Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006795.1 Corchorus capsularis cultivar CVL-1 contig06816, 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: 15070
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:698 original size:25 final size:26
Alignment explanation
Indices: 660--714 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
650 AGTAACAACC
* *
660 AAAATGCCCATAA-GCAAAAATGACT
1 AAAATACCCATAAGGCAAAAATGACA
* *
685 AAAATACCCCTAAGGTAAAAATGACA
1 AAAATACCCATAAGGCAAAAATGACA
711 AAAA
1 AAAA
715 ATTCCTTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.56, C:0.18, G:0.11, T:0.15
Consensus pattern (26 bp):
AAAATACCCATAAGGCAAAAATGACA
Found at i:7510 original size:15 final size:16
Alignment explanation
Indices: 7452--7526 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 16
7442 GGTTCGGTGC
7452 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
* * *
7468 TTCAGCTTCAGGTATT
1 TTCGGGTTCGGGTATT
*
7484 TTAGGGTTCGGGTA-T
1 TTCGGGTTCGGGTATT
*
7499 TTCGGATTCGGGTATT
1 TTCGGGTTCGGGTATT
*
7515 TTCAGGTTCGGG
1 TTCGGGTTCGGG
7527 CTCGGATCGG
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
15 13 0.28
16 34 0.72
ACGTcount: A:0.12, C:0.13, G:0.33, T:0.41
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:7516 original size:31 final size:33
Alignment explanation
Indices: 7455--7526 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 33
7445 TCGGTGCTTC
*
7455 GGGTTCGGGTATTTTCAGCTTCAGGTATTTT-A
1 GGGTTCGGGTATTTTCAGATTCAGGTATTTTCA
* *
7487 GGGTTCGGGTA-TTTCGGATTCGGGTATTTTCA
1 GGGTTCGGGTATTTTCAGATTCAGGTATTTTCA
7519 -GGTTCGGG
1 GGGTTCGGG
7527 CTCGGATCGG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.12, C:0.12, G:0.35, T:0.40
Consensus pattern (33 bp):
GGGTTCGGGTATTTTCAGATTCAGGTATTTTCA
Found at i:7556 original size:17 final size:17
Alignment explanation
Indices: 7516--7563 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
7506 TCGGGTATTT
*
7516 TCAGGTTCGGGCTCGGA
1 TCAGGTTCGGGTTCGGA
* *
7533 TCGGGTTCGGGTTCGGG
1 TCAGGTTCGGGTTCGGA
*
7550 TCAGGTTCAGGTTC
1 TCAGGTTCGGGTTC
7564 ATTTTCGGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.08, C:0.21, G:0.42, T:0.29
Consensus pattern (17 bp):
TCAGGTTCGGGTTCGGA
Found at i:8411 original size:6 final size:6
Alignment explanation
Indices: 8400--8448 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
8390 TTCGGGTAAT
8400 TTCGGG TTCGGG TTCGGG --CGGG TTCGGG --CGGG TTTCGGG TTTCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG -TTCGGG -TTCGGG
8446 TTC
1 TTC
8449 ATTTTGCCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 8 0.21
6 19 0.50
7 11 0.29
ACGTcount: A:0.00, C:0.18, G:0.49, T:0.33
Consensus pattern (6 bp):
TTCGGG
Found at i:8438 original size:11 final size:10
Alignment explanation
Indices: 8408--8438 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
8398 ATTTCGGGTT
8408 CGGGTTCGGG
1 CGGGTTCGGG
8418 CGGGTTCGGG
1 CGGGTTCGGG
8428 CGGGTTTCGGG
1 CGGG-TTCGGG
8439 TTTCGGGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (10 bp):
CGGGTTCGGG
Found at i:9601 original size:437 final size:435
Alignment explanation
Indices: 8645--9877 Score: 1384
Period size: 437 Copynumber: 2.8 Consensus size: 435
8635 CCCGCTTATA
* * *
8645 ATAAACAAATCATTTTTTTGCTGGTTTATTTATCAAACGTTCCCT-ATACTTTTATGCTTTATGC
1 ATAAACAAATCATTTTTTTGCTGGATTATTTATCAAATG-ACCCTCATACTTTTATGCTTTATGC
* * * * *
8709 TATTTAGTCCCTCACAATT-TTTGGGTTGGACGACTTAACGTTTCAGCTTTGATTCTTTTATTTT
65 TATTTAAT-CCTTACAATTATAT--GTTGGACGA-TTAACGTTTCGGCTTTAATT-TTTTATTTT
* *
8773 TTGTTT-TGTTTGTCCGATCAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAA
125 TT-TTTCTATTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAA
* ** ** * *
