Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018264.1 Corchorus olitorius cultivar O-4 contig18297, 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: 77394
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:14848 original size:348 final size:348
Alignment explanation
Indices: 14211--14887 Score: 1043
Period size: 348 Copynumber: 1.9 Consensus size: 348
14201 TTGTAATTGA
14211 GCTTCTTCCATTCCTTTCTGCAACTCTATTTCTATATTTTTCTTCCCAAATTCAATCTCCCTCTT
1 GCTTCTTCCATTCCTTTCTGCAACTCTATTTCTATATTTTTCTTCCCAAATTCAATCTCCCTCTT
* *
14276 CTCTTCAGCCAGTTGAGATAAATCATTCTGTGCAACAACCAATGCATCTTCAAGGGATTTCATAG
66 CTCTTCAGCCAGTTGAGATAAATCATTCTGCGCAACAACCAATGCATCTTCAACGGATTTCATAG
* * *
14341 ATGCTTGGGCTTCTGCTAACTTGCCAGCCAGGTTACTAGCCTCTTCCTTCACTTCCCTCAATTCT
131 ATGCTTCGGCTTCTGCTAACTTGCCAGCCAGATTACTAGCCTCTTCCTTCACTTCCCTCAACTCT
* * * * *
14406 TTCTCAGTCTGTGTCTTTGCAGTCTGACAATCATCAATATACCCGGCAAGCCAGTTCAGCTTCTC
196 TTCTCAGTCTGTGCCTTGGCAGTCTGACAATCATCAATATACCCAGCAAGCCACTCCAGCTTCTC
* * *
14471 AGTAGGCTCTTCAAATTGTAAATCAACTGGAATAACAATGCGATCAATCACTTCGCTCACTCTCT
261 AGTAGGCTCTTCAAATTCTAAAGCAACTGGAATAACAATGCGATCAATCACTTCACTCACTCTCT
14536 GCAATATACTCTTTTGCAAATGT
326 GCAATATACTCTTTTGCAAATGT
* *
14559 GCTTCTTCCATTGCTTTCTGCAACTCTATTTCTATATTTTTCTTCCCAAATTCCATCTCCCTCTT
1 GCTTCTTCCATTCCTTTCTGCAACTCTATTTCTATATTTTTCTTCCCAAATTCAATCTCCCTCTT
* ** * ** * *
14624 CTCTTCGGCCAGTTGATTTGAATCATTCTGCGCAACAGTCAATGCATCTTCCACTGATTTCATAG
66 CTCTTCAGCCAGTTGAGATAAATCATTCTGCGCAACAACCAATGCATCTTCAACGGATTTCATAG
* * *
14689 TTGCTTCGGCTTCTGCTAACTTGCCAGCCAGATTACTAGCCTCTTCCTTTACTTCTCTCAACTCT
131 ATGCTTCGGCTTCTGCTAACTTGCCAGCCAGATTACTAGCCTCTTCCTTCACTTCCCTCAACTCT
*
14754 TGT-TCAGTCTGTGCCTTGGCAGTCTGACAATCATCTATATACCCAGCAAGCCACTCCAGCTTCT
196 T-TCTCAGTCTGTGCCTTGGCAGTCTGACAATCATCAATATACCCAGCAAGCCACTCCAGCTTCT
* * * *
14818 CTA-TAGGCTCTTGAAATTCTAAAGCAACTGGAATAACAATGCGGTCAATTACTTCACTTACTCT
260 C-AGTAGGCTCTTCAAATTCTAAAGCAACTGGAATAACAATGCGATCAATCACTTCACTCACTCT
14882 CTGCAA
324 CTGCAA
14888 GATGTTATTG
Statistics
Matches: 296, Mismatches: 31, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
348 294 0.99
349 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (348 bp):
GCTTCTTCCATTCCTTTCTGCAACTCTATTTCTATATTTTTCTTCCCAAATTCAATCTCCCTCTT
CTCTTCAGCCAGTTGAGATAAATCATTCTGCGCAACAACCAATGCATCTTCAACGGATTTCATAG
ATGCTTCGGCTTCTGCTAACTTGCCAGCCAGATTACTAGCCTCTTCCTTCACTTCCCTCAACTCT
TTCTCAGTCTGTGCCTTGGCAGTCTGACAATCATCAATATACCCAGCAAGCCACTCCAGCTTCTC
AGTAGGCTCTTCAAATTCTAAAGCAACTGGAATAACAATGCGATCAATCACTTCACTCACTCTCT
GCAATATACTCTTTTGCAAATGT
Found at i:17053 original size:18 final size:18
Alignment explanation
Indices: 17030--17065 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17020 GTTCCATTTC
*
17030 ATCAACAAATTGATTGTT
1 ATCAACAAATTCATTGTT
*
17048 ATCAACAACTTCATTGTT
1 ATCAACAAATTCATTGTT
17066 GTGTGTACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (18 bp):
ATCAACAAATTCATTGTT
Found at i:19488 original size:3 final size:3
Alignment explanation
Indices: 19480--19598 Score: 211
Period size: 3 Copynumber: 39.7 Consensus size: 3
19470 ATGAATTTAT
19480 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
* *
19528 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TCT TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
*
