Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000058.1 Corchorus olitorius cultivar O-4 contig00058, 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, 603
Length: 1005
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Found at i:359 original size:10 final size:10
Alignment explanation
Indices: 344--381 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
334 CCAAATTTCC
344 TTCTTTTCTT
1 TTCTTTTCTT
354 TTCTTTTCTT
1 TTCTTTTCTT
364 TTC-TTTCTT
1 TTCTTTTCTT
*
373 CT-TTTTCTT
1 TTCTTTTCTT
382 CATTCTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 13 0.50
10 13 0.50
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTCTTTTCTT
Found at i:372 original size:4 final size:5
Alignment explanation
Indices: 344--381 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
334 CCAAATTTCC
*
344 TTCTT TTCTT TTCTT TTCTT TTC-T TTCTT CT-TT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
382 CATTCTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:389 original size:16 final size:17
Alignment explanation
Indices: 354--391 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
344 TTCTTTTCTT
* *
354 TTCTTTTCTTTTCTTTC
1 TTCTTTTCTCTTCATTC
371 TTCTTTT-TCTTCATTC
1 TTCTTTTCTCTTCATTC
387 TTCTT
1 TTCTT
392 CGTTATGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (17 bp):
TTCTTTTCTCTTCATTC
Found at i:419 original size:6 final size:6
Alignment explanation
Indices: 408--441 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
398 GGGCTAGGCC
*
408 CTTTTT CTTTTT CTTATT CTTTTT CTTATTT CTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTT-TTT CTT
442 ATGGGCTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (6 bp):
CTTTTT
Found at i:439 original size:19 final size:18
Alignment explanation
Indices: 408--443 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
398 GGGCTAGGCC
408 CTTTTTCTTTTTCTTATT
1 CTTTTTCTTTTTCTTATT
426 CTTTTTCTTATTTCTTAT
1 CTTTTTCTT-TTTCTTAT
444 GGGCTAGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (18 bp):
CTTTTTCTTTTTCTTATT
Found at i:449 original size:46 final size:46
Alignment explanation
Indices: 362--483 Score: 151
Period size: 46 Copynumber: 2.6 Consensus size: 46
352 TTTTCTTTTC
* *
362 TTTTCTTTCTTCTTTTTCTTCATTCTT-CTTCGTTATGGGCTAGGCCCT
1 TTTTCTTT-TTC-TTTTCTT-TTTCTTATTTCGTTATGGGCTAGGCCCT
410 TTTTCTTTTTCTTATTCTTTTTCTTATTTC-TTATGGGCTAGGCCCT
1 TTTTCTTTTTCTT-TTCTTTTTCTTATTTCGTTATGGGCTAGGCCCT
*
456 TTTTC-TTTTCTTTTCTTTTGTTTTATTT
1 TTTTCTTTTTCTTTTCTTTT-TCTTATTT
484 ATTTATTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
44 7 0.10
45 14 0.21
46 28 0.41
47 11 0.16
48 8 0.12
ACGTcount: A:0.07, C:0.20, G:0.10, T:0.64
Consensus pattern (46 bp):
TTTTCTTTTTCTTTTCTTTTTCTTATTTCGTTATGGGCTAGGCCCT
Found at i:581 original size:22 final size:22
Alignment explanation
Indices: 551--592 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
541 AGCGGGCCGC
*
551 GCGCTGGCCCAAGCGGCCTGCA
1 GCGCAGGCCCAAGCGGCCTGCA
**
573 GCGCAGGCCCGCGCGGCCTG
1 GCGCAGGCCCAAGCGGCCTG
593 GTGGCCTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.43, G:0.40, T:0.07
Consensus pattern (22 bp):
GCGCAGGCCCAAGCGGCCTGCA
Done.