Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007236.1 Corchorus capsularis cultivar CVL-1 contig07257, 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: 16800
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Found at i:2078 original size:34 final size:34
Alignment explanation
Indices: 2007--2100 Score: 120
Period size: 34 Copynumber: 2.7 Consensus size: 34
1997 CATTCAGTTG
*
2007 ATTGACCCAGGGCGGTCTC-CATTCAGTAAATTTCA
1 ATTGA-CCAGGGCGGTCTCTC-TTCAATAAATTTCA
2042 ATTGATCCAGGGCGGTCTCTCTTCAAT-AATTTCA
1 ATTGA-CCAGGGCGGTCTCTCTTCAATAAATTTCA
*
2076 ATTGACCTAGGGCGGTCTTTCTTCA
1 ATTGACC-AGGGCGGTCTCTCTTCA
2101 GTTGCTTTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
33 2 0.04
34 28 0.52
35 23 0.43
36 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (34 bp):
ATTGACCAGGGCGGTCTCTCTTCAATAAATTTCA
Found at i:11721 original size:63 final size:60
Alignment explanation
Indices: 11646--11859 Score: 194
Period size: 63 Copynumber: 3.3 Consensus size: 60
11636 TGACATCCAT
* * *
11646 AATTAAATACATAGTCTAGACACATCATGCACTGCTGAATAATACCATAAATTCCGAGTACA
1 AATTAAACACATAGTCT-GA-ACATCATCCACTGCTGAATAATACCATAAACTCCGAGTACA
* * * *
11708 CAATTAAACACATAGTCTGAAAATAGCATCCACTGCTGAATAATACCATGAACTCCAAATACA
1 -AATTAAACACATAGTCTGAACAT--CATCCACTGCTGAATAATACCATAAACTCCGAGTACA
* * *
11771 AGTATTGAATAATAACATAGTCTGGAAACACCATCCCCTGCTGAATAATACCATAAACTCCGAGT
1 A--ATT--A-AA-CACATAGTCT-G-AACATCATCCACTGCTGAATAATACCATAAACTCCGAGT
11836 ACA
58 ACA
* *
11839 TAATTAAACATATTGTCTGAA
1 -AATTAAACACATAGTCTGAA
11860 AATACCACCA
Statistics
Matches: 123, Mismatches: 17, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
61 5 0.04
62 4 0.03
63 55 0.45
64 5 0.04
65 1 0.01
66 1 0.01
67 5 0.04
68 42 0.34
69 2 0.02
70 3 0.02
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.25
Consensus pattern (60 bp):
AATTAAACACATAGTCTGAACATCATCCACTGCTGAATAATACCATAAACTCCGAGTACA
Found at i:15429 original size:28 final size:25
Alignment explanation
Indices: 15367--15544 Score: 120
Period size: 27 Copynumber: 7.0 Consensus size: 25
15357 TATTTCTTGA
15367 TTACTAATTACCATTTTTACTCTTT
1 TTACTAATTACCATTTTTACTCTTT
* *
15392 GTACTGATTACCATATTTTTACTCTTTT
1 TTACTAATTACC--ATTTTTACTC-TTT
**
15420 TTACTAATTACC-CCTTT--TC---
1 TTACTAATTACCATTTTTACTCTTT
*
15439 TTACTGAA-TACCACATTTTACTCTTTT
1 TTACT-AATTACCA-TTTTTACTC-TTT
* *
15466 TTACTGATCACCATTTTTTACTCTTT
1 TTACTAATTACCA-TTTTTACTCTTT
15492 ATTACTAATTACTC-TCTTTTACTCTTTT
1 -TTACTAATTAC-CAT-TTTTACTC-TTT
*
15520 TTACTGATTACCACTTTTTACTCTT
1 TTACTAATTACCA-TTTTTACTCTT
15545 CTTCTTTTCC
Statistics
Matches: 119, Mismatches: 15, Indels: 37
0.70 0.09 0.22
Matches are distributed among these distances:
19 9 0.08
20 2 0.02
21 3 0.03
23 4 0.03
25 13 0.11
26 8 0.07
27 62 0.52
28 18 0.15
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (25 bp):
TTACTAATTACCATTTTTACTCTTT
Found at i:15478 original size:27 final size:27
Alignment explanation
Indices: 15433--15544 Score: 136
Period size: 27 Copynumber: 4.1 Consensus size: 27
