Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010719.1 Corchorus capsularis cultivar CVL-1 contig10740, 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: 15112
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:8472 original size:2 final size:2
Alignment explanation
Indices: 8467--8506 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
8457 TTATAATTTT
8467 TA TA TA TA T- TA TA -A TA TA TA TA -A TA TA TGA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
8507 ATTTATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.09
2 29 0.85
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:8486 original size:14 final size:14
Alignment explanation
Indices: 8467--8517 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
8457 TTATAATTTT
8467 TATATATATTATAA
1 TATATATATTATAA
*
8481 TATATATAATAT-A
1 TATATATATTATAA
8494 TGATATATA-TATAA
1 T-ATATATATTATAA
8508 T-T-TATATTAT
1 TATATATATTAT
8518 TGATCGTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 4 0.12
12 4 0.12
13 5 0.15
14 20 0.61
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TATATATATTATAA
Found at i:8488 original size:18 final size:18
Alignment explanation
Indices: 8457--8506 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
8447 ATTATCTTTT
* *
8457 TTATAATTTTTATATATA
1 TTATAATATATATATATA
8475 TTATAATATATATA-ATA
1 TTATAATATATATATATA
*
8492 -TATGATATATATATA
1 TTATAATATATATATA
8507 ATTTATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 12 0.43
17 4 0.14
18 12 0.43
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATAATATATATATATA
Found at i:8725 original size:21 final size:20
Alignment explanation
Indices: 8686--8730 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
8676 AATTATCAAT
* *
8686 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
8706 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
8727 TAAA
1 TAAA
8731 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:9484 original size:18 final size:17
Alignment explanation
Indices: 9461--9496 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
9451 CTCAACCTAA
9461 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
9479 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
9496 A
1 A
9497 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:10125 original size:19 final size:18
Alignment explanation
Indices: 10092--10127 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10082 TTGAAATAAT
10092 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
10110 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
10128 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:10719 original size:14 final size:15
Alignment explanation
Indices: 10696--10728 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
10686 AGTTGTTCGA
10696 TTTTCGATTTTCAAT
1 TTTTCGATTTTCAAT
10711 TTTTC-ATTTTCAAT
1 TTTTCGATTTTCAAT
10725 TTTT
1 TTTT
10729 GATGGGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTCGATTTTCAAT
Found at i:11168 original size:7 final size:7
Alignment explanation
Indices: 11156--11193 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
11146 TCAGTTGTTT
11156 GATTTTC
1 GATTTTC
11163 GATTTTC
1 GATTTTC
11170 GATTTTTC
1 GA-TTTTC
11178 G-TTTTC
1 GATTTTC
*
11184 AATTTTC
1 GATTTTC
11191 GAT
1 GAT
11194 GGGTTTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 5 0.19
7 16 0.59
8 6 0.22
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (7 bp):
GATTTTC
Found at i:11363 original size:462 final size:461
Alignment explanation
Indices: 10550--11477 Score: 1667
Period size: 462 Copynumber: 2.0 Consensus size: 461
10540 TCTTTCGATC
10550 TGCTTGTTGGTGTTTTTGAGTTGGATTTCGATGGAAATCTCACTCCTCTTCAATCTTCGTCTCTT
1 TGCTTGTTGGTGTTTTTGAGTTGGATTTCGATGGAAATCTCACTCCTCTTCAATCTTCGTCTCTT
*
