Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006415.1 Corchorus olitorius cultivar O-4 contig06440, 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: 1707
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Found at i:266 original size:29 final size:28
Alignment explanation
Indices: 225--284 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
215 GATTCCAAAA
225 AAAAGTTTATAAAT-TTTTCATTAAACTT
1 AAAAGTTTATAAATATTTTC-TTAAACTT
* *
253 AAAAGCTTTTTAAATAGTTTTCTTAAATTT
1 AAAAG-TTTATAAATA-TTTTCTTAAACTT
283 AA
1 AA
285 TCAATCACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 8 0.30
30 9 0.33
31 5 0.19
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (28 bp):
AAAAGTTTATAAATATTTTCTTAAACTT
Found at i:329 original size:86 final size:86
Alignment explanation
Indices: 231--396 Score: 280
Period size: 86 Copynumber: 1.9 Consensus size: 86
221 AAAAAAAAGT
*
231 TTATAAATTTTTCATTAAACTTAA-AAGCTTTTTAAATAGTTTTCTTAAATTTAATCAATCACCT
1 TTATAAATTTTTCATTAAACTTAACAA-CCTTTTAAATAGTTTTCTTAAATTTAATCAATCACCT
295 CGTTTAAAATTTTTTGGTAAGC
65 CGTTTAAAATTTTTTGGTAAGC
* *
317 TTATAAATTTTTCATTAAACTTAACAACCTTTTAAATAGTTTTCTTAAATTTATTTAATCACCTC
1 TTATAAATTTTTCATTAAACTTAACAACCTTTTAAATAGTTTTCTTAAATTTAATCAATCACCTC
*
382 GTTTAAGATTTTTTG
66 GTTTAAAATTTTTTG
397 TGATCTTATT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
86 73 0.97
87 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (86 bp):
TTATAAATTTTTCATTAAACTTAACAACCTTTTAAATAGTTTTCTTAAATTTAATCAATCACCTC
GTTTAAAATTTTTTGGTAAGC
Found at i:483 original size:20 final size:21
Alignment explanation
Indices: 460--503 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
450 CCTTGTAAGA
460 TTTATAGTTAA-CTTATGAA-T
1 TTTATAG-TAACCTTATGAAGT
480 TTTATAGTAACCTTATGAAGT
1 TTTATAGTAACCTTATGAAGT
501 TTT
1 TTT
504 TTTTAGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.68
21 4 0.18
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (21 bp):
TTTATAGTAACCTTATGAAGT
Found at i:510 original size:23 final size:23
Alignment explanation
Indices: 479--528 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
469 AACTTATGAA
479 TTTTATAGTAACCTTA-TGAAGTT
1 TTTTATAGTAACCTTATTG-AGTT
* *
502 TTTTTTAGTAACTTTATTGAGTT
1 TTTTATAGTAACCTTATTGAGTT
525 TTTT
1 TTTT
529 CAGAAATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (23 bp):
TTTTATAGTAACCTTATTGAGTT
Found at i:823 original size:22 final size:22
Alignment explanation
Indices: 798--839 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
788 TTTTAAGCAA
798 CCTTACTA-AATGTTTTAGTAAC
1 CCTTACTACAAT-TTTTAGTAAC
*
820 CCTTATTACAATTTTTAGTA
1 CCTTACTACAATTTTTAGTA
840 GGCTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (22 bp):
CCTTACTACAATTTTTAGTAAC
Found at i:936 original size:20 final size:21
Alignment explanation
Indices: 913--956 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
903 CCTTGTAAGA
913 TTTATAGTTAA-CTTATGAA-T
1 TTTATAG-TAACCTTATGAAGT
933 TTTATAGTAACCTTATGAAGT
1 TTTATAGTAACCTTATGAAGT
954 TTT
1 TTT
957 TTTTGAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.68
21 4 0.18
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (21 bp):
TTTATAGTAACCTTATGAAGT
Found at i:1154 original size:21 final size:21
Alignment explanation
