Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015684.1 Corchorus capsularis cultivar CVL-1 contig15705, 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: 9208
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:2976 original size:11 final size:11
Alignment explanation
Indices: 2960--2998 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
2950 TCCCTCCTGA
2960 AAAAAAAGAAG
1 AAAAAAAGAAG
2971 AAAAAAAATGAAG
1 -AAAAAAA-GAAG
*
2984 AAAAAAAAAAG
1 AAAAAAAGAAG
2995 AAAA
1 AAAA
2999 GAGAAAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 7 0.28
12 14 0.56
13 4 0.16
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:2977 original size:13 final size:13
Alignment explanation
Indices: 2959--2992 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2949 TTCCCTCCTG
2959 AAAAAAAAGAAGA
1 AAAAAAAAGAAGA
*
2972 AAAAAAATGAAGA
1 AAAAAAAAGAAGA
2985 AAAAAAAA
1 AAAAAAAA
2993 AGAAAAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAAAAAAGAAGA
Found at i:3007 original size:11 final size:11
Alignment explanation
Indices: 2958--2998 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 11
2948 ATTCCCTCCT
2958 GAAAAAAAAGAA
1 GAAAAAAAA-AA
2970 GAAAAAAAATGAA
1 GAAAAAAAA--AA
2983 GAAAAAAAAAA
1 GAAAAAAAAAA
2994 GAAAA
1 GAAAA
2999 GAGAAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.25
12 9 0.32
13 12 0.43
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:3097 original size:25 final size:26
Alignment explanation
Indices: 3067--3121 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
3057 CGAGAAGTAT
* *
3067 TTTTCAAAAATTA-TTTTCGAAAAGG
1 TTTTCAAAAATGAGTTTTCAAAAAGG
*
3092 TTTTCAAAAATGAGTTTTCAAAAAGT
1 TTTTCAAAAATGAGTTTTCAAAAAGG
3118 TTTT
1 TTTT
3122 TGAGTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (26 bp):
TTTTCAAAAATGAGTTTTCAAAAAGG
Found at i:3108 original size:14 final size:14
Alignment explanation
Indices: 3067--3115 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
3057 CGAGAAGTAT
*
3067 TTTTCAAAAATTA-
1 TTTTCAAAAATGAG
*
3080 TTTTCGAAAA-G-G
1 TTTTCAAAAATGAG
3092 TTTTCAAAAATGAG
1 TTTTCAAAAATGAG
3106 TTTTCAAAAA
1 TTTTCAAAAA
3116 GTTTTTTGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 9 0.30
13 10 0.33
14 11 0.37
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (14 bp):
TTTTCAAAAATGAG
Found at i:3771 original size:22 final size:23
Alignment explanation
Indices: 3723--3769 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
3713 AACAAAAAAG
*
3723 AAAGAAGAAATTGATTTTTCACA
1 AAAGAAGAAAATGATTTTTCACA
*
3746 AAAGAA-AAAATG-TTTTTCTCA
1 AAAGAAGAAAATGATTTTTCACA
3767 AAA
1 AAA
3770 AGGTTTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (23 bp):
AAAGAAGAAAATGATTTTTCACA
