Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014876.1 Corchorus capsularis cultivar CVL-1 contig14897, 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: 46337
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:279 original size:22 final size:22
Alignment explanation
Indices: 251--454 Score: 139
Period size: 22 Copynumber: 9.2 Consensus size: 22
241 TGTCTCTATG
251 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
273 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
296 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
317 TGGTTACCAAAATTTCAT-AGTA
1 TGGTTATCAAAATTTCATAAG-A
*
339 TGGTTACCAAAATTTCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
* *
361 TGATTACCAAAATTTCAT-AGTA
1 TGGTTATCAAAATTTCATAAG-A
* *
383 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
405 TCAGGTTATTAAAATCTCTTAGGC
1 T--GGTTATCAAAATTTCATAAGA
** *
429 TGGTTATTGAAATTTCATAAGG
1 TGGTTATCAAAATTTCATAAGA
451 TGGT
1 TGGT
455 CAATTATCAC
Statistics
Matches: 148, Mismatches: 24, Indels: 20
0.77 0.12 0.10
Matches are distributed among these distances:
20 2 0.01
21 1 0.01
22 122 0.82
23 5 0.03
24 18 0.12
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:321 original size:44 final size:44
Alignment explanation
Indices: 251--402 Score: 182
Period size: 44 Copynumber: 3.5 Consensus size: 44
241 TGTCTCTATG
* * ** * *
251 TGGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCATGAGGA
1 TGGTTACCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT-AGTA
* *
296 -GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATAGTA
1 TGGTTACCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGTA
* *
339 TGGTTACCAAAATTTCATAATGTGATTACCAAAATTTCATAGTA
1 TGGTTACCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGTA
383 TGGTTACCAAAATTTCATAG
1 TGGTTACCAAAATTTCATAG
403 GATCAGGTTA
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
43 5 0.05
44 89 0.95
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (44 bp):
TGGTTACCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGTA
Found at i:328 original size:66 final size:66
Alignment explanation
Indices: 249--419 Score: 200
Period size: 66 Copynumber: 2.6 Consensus size: 66
239 CTTGTCTCTA
* * * * *
249 TGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCATA
1 TGTGGTTACCAAAATTTCATAAGATGGTTATTAAAATTTCATAAGGAGATTACCAAAATTCCATA
314 G
66 G
** * * *
315 TGTGGTTACCAAAATTTCAT-AGTATGGTTACCAAAATTTCATAATGTGATTACCAAAATTTCAT
1 TGTGGTTACCAAAATTTCATAAG-ATGGTTATTAAAATTTCATAAGGAGATTACCAAAATTCCAT
379 AG
65 AG
* *
381 TATGGTTACCAAAATTTCATAGGATCAGGTTATTAAAAT
1 TGTGGTTACCAAAATTTCATAAGAT--GGTTATTAAAAT
420 CTCTTAGGCT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
65 2 0.02
66 74 0.85
67 1 0.01
68 10 0.11
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (66 bp):
TGTGGTTACCAAAATTTCATAAGATGGTTATTAAAATTTCATAAGGAGATTACCAAAATTCCATA
G
Found at i:528 original size:22 final size:22
Alignment explanation
Indices: 496--550 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
486 AAGAGATTAT
*
496 CAAAATGTCATAGCGAGGTTAA
1 CAAAATTTCATAGCGAGGTTAA
* *
518 -AAGAATTTCATAGTGTGGTTAA
1 CAA-AATTTCATAGCGAGGTTAA
540 CAAAATTTCAT
1 CAAAATTTCAT
551 TAAATATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 2 0.07
22 24 0.86
23 2 0.07
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (22 bp):
CAAAATTTCATAGCGAGGTTAA
Found at i:615 original size:22 final size:22
Alignment explanation
Indices: 566--627 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
556 ATTTCATGGG
* *
566 GAGGTTATCAAAATTTTATAGT
1 GAGGTTATCAAAATCTCATAGT
*
588 GTGGTTATCAAAATCTCATA-T
1 GAGGTTATCAAAATCTCATAGT
609 GAAGGTTAT-AAAAGTCTCA
1 G-AGGTTATCAAAA-TCTCA
628 ATTTCATAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.18
22 28 0.82
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (22 bp):
GAGGTTATCAAAATCTCATAGT
Found at i:744 original size:22 final size:22
Alignment explanation
Indices: 644--873 Score: 78
Period size: 22 Copynumber: 10.5 Consensus size: 22
634 TAAGGAGTAC
* *
644 CAAAATTTGATAG-AAGGTTAT
1 CAAAATTTCATAGAAAGATTAT
* * **
665 C-AAATCTCATATAGTGATTAT
1 CAAAATTTCATAGAAAGATTAT
* **
686 CGAAATTTCATATAGATCGAATTAT
1 CAAAATTTC--ATAGAAAG-ATTAT
711 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAAAGATTAT
***
732 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAG-AAAGATTAT
* ** *
754 CAAAATTTCAAAGCGAGGTTAT
1 CAAAATTTCATAGAAAGATTAT
* * **
776 TAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-AAGATTAT
* ** * * *
798 CAGAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAGAAAGATTAT
* *
820 CAAAATTTTATA-AAGAGACTAT
1 CAAAATTTCATAGAA-AGATTAT
*
842 CAAAATTTCATA-AAGAGGTTAT
1 CAAAATTTCATAGAA-AGATTAT
*
864 CAAATTTTCA
1 CAAAATTTCA
874 AAATGTGATT
Statistics
Matches: 153, Mismatches: 45, Indels: 21
0.70 0.21 0.10
Matches are distributed among these distances:
20 8 0.05
