Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005295.1 Corchorus capsularis cultivar CVL-1 contig05313, 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: 6141
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Found at i:1569 original size:5 final size:5
Alignment explanation
Indices: 1559--1598 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
1549 ACAATATTAC
1559 ATAAA ATAAA ATAAA ATAAA ATAAA TATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA -ATAAA ATAAA ATAA
1599 TATCTAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:1766 original size:3 final size:3
Alignment explanation
Indices: 1758--1787 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1748 TAATTTCTAG
1758 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1788 TTAACATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3120 original size:13 final size:13
Alignment explanation
Indices: 3078--3173 Score: 62
Period size: 13 Copynumber: 7.3 Consensus size: 13
3068 GTTGTACTTA
3078 GGAGGTCACGTGTT
1 GGAGGTCACGTG-T
*
3092 GAAGGTGTC-CGT-T
1 GGA-G-GTCACGTGT
3105 GGAGGTCACGTGT
1 GGAGGTCACGTGT
3118 GGAGTTGT-AC-T-T
1 GGAG--GTCACGTGT
3130 CGGAGGTCACGTGT
1 -GGAGGTCACGTGT
3144 GGA-GTCGTACGT-T
1 GGAGGTC--ACGTGT
3157 GGAGGTCACGTGT
1 GGAGGTCACGTGT
3170 GGAG
1 GGAG
3174 TGCCAGCTGG
Statistics
Matches: 66, Mismatches: 2, Indels: 29
0.68 0.02 0.30
Matches are distributed among these distances:
11 5 0.08
12 14 0.21
13 26 0.39
14 12 0.18
15 6 0.09
16 3 0.05
ACGTcount: A:0.16, C:0.15, G:0.43, T:0.27
Consensus pattern (13 bp):
GGAGGTCACGTGT
Found at i:3135 original size:53 final size:52
Alignment explanation
Indices: 3054--3174 Score: 181
Period size: 53 Copynumber: 2.3 Consensus size: 52
3044 CGCACGCGCA
* *
3054 AGGTCACCTGTGGAGTTGTACTTAGGAGGTCACGTGTTGAAGGT-GTCCGTTGG
1 AGGTCACGTGTGGAGTTGTACTTAGGAGGTCACGTG-TGAA-GTCGTACGTTGG
* *
3107 AGGTCACGTGTGGAGTTGTACTTCGGAGGTCACGTGTGGAGTCGTACGTTGG
1 AGGTCACGTGTGGAGTTGTACTTAGGAGGTCACGTGTGAAGTCGTACGTTGG
3159 AGGTCACGTGTGGAGT
1 AGGTCACGTGTGGAGT
3175 GCCAGCTGGC
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.03
52 27 0.43
53 34 0.54
ACGTcount: A:0.17, C:0.15, G:0.40, T:0.29
Consensus pattern (52 bp):
AGGTCACGTGTGGAGTTGTACTTAGGAGGTCACGTGTGAAGTCGTACGTTGG
Found at i:3141 original size:26 final size:26
Alignment explanation
Indices: 3054--3174 Score: 156
Period size: 26 Copynumber: 4.6 Consensus size: 26
3044 CGCACGCGCA
*
3054 AGGTCACCTGTGGAGTTGTAC-TTAGG
1 AGGTCACGTGTGGAGTTGTACGTT-GG
* * *
3080 AGGTCACGTGTTGAAGGTGTCCGTTGG
1 AGGTCACGTG-TGGAGTTGTACGTTGG
3107 AGGTCACGTGTGGAGTTGTAC-TTCGG
1 AGGTCACGTGTGGAGTTGTACGTT-GG
*
3133 AGGTCACGTGTGGAGTCGTACGTTGG
1 AGGTCACGTGTGGAGTTGTACGTTGG
3159 AGGTCACGTGTGGAGT
1 AGGTCACGTGTGGAGT
3175 GCCAGCTGGC
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.02
26 57 0.69
27 22 0.27
28 2 0.02
ACGTcount: A:0.17, C:0.15, G:0.40, T:0.29
Consensus pattern (26 bp):
AGGTCACGTGTGGAGTTGTACGTTGG
Found at i:3235 original size:15 final size:15
Alignment explanation
