Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020328.1 Corchorus olitorius cultivar O-4 contig20361, 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: 70625
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1312 original size:31 final size:31
Alignment explanation
Indices: 1277--1413 Score: 148
Period size: 31 Copynumber: 4.4 Consensus size: 31
1267 TTTGTGCACG
**
1277 TGGCATGCCACGTGTCACTTTTTGAAACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
*
1308 TGGCATGCCACGTGTCACTTTTGGGTACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
* ** * *
1339 TGGCGTGATACGTGTCACCTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
* * * * * *
1370 TGGCGTGCCACATGTCGCTTTTTTGTATACG
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
1401 TGGCATGCCACGT
1 TGGCATGCCACGT
1414 CGGACACCGT
Statistics
Matches: 88, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGGTACACA
Found at i:25975 original size:135 final size:123
Alignment explanation
Indices: 25739--25997 Score: 338
Period size: 135 Copynumber: 2.0 Consensus size: 123
25729 CATTGTTTAA
* * *
25739 ACTTTTATACTTTTACTCAATTAAAAACTCTATTTTTATTTAATTGAATCTAATATCTTTATAAT
1 ACTTTTACACTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
* * *
25804 TTTTACCATTTTTCTATTTTAATTAAAAAATTTATATATATTAGAATTATTTAAATAT
66 TTTTAACATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTATTTAAATAT
*
25862 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTATTTAATTAAATCTAATATCCTTA
1 ACTTTTACACTTTTACTCAACTAAAAACTCTA---TT-TTTATTTAATTAAATCTAATAT-CTT-
*
25927 TACATATTTTATTTTTAACATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTA
60 T--ATA----ATTTTTAACATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTATTTA
25992 AATAT
119 AATAT
25997 A
1 A
25998 TTTCTTAAAT
Statistics
Matches: 116, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
123 29 0.25
126 2 0.02
127 21 0.18
128 3 0.03
129 1 0.01
131 3 0.03
135 57 0.49
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (123 bp):
ACTTTTACACTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
TTTTAACATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTATTTAAATAT
Found at i:26019 original size:14 final size:13
Alignment explanation
Indices: 25983--26021 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
25973 TATATATTAG
25983 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
25996 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
26010 AATTTTTTAAAT
1 AATTTTTTAAAT
26022 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:26287 original size:15 final size:15
Alignment explanation
Indices: 26241--26288 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
