Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006295.1 Corchorus capsularis cultivar CVL-1 contig06315, 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: 45261
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:254 original size:78 final size:78
Alignment explanation
Indices: 11--255 Score: 348
Period size: 84 Copynumber: 3.1 Consensus size: 78
1 TTTTTTAAAT
** *
11 TAAAATAGTAAAATTTTAAAATATAATAGTTATAAGGATATTAAATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
76 -TTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
88 TAAAATAGTAAAATGGTAAAATATAATAGTCATAAGGATTCACTCATTATATTTAATTATATAAA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGG----A-T-ATTATATTTAATTATATAAA
*
153 AATAGAGTTTTTAGTTGAA
60 AATAGAGTTTTTAGTTGAG
* * * *
172 TAAAATAGTAACATGGTAAAATAAAATAGTTATGAGGATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
237 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
250 TAAAAT
1 TAAAAT
256 TATAAAAACC
Statistics
Matches: 150, Mismatches: 11, Indels: 13
0.86 0.06 0.07
Matches are distributed among these distances:
77 34 0.23
78 43 0.29
79 1 0.01
80 1 0.01
81 1 0.01
82 1 0.01
83 25 0.17
84 44 0.29
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:5099 original size:6 final size:6
Alignment explanation
Indices: 5088--5114 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5078 ATAATATATT
5088 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
5115 GCCTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:7781 original size:31 final size:32
Alignment explanation
Indices: 7746--7806 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
7736 ATGTTTTTCG
7746 ATTGTACCCTTATTT-TTAAAACATATTTCCA
1 ATTGTACCCTTATTTCTTAAAACATATTTCCA
* *
7777 ATTGTACCCTTTTTTCTTAAAACGTATTTC
1 ATTGTACCCTTATTTCTTAAAACATATTTC
7807 TAAATTGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (32 bp):
ATTGTACCCTTATTTCTTAAAACATATTTCCA
Found at i:8205 original size:19 final size:20
Alignment explanation
Indices: 8178--8215 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
8168 TACTATTATT
8178 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
8198 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
8216 AATGTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:8442 original size:22 final size:22
Alignment explanation
Indices: 8390--8509 Score: 120
Period size: 22 Copynumber: 5.5 Consensus size: 22
8380 TGGTTATTAT
* *
8390 AATTTCATGAG-GAGGTTAACAA
1 AATTTCAT-AGTGTGGTTACCAA
* * * *
8412 AACTCCATAGTGTGCTTATCAA
1 AATTTCATAGTGTGGTTACCAA
*
8434 AATTTCATA-TG-GAAGTTATCAA
1 AATTTCATAGTGTG--GTTACCAA
*
8456 AATTTTATAGTGTGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
8478 AATTTCATAGTGTGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
8500 AATTTCATAG
1 AATTTCATAG
8510 GATCAGGTTA
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
20 1 0.01
21 4 0.05
22 74 0.90
23 2 0.02
24 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTACCAA
Found at i:8543 original size:22 final size:22
Alignment explanation
Indices: 8380--8563 Score: 117
Period size: 22 Copynumber: 8.3 Consensus size: 22
8370 TGTCTCTATG
*
8380 TGGTTATTATAATTTCATGAGGA
1 TGGTTATTAAAATTTCAT-AGGA
** * *
8403 -GGTTAACAAAACTCCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
* *
8424 TGCTTATCAAAATTTCATATGGA
1 TGGTTATTAAAATTTCATA-GGA
* * *
8447 -AGTTATCAAAATTTTATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
**
8468 TGGTTACCAAAATTTCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
**
8490 TGGTTACCAAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGA
* *
8512 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATTAAAATTTCATAGGA
*
8536 TGGTTATTGAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGA
8558 TGGTTA
1 TGGTTA
8564 ATTATCACAA
Statistics
Matches: 130, Mismatches: 22, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
21 4 0.03
22 107 0.82
23 1 0.01
24 18 0.14
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGA
Found at i:8624 original size:22 final size:22
Alignment explanation
Indices: 8599--9018 Score: 167
Period size: 22 Copynumber: 18.9 Consensus size: 22
8589 ATCAAAGAGA
*
8599 TTATCAAAATGTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
*
8621 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
8643 TTAACAAAATTTCATTAG-AAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
8665 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* * *
8687 TTATCAAAATTTTATAGTGTGAT
1 TTATCAAAATTTCATAGTGAG-G
8710 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* * *
8732 TTAT-AAAAGTCTCAATTTAATAAGG
1 TTATCAAAA-TTTC-A--TAGTGAGG
* * * * *
