Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006713.1 Corchorus capsularis cultivar CVL-1 contig06734, 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: 15914
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:412 original size:16 final size:16
Alignment explanation
Indices: 393--449 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
383 AATCTATGAG
393 CCAACAAATCTCTTCC
1 CCAACAAATCTCTTCC
* ***
409 CCAACAAATCTATGAG
1 CCAACAAATCTCTTCC
* *
425 CCAACAAACCCCTTCC
1 CCAACAAATCTCTTCC
441 CCAACAAAT
1 CCAACAAAT
450 ACAATTCAAA
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.39, C:0.40, G:0.04, T:0.18
Consensus pattern (16 bp):
CCAACAAATCTCTTCC
Found at i:424 original size:32 final size:32
Alignment explanation
Indices: 383--449 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
373 CCAAAATGTT
* *
383 AATCTATGAGCCAACAAATCTCTTCCCCAACA
1 AATCTATGAGCCAACAAACCCCTTCCCCAACA
415 AATCTATGAGCCAACAAACCCCTTCCCCAACA
1 AATCTATGAGCCAACAAACCCCTTCCCCAACA
447 AAT
1 AAT
450 ACAATTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.39, C:0.36, G:0.06, T:0.19
Consensus pattern (32 bp):
AATCTATGAGCCAACAAACCCCTTCCCCAACA
Found at i:4393 original size:17 final size:17
Alignment explanation
Indices: 4371--4431 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
4361 AAAATTATTT
4371 TATTTTAATATGTAAAA
1 TATTTTAATATGTAAAA
* **
4388 TATTTTATTAACTAAGAA
1 TATTTTAATATGTAA-AA
*
4406 TATATATATATATGTAAAA
1 TAT-TTTA-ATATGTAAAA
4425 TATTTTA
1 TATTTTA
4432 TTTTAATATA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 12 0.36
18 8 0.24
19 8 0.24
20 5 0.15
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (17 bp):
TATTTTAATATGTAAAA
Found at i:4430 original size:59 final size:61
Alignment explanation
Indices: 4343--4477 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 61
4333 TTTTAATTAT
* *
4343 ATATATTATATATATCCAAAAATTATTTTATTTTAATATGTAAAATATTTTATTAACTAAG-A
1 ATATA-TATATATATCCAAAAATTATTTTATTTTAATATATAAAATATATTATTAA-TAAGTA
** * *
4405 ATATATATATATAT-GTAAAA-TATTTTATTTTAATATATAATATATATTATTAATATGTA
1 ATATATATATATATCCAAAAATTATTTTATTTTAATATATAAAATATATTATTAATAAGTA
4464 ATATATATATATAT
1 ATATATATATATAT
4478 ATGTGTGTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
58 3 0.05
59 45 0.68
60 4 0.06
61 9 0.14
62 5 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (61 bp):
ATATATATATATATCCAAAAATTATTTTATTTTAATATATAAAATATATTATTAATAAGTA
Found at i:4447 original size:7 final size:7
Alignment explanation
Indices: 4435--4478 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
4425 TATTTTATTT
4435 TAATATA
1 TAATATA
4442 TAATATA
1 TAATATA
*
4449 TATTAT-
1 TAATATA
*
4455 TAATATG
1 TAATATA
4462 TAATATA
1 TAATATA
4469 TATATATA
1 TA-ATATA
4477 TA
1 TA
4479 TGTGTGTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
6 5 0.16
7 20 0.62
8 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
TAATATA
Found at i:4457 original size:20 final size:20
Alignment explanation
Indices: 4371--4471 Score: 86
Period size: 20 Copynumber: 5.2 Consensus size: 20
4361 AAAATTATTT
*
4371 TATT-TTAATATGTAAAATA
1 TATTATTAATATGTAATATA
* *
4390 TTTTATTAACTAAG-AATATA
1 TATTATTAA-TATGTAATATA
*
4410 TA-TA-T-ATATGTAAAATA
1 TATTATTAATATGTAATATA
* *
4427 TTTTATTTTAATATATAATATA
1 TATTA--TTAATATGTAATATA
4449 TATTATTAATATGTAATATA
1 TATTATTAATATGTAATATA
4469 TAT
1 TAT
4472 ATATATATGT
Statistics
Matches: 63, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
16 3 0.05
17 7 0.11
18 3 0.05
19 5 0.08
20 27 0.43
21 4 0.06
22 14 0.22
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.50
Consensus pattern (20 bp):
TATTATTAATATGTAATATA
Found at i:4458 original size:13 final size:14
Alignment explanation
Indices: 4438--4479 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
4428 TTTATTTTAA
4438 TATATAATATATAT
1 TATATAATATATAT
