Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013072.1 Corchorus olitorius cultivar O-4 contig13105, 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: 13181
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:686 original size:29 final size:30
Alignment explanation
Indices: 630--687 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
620 ACCCACTTAT
***
630 ACCAAATTAGACCAATTTTTTTTTATAATA
1 ACCAAATTAGACCAATTTTGAATTATAATA
660 ACCAAATTAGACC-ATTTTGAATTATAAT
1 ACCAAATTAGACCAATTTTGAATTATAAT
688 GATATATCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (30 bp):
ACCAAATTAGACCAATTTTGAATTATAATA
Found at i:4183 original size:261 final size:258
Alignment explanation
Indices: 3466--4198 Score: 1148
Period size: 260 Copynumber: 2.8 Consensus size: 258
3456 GCCTGATTTG
*
3466 CTTGAGTATATAATTTCGT-AA-ATATAACCATAAAAACCATAA-ATAATACTATAAATCGTACC
1 CTTGAGTATATAATTTCGTAAATATATAACCATAAAAACCATAATATAATACTATAAATCATACC
* * * *
3528 TTAAACTGATTACCATGATTTTCTTTTTCTTTTAATAGAGGTCGTCGTATGATTGCTGCTCAATA
66 TTAAATTGATTACCATGATTTTCTTTTTCTTTTAATAGAGGTTGTCATATGATTGTTGCTCAATA
*
3593 TTATTTTATTCAAGATCTCCGGTATTTGATAATCATATTAAAATCCGATTAATTTGAAATTGAGT
131 CTATTTTATTCAAGATCTCCGGTATTTGATAATCATATTAAAATCCGATTAATTTGAAATTGAGT
* *
3658 TGCATCGAATTTAACCAGATTTGAGATTCGTTTCTGTTTCTGTCCATTACTGATTTGCTTGAGC
196 TGCATCG-ATTTAACCAGATTTGAGATTCGTTTCTCTTTCTGCCCATTACTGATTTGCTTGAGC
* *
3722 CTTGAGTATATAATTTCATAAATATATAACCATAAAAACCATAGATATAATACTAGAAATCATAC
1 CTTGAGTATATAATTTCGTAAATATATAACCATAAAAACCATA-ATATAATACTATAAATCATAC
*
3787 CTTAAATTGATTACCATGATTTTCCTTTTCTTTTAATAGAGGTTGTCATATGATTGTTGCTCAAT
65 CTTAAATTGATTACCATGATTTTCTTTTTCTTTTAATAGAGGTTGTCATATGATTGTTGCTCAAT
* ** * *
3852 ACTATTTTATTCAAGATGTCTAGTATTTGATAATCGTATTAAAATCCAATTAATTTGAAATTGAG
130 ACTATTTTATTCAAGATCTCCGGTATTTGATAATCATATTAAAATCCGATTAATTTGAAATTGAG
* *
3917 TTGCATCAGATTTAACCAGATTTGAGATTCGTTTCTCTTTTTGCCCATTGCTGATTTGCTTGAGC
195 TTGCATC-GATTTAACCAGATTTGAGATTCGTTTCTCTTTCTGCCCATTACTGATTTGCTTGAGC
3982 CTTGAGTATATAATTTCGTAAATATATAACCATAAAAACCATATATATAATACTATAAATCATAC
1 CTTGAGTATATAATTTCGTAAATATATAACCATAAAAACCATA-ATATAATACTATAAATCATAC
4047 CTTAAAATTGATTACCATGATTTTCTTTTTCTTTTAATAGAGGTTGTCATATGATTGTTGCTCAA
65 CTT-AAATTGATTACCATGATTTTCTTTTTCTTTTAATAGAGGTTGTCATATGATTGTTGCTCAA
* * * * ** **
4112 CACTATTTTATTCAACATTTCCGGTATTTGATAACCATATTAAAATTTGATTAATTCAAAATTGA
129 TACTATTTTATTCAAGATCTCCGGTATTTGATAATCATATTAAAATCCGATTAATTTGAAATTGA
*
4177 GTTGCATCGGACTTAACCAGAT
194 GTTGCATC-GATTTAACCAGAT
4199 AAAACACTTC
Statistics
Matches: 435, Mismatches: 36, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
256 18 0.04
257 2 0.00
258 20 0.05
259 1 0.00
260 260 0.60
261 134 0.31
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (258 bp):
CTTGAGTATATAATTTCGTAAATATATAACCATAAAAACCATAATATAATACTATAAATCATACC
TTAAATTGATTACCATGATTTTCTTTTTCTTTTAATAGAGGTTGTCATATGATTGTTGCTCAATA
CTATTTTATTCAAGATCTCCGGTATTTGATAATCATATTAAAATCCGATTAATTTGAAATTGAGT
TGCATCGATTTAACCAGATTTGAGATTCGTTTCTCTTTCTGCCCATTACTGATTTGCTTGAGC
Found at i:8723 original size:27 final size:27
Alignment explanation
Indices: 8655--8724 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
8645 AGGCCTGCTC
* * *
8655 TGGTTCTGTCCAATTCAGGGAAGGCCT
1 TGGTTGTGTCCAATTCAGGAAAGGCAT
* * * *
8682 TGATGGTATCAAATTCAGGAAAGGCAT
1 TGGTTGTGTCCAATTCAGGAAAGGCAT
8709 TGGTTGTGTCCAATTC
1 TGGTTGTGTCCAATTC
8725 TAGCAAGTCT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (27 bp):
TGGTTGTGTCCAATTCAGGAAAGGCAT
Done.