Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007745.1 Corchorus capsularis cultivar CVL-1 contig07766, 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: 28248
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Found at i:500 original size:76 final size:76
Alignment explanation
Indices: 362--557 Score: 313
Period size: 76 Copynumber: 2.6 Consensus size: 76
352 GGAGACTCCC
** * * *
362 GCGGGTGACGTCTGCTTGGACGTTTAACCTCGTTTAAGA-ATATACGAGGGCACCAGTCTAGGCG
1 GCGGGTGACGTCTGCTTGGACGTTCGACCTCGCTTATGATTTATACGAGGGCACCAGTCTAGGCG
426 CTCAGCCGTCT
66 CTCAGCCGTCT
* * *
437 GCGGGTGACGTCTGCTAGGACATTCGACCTCGCTTATGATTTATACGGGGGCACCAGTCTAGGCG
1 GCGGGTGACGTCTGCTTGGACGTTCGACCTCGCTTATGATTTATACGAGGGCACCAGTCTAGGCG
502 CTCAGCCGTCT
66 CTCAGCCGTCT
513 GCGGGTGACGTCTGCTTGGACGTTCGACCTCGCTTATGATTTATA
1 GCGGGTGACGTCTGCTTGGACGTTCGACCTCGCTTATGATTTATA
558 TGAGAATTTG
Statistics
Matches: 110, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
75 33 0.30
76 77 0.70
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (76 bp):
GCGGGTGACGTCTGCTTGGACGTTCGACCTCGCTTATGATTTATACGAGGGCACCAGTCTAGGCG
CTCAGCCGTCT
Found at i:9422 original size:189 final size:189
Alignment explanation
Indices: 9102--9483 Score: 719
Period size: 189 Copynumber: 2.0 Consensus size: 189
9092 ATGTCTTCTA
*
9102 AACATAACAATAAGCTAATCTAAGATAGAATTAAGGCCCATAATGACCGAATTACACAATGAAAT
1 AACATAACAATAAGCTAATCTAAGATAGAATTAAGGCCCATAATGACCAAATTACACAATGAAAT
*
9167 ATAATCATCCATCGATTTCAAGCAATGTGATGAGCTTGTAATCGATGGGAATATTCTTGTCCAAA
66 ATAATCATCCATCGATTTCAAGCAATGTGATGAGCTTGTAATCGATGGGAATATTCTTGCCCAAA
*
9232 TCTTCATCAAAGCTCTTCAATTGCTCTTCAATGGTCTTCAAGTCTTCCAGATGAGTTCG
131 TCTTCATCAAAGCTCTTCAATTGCTCTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCG
9291 AACATAACAATAAGCTAATCTAAGATAGAATTAAGGCCCATAATGACCAAATTACACAATGAAAT
1 AACATAACAATAAGCTAATCTAAGATAGAATTAAGGCCCATAATGACCAAATTACACAATGAAAT
* *
9356 ATAATCATCCATTGATTTCAAGCAATGTGATGAGCTTGTTATCGATGGGAATATTCTTGCCCAAA
66 ATAATCATCCATCGATTTCAAGCAATGTGATGAGCTTGTAATCGATGGGAATATTCTTGCCCAAA
9421 TCTTCATCAAAGCTCTTCAATTGCTCTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCG
131 TCTTCATCAAAGCTCTTCAATTGCTCTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCG
9480 AACA
1 AACA
9484 AGGCCCATTA
Statistics
Matches: 188, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
189 188 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (189 bp):
AACATAACAATAAGCTAATCTAAGATAGAATTAAGGCCCATAATGACCAAATTACACAATGAAAT
ATAATCATCCATCGATTTCAAGCAATGTGATGAGCTTGTAATCGATGGGAATATTCTTGCCCAAA
TCTTCATCAAAGCTCTTCAATTGCTCTTCAATGGTCTTCAAGTCTTCAAGATGAGTTCG
Found at i:12146 original size:62 final size:62
Alignment explanation
Indices: 12076--12736 Score: 742
Period size: 62 Copynumber: 10.6 Consensus size: 62
12066 AAACATGGCT
* * *
12076 AAACTGACCCTTTGTCTGCAATGGTATTTTGGGAAATAGAATCTAAATGCAGGAATGTGA-A
1 AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAAATTGAATCTAAATGCAGGAATGTGACA
* * * * * *
12137 GAAACTGACCCTTTCTCTGAAAGGGTATTTTGGGAATACT-AAACTTAAATGTAGGAATATGACG
