Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023263.1 Corchorus olitorius cultivar O-4 contig23296, 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: 4344
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:457 original size:22 final size:22
Alignment explanation
Indices: 432--478 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
422 TTTTTAGTTG
*
432 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
454 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
476 AGT
1 AGT
479 TATAAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:468 original size:91 final size:93
Alignment explanation
Indices: 357--539 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 93
347 ACTTTTTAAT
* * *
357 TAAATTAGTAATATCGTAAAAATAAAATA-TGTATAAGGATATTAGATTTAATT-AA-AAAAATA
1 TAAAATAGTAAAATCGTAAAAATAAAATAGT-TATAAGAATATTAGATTTAATTAAATAAAAATA
*
419 GAGTTTTTAGTTGAGTAAAACTATAAAAG
65 GAGTTTTTAGTTGACTAAAACTATAAAAG
*
448 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAG
513 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAACTATAAAA
540 ATTTACACAA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
91 47 0.56
92 3 0.04
93 34 0.40
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:615 original size:31 final size:31
Alignment explanation
Indices: 575--636 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
565 ATATTCGAAA
** *
575 AATAAGGGTATAGTAGGCGATTCAAAAGTTT
1 AATAAGGGTATAACAGACGATTCAAAAGTTT
*
606 AATATGGGTATAACAGACGATTCAAAAGTTT
1 AATAAGGGTATAACAGACGATTCAAAAGTTT
637 TACAAAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (31 bp):
AATAAGGGTATAACAGACGATTCAAAAGTTT
Found at i:3338 original size:198 final size:198
Alignment explanation
Indices: 3090--3561 Score: 782
Period size: 198 Copynumber: 2.4 Consensus size: 198
3080 CATTTACAAT
* *
3090 ACCTTTGTTACTTGGAATATCTCCATCTCTAGCTCCTTTAGTTGAATCTTCATATAGAGAGTCGT
1 ACCTTTGTTACTTGGAATATCTCCATCTCTAGGTCGTTTAGTTGAATCTTCATATAGAGAGTCGT
*
3155 ATCCATCATCGGCATACTGAGAATCATCATTTACACCTTTGTTATTTGGAGCATTATCATGACCT
66 ATCCATCATCAGCATACTGAGAATCATCATTTACACCTTTGTTATTTGGAGCATTATCATGACCT
* * **
3220 CTAGATTCTTTCGAATCTTTATATAAAGAATCATATCCATCATCAGCATACTGGGAATCATCATT
131 CTAGATTCTTTCAAATCTTCATATAAAGAATCATATCCATCATCAGCATACTAAGAATCATCATT
*
3285 TAC
196 CAC
* *
3288 ACCTTTGTTACTTGGAATATCTCCATCTATAGGTCGTTCAGTTGAATCTTCATATAGAGAGTCGT
1 ACCTTTGTTACTTGGAATATCTCCATCTCTAGGTCGTTTAGTTGAATCTTCATATAGAGAGTCGT
* *
3353 ATCCATCATCAGCATATTGAGAATCATCATTTACACCTTTGTTATTTGGAGCATTATCATGACGT
66 ATCCATCATCAGCATACTGAGAATCATCATTTACACCTTTGTTATTTGGAGCATTATCATGACCT
*
3418 CTATATTCTTTCAAATCTTCATATAAAGAATCATATCCATCATCAGCATACTAAGAATCATCATT
131 CTAGATTCTTTCAAATCTTCATATAAAGAATCATATCCATCATCAGCATACTAAGAATCATCATT
3483 CAC
196 CAC
* ** * *
3486 AGCTTTGTTACTTGGAGCATATCCATCTCTAGGTCGTTTAGTTGAATCTTCATATAGAGAGTCAT
1 ACCTTTGTTACTTGGAATATCTCCATCTCTAGGTCGTTTAGTTGAATCTTCATATAGAGAGTCGT
3551 ATCCATCATCA
66 ATCCATCATCA
3562 TGAGAATCAT
Statistics
Matches: 254, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
198 254 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (198 bp):
ACCTTTGTTACTTGGAATATCTCCATCTCTAGGTCGTTTAGTTGAATCTTCATATAGAGAGTCGT
ATCCATCATCAGCATACTGAGAATCATCATTTACACCTTTGTTATTTGGAGCATTATCATGACCT
CTAGATTCTTTCAAATCTTCATATAAAGAATCATATCCATCATCAGCATACTAAGAATCATCATT
CAC
Found at i:3534 original size:99 final size:99
Alignment explanation
Indices: 3090--3561 Score: 507
Period size: 99 Copynumber: 4.8 Consensus size: 99
3080 CATTTACAAT
** * * * *
3090 ACCTTTGTTACTTGGAATATCTCCATCTCTAGCTCCTTTAGTTGAATCTTCATATAGAGAGTCGT
1 ACCTTTGTTACTTGGAGCATATCCATCTCTAGGTCGTTTAGTTGAATCTTCATATAGAGAGTCAT
*
3155 ATCCATCATCGGCATACTGAGAATCATCATTTAC
