Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016320.1 Corchorus olitorius cultivar O-4 contig16353, 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: 36249
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:342 original size:32 final size:32
Alignment explanation
Indices: 279--344 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
269 ATATATATTC
* **
279 AAATGAATTTTAGTTTATCGATGTATTATTTT
1 AAATGAATTTTAGTTTAGCGATGTAAAATTTT
*
311 AAATGAATTTTAGTTT-GGGATGTGAAAATTTT
1 AAATGAATTTTAGTTTAGCGATGT-AAAATTTT
343 AA
1 AA
345 TTTATTGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 5 0.17
32 24 0.83
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.47
Consensus pattern (32 bp):
AAATGAATTTTAGTTTAGCGATGTAAAATTTT
Found at i:4110 original size:15 final size:15
Alignment explanation
Indices: 4073--4116 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4063 AGAAACCGAC
4073 TATATTATTTTATAAA
1 TATATTA-TTTATAAA
* *
4089 AAAATTATTTATAAA
1 TATATTATTTATAAA
*
4104 TATATTATATATA
1 TATATTATTTATA
4117 TTATATATGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATTATTTATAAA
Found at i:5387 original size:10 final size:12
Alignment explanation
Indices: 5369--5410 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
5359 TCTGATATTG
5369 TATATATATGT-
1 TATATATATGTA
*
5380 TA-ATATATATA
1 TATATATATGTA
5391 TATATATATGTA
1 TATATATATGTA
*
5403 TATGTATA
1 TATATATA
5411 CTATATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 7 0.27
11 4 0.15
12 15 0.58
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
TATATATATGTA
Found at i:8140 original size:14 final size:14
Alignment explanation
Indices: 8121--8164 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
8111 ACTTGAGTCA
*
8121 TTGATTTGCTGTTT
1 TTGATTTCCTGTTT
*
8135 TTGATTTCCTATTT
1 TTGATTTCCTGTTT
* *
8149 GTGAGTTCCTGTTT
1 TTGATTTCCTGTTT
8163 TT
1 TT
8165 TAGTTCCTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.09, C:0.11, G:0.18, T:0.61
Consensus pattern (14 bp):
TTGATTTCCTGTTT
Found at i:8169 original size:14 final size:14
Alignment explanation
Indices: 8129--8172 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
8119 CATTGATTTG
*
8129 CTGTTTTTGATTTC
1 CTGTTTTTGAGTTC
* *
8143 CTATTTGTGAGTTC
1 CTGTTTTTGAGTTC
*
8157 CTGTTTTTTAGTTC
1 CTGTTTTTGAGTTC
8171 CT
1 CT
8173 TACTTGCTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (14 bp):
CTGTTTTTGAGTTC
Found at i:8317 original size:37 final size:37
Alignment explanation
Indices: 8276--8425 Score: 152
Period size: 37 Copynumber: 4.2 Consensus size: 37
8266 GTTTATTTAA
*
8276 CTGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACCTC
1 CTGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACTTC
* **** * *
8313 CTG-TTTTTGAGTTCCTGATGGACT-GGT--TTA---A
1 CTGTTTTTTTAGTTCCTG-TTTTTTAGTTCATTACTTC
*
8344 CTATTTTTTTAGTTCCTGTTTTTTAGTTCATTACTTC
1 CTGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACTTC
*
8381 ATGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACTTC
1 CTGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACTTC
8418 CTGTTTTT
1 CTGTTTTT
8426 GGATTCCCCT
Statistics
Matches: 87, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
