Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017712.1 Corchorus olitorius cultivar O-4 contig17745, 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: 69482
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3746 original size:31 final size:31
Alignment explanation
Indices: 3703--3769 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
3693 AAAATGGGTG
*
3703 AGGGA-TCTAATTGCTTAATTAA-TTCAACTTC
1 AGGGACTCTAATTGC-TAACTAAGTTC-ACTTC
*
3734 AGGGACTC-AATTGCTCACTAAGTTCACTTC
1 AGGGACTCTAATTGCTAACTAAGTTCACTTC
3764 AGGGAC
1 AGGGAC
3770 CCATTTGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 16 0.50
31 14 0.44
32 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (31 bp):
AGGGACTCTAATTGCTAACTAAGTTCACTTC
Found at i:4471 original size:17 final size:18
Alignment explanation
Indices: 4448--4482 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4438 AAAATGATTT
4448 AAAAAAAATAGAA-AAAAG
1 AAAAAAAA-AGAAGAAAAG
4466 AAAAAAAAAGAAGAAAA
1 AAAAAAAAAGAAGAAAA
4483 AATGAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAGAAGAAAAG
Found at i:4471 original size:20 final size:21
Alignment explanation
Indices: 4430--4490 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
4420 CGAGTTTTGG
* **
4430 AAAAGAAGAAAATGATTTAAAA
1 AAAAGAAGAAAA-AATGAAAAA
*
4452 AAAA-TAGAAAAAA-GAAAAA
1 AAAAGAAGAAAAAATGAAAAA
4471 AAAAGAAGAAAAAATGAAAA
1 AAAAGAAGAAAAAATGAAAA
4491 TTTTTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.25
20 9 0.28
21 11 0.34
22 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (21 bp):
AAAAGAAGAAAAAATGAAAAA
Found at i:4639 original size:13 final size:12
Alignment explanation
Indices: 4620--4650 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
4610 TTGACTATTT
4620 TTTTTTTAAATA
1 TTTTTTTAAATA
4632 TATTTTTTAAATA
1 T-TTTTTTAAATA
4645 TTTTTT
1 TTTTTT
4651 AATCAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTTTAAATA
Found at i:4645 original size:11 final size:12
Alignment explanation
Indices: 4621--4653 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
4611 TGACTATTTT
4621 TTTTTTAAATATA
1 TTTTTT-AATATA
4634 TTTTTTAA-ATA
1 TTTTTTAATATA
4645 TTTTTTAAT
1 TTTTTTAAT
4654 CAAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 2 0.11
13 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTTTAATATA
Found at i:7544 original size:48 final size:48
Alignment explanation
Indices: 7473--7566 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
7463 GTTCAGCGCG
*
7473 TATCTCGTCCACATCACAATCCAACAGCTCATGATGATCCAAACTGCC
1 TATCTCGTCCACATCACAATCCAACAACTCATGATGATCCAAACTGCC
* * *
7521 TATCTCGTCCGCATCACAATCCAACAACTCCTTATGATCCAAACTG
1 TATCTCGTCCACATCACAATCCAACAACTCATGATGATCCAAACTG
7567 ATCCAAACGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.31, C:0.35, G:0.10, T:0.24
Consensus pattern (48 bp):
TATCTCGTCCACATCACAATCCAACAACTCATGATGATCCAAACTGCC
Found at i:9807 original size:27 final size:29
Alignment explanation
Indices: 9754--9808 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
9744 CTAAATTAAC
* *
9754 ATTATTAAAATATATTTTAATTATGCCATT
1 ATTATTAAAATATA-TTAAAATATGCCATT
9784 ATTATTAAAATATA-TAAAAT-TGCCA
1 ATTATTAAAATATATTAAAATATGCCA
9809 ATATGTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 4 0.17
30 14 0.61
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (29 bp):
ATTATTAAAATATATTAAAATATGCCATT
Found at i:9830 original size:46 final size:43
Alignment explanation
Indices: 9762--9848 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
9752 ACATTATTAA
*
9762 AATATATTTTAATTATGCCATTATTATTAAAATATATAAAATTGCC
1 AATATATTTTAATTATACC---ATTATTAAAATATATAAAATTGCC
* * *
9808 AATATGTTTTGATTATATCATTATTAAAATATATAAAATTG
