Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012875.1 Corchorus olitorius cultivar O-4 contig12908, 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: 14729
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:487 original size:9 final size:9
Alignment explanation
Indices: 473--498 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
463 AATAAACACT
473 AAAACAAAC
1 AAAACAAAC
482 AAAACAAAC
1 AAAACAAAC
491 AAAACAAA
1 AAAACAAA
499 GCAACTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAACAAAC
Found at i:5018 original size:46 final size:46
Alignment explanation
Indices: 4962--5051 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
4952 TGACTTCATA
4962 TGCTAAAGTAAAAGGCTAATGTGACAATAGGACATGAGAATGTGGC
1 TGCTAAAGTAAAAGGCTAATGTGACAATAGGACATGAGAATGTGGC
*
5008 TGCTAAAGTAAAAGGCTAATGTGATAATAGGACATGAGAATGTG
1 TGCTAAAGTAAAAGGCTAATGTGACAATAGGACATGAGAATGTG
5052 ACTTAATCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (46 bp):
TGCTAAAGTAAAAGGCTAATGTGACAATAGGACATGAGAATGTGGC
Found at i:5331 original size:52 final size:52
Alignment explanation
Indices: 5295--5503 Score: 390
Period size: 52 Copynumber: 4.1 Consensus size: 52
5285 TCTAATATAT
5295 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA-TCT-
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
5345 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
5397 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
5449 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA-TCT-
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
5499 TAAAA
1 TAAAA
5504 AAAGGTAATG
Statistics
Matches: 157, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
50 52 0.33
51 6 0.04
52 99 0.63
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (52 bp):
TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
Found at i:5443 original size:102 final size:102
Alignment explanation
Indices: 5294--5503 Score: 388
Period size: 102 Copynumber: 2.1 Consensus size: 102
5284 CTCTAATATA
5294 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA-TCT-TAAAAGGACCGT
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTATAAAAGGACCGT
5357 CTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTC
66 CTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA-TC
5395 TATAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTATAAAAGGACCG
1 T-TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTATAAAAGGACCG
5460 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
65 TCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
5498 TTAAAA
1 TTAAAA
5504 AAAGGTAATG
Statistics
Matches: 106, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
101 1 0.01
102 52 0.49
103 6 0.06
104 47 0.44
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (102 bp):
TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTATAAAAGGACCGT
CTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
Found at i:7029 original size:15 final size:17
Alignment explanation
Indices: 7011--7048 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
7001 ATTTGATATT
7011 TTTTTTGGA-TGA-TGA
1 TTTTTTGGATTGATTGA
7026 TTTTTT-GATTGATTGA
1 TTTTTTGGATTGATTGA
7042 TTTTTTG
1 TTTTTTG
7049 AATTTCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 9 0.45
16 9 0.45
ACGTcount: A:0.16, C:0.00, G:0.21, T:0.63
Consensus pattern (17 bp):
TTTTTTGGATTGATTGA
Found at i:7042 original size:16 final size:14
Alignment explanation
Indices: 7011--7049 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
7001 ATTTGATATT
7011 TTTTTTGGATGATGA
1 TTTTTT-GATGATGA
7026 TTTTTTGATTGATTGA
1 TTTTTTGA-TGA-TGA
7042 TTTTTTGA
1 TTTTTTGA
7050 ATTTCTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 9 0.41
16 11 0.50
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.62
Consensus pattern (14 bp):
TTTTTTGATGATGA
Found at i:9471 original size:23 final size:23
Alignment explanation
Indices: 9433--9495 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
9423 TTGTTTTGTG
* *
9433 TTTTGCGTCGA-AAAAAAAATATAT
1 TTTTGCGTC-ATAAAAAAAAGA-GT
9457 TTTTGCGTCATAAAAAAAAGAGT
1 TTTTGCGTCATAAAAAAAAGAGT
9480 TTTTGCGTCATAAAAA
1 TTTTGCGTCATAAAAA
9496 GAAAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (23 bp):
TTTTGCGTCATAAAAAAAAGAGT
Found at i:13117 original size:15 final size:14
Alignment explanation
Indices: 13097--13126 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
13087 ATCTTTTTAA
13097 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
13112 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
13126 T
1 T
13127 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Done.