Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009010.1 Corchorus capsularis cultivar CVL-1 contig09031, 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: 55272
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:249 original size:2 final size:2
Alignment explanation
Indices: 242--305 Score: 69
Period size: 2 Copynumber: 32.0 Consensus size: 2
232 TCATATGTAG
* * *
242 TA TA TA TA TG TA GTA TA TA TA GTA TA T- TG TA CA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
285 TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
306 ATGGCTTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.04
2 47 0.89
3 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:264 original size:22 final size:21
Alignment explanation
Indices: 234--299 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
224 AAAAATACTC
*
234 ATATGTAGTATATATATGTAGT
1 ATATATAGTATATATATGTA-T
*
256 ATATATAG--TATAT-TGTAC
1 ATATATAGTATATATATGTAT
*
274 ATATATA-TATATATATATAT
1 ATATATAGTATATATATGTAT
294 ATATAT
1 ATATAT
300 TATATAATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 7 0.19
19 9 0.24
20 14 0.38
22 7 0.19
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (21 bp):
ATATATAGTATATATATGTAT
Found at i:8915 original size:2 final size:2
Alignment explanation
Indices: 8908--8937 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8898 CAGCCATGTG
8908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8938 GAGGCAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10167 original size:12 final size:13
Alignment explanation
Indices: 10150--10178 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10140 TTTTAAAGTC
10150 TAATCT-TTCATA
1 TAATCTATTCATA
10162 TAATCTATTCATA
1 TAATCTATTCATA
10175 TAAT
1 TAAT
10179 TATATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATCTATTCATA
Found at i:10316 original size:2 final size:2
Alignment explanation
Indices: 10309--10344 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
10299 ACACTGGTTA
10309 AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10345 ACATATAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13146 original size:2 final size:2
Alignment explanation
Indices: 13139--13184 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
13129 TGAATTCACA
*
13139 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
13181 TC TC
1 TC TC
13185 GTTTTTCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:21723 original size:12 final size:12
Alignment explanation
Indices: 21706--21760 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
21696 AAAAGAGTAA
21706 TAATAATACTAT
1 TAATAATACTAT
21718 TAATAATACTAT
1 TAATAATACTAT
* * *
21730 TAAAAAGAGTAATAA
1 T-AATA-A-TACTAT
21745 TAATAATACTAT
1 TAATAATACTAT
21757 TAAT
1 TAAT
21761 CTATTATGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 21 0.62
13 4 0.12
14 4 0.12
15 5 0.15
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (12 bp):
TAATAATACTAT
Found at i:21735 original size:36 final size:35
Alignment explanation
Indices: 21695--21766 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
21685 CTTATTCAAG
* *
21695 AAAAAGAGTAATAATAATACTATTAATAATACTATT
1 AAAAAGAGTAATAATAATAATACTAATAAT-CTATT
*
21731 AAAAAGAGTAATAATAATAATACTATTAATCTATT
1 AAAAAGAGTAATAATAATAATACTAATAATCTATT
21766 A
1 A
21767 TGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (35 bp):
AAAAAGAGTAATAATAATAATACTAATAATCTATT
Found at i:24309 original size:2 final size:2
Alignment explanation
Indices: 24302--24331 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24292 AAATGACAAC
24302 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24332 TACTCTCTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28623 original size:2 final size:2
Alignment explanation
Indices: 28616--28645 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28606 CTATAGTTTA
28616 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28646 AATGGATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:42601 original size:24 final size:21
Alignment explanation
Indices: 42572--42616 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
42562 AAAGTTGAAT
42572 TTCGGTCGGTATGTTCGAATAGAA
1 TTCGGT-GGT-TGTTCGAA-AGAA
*
42596 TTCGGTGGTTGTTTGAAAGAA
1 TTCGGTGGTTGTTCGAAAGAA
42617 AGTTTAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 3 0.15
24 6 0.30
ACGTcount: A:0.24, C:0.09, G:0.31, T:0.36
Consensus pattern (21 bp):
TTCGGTGGTTGTTCGAAAGAA
Found at i:44869 original size:6 final size:6
Alignment explanation
Indices: 44860--44884 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44850 TGTATAATAA
44860 TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT T
44885 GCTAGTGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:46330 original size:21 final size:21
Alignment explanation
Indices: 46306--46350 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
46296 ATGACACTGG
* *
46306 CCACCTGGGTGATCAGACAAA
1 CCACATGGGTCATCAGACAAA
*
46327 CCACATGGGTCTTCAGACAAA
1 CCACATGGGTCATCAGACAAA
46348 CCA
1 CCA
46351 TGTGGGCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (21 bp):
CCACATGGGTCATCAGACAAA
Done.