21 22 0.14
22 104 0.68
23 2 0.01
24 5 0.03
25 12 0.08
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGAAAGATTAT
Found at i:799 original size:44 final size:44
Alignment explanation
Indices: 706--895 Score: 163
Period size: 44 Copynumber: 4.3 Consensus size: 44
696 TATAGATCGA
* * * *
706 ATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTTG
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-TG
* * *
750 -TTATCAAAATTTCAAAGCGAGGTTATTAAAATTACATAATGTG
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
* * * * * * * *
793 ATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAG
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
* * *
837 ACTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTG
1 ATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGTG
881 ATTA-CAAAAATTTCA
1 ATTATC-AAAATTTCA
896 TAATGGGATT
Statistics
Matches: 112, Mismatches: 30, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
43 15 0.13
44 96 0.86
45 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (44 bp):
ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
Found at i:1017 original size:19 final size:19
Alignment explanation
Indices: 980--1049 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
970 TTATGGAGTA
980 ATCAAAATTTCAAGAAGGAT
1 ATCAAAA-TTCAAGAAGGAT
* *
1000 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGAAGGAT
*
1019 ATCAAAATTTCATATGAAGGTT
1 ATCAAAA-TTCA-A-GAAGGAT
1041 ATCAAAATT
1 ATCAAAATT
1050 TCATTGTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.40
20 11 0.26
21 2 0.05
22 12 0.29
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.29
Consensus pattern (19 bp):
ATCAAAATTCAAGAAGGAT
Found at i:1046 original size:22 final size:22
Alignment explanation
Indices: 980--1557 Score: 179
Period size: 22 Copynumber: 26.6 Consensus size: 22
970 TTATGGAGTA
*
980 ATCAAAATTTCA-A-GAAGGAT
1 ATCAAAATTTCATATGAAGGTT
* * *
1000 ATCAAAA-TTC--AGGGAGGAT
1 ATCAAAATTTCATATGAAGGTT
1019 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
1041 ATCAAAATTTCAT-TGTATA-GTT
1 ATCAAAATTTCATATG-A-AGGTT
* * * *
1063 TTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
1085 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
1107 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
1129 AACAAAAATTT-ATAATG-AGGTT
1 ATC-AAAATTTCAT-ATGAAGGTT
** *
1151 ATCAAAAAATCATAGGGAA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
*
1173 ATCAAAATTT-GT-T----GTT
1 ATCAAAATTTCATATGAAGGTT
* * *
1189 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
1211 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* * *
1234 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
*
1257 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
1279 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
1301 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
1323 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * * *
1345 TTTAAATTTTCATAACGTA-GTT
1 ATCAAAATTTCAT-ATGAAGGTT
* *
1367 ATCAATATATT-ATATGGAGGTT
1 ATCAAAAT-TTCATATGAAGGTT
* * **
1389 ATCAATATCTCATAGTGTCGGTT
1 ATCAAAATTTCATA-TGAAGGTT
1412 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* * *
1435 -TCAAAA-TTCGTTAGGGAGGTT
1 ATCAAAATTTC-ATATGAAGGTT
* * *
1456 AACCAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
** * **
1478 AAAAAAAACTT-ATAAAAAGGTT
1 -ATCAAAATTTCATATGAAGGTT
* * * * **
1500 CTCGAAATTCCAT-GGTATCGTT
1 ATCAAAATTTCATATG-AAGGTT
*
1522 ATTAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
1544 ATCAAAATTTCATA
1 ATCAAAATTTCATA
1558 ATGGGATCAT
Statistics
Matches: 416, Mismatches: 97, Indels: 88
0.69 0.16 0.15
Matches are distributed among these distances:
16 12 0.03
17 1 0.00
18 1 0.00
19 16 0.04
20 10 0.02
21 29 0.07
22 255 0.61
23 91 0.22
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:17331 original size:40 final size:40
Alignment explanation
Indices: 17286--17366 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
17276 TGTGATGCCC
17286 TGCCACCAAAAGTTATTTCAACTCTTGTTTGTTCACATAT
1 TGCCACCAAAAGTTATTTCAACTCTTGTTTGTTCACATAT
*
17326 TGCCACCAAAAGTTATTTCAACTCTTTTTTGTTCACATAT
1 TGCCACCAAAAGTTATTTCAACTCTTGTTTGTTCACATAT
17366 T
1 T
17367 TTCTAGGCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (40 bp):
TGCCACCAAAAGTTATTTCAACTCTTGTTTGTTCACATAT
Found at i:23720 original size:1 final size:1
Alignment explanation
Indices: 23714--23752 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
23704 GACATTAGGG
23714 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23753 TCAAACAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26963 original size:2 final size:2
Alignment explanation
Indices: 26956--26992 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
26946 TTCTTATTCT
*
26956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26993 TGTGGCTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.