Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007477.1 Corchorus capsularis cultivar CVL-1 contig07498, 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: 8317
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:1959 original size:15 final size:16
Alignment explanation
Indices: 1927--1960 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1917 AAGAAAAATT
*
1927 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
1943 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
1958 TAA
1 TAA
1961 GAGAGCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:5358 original size:581 final size:581
Alignment explanation
Indices: 4224--5382 Score: 2212
Period size: 581 Copynumber: 2.0 Consensus size: 581
4214 GTCCTATTCG
4224 TACGAATCTAGTTGTATTAGATTCAAATCCAACCTTTGAATATCCACCAAAGTCGACTTGAACTT
1 TACGAATCTAGTTGTATTAGATTCAAATCCAACCTTTGAATATCCACCAAAGTCGACTTGAACTT
* *
4289 CTTCAACTTCTAGACTTGTATGTCGATGATCTTCACAAAGCTATTCCTCCTCTTTCGTCAGCCTT
66 CTTCAACTCCTAGACTTGTATGTCGATGATCTTCACAAAGCTATCCCTCCTCTTTCGTCAGCCTT
*
4354 AAGCACTCAATTAGACCTGCAATTGAATTCTCAAGATCACAAGATTCACAAACAACTAAGTTATC
131 AAGCACTCAATTAGACCTACAATTGAATTCTCAAGATCACAAGATTCACAAACAACTAAGTTATC
4419 TCAACCTAATTGCTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCTCAAACTAGAACAA
196 TCAACCTAATTGCTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCTCAAACTAGAACAA
4484 TGAAGCTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTATGTTT
261 TGAAGCTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTATGTTT
4549 ACAAGAGGGGGATGGTCCCTTTATATAGTAGTAGGGGACGCATAACCCTTCTCCTAAATCTAAAA
326 ACAAGAGGGGGATGGTCCCTTTATATAGTAGTAGGGGACGCATAACCCTTCTCCTAAATCTAAAA
*
4614 GGAAAACATTACATAAAGGAAGGAACAAGGAAATAGCCTACTCCTTGTCCTACTATGAAAAGTAA
391 GGAAAACATTACATAAAGGAAGGAACAAGGAAATAGCCTACTCCTTGTCCTACTAGGAAAAGTAA
*
4679 ATACATAACTTAATTAAGCAAGGATTGGACTTAGTCAAACAAGGCCCAACCCAATGTCTTCTAAA
456 ATACATAACATAATTAAGCAAGGATTGGACTTAGTCAAACAAGGCCCAACCCAATGTCTTCTAAA
* *
4744 CTAAATAAATAACTAATCTAAGATAGAAATAAAGGCCCAATGACTGAATTACACAATATGA
521 CTAAATAAATAACTAATCTAAGATAGAAATAAAGGACCAATGACCGAATTACACAATATGA
4805 TACGAATCTAGTTGTATTAGATTCAAATCCAACCTTTGAATATCCACCAAAGTCGACTTGAACTT
1 TACGAATCTAGTTGTATTAGATTCAAATCCAACCTTTGAATATCCACCAAAGTCGACTTGAACTT
*
4870 CTTCAACTCCTAGACTTGTATGTCGATGATCTTCACAAAGCTATCCCTCCTCTTTCGTCGGCCTT
66 CTTCAACTCCTAGACTTGTATGTCGATGATCTTCACAAAGCTATCCCTCCTCTTTCGTCAGCCTT
4935 AAGCACTCAATTAGACCTACAATTGAATTCTCAAGATCACAAGATTCACAAACAACTAAGTTATC
131 AAGCACTCAATTAGACCTACAATTGAATTCTCAAGATCACAAGATTCACAAACAACTAAGTTATC
5000 TCAACCTAATTGCTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCTCAAACTAGAACAA
196 TCAACCTAATTGCTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCTCAAACTAGAACAA
5065 TGAAGCTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTATGTTT
261 TGAAGCTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTATGTTT
