Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011990.1 Corchorus olitorius cultivar O-4 contig12023, 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: 15842
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:3814 original size:11 final size:11
Alignment explanation
Indices: 3798--3823 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3788 CTAGCCCTAA
3798 AAAACTAGAAG
1 AAAACTAGAAG
3809 AAAACTAGAAG
1 AAAACTAGAAG
3820 AAAA
1 AAAA
3824 GAAATTATCT
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:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:4552 original size:42 final size:44
Alignment explanation
Indices: 4501--4587 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
4491 TGCATTACCT
* * *
4501 AAATTCTACT-C-CATCTCTAGGTAATTTATCAAAATAAAGCTA
1 AAATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAACTA
* *
4543 AAATTCTACTCCTCTTCTCTATATAATTCATCAAAATAAAACTA
1 AAATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAACTA
4587 A
1 A
4588 TATTAATTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 10 0.26
43 1 0.03
44 27 0.71
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.34
Consensus pattern (44 bp):
AAATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAACTA
Found at i:8468 original size:15 final size:15
Alignment explanation
Indices: 8450--8483 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
8440 AAAATTTTTT
*
8450 TTTTTGATTTTTGCG
1 TTTTTAATTTTTGCG
*
8465 TTTTTAATTTTTGTG
1 TTTTTAATTTTTGCG
8480 TTTT
1 TTTT
8484 GCATTTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.74
Consensus pattern (15 bp):
TTTTTAATTTTTGCG
Found at i:8475 original size:22 final size:22
Alignment explanation
Indices: 8450--8491 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
8440 AAAATTTTTT
*
8450 TTTTTGAT-TTTTGCGTTTTTAA
1 TTTTTG-TGTTTTGCATTTTTAA
8472 TTTTTGTGTTTTGCATTTTT
1 TTTTTGTGTTTTGCATTTTT
8492 CTAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.10, C:0.05, G:0.14, T:0.71
Consensus pattern (22 bp):
TTTTTGTGTTTTGCATTTTTAA
Found at i:12025 original size:11 final size:11
Alignment explanation
Indices: 12009--12034 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11999 CTAGCCCTAA
12009 AAAACTAGAAG
1 AAAACTAGAAG
12020 AAAACTAGAAG
1 AAAACTAGAAG
12031 AAAA
1 AAAA
12035 GAAATTATCT
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:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:12651 original size:29 final size:29
Alignment explanation
Indices: 12597--12671 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
12587 TTAAAACTCC
*
12597 AATCTTC-AATTCTTC--CTCTTGAAATA
1 AATCTTCAAATTCTTCAACTCTTCAAATA
*
12623 AATCTTCAAATTCTTCAAGTCTTCAAATA
1 AATCTTCAAATTCTTCAACTCTTCAAATA
*
12652 AGTCTTCAAATGGTCTTCAA
1 AATCTTCAAAT--TCTTCAA
12672 ACACGAACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.17
27 8 0.20
29 19 0.46
31 7 0.17
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (29 bp):
AATCTTCAAATTCTTCAACTCTTCAAATA
Found at i:12669 original size:11 final size:12
Alignment explanation
Indices: 12639--12672 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12629 CAAATTCTTC
12639 AAGTCTTCAAAT
1 AAGTCTTCAAAT
12651 AAGTCTTCAAAT
1 AAGTCTTCAAAT
*
12663 -GGTCTTCAAA
1 AAGTCTTCAAA
12673 CACGAACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (12 bp):
AAGTCTTCAAAT
Found at i:14230 original size:16 final size:15
Alignment explanation
Indices: 14209--14251 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
14199 AGAAATAGGC
14209 AATCAATCAAAGCAAT
1 AATCAATCAAAGC-AT
*
14225 AATCAACCAAAGCAT
1 AATCAATCAAAGCAT
14240 AA-CAATGCAAAG
1 AATCAAT-CAAAG
14252 AAAAAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 9 0.38
16 12 0.50
ACGTcount: A:0.56, C:0.21, G:0.09, T:0.14
Consensus pattern (15 bp):
AATCAATCAAAGCAT
Done.