Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005492.1 Corchorus capsularis cultivar CVL-1 contig05510, 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: 54696
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1610 original size:30 final size:30
Alignment explanation
Indices: 1574--1634 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
1564 AAACAACTAC
1574 AATTTCTAGCCTTCTATT-TATGATAAATTA
1 AATTTCTAGCCTTCTATTAT-TGATAAATTA
1604 AATTTCTAGCCTTCTATTATTGATAAATTA
1 AATTTCTAGCCTTCTATTATTGATAAATTA
1634 A
1 A
1635 GTTATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (30 bp):
AATTTCTAGCCTTCTATTATTGATAAATTA
Found at i:6012 original size:2 final size:2
Alignment explanation
Indices: 6000--6056 Score: 62
Period size: 2 Copynumber: 28.5 Consensus size: 2
5990 GTTTAACACC
* * * *
6000 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AA AC ACC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
6043 AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A
6057 AGATGTGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
1 1 0.02
2 45 0.94
3 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:23006 original size:425 final size:418
Alignment explanation
Indices: 22077--23088 Score: 1527
Period size: 419 Copynumber: 2.4 Consensus size: 418
22067 GTAACCTGGG
*
22077 CTCGTCGTTACGAGGCCCACCAGTATGGCCCATATATACCTGTCGGATACCAATCTGAACCCAAA
1 CTCGTCGTTACGAGGCCCACCAGTGTGGCCCATATATACCTGTCGGATACCAATCTGAACCCAAA
*
22142 AGCTTAAGCCTAAATGTTCTTAGATCTTTCAGGTATATATGCCACTTTTACAG-CTCATCCCTTT
66 AGCTTAAGCCTAAATGTTCTTGGATCTTTCAGGTATATATGCCACTTTTACAGTC-CATCCCTTT
22206 GTGATGTGTGATGCGACACTCACATGTGAACTCCAACAAACTCCCCCGTTCACATGTACAGCTCT
130 GTGATGTGTGATGCGACACTCACATGTGAACTCCAACAAACTCCCCCGTTCACATGTACAGCTCT
* *
22271 CCCCCGTGCGGTTAACCCGATATTTCTTGGATAACTAGTTAAGTGGCCCGCTTTTTTTGGACTTG
195 CCCCCGTGCGGCTAACCCGATATTTCTTGGATAACCAGTTAAGTGGCCCGCTTTTTTTGGACTTG
* *
22336 TTCACACTTAACCACACCCTTCACCATCTGTGCACCCAATTTTTTTTTCTCCAGAAATACCACAC
260 TTCACACTTAACCACACCCTGCACCATCTGTGCACCAAATTTTTTTTTCTCCAGAAATACCACAC
*
22401 CATTGTGTTTTTTTTATAGCACAGCCGCACCACCAAACTTCAACTGAACCTAGCCCTGATACCAT
325 CATTGTGTTTTTTTTATAGCACAGCCGCACCACCAAACTCCAACTGAACCTAGCCCTGATACCAT
* *
22466 TTGTAAGAGAGAGAAAGAGAGCAACCCGGT
390 TTGTAAGAGAGAG-AAGAAACCAACCCGGT
* * * * *
22496 CTTGTCGTTACGAGGCCCACCAATGTGGCCCATATATACCTATGGGATACCAATATGAACCCAAA
1 CTCGTCGTTACGAGGCCCACCAGTGTGGCCCATATATACCTGTCGGATACCAATCTGAACCCAAA
** * * *
22561 AGCTTAAGCCTATGTGTTCTTGGATCTTTCAGATATATATGCCACTTTTATAGTCCATCCCTATG
66 AGCTTAAGCCTAAATGTTCTTGGATCTTTCAGGTATATATGCCACTTTTACAGTCCATCCCTTTG
22626 TGATGTAG-GATGCGACACTCACATGTGAACTCCAACAAACTCCCCCGTTCACATGTGACAGCTC
131 TGATGT-GTGATGCGACACTCACATGTGAACTCCAACAAACTCCCCCGTTCACATGT-ACAGCTC
**
22690 TCCCCCGTGCGGCTAACCCGATATTTCTTGGATAACCAGTTAAGTGGCCCG-TTCTTTTTGGGTT
194 TCCCCCGTGCGGCTAACCCGATATTTCTTGGATAACCAGTTAAGTGGCCCGCTT-TTTTTGGACT
*
