Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010855.1 Corchorus capsularis cultivar CVL-1 contig10876, 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: 52562
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2922 original size:27 final size:28
Alignment explanation
Indices: 2871--2925 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
2861 AAACTCTTAG
**
2871 GAGATGATGATATATATTTGTAATAAAT
1 GAGATGATGATATATATTTAAAATAAAT
2899 GAGATGAT-ATATATATTTAAAATAAAT
1 GAGATGATGATATATATTTAAAATAAAT
2926 TCCTATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (28 bp):
GAGATGATGATATATATTTAAAATAAAT
Found at i:4449 original size:165 final size:168
Alignment explanation
Indices: 4177--4590 Score: 531
Period size: 165 Copynumber: 2.5 Consensus size: 168
4167 TTCAAACTTG
* * *
4177 ATGATAGCTTCAAACATCCCGAGCAGATGGAAAAACTTGAAGACTCCAATGTTGTTGGAGTCAGG
1 ATGATAGCTTCAAACATCCAGAGCAGATGAAAAAACTTGAAGACACCAATGTTGTTGGAGTCAGG
* *
4242 ACACTTGACCAGTACAGTCCTTTCTCTTCTCTTGGAGTCAAGACACTTG-AT-CA-ATCCAGTCC
66 ACACTTGACCAGTACAGTCCCTTCTCTTCTCTTGGAGTCAAGACACTTGAATCCAGATCAAGTCC
* *
4304 TTCCTTTAAGCACATGTGGGAGCTGATGGAACCACTAC
131 TTCCTCTAAGCACATGTGGGAGCAGATGGAACCACTAC
4342 ATGATAGCTTCAAACATCCAGAGCAGATGAAAAAACTTGAAGACACCAATGTTGTTGGAGTCAGG
1 ATGATAGCTTCAAACATCCAGAGCAGATGAAAAAACTTGAAGACACCAATGTTGTTGGAGTCAGG
*
4407 ACACTTTA-CAG-ATCAAGTCCCTTCTCTTCTCTTGGAGTCAAGACACTTGACCAATCCAGATCA
66 ACACTTGACCAGTA-C-AGTCCCTTCTCTTCTCTTGGAGTCAAGACACTTG---AATCCAGATCA
*
4470 AGTCCTTTCTCTAAGCACATGTGGGAGCAGATGGAACCACTAC
126 AGTCCTTCCTCTAAGCACATGTGGGAGCAGATGGAACCACTAC
** * * * *
4513 ATGATAGCTTAGTGCAGGCA-CCTGAG--GA-GAAAAAACTTGAAGACTCTAATCTTGTTGGAGT
1 ATGATAGC-T--T-CAAACATCCAGAGCAGATGAAAAAACTTGAAGACACCAATGTTGTTGGAGT
* *
4574 CAAGATACTTGACCAGT
62 CAGGACACTTGACCAGT
4591 CCAGATCAAG
Statistics
Matches: 217, Mismatches: 18, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
163 1 0.00
164 4 0.02
165 102 0.47
169 2 0.01
170 2 0.01
171 90 0.41
172 6 0.03
174 6 0.03
175 4 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (168 bp):
ATGATAGCTTCAAACATCCAGAGCAGATGAAAAAACTTGAAGACACCAATGTTGTTGGAGTCAGG
ACACTTGACCAGTACAGTCCCTTCTCTTCTCTTGGAGTCAAGACACTTGAATCCAGATCAAGTCC
TTCCTCTAAGCACATGTGGGAGCAGATGGAACCACTAC
Found at i:5121 original size:204 final size:202
Alignment explanation
Indices: 4772--5183 Score: 743
Period size: 204 Copynumber: 2.0 Consensus size: 202
4762 CTAGCTATAA
4772 TATATATACGGCAAATTATACAATACACCGGCGGTGGAGTTTAGAAAACTACACAAGCGGGTCCT
1 TATATATACGGCAAATTATACAATACACCGGCGGTGGAGTTTAGAAAACTACACAAGCGGGTCCT
4837 GAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAAAAT
66 GAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAAAAT
* *
4902 GGACATGTGTCAACTCCACAAGCCGCTTGTGGAGTCCAAAATTTACACTGCCGGTGTATCATATA
131 GGACATGTGTCAACTCCACAAACCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCATATA
*
4967 ATCACCG
196 ATCACCC
4974 TATATATACAAGGCAAATTATACAATACACCGGCGGTGGAGTTTAGAAAACTACACAAGCGGGTC
1 TATATATAC--GGCAAATTATACAATACACCGGCGGTGGAGTTTAGAAAACTACACAAGCGGGTC
* * *
5039 TTTAAGGGTGACATGTGTCCCTTAGGGATTAGATTGAAATATTTAAAACTTAATTAATTCAAAAA
64 CTGAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAAA
*
5104 ATGGACATGTGTCAACTCCATAAACCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCATA
129 ATGGACATGTGTCAACTCCACAAACCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCATA
5169 TAATCACCC
194 TAATCACCC
5178 TATATA
1 TATATA
5184 CAATGATGCA
Statistics
Matches: 201, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
202 9 0.04