26231 TTCATCATTT
26241 TTTAAAA-CTAATTAA
1 TTTAAAATCTAATT-A
* *
26256 GTTTAAAATTTATTTA
1 -TTTAAAATCTAATTA
26272 TTTAAAATCTAATTA
1 TTTAAAATCTAATTA
26287 TT
1 TT
26289 ATTATTGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 15 0.56
16 8 0.30
17 4 0.15
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (15 bp):
TTTAAAATCTAATTA
Found at i:26973 original size:31 final size:31
Alignment explanation
Indices: 26938--26997 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
26928 TGTGTATATA
**
26938 TTCATGATAATTAAGTATATTTTCTTAATTT
1 TTCATGATAAAAAAGTATATTTTCTTAATTT
**
26969 TTCATTTTAAAAAAGTATATTTTCTTAAT
1 TTCATGATAAAAAAGTATATTTTCTTAAT
26998 AGTATTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (31 bp):
TTCATGATAAAAAAGTATATTTTCTTAATTT
Found at i:29306 original size:11 final size:11
Alignment explanation
Indices: 29290--29319 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
29280 ACATGCTCAA
29290 TTAATATTCGT
1 TTAATATTCGT
29301 TTAATATTCGT
1 TTAATATTCGT
29312 TTATATAT
1 TTA-ATAT
29320 ATATATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (11 bp):
TTAATATTCGT
Found at i:29446 original size:26 final size:26
Alignment explanation
Indices: 29394--29447 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
29384 AATATTTATT
*
29394 TAATATGTAATAAACTTTATTAGAAA
1 TAATATGTAATAAACTTTAATAGAAA
* *
29420 TAATATGTAATTAATTTCTAATA-AAA
1 TAATATGTAATAAACTT-TAATAGAAA
29446 TA
1 TA
29448 TTTCTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.41
Consensus pattern (26 bp):
TAATATGTAATAAACTTTAATAGAAA
Found at i:30488 original size:20 final size:19
Alignment explanation
Indices: 30451--30492 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
30441 GACCAGAGTC
30451 TTAAACCTAAACAATTTTT
1 TTAAACCTAAACAATTTTT
* *
30470 TTAAACCTAATCAAATTTT
1 TTAAACCTAAACAATTTTT
30489 TTAA
1 TTAA
30493 TACTGGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAACCTAAACAATTTTT
Found at i:34891 original size:14 final size:14
Alignment explanation
Indices: 34872--34915 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
34862 CAATTAAACA
34872 ATTGGGGGTGTTTG
1 ATTGGGGGTGTTTG
34886 ATTGGGGGTGTTTG
1 ATTGGGGGTGTTTG
*
34900 GTTGGGGGTGTTTG
1 ATTGGGGGTGTTTG
34914 AT
1 AT
34916 CACCTATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.07, C:0.00, G:0.50, T:0.43
Consensus pattern (14 bp):
ATTGGGGGTGTTTG
Found at i:41468 original size:804 final size:803
Alignment explanation
Indices: 39917--41527 Score: 3109
Period size: 804 Copynumber: 2.0 Consensus size: 803
39907 TGGGGACCAC
39917 GGATGACGTGGTGAACCCGATCCACCTAATAATTTCTCCTTATAGAGTGTAAATTACATAACGAT