31 4 0.05
32 15 0.17
34 6 0.07
36 15 0.17
37 47 0.54
ACGTcount: A:0.13, C:0.15, G:0.13, T:0.59
Consensus pattern (37 bp):
CTGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACTTC
Found at i:8351 original size:68 final size:69
Alignment explanation
Indices: 8271--8398 Score: 213
Period size: 68 Copynumber: 1.9 Consensus size: 69
8261 TTAGTGTTTA
* *
8271 TTTAACTGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACCTCCTG-TTTTTGAGTTCCTGATGGA
1 TTTAACTATTTTTTTAGTTCCTGTTTTTTAGTTCATTACCTCATGTTTTTTGAGTTCCTGATGGA
8335 CTGG
66 CTGG
* *
8339 TTTAACTATTTTTTTAGTTCCTGTTTTTTAGTTCATTACTTCATGTTTTTTTAGTTCCTG
1 TTTAACTATTTTTTTAGTTCCTGTTTTTTAGTTCATTACCTCATGTTTTTTGAGTTCCTG
8399 TTTTTTAGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
68 42 0.76
69 13 0.24
ACGTcount: A:0.14, C:0.15, G:0.14, T:0.57
Consensus pattern (69 bp):
TTTAACTATTTTTTTAGTTCCTGTTTTTTAGTTCATTACCTCATGTTTTTTGAGTTCCTGATGGA
CTGG
Found at i:8483 original size:105 final size:102
Alignment explanation
Indices: 8277--8489 Score: 247
Period size: 105 Copynumber: 2.1 Consensus size: 102
8267 TTTATTTAAC
*
8277 TGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACCTCCTGTTTTTGAGTTCCTGATGGACTGGTTT
1 TGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACCTCCTGTTTTTGAGTTCCTCAT-G--TGGTTT
* **
8342 AACTATTTTTTTAGTTCCTGTTTTTTAGTTCATTACTTCA
63 AACTATTTTTTTAGTTCCAGAATTTTAGTTCATTACTTCA
* * *
8382 TGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACTTCCTGTTTTTG-GATTCC-CCT-TTGTTTAA
1 TGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACCTCCTGTTTTTGAG-TTCCTCATGTGGTTTAA
* *
8444 CTGTTTTTTTGAGTT-CAGAAATTTTAGTTCCTTACTT-A
65 CTATTTTTTT-AGTTCCAG-AATTTTAGTTCATTACTTCA
8482 CTGTTTTT
1 -TGTTTTT
8490 GAGTTGCTGT
Statistics
Matches: 95, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
100 19 0.20
101 26 0.27
104 2 0.02
105 48 0.51
ACGTcount: A:0.14, C:0.15, G:0.14, T:0.57
Consensus pattern (102 bp):
TGTTTTTTTAGTTCCTGTTTTTTAGTTCATTACCTCCTGTTTTTGAGTTCCTCATGTGGTTTAAC
TATTTTTTTAGTTCCAGAATTTTAGTTCATTACTTCA
Found at i:8544 original size:38 final size:41
Alignment explanation
Indices: 8475--8556 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 41
8465 TTTTAGTTCC
*
8475 TTACTTACTGTTTTTGAGTTGCTGTTTGTTTCTTTAACTGTT
1 TTACTTACTGTTTTTGAGTT-CTGTTCGTTTCTTTAACTGTT
*
8517 TTACTTACTGTTTTTTAG-T-TG-TCGTTTCTTTAACTGTT
1 TTACTTACTGTTTTTGAGTTCTGTTCGTTTCTTTAACTGTT
8555 TT
1 TT
8557 TTGGAGTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 18 0.47
39 2 0.05
41 1 0.03
42 17 0.45
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.61
Consensus pattern (41 bp):
TTACTTACTGTTTTTGAGTTCTGTTCGTTTCTTTAACTGTT
Found at i:15694 original size:29 final size:29
Alignment explanation
Indices: 15660--15735 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
15650 ATTTGTAGCG
*
15660 TTTGGACGTTTTGCCCCCTGAACTTCAAT
1 TTTGGACGTTTTGCCCCCTAAACTTCAAT
** *
15689 TTTGGATATTTTACCCCCTAAACTTCAAT
1 TTTGGACGTTTTGCCCCCTAAACTTCAAT
15718 TTTGGGACGTTTTGCCCC
1 TTT-GGACGTTTTGCCCC
15736 TTTAGACTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.39
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCCTAAACTTCAAT
Found at i:15919 original size:78 final size:78