22754 TGTTCACA-TGTAACCACATCCTGCACCATCTGTGCACCAAATTGTTTTTTTTTCTCCAGAAATA
258 TGTTCACACT-TAACCACACCCTGCACCATCTGTGCACCAAA---TTTTTTTTTCTCCAGAAATA
* * * * *
22818 TCACACCATTGTATTTTTTTTTTTTTTTTAGTACAGCCGCACCACCGAACTCCAA-TCGAACCTA
319 CCACACCATTG------TGTTTTTTTTATAGCACAGCCGCACCACCAAACTCCAACT-GAACCTA
**
22882 GTTCTGATACCATTTGT-AG-GAGAG-AGAAACCAACCCGGT
377 GCCCTGATACCATTTGTAAGAGAGAGAAGAAACCAACCCGGT
*
22921 CTCGTCGTTACGAGGCCCACCAGTGTGGCCCATATATACCTGTCGGATACCAATCGGAACCCAAA
1 CTCGTCGTTACGAGGCCCACCAGTGTGGCCCATATATACCTGTCGGATACCAATCTGAACCCAAA
* *
22986 AGTTTAAGCCTAAATGTTCTTGGATCTTTCAGGTATATATGCCACTTCTACAGTCCATCCCTTTG
66 AGCTTAAGCCTAAATGTTCTTGGATCTTTCAGGTATATATGCCACTTTTACAGTCCATCCCTTTG
*
23051 TGATGTGTGATGCGACACTCACATGTGAACTCTAACAA
131 TGATGTGTGATGCGACACTCACATGTGAACTCCAACAA
23089 TACCATATCC
Statistics
Matches: 534, Mismatches: 43, Indels: 26
0.89 0.07 0.04
Matches are distributed among these distances:
419 173 0.32
420 102 0.19
423 30 0.06
424 1 0.00
425 165 0.31
427 5 0.01
428 3 0.01
429 55 0.10
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (418 bp):
CTCGTCGTTACGAGGCCCACCAGTGTGGCCCATATATACCTGTCGGATACCAATCTGAACCCAAA
AGCTTAAGCCTAAATGTTCTTGGATCTTTCAGGTATATATGCCACTTTTACAGTCCATCCCTTTG
TGATGTGTGATGCGACACTCACATGTGAACTCCAACAAACTCCCCCGTTCACATGTACAGCTCTC
CCCCGTGCGGCTAACCCGATATTTCTTGGATAACCAGTTAAGTGGCCCGCTTTTTTTGGACTTGT
TCACACTTAACCACACCCTGCACCATCTGTGCACCAAATTTTTTTTTCTCCAGAAATACCACACC
ATTGTGTTTTTTTTATAGCACAGCCGCACCACCAAACTCCAACTGAACCTAGCCCTGATACCATT
TGTAAGAGAGAGAAGAAACCAACCCGGT
Found at i:32141 original size:41 final size:41
Alignment explanation
Indices: 32082--32159 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
32072 TTTATAACTA
*
32082 GGGGCTAAACCTGGATTTAATTTCTTACCTTAATTATCAGG
1 GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATCAGG
* *
32123 GGGGCTAAACCTGAATTTAATTTGTTTCCTTAATTAT
1 GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTAT
32160 TTAGGAGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (41 bp):
GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATCAGG
Found at i:34528 original size:29 final size:30
Alignment explanation
Indices: 34478--34543 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
34468 TTGCATAAAA
*
34478 ACAGAATT-GAACTAAGCAAAAACAGAATT
1 ACAGAATTAGAACTAAACAAAAACAGAATT
*
34507 ACAGAATTAGAATTAAAC-AAAACAGAATT
1 ACAGAATTAGAACTAAACAAAAACAGAATT
34536 ACA-AATTA
1 ACAGAATTA
34544 AGCATCAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 5 0.15
29 22 0.65
30 7 0.21
ACGTcount: A:0.58, C:0.12, G:0.11, T:0.20
Consensus pattern (30 bp):
ACAGAATTAGAACTAAACAAAAACAGAATT
Found at i:34553 original size:29 final size:28
Alignment explanation
Indices: 34496--34580 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 28
34486 GAACTAAGCA
* *
34496 AAAACAGAATTACAGAATTAGAATTAAAC
1 AAAACAGAATTACA-AATTAGCATCAAAC
34525 AAAACAGAATTACAAATTAAGCATCAAAC
1 AAAACAGAATTACAAATT-AGCATCAAAC
