Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023992.1 Corchorus olitorius cultivar O-4 contig24025, 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: 20664
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5389 original size:29 final size:28
Alignment explanation
Indices: 5294--5398 Score: 95
Period size: 29 Copynumber: 3.7 Consensus size: 28
5284 AGGATCACCT
* ** * *
5294 AGGGGCATTTTGGTCATTTTAAAAAACTC
1 AGGGGCATTATGGTCATTTT-GCACATTC
* * *
5323 AGGGGTATTTTGGTCATTTTTCACATTC
1 AGGGGCATTATGGTCATTTTGCACATTC
*
5351 A-GGGCATTATGGTCATTTCTGCATATTC
1 AGGGGCATTATGGTCATTT-TGCACATTC
*
5379 AGGGGCATTATGATCATTTT
1 AGGGGCATTATGGTCATTTT
5399 AAGTTCAGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
27 15 0.23
28 14 0.22
29 35 0.55
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (28 bp):
AGGGGCATTATGGTCATTTTGCACATTC
Found at i:6056 original size:10 final size:9
Alignment explanation
Indices: 6026--6055 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6016 GTCATTACAC
6026 AAAA-TAAA
1 AAAATTAAA
6034 AAAATTAAA
1 AAAATTAAA
6043 AAAATTAAA
1 AAAATTAAA
6052 AAAA
1 AAAA
6056 AAAACAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAATTAAA
Found at i:7707 original size:2 final size:2
Alignment explanation
Indices: 7702--7727 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7692 ATAAAAAAAA
7702 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
7728 GAAGCTGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8472 original size:41 final size:41
Alignment explanation
Indices: 8395--8474 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
8385 TTCCAATGTA
* * * *
8395 GTCCCTGATTTAGGTTTATGTTTGTTAATTGGTTCAATTCT
1 GTCCCTGATTTAGGTTAATATTTATTAATTGATTCAATTCT
*
8436 GTCCCTGATTTAGAG-TAATATTTATTTATTGATTCAATT
1 GTCCCTGATTTAG-GTTAATATTTATTAATTGATTCAATT
8475 TCAGCCCTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 32 0.97
42 1 0.03
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.50
Consensus pattern (41 bp):
GTCCCTGATTTAGGTTAATATTTATTAATTGATTCAATTCT
Found at i:10764 original size:6 final size:6
Alignment explanation
Indices: 10744--10777 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
10734 AAGTCAACGT
10744 CCCGAA CCC--A CCCGAA CCCGAA CCCGAA CCCGAA
1 CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA
10778 ATTATCCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
6 22 0.85
ACGTcount: A:0.32, C:0.53, G:0.15, T:0.00
Consensus pattern (6 bp):
CCCGAA
Found at i:10786 original size:16 final size:16
Alignment explanation
Indices: 10765--10806 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
10755 CCGAACCCGA
*
10765 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
* *
10781 ATCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
10797 ACCCGAACCC
1 ACCCGAACCC
10807 AGAATAATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.40, G:0.14, T:0.10
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:11309 original size:31 final size:31
Alignment explanation
Indices: 11238--11320 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 31
11228 GTCTATTGTC
* *
11238 TTTTAATTTATTTAATTTAAGGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAGGCTTTAATTT
* *
