Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012945.1 Corchorus capsularis cultivar CVL-1 contig12966, 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: 13118
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:1583 original size:83 final size:81
Alignment explanation
Indices: 1481--1699 Score: 225
Period size: 84 Copynumber: 2.6 Consensus size: 81
1471 TGGAATGTAT
*
1481 ATATGTTTTGGATCATTATTATCAACAT-AGTAATCAG-GAAAAAAAGGGAGCATG-TTA-AA-A
1 ATATGTTTTGGATCATTATTA-C-ACATAAG-CAT--GTGAAAAAAA-GGAGC-TGTTTATAAGA
1541 ACAGGGGCTGTAATCATATGACA
59 ACAGGGGCTGTAATCATATGACA
* * *
1564 ATATGTTTTGGATCTTTATTACACATAAGCATGTTAATAAAAGGAGCTGTTTTTATTAAGAACAG
1 ATATGTTTTGGATCATTATTACACATAAGCATGTGAAAAAAAGGAGCTG--TTTA-TAAGAACAG
*
1629 GGGCTGTAATCATATTACA
63 GGGCTGTAATCATATGACA
* * *
1648 ATATGTTTTGGATCATTATTACACGA-AAGCATGTTAAAAACAGGGGCTGTTT
1 ATATGTTTTGGATCATTATTACAC-ATAAGCATGTGAAAAAAAGGAGCTGTTT
1700 TTATGTTATA
Statistics
Matches: 118, Mismatches: 9, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
78 2 0.02
79 6 0.05
80 6 0.05
81 9 0.08
82 6 0.05
83 22 0.19
84 66 0.56
85 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (81 bp):
ATATGTTTTGGATCATTATTACACATAAGCATGTGAAAAAAAGGAGCTGTTTATAAGAACAGGGG
CTGTAATCATATGACA
Found at i:1643 original size:84 final size:84
Alignment explanation
Indices: 1535--1703 Score: 270
Period size: 84 Copynumber: 2.0 Consensus size: 84
1525 AGGGAGCATG
*
1535 TTAAAAACAGGGGCTGTAATCATATGACAATATGTTTTGGATCTTTATTACAC-ATAAGCATGTT
1 TTAAAAACAGGGGCTGTAATCATATGACAATATGTTTTGGATCATTATTACACGA-AAGCATGTT
1599 AATAAA-AGGAGCTGTTTTTA
65 AA-AAACAGGAGCTGTTTTTA
* *
1619 TTAAGAACAGGGGCTGTAATCATATTACAATATGTTTTGGATCATTATTACACGAAAGCATGTTA
1 TTAAAAACAGGGGCTGTAATCATATGACAATATGTTTTGGATCATTATTACACGAAAGCATGTTA
*
1684 AAAACAGGGGCTGTTTTTA
66 AAAACAGGAGCTGTTTTTA
1703 T
1 T
1704 GTTATAAGAT
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
83 3 0.04
84 75 0.95
85 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (84 bp):
TTAAAAACAGGGGCTGTAATCATATGACAATATGTTTTGGATCATTATTACACGAAAGCATGTTA
AAAACAGGAGCTGTTTTTA
Found at i:5661 original size:95 final size:95
Alignment explanation
Indices: 5556--5808 Score: 445
Period size: 95 Copynumber: 2.7 Consensus size: 95
5546 TTTTTGTTTG
* *
5556 CTGCATTTATATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTATTGCGTTTCTATTATAG
1 CTGCATTTATATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTATTGCATTTCTATTATAC
5621 TAATTTCTATTTTTTGTTTGCTGCATTTTA
66 TAATTTCTATTTTTTGTTTGCTGCATTTTA
5651 CTGCATTTATATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTATTGCATTTCTATTATAC
1 CTGCATTTATATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTATTGCATTTCTATTATAC
*
5716 TAATTTCTGTTTTTTGTTTGCTGCATTTTA
66 TAATTTCTATTTTTTGTTTGCTGCATTTTA
* *
5746 CTGCA-TCATTATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTATTGCATTTATATTAT
1 CTGCATTTA-TATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTATTGCATTTCTATTAT
5809 GCTCATTAAT
Statistics
Matches: 152, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
