Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010105.1 Corchorus capsularis cultivar CVL-1 contig10126, 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: 25629
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:399 original size:54 final size:54
Alignment explanation
Indices: 312--419 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 54
302 AAATTTCAGC
*
312 CAAATCAGATCAAAATGTTAATAATATCTGATTTCTTTCTTCAAAGTTAATTAT
1 CAAATCAGATCAAAATGTTAATAATATCTGATTTCTTTCTTCAAAATTAATTAT
366 CAAATCAG-TCCAAAATGTTAATAATAT-TCGATTTCTTTCTTCAAAATTAATTAT
1 CAAATCAGAT-CAAAATGTTAATAATATCT-GATTTCTTTCTTCAAAATTAATTAT
420 TGATTTCTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
53 2 0.04
54 49 0.96
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (54 bp):
CAAATCAGATCAAAATGTTAATAATATCTGATTTCTTTCTTCAAAATTAATTAT
Found at i:967 original size:2 final size:2
Alignment explanation
Indices: 960--988 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
950 AAGAAAGTAA
960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
989 AACTTCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6471 original size:39 final size:38
Alignment explanation
Indices: 6347--6492 Score: 204
Period size: 38 Copynumber: 3.8 Consensus size: 38
6337 GAGTCTAGCT
*
6347 AACAG-TTAACCCCCCGAGGCACGGGTCCACTCTTACC
1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC
*
6384 AAGAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC
1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC
* * *
6422 AACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTACC
1 AACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTACC
* * *
6461 ATCAGTTTAACCCCCTGCGGCGCGGGTCCACT
1 AACAGTTTAACCCCCTGAGGCACGGGTCCACT
6493 ATGCATAGCC
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
37 4 0.04
38 60 0.62
39 32 0.33
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.23
Consensus pattern (38 bp):
AACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACC
Found at i:6487 original size:77 final size:75
Alignment explanation
Indices: 6347--6492 Score: 202
Period size: 77 Copynumber: 1.9 Consensus size: 75
6337 GAGTCTAGCT
*
6347 AACAGTTAACCCCCCGAGGCACGGGTCCACTCTTACCAAGAGTTTAACCCCCTGAGGCACGGGTC
1 AACAGTTAACCCCCCGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGGTC
6412 CACTCTTACC
66 CACTCTTACC
* * * * * * *
6422 AACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTACCATCAGTTTAACCCCCTGCGGCGCGGG
1 AACAG-TTAACCCCCCGAGGCACGGGTCCACTC-TTACCAACAGTTTAACCCCCTGAGGCACGGG
6487 TCCACT
64 TCCACT
6493 ATGCATAGCC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 5 0.08
76 23 0.38
77 33 0.54
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.23
Consensus pattern (75 bp):
AACAGTTAACCCCCCGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGGTC
CACTCTTACC
Found at i:6701 original size:15 final size:16
Alignment explanation
Indices: 6672--6705 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6662 TCTATAAAAC
*
6672 AATTCATAATTCATAT
1 AATTCATAATACATAT
6688 AATT-ATAATACATAT
1 AATTCATAATACATAT
6703 AAT
1 AAT
6706 CTTTGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTCATAATACATAT
Found at i:7193 original size:40 final size:41
Alignment explanation
Indices: 7149--7231 Score: 132
Period size: 40 Copynumber: 2.0 Consensus size: 41
7139 TATTCTGTAA
* *
7149 TTTGAAAAATTATGGAAAAATA-TAGAAAAATAATAAGTAT
1 TTTGAAAAATTATGGAAAAATACAAAAAAAATAATAAGTAT
*
7189 TTTGAAAAATTATGGAAAAATACAAAAAAAATCATAAGTAT
1 TTTGAAAAATTATGGAAAAATACAAAAAAAATAATAAGTAT
7230 TT
1 TT
7232 CAATAAACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 22 0.56
41 17 0.44
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (41 bp):
TTTGAAAAATTATGGAAAAATACAAAAAAAATAATAAGTAT
Found at i:10247 original size:9 final size:9
Alignment explanation
Indices: 10233--10271 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
10223 TTAATTTCTT
*
10233 TTAATTTAA
1 TTAATTAAA
10242 TTAATTAAA
1 TTAATTAAA
**
10251 TTAAAGAAA
1 TTAATTAAA
10260 TTAATTAAA
1 TTAATTAAA
10269 TTA
1 TTA
10272 CGTTGAAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:12443 original size:15 final size:15
Alignment explanation
Indices: 12423--12455 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12413 ACAAACCATA
12423 ATGGTGCGAACAACC
1 ATGGTGCGAACAACC
*
12438 ATGGTGCGAACAATC
1 ATGGTGCGAACAACC
12453 ATG
1 ATG
12456 TTGTGCAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.18
Consensus pattern (15 bp):
ATGGTGCGAACAACC
Found at i:25071 original size:9 final size:9
Alignment explanation
Indices: 25057--25095 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
25047 TTAATTTCTT
*
25057 TTAATTTAA
1 TTAATTAAA
25066 TTAATTAAA
1 TTAATTAAA
**
25075 TTAAAGAAA
1 TTAATTAAA
25084 TTAATTAAA
1 TTAATTAAA
25093 TTA
1 TTA
25096 TGTTGAAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Done.