Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008564.1 Corchorus capsularis cultivar CVL-1 contig08585, 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: 64065
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:11729 original size:1 final size:1
Alignment explanation
Indices: 11723--11754 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
11713 CAAAATTGAG
11723 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11755 CAAATAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18912 original size:17 final size:17
Alignment explanation
Indices: 18892--18955 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
18882 ATAAAAGATC
18892 ATAAATATTCAAATAGA
1 ATAAATATTCAAATAGA
*
18909 ATAAATATTTAAAT--A
1 ATAAATATTCAAATAGA
* *
18924 ATAATTAATCAAATAGA
1 ATAAATATTCAAATAGA
* *
18941 ACAAATATTTAAATA
1 ATAAATATTCAAATA
18956 ATAATGAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 12 0.32
17 25 0.68
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (17 bp):
ATAAATATTCAAATAGA
Found at i:18936 original size:32 final size:32
Alignment explanation
Indices: 18900--18960 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
18890 TCATAAATAT
*
18900 TCAAATAGAATAAATATTTAAATAATAATTAA
1 TCAAATAGAACAAATATTTAAATAATAATTAA
18932 TCAAATAGAACAAATATTTAAATAATAAT
1 TCAAATAGAACAAATATTTAAATAATAAT
18961 GAATATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (32 bp):
TCAAATAGAACAAATATTTAAATAATAATTAA
Found at i:19450 original size:17 final size:18
Alignment explanation
Indices: 19419--19452 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19409 AAAAAAAAAA
*
19419 AATTCATAATTCATATAT
1 AATTCATAATACATATAT
19437 AATT-ATAATACATATA
1 AATTCATAATACATATA
19453 ATCTTTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTCATAATACATATAT
Found at i:26678 original size:19 final size:20
Alignment explanation
Indices: 26633--26696 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
26623 GAACTAAAGC
*
26633 AAATTAT-AAAGAAAACT-T
1 AAATTATGAAAGAAACCTCT
26651 AAATATATGAAAGAAACCTCT
1 AAAT-TATGAAAGAAACCTCT
*
26672 -AATTATGAATAAGAAACCTCC
1 AAATTATG-A-AAGAAACCTCT
26693 AAAT
1 AAAT
26697 ATAAATAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 4 0.11
19 7 0.18
20 13 0.34
21 11 0.29
22 3 0.08
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (20 bp):
AAATTATGAAAGAAACCTCT
Found at i:26687 original size:21 final size:21
Alignment explanation
Indices: 26661--26715 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
26651 AAATATATGA
* * *
26661 AAGAAACCTCTAATTATGAAT
1 AAGAAACCTCCAAATATAAAT
26682 AAGAAACCTCCAAATATAAAT
1 AAGAAACCTCCAAATATAAAT
*
26703 AAGAGACCTCCAA
1 AAGAAACCTCCAA
26716 CATAGGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.51, C:0.20, G:0.09, T:0.20
Consensus pattern (21 bp):
AAGAAACCTCCAAATATAAAT
Found at i:31326 original size:12 final size:12
Alignment explanation
Indices: 31309--31335 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31299 TGACATGAAA
31309 TTCCAAAAATTC
1 TTCCAAAAATTC
31321 TTCCAAAAATTC
1 TTCCAAAAATTC
31333 TTC
1 TTC
31336 AACAATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (12 bp):
TTCCAAAAATTC
Found at i:51690 original size:33 final size:32
Alignment explanation
Indices: 51648--51750 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 32
51638 ATTAGCATCC
* * *
51648 AAAACAGATTTTGTTTCATCACAAACAACACCT
1 AAAATAGATTTAGTATCATCACAAACAACA-CT
