Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021201.1 Corchorus olitorius cultivar O-4 contig21234, 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: 10033
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:4842 original size:22 final size:22
Alignment explanation
Indices: 4807--4853 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4797 TTTTCACTTG
* *
4807 AGTAAAATTATAAAAGTAAAAT
1 AGTAAAATGATAAAAATAAAAT
* *
4829 AGTAAAATGGTAAAAATAGAAT
1 AGTAAAATGATAAAAATAAAAT
4851 AGT
1 AGT
4854 TATAAGAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.26
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:4852 original size:93 final size:93
Alignment explanation
Indices: 4730--4914 Score: 255
Period size: 93 Copynumber: 2.0 Consensus size: 93
4720 ACTTTTCAAT
* * * *
4730 TAAATTAGTAATATCGTATAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATGAAAA-TA
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGAATATTAGATTTAATTAAAT-AAAACTA
* *
4794 GAGTTTTCACTTGAGTAAAATTATAAAAG
65 GAGTTTTCACTTGACTAAAACTATAAAAG
* * *
4823 TAAAATAGTAAAATGGTAAAAATAGAATAGTTATAAGAATATTAGATTTAATTAAATAAAACTAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGAATATTAGATTTAATTAAATAAAACTAG
* *
4888 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTCACTTGACTAAAACTATAAAA
4915 ATTTAAACAA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
92 4 0.05
93 76 0.95
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGAATATTAGATTTAATTAAATAAAACTAG
AGTTTTCACTTGACTAAAACTATAAAAG
Found at i:4985 original size:31 final size:31
Alignment explanation
Indices: 4950--5011 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
4940 ATATTCGAAA
4950 AATAAGGGTATAATAGGCGATTCAAAAGTTT
1 AATAAGGGTATAATAGGCGATTCAAAAGTTT
4981 AATAAGGGTATAATAGGCGATTCAAAAGTTT
1 AATAAGGGTATAATAGGCGATTCAAAAGTTT
5012 TACAAAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (31 bp):
AATAAGGGTATAATAGGCGATTCAAAAGTTT
Found at i:5332 original size:53 final size:53
Alignment explanation
Indices: 5249--5514 Score: 238
Period size: 53 Copynumber: 5.1 Consensus size: 53
5239 TGTTTATTCA
* *
5249 ATTGAACCTATTAAATAAGCACACACACCAAATAATACAAAATACAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
5302 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
** * * * * ** * * *** *** * * *
5355 ATTGAA--TAATTCTATTA-TATA-TTA-TTATTATTA-ATTGTGTTGTTTATTCA
1 ATTGAACCT-ATTAAATAAGCACACATACCAAATAATACAAAATG-CAATGA-ACT
* * *
5405 ATTGAACCTATTAAATACGCACACATACTAAATAATACAAAATGCAATGAATT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
*
5458 ATTGAACCTATTAAATACGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
5511 ATTG
1 ATTG
5515 GATTTAAAGA
Statistics
Matches: 161, Mismatches: 43, Indels: 18
0.73 0.19 0.08
Matches are distributed among these distances:
48 3 0.02
49 7 0.04
50 9 0.06
51 8 0.05
52 9 0.06
53 114 0.71
54 8 0.05
55 3 0.02
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.30
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:5487 original size:156 final size:159
Alignment explanation
Indices: 5200--5514 Score: 555
Period size: 156 Copynumber: 2.0 Consensus size: 159
5190 ATTATAAAAT
5200 AATAATTCTAATATATATTATTATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAAT
1 AATAATTCTAATATATATTATTATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAAT
5265 AAGCACACACACCAAATAATACAAAATACAATGAACTATTGAACCTATTAAATAAGCACACATAC
66 AAGCACACACACCAAATAATACAAAATACAATGAACTATTGAACCTATTAAATAAGCACACATAC
5330 CAAATAATACAAAATGCAATGAACTATTG
131 CAAATAATACAAAATGCAATGAACTATTG
5359 AATAATTCT-AT-TATA-TATTATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAAT
1 AATAATTCTAATATATATTATTATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAAT
* * * * * *
5421 ACGCACACATACTAAATAATACAAAATGCAATGAATTATTGAACCTATTAAATACGCACACATAC
66 AAGCACACACACCAAATAATACAAAATACAATGAACTATTGAACCTATTAAATAAGCACACATAC
5486 CAAATAATACAAAATGCAATGAACTATTG
131 CAAATAATACAAAATGCAATGAACTATTG
5515 GATTTAAAGA
Statistics
Matches: 150, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
156 135 0.90
157 4 0.03
158 2 0.01
159 9 0.06
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (159 bp):
AATAATTCTAATATATATTATTATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAAT
AAGCACACACACCAAATAATACAAAATACAATGAACTATTGAACCTATTAAATAAGCACACATAC
CAAATAATACAAAATGCAATGAACTATTG
Found at i:8194 original size:7 final size:7
Alignment explanation
Indices: 8182--8210 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
8172 TTAAGGTTTT
8182 AAAGTCA
1 AAAGTCA
8189 AAAGTCA
1 AAAGTCA
8196 AAAGTCA
1 AAAGTCA
8203 AAAGTCA
1 AAAGTCA
8210 A
1 A
8211 TCCTTTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAGTCA
Done.