1 -AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAA-ATTGAATC-TAAATGCAGGAATGTGACA
* * * *
12201 AAATTGACCCTTTGTCTAAAAGGGTATTTTGGGAAATAGAATCTAAGTGCAGGAATGTGA-A
1 AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAAATTGAATCTAAATGCAGGAATGTGACA
* * * * *
12262 GAAACTGACCCTTTGTCGGAAAGGGTATTCTGGGAAATTGAAACTAAATGCAAGAGTGTGACA
1 -AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAAATTGAATCTAAATGCAGGAATGTGACA
* * *
12325 AAACTAACCCTTTGTCTGAAAGGGTATTTTGGGAAATAGAATCTAAGTGCAGGAATGTGA-A
1 AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAAATTGAATCTAAATGCAGGAATGTGACA
* * * * *
12386 GAAACTGACCCTTTGTCGGAAAGGGTATTCTGGGAAATTGAAACTAAATGCAAGAGTGTGACA
1 -AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAAATTGAATCTAAATGCAGGAATGTGACA
* * * * * *
12449 AAATTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAATTGAAACTGAATGCTAGAAATGTGACA
1 AAACTGACCCTTTGTCTGAAAGGGTATTTTGGG-AAATTGAATCTAAATGC-AGGAATGTGACA
* * *
12513 AAACTAACCCTTTGTCTGAAAGGGTATTTTGGGAACTTGAATCTAAGA-GCAAGAATGTGACA
1 AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAAATTGAATCTAA-ATGCAGGAATGTGACA
* * * * * *
12575 AAATTAACCCTTTGTCCGAAAGGGTATTTTGGGAAAATTGAAACTGAATGCTAGAAATGTGACA
1 AAACTGACCCTTTGTCTGAAAGGGTATTTTGGG-AAATTGAATCTAAATGC-AGGAATGTGACA
* * * *
12639 AAACTAACCCTTTGTCTGAAATGGTATTTTGGGAACTTGAATCTAAGA-GCAAGAATGTGA-A
1 AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAAATTGAATCTAA-ATGCAGGAATGTGACA
* *
12700 GAAACTGACACTTTGTCCGAAAGGGTATTTTGGGAAA
1 -AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAAA
12737 AAGCAAGTAA
Statistics
Matches: 504, Mismatches: 79, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
61 2 0.00
62 315 0.62
63 105 0.21
64 82 0.16
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (62 bp):
AAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAAATTGAATCTAAATGCAGGAATGTGACA
Found at i:12575 original size:126 final size:123
Alignment explanation
Indices: 12082--12736 Score: 800
Period size: 126 Copynumber: 5.2 Consensus size: 123
12072 GGCTAAACTG
* * *
12082 ACCCTTTGTCTGCAATGGTATTTTGGGAAATAGAATCTAAATGCAGGAATGTGAAGAAACTGACC
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAATCT-AATGCAGGAATGTGAAGAAACTGACC
* * * * * * *
12147 CTTTCTCTGAAAGGGTATTTTGGGAATACT-AAACTTAAATGTAGGAATATGACGAAATTG
65 CTTTGTCTGAAAGGGTATTTTGGGAA-ATTGAAAC-TAAATGCAAGAATGTGACAAAATTA
**
12207 ACCCTTTGTCTAAAAGGGTATTTTGGGAAATAGAATCTAAGTGCAGGAATGTGAAGAAACTGACC
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAATCTAA-TGCAGGAATGTGAAGAAACTGACC
* * * *
12272 CTTTGTCGGAAAGGGTATTCTGGGAAATTGAAACTAAATGCAAGAGTGTGACAAAACTA
65 CTTTGTCTGAAAGGGTATTTTGGGAAATTGAAACTAAATGCAAGAATGTGACAAAATTA
*
12331 ACCCTTTGTCTGAAAGGGTATTTTGGGAAATAGAATCTAAGTGCAGGAATGTGAAGAAACTGACC
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAATCTAA-TGCAGGAATGTGAAGAAACTGACC
* * *
12396 CTTTGTCGGAAAGGGTATTCTGGGAAATTGAAACTAAATGCAAGAGTGTGACAAAATTA
65 CTTTGTCTGAAAGGGTATTTTGGGAAATTGAAACTAAATGCAAGAATGTGACAAAATTA
* * * *
12455 ACCCTTTGTCCGAAAGGGTATTTTGGGAAAATTGAAACTGAATGCTAGAAATGTGACA-AAACTA
1 ACCCTTTGTCCGAAAGGGTATTTTGGG-AAATAGAATCT-AATGC-AGGAATGTGA-AGAAACTG
