Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018919.1 Corchorus olitorius cultivar O-4 contig18952, 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: 77214
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:720 original size:19 final size:18
Alignment explanation
Indices: 696--731 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
686 TGAAGACTTA
696 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
715 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
732 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:738 original size:30 final size:30
Alignment explanation
Indices: 684--743 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
674 GAAGTTCGTG
* *
684 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
714 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
744 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:9937 original size:17 final size:16
Alignment explanation
Indices: 9915--9960 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
9905 TAAATATGTG
9915 ATATAATAATAATATAT
1 ATATAATAATAAT-TAT
*
9932 ATATAATATTTAATTAT
1 ATATAATA-ATAATTAT
9949 ATATAATAATAA
1 ATATAATAATAA
9961 ACGGTCGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.12
17 19 0.73
18 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAATAATAATTAT
Found at i:9950 original size:21 final size:20
Alignment explanation
Indices: 9921--9959 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9911 TGTGATATAA
9921 TAATAATATATATATAATATT
1 TAATAATATATA-ATAATATT
*
9942 TAATTATATATAATAATA
1 TAATAATATATAATAATA
9960 AACGGTCGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATAATATATAATAATATT
Found at i:17679 original size:20 final size:20
Alignment explanation
Indices: 17651--17692 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
17641 AGCGCTCAAA
*
17651 AGTGGGTCCAAGGCGTCAGC
1 AGTGAGTCCAAGGCGTCAGC
* *
17671 AGTGAGTCCGAGGTGTCAGC
1 AGTGAGTCCAAGGCGTCAGC
17691 AG
1 AG
17693 AGGACCCTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.17
Consensus pattern (20 bp):
AGTGAGTCCAAGGCGTCAGC
Found at i:22311 original size:19 final size:19
Alignment explanation
Indices: 22275--22311 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22265 TTCATTTAGG
* *
22275 ACTGACTATTAGTTTCTTC
1 ACTGACTATTAATCTCTTC
22294 ACTGACTATTAATCTCTT
1 ACTGACTATTAATCTCTT
22312 ATGGAGCTTA
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:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (19 bp):
ACTGACTATTAATCTCTTC
Found at i:23499 original size:201 final size:201
Alignment explanation
Indices: 23154--23553 Score: 800
Period size: 201 Copynumber: 2.0 Consensus size: 201
23144 TGTTCTTTGA
23154 TATGTTTGGAGAAAACTGCATAAACTACTGGATCTAATTATTGAAAATTGACAATGTTAGCACCT
1 TATGTTTGGAGAAAACTGCATAAACTACTGGATCTAATTATTGAAAATTGACAATGTTAGCACCT
23219 TTTTCTACATGTTTGGTTAATGAGTTACATTTTAACTCATACAAGCCAGTTGTACTTAGGAAGAT
66 TTTTCTACATGTTTGGTTAATGAGTTACATTTTAACTCATACAAGCCAGTTGTACTTAGGAAGAT
23284 GCTCTTGATATACTTTCCCATTTATGAGAGAGAATATTTGTAAATGCTTACTTTTGCATGTGAAA
131 GCTCTTGATATACTTTCCCATTTATGAGAGAGAATATTTGTAAATGCTTACTTTTGCATGTGAAA
23349 TGTGAG
196 TGTGAG
23355 TATGTTTGGAGAAAACTGCATAAACTACTGGATCTAATTATTGAAAATTGACAATGTTAGCACCT
1 TATGTTTGGAGAAAACTGCATAAACTACTGGATCTAATTATTGAAAATTGACAATGTTAGCACCT
23420 TTTTCTACATGTTTGGTTAATGAGTTACATTTTAACTCATACAAGCCAGTTGTACTTAGGAAGAT
66 TTTTCTACATGTTTGGTTAATGAGTTACATTTTAACTCATACAAGCCAGTTGTACTTAGGAAGAT
23485 GCTCTTGATATACTTTCCCATTTATGAGAGAGAATATTTGTAAATGCTTACTTTTGCATGTGAAA
131 GCTCTTGATATACTTTCCCATTTATGAGAGAGAATATTTGTAAATGCTTACTTTTGCATGTGAAA
23550 TGTG
196 TGTG
23554 TCAGACAAAC