1 GGATGACGTGGTGAACCCGATCCACCTAATAATTTCTCCTTATAGAGTGTAAATTACATAACGAT
39982 CCTATCTTAATCCAAAATCAAAATTTACTCTACATCCAAAATCACCAAATCCAACTCCAACTTTT
66 CCTATCTTAATCCAAAATCAAAATTTACTCTACATCCAAAATCACCAAATCCAACTCCAACTTTT
*
40047 ATTAATTACTTTAACTTACTTAATTTAAGCTCTAATTAACCCTAGTTAAAGTTTAATAATTTTAT
131 ATTAATTACTTTAACTTACTTAATTTAACCTCTAATTAACCCTAGTTAAAGTTTAATAATTTTAT
40112 TAATCATGCAAGGAATTTTTTCCCAGGTCTCAAGACAGATTTTTCTTTCATGCTAAATCAATCTT
196 TAATCATGCAAGGAATTTTTTCCCAGGTCTCAAGACAGATTTTTCTTTCATGCTAAATCAATCTT
40177 TTGTTTTTCGTAATTTTCATTTTAAAAAGAAGAGAGAGAGAAATTTTTTTTTGGCAAAGTTTCTT
261 TTGTTTTTCGTAATTTTCATTTTAAAAAGAAGAGAGAGAGAAATTTTTTTTTGGCAAAGTTTCTT
40242 AATTAAGAATAGAGTTGGAGTCGGATTTGGTGAAATAGGGTATATAATAAAATTAGACTTTAGTT
326 AATTAAGAATAGAGTTGGAGTCGGATTTGGTGAAATAGGGTATATAATAAAATTAGACTTTAGTT
40307 CAAAATAGGTTCTTGTTGCGCCAAAAATCTCTTGCTAGAGTTTTCGCGGTGAATTCTTTATGACA
391 CAAAATAGGTTCTTGTTGCGCCAAAAATCTCTTGCTAGAGTTTTCGCGGTGAATTCTTTATGACA
*
40372 GCATAGGGGCGTGCCAGTCAATTTGCTGAAATTGACAAAGAATTGTAAAAACTGAATCTGGTGCG
456 GCATAGGGGCGTGCCAGTCAATTTGCTGAAAATGACAAAGAATTGTAAAAACTGAATCTGGTGCG
40437 CGGAGCAGCAGATTAAAAGATCGGAACGATTGTGGGGACTGGATCAAAGTCACACCGGAGCATTT
521 CGGAGCAGCAGATTAAAAGATCGGAACGATTGTGGGGACTGGATCAAAGTCACACCGGAGCATTT
*
40502 AAATCATTGGATCCGTACAAATTATTCTCCATAACTGGGCCTTCCTCTACTTTTTTAATTGGATC
586 AAATCATTGGATCCGTACAAATTATTCTCCATAACTGGGCCTTCCTCTACTTTTTTAACTGGATC
40567 AGATCTGTGAGATCTGTTCTTGATTGAAATTGAAAGAAAATAACAACTTGATTGTTATTGATGAA
651 AGATCTGTGAGATCTGTTCTTGATTGAAATTGAAAGAAAATAACAACTTGATTGTTATTGATGAA
40632 AGGGAAACACATGTACAGTGTTTTGTGTCTGAAGACAAGATTGAAACAAGAGAAAAACACTAAAA
716 AGGGAAACACATGTACAGTGTTTTGTGTCTGAAGACAAGATTGAAACAAGAGAAAAACACTAAAA
40697 GAGTGTTTGAATGTCCTGAGACA
781 GAGTGTTTGAATGTCCTGAGACA
*
40720 GGAT-ACGTGGTGAACCCGATCCGCCTAATAATTTCTCCTTATAGAGTGTAAATTACATAACGAT
1 GGATGACGTGGTGAACCCGATCCACCTAATAATTTCTCCTTATAGAGTGTAAATTACATAACGAT
40784 CCTATCTTAATCCAAAATCAAAATTTACTCTACATCCAAAATCACCAAATCCAACTCCAACTTTT
66 CCTATCTTAATCCAAAATCAAAATTTACTCTACATCCAAAATCACCAAATCCAACTCCAACTTTT
40849 ATTAATTACTTTAACTTACTTAATTTAACCTCTAATTAACCCTAGTTAAAGTTTAATAATTTTAT
131 ATTAATTACTTTAACTTACTTAATTTAACCTCTAATTAACCCTAGTTAAAGTTTAATAATTTTAT
40914 TAATCATGCAAGGAATTTTTTTCCCAGGTCTCAAGACAGATTTTTCTTTCATGCTAAATCAATCT
196 TAATCATGCAAGGAA-TTTTTTCCCAGGTCTCAAGACAGATTTTTCTTTCATGCTAAATCAATCT
*
40979 TTTGTTTTTCGTAAGATTTTCATTTTAAAAAG-AGAGAGAGAGAGATTTTTTTTTGGCAAAGTTT
260 TTTGTTTTTCGT-A-ATTTTCATTTTAAAAAGAAGAGAGAGAGAAATTTTTTTTTGGCAAAGTTT
41043 CTTAATTAAGAATAGAGTTGGAGTCGGATTTGGTGAAATAGGGTATATAATAAAATTAGACTTTA
323 CTTAATTAAGAATAGAGTTGGAGTCGGATTTGGTGAAATAGGGTATATAATAAAATTAGACTTTA
