Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015903.1 Corchorus capsularis cultivar CVL-1 contig15924, 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: 10934
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.39
Found at i:488 original size:16 final size:16
Alignment explanation
Indices: 469--508 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
459 CCACGTTCAA
*
469 GAATAATGCCATTTTG
1 GAATAATACCATTTTG
485 GAATAATACCATTTTG
1 GAATAATACCATTTTG
*
501 GAGTAATA
1 GAATAATA
509 ACGTGCTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (16 bp):
GAATAATACCATTTTG
Found at i:840 original size:21 final size:21
Alignment explanation
Indices: 816--860 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
806 TTTGTCTATT
816 TAATTTTAAATTGTTT-TTCTC
1 TAATTTT-AATTGTTTGTTCTC
**
837 TAATTTTTTTTGTTTGTTCTC
1 TAATTTTAATTGTTTGTTCTC
858 TAA
1 TAA
861 CCCACGAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (21 bp):
TAATTTTAATTGTTTGTTCTC
Found at i:973 original size:86 final size:84
Alignment explanation
Indices: 787--996 Score: 357
Period size: 86 Copynumber: 2.5 Consensus size: 84
777 ATCACTATTC
* * *
787 TTTGGTTTGTTCTCTCACTTTTGTCTATTTAATTTTAAATTGTTTTTCTCTAATTTTTTTTGTTT
1 TTTGGTTTGTTCTCTCACTTTTGTCTATTTAATTTTACATTGTTTTTCTCCAATTTTTTTTATTT
852 GTTCTCTAACCCACGAGCT
66 GTTCTCTAACCCACGAGCT
871 TTTGGTTTGTTCTCTCACTTTTGTCTATTTAATTTTACATTGTTTTCTTCTCCAATTTTTTTTAT
1 TTTGGTTTGTTCTCTCACTTTTGTCTATTTAATTTTACATTG-TTT-TTCTCCAATTTTTTTTAT
936 TTGTTCTCTAACCCACGAGCT
64 TTGTTCTCTAACCCACGAGCT
* *
957 TTTGGTTTGTTATCTCACTTTTATCTATTTAATTTTACAT
1 TTTGGTTTGTTCTCTCACTTTTGTCTATTTAATTTTACAT
997 GAATTTCATA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
84 41 0.34
85 3 0.03
86 75 0.63
ACGTcount: A:0.16, C:0.17, G:0.10, T:0.57
Consensus pattern (84 bp):
TTTGGTTTGTTCTCTCACTTTTGTCTATTTAATTTTACATTGTTTTTCTCCAATTTTTTTTATTT
GTTCTCTAACCCACGAGCT
Found at i:3532 original size:11 final size:11
Alignment explanation
Indices: 3489--3526 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3479 TTCCTATATA
*
3489 AAATAAATTAT
1 AAATTAATTAT
3500 CAAA-TAATTAT
1 -AAATTAATTAT
3511 AAATTAATTAT
1 AAATTAATTAT
3522 AAATT
1 AAATT
3527 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:3912 original size:41 final size:42
Alignment explanation
Indices: 3839--3922 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
3829 ACAAAATTTC
3839 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
*
3881 ATTTCTTAACTGAA-TTTTCTTAAAAGCATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
3922 A
1 A
3923 CAGCCGCACG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 27 0.66
42 14 0.34
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (42 bp):
ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
Found at i:4182 original size:20 final size:19
Alignment explanation
Indices: 4157--4209 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
4147 TCCTCTTTTC
4157 TATCTCCTTATTTTTACTTA
1 TATCTCCTTATTTTTA-TTA
* * *
4177 TATCTCCTAATTTCTATTC
1 TATCTCCTTATTTTTATTA
4196 TATCTCCTTATTTT
1 TATCTCCTTATTTT
4210 CACTCCTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (19 bp):
TATCTCCTTATTTTTATTA
Found at i:4201 original size:19 final size:20
Alignment explanation
Indices: 4154--4208 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
4144 CACTCCTCTT
*
4154 TTCTATCTCCTTATTTTTAC
1 TTCTATCTCCTTATTTCTAC
* *
4174 TTATATCTCCTAATTTCTA-
1 TTCTATCTCCTTATTTCTAC
4193 TTCTATCTCCTTATTT
1 TTCTATCTCCTTATTT
4209 TCACTCCTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (20 bp):
TTCTATCTCCTTATTTCTAC
Found at i:5656 original size:198 final size:197
Alignment explanation
Indices: 5132--5864 Score: 851
Period size: 199 Copynumber: 3.7 Consensus size: 197
5122 ATACATTGTT
* * ** * * * *
5132 AGTGAAGTTTAGCAGACTGCACAAACGAGGTTTAAGGGTTGGCATATGTCCCCTTAGGGAATATG
1 AGTGAAATTTAGCAGACTGTACGTATGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATG
* *
5197 TATTAATATTAAATATTTAATTAAGTATGAAATGGGGTATGACGGTATGTGTCAACTTCTTAACC
66 TATTAATATTAAATATTTAATTAATTAT-AAA------ATG-GGGTATGTGTCAACTTCTTAACC
* * * * * * *
5262 CACTTATAGAGTCTAAATTTTACACT-AAAAGTGTATTGAATAATAATCCTGTAAGAAAAATTAT
123 CGCTTATGGAGTCCAAAATTTACACTGACAA-TGTATTGTATAATAATCCTATAAGAAAAATTAT
5326 ACAATACACTGTC
187 ACAATAC-C-GTC
* ** *
5339 AGTGAAATTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGATATGTGTCCCCTTAGGGAATATG
1 AGTGAAATTTAGCAGACTGTACGTATGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATG
** * * * *
5404 TATTAATATTATTTTTTTAATTAATTATGAAATGAGGTATATGTCAACTTCTTAACCCGCTTATG
