Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008913.1 Corchorus capsularis cultivar CVL-1 contig08934, 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: 7671
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Found at i:350 original size:15 final size:15
Alignment explanation
Indices: 330--366 Score: 60
Period size: 13 Copynumber: 2.6 Consensus size: 15
320 CATCAGGATC
330 AATTTTTTAAAAAAT
1 AATTTTTTAAAAAAT
345 AA--TTTTAAAAAAT
1 AATTTTTTAAAAAAT
358 AATTTTTTA
1 AATTTTTTA
367 TGTTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.65
15 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTTTTTAAAAAAT
Found at i:500 original size:12 final size:12
Alignment explanation
Indices: 485--547 Score: 56
Period size: 12 Copynumber: 4.9 Consensus size: 12
475 GTAATTATTA
485 TTGTATGTAATT
1 TTGTATGTAATT
*
497 TTGTAAGTAATT
1 TTGTATGTAATT
509 TT-TATGTTAATTATT
1 TTGTATG-T-A--ATT
524 ATTGTATGTAATT
1 -TTGTATGTAATT
*
537 TTGTAAGTAAT
1 TTGTATGTAAT
548 ATTTTTTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 3 0.07
12 24 0.57
13 4 0.10
15 4 0.10
16 3 0.07
17 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (12 bp):
TTGTATGTAATT
Found at i:520 original size:40 final size:41
Alignment explanation
Indices: 476--552 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 41
466 GACATGTTTG
476 TAATTATTATTGTATGTAATTTTGTAAGTAAT-TTTTATGT
1 TAATTATTATTGTATGTAATTTTGTAAGTAATATTTTATGT
516 TAATTATTATTGTATGTAATTTTGTAAGTAATATTTT
1 TAATTATTATTGTATGTAATTTTGTAAGTAATATTTT
553 TTAAGTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (41 bp):
TAATTATTATTGTATGTAATTTTGTAAGTAATATTTTATGT
Found at i:528 original size:28 final size:25
Alignment explanation
Indices: 494--565 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 25
484 ATTGTATGTA
*
494 ATTTTGTAAGTAATTTTTATGTTAATT
1 ATTTTGTAAGTAATTTTTAAG-TAA-T
*
521 ATTATTGTATGTAATTTTGTAAGTAAT
1 ATT-TTGTAAGTAATTTT-TAAGTAAT
*
548 ATTTTTTAAGTAATTTTT
1 ATTTTGTAAGTAATTTTT
566 TTGTAAGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 1 0.03
26 12 0.31
27 7 0.18
28 16 0.41
29 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (25 bp):
ATTTTGTAAGTAATTTTTAAGTAAT
Found at i:557 original size:14 final size:14
Alignment explanation
Indices: 534--579 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
524 ATTGTATGTA
*
534 ATTTTGTAAGTAAT
1 ATTTTTTAAGTAAT
548 ATTTTTTAAGTAAT
1 ATTTTTTAAGTAAT
*
562 TTTTTTGTAAGTAAT
1 ATTTTT-TAAGTAAT
577 ATT
1 ATT
580 ACATACAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.57
Consensus pattern (14 bp):
ATTTTTTAAGTAAT
Found at i:567 original size:15 final size:15
Alignment explanation
Indices: 494--576 Score: 65
Period size: 15 Copynumber: 5.9 Consensus size: 15
484 ATTGTATGTA
494 ATTTTGTAAGTAATT
1 ATTTTGTAAGTAATT
509 -TTTATGT---TAATT
1 ATTT-TGTAAGTAATT
*
521 ATTATTGTATGT-A--
1 ATT-TTGTAAGTAATT
534 ATTTTGTAAGTAA-T
1 ATTTTGTAAGTAATT
*
548 ATTTTTTAAGTAATT
1 ATTTTGTAAGTAATT
*
563 TTTTTGTAAGTAAT
1 ATTTTGTAAGTAAT
577 ATTACATACA
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
12 12 0.22
13 9 0.16
14 16 0.29
15 17 0.31
16 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (15 bp):
ATTTTGTAAGTAATT
Found at i:4450 original size:27 final size:26
Alignment explanation
Indices: 4406--4456 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
4396 AATATATAAA
4406 TTATTATAAAACATTAAAATTAAAAAC
1 TTATTATAAAACATT-AAATTAAAAAC
*
4433 TTATATATAAATCA-TAAATTAAAA
1 TTAT-TATAAAACATTAAATTAAAA
4457 CTAAAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 5 0.23
28 8 0.36
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
TTATTATAAAACATTAAATTAAAAAC
Found at i:6277 original size:26 final size:26
Alignment explanation
Indices: 6248--6302 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
6238 AATATTTTAT
*
6248 TAAATAAGAATGTATATATATATATG
1 TAAATAAGAATATATATATATATATG
6274 TAAATAAGAATATATATATATATATG
1 TAAATAAGAATATATATATATATATG
6300 TAA
1 TAA
6303 TAATTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (26 bp):
TAAATAAGAATATATATATATATATG
Found at i:6334 original size:18 final size:17
Alignment explanation
Indices: 6309--6346 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
6299 GTAATAATTT
6309 TATTTTAATATATAATA
1 TATTTTAATATATAATA
*
6326 TATTATTAATATGTAATA
1 TATT-TTAATATATAATA
6344 TAT
1 TAT
6347 ATACGTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTTAATATATAATA
Found at i:6355 original size:20 final size:18
Alignment explanation
Indices: 6314--6359 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
6304 AATTTTATTT
*
6314 TAATATATAATATATTAT
1 TAATATATAATATATTAG
*
6332 TAATATGTAATATATATACG
1 TAATATATAATATAT-TA-G
6352 TAATATAT
1 TAATATAT
6360 TCAAACCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 14 0.61
19 2 0.09
20 7 0.30
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (18 bp):
TAATATATAATATATTAG
Done.