Found at i:5638 original size:29 final size:29
Alignment explanation
Indices: 5590--5645 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5580 AATTTAAACA
*
5590 GATCCAGGGAGGTCCATCTTAAGTTAATT
1 GATCCAGGGAGATCCATCTTAAGTTAATT
* * *
5619 GATCCAGGGCGATCCTTCTTCAGTTAA
1 GATCCAGGGAGATCCATCTTAAGTTAA
5646 ATTCAAATGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (29 bp):
GATCCAGGGAGATCCATCTTAAGTTAATT
Found at i:5686 original size:35 final size:34
Alignment explanation
Indices: 5618--5713 Score: 102
Period size: 35 Copynumber: 2.8 Consensus size: 34
5608 TTAAGTTAAT
* * *
5618 TGATCCAGGGCGATCCTTCTTCAGTTAAATTCAAA
1 TGATCCAGGGCGATCATTCTTCAATTTAATTC-AA
* * *
5653 TGGTCCAAGGCGATCATTCTTCAATTTACTTCAA
1 TGATCCAGGGCGATCATTCTTCAATTTAATTCAA
* * *
5687 TGATCCAGGGTGGTCTTTCTTCAATTT
1 TGATCCAGGGCGATCATTCTTCAATTT
5714 TCCTAATTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
34 24 0.48
35 26 0.52
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (34 bp):
TGATCCAGGGCGATCATTCTTCAATTTAATTCAA
Found at i:5806 original size:36 final size:36
Alignment explanation
Indices: 5766--6143 Score: 249
Period size: 36 Copynumber: 10.6 Consensus size: 36
5756 TCAATGACCC
* * * *
5766 AGGGTGGTTGCTCTTAAGTTCAGTTCGGAATGATCG
1 AGGGTGGTTGTTCTTCAGTTTAGTTCAGAATGATCG
* * * ** *
5802 AGGGTGGTCGTT-TCTCAGTTTATTTCAG-TTGGCCC
1 AGGGTGGTTGTTCT-TCAGTTTAGTTCAGAATGATCG
* * * *
5837 AGGGTGGTCT-ATCTTTAGGTTGAG-TAAGAATGATCG
1 AGGGTGGT-TGTTCTTCA-GTTTAGTTCAGAATGATCG
*
5873 AGGGTGGTTGTTCTTCAGTTTA-TGTCGGAATGATCG
1 AGGGTGGTTGTTCTTCAGTTTAGT-TCAGAATGATCG
* * **
5909 AGGGTGGTCGTTCTTCAGTTCAGTTTGGAATGATCG
1 AGGGTGGTTGTTCTTCAGTTTAGTTCAGAATGATCG
* *
5945 AGGGTGGTCT-TTCATCAGTTTGAG-TCAGAATCATCG
1 AGGGTGGT-TGTTCTTCAGTTT-AGTTCAGAATGATCG
* * *
5981 ATGGTGGTTATTCTTCAGTTTAGTCCAGAATGATCG
1 AGGGTGGTTGTTCTTCAGTTTAGTTCAGAATGATCG
* * * *
6017 AGGGTGGTTGTTCTTCAGTTTATTTCAG-TTGACCC
1 AGGGTGGTTGTTCTTCAGTTTAGTTCAGAATGATCG
* * * * *
6052 ATGGTGGTCT-TTCTTCAATTT-GCGTCGGAGTGATCG
1 AGGGTGGT-TGTTCTTCAGTTTAG-TTCAGAATGATCG
* * * *
6088 AGGGTGGTCGTTCTTCTGTTCAGTTCTA-AATGATCC
1 AGGGTGGTTGTTCTTCAGTTTAGTTC-AGAATGATCG
6124 AGGGTGGTCT-TTCTTCAGTT
1 AGGGTGGT-TGTTCTTCAGTT
6144 ACTTATTCTA
Statistics
Matches: 258, Mismatches: 64, Indels: 40
0.71 0.18 0.11
Matches are distributed among these distances:
35 50 0.19
36 204 0.79
37 4 0.02
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (36 bp):
AGGGTGGTTGTTCTTCAGTTTAGTTCAGAATGATCG
Found at i:5951 original size:72 final size:72
Alignment explanation
Indices: 5758--6143 Score: 290
Period size: 72 Copynumber: 5.4 Consensus size: 72
5748 TTATTGCTTC
* * * * *
5758 AATGACCCAGGGTGGTTGCTCTTAAGTTCAGTTCGGAATGATCGAGGGTGGTCGTT-TCTCAGTT
1 AATGATCCAGGGTGGTCGTTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTTGTTCT-TCAGTT
