Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024302.1 Corchorus olitorius cultivar O-4 contig24335, 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: 26769
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:532 original size:20 final size:20
Alignment explanation
Indices: 507--547 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
497 AACAAATTTG
*
507 TTATTAATAATAATTTTATT
1 TTATTAATAATAATTTGATT
527 TTATTAATAATAATTTGATT
1 TTATTAATAATAATTTGATT
547 T
1 T
548 CCAAAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTATTAATAATAATTTGATT
Found at i:5729 original size:13 final size:13
Alignment explanation
Indices: 5711--5736 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5701 AATAATCGAT
5711 TTTAAAAAAAGTA
1 TTTAAAAAAAGTA
5724 TTTAAAAAAAGTA
1 TTTAAAAAAAGTA
5737 CAAATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTAAAAAAAGTA
Found at i:10665 original size:40 final size:40
Alignment explanation
Indices: 10587--10668 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
10577 TCAGGGGTAA
* * **
10587 AATTGAATCAATTAACAAATAAACATTCCAATTGGGGACT
1 AATTGAATCAATTAACAAATAAACACTCAAATCAGGGACT
10627 AATTGAATCAATTAACGAACATAAAC-CT-AAATCAGGGACT
1 AATTGAATCAATTAAC-AA-ATAAACACTCAAATCAGGGACT
10667 AA
1 AA
10669 GGTGAAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 27 0.75
41 3 0.08
42 6 0.17
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (40 bp):
AATTGAATCAATTAACAAATAAACACTCAAATCAGGGACT
Found at i:12927 original size:26 final size:26
Alignment explanation
Indices: 12891--12984 Score: 134
Period size: 26 Copynumber: 3.6 Consensus size: 26
12881 TAATTACTAA
12891 TAATTACTAATGTGAATGCTAATGCC
1 TAATTACTAATGTGAATGCTAATGCC
*
12917 TAATTACTAATGTGGATGCTAATGCC
1 TAATTACTAATGTGAATGCTAATGCC
* * * * *
12943 TAACTACTAATGTGGATACTATTACC
1 TAATTACTAATGTGAATGCTAATGCC
12969 TAATTACTAATGTGAA
1 TAATTACTAATGTGAA
12985 AAAAAAATGC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (26 bp):
TAATTACTAATGTGAATGCTAATGCC
Found at i:15616 original size:21 final size:21
Alignment explanation
Indices: 15592--15645 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
15582 ACCTACCACT
**
15592 GTGCCATCACCAGTTAAGCCC
1 GTGCCATCACCAGCCAAGCCC
* *
15613 GTGCCACCACCAGCCATGCCC
1 GTGCCATCACCAGCCAAGCCC
15634 GTGCCATCACCA
1 GTGCCATCACCA
15646 TTTAGTGCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.44, G:0.19, T:0.15
Consensus pattern (21 bp):
GTGCCATCACCAGCCAAGCCC
Found at i:16316 original size:15 final size:15
Alignment explanation
Indices: 16296--16326 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16286 TCTAATAGAG
16296 AGTCTACATGCATAA
1 AGTCTACATGCATAA
16311 AGTCTACATGCATAA
1 AGTCTACATGCATAA
16326 A
1 A
16327 TACATGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (15 bp):
AGTCTACATGCATAA
Found at i:20891 original size:10 final size:10
Alignment explanation
Indices: 20876--20903 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
20866 TTTATTAAGA
20876 AATTATCTCT
1 AATTATCTCT
20886 AATTATCTCT
1 AATTATCTCT
20896 AATTATCT
1 AATTATCT
20904 TGTTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTATCTCT
Found at i:24136 original size:19 final size:18
Alignment explanation
Indices: 24103--24138 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24093 TGGAAATAAT
24103 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
24121 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
24139 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.