Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002139.1 Corchorus capsularis cultivar CVL-1 contig02143, 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, 850
Length: 1417
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Found at i:292 original size:13 final size:13
Alignment explanation
Indices: 276--302 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
266 TTTTTTCCCC
276 TCTTTTTTTTATT
1 TCTTTTTTTTATT
289 TCTTTTTTTTATT
1 TCTTTTTTTTATT
302 T
1 T
303 TATTCCCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (13 bp):
TCTTTTTTTTATT
Found at i:815 original size:18 final size:18
Alignment explanation
Indices: 792--842 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
782 AGTTCTTTTC
792 TTTCTATTCTATTAGTAT
1 TTTCTATTCTATTAGTAT
810 TTTCTATTCTA-T--T-T
1 TTTCTATTCTATTAGTAT
824 TTTCTATTCTATTAGTAT
1 TTTCTATTCTATTAGTAT
842 T
1 T
843 AGAATTAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.41
15 2 0.07
17 2 0.07
18 13 0.45
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTCTATTCTATTAGTAT
Found at i:828 original size:14 final size:14
Alignment explanation
Indices: 809--836 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
799 TCTATTAGTA
809 TTTTCTATTCTATT
1 TTTTCTATTCTATT
823 TTTTCTATTCTATT
1 TTTTCTATTCTATT
837 AGTATTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:844 original size:6 final size:6
Alignment explanation
Indices: 833--895 Score: 71
Period size: 6 Copynumber: 11.2 Consensus size: 6
823 TTTTCTATTC
* * *
833 TATTAG TATTAG AATTAG TATTAG -ATTAG TATT-C TATT-C TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
878 TATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG T
896 TAGTGATCCC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
5 19 0.38
6 31 0.62
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.49
Consensus pattern (6 bp):
TATTAG
Found at i:860 original size:11 final size:11
Alignment explanation
Indices: 834--899 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 11
824 TTTCTATTCT
834 ATTAGTATTAG
1 ATTAGTATTAG
845 AATTAGTATTAG
1 -ATTAGTATTAG
*
857 ATTAGTATTCTATTCT
1 ATTAGTA-T-TA---G
873 ATTAGTATTAG
1 ATTAGTATTAG
884 ATTAGTATTAG
1 ATTAGTATTAG
895 -TTAGT
1 ATTAGT
900 GATCCCGGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
10 5 0.11
11 18 0.38
12 12 0.26
13 2 0.04
14 2 0.04
15 1 0.02
16 7 0.15
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.48
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:870 original size:39 final size:37
Alignment explanation
Indices: 825--899 Score: 132
Period size: 39 Copynumber: 2.0 Consensus size: 37
815 ATTCTATTTT
825 TTCTATTCTATTAGTATTAGAATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAG-ATTAGTATTAG-TTAGTA
864 TTCTATTCTATTAGTATTAGATTAGTATTAGTTAGT
1 TTCTATTCTATTAGTATTAGATTAGTATTAGTTAGT
900 GATCCCGGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 5 0.14
38 11 0.31
39 20 0.56
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (37 bp):
TTCTATTCTATTAGTATTAGATTAGTATTAGTTAGTA
Done.