Alignment explanation
Indices: 15790--15961 Score: 317
Period size: 78 Copynumber: 2.2 Consensus size: 78
15780 GTGGCACAAA
*
15790 AATGCCATGTGGCATTGCCATGTCAGACCAATTCGGCCCACGTGGCCTTGCCACGTCGGACAAAA
1 AATGCCACGTGGCATTGCCATGTCAGACCAATTCGGCCCACGTGGCCTTGCCACGTCGGACAAAA
* *
15855 CCGCTGACGTGGC
66 CCACTGACATGGC
15868 AATGCCACGTGGCATTGCCATGTCAGACCAATTCGGCCCACGTGGCCTTGCCACGTCGGACAAAA
1 AATGCCACGTGGCATTGCCATGTCAGACCAATTCGGCCCACGTGGCCTTGCCACGTCGGACAAAA
15933 CCACTGACATGGC
66 CCACTGACATGGC
15946 AATGCCACGTGGCATT
1 AATGCCACGTGGCATT
15962 TTTGTGACAC
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 91 1.00
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (78 bp):
AATGCCACGTGGCATTGCCATGTCAGACCAATTCGGCCCACGTGGCCTTGCCACGTCGGACAAAA
CCACTGACATGGC
Found at i:23358 original size:84 final size:84
Alignment explanation
Indices: 23217--23370 Score: 290
Period size: 84 Copynumber: 1.8 Consensus size: 84
23207 AATAAAGGTT
*
23217 GTGCAATAGCTCTGAGTTTCAAAAGCTTCCTTAATGTCCAGCTGATATTGTTGGTGATTTGAAAA
1 GTGCAATAGCTCTAAGTTTCAAAAGCTTCCTTAATGTCCAGCTGATATTGTTGGTGATTTGAAAA
23282 TTCCAGAAAATTCCAGAAC
66 TTCCAGAAAATTCCAGAAC
*
23301 GTGCAATAGCTCTAAGTTTCAAAAGCTTCCTTAATGTCCAGTTGATATTGTTGGTGATTTGAAAA
1 GTGCAATAGCTCTAAGTTTCAAAAGCTTCCTTAATGTCCAGCTGATATTGTTGGTGATTTGAAAA
23366 TTCCA
66 TTCCA
23371 TAACGTGCTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 68 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (84 bp):
GTGCAATAGCTCTAAGTTTCAAAAGCTTCCTTAATGTCCAGCTGATATTGTTGGTGATTTGAAAA
TTCCAGAAAATTCCAGAAC
Found at i:26617 original size:27 final size:27
Alignment explanation
Indices: 26575--26631 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
26565 AAGACTACCT
* *
26575 TCAGGATGAAGCTCTTCGGGTTCAGAA
1 TCAGGATGAAGCTCTTCAGATTCAGAA
* *
26602 TCAGGATGGAGGTCTTCAGATTCAGAA
1 TCAGGATGAAGCTCTTCAGATTCAGAA
26629 TCA
1 TCA
26632 TACTCGGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (27 bp):
TCAGGATGAAGCTCTTCAGATTCAGAA
Found at i:26706 original size:33 final size:33
Alignment explanation
Indices: 26664--26735 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
26654 AAAGACAAGC
*
26664 AAAATAAACATGGAATTAACAATTATTGCCAAA
1 AAAAAAAACATGGAATTAACAATTATTGCCAAA
26697 AAAAAAAACATGGAATTAACAATTATTGCCAAA
1 AAAAAAAACATGGAATTAACAATTATTGCCAAA
26730 AAAAAA
1 AAAAAA
26736 TGGAATTAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.21
Consensus pattern (33 bp):
AAAAAAAACATGGAATTAACAATTATTGCCAAA
Found at i:26738 original size:29 final size:29
Alignment explanation
Indices: 26663--26747 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 29
26653 CAAAGACAAG
*
26663 CAAAATAAACATGGAATTAACAATTATTGC
1 CAAAA-AAAAATGGAATTAACAATTATTGC
26693 CAAAAAAAAAAACATGGAATTAACAATTATTGC
1 C---AAAAAAAA-ATGGAATTAACAATTATTGC
26726 CAAAAAAAAATGGAATTAACAA
1 CAAAAAAAAATGGAATTAACAA
26748 CAAAAAATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
29 13 0.26
30 9 0.18
32 3 0.06
33 25 0.50
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (29 bp):
CAAAAAAAAATGGAATTAACAATTATTGC
Found at i:27124 original size:30 final size:31
Alignment explanation
Indices: 27072--27133 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