41108 GTTCAAAATAGGTTCTTGTTGCGCCAAAAATCTCTTGCTAGAGTTTTCGCGGTGAATTCTTTATG
388 GTTCAAAATAGGTTCTTGTTGCGCCAAAAATCTCTTGCTAGAGTTTTCGCGGTGAATTCTTTATG
*
41173 ACAGCATAGGGGCGTGCCAGTCAATTTGCTGAAAATGACAAAGAATTGTAAAAACTGGATCTGGT
453 ACAGCATAGGGGCGTGCCAGTCAATTTGCTGAAAATGACAAAGAATTGTAAAAACTGAATCTGGT
*
41238 GCGCGGAGCAGCAGATTAAAAGATCGGAGCGATTGTGGGGACTGGATCAAAGTCACACCGGAGCA
518 GCGCGGAGCAGCAGATTAAAAGATCGGAACGATTGTGGGGACTGGATCAAAGTCACACCGGAGCA
41303 TTTAAATCATTGGATCCGTACAAATTATTCTCCATAACTGGGCCTTCCTCTACTTTTTTAACTGG
583 TTTAAATCATTGGATCCGTACAAATTATTCTCCATAACTGGGCCTTCCTCTACTTTTTTAACTGG
41368 ATCAGATCTGTGAGATCTGTTCTTGATTGAAATTGAAAGAAAATAACAACTTGATTGTTATTGAT
648 ATCAGATCTGTGAGATCTGTTCTTGATTGAAATTGAAAGAAAATAACAACTTGATTGTTATTGAT
*
41433 GAAAGGGACACACATGTACAGTGTTTTGTGTCTGAAGACAAGATTGAAACAAGAGAAAAACACTA
713 GAAAGGGAAACACATGTACAGTGTTTTGTGTCTGAAGACAAGATTGAAACAAGAGAAAAACACTA
41498 AAAGAGTGTTTGAATGTCCTGAGACA
778 AAAGAGTGTTTGAATGTCCTGAGACA
41524 GGAT
1 GGAT
41528 CTAAACAAGG
Statistics
Matches: 797, Mismatches: 8, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
802 203 0.25
803 65 0.08
804 512 0.64
805 17 0.02
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (803 bp):
GGATGACGTGGTGAACCCGATCCACCTAATAATTTCTCCTTATAGAGTGTAAATTACATAACGAT
CCTATCTTAATCCAAAATCAAAATTTACTCTACATCCAAAATCACCAAATCCAACTCCAACTTTT
ATTAATTACTTTAACTTACTTAATTTAACCTCTAATTAACCCTAGTTAAAGTTTAATAATTTTAT
TAATCATGCAAGGAATTTTTTCCCAGGTCTCAAGACAGATTTTTCTTTCATGCTAAATCAATCTT
TTGTTTTTCGTAATTTTCATTTTAAAAAGAAGAGAGAGAGAAATTTTTTTTTGGCAAAGTTTCTT
AATTAAGAATAGAGTTGGAGTCGGATTTGGTGAAATAGGGTATATAATAAAATTAGACTTTAGTT
CAAAATAGGTTCTTGTTGCGCCAAAAATCTCTTGCTAGAGTTTTCGCGGTGAATTCTTTATGACA
GCATAGGGGCGTGCCAGTCAATTTGCTGAAAATGACAAAGAATTGTAAAAACTGAATCTGGTGCG
CGGAGCAGCAGATTAAAAGATCGGAACGATTGTGGGGACTGGATCAAAGTCACACCGGAGCATTT
AAATCATTGGATCCGTACAAATTATTCTCCATAACTGGGCCTTCCTCTACTTTTTTAACTGGATC
AGATCTGTGAGATCTGTTCTTGATTGAAATTGAAAGAAAATAACAACTTGATTGTTATTGATGAA
AGGGAAACACATGTACAGTGTTTTGTGTCTGAAGACAAGATTGAAACAAGAGAAAAACACTAAAA
GAGTGTTTGAATGTCCTGAGACA
Found at i:50508 original size:81 final size:81
Alignment explanation
Indices: 50368--50764 Score: 566
Period size: 81 Copynumber: 4.9 Consensus size: 81
50358 TTCAATCGGA
** * * * *
50368 GTCTCATTAAGGGACGTTCGTCCTCACTAATAATTATACGAGGACACTCGTCTAAGTGTT-AATC
1 GTCTCATTAAGGGACGTTCGTCCTCTTTAATAGTTATACGGGGACACCCGTCTAGGTGTTCAA-C
* *
50432 CGTTATAGAGGAAGAAC
65 CGTTGTAGAGGAAAAAC
* * *
50449 GTCTCATTAGGGGACGTTCGTCCTCTTTAATAGTTATACGGGGACACCCGTCTGGGTGTTCAGCC
1 GTCTCATTAAGGGACGTTCGTCCTCTTTAATAGTTATACGGGGACACCCGTCTAGGTGTTCAACC
* *
50514 GTTGTGGAGAAAAAAC
66 GTTGTAGAGGAAAAAC
* *
