Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016183.1 Corchorus olitorius cultivar O-4 contig16216, 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: 53124
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:54 original size:29 final size:27
Alignment explanation
Indices: 17--71 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
7 AAAAAATAAA
17 AATAAAAAGCCAGAAAACGAATAAAAAAG
1 AATAAAAAG-CAGAAAA-GAATAAAAAAG
**
46 AATAAAAAGGTGAAAAGAATAAAAAA
1 AATAAAAAGCAGAAAAGAATAAAAAA
72 TAAAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.42
28 5 0.21
29 9 0.38
ACGTcount: A:0.71, C:0.05, G:0.15, T:0.09
Consensus pattern (27 bp):
AATAAAAAGCAGAAAAGAATAAAAAAG
Found at i:78 original size:17 final size:17
Alignment explanation
Indices: 36--78 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
26 CCAGAAAACG
36 AATAAAAAAGAATAAAA
1 AATAAAAAAGAATAAAA
* *
53 AGGT-GAAAAGAATAAAA
1 A-ATAAAAAAGAATAAAA
70 AATAAAAAA
1 AATAAAAAA
79 TAAAAAAGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 4
0.71 0.14 0.14
Matches are distributed among these distances:
16 1 0.05
17 18 0.90
18 1 0.05
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
AATAAAAAAGAATAAAA
Found at i:82 original size:14 final size:15
Alignment explanation
Indices: 41--85 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
31 AAACGAATAA
*
41 AAAAGAATAAAAAGGT
1 AAAAGAATAAAAA-AT
57 GAAAAGAATAAAAAAT
1 -AAAAGAATAAAAAAT
73 AAAA-AATAAAAAA
1 AAAAGAATAAAAAA
86 GTTAAAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 4 0.15
16 1 0.04
17 13 0.48
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (15 bp):
AAAAGAATAAAAAAT
Found at i:5484 original size:20 final size:19
Alignment explanation
Indices: 5444--5481 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5434 TTCTTGAAAA
* *
5444 AAAATAGTCACGTGGCATT
1 AAAATAGCCACGTGGAATT
5463 AAAATAGCCACGTGGAATT
1 AAAATAGCCACGTGGAATT
5482 TAATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (19 bp):
AAAATAGCCACGTGGAATT
Found at i:23934 original size:13 final size:13
Alignment explanation
Indices: 23916--23941 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23906 GGAGTTCATT
23916 TTATACTCTATTC
1 TTATACTCTATTC
23929 TTATACTCTATTC
1 TTATACTCTATTC
23942 GATTTCTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATACTCTATTC
Found at i:38639 original size:57 final size:57
Alignment explanation
Indices: 38512--38625 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 57
38502 CACAATTCTT
* * * * *
38512 AATTCTATCCTTAAGTAACCTCATGTTTTCACAATTCTATCCAAATTGATGTCCCGT
1 AATTCTAGCCTTAAGTAACCTCATGTTTTCACAATTCTATCCAAACTAATGGCCCGG
* * *
38569 AATTCTATCCTTAAGTAACCTCGTGTTTTCACAGTTCTATCCAAACTAATGGCCCGG
1 AATTCTAGCCTTAAGTAACCTCATGTTTTCACAATTCTATCCAAACTAATGGCCCGG
38626 GTTTCGTGCC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36
Consensus pattern (57 bp):
AATTCTAGCCTTAAGTAACCTCATGTTTTCACAATTCTATCCAAACTAATGGCCCGG
Found at i:50044 original size:228 final size:228
Alignment explanation
Indices: 49647--50106 Score: 850
Period size: 228 Copynumber: 2.0 Consensus size: 228
49637 AATCTATATC
49647 TATATCTATACTATATTAAAAAATACATTCTTTTGTAAAACTTTTGAATCGCCCATTATACCCTT
1 TATATCTATACTATATTAAAAAATACATTCTTTTGTAAAACTTTTGAATCGCCCATTATACCCTT
* *
49712 ATTTCTTGAATATATTTCTTAAATGTTATTACTTAAACAATTATAGTTTTATTCTACTAAAAACT
66 ATTTCTTGAATATATTTCTTAAATGTCATTACTTAAACAATTATAGATTTATTCTACTAAAAACT
*
49777 TTATTTTTATTTAATTAAATCTAATATATTTATAATTACTTTATTTTTACCATTTTACTATTTTT
131 CTATTTTTATTTAATTAAATCTAATATATTTATAATTACTTTATTTTTACCATTTTACTATTTTT
49842 CATTAAAAACTTGGATATATTAAAAAAATTTAA
196 CATTAAAAACTTGGATATATTAAAAAAATTTAA
*
49875 TATATCTATACTATATTAAAAAATACGTTCTTTTGTAAAACTTTTGAATCGCCCATTATACCCTT
1 TATATCTATACTATATTAAAAAATACATTCTTTTGTAAAACTTTTGAATCGCCCATTATACCCTT
*
49940 ATTT-TTCGAATATATTTCTTAAATGTCATTACTTAAACAGTTATAGATTTATTCTACTAAAAAC
66 ATTTCTT-GAATATATTTCTTAAATGTCATTACTTAAACAATTATAGATTTATTCTACTAAAAAC
*
50004 TCTATTTTTATTTAATTAAATCTAATATCTTTATAATTACTTTATTTTTACCATTTTACTATTTT
130 TCTATTTTTATTTAATTAAATCTAATATATTTATAATTACTTTATTTTTACCATTTTACTATTTT
50069 TCATTAAAAACTTGGATATATTAAAAAAATTTAA
195 TCATTAAAAACTTGGATATATTAAAAAAATTTAA
50103 TATA
1 TATA
50107 CAGTTTTATT
Statistics
Matches: 225, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
227 2 0.01
228 223 0.99
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (228 bp):
TATATCTATACTATATTAAAAAATACATTCTTTTGTAAAACTTTTGAATCGCCCATTATACCCTT
ATTTCTTGAATATATTTCTTAAATGTCATTACTTAAACAATTATAGATTTATTCTACTAAAAACT
CTATTTTTATTTAATTAAATCTAATATATTTATAATTACTTTATTTTTACCATTTTACTATTTTT
CATTAAAAACTTGGATATATTAAAAAAATTTAA
Found at i:51837 original size:26 final size:26
Alignment explanation
Indices: 51783--51831 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
51773 ATATATTAGA
*
51783 ATTTTTAAAATATATTCTTTTACAAT
1 ATTTTTAAAATATAATCTTTTACAAT
51809 ATTTTTAGAAATA-AAT-TTTTACA
1 ATTTTTA-AAATATAATCTTTTACA
51832 GTTATTCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 9 0.43
27 5 0.24
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (26 bp):
ATTTTTAAAATATAATCTTTTACAAT
Done.