* *
4452 TAT-TAATATGTAA
1 TATATAATATATAT
4465 TATATATATATATAT
1 TATATA-ATATATAT
4480 GTGTGTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.50
14 5 0.23
15 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TATATAATATATAT
Found at i:7588 original size:20 final size:20
Alignment explanation
Indices: 7563--7603 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7553 ATGAGATGTC
* * *
7563 TTAAAAATCCATTTGACATA
1 TTAAAAACCCACTTAACATA
7583 TTAAAAACCCACTTAACATA
1 TTAAAAACCCACTTAACATA
7603 T
1 T
7604 CAATAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (20 bp):
TTAAAAACCCACTTAACATA
Found at i:10153 original size:78 final size:75
Alignment explanation
Indices: 9985--10241 Score: 286
Period size: 74 Copynumber: 3.4 Consensus size: 75
9975 GGGCCATTCA
* * * * *
9985 CCCTGCTAGCCCTCCTCTAGA-CCTGCCACTGAATAGAATACATGGCAACATAATATTAAAGGGA
1 CCCTGCCAGCCATCCTCTAGATCC-GCCACTGAATAGAATACGTCGCAACATGATATTAAAGGGA
10049 CACAACATGG-
65 CACAACATGGC
* * * *
10059 CCCTACTAGCCCTCCTCTAGATCCGCCACTGAATACTGAATAGGATACGCAACATGATATTAAAG
1 CCCTGCCAGCCATCCTCTAGATCCGCCACTGAATA--GAATACG-T-CGCAACATGATATTAAAG
* *
10124 GGA-TCAATATGGC
62 GGACACAACATGGC
* * * * *
10137 CCCTGCCAGCCATCCTCTAGATCCGTCACCGAATAGGATACGTGGCAACATGATATTCAAGGGAC
1 CCCTGCCAGCCATCCTCTAGATCCGCCACTGAATAGAATACGTCGCAACATGATATTAAAGGGAC
*
10202 ACAACATAGC
66 ACAACATGGC
*
10212 CCCTGCCAGCCTTCCTCTAGATCCGCCACT
1 CCCTGCCAGCCATCCTCTAGATCCGCCACT
10242 TAGGCCTTGT
Statistics
Matches: 154, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
74 50 0.32
75 37 0.24
76 10 0.06
77 8 0.05
78 49 0.32
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (75 bp):
CCCTGCCAGCCATCCTCTAGATCCGCCACTGAATAGAATACGTCGCAACATGATATTAAAGGGAC
ACAACATGGC
Found at i:10229 original size:75 final size:71
Alignment explanation
Indices: 10096--10236 Score: 201
Period size: 75 Copynumber: 1.9 Consensus size: 71
10086 ACTGAATACT
* * *
10096 GAATAGGATACGCAACATGATATTAAAGGGATCAATATGGCCCCTGCCAGCCATCCTCTAGATCC
1 GAATAGGATACGCAACATGATATTAAAGGGAACAACATAGCCCCTGCCAGCCATCCTCTAGATCC
10161 GTCACC
66 GTCACC
* *
10167 GAATAGGATACGTGGCAACATGATATTCAAGGGACACAACATAGCCCCTGCCAGCCTTCCTCTAG
1 GAATAGGATAC---GCAACATGATATTAAAGGGA-ACAACATAGCCCCTGCCAGCCATCCTCTAG
10232 ATCCG
62 ATCCG
10237 CCACTTAGGC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
71 11 0.18
74 19 0.31
75 31 0.51
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (71 bp):
GAATAGGATACGCAACATGATATTAAAGGGAACAACATAGCCCCTGCCAGCCATCCTCTAGATCC
GTCACC
Found at i:10298 original size:18 final size:15
Alignment explanation
Indices: 10262--10291 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10252 TCGGAATAGA
10262 GGTGAGATTGAAAAT
1 GGTGAGATTGAAAAT
10277 GGTGAGATTGAAAAT
1 GGTGAGATTGAAAAT
10292 AATGGTGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (15 bp):
GGTGAGATTGAAAAT
Found at i:10667 original size:26 final size:25
Alignment explanation
Indices: 10600--10670 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 25
10590 ATATAAATTA
10600 CTAAAATAAATGTAT-TATATTATG-
1 CTAAAATAAATGTATATATA-TATGT
*
10624 GTAAAA-AAATG--TAT-TATATGT
1 CTAAAATAAATGTATATATATATGT
10645 CTAAAATAAATGTAATATATATATGT
1 CTAAAATAAATGT-ATATATATATGT
10671 ATTAATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
20 4 0.11
21 8 0.21
22 6 0.16
23 5 0.13
24 5 0.13
25 3 0.08
26 7 0.18
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (25 bp):
CTAAAATAAATGTATATATATATGT
Found at i:11557 original size:24 final size:24
Alignment explanation
Indices: 11516--11561 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
11506 ACTTCATATA
* *
11516 CCGGATTAGGGCGGGTCAATTAAT
1 CCGGATTAGGACGAGTCAATTAAT
*
11540 CCGGATTAGGATGAGTCAATTA
1 CCGGATTAGGACGAGTCAATTA
11562 CATAAACGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (24 bp):
CCGGATTAGGACGAGTCAATTAAT
Done.