Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008912.1 Corchorus capsularis cultivar CVL-1 contig08933, 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: 43224
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:4526 original size:12 final size:12
Alignment explanation
Indices: 4509--4533 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4499 ATCTGGCAAT
4509 TTGTGTTTCGTG
1 TTGTGTTTCGTG
4521 TTGTGTTTCGTG
1 TTGTGTTTCGTG
4533 T
1 T
4534 CGTATAAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.32, T:0.60
Consensus pattern (12 bp):
TTGTGTTTCGTG
Found at i:14739 original size:17 final size:17
Alignment explanation
Indices: 14717--14770 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
14707 TCCATACCAC
*
14717 ATGACTAGTAATGTTTT
1 ATGACTAGTAATATTTT
*
14734 ATGACTAATGATGATATTTT
1 ATGACT-A-G-TAATATTTT
14754 ATGACTAGTAATATTTT
1 ATGACTAGTAATATTTT
14771 CCGAATCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 14 0.45
18 2 0.06
19 2 0.06
20 13 0.42
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (17 bp):
ATGACTAGTAATATTTT
Found at i:21478 original size:21 final size:20
Alignment explanation
Indices: 21452--21495 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
21442 GTAGAAAGCA
21452 TTATAACTATTTTAATAACTT
1 TTATAACTATTTTAATAA-TT
* *
21473 TTATAACTTTTTTAGTAATT
1 TTATAACTATTTTAATAATT
21493 TTA
1 TTA
21496 GATTACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATAACTATTTTAATAATT
Found at i:21913 original size:4 final size:4
Alignment explanation
Indices: 21904--21930 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21894 TTCATAATCT
21904 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
21931 TTTTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:37190 original size:18 final size:18
Alignment explanation
Indices: 37154--37188 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
37144 GTAGAACCAT
*
37154 GAAAGAGAAAGAAGAAAA
1 GAAAAAGAAAGAAGAAAA
37172 GAAAAAGAAA-AAGAAAA
1 GAAAAAGAAAGAAGAAAA
37189 AGGAAGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
GAAAAAGAAAGAAGAAAA
Found at i:37477 original size:43 final size:43
Alignment explanation
Indices: 37419--37507 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
37409 CTGCAAGCAG
37419 AAAAACTATGCAACTGAGAAATTTTACAGACTAAGGGCTCAAA
1 AAAAACTATGCAACTGAGAAATTTTACAGACTAAGGGCTCAAA
37462 AAAAACTATGCAACTGAGAAATTTTACAGACTAAGGGCTCAAA
1 AAAAACTATGCAACTGAGAAATTTTACAGACTAAGGGCTCAAA
37505 AAA
1 AAA
37508 TAGCAGAGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (43 bp):
AAAAACTATGCAACTGAGAAATTTTACAGACTAAGGGCTCAAA
Found at i:40466 original size:22 final size:24
Alignment explanation
Indices: 40422--40471 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
40412 TAATTAAATT
40422 AATATTTAAACTTTTTTTGAGTA-
1 AATATTTAAACTTTTTTTGAGTAG
40445 AATATTTAAACTTTTTTT-AGTAG
1 AATATTTAAACTTTTTTTGAGTAG
40468 AATA
1 AATA
40472 ATAAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
AATATTTAAACTTTTTTTGAGTAG
Found at i:40983 original size:2 final size:2
Alignment explanation
Indices: 40976--41006 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
40966 GCTAAAAGAA
40976 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41007 CAATTAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41064 original size:115 final size:115
Alignment explanation
Indices: 40873--41091 Score: 429
Period size: 115 Copynumber: 1.9 Consensus size: 115
40863 AAGAGTATAT
*
40873 TATATATATATATATATATCAATTAATGAATCAAACGTTAAATTAACCATGATAAACTATCAATT
1 TATATATATATATATATATCAATTAATGAATCAAACGTTAAACTAACCATGATAAACTATCAATT
40938 ACACAGTCAAATGTTAGATAGTTGCATTGCTAAAAGAAATATATATAATA
66 ACACAGTCAAATGTTAGATAGTTGCATTGCTAAAAGAAATATATATAATA
40988 TATATATATATATATATATCAATTAATGAATCAAACGTTAAACTAACCATGATAAACTATCAATT
1 TATATATATATATATATATCAATTAATGAATCAAACGTTAAACTAACCATGATAAACTATCAATT
41053 ACACAGTCAAATGTTAGATAGTTGCATTGCTAAAAGAAA
66 ACACAGTCAAATGTTAGATAGTTGCATTGCTAAAAGAAA
41092 AAAATATCTG
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 103 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (115 bp):
TATATATATATATATATATCAATTAATGAATCAAACGTTAAACTAACCATGATAAACTATCAATT
ACACAGTCAAATGTTAGATAGTTGCATTGCTAAAAGAAATATATATAATA
Done.