Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019435.1 Corchorus olitorius cultivar O-4 contig19468, 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: 58012
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:831 original size:19 final size:20
Alignment explanation
Indices: 804--842 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
794 TTTTGAGAAA
*
804 AACAGAGTGAGATTT-AGAT
1 AACAAAGTGAGATTTGAGAT
823 AACAAAGTGAGATTTGAGAT
1 AACAAAGTGAGATTTGAGAT
843 GGGAAAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.26
Consensus pattern (20 bp):
AACAAAGTGAGATTTGAGAT
Found at i:1368 original size:21 final size:21
Alignment explanation
Indices: 1322--1368 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1312 CTTGCGTGCT
*
1322 TCTCAATTAGCACTTCAACAA
1 TCTCTATTAGCACTTCAACAA
1343 TCTCTATTAGCACTTCAACAA
1 TCTCTATTAGCACTTCAACAA
1364 TCTCT
1 TCTCT
1369 GGAAACCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (21 bp):
TCTCTATTAGCACTTCAACAA
Found at i:4590 original size:42 final size:44
Alignment explanation
Indices: 4540--4633 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 44
4530 AGTGCATTAC
*
4540 CTAA-ATTCTACT-T-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
4581 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
4626 CTAATATT
1 CTAATATT
4634 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 8 0.17
44 1 0.02
45 35 0.73
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:5655 original size:78 final size:79
Alignment explanation
Indices: 5522--5691 Score: 290
Period size: 78 Copynumber: 2.2 Consensus size: 79
5512 TTGTTTAAAC
5522 TTTTA-TAGTTTTACTCAACTAAAAACTCTAATTTTTATTTAATTAAATCTAATATCTTTATAAC
1 TTTTACTA-TTTTACTCAACTAAAAACTCTAATTTTTATTTAATTAAATCTAATATCTTTATAAC
*
5586 TATTTTATTTTACCA
65 TATTCTATTTTACCA
*
5601 TTTTACTATTTTACTCAACTAAAAACT-TTATTTTTATTTAATTAAATCTAATATCTTTATAACT
1 TTTTACTATTTTACTCAACTAAAAACTCTAATTTTTATTTAATTAAATCTAATATCTTTATAACT
*
5665 ATTCTATTTTAGCA
66 ATTCTATTTTACCA
5679 TTTTACTATTTTA
1 TTTTACTATTTTA
5692 ATTAAAAAAA
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
78 61 0.70
79 24 0.28
80 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.52
Consensus pattern (79 bp):
TTTTACTATTTTACTCAACTAAAAACTCTAATTTTTATTTAATTAAATCTAATATCTTTATAACT
ATTCTATTTTACCA
Found at i:5725 original size:78 final size:77
Alignment explanation
Indices: 5522--5718 Score: 227
Period size: 78 Copynumber: 2.5 Consensus size: 77
5512 TTGTTTAAAC
* * **
5522 TTTTA-TAGTTTTACTCAACTAAAAACTCTAATTTTTATTTAATTAAATCTAATATCTTTATAAC
1 TTTTACTA-TTTTAATCAAC-AAAAACT-TTATTTAGATTTAATTAAATCTAATATCTTTATAAC
*
5586 TATTTTATTTTACCA
63 TATTCTATTTTACCA
* **
5601 TTTTACTATTTTACTCAACTAAAAACTTTATTTTTATTTAATTAAATCTAATATCTTTATAACTA
1 TTTTACTATTTTAATCAAC-AAAAACTTTATTTAGATTTAATTAAATCTAATATCTTTATAACTA
*
5666 TTCTATTTTAGCA
65 TTCTATTTTACCA
*
5679 TTTTACTATTTTAATTAA-AAAAACTTGATATATTAGATTT
1 TTTTACTATTTTAATCAACAAAAACTT--TAT-TTAGATTT
5719 TTTAAATATA
Statistics
Matches: 107, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
76 8 0.07
78 67 0.63
79 30 0.28
80 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (77 bp):
TTTTACTATTTTAATCAACAAAAACTTTATTTAGATTTAATTAAATCTAATATCTTTATAACTAT
TCTATTTTACCA
