Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010598.1 Corchorus capsularis cultivar CVL-1 contig10619, 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: 9766
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:399 original size:31 final size:31
Alignment explanation
Indices: 361--491 Score: 131
Period size: 31 Copynumber: 4.5 Consensus size: 31
351 GGTGTCCGAC
*
361 GTGGCACGCCACGTGTACCAAAAAGTAACAT
1 GTGGCACGCCACATGTACCAAAAAGTAACAT
392 GTGGCACGCCACATGTACCAAAAAGT--C--
1 GTGGCACGCCACATGTACCAAAAAGTAACAT
419 GT-----GCCACATGTACCAAAAAGTGACACAT
1 GTGGCACGCCACATGTACCAAAAAGT-A-ACAT
* *
447 GT--CACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCACGCCACATGTACCAAAAAGTAACAT
*
476 GTGGCATGCCACATGT
1 GTGGCACGCCACATGT
492 TTCAAAAATG
Statistics
Matches: 84, Mismatches: 5, Indels: 22
0.76 0.05 0.20
Matches are distributed among these distances:
22 19 0.23
26 1 0.01
27 2 0.02
28 2 0.02
29 7 0.08
31 53 0.63
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.18
Consensus pattern (31 bp):
GTGGCACGCCACATGTACCAAAAAGTAACAT
Found at i:447 original size:19 final size:20
Alignment explanation
Indices: 401--448 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
391 TGTGGCACGC
*
401 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
423 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
442 CACATGT
1 CACATGT
449 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:453 original size:53 final size:52
Alignment explanation
Indices: 368--470 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 52
358 GACGTGGCAC
*
368 GCCACGTGTACCAAAAAGTAACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTAACATGT-GCACGCCACATGTACCAAAAAGTCGT
*
421 GCCACATGTACCAAAAAGTGACACATGT-CACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGT-A-ACATGTGCACGCCACATGTACCAAAAAGT
471 GACATGTGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
53 39 0.85
54 1 0.02
55 6 0.13
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (52 bp):
GCCACATGTACCAAAAAGTAACATGTGCACGCCACATGTACCAAAAAGTCGT
Found at i:498 original size:31 final size:31
Alignment explanation
Indices: 420--513 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 31
410 CAAAAAGTCG
* *
420 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* * *
451 CGCCACGTGTACCAAAAAGTGACATGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** *
482 TGCCACATGTTTCAAAAA-TGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
512 TG
1 TG
514 TCACGTGCAC
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 12 0.23
31 40 0.77
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:6189 original size:20 final size:20
Alignment explanation
Indices: 6153--6190 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6143 ATAGAAAGTA
*
6153 GAAAATGAAAACCGTTTTTC
1 GAAAATGAAAAACGTTTTTC
*
6173 GAAAATGAAAAATGTTTT
1 GAAAATGAAAAACGTTTT
6191 ACATTACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (20 bp):
GAAAATGAAAAACGTTTTTC
Found at i:8230 original size:20 final size:20
Alignment explanation
Indices: 8205--8250 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
8195 ATGGTTGATT
8205 GGATTTCAGATACACTTAGG
1 GGATTTCAGATACACTTAGG
*
8225 GGATTTCAGTTACACTTAGG
1 GGATTTCAGATACACTTAGG
*
8245 GTATTT
1 GGATTT
8251 GTTTCAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (20 bp):
GGATTTCAGATACACTTAGG
Found at i:9766 original size:21 final size:19
Alignment explanation
Indices: 9712--9766 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
9702 AATGCATCAA
9712 ATATAAACTCATTATATATAT
1 ATATAAA-T-ATTATATATAT
9733 ATAT-AATATTTATATATATTT
1 ATATAAATA-TTATATATA--T
9754 ATATAAATATTAT
1 ATATAAATATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.03
19 10 0.33
20 2 0.07
21 13 0.43
22 4 0.13
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATAAATATTATATATAT
Done.