27062 TTGGGTAGCT
27072 AGGTTTCAGAAAGGGTTTTGGCCAAAAAAAA
1 AGGTTTCAGAAAGGGTTTTGGCCAAAAAAAA
27103 AGGTTTCAGAAAGGG-TTTGGCCAAAAAAAA
1 AGGTTTCAGAAAGGGTTTTGGCCAAAAAAAA
27133 A
1 A
27134 AAAGTTTCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.21
Consensus pattern (31 bp):
AGGTTTCAGAAAGGGTTTTGGCCAAAAAAAA
Found at i:27134 original size:31 final size:32
Alignment explanation
Indices: 27072--27146 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
27062 TTGGGTAGCT
27072 AGGTTTCAGAAAGGGTTTTGGCC-AAAAAAAA
1 AGGTTTCAGAAAGGGTTTTGGCCAAAAAAAAA
27103 AGGTTTCAGAAAGGG-TTTGGCCAAAAAAAAAA
1 AGGTTTCAGAAAGGGTTTTGGCC-AAAAAAAAA
*
27135 AAGTTTCAGAAA
1 AGGTTTCAGAAA
27147 AAAATGCGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 7 0.17
31 15 0.37
32 19 0.46
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.21
Consensus pattern (32 bp):
AGGTTTCAGAAAGGGTTTTGGCCAAAAAAAAA
Found at i:29060 original size:80 final size:80
Alignment explanation
Indices: 28947--29104 Score: 289
Period size: 80 Copynumber: 2.0 Consensus size: 80
28937 GCATTCGTTC
*
28947 TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTTCAGCCAACCCATCTTCAAAA
1 TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
29012 GTCGTCTAAGATCCA
66 GTCGTCTAAGATCCA
* *
29027 TGCAACTCCCCCTCGTTTTTATTTCCCTTCCCAAAATAGGTTTTCCAGCCGACCCATCTTCAAAA
1 TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
29092 GTCGTCTAAGATC
66 GTCGTCTAAGATC
29105 TGAAACCTCT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.24, C:0.34, G:0.11, T:0.32
Consensus pattern (80 bp):
TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
GTCGTCTAAGATCCA
Found at i:29597 original size:22 final size:22
Alignment explanation
Indices: 29569--29610 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
29559 TTTGGAGGAC
29569 AAGGAAAATATAAAGTAAAAAA
1 AAGGAAAATATAAAGTAAAAAA
29591 AAGGAAAATATAAAGTAAAA
1 AAGGAAAATATAAAGTAAAA
29611 TTTTCTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (22 bp):
AAGGAAAATATAAAGTAAAAAA
Found at i:29605 original size:12 final size:12
Alignment explanation
Indices: 29569--29611 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
29559 TTTGGAGGAC
29569 AAGGAAAATATA
1 AAGGAAAATATA
*
29581 AAGTAAAA-A-A
1 AAGGAAAATATA
29591 AAGGAAAATATA
1 AAGGAAAATATA
*
29603 AAGTAAAAT
1 AAGGAAAAT
29612 TTTCTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 16 0.62
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (12 bp):
AAGGAAAATATA
Found at i:34594 original size:28 final size:28
Alignment explanation
Indices: 34536--34591 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
34526 CTAATTCAAT
* *
34536 ATAAGAACATTTTCCTTTTTTTCTTATA
1 ATAAGAACATTTTACTTTCTTTCTTATA
34564 ATAAGAACATTTTAC-TTCTTTCTTATA
1 ATAAGAACATTTTACTTTCTTTCTTATA
34591 A
1 A
34592 ATATGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (28 bp):
ATAAGAACATTTTACTTTCTTTCTTATA
Found at i:35301 original size:4 final size:4
Alignment explanation
Indices: 35292--35318 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
35282 AAAGTGACTC
35292 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
35319 CTCGTTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Done.