Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007360.1 Corchorus olitorius cultivar O-4 contig07385, 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: 2210
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:627 original size:60 final size:60
Alignment explanation
Indices: 533--694 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
523 GCTAATTGCT
*
533 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGG-CTTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CAAAAATGCTCAAATAAGGGTC-TGATCTTTTAATTTGGC
* *
593 CAAATAAGGGCCTAACGTTATCGAAAATGGTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
*
653 CAAATAAGGGCCTAACGTTATAAAAAATGCTCAAATAAGGGT
1 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGT
695 TTGGCGTCAG
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
60 93 0.98
61 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
Found at i:631 original size:31 final size:29
Alignment explanation
Indices: 532--693 Score: 103
Period size: 31 Copynumber: 5.4 Consensus size: 29
522 GGCTAATTGC
* *
532 TCAAATAAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAACGTTT--TAAAATGG
* * **
563 TCAAATAAGGGCTTGATC-TTTTAATTTGG
1 TCAAATAAGGGCCT-AACGTTTTAAAATGG
* *
592 CCAAATAAGGGCCTAACGTTATCGAAAATGG
1 TCAAATAAGGGCCTAACGTT-T-TAAAATGG
* * **
623 TCAAATAAGGGTCTGATC-TTTTAATTTGG
1 TCAAATAAGGGCCT-AACGTTTTAAAATGG
* * *
652 CCAAATAAGGGCCTAACGTTATAAAAAATGC
1 TCAAATAAGGGCCTAACGTT-T-TAAAATGG
683 TCAAATAAGGG
1 TCAAATAAGGG
694 TTTGGCGTCA
Statistics
Matches: 97, Mismatches: 26, Indels: 16
0.70 0.19 0.12
Matches are distributed among these distances:
28 4 0.04
29 37 0.38
30 3 0.03
31 49 0.51
32 4 0.04
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (29 bp):
TCAAATAAGGGCCTAACGTTTTAAAATGG
Found at i:662 original size:29 final size:28
Alignment explanation
Indices: 564--663 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 28
554 CCAAAATGCT
564 CAAATAAGGGCTTGATCTTTTAATTTGGC
1 CAAATAAGGGC-TGATCTTTTAATTTGGC
* * ** *
593 CAAATAAGGGCCT-AACGTTATCGAAAATGGT
1 CAAATAAGGG-CTGATC-TT-T-TAATTTGGC
624 CAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGG-CTGATCTTTTAATTTGGC
653 CAAATAAGGGC
1 CAAATAAGGGC
664 CTAACGTTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
28 3 0.05
29 28 0.51
30 3 0.05
31 19 0.35
32 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (28 bp):
CAAATAAGGGCTGATCTTTTAATTTGGC
Found at i:778 original size:31 final size:31
Alignment explanation
Indices: 735--902 Score: 136
Period size: 31 Copynumber: 5.5 Consensus size: 31
725 TTTCGACGCC
*
735 AGGCCCTAATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
** * *
766 AGGCCCTTATTTG-GCCAAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
*
795 AGACCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
* ** * *
826 AGGTCCTTATTTG-GTCAAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
*
855 AAGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
886 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
903 ATTAGCCATA
Statistics
Matches: 102, Mismatches: 23, Indels: 24
0.68 0.15 0.16
Matches are distributed among these distances:
28 8 0.08
29 33 0.32
30 4 0.04
31 49 0.48
32 8 0.08
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTT
Found at i:815 original size:60 final size:60
Alignment explanation
Indices: 737--898 Score: 281
Period size: 60 Copynumber: 2.7 Consensus size: 60
727 TCGACGCCAG
*
737 GCCCTAATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC-A
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAA
* *
796 GACCCTTATTTGAGCATTTTGGCAAACGTTAGGTCCTTATTTGGTCAAATTAAAAGATCAA
1 G-CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAA
857 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
899 AGCAATTAGC
Statistics
Matches: 97, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
59 1 0.01
60 94 0.97
61 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAA
Done.