5130 ACAAGAGGGGGATGGTCCCTTTATATAGTAGTAGGGGACGCATAACCCTTCTCCTAAATCTAAAA
326 ACAAGAGGGGGATGGTCCCTTTATATAGTAGTAGGGGACGCATAACCCTTCTCCTAAATCTAAAA
5195 GGAAAACATTACATAAAGGAAGGAACAAGGAAATAGCCTACTCCTTGTCCTACTAGGAAAAGTAA
391 GGAAAACATTACATAAAGGAAGGAACAAGGAAATAGCCTACTCCTTGTCCTACTAGGAAAAGTAA
*
5260 ATAACATTACATAATTAAGCAAGGATTGGACTTAGTCAAACAAGGCCCAACCCAATGTCTTCTAA
456 AT-ACATAACATAATTAAGCAAGGATTGGACTTAGTCAAACAAGGCCCAACCCAATGTCTTCTAA
*
5325 ACTAAATAAATAACTAATCTAAGATAG-AATAAAGGACCAATGGCCGAATTACACAATA
520 ACTAAATAAATAACTAATCTAAGATAGAAATAAAGGACCAATGACCGAATTACACAATA
5383 CTAAAGCCTA
Statistics
Matches: 567, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
581 480 0.85
582 87 0.15
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (581 bp):
TACGAATCTAGTTGTATTAGATTCAAATCCAACCTTTGAATATCCACCAAAGTCGACTTGAACTT
CTTCAACTCCTAGACTTGTATGTCGATGATCTTCACAAAGCTATCCCTCCTCTTTCGTCAGCCTT
AAGCACTCAATTAGACCTACAATTGAATTCTCAAGATCACAAGATTCACAAACAACTAAGTTATC
TCAACCTAATTGCTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCTCAAACTAGAACAA
TGAAGCTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTATGTTT
ACAAGAGGGGGATGGTCCCTTTATATAGTAGTAGGGGACGCATAACCCTTCTCCTAAATCTAAAA
GGAAAACATTACATAAAGGAAGGAACAAGGAAATAGCCTACTCCTTGTCCTACTAGGAAAAGTAA
ATACATAACATAATTAAGCAAGGATTGGACTTAGTCAAACAAGGCCCAACCCAATGTCTTCTAAA
CTAAATAAATAACTAATCTAAGATAGAAATAAAGGACCAATGACCGAATTACACAATATGA
Found at i:6573 original size:30 final size:30
Alignment explanation
Indices: 6537--6619 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 30
6527 TTCTCGTCAC
6537 CCAAAACAGATTTATTTTCAATGC-CATCAA
1 CCAAAACAGA-TTATTTTCAATGCTCATCAA
* *
6567 CCAAAACAGGATTATTTGCAATGCTATGATCAA
1 CCAAAACA-GATTATTTTCAATGC--TCATCAA
*
6600 CCAAAACAGAATTGTTTTCA
1 CCAAAACAG-ATTATTTTCA
6620 TCACAATTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 20 0.45
31 2 0.05
32 1 0.02
33 21 0.48
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (30 bp):
CCAAAACAGATTATTTTCAATGCTCATCAA
Found at i:6713 original size:33 final size:32
Alignment explanation
Indices: 6633--6730 Score: 106
Period size: 33 Copynumber: 3.0 Consensus size: 32
6623 CAATTAGCAT
*
6633 CCAAAATAGATTTAGTTTCATCACAAACAACA
1 CCAAAATAGATTTAGTATCATCACAAACAACA
* * *
6665 CCTAAAACAGATTTAGTGTCATTACAAACAACA
1 CC-AAAATAGATTTAGTATCATCACAAACAACA
* * * *
6698 CTCAAATTAGGTTTAGTATCATCGCAATCAACA
1 C-CAAAATAGATTTAGTATCATCACAAACAACA
6731 TCTATAACAC
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
32 2 0.04
33 51 0.94
34 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (32 bp):
CCAAAATAGATTTAGTATCATCACAAACAACA
Found at i:8133 original size:10 final size:9
Alignment explanation
Indices: 8113--8147 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
8103 TCTGGTCGAA
8113 ATTTTTTTT
1 ATTTTTTTT
8122 ATTTTATTTT
1 ATTTT-TTTT
8132 ATTTTTTTAT
1 ATTTTTTT-T
8142 ATTTTT
1 ATTTTT
8148 CGATATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Done.