Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021710.1 Corchorus olitorius cultivar O-4 contig21743, 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: 16685
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:459 original size:2 final size:2
Alignment explanation
Indices: 452--495 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
442 ATAGTAAGGA
452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
493 AT A
1 AT A
496 CAAGCGGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3244 original size:19 final size:19
Alignment explanation
Indices: 3204--3240 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3194 AATTTTTAAG
3204 TAAAAATTTAATATATAAA
1 TAAAAATTTAATATATAAA
3223 TAAAAATTTAATAT-TAAA
1 TAAAAATTTAATATATAAA
3241 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATTTAATATATAAA
Found at i:14565 original size:39 final size:39
Alignment explanation
Indices: 14511--14588 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
14501 CACTGCAGTC
*
14511 AAGAATGGTGATAGAAAGAAACCCATTGAGGAAGAAGAG
1 AAGAAAGGTGATAGAAAGAAACCCATTGAGGAAGAAGAG
14550 AAGAAAGGTGATAGAAAGAAACCCATTGAGGAAGAAGAG
1 AAGAAAGGTGATAGAAAGAAACCCATTGAGGAAGAAGAG
14589 GTAATCATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.50, C:0.08, G:0.31, T:0.12
Consensus pattern (39 bp):
AAGAAAGGTGATAGAAAGAAACCCATTGAGGAAGAAGAG
Found at i:15523 original size:2 final size:2
Alignment explanation
Indices: 15516--15542 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15506 AACAATACTA
15516 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15543 AACCAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16007 original size:30 final size:30
Alignment explanation
Indices: 15944--16034 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
15934 TTTTGTAAAA
* * *
15944 CTTTTGAATCGACTATTATATTCATATTTTT
1 CTTTTAAATCGACTATTATATCCTTA-TTTT
15975 CTTTTAAATCGACTATTATATCCTTATTTT
1 CTTTTAAATCGACTATTATATCCTTATTTT
* *
16005 CTTTTAAATCGACCATTATACCCTTATTTT
1 CTTTTAAATCGACTATTATATCCTTATTTT
16035 TCGAATATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 32 0.58
31 23 0.42
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.52
Consensus pattern (30 bp):
CTTTTAAATCGACTATTATATCCTTATTTT
Found at i:16204 original size:85 final size:85
Alignment explanation
Indices: 16104--16278 Score: 264
Period size: 85 Copynumber: 2.1 Consensus size: 85
16094 TCTATTTTTG
16104 TTTAATTAAATCTAATCTCTTTATAACTATTTTG-TTTTTACC-ATTTTACTATTTTAATTAAAA
1 TTTAATTAAATCTAATCTCTTTATAACTA-TTTGATTTTTACCAATTTTACTATTTTAATT-AAA
* *
16167 AAACTTAGATATGTTATAAATT
64 AAACTTAGATATATTAGAAATT
* *
16189 TTTAATTAAATCTAATTTCTTTATAACTATTTGATTTTTACCAATTTTACTATTTTAATTACAAA
1 TTTAATTAAATCTAATCTCTTTATAACTATTTGATTTTTACCAATTTTACTATTTTAATTAAAAA
* *
16254 ACTTAGGTATATTAGAATTT
66 ACTTAGATATATTAGAAATT
16274 TTTAA
1 TTTAA
16279 ATATATTTCT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
84 4 0.05
85 61 0.74
86 17 0.21
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (85 bp):
TTTAATTAAATCTAATCTCTTTATAACTATTTGATTTTTACCAATTTTACTATTTTAATTAAAAA
ACTTAGATATATTAGAAATT
Found at i:16545 original size:82 final size:84
Alignment explanation
Indices: 16445--16601 Score: 239
Period size: 82 Copynumber: 1.9 Consensus size: 84
16435 ACACTTTTTG
* *
16445 ATCTTTTTATAACTATTTTATTTTTACCAGTT-TACTATTTTAATT-AAAAAATT-GATATATTA
1 ATCTCTTTATAACTATTTTATTTTTACCA-TTAAACTATTTTAATTGAAAAAATTAGATATATTA
16507 GAATTTTTTAATTAAATCTA
65 GAATTTTTTAATTAAATCTA
* * *
16527 ATCTCTTTATAACTATTTTATTTTTACCATTAAACTATTTTAATTGCAAAACTTAGATATATTAT
1 ATCTCTTTATAACTATTTTATTTTTACCATTAAACTATTTTAATTGAAAAAATTAGATATATTAG
16592 AATTTTTTAA
66 AATTTTTTAA
16602 ATATATATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
81 2 0.03
82 40 0.60
83 6 0.09
84 19 0.28
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (84 bp):
ATCTCTTTATAACTATTTTATTTTTACCATTAAACTATTTTAATTGAAAAAATTAGATATATTAG
AATTTTTTAATTAAATCTA
Done.