Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014596.1 Corchorus olitorius cultivar O-4 contig14629, 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: 31358
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:15452 original size:29 final size:30
Alignment explanation
Indices: 15394--15454 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
15384 ATTCTAATTA
* *
15394 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
15424 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
15453 AT
1 AT
15455 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:25362 original size:21 final size:21
Alignment explanation
Indices: 25338--25403 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 21
25328 TCCACGATTT
25338 AATTCAAGATTCAAACACTTA
1 AATTCAAGATTCAAACACTTA
* **** *
25359 AATT--GGATTTTCGCACTCA
1 AATTCAAGATTCAAACACTTA
25378 TAATTCAAGATTCAAACACTTA
1 -AATTCAAGATTCAAACACTTA
25400 AATT
1 AATT
25404 GGATTTTCGC
Statistics
Matches: 30, Mismatches: 12, Indels: 6
0.62 0.25 0.12
Matches are distributed among these distances:
19 9 0.30
20 4 0.13
21 8 0.27
22 9 0.30
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (21 bp):
AATTCAAGATTCAAACACTTA
Found at i:25394 original size:41 final size:41
Alignment explanation
Indices: 25337--25419 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
25327 CTCCACGATT
25337 TAATTCAAGATTCAAACACTTAAATTGGATTTTCGCACTCA
1 TAATTCAAGATTCAAACACTTAAATTGGATTTTCGCACTCA
25378 TAATTCAAGATTCAAACACTTAAATTGGATTTTCGCACTCA
1 TAATTCAAGATTCAAACACTTAAATTGGATTTTCGCACTCA
25419 T
1 T
25420 TTAGTATGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (41 bp):
TAATTCAAGATTCAAACACTTAAATTGGATTTTCGCACTCA
Found at i:26316 original size:107 final size:104
Alignment explanation
Indices: 26084--26342 Score: 394
Period size: 107 Copynumber: 2.5 Consensus size: 104
26074 AATTTTTCTA
* **
26084 ACCCTTAAAATAAAATTTTAATTTTAATTTGGGCTAAACTTAGT-AAATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
*
26148 TTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* *
26187 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
26252 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
* *
26294 ACCCTTAAAATAAAAATAAAATTTTAATTTTAGGTTAAACTTAGTGAAA
1 ACCCTTAAAATAAAAATAAAATTTTAA-TTTGGGCTAAACTTAGTGAAA
26343 CTAAGGCTAA
Statistics
Matches: 142, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
103 27 0.19
104 14 0.10
105 38 0.27
107 60 0.42
108 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:30076 original size:22 final size:22
Alignment explanation
Indices: 30048--30092 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
30038 TTCTTGTTCC
30048 TCATTGTTAACTCAAAAAGACT
1 TCATTGTTAACTCAAAAAGACT
30070 TCATTGTTAACTCAAAAAGACT
1 TCATTGTTAACTCAAAAAGACT
30092 T
1 T
30093 TGGAAAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (22 bp):
TCATTGTTAACTCAAAAAGACT
Found at i:30853 original size:2 final size:2
Alignment explanation
Indices: 30841--30872 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
30831 ATATCTATCC
*
30841 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30873 TTGGGTACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30856 original size:12 final size:12
Alignment explanation
Indices: 30830--30870 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
30820 CTTCCTTGTG
**
30830 TATATCTATCCA
1 TATATCTATATA
30842 TATATCTATATA
1 TATATCTATATA
*
30854 TATATATATATA
1 TATATCTATATA
30866 TATAT
1 TATAT
30871 ATTTGGGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (12 bp):
TATATCTATATA
Done.