Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018541.1 Corchorus olitorius cultivar O-4 contig18574, 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: 5740
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Found at i:1461 original size:651 final size:649
Alignment explanation
Indices: 221--1520 Score: 2530
Period size: 651 Copynumber: 2.0 Consensus size: 649
211 GTTTTCACTT
221 CTCACCGCAACATTTTGAGGTAAATCTGGATTTATTTGTTGATTATATTATTTGATACTTAAATT
1 CTCACCGCAACATTTTGAGGTAAATCTGGATTTATTTGTTGATTATATTATTTGATACTTAAATT
286 TAAATTAACCATTTCCTTATTCCTCTTTTATTTCACAATTTTTTTTTCTACATTTCCAAAAGCAC
66 TAAATTAACCATTTCCTTATTCCTCTTTTATTTCACAATTTTTTTTTCTACATTTCCAAAAGCAC
351 AGTTAGCCAATACTAAGTACAATCATTTTGTGATACATTGTGTAAATTACATATGCTCCTGCAAA
131 AGTTAGCCAATACTAAGTACAATCATTTTGTGATACATTGTGTAAATTACATATGCTCCTGCAAA
416 TGCTCTCAACTAATTCAATTTTCCTACAACAACTATACATGCTCCTTGAATACAAAAATTAGGTC
196 TGCTCTCAACTAATTCAATTTTCCTACAACAACTATACATGCTCCTTGAATACAAAAATTAGGTC
481 TTCCTCATGCAGAAGCCAAATTCTTCCACCTACCCGAGTTCAGTAATTTAACAATTGCAATCAAG
261 TTCCTCATGCAGAAGCCAAATTCTTCCACCTACCCGAGTTCAGTAATTTAACAATTGCAATCAAG
546 ATTAAAAAAAACCGTAGTGTACTATGTTTTTTTAGATAATCAACATACATTTTAAGTAAACAATT
326 ATTAAAAAAAACCGTAGTGTACTATGTTTTTTTAGATAATCAACATACATTTTAAGTAAACAATT
611 AATATTAGTTTTATTTTGATGAATTATCTAGAGATGAAGGAGTAGAATATTAGCTTTATTTTGAT
391 AATATTAGTTTTATTTTGATGAATTATCTAGAGATGAAGGAGTAGAATATTAGCTTTATTTTGAT
676 GAATTACCTAGAGATGGAGTAGAATTTAGGTAATGCACTTTTAGAATGAAAGAGAGGTCATGTGT
456 GAATTACCTAGAGATGGAGTAGAATTTAGGTAATGCACTTTTAGAATGAAAGAGAGGTCATGTGT
*
741 TTTGCTTTATATATGCGAATTATTTGTTTCGATGTATTCTCCTAATTGTTTAACTTACAGTTAAT
521 TTTGCTTTATATATGCGAATTATTTGTTTCGATGTATTCTCCTAATTGTTTAACTTACAGCTAAT
806 GCAATATCTTCTTACTAACCGACTTAAACAACTACAAAAAATATAGCCCTGATAAGAAGATGAC
586 GCAATATCTTCTTACTAACCGACTTAAACAACTACAAAAAATATAGCCCTGATAAGAAGATGAC
870 CTCACCGCAACATTTTGAGGTAAATCTGGATTTATTTGTTGATTATATTATTTGATACTTAAATT
1 CTCACCGCAACATTTTGAGGTAAATCTGGATTTATTTGTTGATTATATTATTTGATACTTAAATT
935 TAAATTAACCATTTCCTTATTCCTCTTTTATTTCACAA-TTTTTTTTCTACATTTCCAAAAGCAC
66 TAAATTAACCATTTCCTTATTCCTCTTTTATTTCACAATTTTTTTTTCTACATTTCCAAAAGCAC
999 AGTTAGCCAATACTAAGTACAATCATTTTGTGATACATTGTGTAAATTACATATGCTCCTGCAAA
131 AGTTAGCCAATACTAAGTACAATCATTTTGTGATACATTGTGTAAATTACATATGCTCCTGCAAA
*
1064 TGCTCTCAACTAATTCAATTTTCCTACGACAACTATACATGCTCCTTGAATACAAAAAATTAGGT
196 TGCTCTCAACTAATTCAATTTTCCTACAACAACTATACATGCTCCTTGAATAC-AAAAATTAGGT
*
1129 CTTCCTCATGCAGAAGCTAAATTCTTCCACCTACCCGAGTTCAGTAATTTAACAATTGCAATCAA
260 CTTCCTCATGCAGAAGCCAAATTCTTCCACCTACCCGAGTTCAGTAATTTAACAATTGCAATCAA
1194 GATTAAAAAAAAAACCGTAGTGTACTATGTTTTTTTAGATAATCAACATACATTTTAAGTAAACA
325 GATT--AAAAAAAACCGTAGTGTACTATGTTTTTTTAGATAATCAACATACATTTTAAGTAAACA
1259 ATTAATATTAGTTTTATTTTGATGAATTATCTAGAGATGAAGGAGTAGAATATTAGCTTTATTTT
388 ATTAATATTAGTTTTATTTTGATGAATTATCTAGAGATGAAGGAGTAGAATATTAGCTTTATTTT
1324 GATGAATTACCTAGAGATGGAGTAGAATTTAGGTAATGCACTTTTAGAATGAAAGAGAGGTCATG