66 ATCCATCATCAGCATACTGAGAATCATCATTTAC
* * * * *
3189 ACCTTTGTTATTTGGAGCATTAT-CATGACCTCTAGAT--TCTT--TCGAATCTTTATATAAAGA
1 ACCTTTGTTACTTGGAGCA-TATCCAT---CTCTAGGTCGT-TTAGTTGAATCTTCATATAGAGA
* *
3249 ATCATATCCATCATCAGCATACTGGGAATCATCATTTAC
61 GTCATATCCATCATCAGCATACTGAGAATCATCATTTAC
** * * * *
3288 ACCTTTGTTACTTGGAATATCTCCATCTATAGGTCGTTCAGTTGAATCTTCATATAGAGAGTCGT
1 ACCTTTGTTACTTGGAGCATATCCATCTCTAGGTCGTTTAGTTGAATCTTCATATAGAGAGTCAT
*
3353 ATCCATCATCAGCATATTGAGAATCATCATTTAC
66 ATCCATCATCAGCATACTGAGAATCATCATTTAC
* * * *
3387 ACCTTTGTTATTTGGAGCATTAT-CATGACGTCTA--T-ATTCT--TTCAAATCTTCATATAAAG
1 ACCTTTGTTACTTGGAGCA-TATCCAT--C-TCTAGGTCGTT-TAGTT-GAATCTTCATATAGAG
* * *
3446 AATCATATCCATCATCAGCATACTAAGAATCATCATTCAC
60 AGTCATATCCATCATCAGCATACTGAGAATCATCATTTAC
*
3486 AGCTTTGTTACTTGGAGCATATCCATCTCTAGGTCGTTTAGTTGAATCTTCATATAGAGAGTCAT
1 ACCTTTGTTACTTGGAGCATATCCATCTCTAGGTCGTTTAGTTGAATCTTCATATAGAGAGTCAT
3551 ATCCATCATCA
66 ATCCATCATCA
3562 TGAGAATCAT
Statistics
Matches: 305, Mismatches: 46, Indels: 44
0.77 0.12 0.11
Matches are distributed among these distances:
96 10 0.03
97 2 0.01
98 10 0.03
99 262 0.86
100 8 0.03
101 3 0.01
102 10 0.03
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (99 bp):
ACCTTTGTTACTTGGAGCATATCCATCTCTAGGTCGTTTAGTTGAATCTTCATATAGAGAGTCAT
ATCCATCATCAGCATACTGAGAATCATCATTTAC
Found at i:4051 original size:123 final size:123
Alignment explanation
Indices: 3853--4106 Score: 364
Period size: 132 Copynumber: 2.0 Consensus size: 123
3843 ATTGTTTAAA
* * *
3853 CTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATAATT
1 CTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAACCTTATAATT
**
3918 TTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATG
66 TTTTTCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATG
*
3976 CTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATAACCTTATACC
1 CTTTTACAGTTTTACTCAACTAAAAACTCTA-ATTTTATTTAATTAAATCTAATAACCTTATA--
*
4041 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAACTTATATATATTAGAATTTTTTAAATA
63 -A--TT-TTTTT--CATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
4106 T
122 T
4107 ATTTCTTAAA
Statistics
Matches: 115, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
123 30 0.26
124 28 0.24
127 1 0.01
129 2 0.02
130 3 0.03
132 51 0.44
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (123 bp):
CTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAACCTTATAATT
TTTTTCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATATG
Found at i:4129 original size:14 final size:13
Alignment explanation
Indices: 4093--4131 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
4083 TATATATTAG
4093 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
4106 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
4120 AATTTTTTAAAT
1 AATTTTTTAAAT
4132 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:4285 original size:85 final size:86
Alignment explanation
Indices: 4148--4318 Score: 308
Period size: 85 Copynumber: 2.0 Consensus size: 86
4138 ATTTTTTTAG
*
4148 AAATAAACTTTTACAGTTATTCTACTAAAAAAATCTATTTTTATTTAATTAAATTCAATATTATT
1 AAATAAACTTTTACAATTATTCTACTAAAAAAATCTATTTTTATTTAATTAAATTCAATATTATT
4213 ATAAATATTTTATTTTTACCA
66 ATAAATATTTTATTTTTACCA
4234 AAATAAACTTTTACAATTATTCTACT-AAAAAATCTATTTTTATTTAATTAAATTCAATATTATT
1 AAATAAACTTTTACAATTATTCTACTAAAAAAATCTATTTTTATTTAATTAAATTCAATATTATT
* *
4298 ATGACTATTTTATTTTTACCA
66 ATAAATATTTTATTTTTACCA
4319 TTTTAATTTT
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
85 57 0.70
86 25 0.30
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (86 bp):
AAATAAACTTTTACAATTATTCTACTAAAAAAATCTATTTTTATTTAATTAAATTCAATATTATT
ATAAATATTTTATTTTTACCA
Done.