204 192 0.96
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (202 bp):
TATATATACGGCAAATTATACAATACACCGGCGGTGGAGTTTAGAAAACTACACAAGCGGGTCCT
GAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAAAAT
GGACATGTGTCAACTCCACAAACCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCATATA
ATCACCC
Found at i:6747 original size:22 final size:21
Alignment explanation
Indices: 6722--6762 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
6712 TATACTGTAC
*
6722 CTATTTCGGTTGCTTCTGTTTA
1 CTATTTCGGTT-CTCCTGTTTA
6744 CTATTTCGGTTCTCCTGTT
1 CTATTTCGGTTCTCCTGTT
6763 ATTTCTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.07, C:0.22, G:0.17, T:0.54
Consensus pattern (21 bp):
CTATTTCGGTTCTCCTGTTTA
Found at i:9816 original size:132 final size:132
Alignment explanation
Indices: 9579--9835 Score: 374
Period size: 132 Copynumber: 1.9 Consensus size: 132
9569 GGACTTTTTT
* *
9579 CTGTCAAATCCGGTGTTTTTAGTTTCGGAGTCCTGCTATTGGAGATAATAAGTGGCAAAAGGAAC
1 CTGTCAAATCCGGTGTTTTCAGTTTCGGAGTCCTGCTATTGGAGATAATAAGCGGCAAAAGGAAC
* * * *
9644 AGTGGGTTTTATATTTGGGAGCATGGTGAAAGCCTCCTAACTTTTGTAAGTTTCTAAATCCTATT
66 AATAGGTTTCATATTTCGGAGCATGGTGAAAGCCTCCTAACTTTTGTAAGTTTCTAAATCCTATT
9709 TC
131 TC
* * *
9711 CTGTCAAAT-CGGATGTTTTCAGTTTTGGAGTCCTGTTATTGGAGATAATAAGCGGGAAAAGGAA
1 CTGTCAAATCCGG-TGTTTTCAGTTTCGGAGTCCTGCTATTGGAGATAATAAGCGGCAAAAGGAA
* * *
9775 CAATAGGTTTCATCA-TTCGGAGCGTGGTGAAAGCCTCCTAACTTTTGTACGTTTTTAAATC
65 CAATAGGTTTCAT-ATTTCGGAGCATGGTGAAAGCCTCCTAACTTTTGTAAGTTTCTAAATC
9836 ATTTTCTTCA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
131 3 0.03
132 107 0.96
133 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (132 bp):
CTGTCAAATCCGGTGTTTTCAGTTTCGGAGTCCTGCTATTGGAGATAATAAGCGGCAAAAGGAAC
AATAGGTTTCATATTTCGGAGCATGGTGAAAGCCTCCTAACTTTTGTAAGTTTCTAAATCCTATT
TC
Found at i:12678 original size:3 final size:3
Alignment explanation
Indices: 12670--12703 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
12660 CCTCCGCCAT
*
12670 CTC CTC CTC CTC CTC CTT CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
12704 CTCTACAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:33175 original size:24 final size:24
Alignment explanation
Indices: 33136--33190 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
33126 CGACGCCAAT
* *
33136 ATCTCCAATACTATCTCCGTCACC
1 ATCTCCAAGACCATCTCCGTCACC
*
33160 ATCTCCAAGACCATCTCTGTCACC
1 ATCTCCAAGACCATCTCCGTCACC
33184 ATCTCCA
1 ATCTCCA
33191 CCATCTTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.42, G:0.05, T:0.27
Consensus pattern (24 bp):
ATCTCCAAGACCATCTCCGTCACC
Found at i:34075 original size:22 final size:22
Alignment explanation
Indices: 34033--34076 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
34023 AGTATTAATG
* *
34033 AGTTAAAATAATACAAGTTAAA
1 AGTTAAAAAAATACAAATTAAA
34055 AGTTAAAAGAAATA-AAATTAAA
1 AGTTAAAA-AAATACAAATTAAA
34077 GGACTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (22 bp):
AGTTAAAAAAATACAAATTAAA
Found at i:51832 original size:24 final size:24
Alignment explanation
Indices: 51757--51825 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
51747 GATGATCCAC
**
51757 ATGATGCTATTTTAGATGCTGTTA
1 ATGATGCTGGTTTAGATGCTGTTA
* *
51781 ATGATGTTGGTTT-GAATGATGTTA
1 ATGATGCTGGTTTAG-ATGCTGTTA
51805 ATGATGCTGGTTTAGATGCTG
1 ATGATGCTGGTTTAGATGCTG
51826 AAAATGAGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 1 0.03
24 35 0.95
25 1 0.03
ACGTcount: A:0.23, C:0.06, G:0.28, T:0.43
Consensus pattern (24 bp):
ATGATGCTGGTTTAGATGCTGTTA
Done.