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 199 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (201 bp):
TATGTTTGGAGAAAACTGCATAAACTACTGGATCTAATTATTGAAAATTGACAATGTTAGCACCT
TTTTCTACATGTTTGGTTAATGAGTTACATTTTAACTCATACAAGCCAGTTGTACTTAGGAAGAT
GCTCTTGATATACTTTCCCATTTATGAGAGAGAATATTTGTAAATGCTTACTTTTGCATGTGAAA
TGTGAG
Found at i:32384 original size:13 final size:13
Alignment explanation
Indices: 32366--32391 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32356 GAGAGGACTC
32366 CATGATCAATATA
1 CATGATCAATATA
32379 CATGATCAATATA
1 CATGATCAATATA
32392 TTAAGGGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
CATGATCAATATA
Found at i:34299 original size:19 final size:18
Alignment explanation
Indices: 34266--34301 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34256 TTAAGATAAT
34266 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
34284 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
34302 TAAGTTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:34656 original size:49 final size:47
Alignment explanation
Indices: 34558--34691 Score: 180
Period size: 49 Copynumber: 2.8 Consensus size: 47
34548 AGCGTGCCAA
* * * * *
34558 TCAATTTTGTCCAAAAATTGATAAAAAGTGCAATGAAAAGTAAATAT
1 TCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGGAAAAATAAAGAT
34605 TCAATTTTGTCTTAAAAATTGAGAAAAAGGTGCAAGGAAAAATAAAGAT
1 TCAATTTTGTC-TAAAAATTGAGAAAAA-GTGCAAGGAAAAATAAAGAT
*
34654 TCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGGAAA
1 TCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGGAAA
34692 TGTAAATGAT
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
47 17 0.22
48 18 0.23
49 43 0.55
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.28
Consensus pattern (47 bp):
TCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGGAAAAATAAAGAT
Found at i:42106 original size:24 final size:24
Alignment explanation
Indices: 42079--42134 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
42069 CCACTTTGTG
42079 ATTTTGGTGCTTATGGATAATTAA
1 ATTTTGGTGCTTATGGATAATTAA
42103 ATTTTGGTGCTTATGGATAATTAA
1 ATTTTGGTGCTTATGGATAATTAA
42127 ATTTTGGT
1 ATTTTGGT
42135 TTATGCACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.04, G:0.21, T:0.48
Consensus pattern (24 bp):
ATTTTGGTGCTTATGGATAATTAA
Found at i:50925 original size:49 final size:48
Alignment explanation
Indices: 50845--50969 Score: 162
Period size: 49 Copynumber: 2.6 Consensus size: 48
50835 AGCGTGCCAA
* * * *
50845 TCAATTTTGTCCAAAAATTGATAAAAA-GTGCAATGAAAAATAAATAT
1 TCAATTTTGTCTAAAAATTGAGAAAAAGGTGCAAGGAAAAATAAAGAT
* *
50892 TCAATTTTGTCTTAAAAAATGAGAAAAAGGTGCAAGGAAAAATAAAGGT
1 TCAATTTTGTC-TAAAAATTGAGAAAAAGGTGCAAGGAAAAATAAAGAT
*
50941 TCAATTTTGTAGTAAAAATTGAGAAAAAG
1 TCAATTTTGT-CTAAAAATTGAGAAAAAG
50970 TACAGGAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 11 0.16
48 13 0.19
49 43 0.64
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (48 bp):
TCAATTTTGTCTAAAAATTGAGAAAAAGGTGCAAGGAAAAATAAAGAT
Found at i:53131 original size:18 final size:18
Alignment explanation
Indices: 53097--53131 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53087 CTCTTCTATC
*
53097 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
53115 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
53132 GTAATTACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:53426 original size:20 final size:21
Alignment explanation
Indices: 53401--53449 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
53391 AATATATACA
*
53401 TGAAAAA-TCAAAAAGAATTT
1 TGAAAAACTCAAAAAAAATTT
53421 TGAAAAATCTCAAAAAAAATTT
1 TGAAAAA-CTCAAAAAAAATTT
*
53443 CGAAAAA
1 TGAAAAA
53450 ATTTCTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