Found at i:9618 original size:31 final size:31
Alignment explanation
Indices: 9562--9620 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
9552 TTTGTAAAAC
* *
9562 TTTTGAAACGCCTATTGTACCCTTATTTAAT
1 TTTTGAAACACCTATTATACCCTTATTTAAT
**
9593 TTTTGAAACACCTATTATATTCTTATTT
1 TTTTGAAACACCTATTATACCCTTATTT
9621 TTCTAACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (31 bp):
TTTTGAAACACCTATTATACCCTTATTTAAT
Found at i:10285 original size:50 final size:50
Alignment explanation
Indices: 10223--10320 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 50
10213 AATTAATCTC
* * *
10223 TGTTCATGATGTTTTTGTTTCTGTATTCCCTTATGTATCCAGACTTATAT
1 TGTTAATGATGTTTCTGTTTCTCTATTCCCTTATGTATCCAGACTTATAT
* * *
10273 TGTTAATGATGTTTCTGTTTTTCTATTCCTTTGTGTATCCAGACTTAT
1 TGTTAATGATGTTTCTGTTTCTCTATTCCCTTATGTATCCAGACTTAT
10321 TAATCAAACC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.17, C:0.15, G:0.14, T:0.53
Consensus pattern (50 bp):
TGTTAATGATGTTTCTGTTTCTCTATTCCCTTATGTATCCAGACTTATAT
Found at i:10509 original size:23 final size:23
Alignment explanation
Indices: 10476--10520 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
10466 TTTAGCTTTT
10476 ATGTCACATCTCACGTAGGATTC
1 ATGTCACATCTCACGTAGGATTC
* *
10499 ATGTCATATCTCACTTAGGATT
1 ATGTCACATCTCACGTAGGATT
10521 TAACATAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (23 bp):
ATGTCACATCTCACGTAGGATTC
Found at i:12352 original size:23 final size:22
Alignment explanation
Indices: 12326--12369 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12316 AAAAAACCAA
*
12326 GCTCCGTGCTTATTTTCACTCTG
1 GCTCCGTGC-CATTTTCACTCTG
*
12349 GCTCTGTGCCATTTTCACTCT
1 GCTCCGTGCCATTTTCACTCT
12370 TGTTCATCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.09, C:0.32, G:0.16, T:0.43
Consensus pattern (22 bp):
GCTCCGTGCCATTTTCACTCTG
Found at i:16707 original size:2 final size:2
Alignment explanation
Indices: 16700--16727 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16690 TTGCTTGGAA
16700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16728 TAATTTAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20083 original size:13 final size:13
Alignment explanation
Indices: 20065--20092 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20055 CCAACTCTTC
20065 TTTTACTAAAGAA
1 TTTTACTAAAGAA
20078 TTTTACTAAAGAA
1 TTTTACTAAAGAA
20091 TT
1 TT
20093 GTGTGTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (13 bp):
TTTTACTAAAGAA
Found at i:24054 original size:19 final size:20
Alignment explanation
Indices: 24027--24065 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
24017 TTAATGCAAG
*
24027 ACTACATTTTCA-AGAAATT
1 ACTACATTTACAGAGAAATT
*
24046 ACTATATTTACAGAGAAATT
1 ACTACATTTACAGAGAAATT
24066 TTTTATATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (20 bp):
ACTACATTTACAGAGAAATT
Found at i:32657 original size:32 final size:32
Alignment explanation
Indices: 32616--32689 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
32606 ATTATGGGGA
32616 TCGAGCTCGACTCGATACTCGTATCGAGCTAC
1 TCGAGCTCGACTCGATACTCGTATCGAGCTAC
32648 TCGAGCTCGACTCGATACTCGTATCGAGCTAC
1 TCGAGCTCGACTCGATACTCGTATCGAGCTAC
32680 TCGAGCTCGA
1 TCGAGCTCGA
32690 TCGGTAAGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (32 bp):
