Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009704.1 Corchorus capsularis cultivar CVL-1 contig09725, 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: 13242
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Found at i:2088 original size:587 final size:585
Alignment explanation
Indices: 972--2141 Score: 2157
Period size: 587 Copynumber: 2.0 Consensus size: 585
962 CCTCAAATTA
* *
972 TTTTTCTGAAAGAAAAAAAAATTGCCATTACCTTTTTTTCTCTCTTAACTCTTAGGTCTTACTTT
1 TTTTTCCGAAAGAAAAAAAAATTGCCATTACCTTTTTTTCTCTCTTAACTCTCAGGTCTTACTTT
1037 ATTTAGATTTTCTCTCATTTTTTCGATCTAAAATTTTTCCGGTTTGCATGGAACTTTTGGAGAAA
66 ATTTAGATTTTCTCTCATTTTTTCGATCTAAAATTTTTCCGGTTTGCATGGAACTTTTGGAGAAA
*
1102 TGACAATATATAACGATAATAACTAACTCTCAGTTCTTTCTCCGTGTTTCTTTTCCCCCTATTCT
131 TGACAATATATAACGATAATAACTAACTCTCAGTTCTTTCTCAGTGTTTCTTTTCCCCCTATTCT
* * *
1167 TTAAGCCCTATTTTTTTTCCTACAATGTATATATCAATGCACCGACCTGGAAGTCAATATAGTAG
196 TTAAGCCCTATTTTTTTTCCTACAATGTATATATCAATGCACCGACCTGGAAATCAATATAATAA
*
1232 GTTATTTTTTTTGCATTAACGAGATTTTTCATTTGTGTTCTCCTTTGATTCATTTTTTTAATGTT
261 GTTATTTTTTTTGCATTAACGAGATTCTTCATTTGTGTTCTCCTTTGATTCATTTTTTTAATGTT
1297 CTTCAAATCATTTCTATGTTCTGTTTTATGATTTCTCTATACTAGAATTGACAAATTTAGAGGTC
326 CTTCAAATCATTTCTATGTTCTGTTTTATGATTTCTCTATACTAGAATTGACAAATTTAGAGGTC
1362 TTTTTCTTTTTTGGGTTTTCAGCAGAATCTCTCATTGAACAAAAATTTGGATCAATATGGATAAG
391 TTTTTCTTTTTTGGGTTTTCAGCAGAATCTCTCATTGAACAAAAATTTGGATCAATATGGATAAG
1427 AACTTTTCAAATATATGATTAATATGAATGAAATTGATATTCATGTTTTATATGCCTATCTTTCA
456 AACTTTTCAAATATATGATTAATATGAATGAAATTGATATTCATGTTTTATATGCCTATCTTTCA
*
1492 TTCTATATATATATTCTCTTGTTCATTGGTCAACGATGCTACCATTGTTGCCTTAGAGAACAATA
521 TTC--TATATATATTCTCTTGTTCATTGGTCAACGATGCTACCATTGTTGCATTAGAGAACAATA
1557 TT
584 TT
1559 TTTTTCCGAAAGAAAAAAAAATTGCCATTACCTTTTTTTCTCTCTTAACTCTCAGGTCTTACTTT
1 TTTTTCCGAAAGAAAAAAAAATTGCCATTACCTTTTTTTCTCTCTTAACTCTCAGGTCTTACTTT
* *
1624 ATTTAGTTTTTCTCTCATTTTTTCGATCTAAAATTTTTCCGGTTTGCATGGCACTTTTGGAGAAA
66 ATTTAGATTTTCTCTCATTTTTTCGATCTAAAATTTTTCCGGTTTGCATGGAACTTTTGGAGAAA
1689 TGACAATATATAACGATAATAACTAACTCTCAGTTCTTTCTCAGTGTTTCTTTTCCCCCTATTCT
131 TGACAATATATAACGATAATAACTAACTCTCAGTTCTTTCTCAGTGTTTCTTTTCCCCCTATTCT
* *
1754 TTAAGCCCTATTTTTTTT-CTACATTGTATATATCAATGCACTGACCTGGAAATCAATATAATAA
196 TTAAGCCCTATTTTTTTTCCTACAATGTATATATCAATGCACCGACCTGGAAATCAATATAATAA
1818 GTTA-TTTTTTTGCATTAACGAGATTCTTCATTTGTGTTCTCCTTTGATTCA-TTTTTTAATGTT
261 GTTATTTTTTTTGCATTAACGAGATTCTTCATTTGTGTTCTCCTTTGATTCATTTTTTTAATGTT
* *
1881 CTTCTAATCATTTCTATGTTCTGTTTTATGATTTCTCTATACTAGAATTGGCAAATTTAGAGGTC
326 CTTCAAATCATTTCTATGTTCTGTTTTATGATTTCTCTATACTAGAATTGACAAATTTAGAGGTC
*
1946 TTTTTTCTTTTTTGGGTTTTCAGCAGAATCTCTCATTGCACAAAAATTTGGATCAATATGGATAA
391 -TTTTTCTTTTTTGGGTTTTCAGCAGAATCTCTCATTGAACAAAAATTTGGATCAATATGGATAA
2011 GAACTTTTCAAATATATGATTAATATGAATGAAATTGATATTCATGTTTTATATGCCTATCTTTC
