Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014296.1 Corchorus olitorius cultivar O-4 contig14329, 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: 6725
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:718 original size:36 final size:35
Alignment explanation
Indices: 668--736 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 35
658 TGGCTGAGTA
*
668 TTGGTTAGATAATATAGATATTTCAAGGAGTCTAT
1 TTGGTCAGATAATATAGATATTTCAAGGAGTCTAT
703 TTGGTCAGATGAATATAGATATTTCAAGGAGTCT
1 TTGGTCAGAT-AATATAGATATTTCAAGGAGTCT
737 TTATGCCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 9 0.28
36 23 0.72
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (35 bp):
TTGGTCAGATAATATAGATATTTCAAGGAGTCTAT
Found at i:3279 original size:18 final size:19
Alignment explanation
Indices: 3252--3302 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
3242 CAAGATAATG
*
3252 CTTATCTTACTATCTTA-T
1 CTTATATTACTATCTTATT
3270 CTTATATTACTATCTTATT
1 CTTATATTACTATCTTATT
*
3289 ATTACTATTACTAT
1 CTTA-TATTACTAT
3303 TATTACTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 16 0.55
19 4 0.14
20 9 0.31
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (19 bp):
CTTATATTACTATCTTATT
Found at i:3283 original size:13 final size:14
Alignment explanation
Indices: 3267--3311 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
3257 CTTACTATCT
3267 TATCTTA-TATTAC
1 TATCTTATTATTAC
3280 TATCTTATTATTAC
1 TATCTTATTATTAC
3294 TAT-TACTATTATTAC
1 TATCT--TATTATTAC
3309 TAT
1 TAT
3312 TACTATTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.28
14 9 0.31
15 12 0.41
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (14 bp):
TATCTTATTATTAC
Found at i:3299 original size:6 final size:6
Alignment explanation
Indices: 3274--3322 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
3264 TCTTATCTTA
*
3274 TATTAC TATCTTAT TATTAC TATTAC TA-T-- TATTAC TATTAC TATTAC
1 TATTAC TA--TTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC
3321 TA
1 TA
3323 CTATATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 1 0.03
6 27 0.75
8 5 0.14
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAC
Found at i:3305 original size:15 final size:15
Alignment explanation
Indices: 3285--3326 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
3275 ATTACTATCT
3285 TATTATTACTATTAC
1 TATTATTACTATTAC
3300 TATTATTACTATTAC
1 TATTATTACTATTAC
*
3315 TATTACTACTAT
1 TATTATTACTAT
3327 ATATAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATTACTATTAC
Found at i:6249 original size:31 final size:31
Alignment explanation
Indices: 6214--6348 Score: 143
Period size: 31 Copynumber: 4.5 Consensus size: 31
6204 ATTGAACTAC
*
6214 ATGAACTGTATGCAATAACAATAGACCTAAA
1 ATGAACTGTATGCAATAACGATAGACCTAAA
6245 ATGAACTGTATGCAATAACGATAGACCT---
1 ATGAACTGTATGCAATAACGATAGACCTAAA
* *
6273 A-GAACTATATGCAATAATGATAGACCTAAA
1 ATGAACTGTATGCAATAACGATAGACCTAAA
** ** * *
6303 ATGAACTACATGTTATGACGATAAACCTAAAA
1 ATGAACTGTATGCAATAACGATAGACCT-AAA
*
6335 ATGAACTATATGCA
1 ATGAACTGTATGCA
6349 CCAGCCACAC
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
27 24 0.28
28 1 0.01
30 1 0.01
31 47 0.54
32 14 0.16
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (31 bp):
ATGAACTGTATGCAATAACGATAGACCTAAA
Found at i:6324 original size:58 final size:58
Alignment explanation
Indices: 6216--6331 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 58
6206 TGAACTACAT
* ** *
6216 GAACTGTATGCAATAACAATAGACCTAAAATGAACTGTATGCAATAACGATAGACCTA
1 GAACTATATGCAATAACAATAGACCTAAAATGAACTACATGCAATAACGATAAACCTA
** ** *
6274 GAACTATATGCAATAATGATAGACCTAAAATGAACTACATGTTATGACGATAAACCTA
1 GAACTATATGCAATAACAATAGACCTAAAATGAACTACATGCAATAACGATAAACCTA
6332 AAAATGAACT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (58 bp):
GAACTATATGCAATAACAATAGACCTAAAATGAACTACATGCAATAACGATAAACCTA
Done.