Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008033.1 Corchorus capsularis cultivar CVL-1 contig08054, 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: 31532
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:441 original size:4 final size:4
Alignment explanation
Indices: 432--473 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
422 TCTCATCTCT
432 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
474 TCTATTCTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:5729 original size:29 final size:30
Alignment explanation
Indices: 5676--5734 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5666 ATCTATGGAT
*
5676 TACTATGTAATTTTTCCATTTTTGGGGGAC
1 TACTATGCAATTTTTCCATTTTTGGGGGAC
*
5706 TACTATGCAATTTTTCCATTTTGGGGGGA
1 TACTATGCAATTTTTCCATTTTTGGGGGA
5735 GGGCATGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (30 bp):
TACTATGCAATTTTTCCATTTTTGGGGGAC
Found at i:7782 original size:11 final size:11
Alignment explanation
Indices: 7766--7800 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
7756 TTGACAGCGC
7766 AACAAAAACAA
1 AACAAAAACAA
*
7777 AACAAAAACGA
1 AACAAAAACAA
7788 AACAAAAACAA
1 AACAAAAACAA
7799 AA
1 AA
7801 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:7862 original size:13 final size:13
Alignment explanation
Indices: 7844--7868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7834 TTAGAATTCC
7844 AAATAATATTTAT
1 AAATAATATTTAT
7857 AAATAATATTTA
1 AAATAATATTTA
7869 GAATATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:10618 original size:36 final size:36
Alignment explanation
Indices: 10574--10656 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
10564 CGAGCAGGAC
** * *
10574 ATATATAGTATGGTGTGTGTGTGTGTGTGTATACAT
1 ATATATAGTATAATGTGTGTGTGTGTATATATACAT
*
10610 ATATATAGTATAATGTGTGTGTGTGTATATATATAT
1 ATATATAGTATAATGTGTGTGTGTGTATATATACAT
10646 ATATATA-TATA
1 ATATATAGTATA
10657 TATAGTATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 4 0.10
36 38 0.90
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (36 bp):
ATATATAGTATAATGTGTGTGTGTGTATATATACAT
Found at i:10627 original size:32 final size:31
Alignment explanation
Indices: 10591--10652 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
10581 GTATGGTGTG
10591 TGTGTGTGTGTGTATACATATATATAGTATAA
1 TGTGTGTGTGTGTATACATATATATA-TATAA
*
10623 TGTGTGTGTGTGTATATATATATATATATA
1 TGTGTGTGTGTGTATACATATATATATATA
10653 TATATATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.47
Consensus pattern (31 bp):
TGTGTGTGTGTGTATACATATATATATATAA
Found at i:10640 original size:2 final size:2
Alignment explanation
Indices: 10635--10670 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
10625 TGTGTGTGTG
10635 TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
10671 AATCCCATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:14159 original size:2 final size:2
Alignment explanation
Indices: 14152--14212 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
14142 AAGATTAAAA
14152 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
14194 AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC A
14213 TTTCACTCCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20781 original size:15 final size:15
Alignment explanation
Indices: 20761--20792 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20751 TATTTGAAAG
20761 TAATTCCTTAATGGC
1 TAATTCCTTAATGGC
20776 TAATTCCTTAATGGC
1 TAATTCCTTAATGGC
20791 TA
1 TA
20793 TTAAGGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (15 bp):
TAATTCCTTAATGGC
Found at i:21993 original size:44 final size:45
Alignment explanation
Indices: 21944--22032 Score: 126
Period size: 47 Copynumber: 2.0 Consensus size: 45
21934 TTCATTAGTT
* *
21944 CTATCAATTC-GCTTTTTTTTTTAATAGAAGGTTCAGGTGAGATC
1 CTATCAATTCTGCTTTTTTTTTTAATAGAAAGTTCAAGTGAGATC
*
21988 CTATCAATTCATTTCTTTTTTTTTTAATAGAAAGTTCAAGTGAGA
1 CTATCAATTC--TGCTTTTTTTTTTAATAGAAAGTTCAAGTGAGA
22033 AGAGACTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 10 0.26
47 29 0.74
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (45 bp):
CTATCAATTCTGCTTTTTTTTTTAATAGAAAGTTCAAGTGAGATC
Found at i:22102 original size:32 final size:32
Alignment explanation
Indices: 22065--22125 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
22055 AAGACATACC
*
22065 ACAAGTCTCAGAAATGATTTATAGTGTTAATT
1 ACAAGTCTCAGAAAAGATTTATAGTGTTAATT
* *
22097 ACAAGTCTCTGAAAAGGTTTATAGTGTTA
1 ACAAGTCTCAGAAAAGATTTATAGTGTTA
22126 CTTATAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (32 bp):
ACAAGTCTCAGAAAAGATTTATAGTGTTAATT
Done.