Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014083.1 Corchorus olitorius cultivar O-4 contig14116, 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: 30508
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4719 original size:21 final size:21
Alignment explanation
Indices: 4695--4744 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
4685 CTTAGGCAAT
4695 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
4716 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
4737 TCCAATGA
1 TCCAATGA
4745 TCTCCTAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:5371 original size:5 final size:5
Alignment explanation
Indices: 5358--5420 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
5348 TTAAAGATGA
* *
5358 AAAAA AAAAC AAAAAC AAAAA AAAAC AAAAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC -AAAAC AAAAC AAAAC --AAAAC AAAAC AAAAC AAAAC
5406 -AAAC -AAAC -AAAC AAA
1 AAAAC AAAAC AAAAC AAA
5421 CAGTGCGTGC
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
4 12 0.24
5 29 0.57
6 5 0.10
7 5 0.10
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:5379 original size:17 final size:17
Alignment explanation
Indices: 5357--5420 Score: 71
Period size: 16 Copynumber: 3.8 Consensus size: 17
5347 GTTAAAGATG
5357 AAAAAAAAAACAAAAAC
1 AAAAAAAAAACAAAAAC
5374 -AAAAAAAAACAAAAA-
1 AAAAAAAAAACAAAAAC
*
5389 ACAAAACAAAAC-AAAAC
1 A-AAAAAAAAACAAAAAC
*
5406 AAACAAACAAACAAA
1 AAA-AAAAAAACAAA
5421 CAGTGCGTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 21 0.54
17 16 0.41
18 2 0.05
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAC
Found at i:5411 original size:4 final size:4
Alignment explanation
Indices: 5370--5422 Score: 58
Period size: 4 Copynumber: 13.2 Consensus size: 4
5360 AAAAAAACAA
5370 AAAC AAA- AAA- AAAC AAA- AAAC AAAAC AAAAC AAAAC AAAC AAAC AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC -AAAC -AAAC -AAAC AAAC AAAC AAAC
5418 AAAC A
1 AAAC A
5423 GTGCGTGCGA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
3 9 0.20
4 23 0.50
5 14 0.30
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:5417 original size:22 final size:22
Alignment explanation
Indices: 5357--5420 Score: 87
Period size: 22 Copynumber: 2.9 Consensus size: 22
5347 GTTAAAGATG
5357 AAAA-AAAAAACAAAAACAAAAA
1 AAAACAAAAAAC-AAAACAAAAA
*
5379 AAAACAAAAAACAAAACAAAAC
1 AAAACAAAAAACAAAACAAAAA
5401 AAAACAAACAAAC-AAACAAA
1 AAAACAAA-AAACAAAACAAA
5421 CAGTGCGTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 28 0.72
23 11 0.28
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (22 bp):
AAAACAAAAAACAAAACAAAAA
Found at i:17716 original size:22 final size:21
Alignment explanation
Indices: 17691--17735 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17681 TTAAGGAAAG
17691 AATTAAAAAATATTAATTAAAA
1 AATTAAAAAATA-TAATTAAAA
** *
17713 AATTAATTATTATAATTAAAA
1 AATTAAAAAATATAATTAAAA
17734 AA
1 AA
17736 GGAAGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTAAAAAATATAATTAAAA
Found at i:18026 original size:17 final size:17
Alignment explanation
Indices: 18004--18037 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17994 AATAAAATAA
*
18004 TAAAAATTATTAAAAAT
1 TAAAAATAATTAAAAAT
18021 TAAAAATAATTAAAAAT
1 TAAAAATAATTAAAAAT
18038 GAATTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAATAATTAAAAAT
Found at i:20447 original size:2 final size:2
Alignment explanation
Indices: 20440--20465 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20430 TGTCAAGAAC
20440 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
20466 GAGACATTTA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20651 original size:6 final size:6
Alignment explanation
Indices: 20642--20669 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20632 AATGCAATGA
20642 GGGATT GGGATT GGGATT GGGATT GGGA
1 GGGATT GGGATT GGGATT GGGATT GGGA
20670 GCATTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.54, T:0.29
Consensus pattern (6 bp):
GGGATT
Found at i:21872 original size:6 final size:6
Alignment explanation
Indices: 21861--21904 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
21851 CAGGCTGCAC
21861 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CA
1 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CA
21905 TCCGTTAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:22060 original size:39 final size:38
Alignment explanation
Indices: 21934--22081 Score: 226
Period size: 38 Copynumber: 3.9 Consensus size: 38
21924 TCGAGTCTAG
21934 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
21971 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
22009 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* **
22048 CCATCAGTTTAACCCCCTGAGATACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
22082 ATGCACAGCC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
37 7 0.07
38 62 0.61
39 33 0.32
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:22068 original size:77 final size:75
Alignment explanation
Indices: 21934--22081 Score: 224
Period size: 77 Copynumber: 1.9 Consensus size: 75
21924 TCGAGTCTAG
*
21934 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
1 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGACACGGG
21999 TCCACTCTTA
66 TCCACTCTTA
* * * * *
22009 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTACCATCAGTTTAACCCCCTGAGATACG
1 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTC-TTACCAACAGTTTAACCCCCTGAGACACG
22074 GGTCCACT
64 GGTCCACT
22082 ATGCACAGCC
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 7 0.11
76 24 0.37
77 34 0.52
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (75 bp):
CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGACACGGG
TCCACTCTTA
Found at i:29388 original size:21 final size:21
Alignment explanation
Indices: 29362--29402 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
29352 ACATAAAGAA
*
29362 GTTTCAAGCTCATTGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
29383 GTTTCAAGCTCATCGGAGTT
1 GTTTCAAGCTCATCGGAGTT
29403 ACCTAAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Found at i:29689 original size:65 final size:65
Alignment explanation
Indices: 29584--29713 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
29574 GCTTGCTATT
* *
29584 GATTCCAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTTGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
* *
29649 GATTCAAACTTTCTGCACTAGCCTAGGCGTGGGTATGCCAAGGGTACCCCATGCATGGGTAGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
29714 CAGGTTTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (65 bp):
GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
Found at i:30353 original size:28 final size:25
Alignment explanation
Indices: 30316--30368 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
30306 AATCTATCCT
*
30316 TCTACTCATCTATCATCAAGTTTTTCA
1 TCTACTCATCCATCA--AAGTTTTTCA
30343 TCTATCTCATCCATCAAAGTTTTTCA
1 TCTA-CTCATCCATCAAAGTTTTTCA
30369 AATTTTCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 4 0.17
28 10 0.42
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.43
Consensus pattern (25 bp):
TCTACTCATCCATCAAAGTTTTTCA
Done.