Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015777.1 Corchorus capsularis cultivar CVL-1 contig15798, 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: 28498
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--29 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30 CCGTGGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3424 original size:14 final size:14
Alignment explanation
Indices: 3405--3434 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3395 TAGTCACTTA
3405 ATTTGATCTGTTTG
1 ATTTGATCTGTTTG
3419 ATTTGATCTGTTTG
1 ATTTGATCTGTTTG
3433 AT
1 AT
3435 GCCTTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.57
Consensus pattern (14 bp):
ATTTGATCTGTTTG
Found at i:5499 original size:25 final size:25
Alignment explanation
Indices: 5467--5517 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
5457 TTGCTAGTTG
5467 TGATTAATGCTCCA-TGTTTGCATGT
1 TGATTAAT-CTCCAGTGTTTGCATGT
*
5492 TGATTAATTTCCAGTGTTTGCATGT
1 TGATTAATCTCCAGTGTTTGCATGT
5517 T
1 T
5518 CCTTGGTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.47
Consensus pattern (25 bp):
TGATTAATCTCCAGTGTTTGCATGT
Found at i:11502 original size:16 final size:17
Alignment explanation
Indices: 11462--11505 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
11452 TGCCGTTTTC
*
11462 GGGTTCGGGTTTAAGTT
1 GGGTTCGGGTTAAAGTT
*
11479 GGGTTCGGGTTAAATTT
1 GGGTTCGGGTTAAAGTT
11496 GGG-TCGGGTT
1 GGGTTCGGGTT
11506 GATTCGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.11, C:0.07, G:0.43, T:0.39
Consensus pattern (17 bp):
GGGTTCGGGTTAAAGTT
Found at i:11517 original size:32 final size:32
Alignment explanation
Indices: 11479--11551 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
11469 GGTTTAAGTT
* * *
11479 GGGTTCGGGTTAAATTTGGGTCGGGTTGATTC
1 GGGTTCGGGTCAAATTTGGGTCAGGTTAATTC
* *
11511 GGGTTCGGGTCCATTTTGGGTCAGGTTAATTC
1 GGGTTCGGGTCAAATTTGGGTCAGGTTAATTC
*
11543 GGGGTCGGG
1 GGGTTCGGG
11552 CTCGGATTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.11, C:0.12, G:0.42, T:0.34
Consensus pattern (32 bp):
GGGTTCGGGTCAAATTTGGGTCAGGTTAATTC
Found at i:11518 original size:16 final size:16
Alignment explanation
Indices: 11459--11551 Score: 66
Period size: 16 Copynumber: 5.8 Consensus size: 16
11449 TCATGCCGTT
11459 TTCGGGTTCGGGTTTAA
1 TTCGGGTTCGGG-TTAA
11476 GTT-GGGTTCGGGTTAAA
1 -TTCGGGTTCGGGTT-AA
* *
11493 TTTGGG-TCGGGTTGA
1 TTCGGGTTCGGGTTAA
* *
11508 TTCGGGTTCGGGTCCAT
1 TTCGGGTTCGGGT-TAA
* *
11525 TTTGGG-TCAGGTTAA
1 TTCGGGTTCGGGTTAA
*
11540 TTCGGGGTCGGG
1 TTCGGGTTCGGG
11552 CTCGGATTGG
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
15 12 0.20
16 26 0.44
17 19 0.32
18 2 0.03
ACGTcount: A:0.11, C:0.12, G:0.41, T:0.37
Consensus pattern (16 bp):
TTCGGGTTCGGGTTAA
Found at i:11726 original size:20 final size:20
Alignment explanation
Indices: 11693--11731 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11683 CATGGATGAA
*
11693 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
11713 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
11732 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:11832 original size:16 final size:16
Alignment explanation
Indices: 11751--11838 Score: 63
Period size: 16 Copynumber: 5.5 Consensus size: 16
11741 TTTTTTCAGG
* *
11751 TTCGGATTCGGGTTTT
1 TTCGGGTTCAGGTTTT
* *
11767 TTCAGGTTTCA-GATTT
1 TTC-GGGTTCAGGTTTT
* *
11783 TTCGGGTTCTGATTTT
1 TTCGGGTTCAGGTTTT
* *
11799 TTCGGGTT-TGAGCTTT