8837 -GTTCTATGAAGGACTCAAAAAACAATTTAAATGTTTTCATTCAAAAAAATGCTTCTGAAATTTT
189 CTTTC-ATGAAGGACTCAAAAGCCAATTTTGATGTTTTGATTCAAAAAAATGCTTCTAAAATTTT
* * *
8901 GTGGTCTCGATTACCGGTCTATTTGATATCGTATAAATTTCAGTCCACATGTCCGATTGAGGTTG
253 GTGGTCTCGATTACCGGTCTATCTAATATCGTATAAATTTCAGTCCACATGTCCGATTGAGATTG
* * *
8966 TTCGAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACTTTCGTTAAGGGCCTGAAAGCTAAAT
318 TTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGTCAAGGGCCTGAAAGCTAAAT
9031 TGATTAATGAGTTTCGTGGAGGATTCAAGAGGGAATTTTTATGTTTGGTCTTC
383 TGATTAATGAGTTTCGTGGAGGATTCAAGAGGGAATTTTTATGTTTGGTCTTC
* * * **
9084 ATAAACAAATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATGCT
1 ATAAACAAATCATTTTTTTGCTGGATTATTTATCAAATGACCCTCATACTTTTATGCTTTATGCT
* *
9149 ATTTAATCCTTACAATTATATATTGGACGATTGAATGTTTCGGCTTTAATTGTTTTATTTTTTTT
66 ATTTAATCCTTACAATTATATGTTGGACGATT-AACGTTTCGGCTTTAATT-TTTTATTTTTTTT
* * * * *
9214 TCTATTTGACCGATCAAGGTGATTCAGGTGTCTATTTAAAGGTAATTCCATGGTCTACAACTTTC
129 TCTATTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTC
*
9279 ATGAAGGACTCAAAAGCCAATTTTGATGTTTTGATTCTAAAAAATGCTTCTAAAATTTTGTGGTC
194 ATGAAGGACTCAAAAGCCAATTTTGATGTTTTGATTCAAAAAAATGCTTCTAAAATTTTGTGGTC
** * * * *
9344 TCGATTGTCGGTCTATCTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAGATTGTTCAAG
259 TCGATTACCGGTCTATCTAATATCGTATAAATTTCAGTCCACATGTCCGATTGAGATTGTTCAAG
* * * * * *
9409 TGTCGGTTGAAAGGTTATTGTGTTATCTACGACTTTCG-CCATGGCTTGAAAGCTGAATTTGATT
324 TGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGTCAAGGGCCTGAAAGCT-AAATTGATT
*
9473 GATGAGTTTCGTGGA-GAGTTCAAGAGGGAATTTTTATGTTTGGTCCTT-
388 AATGAGTTTCGTGGAGGA-TTCAAGAGGGAATTTTTATGTTTGGT-CTTC
** * *
9521 ATAAACAAAT-ATTTTTTCCCTGGATTATTTATCAAATGACCCTCATAGTTTTATGCTTTGTGCT
1 ATAAACAAATCATTTTTTTGCTGGATTATTTATCAAATGACCCTCATACTTTTATGCTTTATGCT
** * * * * *
9585 ATTTAATCCTTTACAATTATGGGTTGAACGATTTAACATGTCGACTTTTATTTTTGTATTTTTTT
66 ATTTAATCC-TTACAATTATATGTTGGACGA-TTAACGTTTCGGCTTTAATTTTT-TATTTTTTT
* * * * * *
9650 GTTCTATTTGTCGGATCAAGGTAATTCAAGTGTCTATTGAAAGATAATTTAATGATTTACAACTT
128 -TTCTATTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTT
* * * * *
9715 TTATGAAGAACTCGAAAGCCAA-TTTGATGTTTTG-------AAAATGCTTCTGAAATTTTGTTG
192 TCATGAAGGACTCAAAAGCCAATTTTGATGTTTTGATTCAAAAAAATGCTTCTAAAATTTTGTGG
* * * * * ** * * *
9772 TCTCGATTTCGCCGGTCTATTTAATATCTTTTAATTTTTTGTTCATATGTCCGATTGA-ACTTAT
257 TCTCGA-TT-ACCGGTCTATCTAATATCGTATAAATTTCAGTCCACATGTCCGATTGAGA-TTGT
* * * ** *
9836 TCGAGTGTTGATTAAAAGGTTATTGCATGATTTACGACTTTC
319 TCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTC
9878 ATGAAGGACT
Statistics
Matches: 677, Mismatches: 102, Indels: 37
0.83 0.12 0.05
Matches are distributed among these distances:
430 27 0.04
431 3 0.00
432 75 0.11
436 76 0.11
437 342 0.51
438 93 0.14
439 61 0.09
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.42
Consensus pattern (435 bp):
ATAAACAAATCATTTTTTTGCTGGATTATTTATCAAATGACCCTCATACTTTTATGCTTTATGCT
ATTTAATCCTTACAATTATATGTTGGACGATTAACGTTTCGGCTTTAATTTTTTATTTTTTTTTC
TATTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCAT
GAAGGACTCAAAAGCCAATTTTGATGTTTTGATTCAAAAAAATGCTTCTAAAATTTTGTGGTCTC
GATTACCGGTCTATCTAATATCGTATAAATTTCAGTCCACATGTCCGATTGAGATTGTTCAAGTG
TCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGTCAAGGGCCTGAAAGCTAAATTGATTAAT
GAGTTTCGTGGAGGATTCAAGAGGGAATTTTTATGTTTGGTCTTC
Found at i:13093 original size:12 final size:13
Alignment explanation
Indices: 13078--13111 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
13068 AATCTAAATC
*
13078 TAAAGCAGATT-A
1 TAAAGCAAATTAA
13090 TAAAGCAAATTAA
1 TAAAGCAAATTAA
13103 TAAAGCAAA
1 TAAAGCAAA
13112 CAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Done.