Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006936.1 Corchorus capsularis cultivar CVL-1 contig06957, 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: 18634
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:102 original size:31 final size:31
Alignment explanation
Indices: 62--202 Score: 165
Period size: 31 Copynumber: 4.5 Consensus size: 31
52 ACAATGTCCG
62 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * *
93 ATGTGGCACGCCACATATACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
124 ACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* ** ** * *
155 ACGTGGCATGCCATATGTTTCAAAAAATGGC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
*
186 ACGTGGCATGCCACGTG
1 ACGTGGCACGCCACGTG
203 CACAAAAGGA
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 91 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:199 original size:62 final size:62
Alignment explanation
Indices: 62--202 Score: 183
Period size: 62 Copynumber: 2.3 Consensus size: 62
52 ACAATGTCCG
* *
62 ACGTGGCACGCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATATACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATATACCAAAAAATGAC
* * * * * ** *
124 ACATGTCACGCCACGTGTACCAAAAAGTGACACGTGGCATGCCATATGTTTCAAAAAATGGC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATATACCAAAAAATGAC
*
186 ACGTGGCATGCCACGTG
1 ACGTGGCACGCCACGTG
203 CACAAAAGGA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (62 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGACACGTGGCACGCCACATATACCAAAAAATGAC
Found at i:733 original size:33 final size:32
Alignment explanation
Indices: 696--803 Score: 135
Period size: 33 Copynumber: 3.3 Consensus size: 32
686 GCCGAGTCAT
* **
696 GTGGCCGGGTGTGGCCAGGCATGGCCATGTCGC
1 GTGGCC-GGTGTGGCCGGGCATCTCCATGTCGC
729 GTGGCCGGTGATGGCCGGGCATCTCCATGTCGC
1 GTGGCCGGTG-TGGCCGGGCATCTCCATGTCGC
* * *
762 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATCTCCATGTCGC
795 GTGGCCGGT
1 GTGGCCGGT
804 CACAAGTGCT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 7 0.11
33 59 0.89
ACGTcount: A:0.09, C:0.29, G:0.42, T:0.20
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATCTCCATGTCGC
Found at i:2691 original size:18 final size:18
Alignment explanation
Indices: 2670--2706 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2660 CTATTTGAAT
2670 AGGTATAAACTACCAAAA
1 AGGTATAAACTACCAAAA
2688 AGGTATAAACTACCAAAA
1 AGGTATAAACTACCAAAA
2706 A
1 A
2707 CTGTCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (18 bp):
AGGTATAAACTACCAAAA
Found at i:13963 original size:19 final size:21
Alignment explanation
Indices: 13939--13982 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
13929 AAATGTGAAA
*
13939 TCCCCAAA-GTCAAAA-CCCT
1 TCCCCAAAGGCCAAAATCCCT
13958 TCCCCAAAGGCCAAAATCCCT
1 TCCCCAAAGGCCAAAATCCCT
13979 TCCC
1 TCCC
13983 ATTTCTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 6 0.27
21 8 0.36
ACGTcount: A:0.32, C:0.45, G:0.07, T:0.16
Consensus pattern (21 bp):
TCCCCAAAGGCCAAAATCCCT
Found at i:18399 original size:21 final size:21
Alignment explanation
Indices: 18375--18418 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18365 TTAATGGGGG
*
18375 TTGCTAAAT-ACCGCCCTATTT
1 TTGCT-AATCACCGCCCCATTT
*
18396 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
18417 TT
1 TT
18419 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:18554 original size:32 final size:32
Alignment explanation
Indices: 18475--18591 Score: 162
Period size: 32 Copynumber: 3.6 Consensus size: 32
18465 AGCCACGCGG
* * *
18475 AGCCTCCCCACTAGGACGGCTCTGCCACGGCGG
1 AGCCGCCCCACCAGGACGGCTCTGCCACGGC-T
* *
18508 AGCCTCCCCACCAGGACGGCTCTGCCACGGTT
1 AGCCGCCCCACCAGGACGGCTCTGCCACGGCT
18540 AGCCGCCCCACCAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACCAGGACGGCTCTGCCACGGCT
* *
18572 AGCCGCCCCACTAGGGCGGC
1 AGCCGCCCCACCAGGACGGC
18592 AAGGCTTTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 48 0.62
33 29 0.38
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.11
Consensus pattern (32 bp):
AGCCGCCCCACCAGGACGGCTCTGCCACGGCT
Done.