19576 TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TC
19599 GCTATCTTCC
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 110 1.00
ACGTcount: A:0.30, C:0.34, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:21196 original size:21 final size:21
Alignment explanation
Indices: 21170--21212 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
21160 CATATATTGC
21170 ATGAAAAACATTCACCAGAAA
1 ATGAAAAACATTCACCAGAAA
*
21191 ATGAAAAACGTTCACCAGAAA
1 ATGAAAAACATTCACCAGAAA
21212 A
1 A
21213 CTGTAGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.14
Consensus pattern (21 bp):
ATGAAAAACATTCACCAGAAA
Found at i:21988 original size:19 final size:19
Alignment explanation
Indices: 21961--22005 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
21951 TTATTGGCAA
* *
21961 TTTTCCTTTTTT-CTTTTT
1 TTTTTCTTTTTTCCTTTAT
21979 CTTTTTCTTTTTTCCTTTAT
1 -TTTTTCTTTTTTCCTTTAT
21999 TTTTTCT
1 TTTTTCT
22006 AATAATAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTTTCCTTTAT
Found at i:34742 original size:25 final size:24
Alignment explanation
Indices: 34697--34750 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
34687 AGAATCTATA
* * *
34697 TATATATATATATATATTATTCTG
1 TATATATATATACACAGTATTCTG
34721 TATATATACTATACACAGTATTCTG
1 TATATATA-TATACACAGTATTCTG
34746 TATAT
1 TATAT
34751 GAATCAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (24 bp):
TATATATATATACACAGTATTCTG
Found at i:35821 original size:25 final size:25
Alignment explanation
Indices: 35778--35829 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
35768 AATTTAAATT
35778 TATAAAATATTATATATATATATTA
1 TATAAAATATTATATATATATATTA
*
35803 TATAAAGTA-TATATAATATATATTA
1 TATAAAATATTATAT-ATATATATTA
35828 TA
1 TA
35830 AGGTCGGTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TATAAAATATTATATATATATATTA
Found at i:40716 original size:15 final size:15
Alignment explanation
Indices: 40693--40722 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40683 GTCCTTCAAA
*
40693 TTCAGGTTCAGACTC
1 TTCAAGTTCAGACTC
40708 TTCAAGTTCAGACTC
1 TTCAAGTTCAGACTC
40723 AAGCGCTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (15 bp):
TTCAAGTTCAGACTC
Found at i:41158 original size:6 final size:6
Alignment explanation
Indices: 41142--41237 Score: 93
Period size: 6 Copynumber: 16.0 Consensus size: 6
41132 ACTGGTACTA
* * * * * *
41142 GTTCAG ATTCAG CTTCAG GTTCAA GTTCAA GTTCAG GTTCAG ATTCAA
1 GTTCAG GTTCAG GTTCAG GTTCAG GTTCAG GTTCAG GTTCAG GTTCAG
** * * *
41190 GTTCAG GTTCAG GTTCAG GTTCAG ACTCAG GCTCAG GCTCAG GCTCAG
1 GTTCAG GTTCAG GTTCAG GTTCAG GTTCAG GTTCAG GTTCAG GTTCAG
41238 CTTCTAGCCC
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 78 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (6 bp):
GTTCAG
Found at i:43055 original size:69 final size:69
Alignment explanation
Indices: 42944--43081 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
42934 TTTTACCGAG
42944 TTTGATTCGTGTCGATAGTTGTATAAGAATCATTGCAATCTCCATTTGTTTGGAAAAGTAGCTCT
1 TTTGATTCGTGTCGATAGTTGTATAAGAATCATTGCAATCTCCATTTGTTTGGAAAAGTAGCTCT
43009 TTCC
66 TTCC
43013 TTTGATTCGTGTCGATAGTTGTATAAGAATCATTGCAATCTCCATTTGTTTGGAAAAGTAGCTCT
1 TTTGATTCGTGTCGATAGTTGTATAAGAATCATTGCAATCTCCATTTGTTTGGAAAAGTAGCTCT
43078 TTCC
66 TTCC
43082 ACAGCTCCAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (69 bp):