22 18 0.72
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.22
Consensus pattern (21 bp):
TGAAAAACTCAAAAAAAATTT
Found at i:58280 original size:19 final size:18
Alignment explanation
Indices: 58247--58282 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
58237 TTGAGATAAT
58247 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
58265 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
58283 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:58779 original size:29 final size:29
Alignment explanation
Indices: 58737--58794 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
58727 GGAAATTCAT
*
58737 GTAAACATTAGTGGGACTAACTGGAGCAC
1 GTAAACATTAGTGGGACTAACTAGAGCAC
*
58766 GTAAACATTAGTGGGACTAATTAGAGCAC
1 GTAAACATTAGTGGGACTAACTAGAGCAC
58795 AAAAATTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (29 bp):
GTAAACATTAGTGGGACTAACTAGAGCAC
Found at i:59322 original size:32 final size:33
Alignment explanation
Indices: 59263--59325 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
59253 AACTTGTTAA
59263 GGCGTGATGAAGGCCCGTGTAACTTCATTGGAAC
1 GGCGTGATGAAGGCCCG-GTAACTTCATTGGAAC
59297 GGCGTGATGAAGGCCC-GTAACTTCATTGG
1 GGCGTGATGAAGGCCCGGTAACTTCATTGG
59326 TTGTAAGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.45
34 16 0.55
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (33 bp):
GGCGTGATGAAGGCCCGGTAACTTCATTGGAAC
Found at i:63135 original size:15 final size:15
Alignment explanation
Indices: 63115--63147 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
63105 ATCTTTTTTC
63115 TATCTGACTTATGAT
1 TATCTGACTTATGAT
63130 TATCTGACTTATGAT
1 TATCTGACTTATGAT
63145 TAT
1 TAT
63148 GGTGGCACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (15 bp):
TATCTGACTTATGAT
Found at i:66287 original size:5 final size:5
Alignment explanation
Indices: 66277--66306 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
66267 GGCTGACTTA
66277 CTAAT CTAAT CTAAT CTAAT CTAAT CTAAT
1 CTAAT CTAAT CTAAT CTAAT CTAAT CTAAT
66307 GCTGCTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
CTAAT
Found at i:75920 original size:6 final size:6
Alignment explanation
Indices: 75911--75944 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
75901 TTGTGATTGT
*
75911 CGCCTC CGCCTC CGCCTC CGCCTC CTCCTC CGCC
1 CGCCTC CGCCTC CGCCTC CGCCTC CGCCTC CGCC
75945 ACTGCCGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.68, G:0.15, T:0.18
Consensus pattern (6 bp):
CGCCTC
Found at i:76461 original size:6 final size:6
Alignment explanation
Indices: 76446--76478 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
76436 CAAAGCAATG
*
76446 TTTTTT TTTTTC TTTTTC TTTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT
76479 CTTTTTTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTC
Found at i:76485 original size:12 final size:11
Alignment explanation
Indices: 76447--76485 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
76437 AAAGCAATGT
76447 TTTTTTTTTTC
1 TTTTTTTTTTC
76458 TTTTTCTTTTTC
1 TTTTT-TTTTTC
*
76470 -TTTTTCTTTC
1 TTTTTTTTTTC
76480 TTTTTT
1 TTTTTT
76486 CACTCATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 5 0.20
11 14 0.56
12 6 0.24
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:76485 original size:18 final size:16
Alignment explanation
Indices: 76446--76485 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
76436 CAAAGCAATG
76446 TTTTTTTTTTTCTTTT
1 TTTTTTTTTTTCTTTT
*
76462 TCTTTTTCTTTTTCTTTC
1 T-TTTTT-TTTTTCTTTT
76480 TTTTTT
1 TTTTTT
76486 CACTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 10 0.48
18 10 0.48
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTTCTTTT
Done.