1 AATATATTTTAATTATACCATTATTAAAATATATAAAATTG
9849 TCTTTATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 22 0.59
46 15 0.41
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (43 bp):
AATATATTTTAATTATACCATTATTAAAATATATAAAATTGCC
Found at i:10776 original size:22 final size:22
Alignment explanation
Indices: 10722--10884 Score: 120
Period size: 22 Copynumber: 7.3 Consensus size: 22
10712 AAAAATTAAT
10722 AAAATTTCATAGAGAGGTTATC
1 AAAATTTCATAGAGAGGTTATC
**
10744 AAAAAAATCATATG-GAGGTTATC
1 -AAAATTTCATA-GAGAGGTTATC
* *
10767 AAAATTTCATAGAAAGGTTTATT
1 AAAATTTCATAGAGAGG-TTATC
**
10790 AAAATTTCATAGTTAGGTTATC
1 AAAATTTCATAGAGAGGTTATC
** * * *
10812 AGTATTTCATTGGGAGTTTATC
1 AAAATTTCATAGAGAGGTTATC
*
10834 ACAATTTCAT--A-AGGTAATCATC
1 AAAATTTCATAGAGAGGT--T-ATC
10856 AAAATTTCATAGTA-AGGTTATC
1 AAAATTTCATAG-AGAGGTTATC
10878 AAAATTT
1 AAAATTT
10885 GGTGGTTATC
Statistics
Matches: 111, Mismatches: 20, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
19 3 0.03
21 2 0.02
22 62 0.56
23 38 0.34
24 1 0.01
25 5 0.05
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGAGAGGTTATC
Found at i:10800 original size:45 final size:43
Alignment explanation
Indices: 10722--10905 Score: 137
Period size: 45 Copynumber: 4.3 Consensus size: 43
10712 AAAAATTAAT
* **
10722 AAAATTTCATAGAGAGGTTATCAAAAAAATCATATGGAGGTTATC
1 AAAATTTCATAGAAAGGTTATC-AAAATTTCATA-GGAGGTTATC
* *
10767 AAAATTTCATAGAAAGGTTTATTAAAATTTCATAGTTAGGTTATC
1 AAAATTTCATAGAAAGG-TTATCAAAATTTCATAG-GAGGTTATC
** * ** * *
10812 AGTATTTCATTGGGAGTTTATCACAATTTCATA--AGGTAATCATC
1 AAAATTTCATAGAAAGGTTATCAAAATTTCATAGGAGGT--T-ATC
* *
10856 AAAATTTCATAGTAAGGTTATCAAAA-TT--T-GGTGGTTATC
1 AAAATTTCATAGAAAGGTTATCAAAATTTCATAGGAGGTTATC
10895 AAAATTTCATA
1 AAAATTTCATA
10906 AAAATATTTA
Statistics
Matches: 111, Mismatches: 21, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
39 14 0.13
40 1 0.01
41 5 0.05
42 3 0.03
43 3 0.03
44 37 0.33
45 44 0.40
46 4 0.04
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (43 bp):
AAAATTTCATAGAAAGGTTATCAAAATTTCATAGGAGGTTATC
Found at i:14356 original size:23 final size:24
Alignment explanation
Indices: 14321--14376 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
14311 AATTAATTTA
*
14321 AAAAAAAAGTAAATCCAAGTAATG
1 AAAAAAAAGTAAATCCAAATAATG
* *
14345 AAAAAAAA-TAAATCTAAATAATT
1 AAAAAAAAGTAAATCCAAATAATG
14368 AATAAAAAA
1 AA-AAAAAA
14377 ATCGATAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (24 bp):
AAAAAAAAGTAAATCCAAATAATG
Found at i:22001 original size:22 final size:22
Alignment explanation
Indices: 21965--22008 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
21955 AATTGCAGGA
*
21965 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
21987 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
22009 GCGTAGGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Found at i:22022 original size:52 final size:52
Alignment explanation
Indices: 21961--22063 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
21951 CAAGAATTGC
*
21961 AGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGACAGAAGTTGTTGCGT
1 AGGACAACTTCGGCCCAAAACTTGTTCAACTTCGGGACAGAAGTTGTTGCGT
*
22013 AGGACAACTTCGGCCTAAAACTTGTTCAACTTCGGGACAGAAGTTGTTGCG
1 AGGACAACTTCGGCCCAAAACTTGTTCAACTTCGGGACAGAAGTTGTTGCG
22064 GAAAGAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (52 bp):
AGGACAACTTCGGCCCAAAACTTGTTCAACTTCGGGACAGAAGTTGTTGCGT
Found at i:32469 original size:15 final size:16
Alignment explanation
Indices: 32449--32484 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
32439 CGCTCAAATG
32449 TCGGGTC-TTCTGGGT
1 TCGGGTCATTCTGGGT
32464 TCGGGTCAATTCTGGGT
1 TCGGGTC-ATTCTGGGT
32481 TCGG
1 TCGG
