Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021029.1 Corchorus olitorius cultivar O-4 contig21062, 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: 28367
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4567 original size:2 final size:2
Alignment explanation
Indices: 4544--4584 Score: 50
Period size: 2 Copynumber: 20.5 Consensus size: 2
4534 CGACCCCGAA
4544 AT AT AT A- AT AT ACT CAT A- AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT A
4585 CACACACACT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 2 0.06
2 30 0.86
3 2 0.06
4 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4671 original size:14 final size:14
Alignment explanation
Indices: 4654--4702 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
4644 AAGATGATAA
4654 TTATTTCATGAATT
1 TTATTTCATGAATT
* *
4668 TTATTTGAATG-ATAA
1 TTATTT-CATGAAT-T
4683 TTATTTCATGAATT
1 TTATTTCATGAATT
4697 TTATTT
1 TTATTT
4703 GGATGATGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (14 bp):
TTATTTCATGAATT
Found at i:4689 original size:29 final size:29
Alignment explanation
Indices: 4647--4709 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
4637 GAAGTGCAAG
4647 ATGATAATTATTTCATGAATTTTATTTGA
1 ATGATAATTATTTCATGAATTTTATTTGA
*
4676 ATGATAATTATTTCATGAATTTTATTTGG
1 ATGATAATTATTTCATGAATTTTATTTGA
4705 ATGAT
1 ATGAT
4710 GGATTTGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (29 bp):
ATGATAATTATTTCATGAATTTTATTTGA
Found at i:12210 original size:32 final size:31
Alignment explanation
Indices: 12165--12253 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 31
12155 ACCTGAACCC
*
12165 AAAAAACCCGAACCCG-GAAAAGCTCAAACTCG
1 AAAAAA-CCGAACCCGAGAAAACCT-AAACTCG
*
12197 AAAAAACCAGAACCCGATAAAACCTAAACTCG
1 AAAAAACC-GAACCCGAGAAAACCTAAACTCG
* *
12229 AAAAAATCCGAACCTGAAAAAACCT
1 AAAAAA-CCGAACCCGAGAAAACCT
12254 GAATTCAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 2 0.04
32 40 0.80
33 8 0.16
ACGTcount: A:0.52, C:0.28, G:0.11, T:0.09
Consensus pattern (31 bp):
AAAAAACCGAACCCGAGAAAACCTAAACTCG
Found at i:16354 original size:6 final size:6
Alignment explanation
Indices: 16343--16389 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
16333 TACACATTCC
16343 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG
16390 AGTGAGGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (6 bp):
TACTGT
Found at i:22340 original size:21 final size:22
Alignment explanation
Indices: 22314--22367 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
22304 CATATGGAGT
* *
22314 TTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTAATAGGGTAA
22335 TTATCAAAATTTAATAGGGTAA
1 TTATCAAAATTTAATAGGGTAA
22357 -TATCAAAATTT
1 TTATCAAAATTT
22368 CATAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTAATAGGGTAA
Found at i:22517 original size:27 final size:26
Alignment explanation
Indices: 22487--22548 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
22477 TACCCTTTTT
22487 TTAAAATATATTTCTAA-ATTGCCATTA
1 TTAAAATATATTT-TAATATT-CCATTA
22514 TT-AAATAATATTTTAATTATTCCATTA
1 TTAAAAT-ATATTTTAA-TATTCCATTA
22541 TTAAAATA
1 TTAAAATA
22549 ATAGAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
26 7 0.23
27 17 0.55
28 7 0.23
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.47
Consensus pattern (26 bp):
TTAAAATATATTTTAATATTCCATTA
Found at i:26692 original size:34 final size:34
Alignment explanation
Indices: 26649--26717 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
26639 TGTTGATCCA
*
26649 TAGAGCATCCCTCTTCCTTTGATGAATCTTATCT
1 TAGAGCATCCCTCTTCCTTTGATAAATCTTATCT
*
26683 TAGAGCATCCCTCTTCGTTTGATAAATCTTATCT
1 TAGAGCATCCCTCTTCCTTTGATAAATCTTATCT
26717 T
1 T
26718 TTGTTTGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.42
Consensus pattern (34 bp):
TAGAGCATCCCTCTTCCTTTGATAAATCTTATCT
Found at i:28319 original size:2 final size:2
Alignment explanation
Indices: 28312--28359 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
28302 TCTTTTACAC
28312 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28354 TA TA TA
1 TA TA TA
28360 CGTACGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.