Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011323.1 Corchorus olitorius cultivar O-4 contig11356, 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: 37330
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1783 original size:11 final size:11
Alignment explanation
Indices: 1767--1792 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1757 AGATAATTTC
1767 TTTTCTTCTAG
1 TTTTCTTCTAG
1778 TTTTCTTCTAG
1 TTTTCTTCTAG
1789 TTTT
1 TTTT
1793 TTAGGCAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:3462 original size:52 final size:52
Alignment explanation
Indices: 3396--3494 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
3386 GTCTATCTAG
*
3396 ATAGACAAAAAATCATTCATAAATGCACTGAGTTGAATGTTGTGTCAGTTTT
1 ATAGAAAAAAAATCATTCATAAATGCACTGAGTTGAATGTTGTGTCAGTTTT
* *
3448 ATAGAAAAAAAATCATTCATTAATGCACTGGGTTGAATGTTGTGTCA
1 ATAGAAAAAAAATCATTCATAAATGCACTGAGTTGAATGTTGTGTCA
3495 CCTTTTTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (52 bp):
ATAGAAAAAAAATCATTCATAAATGCACTGAGTTGAATGTTGTGTCAGTTTT
Found at i:12206 original size:16 final size:16
Alignment explanation
Indices: 12181--12214 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12171 GGAATCAAGG
*
12181 AATAAGCAATCAAAGC
1 AATAACCAATCAAAGC
12197 AATAACCAATCAAAGC
1 AATAACCAATCAAAGC
12213 AA
1 AA
12215 AGCAAAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.12
Consensus pattern (16 bp):
AATAACCAATCAAAGC
Found at i:12378 original size:15 final size:15
Alignment explanation
Indices: 12358--12389 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12348 ATGAAATCCT
12358 ATAAAAGAAAGAAAA
1 ATAAAAGAAAGAAAA
12373 ATAAAAGAAAGAAAA
1 ATAAAAGAAAGAAAA
12388 AT
1 AT
12390 TAAGGGTTAG
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:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (15 bp):
ATAAAAGAAAGAAAA
Found at i:29715 original size:19 final size:16
Alignment explanation
Indices: 29694--29763 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
29684 GACCGGTGGT
29694 GGTGGTGGCCGGCGGC
1 GGTGGTGGCCGGCGGC
29710 GGTGGTGGCCGGCGGC
1 GGTGGTGGCCGGCGGC
*
29726 GGTGATGGCCGGCGGC
1 GGTGGTGGCCGGCGGC
* *
29742 GGTTGTGG-TGGCCGGC
1 GGTGGTGGCCGG-CGGC
29758 GGTGGT
1 GGTGGT
29764 TGGTTTCCGG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
15 2 0.04
16 46 0.96
ACGTcount: A:0.01, C:0.21, G:0.60, T:0.17
Consensus pattern (16 bp):
GGTGGTGGCCGGCGGC
Found at i:35495 original size:19 final size:19
Alignment explanation
Indices: 35453--35495 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
35443 TTCCCCTAAG
*
35453 AAAAAGAAGAAAAAATGAT
1 AAAAAGAAGAAAAAATGAA
*
35472 GAAAAGAAGAAAAAATGAA
1 AAAAAGAAGAAAAAATGAA
35491 AAAAA
1 AAAAA
35496 AGCACTTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (19 bp):
AAAAAGAAGAAAAAATGAA
Found at i:36349 original size:12 final size:12
Alignment explanation
Indices: 36332--36356 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36322 TCTCAAGTGC
36332 AAAAAAAAAAAG
1 AAAAAAAAAAAG
36344 AAAAAAAAAAAG
1 AAAAAAAAAAAG
36356 A
1 A
36357 CAAGGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Done.