Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021149.1 Corchorus olitorius cultivar O-4 contig21182, 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: 7046
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Found at i:418 original size:11 final size:11
Alignment explanation
Indices: 398--460 Score: 74
Period size: 11 Copynumber: 5.8 Consensus size: 11
388 TTATTTCTTA
*
398 TTTTCCTTTTT
1 TTTTCTTTTTT
409 TTTTC-TTTTT
1 TTTTCTTTTTT
*
419 TCTTCTTTTTT
1 TTTTCTTTTTT
* *
430 TTTCCTTTTTC
1 TTTTCTTTTTT
*
441 TTTTCTTTTCT
1 TTTTCTTTTTT
452 TTTTCTTTT
1 TTTTCTTTT
461 CCCTTTTTCC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
10 9 0.20
11 35 0.80
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:420 original size:26 final size:25
Alignment explanation
Indices: 367--444 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 25
357 TTATCCATAA
* *
367 TTTTC-TATTTTC-TATTTTCTCTT
1 TTTTCTTATTTTCTTTTTTTTTCTT
*
390 ATTTCTTATTTTCCTTTTTTTTTCTT
1 TTTTCTTATTTT-CTTTTTTTTTCTT
* *
416 TTTTCTTCTTTTTTTTTCCTTTTTCTT
1 TTTTCTTATTTTCTTTT--TTTTTCTT
443 TT
1 TT
445 CTTTTCTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
23 4 0.09
24 6 0.14
25 5 0.11
26 19 0.43
27 10 0.23
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTCTTATTTTCTTTTTTTTTCTT
Found at i:427 original size:17 final size:17
Alignment explanation
Indices: 369--429 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
359 ATCCATAATT
* *
369 TTCTATTTTCTATTTTC
1 TTCTTTTTTCTTTTTTC
*
386 -TCTTATTTCTTATTTTCC
1 TTCTTTTTTCTT-TTTT-C
*
404 TTTTTTTTTCTTTTTTC
1 TTCTTTTTTCTTTTTTC
421 TTCTTTTTT
1 TTCTTTTTT
430 TTTCCTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 8 0.23
17 13 0.37
18 5 0.14
19 9 0.26
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCTTTTTTCTTTTTTC
Found at i:461 original size:16 final size:16
Alignment explanation
Indices: 367--461 Score: 81
Period size: 16 Copynumber: 6.0 Consensus size: 16
357 TTATCCATAA
*
367 TTTTCTATTTTCTATT-
1 TTTTCT-TTTTCTTTTC
* *
383 TTCTCTTATTTCTTAT-
1 TTTTCTT-TTTCTTTTC
*
399 TTTCCTTTTT-TTTTC
1 TTTTCTTTTTCTTTTC
* *
414 TTTT-TTCTTCTTTTT
1 TTTTCTTTTTCTTTTC
429 TTTTCCTTTTTCTTTTC
1 TTTT-CTTTTTCTTTTC
446 TTTTCTTTTTCTTTTC
1 TTTTCTTTTTCTTTTC
462 CCTTTTTCCC
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
14 7 0.11
15 15 0.24
16 28 0.44
17 13 0.21
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:477 original size:37 final size:32
Alignment explanation
Indices: 374--460 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 32
364 TAATTTTCTA
*
374 TTTTCTATTTTCTCTTATTTCTTATTTTCCTTTTT-
1 TTTTCT-TTTT-TCTTCTTT-TT-TTTTCCTTTTTC
409 TTTTCTTTTTTCTTCTTTTTTTTTCCTTTTTC
1 TTTTCTTTTTTCTTCTTTTTTTTTCCTTTTTC
*
441 TTTTCTTTTCTTTTTCTTTT
1 TTTTCTTTT-TTCTTCTTTT
461 CCCTTTTTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
31 11 0.23
32 11 0.23
33 16 0.33
34 4 0.08
35 6 0.12
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (32 bp):
TTTTCTTTTTTCTTCTTTTTTTTTCCTTTTTC
Done.