Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022960.1 Corchorus olitorius cultivar O-4 contig22993, 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: 16048
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Found at i:303 original size:10 final size:10
Alignment explanation
Indices: 288--330 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
278 GATATGTTAT
288 AAAAACAAAA
1 AAAAACAAAA
298 AAAAACAAAA
1 AAAAACAAAA
**
308 CCAAACAAAA
1 AAAAACAAAA
* *
318 AGAAAGAAAA
1 AAAAACAAAA
328 AAA
1 AAA
331 GTGCAAAACA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:458 original size:26 final size:27
Alignment explanation
Indices: 400--469 Score: 115
Period size: 26 Copynumber: 2.6 Consensus size: 27
390 ACAGTAATTT
* *
400 TGACAAAAATGCCCCTGGGGCGAAAAA
1 TGACCAAAATGCCCCTGAGGCGAAAAA
427 TGACCAAAATGCCCCTGAGGC-AAAAA
1 TGACCAAAATGCCCCTGAGGCGAAAAA
453 TGACCAAAATGCCCCTG
1 TGACCAAAATGCCCCTG
470 GTGAATTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 22 0.54
27 19 0.46
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (27 bp):
TGACCAAAATGCCCCTGAGGCGAAAAA
Found at i:941 original size:25 final size:25
Alignment explanation
Indices: 912--962 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
902 ATATCTACAT
*
912 ACTCATCTATCTTACTATTCATTTA
1 ACTCATCTATCTCACTATTCATTTA
937 ACTCATCTATCTCACTATTCATTTA
1 ACTCATCTATCTCACTATTCATTTA
962 A
1 A
963 GTATGTAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.45
Consensus pattern (25 bp):
ACTCATCTATCTCACTATTCATTTA
Found at i:3793 original size:68 final size:68
Alignment explanation
Indices: 3683--3891 Score: 391
Period size: 68 Copynumber: 3.1 Consensus size: 68
3673 GCCAAAAATA
* * *
3683 TAATTTGATGAGTTTAAGTCATACTTTGCGGACCGATTCACTCCCTCAGGGCCATCTTAATTGTT
1 TAATTCGATGAGTTTAAGTCATACTTTGCGGACCGATACACTCCCTCAGGGCCATCTTTATTGTT
3748 TGT
66 TGT
3751 TAATTCGATGAGTTTAAGTCATACTTTGCGGACCGATACACTCCCTCAGGGCCATCTTTATTGTT
1 TAATTCGATGAGTTTAAGTCATACTTTGCGGACCGATACACTCCCTCAGGGCCATCTTTATTGTT
3816 TGT
66 TGT
3819 TAATTCGATGAGTTTAAGTCATACTTTGCGGACCGATACACTCCCTCAGGGCCATCTTTATTGTT
1 TAATTCGATGAGTTTAAGTCATACTTTGCGGACCGATACACTCCCTCAGGGCCATCTTTATTGTT
3884 TGT
66 TGT
3887 TAATT
1 TAATT
3892 GTTAGTGACT
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 138 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (68 bp):
TAATTCGATGAGTTTAAGTCATACTTTGCGGACCGATACACTCCCTCAGGGCCATCTTTATTGTT
TGT
Found at i:4592 original size:24 final size:24
Alignment explanation
Indices: 4564--4687 Score: 135
Period size: 24 Copynumber: 5.2 Consensus size: 24
4554 GGTGGTTATG
4564 GTGGCGGTGGTCAAGGAGGAGGAA
1 GTGGCGGTGGTCAAGGAGGAGGAA
* *
4588 GTGGCGGTGG-CAAAGGAGGTGGTA
1 GTGGCGGTGGTC-AAGGAGGAGGAA
*
4612 GTGGCGGTGGTCGAGGAGGAGGAA
1 GTGGCGGTGGTCAAGGAGGAGGAA
* * *
4636 GTCGCGGTGG-CAAAGGAGGTGGTA
1 GTGGCGGTGGTC-AAGGAGGAGGAA
* * *
4660 GTGGCGGCGGTAAAGGAGGAGGCA
1 GTGGCGGTGGTCAAGGAGGAGGAA
4684 GTGG
1 GTGG
4688 TTCAGGTGGC
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
23 2 0.02
24 79 0.96
25 1 0.01
ACGTcount: A:0.22, C:0.10, G:0.55, T:0.14
Consensus pattern (24 bp):
GTGGCGGTGGTCAAGGAGGAGGAA
Found at i:4616 original size:48 final size:48
Alignment explanation
Indices: 4564--4687 Score: 203