10615 TCGCACAGTCTGATTCAGTGAACCCGTGTTTCATTTCAAAATTTTCAATTTGGGTAAGTGAACCC
66 TCGCACAGTCTGATTCAGTGAACCCGTGTTTCATTTCAAAATTTTCAATTTAGGTAAGTGAACCC
*
10680 TTGTTCAGTTGTTCGATTTTCGATTTTCAATTTTTCATTTTCAATTTTTGATGGGTTTCTTAATT
131 TTGTTCAGTTGTTCGATTTTCGATTTTCAATTTTTCATTTTCAATTTTCGATGGGTTTCTTAATT
10745 TCTTTAATCTGTACTAACTATAAGTTTTAATTTGTTTATGTGGGTGGAATTAGGACTTGGAGTTT
196 TCTTTAATCTGTACTAACTATAAGTTTTAATTTGTTTATGTGGGTGGAATTAGGACTTGGAGTTT
*
10810 CGATTTCAAATTCAGAGGCTCAGAGCAATCCTCTTTAAATTCTTGTATACCTCTCGAGTCTCGTC
261 CGATTTCAAATTCAGAGGCTCAGAGCAATCCTCTATAAATTCTTGTATACCTCTCGAGTCTCGTC
* *
10875 TGAATTCTTGTCCTTCTTTAAGGAGCAAATTTTGAGGTAAATTAACTTGAATTATTCCATTTTCA
326 TGAATTCTTGTCCTTCTTTAAGGAGCAAATTTTGAGGTAAATTAACATGAATTATTCAATTTTCA
* *
10940 TTCATACCTTTTTCTTTGCATTCTCTCTTTCTTATTTTGTTGGTTCTTTGATCTCGTGCTTATTG
391 TTCATACCTTTTT-TTTGCATTCTCTCTTCCTTATTTTGTTGGTTCTGTGATCTCGTGCTTATTG
11005 CTTTTCT
455 CTTTTCT
* *
11012 TGCTTGTTGGTGTTTTTGAGTTGGCTTTCGATGGAAATCTTACTCCTCTTCAATCTTCGTCTCTT
1 TGCTTGTTGGTGTTTTTGAGTTGGATTTCGATGGAAATCTCACTCCTCTTCAATCTTCGTCTCTT
* * * * *
11077 TCGCATAGTCTGATTTAGTGAACCCTTGTTTGATTTCAAAATTTTCGATTTAGGTAAGTGAACCC
66 TCGCACAGTCTGATTCAGTGAACCCGTGTTTCATTTCAAAATTTTCAATTTAGGTAAGTGAACCC
* * *
11142 TTGTTCAGTTGTTTGATTTTCGATTTTCGATTTTTCGTTTTCAATTTTCGATGGGTTTCTTAATT
131 TTGTTCAGTTGTTCGATTTTCGATTTTCAATTTTTCATTTTCAATTTTCGATGGGTTTCTTAATT
*
11207 TCTTTAATCTGTACTGACTATAAGTTTTAATTTGTTTATGTGGGTGGAATTAGGACTTGGAGTTT
196 TCTTTAATCTGTACTAACTATAAGTTTTAATTTGTTTATGTGGGTGGAATTAGGACTTGGAGTTT
* *
11272 CGGTTTCAAATTCAGAGGCTCAGAGCAATCCTCTATGAATTCTTGTATACCTCTCGAGTCTCGTC
261 CGATTTCAAATTCAGAGGCTCAGAGCAATCCTCTATAAATTCTTGTATACCTCTCGAGTCTCGTC
11337 TGAATTCTTGTCCTTCTTTAAGGAGCAAATTTTGAGGTAAATTAACATGAATTATTCAATTTTCA
326 TGAATTCTTGTCCTTCTTTAAGGAGCAAATTTTGAGGTAAATTAACATGAATTATTCAATTTTCA
11402 TTCATACCTTTTTTTTGCATTCTCTCTTCCTTATTTTGTTGGTTCTGTGATCTCGTGCTTATTGC
391 TTCATACCTTTTTTTTGCATTCTCTCTTCCTTATTTTGTTGGTTCTGTGATCTCGTGCTTATTGC
11467 TTTTCT
456 TTTTCT
11473 TGCTT
1 TGCTT
11478 TTCTTGGTTA
Statistics
Matches: 446, Mismatches: 20, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
461 61 0.14
462 385 0.86
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (461 bp):
TGCTTGTTGGTGTTTTTGAGTTGGATTTCGATGGAAATCTCACTCCTCTTCAATCTTCGTCTCTT
TCGCACAGTCTGATTCAGTGAACCCGTGTTTCATTTCAAAATTTTCAATTTAGGTAAGTGAACCC
TTGTTCAGTTGTTCGATTTTCGATTTTCAATTTTTCATTTTCAATTTTCGATGGGTTTCTTAATT
TCTTTAATCTGTACTAACTATAAGTTTTAATTTGTTTATGTGGGTGGAATTAGGACTTGGAGTTT
CGATTTCAAATTCAGAGGCTCAGAGCAATCCTCTATAAATTCTTGTATACCTCTCGAGTCTCGTC
TGAATTCTTGTCCTTCTTTAAGGAGCAAATTTTGAGGTAAATTAACATGAATTATTCAATTTTCA
TTCATACCTTTTTTTTGCATTCTCTCTTCCTTATTTTGTTGGTTCTGTGATCTCGTGCTTATTGC
TTTTCT
Found at i:12389 original size:34 final size:35
Alignment explanation
Indices: 12331--12431 Score: 186
Period size: 34 Copynumber: 2.9 Consensus size: 35
12321 CCAAATTGAG
12331 TTAATTAGGTTGCATTTCAGTTTTGCATTTCAGAT
1 TTAATTAGGTTGCATTTCAGTTTTGCATTTCAGAT
*
12366 TTAGTTAGGTTGCA-TTCAGTTTTGCATTTCAGAT
1 TTAATTAGGTTGCATTTCAGTTTTGCATTTCAGAT
12400 TTAATTAGGTTGCATTTCAGTTTTGCATTTCA
1 TTAATTAGGTTGCATTTCAGTTTTGCATTTCA
12432 ACCTTTATAC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 33 0.52
35 30 0.48
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.49
Consensus pattern (35 bp):
TTAATTAGGTTGCATTTCAGTTTTGCATTTCAGAT
Found at i:14605 original size:27 final size:27
Alignment explanation
Indices: 14575--14653 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
14565 GCATTGGGGT
*
14575 CGCCCAAGGGTATTTTGGTCATTTTCA
1 CGCCCAAGGGCATTTTGGTCATTTTCA
* *
14602 CGCCCAGGGGCATTTTGGTCATTTTTA
1 CGCCCAAGGGCATTTTGGTCATTTTCA
* * ** *
14629 CACTCGGGGGCATTTTAGTCATTTT
1 CGCCCAAGGGCATTTTGGTCATTTT
14654 TTAATTTCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (27 bp):
CGCCCAAGGGCATTTTGGTCATTTTCA
Done.