32485 TCGTTTTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
17 12 0.63
ACGTcount: A:0.06, C:0.19, G:0.39, T:0.36
Consensus pattern (16 bp):
TCGGGTCATTCTGGGT
Found at i:33372 original size:15 final size:15
Alignment explanation
Indices: 33352--33389 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
33342 GCTAAACTTC
*
33352 ATTATATGAACAATT
1 ATTATATGAACAATA
*
33367 ATTATATGAATAATA
1 ATTATATGAACAATA
33382 ATT-TATGA
1 ATTATATGA
33390 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (15 bp):
ATTATATGAACAATA
Found at i:33879 original size:31 final size:31
Alignment explanation
Indices: 33844--33905 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
33834 CCTAACCCTA
33844 GACCCAG-TAGAGCCGAGA-CCCGAATGACCTG
1 GACCCAGATA-AGCCGA-ATCCCGAATGACCTG
*
33875 GACCCAGATAAGCCGAATCCTGAATGACCTG
1 GACCCAGATAAGCCGAATCCCGAATGACCTG
33906 AGAAATTACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 1 0.04
31 25 0.89
32 2 0.07
ACGTcount: A:0.31, C:0.31, G:0.26, T:0.13
Consensus pattern (31 bp):
GACCCAGATAAGCCGAATCCCGAATGACCTG
Found at i:34477 original size:23 final size:22
Alignment explanation
Indices: 34428--34477 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
34418 GTTTTTTAAT
*
34428 TAAAATAGTAAAATGATAAAAA
1 TAAAATAGTAAAATAATAAAAA
* *
34450 TAAAATAGGTATAATAATATAAA
1 TAAAATA-GTAAAATAATAAAAA
34473 TAAAA
1 TAAAA
34478 AATAGAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (22 bp):
TAAAATAGTAAAATAATAAAAA
Found at i:35707 original size:15 final size:15
Alignment explanation
Indices: 35689--35719 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35679 CAAGGGCTGA
*
35689 AATTAATTAATTATT
1 AATTAAATAATTATT
35704 AATTAAATAATTATT
1 AATTAAATAATTATT
35719 A
1 A
35720 TTTTCTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAAATAATTATT
Found at i:54883 original size:49 final size:49
Alignment explanation
Indices: 54818--54916 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
54808 CAAATCAACG
* * *
54818 AATCGTTATAATAATAAACAAATCAATGAGTGTCAAATATGCTAAACAC
1 AATCGTCATAACAATAAACAAATCAAAGAGTGTCAAATATGCTAAACAC
*
54867 AATCGTCATAACAATAAACATATCAAAGAGTGTCAAATATGCTAAACAC
1 AATCGTCATAACAATAAACAAATCAAAGAGTGTCAAATATGCTAAACAC
54916 A
1 A
54917 TTTGACAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.24
Consensus pattern (49 bp):
AATCGTCATAACAATAAACAAATCAAAGAGTGTCAAATATGCTAAACAC
Found at i:55620 original size:50 final size:51
Alignment explanation
Indices: 55561--55664 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
55551 GTAGAAAAAA
*
55561 AAACCCAGCTCCTTGAA-TTTTTCCATTTCCTTAACAAGCATGTCTTACTG
1 AAACCCAGCTCCTTGAATTTTTTCCATCTCCTTAACAAGCATGTCTTACTG
*
55611 AAACCCAGCTCCTTGAATTTTTTTCATCTCCTTAACAAGCATGTCTTACTG
1 AAACCCAGCTCCTTGAATTTTTTCCATCTCCTTAACAAGCATGTCTTACTG
55662 AAA
1 AAA
55665 TTTTGTTGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 17 0.33
51 34 0.67
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.36
Consensus pattern (51 bp):
AAACCCAGCTCCTTGAATTTTTTCCATCTCCTTAACAAGCATGTCTTACTG
Found at i:57599 original size:3 final size:3
Alignment explanation
Indices: 57591--57616 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
57581 AGCTATCAGA
57591 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
57617 AAGGGCTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:58892 original size:13 final size:12
Alignment explanation
Indices: 58874--58918 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
58864 ATTTTATTAC
58874 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
58887 TGTTTTATAAAT
1 TGTTTTATAAAT
*
58899 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
58913 TGTTTT
1 TGTTTT
58919 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Done.