Period size: 48 Copynumber: 2.6 Consensus size: 48
4554 GGTGGTTATG
4564 GTGGCGGTGGTCAAGGAGGAGGAAGTGGCGGTGGCAAAGGAGGTGGTA
1 GTGGCGGTGGTCAAGGAGGAGGAAGTGGCGGTGGCAAAGGAGGTGGTA
* *
4612 GTGGCGGTGGTCGAGGAGGAGGAAGTCGCGGTGGCAAAGGAGGTGGTA
1 GTGGCGGTGGTCAAGGAGGAGGAAGTGGCGGTGGCAAAGGAGGTGGTA
* * *
4660 GTGGCGGCGGTAAAGGAGGAGGCAGTGG
1 GTGGCGGTGGTCAAGGAGGAGGAAGTGG
4688 TTCAGGTGGC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.22, C:0.10, G:0.55, T:0.14
Consensus pattern (48 bp):
GTGGCGGTGGTCAAGGAGGAGGAAGTGGCGGTGGCAAAGGAGGTGGTA
Found at i:4738 original size:42 final size:42
Alignment explanation
Indices: 4694--4840 Score: 215
Period size: 42 Copynumber: 3.5 Consensus size: 42
4684 GTGGTTCAGG
* **
4694 TGGCGGCGGTCAAGGAGGAGGAAGCAGCA-GTGGTGGTTATGG
1 TGGCGGCGGCCAAGGAGGAGGAAGCAG-AGGTGGTGGTTATCA
* * *
4736 TGGTGGCGGCCAAGGAGGAGGAAGCGGAGGTGGTGGTTCTCA
1 TGGCGGCGGCCAAGGAGGAGGAAGCAGAGGTGGTGGTTATCA
*
4778 TGGCGGCGGCCAAGGAGGAGGAAGCAGAGGTGGTGGTTCTCA
1 TGGCGGCGGCCAAGGAGGAGGAAGCAGAGGTGGTGGTTATCA
4820 TGGCGGCGGCCAAGGAGGAGG
1 TGGCGGCGGCCAAGGAGGAGG
4841 CAGCGGTGGC
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
41 1 0.01
42 95 0.99
ACGTcount: A:0.20, C:0.15, G:0.50, T:0.14
Consensus pattern (42 bp):
TGGCGGCGGCCAAGGAGGAGGAAGCAGAGGTGGTGGTTATCA
Found at i:4765 original size:84 final size:84
Alignment explanation
Indices: 4677--4846 Score: 225
Period size: 84 Copynumber: 2.0 Consensus size: 84
4667 CGGTAAAGGA
** * ** *
4677 GGAGGCAGTGGTTCAGGTGGCGGCGGTCAAGGAGGAGGAAGCAGCA-GTGGTGGTTATGGTGGTG
1 GGAGGCAGTGGTTCACATGGCGGCGGCCAAGGAGGAGGAAGCAG-AGGTGGTGGTTATCATGGCG
4741 GCGGCCAAGGAGGAGGAAGC
65 GCGGCCAAGGAGGAGGAAGC
** * *
4761 GGAGGTGGTGGTTCTCATGGCGGCGGCCAAGGAGGAGGAAGCAGAGGTGGTGGTTCTCATGGCGG
1 GGAGGCAGTGGTTCACATGGCGGCGGCCAAGGAGGAGGAAGCAGAGGTGGTGGTTATCATGGCGG
*
4826 CGGCCAAGGAGGAGGCAGC
66 CGGCCAAGGAGGAGGAAGC
4845 GG
1 GG
4847 TGGCGGTAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
83 1 0.01
84 73 0.99
ACGTcount: A:0.20, C:0.15, G:0.51, T:0.14
Consensus pattern (84 bp):
GGAGGCAGTGGTTCACATGGCGGCGGCCAAGGAGGAGGAAGCAGAGGTGGTGGTTATCATGGCGG
CGGCCAAGGAGGAGGAAGC
Found at i:4851 original size:24 final size:24
Alignment explanation
Indices: 4824--4870 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4814 TTCTCATGGC
* *
4824 GGCGGCCAAGGAGGAGGCAGCGGT
1 GGCGGCAAAGGAGGAGGAAGCGGT
*
4848 GGCGGTAAAGGAGGAGGAAGCGG
1 GGCGGCAAAGGAGGAGGAAGCGG
4871 AGGTGGTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.55, T:0.04
Consensus pattern (24 bp):
GGCGGCAAAGGAGGAGGAAGCGGT
Found at i:4860 original size:66 final size:66
Alignment explanation
Indices: 4789--5035 Score: 410
Period size: 66 Copynumber: 3.8 Consensus size: 66
4779 GGCGGCGGCC
*
4789 AAGGAGGAGGAAGCAGAGGTGGTGGTTCTCATGGCGGCGGCCAAGGAGGAGGCAGCGGTGGCGGT
1 AAGGAGGAGGAAGCGGAGGTGGTGGTTCTCATGGCGGCGGCCAAGGAGGAGGCAGCGGTGGCGGT
4854 A
66 A
4855 AAGGAGGAGGAAGCGGAGGTGGTGGTTCTCATGGCGGCGGCCAAGGAGGAGGCAGCGGTGGCGGT
1 AAGGAGGAGGAAGCGGAGGTGGTGGTTCTCATGGCGGCGGCCAAGGAGGAGGCAGCGGTGGCGGT
4920 A
66 A
* *
4921 AAGGAGGAGGAAGTGGAGGTGGTGGTTCTCATGGCGGCGGCCAAGGAGGAGGAAGCGGTGGCGGT
1 AAGGAGGAGGAAGCGGAGGTGGTGGTTCTCATGGCGGCGGCCAAGGAGGAGGCAGCGGTGGCGGT
4986 A
66 A
* * * *