94 2 0.01
95 150 0.99
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (95 bp):
CTGCATTTATATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTATTGCATTTCTATTATAC
TAATTTCTATTTTTTGTTTGCTGCATTTTA
Found at i:5828 original size:48 final size:48
Alignment explanation
Indices: 5557--5813 Score: 353
Period size: 48 Copynumber: 5.4 Consensus size: 48
5547 TTTTGTTTGC
5557 TGCATTTATATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTAT
1 TGCATTTATATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTAT
* * * * * *
5605 TGCGTTTCTATTATAGT--AATTTCTATTTTTTGTTTGCTGCATTTTAC
1 TGCATTTATATTATACTCAAAATTCT-GTTTTTGTTTGCTGCATTTTAT
5652 TGCATTTATATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTAT
1 TGCATTTATATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTAT
* * *
5700 TGCATTTCTATTATACT--AATTTCTGTTTTTTGTTTGCTGCATTTTAC
1 TGCATTTATATTATACTCAAAATTCTG-TTTTTGTTTGCTGCATTTTAT
*
5747 TGCA-TCATTATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTAT
1 TGCATTTA-TATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTAT
*
5795 TGCATTTATATTATGCTCA
1 TGCATTTATATTATACTCA
5814 TTAATTTTGT
Statistics
Matches: 180, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
46 14 0.08
47 67 0.37
48 84 0.47
49 15 0.08
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (48 bp):
TGCATTTATATTATACTCAAAATTCTGTTTTTGTTTGCTGCATTTTAT
Found at i:8707 original size:21 final size:21
Alignment explanation
Indices: 8683--8731 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
8673 CAGCTGGGGG
* * *
8683 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
8704 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
8725 CCCATGT
1 CCCATGT
8732 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:10377 original size:169 final size:169
Alignment explanation
Indices: 10098--10435 Score: 667
Period size: 169 Copynumber: 2.0 Consensus size: 169
10088 AACCTAAGAC
10098 TGAAGGGGTACTTAGGAGGTGTTATGTCACCTGAGGGTTTACTTAACTAGAACGATACCCACAAA
1 TGAAGGGGTACTTAGGAGGTGTTATGTCACCTGAGGGTTTACTTAACTAGAACGATACCCACAAA
10163 CATTTTATTCATTAAAACTAAGTAAACTAAGACGACTAATATATTAACTAGAACGATACATTAAG
66 CATTTTATTCATTAAAACTAAGTAAACTAAGACGACTAATATATTAACTAGAACGATACATTAAG
10228 CATTCACCTATTTCCTCCCCCACACTTAAATTCAACATT
131 CATTCACCTATTTCCTCCCCCACACTTAAATTCAACATT
*
10267 TGAAGGGGTACTTAGGAGGTGTTATGTCACCTGAGGGTTTACTTAACTAGAACGATACCTACAAA
1 TGAAGGGGTACTTAGGAGGTGTTATGTCACCTGAGGGTTTACTTAACTAGAACGATACCCACAAA
10332 CATTTTATTCATTAAAACTAAGTAAACTAAGACGACTAATATATTAACTAGAACGATACATTAAG
66 CATTTTATTCATTAAAACTAAGTAAACTAAGACGACTAATATATTAACTAGAACGATACATTAAG
10397 CATTCACCTATTTCCTCCCCCACACTTAAATTCAACATT
131 CATTCACCTATTTCCTCCCCCACACTTAAATTCAACATT
10436 GTCCTCAATG
Statistics
Matches: 168, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 168 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (169 bp):
TGAAGGGGTACTTAGGAGGTGTTATGTCACCTGAGGGTTTACTTAACTAGAACGATACCCACAAA
CATTTTATTCATTAAAACTAAGTAAACTAAGACGACTAATATATTAACTAGAACGATACATTAAG
CATTCACCTATTTCCTCCCCCACACTTAAATTCAACATT
Done.