TTTGATTCGTGTCGATAGTTGTATAAGAATCATTGCAATCTCCATTTGTTTGGAAAAGTAGCTCT
TTCC
Found at i:47570 original size:23 final size:23
Alignment explanation
Indices: 47540--47583 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
47530 AGTTGGGTAC
47540 ATGTAAAATTTCAACAAAATCCG
1 ATGTAAAATTTCAACAAAATCCG
47563 ATGTAAAATTTCAACAAAATC
1 ATGTAAAATTTCAACAAAATC
47584 TGATATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (23 bp):
ATGTAAAATTTCAACAAAATCCG
Found at i:54404 original size:18 final size:18
Alignment explanation
Indices: 54376--54417 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
54366 TAATAAAAAA
54376 CAGTAAGCCTGTGTTATAG
1 CAGT-AGCCTGTGTTATAG
54395 CAGTAGCCTGTGTTATAG
1 CAGTAGCCTGTGTTATAG
54413 CAGTA
1 CAGTA
54418 TTTGTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (18 bp):
CAGTAGCCTGTGTTATAG
Found at i:59402 original size:21 final size:22
Alignment explanation
Indices: 59377--59417 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
59367 AAATGATTCT
59377 TTTGAAAATTT-A-TTTTTAGGC
1 TTTG-AAATTTCAGTTTTTAGGC
59398 TTTGAAATTTCAGTTTTTAG
1 TTTGAAATTTCAGTTTTTAG
59418 TAAATGTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.54
Consensus pattern (22 bp):
TTTGAAATTTCAGTTTTTAGGC
Found at i:66987 original size:29 final size:30
Alignment explanation
Indices: 66937--67025 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 30
66927 CTTTTTGAAA
66937 CACATGGTCACTTTTTTGGTACACATGGCGTG
1 CACAT-GTCAC-TTTTTGGTACACATGGCGTG
* *
66969 -ATATGTCACTTTTTGGTACACATGGTGTG
1 CACATGTCACTTTTTGGTACACATGGCGTG
* *
66998 TCACATGTCGCTTTTTGGTACACGTGGC
1 -CACATGTCACTTTTTGGTACACATGGC
67026 ATGCCATCGT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 19 0.39
30 5 0.10
31 25 0.51
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (30 bp):
CACATGTCACTTTTTGGTACACATGGCGTG
Found at i:76374 original size:18 final size:18
Alignment explanation
Indices: 76353--76387 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
76343 GTAATTTTGC
76353 TTTTTCCTTTTCTTTTCT
1 TTTTTCCTTTTCTTTTCT
* *
76371 TTTTTCTTTTTTTTTTC
1 TTTTTCCTTTTCTTTTC
76388 GCCAGAGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTCCTTTTCTTTTCT
Found at i:76385 original size:17 final size:17
Alignment explanation
Indices: 76347--76385 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
76337 AATTCGGTAA
*
76347 TTTTGCTTTTTCCTTTT
1 TTTTTCTTTTTCCTTTT
* *
76364 CTTTTCTTTTTTCTTTT
1 TTTTTCTTTTTCCTTTT
76381 TTTTT
1 TTTTT
76386 TCGCCAGAGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTTTCCTTTT
Found at i:76950 original size:39 final size:40
Alignment explanation
Indices: 76894--76974 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
76884 TTTAATTCCT
76894 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
76934 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
76973 AT
1 AT
76975 TCTTAGATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:77000 original size:24 final size:23
Alignment explanation
Indices: 76965--77010 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
76955 AATACTTACA
76965 TTAATTAAATTCTTAGATATTTT
1 TTAATTAAATTCTTAGATATTTT
*
76988 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGATATTT
77011 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (23 bp):
TTAATTAAATTCTTAGATATTTT
Done.