Indices: 3215--3243 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3205 TTGTGGTCAT
3215 AGGTGGTCGAGCGCC
1 AGGTGGTCGAGCGCC
3230 AGGTGGTCGAGCGC
1 AGGTGGTCGAGCGC
3244 TGGGCTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.24, G:0.48, T:0.14
Consensus pattern (15 bp):
AGGTGGTCGAGCGCC
Found at i:3672 original size:28 final size:28
Alignment explanation
Indices: 3641--3725 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
3631 GCTCGACCAC
3641 ATATGGAGATGGTGGGTCGAGCGCCCAT
1 ATATGGAGATGGTGGGTCGAGCGCCCAT
* * ** *
3669 ATATGG-GCT--T-GAT-GCTCGCCCAC
1 ATATGGAGATGGTGGGTCGAGCGCCCAT
* *
3692 ACATGAAGATGGTGGGTCGAGCGCCCAT
1 ATATGGAGATGGTGGGTCGAGCGCCCAT
3720 ATATGG
1 ATATGG
3726 GGTTGGCGTT
Statistics
Matches: 38, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
23 11 0.29
24 4 0.11
25 1 0.03
26 1 0.03
27 4 0.11
28 17 0.45
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (28 bp):
ATATGGAGATGGTGGGTCGAGCGCCCAT
Found at i:3702 original size:51 final size:51
Alignment explanation
Indices: 3630--3774 Score: 211
Period size: 51 Copynumber: 2.8 Consensus size: 51
3620 CGAGCGTGGG
* * *
3630 CGCTCGACCACATATGGAGATGGTGGGTCGAGCGCCCATATATGGGCTTGA
1 CGCTCGCCCACACATGAAGATGGTGGGTCGAGCGCCCATATATGGGCTTGA
* * *
3681 TGCTCGCCCACACATGAAGATGGTGGGTCGAGCGCCCATATATGGGGTTGG
1 CGCTCGCCCACACATGAAGATGGTGGGTCGAGCGCCCATATATGGGCTTGA
*
3732 CGTTCGCCCACACATGAATG-TGGTGGGTCGAGCGCCCATATAT
1 CGCTCGCCCACACATGAA-GATGGTGGGTCGAGCGCCCATATAT
3775 ATAGGGCAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
51 84 0.99
52 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.22
Consensus pattern (51 bp):
CGCTCGCCCACACATGAAGATGGTGGGTCGAGCGCCCATATATGGGCTTGA
Found at i:3836 original size:14 final size:15
Alignment explanation
Indices: 3803--3837 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3793 TTGCCTTTTT
3803 TTTTTTGAAATTCAA
1 TTTTTTGAAATTCAA
*
3818 ATTTTTGAAATT-AA
1 TTTTTTGAAATTCAA
3832 TTTTTT
1 TTTTTT
3838 TTTGCTAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (15 bp):
TTTTTTGAAATTCAA
Found at i:4024 original size:37 final size:37
Alignment explanation
Indices: 3983--4090 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
3973 GTGGTGGTCA
* *
3983 ACACATTTTGTCAACTTGTCGAGCGATGTGGCAGTCG
1 ACACATTTTGTCAGCTTGTCGAGCGACGTGGCAGTCG
* * *
4020 ACACATTTTGTCAGTTTGTCGAGCGACATGGCGGTCG
1 ACACATTTTGTCAGCTTGTCGAGCGACGTGGCAGTCG
4057 ACACATTTTGTCAGCTTTGTCGAGCGACGTGGCA
1 ACACATTTTGTCAGC-TTGTCGAGCGACGTGGCA
4091 TGAAAATGAC
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
37 46 0.74
38 16 0.26
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (37 bp):
ACACATTTTGTCAGCTTGTCGAGCGACGTGGCAGTCG
Found at i:4486 original size:6 final size:6
Alignment explanation
Indices: 4475--4503 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4465 GGCGCCCAAC
4475 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
4504 GGGTGTCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:5102 original size:50 final size:51
Alignment explanation
Indices: 5048--5156 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 51