1 TTCGGGTTCAG-GTTTT
11815 TTCGGGTTCAGGTTTT
1 TTCGGGTTCAGGTTTT
*
11831 TTTGGGTT
1 TTCGGGTT
11839 TGGGTTCGGA
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
15 7 0.12
16 43 0.77
17 6 0.11
ACGTcount: A:0.08, C:0.11, G:0.28, T:0.52
Consensus pattern (16 bp):
TTCGGGTTCAGGTTTT
Found at i:11838 original size:32 final size:32
Alignment explanation
Indices: 11751--11840 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
11741 TTTTTTCAGG
* * * *
11751 TTCGGATTCGGGTTTTTTCAGGTTTCAGATTT
1 TTCGGGTTCAGGTTTTTTCGGGTTTGAGATTT
* * *
11783 TTCGGGTTCTGATTTTTTCGGGTTTGAGCTTT
1 TTCGGGTTCAGGTTTTTTCGGGTTTGAGATTT
*
11815 TTCGGGTTCAGGTTTTTTTGGGTTTG
1 TTCGGGTTCAGGTTTTTTCGGGTTTG
11841 GGTTCGGACG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.08, C:0.11, G:0.29, T:0.52
Consensus pattern (32 bp):
TTCGGGTTCAGGTTTTTTCGGGTTTGAGATTT
Found at i:11844 original size:16 final size:16
Alignment explanation
Indices: 11760--11844 Score: 64
Period size: 16 Copynumber: 5.3 Consensus size: 16
11750 GTTCGGATTC
*
11760 GGGTTTTTTCAGGTTT
1 GGGTTTTTTCGGGTTT
** *
11776 CAGATTTTTCGGGTTCT
1 GGGTTTTTTCGGGTT-T
*
11793 -GATTTTTTCGGGTTT
1 GGGTTTTTTCGGGTTT
* * *
11808 GAGCTTTTTCGGGTTC
1 GGGTTTTTTCGGGTTT
* *
11824 AGGTTTTTTTGGGTTT
1 GGGTTTTTTCGGGTTT
11840 GGGTT
1 GGGTT
11845 CGGACGGGTT
Statistics
Matches: 50, Mismatches: 17, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
15 1 0.02
16 48 0.96
17 1 0.02
ACGTcount: A:0.07, C:0.09, G:0.31, T:0.53
Consensus pattern (16 bp):
GGGTTTTTTCGGGTTT
Found at i:20400 original size:31 final size:31
Alignment explanation
Indices: 20244--20415 Score: 200
Period size: 31 Copynumber: 5.5 Consensus size: 31
20234 TCCTTTTGTG
* * * **
20244 CACGTGGCATGCCACATGTCACTTTTTGAAA
1 CACGTGGCGTGACACGTGTCACTTTTTGGTA
*
20275 CATGTGGCGTGACACGTGTCACTTTTTGGTA
1 CACGTGGCGTGACACGTGTCACTTTTTGGTA
*
20306 AACGTGGCGTGACACGTGTCACTTTTTGGTA
1 CACGTGGCGTGACACGTGTCACTTTTTGGTA
* *
20337 CACGTGACGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGACACGTGTCACTTTTTGGTA
* * * *
20368 CACGTGGCGTGCCACATATCACTTTTTTGTA
1 CACGTGGCGTGACACGTGTCACTTTTTGGTA
* * *
20399 CACTTGGCATGCCACGT
1 CACGTGGCGTGACACGT
20416 CGGTCACCGT
Statistics
Matches: 121, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 121 1.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (31 bp):
CACGTGGCGTGACACGTGTCACTTTTTGGTA
Found at i:27082 original size:16 final size:16
Alignment explanation
Indices: 27061--27091 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27051 TTGAAAAATA
27061 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
27077 TTACTAAATTTTTAT
1 TTACTAAATATTTAT
27092 AATATGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:27955 original size:231 final size:230
Alignment explanation
Indices: 27554--28003 Score: 623
Period size: 231 Copynumber: 1.9 Consensus size: 230
27544 CTAAGGGGAT
* * * *
27554 ACATGTCAACCCTTAAACCATGCACGTACAGTCTACTAAACTCTACTGACGGTGTATTGTATAAT
1 ACATGTCAACCCTTAAACCACGCACGTACAGTCTACTAAACTCCACTAACAGTGTATTGTATAAT
*
27619 TTTTTTTGTAGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCACAACCGAGTTAA
66 TTTTTTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCACAACCGAGTTAA
* ** * * ** *
27684 GAAGTTGACACATACCTTATTTCATAATTAATTAGATATAA-ATTATTAATTCACATTCCCTAAG
131 GAAGTTGACACACACCCCATTTCACAATTAATTAGATATAAGAATATTAATAAACATTCCATAAG
*
27748 AGGATACATGTTAACCCTTAAACACGCGCTAGGAC
196 AGGATACATGTCAACCCTTAAACACGCGCTAGGAC
