Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007475.1 Corchorus capsularis cultivar CVL-1 contig07496, 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: 44183
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:6137 original size:112 final size:112
Alignment explanation
Indices: 5932--6164 Score: 452
Period size: 112 Copynumber: 2.1 Consensus size: 112
5922 CTGTTTTCAT
5932 TCAATTTG--AATCTGCTTGTCAACCTTCACATTTCTTCTTTCAAATCATTCCAAATTACTATGT
1 TCAATTTGACAATCTGCTTGTCAACCTTCACATTTCTTCTTTCAAATCATTCCAAATTACTATGT
5995 ATTGTATGAAGCTTAGCATTGTGGTGGAATGGCAACATGGTGACTCC
66 ATTGTATGAAGCTTAGCATTGTGGTGGAATGGCAACATGGTGACTCC
6042 TCAATTTGACAATCTGCTTGTCAACCTTCACATTTCTTCTTTCAAATCATTCCAAATTACTATGT
1 TCAATTTGACAATCTGCTTGTCAACCTTCACATTTCTTCTTTCAAATCATTCCAAATTACTATGT
6107 ATTGTATGAAGCTTAGCATTGTGGTGGAATGGCAACATGGTGACTCC
66 ATTGTATGAAGCTTAGCATTGTGGTGGAATGGCAACATGGTGACTCC
6154 TCAATTTGACA
1 TCAATTTGACA
6165 TCGCAACACC
Statistics
Matches: 121, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
110 8 0.07
112 113 0.93
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (112 bp):
TCAATTTGACAATCTGCTTGTCAACCTTCACATTTCTTCTTTCAAATCATTCCAAATTACTATGT
ATTGTATGAAGCTTAGCATTGTGGTGGAATGGCAACATGGTGACTCC
Found at i:6951 original size:32 final size:32
Alignment explanation
Indices: 6904--7004 Score: 114
Period size: 32 Copynumber: 3.1 Consensus size: 32
6894 CTCAACCACC
* *
6904 GGGGCAGCCTGCCGTGGCAAAGTCGCCCCAG-
1 GGGGCGGCCTGCCGTGGCAAAGCCGCCCCAGT
*
6935 GAGGGCGGCCTGCCGTGGCGAAGCCGCCCCAGT
1 G-GGGCGGCCTGCCGTGGCAAAGCCGCCCCAGT
* * **
6968 GGGACGGCCTGCCCATGGTGAAGCCGCCCCAGT
1 GGGGCGGCCTG-CCGTGGCAAAGCCGCCCCAGT
7001 GGGG
1 GGGG
7005 AGACTCTGTC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
31 1 0.02
32 36 0.60
33 23 0.38
ACGTcount: A:0.14, C:0.35, G:0.42, T:0.10
Consensus pattern (32 bp):
GGGGCGGCCTGCCGTGGCAAAGCCGCCCCAGT
Found at i:7713 original size:7 final size:7
Alignment explanation
Indices: 7701--7727 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
7691 ATTTTCCCTC
7701 CTCACTT
1 CTCACTT
7708 CTCACTT
1 CTCACTT
7715 CTCACTT
1 CTCACTT
7722 CTCACT
1 CTCACT
7728 CGGATTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.44, G:0.00, T:0.41
Consensus pattern (7 bp):
CTCACTT
Found at i:8588 original size:16 final size:16
Alignment explanation
Indices: 8567--8597 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8557 TTTCTCGTAT
8567 CTTATATATATTTGTA
1 CTTATATATATTTGTA
8583 CTTATATATATTTGT
1 CTTATATATATTTGT
8598 TTTCTACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
CTTATATATATTTGTA
Found at i:20519 original size:46 final size:46
Alignment explanation
Indices: 20458--20568 Score: 195
Period size: 46 Copynumber: 2.4 Consensus size: 46
20448 AAACTTCTTT
*
20458 TGCCTTTTCACGCATGGTTGTCTGATTTTAAATTACATCCTTCTAC
1 TGCCTTTTCATGCATGGTTGTCTGATTTTAAATTACATCCTTCTAC
* *
20504 TGCCTTTTCATGCATGGTTGTCTGATTTTAAGTTACATCCTTCTAT
1 TGCCTTTTCATGCATGGTTGTCTGATTTTAAATTACATCCTTCTAC
20550 TGCCTTTTCATGCATGGTT
1 TGCCTTTTCATGCATGGTT
20569 TACTTCAGGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (46 bp):
TGCCTTTTCATGCATGGTTGTCTGATTTTAAATTACATCCTTCTAC
Found at i:38454 original size:53 final size:56
Alignment explanation
Indices: 38362--38471 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 56
38352 AGATAGTAAG
38362 ATTATATTGTTTTTAGGTGATGAAGTCAATTATTAGAAATGTGAATGTAAATGCAA
1 ATTATATTGTTTTTAGGTGATGAAGTCAATTATTAGAAATGTGAATGTAAATGCAA
38418 ATTATATTGTTTTTA-G-G-TGAAGTCAATTATTAGAAATGTGAATGTAAATGCAA
1 ATTATATTGTTTTTAGGTGATGAAGTCAATTATTAGAAATGTGAATGTAAATGCAA
38471 A
1 A
38472 GAACCTTGGA
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
53 37 0.69
54 1 0.02
55 1 0.02
56 15 0.28
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (56 bp):
ATTATATTGTTTTTAGGTGATGAAGTCAATTATTAGAAATGTGAATGTAAATGCAA
Found at i:40217 original size:11 final size:11
Alignment explanation
Indices: 40193--40227 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40183 TTGACAGCGC
40193 AACAAAAACAA
1 AACAAAAACAA
* *
40204 AACGAAAACGA
1 AACAAAAACAA
40215 AACAAAAACAA
1 AACAAAAACAA
40226 AA
1 AA
40228 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Done.