Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013364.1 Corchorus olitorius cultivar O-4 contig13397, 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: 26955
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:5084 original size:12 final size:12
Alignment explanation
Indices: 5067--5091 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5057 TCAAACACAA
5067 CCCTTTCATCAT
1 CCCTTTCATCAT
5079 CCCTTTCATCAT
1 CCCTTTCATCAT
5091 C
1 C
5092 TCCATCTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.40
Consensus pattern (12 bp):
CCCTTTCATCAT
Found at i:6267 original size:2 final size:2
Alignment explanation
Indices: 6262--6289 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6252 TTCCTCACAA
6262 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
6290 ATACCTTGTT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:12257 original size:18 final size:18
Alignment explanation
Indices: 12234--12268 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12224 TCTTTCTTTC
12234 TTTTTTTGATTTTTATTA
1 TTTTTTTGATTTTTATTA
12252 TTTTTTTGATTTTTATT
1 TTTTTTTGATTTTTATT
12269 TTGATTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTTTTTGATTTTTATTA
Found at i:12276 original size:18 final size:18
Alignment explanation
Indices: 12237--12279 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12227 TTCTTTCTTT
*
12237 TTTTGATTTTTATTATTT
1 TTTTGATTTTTATTATTA
12255 TTTTGATTTTTATT-TTGA
1 TTTTGATTTTTATTATT-A
12273 TTTTGAT
1 TTTTGAT
12280 GATGATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (18 bp):
TTTTGATTTTTATTATTA
Found at i:12686 original size:22 final size:21
Alignment explanation
Indices: 12646--12689 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
12636 TCCAAGTGCC
12646 TTTATTTTCCTTTTTTCATTT
1 TTTATTTTCCTTTTTTCATTT
12667 TTTATTTT-CTTCATTTTCATTT
1 TTTATTTTCCTT--TTTTCATTT
12689 T
1 T
12690 CATTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 10 0.48
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTTTCCTTTTTTCATTT
Found at i:12688 original size:15 final size:15
Alignment explanation
Indices: 12649--12690 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
12639 AAGTGCCTTT
*
12649 ATTTTCCTTTT-TTC
1 ATTTTCATTTTCTTC
*
12663 ATTTTTTATTTTCTTC
1 A-TTTTCATTTTCTTC
12679 ATTTTCATTTTC
1 ATTTTCATTTTC
12691 ATTTTTTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.78
16 4 0.17
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTCATTTTCTTC
Found at i:13650 original size:21 final size:21
Alignment explanation
Indices: 13620--13659 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13610 CTAAAAACAG
*
13620 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
*
13641 GACAACTCCTGTCCAGGAC
1 GACAACTCCTGCCCAGGAC
13660 CTGGTCTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.23, T:0.17
Consensus pattern (21 bp):
GACAACTCCTGCCCAGGACTT
Found at i:13713 original size:71 final size:70
Alignment explanation
Indices: 13612--13798 Score: 286
Period size: 71 Copynumber: 2.6 Consensus size: 70
13602 ATTGAAGCCT
* * *
13612 AAAAA-CAGGACAAGTCCTGCCCAGGACTTGACAACTCCTGTCCAGGACCTGGTCTGTTGAAAGA
1 AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAA
13676 CGGAA
66 CGGAA
* *
13681 GAAAAATCAGAACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAA
1 -AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAA
13746 ACGGAA
65 ACGGAA
*
13752 AAAAATTCAGAACAAGTCCTGTCCAGGACTTGGACAACTCCTGCCCA
1 AAAAA-TCAGAACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCA
13799 TGACTTGTTG
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
70 10 0.09
71 82 0.77
72 15 0.14
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.18
Consensus pattern (70 bp):
AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAA
CGGAA
Found at i:13718 original size:21 final size:21
Alignment explanation
Indices: 13692--13733 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
13682 AAAAATCAGA
13692 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
13713 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
13734 GTCTGTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.38, G:0.19, T:0.19
Consensus pattern (21 bp):
ACAACTCCTGCCCAGGACTTG
Found at i:13793 original size:22 final size:22
Alignment explanation
Indices: 13763--13805 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13753 AAAATTCAGA
* *
13763 ACAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
*
13785 ACAACTCCTGCCCATGACTTG
1 ACAACTCCTGCCCAGGACTTG
13806 TTGCGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:16031 original size:15 final size:14
Alignment explanation
Indices: 16007--16036 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
15997 CAATAACATC
16007 AAACAAACAAAACA
1 AAACAAACAAAACA
16021 AAACGAAACAAAACA
1 AAAC-AAACAAAACA
16036 A
1 A
16037 GGCAACCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.77, C:0.20, G:0.03, T:0.00
Consensus pattern (14 bp):
AAACAAACAAAACA
Found at i:20355 original size:28 final size:27
Alignment explanation
Indices: 20252--20353 Score: 132
Period size: 28 Copynumber: 3.7 Consensus size: 27
20242 TGTGAGCTTG
20252 AAATGACCAAAATGCCCCTGAATGTAA
1 AAATGACCAAAATGCCCCTGAATGTAA
**
20279 AAATGACCAAAATGCCCCCTGAATGTGC
1 AAATGACCAAAATG-CCCCTGAATGTAA
* * *
20307 AAATGACTAAAATGCCCCTAGATTTTAA
1 AAATGACCAAAATGCCCCT-GAATGTAA
*
20335 AAATGACCGAAATGCCCCT
1 AAATGACCAAAATGCCCCT
20354 AGTTGATGCT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 19 0.30
28 45 0.70
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATGTAA
Found at i:21570 original size:16 final size:15
Alignment explanation
Indices: 21541--21573 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
21531 GACAGAAATT
21541 AATTAAACAGAAAAC
1 AATTAAACAGAAAAC
21556 AATTAAACTAGAAAAC
1 AATTAAAC-AGAAAAC
21572 AA
1 AA
21574 AGCAGAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (15 bp):
AATTAAACAGAAAAC
Found at i:24852 original size:21 final size:21
Alignment explanation
Indices: 24823--24887 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
24813 GGCTTGGAAT
*
24823 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATGGCC
* **
24844 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATGGCC
*
24865 GGTGGTGGCACGGTGAATGGCC
1 GGTGGTGGCACGG-GCATGGCC
24887 G
1 G
24888 ATAATGGCTT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 30 0.86
22 5 0.14
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.17
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATGGCC
Done.