TCGAGCTCGACTCGATACTCGTATCGAGCTAC
Found at i:32891 original size:15 final size:14
Alignment explanation
Indices: 32871--32924 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
32861 CAAAAAAATC
32871 GAATAACATCCATAT
1 GAATAAC-TCCATAT
32886 GAATAACTCCAAATAT
1 GAATAACTCC--ATAT
*
32902 GAATAACTCCAAAGT
1 GAATAACTCCATA-T
32917 GAATAACT
1 GAATAACT
32925 TGAATACATG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
14 5 0.14
15 16 0.46
16 14 0.40
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.24
Consensus pattern (14 bp):
GAATAACTCCATAT
Found at i:32903 original size:16 final size:16
Alignment explanation
Indices: 32882--32924 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
32872 AATAACATCC
32882 ATATGAATAACTCCAA
1 ATATGAATAACTCCAA
32898 ATATGAATAACTCCAA
1 ATATGAATAACTCCAA
*
32914 A-GTGAATAACT
1 ATATGAATAACT
32925 TGAATACATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (16 bp):
ATATGAATAACTCCAA
Found at i:41741 original size:13 final size:12
Alignment explanation
Indices: 41709--41741 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
41699 GTTTTGATAA
41709 ATTTTTATTTTC
1 ATTTTTATTTTC
41721 ATTTTTATTTTC
1 ATTTTTATTTTC
41733 ATTTCTTAT
1 ATTT-TTAT
41742 ATTTGTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (12 bp):
ATTTTTATTTTC
Found at i:49302 original size:21 final size:19
Alignment explanation
Indices: 49245--49302 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
49235 CTGTTTAGCA
49245 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* * *
49264 ACTGTACAGATTAAATTAGGT
1 ACTGTACAGATGAGATTA--C
49285 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
49303 TTAGAGTAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:50606 original size:28 final size:29
Alignment explanation
Indices: 50525--50650 Score: 175
Period size: 29 Copynumber: 4.4 Consensus size: 29
50515 GGGTCAGTAA
*
50525 AGGGGCATTTTGGTCA-TTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
* *
50553 AGGGGGCATTTTGGTCACTTTCGCACATCC
1 A-GGGGCATTTTGGTCATTTTTGCACATCC
*
50583 AGAGGCA-TTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
*
50611 AGGGGCATTTTGGTCATTTTTGCACATAC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
*
50640 AGGGTCATTTT
1 AGGGGCATTTT
50651 TGCACATCTA
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
28 26 0.30
29 50 0.57
30 11 0.13
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.37
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCACATCC
Found at i:50621 original size:57 final size:58
Alignment explanation
Indices: 50528--50650 Score: 171
Period size: 57 Copynumber: 2.1 Consensus size: 58
50518 TCAGTAAAGG
*
50528 GGCATTTTGGTCATTTTGCATATCCAGGGGGCATTTTGGTCACTTTCGCACATCCAGA
1 GGCATTTTGGTCATTTTGCACATCCAGGGGGCATTTTGGTCACTTTCGCACATCCAGA
* * *
50586 GGCA-TTTGGTCATTTTTGCACATCCA-GGGGCATTTTGGTCATTTTTGCACATACAG-
1 GGCATTTTGGTCA-TTTTGCACATCCAGGGGGCATTTTGGTCACTTTCGCACATCCAGA
50642 GGTCATTTT
1 GG-CATTTT
50651 TGCACATCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
56 2 0.03
57 37 0.64
58 19 0.33
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (58 bp):
GGCATTTTGGTCATTTTGCACATCCAGGGGGCATTTTGGTCACTTTCGCACATCCAGA
Done.