Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008617.1 Corchorus capsularis cultivar CVL-1 contig08638, 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: 19873
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:8894 original size:72 final size:72
Alignment explanation
Indices: 8791--9283 Score: 659
Period size: 72 Copynumber: 6.8 Consensus size: 72
8781 GTAGTAGCAT
*
8791 GGATTGTGCGAAGGACTGCC-AATGTGGGAACTGCCTCGGCTACAATCGCAATGGGGAAGATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
8855 CACATAA
66 CACATAA
* * * * *
8862 GGATTGTGTGAAGAACTGGCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGATGAATATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
*
8927 CGCATAA
66 CACATAA
* * * *
8934 GGGTTGTGCGAAGGACTGCCAAATGTGGGAAATGCCTCGGCTACAATCGCAATGATGAATATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
*
8999 CGCATAA
66 CACATAA
* * * *
9006 GGGTTGTGCGAAGGACTGCCAAATGTGGGAAATGCCTCGGCTACAATCGCAATGATGAATATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
*
9071 CGCATAA
66 CACATAA
* * * *
9078 GGGTTGTGCGAAGAACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAAT-ATGGAAGATTA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATAA
**
9142 TCATGTAA
65 TCACATAA
* * *
9150 GGATTTGTGCGAAGGACTGCCACATGTGGGAACTGCCTCGGCTACAACCGCAAT-ATGGAAGATT
1 GGA-TTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATA
**
9214 ATCATGTAA
64 ATCACATAA
* * *
9223 GGATTGTGCGAAGGACTGCCAAATGTGAGAACTGTCTCGGCTACAATCGCAATGAAGAAGA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGA
9284 AGACCATGGG
Statistics
Matches: 389, Mismatches: 29, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
71 18 0.05
72 300 0.77
73 71 0.18
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (72 bp):
GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
CACATAA
Found at i:9264 original size:217 final size:216
Alignment explanation
Indices: 8791--9283 Score: 695
Period size: 217 Copynumber: 2.3 Consensus size: 216
8781 GTAGTAGCAT
*
8791 GGATTGTGCGAAGGACTGCC-AATGTGGGAACTGCCTCGGCTACAATCGCAATGGGGAAGATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
* * *
8855 CACATAAGGATTGTGTGAAGAACTGGCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGATGA
66 CACATAAGGATTGTGCGAAGAACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATGATGA
* * *
8920 ATATAATCGCATAAGGGTTGTGCGAAGGACTGCCAAATGTGGGAAATGCCTCGGCTACAATCGCA
131 AGATAATCACATAAGGGTTGTGCGAAGGACTGCCAAATGTGGGAAATGCCTCGGCTACAACCGCA
* *
8985 ATGATGAATATAATCGCATAA
196 ATGATGAAGATAATCACATAA
* * * *
9006 GGGTTGTGCGAAGGACTGCCAAATGTGGGAAATGCCTCGGCTACAATCGCAATGATGAATATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
* *
9071 CGCATAAGGGTTGTGCGAAGAACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAAT-ATGG
66 CACATAAGGATTGTGCGAAGAACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATGAT-G
* ** * * *
9135 AAGATTATCATGTAAGGATTTGTGCGAAGGACTGCCACATGTGGGAACTGCCTCGGCTACAACCG
130 AAGATAATCACATAAGG-GTTGTGCGAAGGACTGCCAAATGTGGGAAATGCCTCGGCTACAACCG
* **
9200 CAAT-ATGGAAGATTATCATGTAA
194 CAATGAT-GAAGATAATCACATAA
* * *
9223 GGATTGTGCGAAGGACTGCCAAATGTGAGAACTGTCTCGGCTACAATCGCAATGAAGAAGA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGA
9284 AGACCATGGG
Statistics
Matches: 244, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
215 21 0.09
216 110 0.45
217 113 0.46
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (216 bp):
GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
CACATAAGGATTGTGCGAAGAACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAATGATGA
AGATAATCACATAAGGGTTGTGCGAAGGACTGCCAAATGTGGGAAATGCCTCGGCTACAACCGCA
ATGATGAAGATAATCACATAA
Found at i:9755 original size:34 final size:35
Alignment explanation
Indices: 9644--9773 Score: 118
Period size: 35 Copynumber: 3.7 Consensus size: 35
9634 TCGTTGTTGA
* * * *
9644 AGCCCCCAAGTATTGAATGAAGAATGAGTTGCTGG
1 AGCCCCCAAGTGTTGAACGATGAATGGGTTGCTGG
** * * * *
9679 AGTACCCAACTGTTGAATGGTGAATGGGTTGTTGG
1 AGCCCCCAAGTGTTGAACGATGAATGGGTTGCTGG
* *
9714 AGTCCCCAAGTGTTGAACGATGAA-GGGTTGCTGC
1 AGCCCCCAAGTGTTGAACGATGAATGGGTTGCTGG
*
9748 AGCCCCCAAGTGCTGAATCTGATGAA
1 AGCCCCCAAGTGTTGAA-C-GATGAA
9774 ATATGTCGTA
Statistics
Matches: 77, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
34 23 0.30
35 48 0.62
36 6 0.08
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (35 bp):
AGCCCCCAAGTGTTGAACGATGAATGGGTTGCTGG
Found at i:14998 original size:14 final size:14
Alignment explanation
Indices: 14981--15013 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
14971 ATTTGAAGTA
14981 AATAAATATAGATT
1 AATAAATATAGATT
*
14995 AATATATATAGATT
1 AATAAATATAGATT
15009 AATAA
1 AATAA
15014 CAAAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (14 bp):
AATAAATATAGATT
Found at i:15747 original size:14 final size:14
Alignment explanation
Indices: 15730--15769 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
15720 ATTAATTTTA
15730 AATATATTATATAT
1 AATATATTATATAT
*
15744 AATAAATTATATA-
1 AATATATTATATAT
15757 AA-ATATTATATAT
1 AATATATTATATAT
15770 TTTAGCGACG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 12 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATATTATATAT
Found at i:16532 original size:20 final size:21
Alignment explanation
Indices: 16507--16552 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
16497 TCAAAACAAA
*
16507 ATAAAAACTACCCATTTTA-G
1 ATAAAAACTACCCATTATAGG
*
16527 ATAAAAACTACCTATTATAGG
1 ATAAAAACTACCCATTATAGG
16548 ATAAA
1 ATAAA
16553 TATAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (21 bp):
ATAAAAACTACCCATTATAGG
Found at i:16736 original size:26 final size:27
Alignment explanation
Indices: 16699--16755 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 27
16689 TCCTTTTTTC
16699 AAAAATATTTTTAAATT-GTC-ATTATT
1 AAAAATATTTTT-AATTAGTCTATTATT
*
16725 AAAAAT-TATTTTAATTATTCTATTATT
1 AAAAATAT-TTTTAATTAGTCTATTATT
16752 AAAA
1 AAAA
16756 TAATGAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 5 0.19
26 12 0.44
27 10 0.37
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAATATTTTTAATTAGTCTATTATT
Found at i:17476 original size:14 final size:14
Alignment explanation
Indices: 17459--17497 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
17449 AATATATTTG
17459 TATCTATATAAATC
1 TATCTATATAAATC
**
17473 TATCTATATCTATC
1 TATCTATATAAATC
17487 TATACTATATA
1 TAT-CTATATA
17498 TAAAAGTACG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (14 bp):
TATCTATATAAATC
Done.