*
5822 TATTTCAG
65 TATGTCAG
* ** * * **
5830 -TTGGCCCAGGGTGGTC-TATCTTTAGGTTGAG-TAAGAATGATCGAGGGTGGTTGTTCTTCAGT
1 AATGATCCAGGGTGGTCGT-TCTTCA-GTTCAGTTCGGAATGATCGAGGGTGGTTGTTCTTCAGT
*
5892 TTATGTCGG
64 TTATGTCAG
* * *
5901 AATGATCGAGGGTGGTCGTTCTTCAGTTCAGTTTGGAATGATCGAGGGTGGTCT-TTCATCAGTT
1 AATGATCCAGGGTGGTCGTTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGT-TGTTCTTCAGTT
5965 TGA-GTCAG
65 T-ATGTCAG
* * * ** * * *
5973 AATCATCGATGGTGGTTATTCTTCAGTTTAGTCCAGAATGATCGAGGGTGGTTGTTCTTCAGTTT
1 AATGATCCAGGGTGGTCGTTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTTGTTCTTCAGTTT
*
6038 ATTTCAG
66 ATGTCAG
* * * * * * * *
6045 -TTGACCCATGGTGGTCTTTCTTCAATTTGC-G-TCGGAGTGATCGAGGGTGGTCGTTCTTCTGT
1 AATGATCCAGGGTGGTCGTTCTTC-AGTT-CAGTTCGGAATGATCGAGGGTGGTTGTTCTTCAGT
*
6107 TCA-GTTCTA-
64 TTATG-TC-AG
*
6116 AATGATCCAGGGTGGTCTTTCTTCAGTT
1 AATGATCCAGGGTGGTCGTTCTTCAGTT
6144 ACTTATTCTA
Statistics
Matches: 249, Mismatches: 50, Indels: 31
0.75 0.15 0.09
Matches are distributed among these distances:
71 108 0.43
72 138 0.55
73 3 0.01
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.37
Consensus pattern (72 bp):
AATGATCCAGGGTGGTCGTTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTTGTTCTTCAGTTT
ATGTCAG
Found at i:5989 original size:108 final size:106
Alignment explanation
Indices: 5766--6143 Score: 337
Period size: 107 Copynumber: 3.5 Consensus size: 106
5756 TCAATGACCC
* * * *
5766 AGGGTGGTTGCTCTTAAGTTCAGTTCGGAATGATCGAGGGTGGTCGTT-TCTCAGTTTATTTCAG
1 AGGGTGGTTGTTCTTCAGTTTAG-TCGGAATGATCGAGGGTGGTCGTTCT-TCAGTTCATTTCAG
* * * * *
5830 TTGGCCCAGGGTGGTCTATCTTTAGGTTGAGTAAGAATGATCG
64 ATGACCCAGGGTGGTCTATCATCAGGTTGAGTAAGAATCATCG
*
5873 AGGGTGGTTGTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTCGTTCTTCAGTTCAGTTT-GG
1 AGGGTGGTTGTTCTTCAGTTTA-GTCGGAATGATCGAGGGTGGTCGTTCTTCAGTTCA-TTTCAG
* * * * *
5937 AATGATCGAGGGTGGTCTTTCATCAGTTTGAGTCAGAATCATCG
64 -ATGACCCAGGGTGGTCTATCATCAGGTTGAGTAAGAATCATCG
* * * * * *
5981 ATGGTGGTTATTCTTCAGTTTAGTCCAGAATGATCGAGGGTGGTTGTTCTTCAGTTTATTTCAGT
1 AGGGTGGTTGTTCTTCAGTTTAGT-CGGAATGATCGAGGGTGGTCGTTCTTCAGTTCATTTCAGA
* * * ** * ** * *
6046 TGACCCATGGTGGTCTTTCTTCAATTTGCGTCGGAGTGATCG
65 TGACCCAGGGTGGTCTATCATCAGGTTGAGTAAGAATCATCG
* * * ** * *
6088 AGGGTGGTCGTTCTTCTGTTCAGTTCTAAATGATCCAGGGTGGTCTTTCTTCAGTT
1 AGGGTGGTTGTTCTTCAGTTTAG-TCGGAATGATCGAGGGTGGTCGTTCTTCAGTT
6144 ACTTATTCTA
Statistics
Matches: 223, Mismatches: 41, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
107 133 0.60
108 90 0.40
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (106 bp):
AGGGTGGTTGTTCTTCAGTTTAGTCGGAATGATCGAGGGTGGTCGTTCTTCAGTTCATTTCAGAT
GACCCAGGGTGGTCTATCATCAGGTTGAGTAAGAATCATCG
Done.