11269 TAATT-ATTTGTTTAATTTAATGC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAGGCTTTAATTT
*
11299 GTTTTAATTTGTAATAATTTAA
1 -TTTTAATTTGT-TTAATTTAA
11321 AATTTATTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
30 8 0.19
31 24 0.57
32 10 0.24
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGGCTTTAATTT
Found at i:11601 original size:21 final size:20
Alignment explanation
Indices: 11571--11624 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
11561 TTATATATAT
11571 ATATATATATATATTGATAATC
1 ATAT-TATATATATT-ATAATC
* * *
11593 ATGTTATATTATATTATTATT
1 ATATTATA-TATATTATAATC
11614 ATATTATATAT
1 ATATTATATAT
11625 TATCAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 3 0.11
21 15 0.56
22 9 0.33
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
ATATTATATATATTATAATC
Found at i:11615 original size:11 final size:12
Alignment explanation
Indices: 11561--11627 Score: 56
Period size: 11 Copynumber: 5.9 Consensus size: 12
11551 TATTCAATCT
11561 TTATATA-TATA
1 TTATATATTATA
11572 -TATATATATATA
1 TTATATAT-TATA
*
11584 TTGATA-ATCAT-
1 TT-ATATATTATA
*
11595 GT-TATATTATA
1 TTATATATTATA
11606 TTAT-TATTATA
1 TTATATATTATA
11617 TTATATATTAT
1 TTATATATTAT
11628 CAATAAACTT
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
9 2 0.05
10 10 0.23
11 13 0.30
12 13 0.30
13 3 0.07
14 3 0.07
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (12 bp):
TTATATATTATA
Found at i:11617 original size:16 final size:15
Alignment explanation
Indices: 11596--11627 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
11586 GATAATCATG
11596 TTATATTATATTATTA
1 TTATATTATA-TATTA
11612 TTATATTATATATTA
1 TTATATTATATATTA
11627 T
1 T
11628 CAATAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATATTATATATTA
Found at i:11803 original size:32 final size:32
Alignment explanation
Indices: 11761--11838 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
11751 CAAACCCGAG
*
11761 CCCGAACCCGAAAATA-CTCAAACCCGACATAA
1 CCCGAACCCGAAAATACCT-AAACCCGACAGAA
* *
11793 CCCGAGCCCGAAAATACCTGAACCCGACAGAA
1 CCCGAACCCGAAAATACCTAAACCCGACAGAA
*
11825 CCCGAACCTGAAAA
1 CCCGAACCCGAAAA
11839 AGCCCGACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 38 0.95
33 2 0.05
ACGTcount: A:0.41, C:0.37, G:0.14, T:0.08
Consensus pattern (32 bp):
CCCGAACCCGAAAATACCTAAACCCGACAGAA
Found at i:11831 original size:16 final size:16
Alignment explanation
Indices: 11761--11851 Score: 62
Period size: 16 Copynumber: 5.7 Consensus size: 16
11751 CAAACCCGAG
11761 CCCGAACCCGA-AAATA
1 CCCGAACCCGACAAA-A
* * *
11777 CTCAAACCCGACATAA
1 CCCGAACCCGACAAAA
*
11793 CCCGAGCCCGA-AAATA
1 CCCGAACCCGACAAA-A
* *
11809 CCTGAACCCGACAGAA
1 CCCGAACCCGACAAAA
*
11825 CCCGAACCTGA-AAAA
1 CCCGAACCCGACAAAA
*
11840 GCCCGACCCCGA
1 -CCCGAACCCGA
11852 ACCCGCCCAA
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
15 5 0.09
16 47 0.84
17 4 0.07
ACGTcount: A:0.38, C:0.40, G:0.15, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGACAAAA
Found at i:11851 original size:32 final size:32
Alignment explanation
Indices: 11761--11851 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
11751 CAAACCCGAG
* * *
11761 CCCGAACCCGAAAATACTCAAACCCGACATAA
1 CCCGAACCCGAAAATACCCGAACCCGACAGAA
* *