* **
51681 AAAATAGATTTAGTGTCATTGCAAACAACACT
1 AAAATAGATTTAGTATCATCACAAACAACACT
* *
51713 CAAATTAGGTTTAGTATCATCACAAACAACATCT
1 -AAAATAGATTTAGTATCATCACAAACAACA-CT
51747 AAAA
1 AAAA
51751 CACTCTTTGC
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
32 2 0.04
33 53 0.93
34 2 0.04
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (32 bp):
AAAATAGATTTAGTATCATCACAAACAACACT
Found at i:56879 original size:2 final size:2
Alignment explanation
Indices: 56872--56912 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
56862 ATACAATGTT
* *
56872 TA TA TA TA TA TA AA TA TA TA TA TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56913 TCAATTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:57110 original size:61 final size:61
Alignment explanation
Indices: 57045--57178 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
57035 TAAAAAACAC
* * *
57045 TTAAATATAGCGACGTCTAGACGCCGTTA-TATTTAAGGGTTTTTTTAAGAA-AAATCTCAAA
1 TTAAATATAGCGACATCTAGACGCCGCTATTA-TTAAGGG-TTTTTTAAAAATAAATCTCAAA
* * * *
57106 TTAAATTTTGCGTCATTTAGACGCCGCTATTATTAAGGGTTTTTTAAAAATAAATCTCAAA
1 TTAAATATAGCGACATCTAGACGCCGCTATTATTAAGGGTTTTTTAAAAATAAATCTCAAA
*
57167 TTAAATGTAGCG
1 TTAAATATAGCG
57179 GCGTTTCTTG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 10 0.16
61 50 0.81
62 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (61 bp):
TTAAATATAGCGACATCTAGACGCCGCTATTATTAAGGGTTTTTTAAAAATAAATCTCAAA
Found at i:57263 original size:2 final size:2
Alignment explanation
Indices: 57256--57284 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57246 TTAAATTGAA
57256 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
57285 AACATTGTAC
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:61451 original size:163 final size:163
Alignment explanation
Indices: 61154--61456 Score: 389
Period size: 163 Copynumber: 1.9 Consensus size: 163
61144 AGTTGTAAAC
* *
61154 TTTTCTTTGTTTTAGGAAGAGAGAATTTTTCCCTCCAAAAAAAAGGAAAAAATAAATCTCTCCCT
1 TTTTCTTTGTTTTAGGAAGAGAGAATTTTTCCCTCCAAAAAAAAGGAAAAAAAAAATCTCTCACT
* * * * ** * *
61219 CCATATATTATAATAGCGGCGCTTCGTTTTCTAGACGCCGCTATTTAGCGGCATCTGGTTTGTAA
66 CCATATATTATAATAGCGGCGCTTCG-TATCAAAACGCCACTAAATAGCGGCATCTGCTTTGAAA
*
61284 ACGCCTCTATTTATTATAGACGTAAAGTTCGAAA
130 ACGCCGCTATTTATTATAGACGTAAAGTTCGAAA
** *
61318 TTTTCTTTGTTTTAGGGGGAGGGAATTTTTCCCTCCAAAAAAAA-GAAAAAAAAAATCTCTCACT
1 TTTTCTTTGTTTTAGGAAGAGAGAATTTTTCCCTCCAAAAAAAAGGAAAAAAAAAATCTCTCACT
* *
61382 CCATATATTA-ATATGGCGGCGTCTTAC-TATCAAAACGCCACTAAATAGCGGCGTCTGACTTT-
66 CCATATATTATA-ATAGCGGCG-CTT-CGTATCAAAACGCCACTAAATAGCGGCATCTG-CTTTG
61444 AAAACGCCGCTAT
127 AAAACGCCGCTAT
61457 ATTCAATTTC
Statistics
Matches: 119, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
162 1 0.01
163 70 0.59
164 47 0.39
165 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (163 bp):
TTTTCTTTGTTTTAGGAAGAGAGAATTTTTCCCTCCAAAAAAAAGGAAAAAAAAAATCTCTCACT
CCATATATTATAATAGCGGCGCTTCGTATCAAAACGCCACTAAATAGCGGCATCTGCTTTGAAAA
CGCCGCTATTTATTATAGACGTAAAGTTCGAAA
Found at i:63850 original size:24 final size:24
Alignment explanation
Indices: 63805--63850 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
63795 AAGGAAAATC
* *
63805 AGTAAAACCAGGATCATAAATCAT
1 AGTAAAACCAAGATAATAAATCAT
* *
63829 AGTAAAATCAAGATAATCAATC
1 AGTAAAACCAAGATAATAAATC
63851 CAAAACCAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (24 bp):
AGTAAAACCAAGATAATAAATCAT
Done.