66 TATTAATATTAAATATTTAATTAATTATAAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATG
* * * *
5469 GAGTCCAAAATTTACACTGACAATGTATTGTATAATAACCCCATAAGAAAGATTGTACAATACCG
131 GAGTCCAAAATTTACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACCG
5534 TC
196 TC
* *
5536 AGTGAAATTTAGCAGACTGTACGTTTGGGGTATAAGGGTTGACATGTGTTCCCCTTAGGGAATAT
1 AGTGAAATTTAGCAGACTGTACGTATGGGGTTTAAGGGTTGACATGTG-TCCCCTTAGGGAATAT
*
5601 GTATCAATATTAAATATTTAATTAATTATAAAATGGGGTATGTGTCAACTTCTTAACCCGCTTAT
65 GTATTAATATTAAATATTTAATTAATTATAAAATGGGGTATGTGTCAACTTCTTAACCCGCTTAT
* * *
5666 GGAGTTCAAAATTTACACTGACAGTGTATTATATAATAATCCTATAAGAAAAATTATACAATACA
130 GGAGTCCAAAATTTACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAAT--A
5731 CCGTC
193 CCGTC
* * ** * * * *
5736 AGTGGAGTTTAGTTGACTGAATGCGCAT--GGTTTAAGGGATGACATGTGTCCGCTTAGGGAATA
1 AGTGAAATTTAGCAGACTG--TACGTATGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
* * * * *
5799 TGTATTAAAATTAAATATTTAATTAATTATGAAATGGGGTGTGTGTCAACTTCTTAATCTGCTTA
64 TGTATTAATATTAAATATTTAATTAATTATAAAATGGGGTATGTGTCAACTTCTTAACCCGCTTA
5864 T
129 T
5865 AAATATTCAT
Statistics
Matches: 459, Mismatches: 61, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
197 46 0.10
198 130 0.28
199 151 0.33
200 45 0.10
202 4 0.01
206 2 0.00
207 81 0.18
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (197 bp):
AGTGAAATTTAGCAGACTGTACGTATGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATG
TATTAATATTAAATATTTAATTAATTATAAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATG
GAGTCCAAAATTTACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACCG
TC
Found at i:7727 original size:87 final size:87
Alignment explanation
Indices: 7608--7787 Score: 272
Period size: 87 Copynumber: 2.1 Consensus size: 87
7598 TAAGATCACT
* * * *
7608 AAAAATCTTAAACGATGTGATTAAATACATTTAAGAAAACTATTTAA-AAAGTTTTTAAGTTTAA
1 AAAAATCTTAAACGAGGTGATTAAATAAATTTAAGAAAACCATTTAATAAA-CTTTTAAGTTTAA
*
7672 TGAAAAATTTATAAACTTACCAA
65 TGAAAAAATTATAAACTTACCAA
*
7695 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACCATTTAATAAACTTTTAAGTTTAAT
1 AAAAATCTTAAACGAGGTGATTAAATAAATTTAAGAAAACCATTTAATAAACTTTTAAGTTTAAT
*
7760 GAAAAAATTATAAGCTTACCAA
66 GAAAAAATTATAAACTTACCAA
*
7782 GAAAAT
1 AAAAAT
7788 TTACAAGGTT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
87 81 0.96
88 3 0.04
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.32
Consensus pattern (87 bp):
AAAAATCTTAAACGAGGTGATTAAATAAATTTAAGAAAACCATTTAATAAACTTTTAAGTTTAAT
GAAAAAATTATAAACTTACCAA
Found at i:7869 original size:21 final size:19
Alignment explanation
Indices: 7822--7870 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
7812 CCAGTTACAA
* *
7822 TAAAAGTTAAATAGTTTAC
1 TAAAAGTTAAATAGATCAC
7841 TAAAAAGTTAAATACGATCATC
1 T-AAAAGTTAAATA-GATCA-C
7863 TAAAAGTT
1 TAAAAGTT
7871 TTCAAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.04
20 12 0.48
21 10 0.40
22 2 0.08
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (19 bp):
TAAAAGTTAAATAGATCAC
Found at i:8382 original size:20 final size:20
Alignment explanation
Indices: 8359--8411 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
8349 AAGGTTTTTT
*
8359 AGGTTATTAAAAAATTTATA
1 AGGTTATTAAAAAATTTAAA
* * *
8379 AGGTGACTAATAAATTTAAA
1 AGGTTATTAAAAAATTTAAA
*
8399 ATGTTATTGAAAA
1 AGGTTATT-AAAA
8412 TCTTAACAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
AGGTTATTAAAAAATTTAAA
Found at i:9199 original size:42 final size:40
Alignment explanation
Indices: 9140--9223 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 40
9130 ATTAATTCCT
9140 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
9180 ATGTAATAATACTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATTAATTAA
9222 AT
1 AT
9224 TCTTAGGTGT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 7 0.17
41 3 0.07
42 31 0.76
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:9448 original size:3 final size:3
Alignment explanation
Indices: 9440--9478 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
9430 ATATATATAT
9440 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9479 TGTTGTATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10116 original size:36 final size:36
Alignment explanation
Indices: 10069--10138 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
10059 GAGATTTTGG
*
10069 AGAAATATGATAA-TCAAAATTATAAAAAATGTAATA
1 AGAAATATGATAACT-AAAATTACAAAAAATGTAATA
10105 AGAAATATGATAACTAAAATTACAAAAAATGTAA
1 AGAAATATGATAACTAAAATTACAAAAAATGTAA
10139 GGTTATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26
Consensus pattern (36 bp):
AGAAATATGATAACTAAAATTACAAAAAATGTAATA
Done.