11793 CCCGAGCCCGAAAATACCTGAACCCGACAGAA
1 CCCGAACCCGAAAATACCCGAACCCGACAGAA
* *
11825 CCCGAACCTGAAAA-AGCCCGACCCCGA
1 CCCGAACCCGAAAATA-CCCGAACCCGA
11852 ACCCGCCCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 1 0.02
32 48 0.98
ACGTcount: A:0.38, C:0.40, G:0.15, T:0.07
Consensus pattern (32 bp):
CCCGAACCCGAAAATACCCGAACCCGACAGAA
Found at i:13662 original size:22 final size:22
Alignment explanation
Indices: 13627--13679 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
13617 AAAAATTAAC
*
13627 AACGCAAAAAAAAAACAAAACAAA
1 AACG-AAACAAAAAA-AAAACAAA
* *
13651 GACGAAACAAAAAAAAAAGAAA
1 AACGAAACAAAAAAAAAACAAA
13673 AACGAAA
1 AACGAAA
13680 ACGATGCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 13 0.52
23 9 0.36
24 3 0.12
ACGTcount: A:0.77, C:0.13, G:0.09, T:0.00
Consensus pattern (22 bp):
AACGAAACAAAAAAAAAACAAA
Found at i:13674 original size:28 final size:27
Alignment explanation
Indices: 13631--13683 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
13621 ATTAACAACG
*
13631 CAAAAAAAAAACAAAAC-AAAGACGAAA
1 CAAAAAAAAAAAAAAACGAAA-ACGAAA
13658 CAAAAAAAAAAGAAAAACGAAAACGA
1 CAAAAAAAAAA-AAAAACGAAAACGA
13684 TGCCAAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 11 0.48
28 9 0.39
29 3 0.13
ACGTcount: A:0.77, C:0.13, G:0.09, T:0.00
Consensus pattern (27 bp):
CAAAAAAAAAAAAAAACGAAAACGAAA
Found at i:14786 original size:108 final size:108
Alignment explanation
Indices: 14592--14832 Score: 301
Period size: 108 Copynumber: 2.2 Consensus size: 108
14582 AATGCTTTGG
*
14592 ATGGGAACTTTCCCATTTTGAAAACTAAAACTGAAAATGATGGGAACTCTCCCTAAATTGAAAAC
1 ATGGGAACTTTCCCAATTTGAAAACTAAAAC--AAAATGATGGGAACTCTCCC-AAATTGAAAAC
14657 TAAAACTTGATGGGAACTTTCCCAATTT-AAAAACTTTCAAAACTGA
63 TAAAACTTGATGGGAACTTTCCCAATTTGAAAAA-TTTCAAAACTGA
* * * * *
14703 ATGGGAACTTTCCCAATTTGAAAACTTAAA-AAATTGGTGGGAACTTTCCC-AATTTAAAATCTT
1 ATGGGAACTTTCCCAATTTGAAAACTAAAACAAAATGATGGGAACTCTCCCAAATTGAAAA-C-T
* * * *
14766 AAAAGC-TGGTGGGAACTTTCCCAATTTGACAAATTTGAAAACTGG
64 AAAA-CTTGATGGGAACTTTCCCAATTTGAAAAATTTCAAAACTGA
14811 ATGGGAACTTTCCCAATTTGAA
1 ATGGGAACTTTCCCAATTTGAA
14833 GACTGGCTAA
Statistics
Matches: 116, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
106 8 0.07
107 1 0.01
108 74 0.64
109 5 0.04
111 28 0.24
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (108 bp):
ATGGGAACTTTCCCAATTTGAAAACTAAAACAAAATGATGGGAACTCTCCCAAATTGAAAACTAA
AACTTGATGGGAACTTTCCCAATTTGAAAAATTTCAAAACTGA
Found at i:14830 original size:37 final size:35
Alignment explanation
Indices: 14630--14832 Score: 225
Period size: 37 Copynumber: 5.7 Consensus size: 35
14620 AACTGAAAAT
* * * *
14630 GATGGGAACTCTCCCTAAATTGAAAA-CTAAAACTT
1 GATGGGAACTTTCCC-AATTTGAAAATTTAAAACTG
*
14665 GATGGGAACTTTCCCAATTTAAAAACTTTCAAAACTG
1 GATGGGAACTTTCCCAATTTGAAAA-TTT-AAAACTG
* * *
14702 AATGGGAACTTTCCCAATTTGAAAACTTAAAAAATTG
1 GATGGGAACTTTCCCAATTTGAAAA-TT-TAAAACTG
14739 G-TGGGAACTTTCCCAATTT-AAAATCTTAAAAGCTG
1 GATGGGAACTTTCCCAATTTGAAAAT-TTAAAA-CTG
14774 G-TGGGAACTTTCCCAATTTGACAAATTTGAAAACTG
1 GATGGGAACTTTCCCAATTTGA-AAATTT-AAAACTG
14810 GATGGGAACTTTCCCAATTTGAA
1 GATGGGAACTTTCCCAATTTGAA
14833 GACTGGCTAA
Statistics
Matches: 146, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
34 13 0.09
35 40 0.27