455 GAACTTTTCAAATATATGATTAATATGAATGAAATTGATATTCATGTTTTATATGCCTATCTTTC
2076 ATTCTATATATATTCTCTTGTTCATTGGTCAACGATGCTACCATTGTTGCATTAGAGAACAATAT
520 ATTCTATATATATTCTCTTGTTCATTGGTCAACGATGCTACCATTGTTGCATTAGAGAACAATAT
2141 T
585 T
2142 ACAATGATGA
Statistics
Matches: 567, Mismatches: 15, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
583 61 0.11
584 75 0.13
585 178 0.31
586 45 0.08
587 208 0.37
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (585 bp):
TTTTTCCGAAAGAAAAAAAAATTGCCATTACCTTTTTTTCTCTCTTAACTCTCAGGTCTTACTTT
ATTTAGATTTTCTCTCATTTTTTCGATCTAAAATTTTTCCGGTTTGCATGGAACTTTTGGAGAAA
TGACAATATATAACGATAATAACTAACTCTCAGTTCTTTCTCAGTGTTTCTTTTCCCCCTATTCT
TTAAGCCCTATTTTTTTTCCTACAATGTATATATCAATGCACCGACCTGGAAATCAATATAATAA
GTTATTTTTTTTGCATTAACGAGATTCTTCATTTGTGTTCTCCTTTGATTCATTTTTTTAATGTT
CTTCAAATCATTTCTATGTTCTGTTTTATGATTTCTCTATACTAGAATTGACAAATTTAGAGGTC
TTTTTCTTTTTTGGGTTTTCAGCAGAATCTCTCATTGAACAAAAATTTGGATCAATATGGATAAG
AACTTTTCAAATATATGATTAATATGAATGAAATTGATATTCATGTTTTATATGCCTATCTTTCA
TTCTATATATATTCTCTTGTTCATTGGTCAACGATGCTACCATTGTTGCATTAGAGAACAATATT
Found at i:2725 original size:23 final size:23
Alignment explanation
Indices: 2695--2740 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2685 ATAATTTTCT
2695 ATAAGAATCATAGTTATCATTCA
1 ATAAGAATCATAGTTATCATTCA
2718 ATAAGAATCATAGTTATCATTCA
1 ATAAGAATCATAGTTATCATTCA
2741 TGGCTACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (23 bp):
ATAAGAATCATAGTTATCATTCA
Found at i:2873 original size:13 final size:13
Alignment explanation
Indices: 2852--2884 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2842 AACGAGATCC
*
2852 AATGTTATATCAG
1 AATGCTATATCAG
2865 AATGCTATATCAG
1 AATGCTATATCAG
2878 AATGCTA
1 AATGCTA
2885 CGCCGAGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (13 bp):
AATGCTATATCAG
Found at i:7965 original size:13 final size:13
Alignment explanation
Indices: 7947--7972 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7937 AATCAATCAA
7947 AAACAAATTTTGC
1 AAACAAATTTTGC
7960 AAACAAATTTTGC
1 AAACAAATTTTGC
7973 TTATGCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
AAACAAATTTTGC
Found at i:9884 original size:21 final size:22
Alignment explanation
Indices: 9838--9884 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
9828 ACTTCAAGAC
* *
9838 TTATCAGCTTAACCTTAACCAT
1 TTATCAGCCTAACCTTAACCAA
9860 TTATCA-CCTAACCTTATA-CAA
1 TTATCAGCCTAACCTTA-ACCAA
9881 TTAT
1 TTAT
9885 TATCTTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (22 bp):
TTATCAGCCTAACCTTAACCAA
Found at i:10224 original size:9 final size:11
Alignment explanation
Indices: 10196--10222 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
10186 GAAGTTTTCA
10196 AATATATGATT
1 AATATATGATT
10207 AATATATGATT
1 AATATATGATT
10218 AATAT
1 AATAT
10223 GAATGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (11 bp):
AATATATGATT
Done.