453 GATGAATTACCTAGAGATGGAGTAGAATTTAGGTAATGCACTTTTAGAATGAAAGAGAGGTCATG
1389 TGTTTTGCTTTATATATGCGAATTATTTGTTTCGATGTATTCTCCTAATTGTTTAACTTACAGCT
518 TGTTTTGCTTTATATATGCGAATTATTTGTTTCGATGTATTCTCCTAATTGTTTAACTTACAGCT
*
1454 AATGCAATATCTTCTTACTAACCGACTTAAACAACTACAAAAAATATAGTCCTGATAAGAAGATG
583 AATGCAATATCTTCTTACTAACCGACTTAAACAACTACAAAAAATATAGCCCTGATAAGAAGATG
1519 AC
648 AC
1521 TGTAGCGCAA
Statistics
Matches: 644, Mismatches: 4, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
648 143 0.22
649 182 0.28
651 319 0.50
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (649 bp):
CTCACCGCAACATTTTGAGGTAAATCTGGATTTATTTGTTGATTATATTATTTGATACTTAAATT
TAAATTAACCATTTCCTTATTCCTCTTTTATTTCACAATTTTTTTTTCTACATTTCCAAAAGCAC
AGTTAGCCAATACTAAGTACAATCATTTTGTGATACATTGTGTAAATTACATATGCTCCTGCAAA
TGCTCTCAACTAATTCAATTTTCCTACAACAACTATACATGCTCCTTGAATACAAAAATTAGGTC
TTCCTCATGCAGAAGCCAAATTCTTCCACCTACCCGAGTTCAGTAATTTAACAATTGCAATCAAG
ATTAAAAAAAACCGTAGTGTACTATGTTTTTTTAGATAATCAACATACATTTTAAGTAAACAATT
AATATTAGTTTTATTTTGATGAATTATCTAGAGATGAAGGAGTAGAATATTAGCTTTATTTTGAT
GAATTACCTAGAGATGGAGTAGAATTTAGGTAATGCACTTTTAGAATGAAAGAGAGGTCATGTGT
TTTGCTTTATATATGCGAATTATTTGTTTCGATGTATTCTCCTAATTGTTTAACTTACAGCTAAT
GCAATATCTTCTTACTAACCGACTTAAACAACTACAAAAAATATAGCCCTGATAAGAAGATGAC
Found at i:2486 original size:16 final size:17
Alignment explanation
Indices: 2462--2494 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2452 ACGGTGTACG
2462 TATAAATTATAT-TTAA
1 TATAAATTATATATTAA
*
2478 TATATATTATATATTAA
1 TATAAATTATATATTAA
2495 CAAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAATTATATATTAA
Found at i:4916 original size:25 final size:25
Alignment explanation
Indices: 4878--4926 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
4868 CCAAACAATC
4878 TTGAGAACTATCGCTCGGTCTCTAT
1 TTGAGAACTATCGCTCGGTCTCTAT
* *
4903 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGAACTATCGCTCGGTCTCTA
4927 CAAACCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.16, C:0.29, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGAACTATCGCTCGGTCTCTAT
Found at i:4952 original size:21 final size:21
Alignment explanation
Indices: 4923--4965 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4913 TCGCTCGGTC
*
4923 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
4943 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
4965 T
1 T
4966 ACACACATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.19
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:5405 original size:20 final size:20
Alignment explanation
Indices: 5377--5421 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5367 GTTCTGTTGT
*
5377 TTAATATCTAACGCAACGAC
1 TTAAGATCTAACGCAACGAC
5397 TTAAGATCTAACGCAACGAC
1 TTAAGATCTAACGCAACGAC
*
5417 CTAAG
1 TTAAG
5422 TGTCCGCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.22
Consensus pattern (20 bp):
TTAAGATCTAACGCAACGAC
Done.