Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009690.1 Corchorus capsularis cultivar CVL-1 contig09711, 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: 52980
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:19717 original size:7 final size:7
Alignment explanation
Indices: 19705--19736 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
19695 ATCAATAGAT
19705 TCATCAA
1 TCATCAA
19712 TCATCAA
1 TCATCAA
19719 TCATCAA
1 TCATCAA
19726 TCATCAA
1 TCATCAA
19733 TCAT
1 TCAT
19737 ACATAGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCAA
Found at i:28092 original size:182 final size:182
Alignment explanation
Indices: 27889--28250 Score: 724
Period size: 182 Copynumber: 2.0 Consensus size: 182
27879 TTATATCCTT
27889 ATTTTTCAAATATATTTCTTAAATACCATTATTTAAATTTTTATAGTTTTACTCAACTAAAAACT
1 ATTTTTCAAATATATTTCTTAAATACCATTATTTAAATTTTTATAGTTTTACTCAACTAAAAACT
27954 CTATTTTTATTTAATTAAATCTAATATCCTTATAAGTACTATTTTATTTTTACCATTTTACTATT
66 CTATTTTTATTTAATTAAATCTAATATCCTTATAAGTACTATTTTATTTTTACCATTTTACTATT
28019 TTAATTAAAAAATACTTTTATAGTTTTACGCAATAAACTTTTGCAGTTATAA
131 TTAATTAAAAAATACTTTTATAGTTTTACGCAATAAACTTTTGCAGTTATAA
28071 ATTTTTCAAATATATTTCTTAAATACCATTATTTAAATTTTTATAGTTTTACTCAACTAAAAACT
1 ATTTTTCAAATATATTTCTTAAATACCATTATTTAAATTTTTATAGTTTTACTCAACTAAAAACT
28136 CTATTTTTATTTAATTAAATCTAATATCCTTATAAGTACTATTTTATTTTTACCATTTTACTATT
66 CTATTTTTATTTAATTAAATCTAATATCCTTATAAGTACTATTTTATTTTTACCATTTTACTATT
28201 TTAATTAAAAAATACTTTTATAGTTTTACGCAATAAACTTTTGCAGTTAT
131 TTAATTAAAAAATACTTTTATAGTTTTACGCAATAAACTTTTGCAGTTAT
28251 TCTACTAAAA
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 180 1.00
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.49
Consensus pattern (182 bp):
ATTTTTCAAATATATTTCTTAAATACCATTATTTAAATTTTTATAGTTTTACTCAACTAAAAACT
CTATTTTTATTTAATTAAATCTAATATCCTTATAAGTACTATTTTATTTTTACCATTTTACTATT
TTAATTAAAAAATACTTTTATAGTTTTACGCAATAAACTTTTGCAGTTATAA
Found at i:28295 original size:182 final size:182
Alignment explanation
Indices: 27896--28297 Score: 621
Period size: 182 Copynumber: 2.2 Consensus size: 182
27886 CTTATTTTTC
* * *
27896 AAATATATTTCTTAAATACCATTATTTAAATTTTTATAGTTTTACTCAACTAAAAACTCTATTTT
1 AAATATATTTCTTAAATACAATAATTCAAATTTTTATAGTTTTACTCAACTAAAAACTCTATTTT
27961 TATTTAATTAAATCTAATATCCTTATAAGTACTATTTTATTTTTACCATTTTACTATTTTAATTA
66 TATTTAATTAAATCTAATATCCTTATAAGTACTATTTTATTTTTACCATTTTACTATTTTAATTA
** **
28026 AAAAATACTTTTATAGTTTTACGCAATAAACTTTTGCAGTTATAAATTTTTC
131 AAAAATACTTTTATAGTTTTACGCAATAAACTTTTGCAGTTATAAATACTAA
* * *
28078 AAATATATTTCTTAAATACCATTATTTAAATTTTTATAGTTTTACTCAACTAAAAACTCTATTTT
1 AAATATATTTCTTAAATACAATAATTCAAATTTTTATAGTTTTACTCAACTAAAAACTCTATTTT
28143 TATTTAATTAAATCTAATATCCTTATAAGTACTATTTTATTTTTACCATTTTACTATTTTAATTA
66 TATTTAATTAAATCTAATATCCTTATAAGTACTATTTTATTTTTACCATTTTACTATTTTAATTA
**
28208 AAAAATACTTTTATAGTTTTACGCAATAAACTTTTGCAGTTAT-TCTACTAA
131 AAAAATACTTTTATAGTTTTACGCAATAAACTTTTGCAGTTATAAATACTAA
* **
28259 AAACTCTATTT-TTATTTA-AATAAATTCAATATTTTTATA
1 AAA-TATATTTCTTAAATACAAT-AATTCAA-ATTTTTATA
28298 AATTTTATCA
Statistics
Matches: 205, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
180 2 0.01
181 15 0.07
182 188 0.92
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (182 bp):
AAATATATTTCTTAAATACAATAATTCAAATTTTTATAGTTTTACTCAACTAAAAACTCTATTTT
TATTTAATTAAATCTAATATCCTTATAAGTACTATTTTATTTTTACCATTTTACTATTTTAATTA
AAAAATACTTTTATAGTTTTACGCAATAAACTTTTGCAGTTATAAATACTAA
Found at i:36031 original size:31 final size:31
Alignment explanation
Indices: 35996--36060 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
35986 AACTGAACAA
35996 ACTCAAACATCCAAGATCTAAAGATCTAGAG
1 ACTCAAACATCCAAGATCTAAAGATCTAGAG
* *
36027 ACTCAAACATCCAAGATCTAAAGATTTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTAGAG
36058 ACT
1 ACT
36061 AGTAACCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTAGAG
Found at i:42133 original size:5 final size:5
Alignment explanation
Indices: 42123--42150 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
42113 ATTAAAGAAC
42123 ATGAA ATGAA ATGAA ATGAA ATGAA ATG
1 ATGAA ATGAA ATGAA ATGAA ATGAA ATG
42151 CTACACACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (5 bp):
ATGAA
Found at i:51085 original size:2 final size:2
Alignment explanation
Indices: 51078--51106 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
51068 TTTTATAGCA
51078 AT 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 AT A
51107 CTAGCTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.