15423 CTAATTACCC
* *
15433 CTTTTCTTACTGAATACCACATTTTACT
1 CTTTT-TTACTGATTACCACTTTTTACT
* *
15461 CTTTTTTACTGATCACCATTTTTTACT
1 CTTTTTTACTGATTACCACTTTTTACT
* * *
15488 CTTTATTACTAATTA-CTCTCTTTTACT
1 CTTTTTTACTGATTACCACT-TTTTACT
15515 CTTTTTTACTGATTACCACTTTTTACT
1 CTTTTTTACTGATTACCACTTTTTACT
15542 CTT
1 CTT
15545 CTTCTTTTCC
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.03
27 60 0.86
28 8 0.11
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.54
Consensus pattern (27 bp):
CTTTTTTACTGATTACCACTTTTTACT
Found at i:15649 original size:13 final size:13
Alignment explanation
Indices: 15631--15658 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15621 CTGATTACTA
15631 TTTTTACTCCTTT
1 TTTTTACTCCTTT
15644 TTTTTACTCCTTT
1 TTTTTACTCCTTT
15657 TT
1 TT
15659 AAATATCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTACTCCTTT
Found at i:15807 original size:72 final size:70
Alignment explanation
Indices: 15712--15855 Score: 175
Period size: 72 Copynumber: 2.0 Consensus size: 70
15702 CACTTTAACC
* * * *
15712 CTTAATTATCGATTCACTGATTACTAT-TTTTACCTTGACT-CTTTAATTACTGATTAATCTCTT
1 CTTAATTATCAATTCACTAATTACTATCTTTTA-CTTGACTAC-TGAATTACTGATT-A-CTATT
15775 ACCTTGACT
62 ACCTTGACT
* * *
15784 CTTAATTATCAATTTACTAATTACTATCTTTTACTTGATTACTGATTTACTGATTACTATTACCT
1 CTTAATTATCAATTCACTAATTACTATCTTTTACTTGACTACTGAATTACTGATTACTATTACCT
15849 TGACT
66 TGACT
15854 CT
1 CT
15856 GATTAATCTC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
70 15 0.24
71 1 0.02
72 41 0.65
73 6 0.10
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (70 bp):
CTTAATTATCAATTCACTAATTACTATCTTTTACTTGACTACTGAATTACTGATTACTATTACCT
TGACT
Found at i:15930 original size:54 final size:55
Alignment explanation
Indices: 15812--16005 Score: 320
Period size: 55 Copynumber: 3.5 Consensus size: 55
15802 AATTACTATC
*
15812 TTTTACTTGATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCT-CT
*
15868 TTTT-CTTAATTACTGATTTACTGATTACTATTA-CTTGACTCTGATTAACCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCT
* *
15921 TTTTACTTAATTACTGATTTACTGGTTACTATTACCTTAACTCTGATTAATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCT
*
15976 TTTTACTTAATTACTAATTTACTGATTACT
1 TTTTACTTAATTACTGATTTACTGATTACT
16006 GATCGTGTCG
Statistics
Matches: 129, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
53 6 0.05
54 45 0.35
55 74 0.57
56 4 0.03
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.49
Consensus pattern (55 bp):
TTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCT
Found at i:16243 original size:12 final size:12
Alignment explanation
Indices: 16228--16272 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
16218 AATCTAAATC
16228 TAAAGCAGATTA
1 TAAAGCAGATTA
*
16240 TAAAGCAAATTA
1 TAAAGCAGATTA
16252 GTAAAGCAGATTAA
1 -TAAAGCAGATT-A
16266 TAAAGCA
1 TAAAGCA
16273 AACAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.38
13 17 0.59
14 1 0.03
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (12 bp):
TAAAGCAGATTA
Done.