* ** * *
27783 ACATGTCAACCCTTAAACCCCGTGCGTGCAGTCTGCTAAACTCCACTAACAGTGTATTGTATAAT
1 ACATGTCAACCCTTAAACCACGCACGTACAGTCTACTAAACTCCACTAACAGTGTATTGTATAA-
* * * * * *
27848 TTTTGTTTTATATGATTATTATACAATATACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTT
65 TTTT-TTTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCACAACCGAGTT
*
27913 AAGAAGTTGACACACACCCCATTTCACAATTAATTAGATATAAGTAATATTAATAAATATTCCAT
129 AAGAAGTTGACACACACCCCATTTCACAATTAATTAGATATAAG-AATATTAATAAACATTCCAT
*
27978 AAGGGGATACATGTCAACCCTTAAAC
193 AAGAGGATACATGTCAACCCTTAAAC
28004 CCCGCACGTG
Statistics
Matches: 190, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
229 55 0.29
230 4 0.02
231 92 0.48
233 39 0.21
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (230 bp):
ACATGTCAACCCTTAAACCACGCACGTACAGTCTACTAAACTCCACTAACAGTGTATTGTATAAT
TTTTTTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCACAACCGAGTTAA
GAAGTTGACACACACCCCATTTCACAATTAATTAGATATAAGAATATTAATAAACATTCCATAAG
AGGATACATGTCAACCCTTAAACACGCGCTAGGAC
Found at i:28382 original size:192 final size:193
Alignment explanation
Indices: 27778--28468 Score: 816
Period size: 192 Copynumber: 3.5 Consensus size: 193
27768 AACACGCGCT
**
27778 AGGACACATGTCAACCCTTAAACCCCGTGCGTGCAGTCTGCTAAACTCCACTAACAGTGTATTGT
1 AGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTAACAGTGTATTGT
* *
27843 ATAATTTTTGTTTTATATGATTATTATACAATATACTGTCAGTGTAAATTTTGGACTCCATAAGC
66 ATAATTTTT-TTTTATAGGATTATTATAC-A-ATA----CAGTGTAAAATTTGGACTCCATAAGC
* * * *
27908 GGGTTAAGAAGTTGACACACACCCCATTTCACAATTAATTAGATATAAGTAATATTAATAAATAT
124 -GGTTAAGAAGTTGACACATACCCTATTTCATAATTAATTAGATATAA--AATATTAATACATAT
*
27973 TCCATAAG
186 TCCCTAAG
* * * * * *
27981 GGGATACATGTCAACCCTTAAACCCCGCACGTGCAGTTTGCTAAACTCTACTAACTGTGTATTGA
1 AGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTAACAGTGTATTGT
* * * * *
28046 ATAA-TTTTTCTTATAGGATTATTAATACACTGCCAGTATAAAATTTTGGACTCTATAAGCGAGT
66 ATAATTTTTTTTTATAGGATTATT-ATACAAT-ACAGTGTAAAA-TTTGGACTCCATAAGCG-GT
** * * * * ** * *
28110 TAAGAAGTTGACAGGTA-TCTCATTTCTTAATAAATTAAATATTTAACATGAATACATATTCCCT
127 TAAGAAGTTGACACATACCCT-ATTTCATAATTAATTAGATATAAAATATTAATACATATTCCCT
28174 AA-
191 AAG
* * * *
28176 AGGGACACATGTCAACCCTTAAATCCTGCACGTGCAGTCTGCTAAAATCCACTTAC-G-GTATTG
1 A-GGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTAACAGTGTATTG
* *
28239 TATAATTTTTTTTTATAGGATTATTATACAATACATTGTAAAATTTGAACTCCATAAGCAGGTTA
65 TATAATTTTTTTTTATAGGATTATTATACAATACAGTGTAAAATTTGGACTCCATAAGC-GGTTA
28304 AGAAGTTGACACATACCCTATTTCATAATTAATTAGATATAAAATATTAATACATATTCCCTAAG
129 AGAAGTTGACACATACCCTATTTCATAATTAATTAGATATAAAATATTAATACATATTCCCTAAG
* * *
28369 AGGACATATGTCAACCCTTAAACCCCGCGCGTGCAGTCTGCTAAACTCCACTGACAGTGTATTGT
1 AGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTAACAGTGTATTGT
* *
28434 ATAATTTTCGTTTTATATGATTATTATACAATACA
66 ATAATTTT-TTTTTATAGGATTATTATACAATACA
28469 CTGTTAGTGT
Statistics
Matches: 411, Mismatches: 64, Indels: 34
0.81 0.13 0.07
Matches are distributed among these distances:
192 117 0.28
193 13 0.03
194 31 0.08
195 43 0.10
196 65 0.16
197 10 0.02
198 48 0.12
200 1 0.00
201 14 0.03
202 8 0.02
203 61 0.15
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (193 bp):
AGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTAACAGTGTATTGT
ATAATTTTTTTTTATAGGATTATTATACAATACAGTGTAAAATTTGGACTCCATAAGCGGTTAAG
AAGTTGACACATACCCTATTTCATAATTAATTAGATATAAAATATTAATACATATTCCCTAAG
Done.