5038 CAGTTAACAT
* * * * *
5048 TTGATTGCTC-CGCTTCCGTTTTGTGTCGCAC-GCCGCGTAGTAGTTGGCTC
1 TTGATTGCTCTCGCTTCCATTTAGTGTCGCACAG-CACGTAGTAGCTGGCAC
*
5098 TTGATTGC-CTTGCTTCCATTTAGTGTCGCACAGCACGTAGTAGCTGGCAC
1 TTGATTGCTCTCGCTTCCATTTAGTGTCGCACAGCACGTAGTAGCTGGCAC
*
5148 TTTATTGCT
1 TTGATTGCT
5157 TTGTTTTCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
49 1 0.02
50 47 0.96
51 1 0.02
ACGTcount: A:0.13, C:0.26, G:0.25, T:0.37
Consensus pattern (51 bp):
TTGATTGCTCTCGCTTCCATTTAGTGTCGCACAGCACGTAGTAGCTGGCAC
Found at i:5168 original size:50 final size:50
Alignment explanation
Indices: 5059--5175 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 50
5049 TGATTGCTCC
* * * * *
5059 GCTTCCGTTTTGTGTCGCACGCCGCGTAGTAGTTGGCTCTTGATTGCCTT
1 GCTTCCATTTAGTGTCGCACGCCACGTAGTAGCTGGCACTTGATTGCCTT
* *
5109 GCTTCCATTTAGTGTCGCACAG-CACGTAGTAGCTGGCACTTTATTGCTTT
1 GCTTCCATTTAGTGTCGCAC-GCCACGTAGTAGCTGGCACTTGATTGCCTT
* * *
5159 GTTTTCATTTTGTGTCG
1 GCTTCCATTTAGTGTCG
5176 TACGTCACTT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 55 0.98
51 1 0.02
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (50 bp):
GCTTCCATTTAGTGTCGCACGCCACGTAGTAGCTGGCACTTGATTGCCTT
Found at i:5747 original size:44 final size:43
Alignment explanation
Indices: 5621--6141 Score: 702
Period size: 44 Copynumber: 11.9 Consensus size: 43
5611 TGACCATCTA
* * * * * *
5621 GTTCTTGTCTTCTTGATTTGATTGTGGTGTGATCGACCGACTT
1 GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* * *
5664 GTTGTTTACTTCTTGCTTTAAATGTGATGTGGTCGATCGACTT
1 GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
*
5707 GTTGTTTAT-TTCTTGCTTTTGAATGTGATGTGGTCGATCGACTT
1 GTTCTTT-TCTTCTTGC-TTTGAATGTGATGTGGTCGATCGACTT
*
5751 GTTCTTGTTCTTCTTGCTTTGTATGTGATGTGGTCGATCGACTT
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
*
5795 GTTCTTGTTCTTCTTGCTTTGTATGTGATGTGGTCGATCGACTT
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
*
5839 GTTCTTGTTCTTCTTGCTTTGAATGCGATGTGGTCGATCGACTT
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
*
5883 GTTCTTGTTCTTCTTGCTTTGTATGTGATGTGGTCGATCGACTT
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
**
5927 GTTCTTGTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACCG
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* * *
5971 GTTCTTTTCTTCTTGGTTTGAATGTGATGTGGTCGATAGACTA
1 GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* * *
6014 GTTACTTCTCTTCTTGGTTTGAATGTGATGTGGTCGATCGACTA
1 GTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* **
6058 GTTACTTCTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACCG
1 GTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
**
6102 GTTCTTTTCTTCTCACTTCTGAATGTGATGTGGTCGATCG
1 GTTCTTTTCTTCTTGCTT-TGAATGTGATGTGGTCGATCG
Statistics
Matches: 440, Mismatches: 32, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
43 96 0.22
44 336 0.76
45 8 0.02
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.46
Consensus pattern (43 bp):
GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
Done.