36 27 0.18
37 66 0.45
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (35 bp):
GATGGGAACTTTCCCAATTTGAAAATTTAAAACTG
Found at i:14929 original size:53 final size:53
Alignment explanation
Indices: 14799--14959 Score: 209
Period size: 53 Copynumber: 3.0 Consensus size: 53
14789 ATTTGACAAA
* *
14799 TTTGAAAACTGGATGGGAACTTTCCCAATTTGAAGACTG-GCTAAATTGAATAC-
1 TTTGAAAACT-GATGGGAACTTTCCCGATTTGAAGA-AGAGCTAAATTGAATACT
* * *
14852 TTTGAAAATTGATGGGAACTTTCCCGATTTGAAGAAGAGCTAGATGGAATACT
1 TTTGAAAACTGATGGGAACTTTCCCGATTTGAAGAAGAGCTAAATTGAATACT
* * * *
14905 TTTGAAAGCTGATGGGAACCTTCCCGACTTGAAAAAGAGCTAAATTGAATACT
1 TTTGAAAACTGATGGGAACTTTCCCGATTTGAAGAAGAGCTAAATTGAATACT
14958 TT
1 TT
14960 GAAGACTTGA
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 1 0.01
52 36 0.38
53 57 0.61
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (53 bp):
TTTGAAAACTGATGGGAACTTTCCCGATTTGAAGAAGAGCTAAATTGAATACT
Found at i:16040 original size:22 final size:22
Alignment explanation
Indices: 16015--16073 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
16005 ACCGCCTCAA
*
16015 CTAGCTTGCAGCGCCGCTCCGC
1 CTAGCTTGCAGCGCCGCTCCAC
16037 CTAGCTTGCAGCGCCGCTCCAC
1 CTAGCTTGCAGCGCCGCTCCAC
16059 CTAGCTTGCAGCGCC
1 CTAGCTTGCAGCGCC
16074 ATCGTCGGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.12, C:0.44, G:0.25, T:0.19
Consensus pattern (22 bp):
CTAGCTTGCAGCGCCGCTCCAC
Found at i:18790 original size:16 final size:15
Alignment explanation
Indices: 18769--18825 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 15
18759 GGTTATCTAC
18769 ATGCTAAATGCTAGAA
1 ATGCTAAATGC-AGAA
18785 ATGCTAAAATGC----
1 ATGCT-AAATGCAGAA
18797 ATGCTAAATGCCAGAA
1 ATGCTAAATG-CAGAA
18813 ATGCTAAAATGCA
1 ATGCT-AAATGCA
18826 TGCTAAATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
11 5 0.15
12 6 0.18
16 12 0.35
17 11 0.32
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.23
Consensus pattern (15 bp):
ATGCTAAATGCAGAA
Found at i:18812 original size:28 final size:28
Alignment explanation
Indices: 18768--18837 Score: 131
Period size: 28 Copynumber: 2.5 Consensus size: 28
18758 TGGTTATCTA
*
18768 CATGCTAAATGCTAGAAATGCTAAAATG
1 CATGCTAAATGCCAGAAATGCTAAAATG
18796 CATGCTAAATGCCAGAAATGCTAAAATG
1 CATGCTAAATGCCAGAAATGCTAAAATG
18824 CATGCTAAATGCCA
1 CATGCTAAATGCCA
18838 AGTGCCCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (28 bp):
CATGCTAAATGCCAGAAATGCTAAAATG
Found at i:19362 original size:27 final size:28
Alignment explanation
Indices: 19332--19386 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
19322 CAACAACTAA
*
19332 AGCCCAAAGTC-ACATGAACCAAATAAG
1 AGCCCAAAGTCAACATAAACCAAATAAG
*
19359 AGCCTAAAGTCAACATAAACCAAATAAG
1 AGCCCAAAGTCAACATAAACCAAATAAG
19387 CAAATGGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.51, C:0.24, G:0.13, T:0.13
Consensus pattern (28 bp):
AGCCCAAAGTCAACATAAACCAAATAAG
Found at i:20465 original size:19 final size:19
Alignment explanation
Indices: 20441--20478 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20431 TTAATGATTA
20441 GCCAACTTATTTTAACTTT
1 GCCAACTTATTTTAACTTT
20460 GCCAACTTATTTTAACTTT
1 GCCAACTTATTTTAACTTT
20479 TAAACTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (19 bp):
GCCAACTTATTTTAACTTT
Done.