Indices: 1103--1156 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1093 TAATTAAACT
*
1103 TTTCAATAACCTCACTAAGCA
1 TTTCAATAATCTCACTAAGCA
1124 TTTCAATAATCTCACTAAGCA
1 TTTCAATAATCTCACTAAGCA
1145 TTTCAATAATCT
1 TTTCAATAATCT
1157 TATATGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (21 bp):
TTTCAATAATCTCACTAAGCA
Found at i:1306 original size:21 final size:22
Alignment explanation
Indices: 1277--1333 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1267 GTAACTTACT
1277 AAATGTTTTAGTAACCCTTATTA
1 AAAT-TTTTAGTAACCCTTATTA
* ** *
1300 CAATTTTTAGTAGGCTTTATTA
1 AAATTTTTAGTAACCCTTATTA
1322 AAA-TTTTAGTAA
1 AAATTTTTAGTAA
1334 TCTTGTAAGC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 8 0.29
22 17 0.61
23 3 0.11
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (22 bp):
AAATTTTTAGTAACCCTTATTA
Found at i:1382 original size:21 final size:21
Alignment explanation
Indices: 1358--1431 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
1348 TATAATAATC
*
1358 TTAAACTCTTTTAGTGA-TTTA
1 TTAAACT-TTTTAGTAACTTTA
1379 TTAAACTTTTTAGTAACTTTA
1 TTAAACTTTTTAGTAACTTTA
** *
1400 TTAAGTTTTTTAATAAAC-TTA
1 TTAAACTTTTTAGT-AACTTTA
1421 TTAAACTTTTT
1 TTAAACTTTTT
1432 TGTGATCTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 8 0.18
21 34 0.76
22 3 0.07
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (21 bp):
TTAAACTTTTTAGTAACTTTA
Found at i:1441 original size:21 final size:21
Alignment explanation
Indices: 1358--1453 Score: 63
Period size: 21 Copynumber: 4.6 Consensus size: 21
1348 TATAATAATC
* *
1358 TTAAACTCTTTTAGTG-ATTTA
1 TTAAACT-TTTTTGTGAACTTA
*
1379 TTAAACTTTTTAGT-AACTTTA
1 TTAAACTTTTTTGTGAAC-TTA
* * *
1400 TT-AAGTTTTTTAATAAACTTA
1 TTAAACTTTTTT-GTGAACTTA
*
1421 TTAAACTTTTTTGTGATCTTA
1 TTAAACTTTTTTGTGAACTTA
**
1442 TTACGCTTTTTT
1 TTAAACTTTTTT
1454 TGTAACATTG
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
20 15 0.25
21 34 0.57
22 11 0.18
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.55
Consensus pattern (21 bp):
TTAAACTTTTTTGTGAACTTA
Found at i:1452 original size:63 final size:63
Alignment explanation
Indices: 1358--1502 Score: 161
Period size: 63 Copynumber: 2.3 Consensus size: 63
1348 TATAATAATC
*
1358 TTAAACTCTTTTAGTGATTTATTAAAC-TTTTTAGTAACTTTATTAAGTTTTTTAATAAAC-TTA
1 TTAAACTCTTTTAGTGATTTATTAAACTTTTTTAGTAACATTATTAAG-TTTTTAAT-AACTTTA
* ** * *
1421 TTAAACT-TTTTTGTGATCTTATTACGCTTTTTTTGTAACATTGTTAAGTTTTTAATAACTTTA
1 TTAAACTCTTTTAGTGAT-TTATTAAACTTTTTTAGTAACATTATTAAGTTTTTAATAACTTTA
1484 TTAAGACTGCTTTGTAGTG
1 TTAA-ACT-CTTT-TAGTG
1503 TGTTAAGTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
62 12 0.18
63 29 0.43
64 20 0.29
66 3 0.04
67 4 0.06
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.52
Consensus pattern (63 bp):
TTAAACTCTTTTAGTGATTTATTAAACTTTTTTAGTAACATTATTAAGTTTTTAATAACTTTA
Found at i:1656 original size:21 final size:20
Alignment explanation
Indices: 1618--1667 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
1608 TTTCAATATA
1618 TAACTTAGTAAGCATTTTAG
1 TAACTTAGTAAGCATTTTAG
* *
1638 TAACTTTGTTAAGCTTTTTAG
1 TAACTTAG-TAAGCATTTTAG
1659 TAACCTTAG
1 TAA-CTTAG
1668 AAAGTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 14 0.56
22 4 0.16
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (20 bp):
TAACTTAGTAAGCATTTTAG
Done.