34554 -AAACAG---TACCAAATTTAGCATCAAAC
1 AAAACAGAATTA-CAAA-TTAGCATCAAAC
34580 A
1 A
34581 GTAGCAAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.04
26 14 0.28
27 2 0.04
28 10 0.20
29 22 0.44
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.19
Consensus pattern (28 bp):
AAAACAGAATTACAAATTAGCATCAAAC
Found at i:34581 original size:22 final size:22
Alignment explanation
Indices: 34553--34595 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34543 AAGCATCAAA
*
34553 CAAACAGTACCAAATTTAGCAT
1 CAAACAGTACCAAATTAAGCAT
*
34575 CAAACAGTAGCAAATTAAGCA
1 CAAACAGTACCAAATTAAGCA
34596 AAATAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.21, G:0.12, T:0.19
Consensus pattern (22 bp):
CAAACAGTACCAAATTAAGCAT
Found at i:35378 original size:23 final size:21
Alignment explanation
Indices: 35337--35378 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
35327 TTGGAGATTT
*
35337 ATTGAAGATATTTTGAAGATC
1 ATTGAAGATATTTTCAAGATC
35358 ATTGAAGAATTATTTTCAAGA
1 ATTGAAG-A-TATTTTCAAGA
35379 AGCAAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (21 bp):
ATTGAAGATATTTTCAAGATC
Found at i:42412 original size:54 final size:55
Alignment explanation
Indices: 42302--42413 Score: 201
Period size: 54 Copynumber: 2.1 Consensus size: 55
42292 AGAAGAAAGA
42302 GAAGAAGTCATATGGTCAAAAATATTTCAAACACTTAATTAATATATACTTAATT
1 GAAGAAGTCATATGGTCAAAAATATTTCAAACACTTAATTAATATATACTTAATT
42357 GAAGAAGTCATATGGTC-AAAA-ATTTCAAACACTTTAATTAATATATACTTAATT
1 GAAGAAGTCATATGGTCAAAAATATTTCAAACAC-TTAATTAATATATACTTAATT
42411 GAA
1 GAA
42414 AGTAGTTGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
53 11 0.20
54 28 0.50
55 17 0.30
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.34
Consensus pattern (55 bp):
GAAGAAGTCATATGGTCAAAAATATTTCAAACACTTAATTAATATATACTTAATT
Found at i:52014 original size:90 final size:91
Alignment explanation
Indices: 51781--52030 Score: 340
Period size: 91 Copynumber: 2.8 Consensus size: 91
51771 GTTGTGGCAA
* * *
51781 AGACCTTTTATGTTAAAAATTGCGGCATAAAATAGAACAAGTCCACTTTCTGACTTGGGTTCGAA
1 AGACCTTTTATGTTGAAAATTGCGGCATAAAATAGAACGAGTCCACTTTCTGCCTTGGGTTCGAA
*
51846 CTTCAAGGGCAGAAAGGATTTTGCAT
66 CTTCAAGGGCAGAAAGGATTTTGCAC
* * * * * * * *
51872 AGACCTTTAAGGTTGAAAGTTGCGGCATAAACTAGAACGAGTTCATTTTCTGCCTTGGATTCAAA
1 AGACCTTTTATGTTGAAAATTGCGGCATAAAATAGAACGAGTCCACTTTCTGCCTTGGGTTCGAA
*
51937 CTTCAAGGGCGGAAAGGATTTTGCAC
66 CTTCAAGGGCAGAAAGGATTTTGCAC
** * *
51963 AGA-CTTTTATGTTGAATTTTACGGCATAAAATAGAACGAGTCCAGTTTCTGCCTTGGGTTCGAA
1 AGACCTTTTATGTTGAAAATTGCGGCATAAAATAGAACGAGTCCACTTTCTGCCTTGGGTTCGAA
52027 CTTC
66 CTTC
52031 TCCTTGTTGA
Statistics
Matches: 136, Mismatches: 23, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
90 55 0.40
91 81 0.60
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (91 bp):
AGACCTTTTATGTTGAAAATTGCGGCATAAAATAGAACGAGTCCACTTTCTGCCTTGGGTTCGAA
CTTCAAGGGCAGAAAGGATTTTGCAC
Done.