4987 AAGGAGGAGGAAGCGGCGGTGGAGGTTC-C--GGAGGCGGGCAAGGAGGAGG
1 AAGGAGGAGGAAGCGGAGGTGGTGGTTCTCATGGCGGCGGCCAAGGAGGAGG
5036 TTATGGCGGC
Statistics
Matches: 173, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
63 18 0.10
65 1 0.01
66 154 0.89
ACGTcount: A:0.23, C:0.14, G:0.52, T:0.11
Consensus pattern (66 bp):
AAGGAGGAGGAAGCGGAGGTGGTGGTTCTCATGGCGGCGGCCAAGGAGGAGGCAGCGGTGGCGGT
A
Found at i:4983 original size:24 final size:24
Alignment explanation
Indices: 4956--5002 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
4946 TTCTCATGGC
*
4956 GGCGGCCAAGGAGGAGGAAGCGGT
1 GGCGGCAAAGGAGGAGGAAGCGGT
*
4980 GGCGGTAAAGGAGGAGGAAGCGG
1 GGCGGCAAAGGAGGAGGAAGCGG
5003 CGGTGGAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.55, T:0.04
Consensus pattern (24 bp):
GGCGGCAAAGGAGGAGGAAGCGGT
Found at i:5004 original size:21 final size:21
Alignment explanation
Indices: 4954--5006 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 21
4944 GGTTCTCATG
**
4954 GCGGCGGCCAAGGAGGAGGAA
1 GCGGCGGTAAAGGAGGAGGAA
4975 GCGGTGGCGGTAAAGGAGGAGGAA
1 GC---GGCGGTAAAGGAGGAGGAA
4999 GCGGCGGT
1 GCGGCGGT
5007 GGAGGTTCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 8 0.30
24 19 0.70
ACGTcount: A:0.25, C:0.15, G:0.55, T:0.06
Consensus pattern (21 bp):
GCGGCGGTAAAGGAGGAGGAA
Found at i:5128 original size:30 final size:32
Alignment explanation
Indices: 5064--5134 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
5054 ACGTGGTGGC
* * *
5064 GGTGGTGGTAAAGGAGGTGGAAGCGGTTCTGGT
1 GGTGGCGGTAAAGGAGGAGGAAGCAG-TCTGGT
5097 GGTGGCGGTAAAGGAGGAGGAAGCAG-C-GGT
1 GGTGGCGGTAAAGGAGGAGGAAGCAGTCTGGT
*
5127 GGAGGCGG
1 GGTGGCGG
5135 CGGAGGCGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.29
31 1 0.03
33 23 0.68
ACGTcount: A:0.21, C:0.08, G:0.55, T:0.15
Consensus pattern (32 bp):
GGTGGCGGTAAAGGAGGAGGAAGCAGTCTGGT
Found at i:5218 original size:120 final size:120
Alignment explanation
Indices: 4977--5192 Score: 333
Period size: 120 Copynumber: 1.8 Consensus size: 120
4967 AGGAGGAAGC
* **
4977 GGTGGCGGTAAAGGAGGAGGAAGCGGCGGTGGAGGTTCCGGAGGCGGGCAAGGAGGAGGTTATGG
1 GGTGGCGGTAAAGGAGGAGGAAGCAGCGGTGGAGGCGCCGGAGGCGGGCAAGGAGGAGGTTATGG
* * * * * *
5042 CGGCGGAGGGGGACGTGGTGGCGGTGGTGGTAAAGGAGGTGGAAGCGGTTCTGGT
66 CGGCGGAGGGGGACGTGGTGGCGGAGGGGGCAAAGGAGGAGGAAGCGGTGCAGGT
*
5097 GGTGGCGGTAAAGGAGGAGGAAGCAGCGGTGGAGGCGGCGGAGGCGGGCAAGGAGGAGGTTATGG
1 GGTGGCGGTAAAGGAGGAGGAAGCAGCGGTGGAGGCGCCGGAGGCGGGCAAGGAGGAGGTTATGG
*
5162 CGGCGGAGGGGGACGTGGTGGTGGAGGGGGC
66 CGGCGGAGGGGGACGTGGTGGCGGAGGGGGC
5193 CATGGCGGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 88 1.00
ACGTcount: A:0.19, C:0.11, G:0.58, T:0.12
Consensus pattern (120 bp):
GGTGGCGGTAAAGGAGGAGGAAGCAGCGGTGGAGGCGCCGGAGGCGGGCAAGGAGGAGGTTATGG
CGGCGGAGGGGGACGTGGTGGCGGAGGGGGCAAAGGAGGAGGAAGCGGTGCAGGT
Found at i:5555 original size:16 final size:17
Alignment explanation
Indices: 5519--5555 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
5509 CTTTGCTGCA
5519 ATAATAGATCATGATCT
1 ATAATAGATCATGATCT
5536 ATAAT-GAT-ATGATGCT
1 ATAATAGATCATGAT-CT
5552 ATAA
1 ATAA
5556 CAAAATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 5 0.26
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (17 bp):
ATAATAGATCATGATCT
Done.