTTGGAAA
1 CTTAAATGCAAAAACA-TGACGAAATTGACCCTTTGACCGAAAGGGTACTTTTGGAAA
28602 GCAAAATAAA
Statistics
Matches: 218, Mismatches: 41, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
68 93 0.43
69 57 0.26
70 17 0.08
71 14 0.06
73 35 0.16
74 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (68 bp):
CTTAAATGCAAAAACATGACGAAATTGACCCTTTGACCGAAAGGGTACTTTTGGAAAATAAAACT
AAA
Found at i:28533 original size:137 final size:137
Alignment explanation
Indices: 28336--28601 Score: 320
Period size: 137 Copynumber: 1.9 Consensus size: 137
28326 AGAGAATTTG
* * * **
28336 AACTTAAATGCAAAAACATATGACAAAATTAACCCTTTGACCGAAAGGGTATTTTTGGAAAGTAA
1 AACTTAAATACAAAAACA-ATGACAAAACTAACCCTTTGACCGAAAGGGTACTTTTGGAAAACAA
* * *
28401 AAATAAACTCACATGCAAAAATA-TGACGAAGTTGACCCTTCGACCGAAATGGTACTTCTGGAAA
65 AAATAAACTCAAATGCAAAAA-AGTGACGAAATTGACCCTTCGACCGAAAGGGTACTTCTGGAAA
28465 ATAAAACTA
129 ATAAAACTA
* * *
28474 AACTTAAATACAAAAAC-ATGACGAAACCTGACCCTTTGACCGAGAGGGTACTTTTGGAAAACAA
1 AACTTAAATACAAAAACAATGAC-AAAACTAACCCTTTGACCGAAAGGGTACTTTTGGAAAACAA
* * * * * * * *
28538 TACTAAACTTAAATGCAAAAAAGTGATGAAATTGACCTTTTGACCGAAAGGGTATTTTTGGAAA
65 AAATAAACTCAAATGCAAAAAAGTGACGAAATTGACCCTTCGACCGAAAGGGTACTTCTGGAAA
28602 GCAAAATAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
136 6 0.06
137 85 0.79
138 16 0.15
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (137 bp):
AACTTAAATACAAAAACAATGACAAAACTAACCCTTTGACCGAAAGGGTACTTTTGGAAAACAAA
AATAAACTCAAATGCAAAAAAGTGACGAAATTGACCCTTCGACCGAAAGGGTACTTCTGGAAAAT
AAAACTA
Found at i:39261 original size:11 final size:12
Alignment explanation
Indices: 39244--39275 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
39234 ATGGTCTTCA
39244 AATCTTCAAAAT
1 AATCTTCAAAAT
39256 -ATCTTC-AAAT
1 AATCTTCAAAAT
39266 AATCTTCAAA
1 AATCTTCAAA
39276 CACGAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.22
11 12 0.67
12 2 0.11
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (12 bp):
AATCTTCAAAAT
Found at i:39721 original size:66 final size:65
Alignment explanation
Indices: 39519--39723 Score: 218
Period size: 66 Copynumber: 3.1 Consensus size: 65
39509 TAGGAAAAAG
* *
39519 AAAATGACAAAACTAACCCTTTGACCAAAAGGGTATTCTTGGAAAG-AGAAAATTAAACT-ACAT
1 AAAATGACAAAATTAACCCTTTGACCGAAA-GGTATTCTTGGAAAGCA-AAAA-TAAACTCACAT
39582 GCA
63 GCA
* * *
39585 AAAAGGACAAAATTAACCCTTTGACTGAAAGTGTATTCTTGGACAA-CAAAAATAAAATCACATG
1 AAAATGACAAAATTAACCCTTTGACCGAAAG-GTATTCTTGGA-AAGCAAAAATAAACTCACATG
*
39649 TA
64 CA
* * * ** *
39651 AAAATGACAAAATTGATCCTTTGACCGATAAGGTATTTTTTCAAAGCAAAAATAAACTCAAATGC
1 AAAATGACAAAATTAACCCTTTGACCGA-AAGGTATTCTTGGAAAGCAAAAATAAACTCACATGC
*
39716 G
65 A
39717 AAAATGA
1 AAAATGA
39724 TGAAACTGAC
Statistics
Matches: 116, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
65 8 0.07
66 102 0.88
67 6 0.05
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (65 bp):
AAAATGACAAAATTAACCCTTTGACCGAAAGGTATTCTTGGAAAGCAAAAATAAACTCACATGCA
