Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007191.1 Corchorus capsularis cultivar CVL-1 contig07212, 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: 18963
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1706 original size:6 final size:6
Alignment explanation
Indices: 1690--1721 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1680 AAAAGCAAGC
1690 AAATC- AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1722 GCAGATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATCT
Found at i:1733 original size:12 final size:13
Alignment explanation
Indices: 1718--1762 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
1708 AATCTAAATC
1718 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
1730 TAAAGCAAATTAA
1 TAAAGCAGATTAA
1743 TAAAGCAGATTAA
1 TAAAGCAGATTAA
1756 TAAAGCA
1 TAAAGCA
1763 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:1769 original size:25 final size:25
Alignment explanation
Indices: 1718--1770 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
1708 AATCTAAATC
*
1718 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
1743 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
1768 TAA
1 TAA
1771 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Found at i:6820 original size:21 final size:21
Alignment explanation
Indices: 6791--6838 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6781 GATTGGAGTA
*
6791 TTTATTTATCTTGTTGCTTAAT
1 TTTATTTATCTTCTTG-TTAAT
*
6813 TTTA-TTATTTTCTTGTTAA-
1 TTTATTTATCTTCTTGTTAAT
6832 TTTATTT
1 TTTATTT
6839 TTATTGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.17
20 6 0.26
21 9 0.39
22 4 0.17
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTATTTATCTTCTTGTTAAT
Found at i:6838 original size:24 final size:25
Alignment explanation
Indices: 6792--6839 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
6782 ATTGGAGTAT
**
6792 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTAATTAATTTTA
*
6817 TTATTT-TCTTGTTAATTTATTTT
1 TTATTTATCTTGTTAATTAATTTT
6840 TATTGTTCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (25 bp):
TTATTTATCTTGTTAATTAATTTTA
Found at i:11987 original size:21 final size:22
Alignment explanation
Indices: 11928--11987 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 22
11918 ATGCTCCCAT
* *
11928 GCAATGGCCGGTCTTAGTCCAAT
1 GCAATGGCCGGTCTT-CTCCAAG
* *
11951 GCGATGGCGCAG-CTTCTCC-AG
1 GCAATGGC-CGGTCTTCTCCAAG
11972 GCAATGGCCGGTCTTC
1 GCAATGGCCGGTCTTC
11988 CACTCCATGT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
20 2 0.07
21 12 0.41
22 3 0.10
23 10 0.34
24 2 0.07
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (22 bp):
GCAATGGCCGGTCTTCTCCAAG
Found at i:14442 original size:42 final size:42
Alignment explanation
Indices: 14366--14445 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
14356 GGTCGAATGG
* *
14366 CCGGTTGTGTCCGGATGGCGCATGCGTTGGCCCGTGCGATGA
1 CCGGTTGTGGCCGGATGGCGCATGCGATGGCCCGTGCGATGA
*** *
14408 CCGGTTGTGGCCGGATGGCTTGTGCGATGTCCCGTGCG
1 CCGGTTGTGGCCGGATGGCGCATGCGATGGCCCGTGCG
14446 GCGTCCCATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.07, C:0.26, G:0.41, T:0.25
Consensus pattern (42 bp):
CCGGTTGTGGCCGGATGGCGCATGCGATGGCCCGTGCGATGA
Found at i:18601 original size:12 final size:13
Alignment explanation
Indices: 18560--18604 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
18550 AATTATTGTT
18560 TGCTTTATTAATC
1 TGCTTTATTAATC
*
18573 TGCTTTATTAATT
1 TGCTTTATTAATC
18586 TGCTTTA-TAATC
1 TGCTTTATTAATC
18598 TGCTTTA
1 TGCTTTA
18605 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:18612 original size:6 final size:6
Alignment explanation
Indices: 18601--18633 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
18591 TATAATCTGC
18601 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
18634 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (6 bp):
TTTAGA
Done.