50530 GTGTCATTAAGGGACGTCCGTCCTC-TTAATAGTTTATACGGGGACACCCGTCTAGGTGTTCAAC
1 GTCTCATTAAGGGACGTTCGTCCTCTTTAATAG-TTATACGGGGACACCCGTCTAGGTGTTCAAC
50594 CGTTGTAGAGGAAAAAC
65 CGTTGTAGAGGAAAAAC
* *
50611 GTCTCATTAGGGGACGTTCGTCCTCTTTAATAGTTATACGGGGACACCCGTTTAGGTGTTCAACC
1 GTCTCATTAAGGGACGTTCGTCCTCTTTAATAGTTATACGGGGACACCCGTCTAGGTGTTCAACC
50676 GTTGTAGAGGAAAAAC
66 GTTGTAGAGGAAAAAC
* * *
50692 GTCTCATT-AGGGACGTTTGTCCTCTTTAATAGTTATACGGGGACACCCGTTTAGGTGTTCAGCC
1 GTCTCATTAAGGGACGTTCGTCCTCTTTAATAGTTATACGGGGACACCCGTCTAGGTGTTCAACC
50756 GTTTGTAGA
66 G-TTGTAGA
50765 TGTATTTGAG
Statistics
Matches: 285, Mismatches: 27, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
80 61 0.21
81 216 0.76
82 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (81 bp):
GTCTCATTAAGGGACGTTCGTCCTCTTTAATAGTTATACGGGGACACCCGTCTAGGTGTTCAACC
GTTGTAGAGGAAAAAC
Found at i:61385 original size:10 final size:10
Alignment explanation
Indices: 61370--61394 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
61360 TTCAATTTAA
61370 TTTAATCGGT
1 TTTAATCGGT
61380 TTTAATCGGT
1 TTTAATCGGT
61390 TTTAA
1 TTTAA
61395 AATAGGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (10 bp):
TTTAATCGGT
Found at i:61526 original size:11 final size:11
Alignment explanation
Indices: 61510--61623 Score: 67
Period size: 11 Copynumber: 10.8 Consensus size: 11
61500 AAAAAATTTG
61510 TTATATATATT
1 TTATATATATT
*
61521 TTATATATATC
1 TTATATATATT
* * *
61532 ATAAATATA-A
1 TTATATATATT
61542 TT-TATATATT
1 TTATATATATT
* *
61552 TTACATGTATT
1 TTATATATATT
61563 TTATATATA--
1 TTATATATATT
* * *
61572 TCATAAATA-A
1 TTATATATATT
*
61582 TTAAATATATT
1 TTATATATATT
*
61593 TTATATATATC
1 TTATATATATT
* *
61604 ATAAATATATT
1 TTATATATATT
*
61615 TGATATATA
1 TTATATATA
61624 ATAGCATAAT
Statistics
Matches: 74, Mismatches: 25, Indels: 8
0.69 0.23 0.07
Matches are distributed among these distances:
9 12 0.16
10 9 0.12
11 53 0.72
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (11 bp):
TTATATATATT
Found at i:65221 original size:2 final size:2
Alignment explanation
Indices: 65214--65249 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
65204 AATCTTGATT
65214 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65250 AAAAAACCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66289 original size:19 final size:19
Alignment explanation
Indices: 66267--66303 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
66257 GTAATATATC
66267 TAAAATCCATTAATACTTG
1 TAAAATCCATTAATACTTG
* *
66286 TAAAATTCATTAGTACTT
1 TAAAATCCATTAATACTT
66304 AGATTCCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (19 bp):
TAAAATCCATTAATACTTG
Done.