8757 AGTACCGAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * ***
8779 TTATC-AAATCTCATAGAGTTA
1 TTATCAAAATTTCATAGTGAGG
* *
8800 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
*
8824 ATTATCAAAATTT-ATA-TGAAGA
1 -TTATCAAAATTTCATAGTG-AGG
**
8846 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* **
8868 TTATCAAAATTTCAAAGCAAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
8890 TTATCAATATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
8912 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * ** **
8934 TCAACAAAATTTTGTAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
8956 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
8978 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
9000 TTA-CAAAAATTTCATAGTG
1 TTATC-AAAATTTCATAGTG
9019 GTATTTCTGG
Statistics
Matches: 292, Mismatches: 82, Indels: 48
0.69 0.19 0.11
Matches are distributed among these distances:
20 9 0.03
21 30 0.10
22 196 0.67
23 28 0.10
24 4 0.01
25 17 0.06
26 5 0.02
27 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:9232 original size:22 final size:22
Alignment explanation
Indices: 9097--9407 Score: 155
Period size: 22 Copynumber: 14.4 Consensus size: 22
9087 TTATGGAGTA
9097 ATCAAAATTTC--AGGGAGGA-T
1 ATCAAAATTTCATAGGGA-GATT
* * * *
9117 ATCAAAATTCCATACGAAGGTT
1 ATCAAAATTTCATAGGGAGATT
**
9139 ATCAAAATTTCATAGTTTAG-TT
1 ATCAAAATTTCATAG-GGAGATT
* *
9161 TTCAAATTTTCATAAGAGG-G-TT
1 ATCAAAATTTCAT-AG-GGAGATT
* *
9183 ATCAAAATTTCATA-GTATG-TAG
1 ATCAAAATTTCATAGGGA-GAT-T
9205 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGATT
* ** *
9227 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGATT
** *
9249 ATCAAAAGATCATAGGGAGCTT
1 ATCAAAATTTCATAGGGAGATT
*
9271 ATCAAAATTT--T---TAG-TT
1 ATCAAAATTTCATAGGGAGATT
* * * *
9287 ATCAAGATTTCATAAGAAAATT
1 ATCAAAATTTCATAGGGAGATT
* * *
9309 ATCAAATTTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGA-GATT
* *
9332 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGGAGA-TT
* * *
9355 ATCAAAATTTTATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGATT
* * *
9377 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGATT
9399 ATCAAAATT
1 ATCAAAATT
9408 CAGAGTGTAA
Statistics
Matches: 219, Mismatches: 54, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 1 0.00
19 1 0.00
20 11 0.05
21 5 0.02
22 144 0.66
23 44 0.20
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGATT
Found at i:9335 original size:23 final size:23
Alignment explanation
Indices: 9307--9391 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
9297 CATAAGAAAA
*
9307 TTATCAAATTTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
9330 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
*
9353 TTATCAAAATTTTATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* *
9375 TTATCACAATTTCATAG
1 TTATCAAAATTTTATAG
9392 TGTGATTATC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
22 15 0.28
23 39 0.72
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:9414 original size:21 final size:22
Alignment explanation
Indices: 9375--9420 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
9365 TATAGCGAGG
* * *
9375 TTATCACAATTTCATAGTGTGA
1 TTATCACAAATTCAGAGTGTAA
9397 TTATCA-AAATTCAGAGTGTAA
1 TTATCACAAATTCAGAGTGTAA
9418 TTA
1 TTA
9421 CTAACAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (22 bp):
TTATCACAAATTCAGAGTGTAA
Found at i:9606 original size:22 final size:22
Alignment explanation
Indices: 9489--9685 Score: 89
Period size: 22 Copynumber: 8.9 Consensus size: 22
9479 TATCATATGG
* * *
9489 AGGTTATCAACATCTCATAATGT
1 AGGTTATCAAAATTTCATAA-GA
* * *
9512 TGGTTATCAAGATTTCATTAGGA
1 AGGTTATCAAAATTTCA-TAAGA
**
9535 A-GTTATCAAAATTTCATATTA
1 AGGTTATCAAAATTTCATAAGA
* *
9556 AGGTCT-TCAAAA-TTCCTTAGA
1 AGGT-TATCAAAATTTCATAAGA
*
9577 GAGGTTAACAAAATTTCATAAGA
1 -AGGTTATCAAAATTTCATAAGA
** *
9600 AGGTTAAAAAAAATTT-ATAAAA
1 AGGTT-ATCAAAATTTCATAAGA
* * * *
9622 AGATTCTCGAAATTCCAT-AGTA
1 AGGTTATCAAAATTTCATAAG-A
** * *
9644 TCGTTATTAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAAGA
* *
9666 AGATTATTAAAATTTCATAA
1 AGGTTATCAAAATTTCATAA
9686 TGGGATCATA
Statistics
Matches: 127, Mismatches: 37, Indels: 21
0.69 0.20 0.11
Matches are distributed among these distances:
21 16 0.13
22 76 0.60
23 33 0.26
24 2 0.02
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAAGA
Found at i:44843 original size:2 final size:2
Alignment explanation
Indices: 44805--44830 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44795 TCAAGTCTTA
44805 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
44831 TAATTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.