Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010847.1 Corchorus capsularis cultivar CVL-1 contig10868, 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: 23427
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:5282 original size:40 final size:40
Alignment explanation
Indices: 5238--5636 Score: 583
Period size: 40 Copynumber: 10.0 Consensus size: 40
5228 TACGCGGCAC
* *
5238 ATTCACATTCAAATTTTCCAATTGACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* *
5278 ATTCACATTCAAATTTTCCAATTTACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
5318 AATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
1 -ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* * *
5359 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* * *
5399 ATTCACATCCAACTTTCCCAAATAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
*
5439 ATTCACATCCAAA-TTTCCAATAAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* *
5478 ATTCACATCCAAAATTTCCAATAAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* * *
5518 ATTCACATTCAAA-ATTCCAATAAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
*
5557 ATTCACATCCAACA-TTTCCAAATAACATTGAACTTGCCTT
1 ATTCACATCCAA-ATTTTCCAATTAACATTGAACTTGCCTT
5597 ATTCACATCCAAA-TTTCCAA-TAGACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTA-ACATTGAACTTGCCTT
5636 A
1 A
5637 ACTCACATTG
Statistics
Matches: 337, Mismatches: 18, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
38 2 0.01
39 97 0.29
40 200 0.59
41 38 0.11
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.35
Consensus pattern (40 bp):
ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
Found at i:5479 original size:79 final size:78
Alignment explanation
Indices: 5238--5636 Score: 584
Period size: 79 Copynumber: 5.0 Consensus size: 78
5228 TACGCGGCAC
* * * * **
5238 ATTCACATTCAAATTTTCCAATTGACATTGAACTTGCCTTATTCACATTCAAATTTTCCAATTTA
1 ATTCACATCCAAA-TTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAA-TTTCCAATAAA
5303 CATTGAACTTGCCTT
64 CATTGAACTTGCCTT
* * **
5318 AATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTTATTCACATCCAACTTTCCCAATTG
1 -ATTCACATCCAAA-TTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTT-CCAATAA
5383 ACATTGAACTTGCCTT
63 ACATTGAACTTGCCTT
*
5399 ATTCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAAC
1 ATTCACATCCAAATTT-CCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAAC
5464 ATTGAACTTGCCTT
65 ATTGAACTTGCCTT
* *
5478 ATTCACATCCAAAATTTCC-AATAAACATTGAACTTGCCTTATTCACATTCAAAATTCCAATAAA
1 ATTCACATCC-AAATTTCCAAAT-AACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAA
5542 CATTGAACTTGCCTT
64 CATTGAACTTGCCTT
*
5557 ATTCACATCCAACATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAGAC
1 ATTCACATCCAA-ATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAAC
5622 ATTGAACTTGCCTT
65 ATTGAACTTGCCTT
5636 A
1 A
5637 ACTCACATTG
Statistics
Matches: 296, Mismatches: 16, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
78 5 0.02
79 160 0.54
80 60 0.20
81 71 0.24
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.35
Consensus pattern (78 bp):
ATTCACATCCAAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACA
TTGAACTTGCCTT
Found at i:5507 original size:119 final size:117
Alignment explanation
Indices: 5238--5645 Score: 595
Period size: 119 Copynumber: 3.4 Consensus size: 117
5228 TACGCGGCAC
* * * *
5238 ATTCACATTCAAATTTTCCAATTGACATTGAACTTGCCTTATTCACATTCAAATTTTCCAATTTA
1 ATTCACATCCAAA-TTTCCAATAGACATTGAACTTGCCTTATTCACATTCAAA-TTTCCAAATAA
*
5303 CATTGAACTTGCCTTAATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
64 CATTGAACTTGCCTT-ATTCACATCCAAA-TTTCCAATAAACATTGAACTTGCCTT
* * * *
5359 ATTCACATCCAACTTTCCCAATTGACATTGAACTTGCCTTATTCACATCCAACTTTCCCAAATAA
1 ATTCACATCCAAATTT-CCAATAGACATTGAACTTGCCTTATTCACATTCAAATTT-CCAAATAA
5424 CATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACATTGAACTTGCCTT
64 CATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACATTGAACTTGCCTT
* *
5478 ATTCACATCCAAAATTTCCAATAAACATTGAACTTGCCTTATTCACATTCAAAATTCC-AATAAA
1 ATTCACATCC-AAATTTCCAATAGACATTGAACTTGCCTTATTCACATTCAAATTTCCAAAT-AA
5542 CATTGAACTTGCCTTATTCACATCCAACATTTCCAA-ATAACATTGAACTTGCCTT
64 CATTGAACTTGCCTTATTCACATCCAA-ATTTCCAATA-AACATTGAACTTGCCTT
*
5597 ATTCACATCCAAATTTCCAATAGACATTGAACTTGCCTTAACTCACATT
1 ATTCACATCCAAATTTCCAATAGACATTGAACTTGCCTT-ATTCACATT
5646 GGCCCTCAAT
Statistics
Matches: 265, Mismatches: 15, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
117 3 0.01
118 60 0.23
119 112 0.42
120 24 0.09
121 66 0.25
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.35
Consensus pattern (117 bp):
ATTCACATCCAAATTTCCAATAGACATTGAACTTGCCTTATTCACATTCAAATTTCCAAATAACA
TTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACATTGAACTTGCCTT
Found at i:13007 original size:2 final size:2
Alignment explanation
Indices: 12991--13048 Score: 55
Period size: 2 Copynumber: 29.0 Consensus size: 2
12981 GGTAAATTGC
* ** * *
12991 AT AT -T AT AA AT AT AT AT AT AT AT AT AT CG AA ACC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
13033 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
13049 CATGTAATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
1 1 0.02
2 44 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:13225 original size:18 final size:18
Alignment explanation
Indices: 13202--13238 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
13192 AATAGTTAAG
13202 TGTCAAAATTTAAACAAA
1 TGTCAAAATTTAAACAAA
13220 TGTCAAAATTTAAACAAA
1 TGTCAAAATTTAAACAAA
13238 T
1 T
13239 TTAAACCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (18 bp):
TGTCAAAATTTAAACAAA
Found at i:16584 original size:76 final size:76
Alignment explanation
Indices: 16456--16605 Score: 205
Period size: 76 Copynumber: 2.0 Consensus size: 76
16446 GAAAAGTAAG
* *
16456 ATGCAAAGCTTCCAGATTTCCACTTATCTTCTAAGTACAAGTACCTTCAGAGCTTA-AGTTCATA
1 ATGCAAAGCTTCCAGATTTCCACTTATCTTCTAAGTACAAATACATTCAGAGCTTACA-TTCATA
*
16520 ATGGCAAGAGAT
65 ATGGAAAGAGAT
* * * *
16532 ATGCAAAGTTTCCAGTTTTGCACTTATCTTACT-AGTACAAATACATTTAGAGCTTACATTCATA
1 ATGCAAAGCTTCCAGATTTCCACTTATCTT-CTAAGTACAAATACATTCAGAGCTTACATTCATA
16596 ATGGAAAGAG
65 ATGGAAAGAG
16606 GCAAAACCTA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
76 62 0.95
77 3 0.05
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (76 bp):
ATGCAAAGCTTCCAGATTTCCACTTATCTTCTAAGTACAAATACATTCAGAGCTTACATTCATAA
TGGAAAGAGAT
Found at i:19066 original size:6 final size:6
Alignment explanation
Indices: 19057--19094 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
19047 AATTTTTCAT
19057 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA -TTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
19095 AACAAGGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Done.