Found at i:39738 original size:66 final size:66
Alignment explanation
Indices: 39519--39755 Score: 167
Period size: 66 Copynumber: 3.6 Consensus size: 66
39509 TAGGAAAAAG
* * * * ** * *
39519 AAAATGACAAAACTAACCCTTTGACCAAAAGGGTATTCTTGGAAAG-AGAAAATTAAA-CTACAT
1 AAAATGACAAAACTGACCCTTTCACCGAAAGGGTATTTTTTCAAAGCA-AAAATAAAATC-AAAT
39582 GCA
64 GCA
* * * * * * * ** *
39585 AAAAGGACAAAATTAACCCTTTGACTGAAAGTGTATTCTTGGACAA-CAAAAATAAAATCACATG
1 AAAATGACAAAACTGACCCTTTCACCGAAAGGGTATTTTTTCA-AAGCAAAAATAAAATCAAATG
*
39649 TA
65 CA
* * * *
39651 AAAATGACAAAATTGATCCTTTGACCGATAA-GGTATTTTTTCAAAGCAAAAATAAACTCAAATG
1 AAAATGACAAAACTGACCCTTTCACCGA-AAGGGTATTTTTTCAAAGCAAAAATAAAATCAAATG
*
39715 CG
65 CA
** *
39717 AAAATGATGAAACTGACCCTTTCAGCGAAAGGGTATTTT
1 AAAATGACAAAACTGACCCTTTCACCGAAAGGGTATTTT
39756 CGTAAAAAAA
Statistics
Matches: 140, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
65 4 0.03
66 130 0.93
67 6 0.04
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (66 bp):
AAAATGACAAAACTGACCCTTTCACCGAAAGGGTATTTTTTCAAAGCAAAAATAAAATCAAATGC
A
Found at i:53238 original size:15 final size:15
Alignment explanation
Indices: 53218--53263 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
53208 AATTTAATTG
53218 TTACTTTCCCTAGAA
1 TTACTTTCCCTAGAA
*
53233 TTACTTTCCCTAAAA
1 TTACTTTCCCTAGAA
* * *
53248 TCACTCTCCCAAGAA
1 TTACTTTCCCTAGAA
53263 T
1 T
53264 CACTCTCCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.35
Consensus pattern (15 bp):
TTACTTTCCCTAGAA
Found at i:53264 original size:15 final size:15
Alignment explanation
Indices: 53224--53271 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
53214 ATTGTTACTT
* * *
53224 TCCCTAGAATTACTT
1 TCCCAAGAATCACTC
53239 TCCCTAA-AATCACTC
1 TCCC-AAGAATCACTC
53254 TCCCAAGAATCACTC
1 TCCCAAGAATCACTC
53269 TCC
1 TCC
53272 TATGGAGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 2 0.07
15 25 0.89
16 1 0.04
ACGTcount: A:0.29, C:0.38, G:0.04, T:0.29
Consensus pattern (15 bp):
TCCCAAGAATCACTC
Found at i:64561 original size:31 final size:32
Alignment explanation
Indices: 64523--64598 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
64513 ATAAAGATAG
*
64523 AAAAAAGTTGATGT-CTTTACCTC-AAAAAG-AA
1 AAAAAAGTTGATGTGC-TT-CCACAAAAAAGAAA
64554 AAAAAAGTTGATGTGCTTCCACAAAAAAAGAAA
1 AAAAAAGTTGATGTGCTTCCAC-AAAAAAGAAA
64587 AAAAAAGTTGAT
1 AAAAAAGTTGAT
64599 AGTTCAAGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 3 0.08
31 16 0.40
32 7 0.17
33 14 0.35
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.22
Consensus pattern (32 bp):
AAAAAAGTTGATGTGCTTCCACAAAAAAGAAA
Found at i:66094 original size:13 final size:13
Alignment explanation
Indices: 66076--66104 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
66066 GTCAGCCATC
66076 AATGAACAAAACA
1 AATGAACAAAACA
66089 AATGAACAAAACA
1 AATGAACAAAACA
66102 AAT
1 AAT
66105 TAACTGTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (13 bp):
AATGAACAAAACA
Done.