* *
12519 ACCCTTTGTCTGAAAGGGTATTTTGGGAACTTGAATCTAAGA-GCAAGAATGTGACAAAATTA
62 ACCCTTTGTCTGAAAGGGTATTTTGGGAAATTGAAACTAA-ATGCAAGAATGTGACAAAATTA
* * * *
12581 ACCCTTTGTCCGAAAGGGTATTTTGGGAAAATTGAAACTGAATGCTAGAAATGTGACA-AAACTA
1 ACCCTTTGTCCGAAAGGGTATTTTGGG-AAATAGAATCT-AATGC-AGGAATGTGA-AGAAACTG
* * * * *
12645 ACCCTTTGTCTGAAATGGTATTTTGGGAACTTGAATCTAAGA-GCAAGAATGTGA-AGAAACTG
62 ACCCTTTGTCTGAAAGGGTATTTTGGGAAATTGAAACTAA-ATGCAAGAATGTGACA-AAATTA
*
12707 ACACTTTGTCCGAAAGGGTATTTTGGGAAA
1 ACCCTTTGTCCGAAAGGGTATTTTGGGAAA
12737 AAGCAAGTAA
Statistics
Matches: 492, Mismatches: 30, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
124 170 0.35
125 102 0.21
126 218 0.44
127 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (123 bp):
ACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAATCTAATGCAGGAATGTGAAGAAACTGACCC
TTTGTCTGAAAGGGTATTTTGGGAAATTGAAACTAAATGCAAGAATGTGACAAAATTA
Found at i:12780 original size:49 final size:49
Alignment explanation
Indices: 12727--12834 Score: 153
Period size: 49 Copynumber: 2.2 Consensus size: 49
12717 CGAAAGGGTA
*
12727 TTTTGGGAAAAAGCAAGTAAAAAGAAGTGCCTTCCGTCCGGGAAGGGCT
1 TTTTGGGAAAAAGCAAGTAAAAAGAAGTGCCTTCCGTCCGGGAAGGGCG
* ** **
12776 TTTTGGGAAAAAGCAGGTAAAAATTAGTGCCTTCCGTCTTGGAAGGGCG
1 TTTTGGGAAAAAGCAAGTAAAAAGAAGTGCCTTCCGTCCGGGAAGGGCG
*
12825 TTTTAGGAAA
1 TTTTGGGAAA
12835 TGTAAGTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (49 bp):
TTTTGGGAAAAAGCAAGTAAAAAGAAGTGCCTTCCGTCCGGGAAGGGCG
Found at i:14098 original size:16 final size:15
Alignment explanation
Indices: 14077--14106 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
14067 CCTCCCACTG
14077 AACTGACTTCACTCTA
1 AACTGACTTC-CTCTA
14093 AACTGACTTCCTCT
1 AACTGACTTCCTCT
14107 TTTTTTCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.33, G:0.07, T:0.33
Consensus pattern (15 bp):
AACTGACTTCCTCTA
Found at i:14628 original size:22 final size:22
Alignment explanation
Indices: 14600--14668 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
14590 TCAATCCCCT
14600 GCAGGAAGGCTTTGGTGACATG
1 GCAGGAAGGCTTTGGTGACATG
* *
14622 GCAGGAAGGCCTTGGTAACATG
1 GCAGGAAGGCTTTGGTGACATG
* *
14644 GCAGG-AGAGCTCTAGTGACATG
1 GCAGGAAG-GCTTTGGTGACATG
14666 GCA
1 GCA
14669 TGTGCAGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
21 2 0.05
22 38 0.95
ACGTcount: A:0.26, C:0.17, G:0.38, T:0.19
Consensus pattern (22 bp):
GCAGGAAGGCTTTGGTGACATG
Found at i:15862 original size:13 final size:13
Alignment explanation
Indices: 15842--15873 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
15832 ATGATTATGC
15842 ATAA-TGCAATTT
1 ATAAGTGCAATTT
15854 ATAAGTGCAATTT
1 ATAAGTGCAATTT
15867 ATAAGTG
1 ATAAGTG
15874 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (13 bp):
ATAAGTGCAATTT
Found at i:19932 original size:2 final size:2
Alignment explanation
Indices: 19925--19954 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19915 ATCCTCACAA
19925 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
19955 ATACCTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Done.