Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011564.1 Corchorus capsularis cultivar CVL-1 contig11585, 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: 36004
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3602 original size:31 final size:31
Alignment explanation
Indices: 3561--3725 Score: 94
Period size: 31 Copynumber: 5.5 Consensus size: 31
3551 AATGACTAAT
* *
3561 TGCTTAAATAAGGGTCTAACGTTTGGCAAAA
1 TGCTCAAATAAGGGTCTAACGTTTGCCAAAA
* * * **
3592 TGCTCAAATAAGGGTATGATC-TTT--TAATT
1 TGCTCAAATAAGGGTCT-AACGTTTGCCAAAA
* *
3621 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGTCTAACGTTTGCCAAAA
** *** **
3652 TGCTCAAATAAAGGCCCGGTC-TTTG--AATT
1 TGCTCAAAT-AAGGGTCTAACGTTTGCCAAAA
3681 TGGC-CAAATAAGGGTCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGTCTAACGTTTGCCAAAA
3712 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
3726 CCTATCTCAT
Statistics
Matches: 95, Mismatches: 27, Indels: 24
0.65 0.18 0.16
Matches are distributed among these distances:
28 7 0.07
29 29 0.31
30 8 0.08
31 43 0.45
32 8 0.08
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGTCTAACGTTTGCCAAAA
Found at i:3634 original size:60 final size:60
Alignment explanation
Indices: 3566--3726 Score: 241
Period size: 60 Copynumber: 2.7 Consensus size: 60
3556 CTAATTGCTT
* * * *
3566 AAATAAGGGTCTAACGTTTGGCAAAATGCTCAAATAAGGGTATGATCTTTTAATTTGGCC
1 AAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCACGATCTTTGAATTTGGCC
* * * * *
3626 AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAAGGCCCGGTCTTTGAATTTGGCC
1 AAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCACGATCTTTGAATTTGGCC
3686 AAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGC
1 AAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGC
3727 CTATCTCATA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 89 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (60 bp):
AAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCACGATCTTTGAATTTGGCC
Found at i:3797 original size:31 final size:31
Alignment explanation
Indices: 3759--3890 Score: 128
Period size: 31 Copynumber: 4.3 Consensus size: 31
3749 TGAAACCAGG
*
3759 CCCTTATTTGAGCATTTTCAATGACGTTAGA
1 CCCTTATTTGAGCATTTTCAATAACGTTAGA
*
3790 CCCTTATTTGAGCATTTTCAATAACGTTAGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGA
** ** *
3821 CCCTTATTTG-GCCAAATT-AA-AA-GATCGGG
1 CCCTTATTTGAG-CATTTTCAATAACG-TTAGA
* * *
3850 TCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCAATAACGTTAGA
3881 CCCTTATTTG
1 CCCTTATTTG
3891 GTCAAATTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
28 1 0.01
29 18 0.22
30 5 0.06
31 57 0.70
32 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCAATAACGTTAGA
Found at i:3863 original size:60 final size:59
Alignment explanation
Indices: 3790--3950 Score: 243
Period size: 60 Copynumber: 2.7 Consensus size: 59
3780 TGACGTTAGA
*
3790 CCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
* *
3850 TCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCAGG
1 CCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
*
3910 CCCTTATTTGAGCATTTTGGCA-AACTTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTT--CATAACGTTAGGCCCTTATTTG
3951 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
60 91 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (59 bp):
CCCTTATTTGAGCATTTTCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGG
Found at i:3915 original size:29 final size:28
Alignment explanation
Indices: 3818--3919 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
3808 CAATAACGTT
3818 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
* * ** * *
3847 GGGTCCTTATTTGAGCATTTTCGATAACG-TT
1 AGGCCCTTATTTG-GCAAATT--A-AAAGATC
3878 AGGCCCTTATTTGGTCAAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
3907 AGGCCCTTATTTG
1 AGGCCCTTATTTG
3920 AGCATTTTGG
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
28 3 0.05
29 30 0.55
30 2 0.04
31 17 0.31
32 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (28 bp):
AGGCCCTTATTTGGCAAATTAAAAGATC
Found at i:14858 original size:18 final size:18
Alignment explanation
Indices: 14819--14858 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
14809 CTACTACATT
*
14819 CAATCAAATTAATTTGCG
1 CAATCAAATTAATTTGCC
14837 CAATCAAATT-ATTTAGCC
1 CAATCAAATTAATTT-GCC
14855 CAAT
1 CAAT
14859 AGGTTATGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (18 bp):
CAATCAAATTAATTTGCC
Found at i:21278 original size:13 final size:13
Alignment explanation
Indices: 21260--21286 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21250 CATGGTTTCT
21260 TATATAATAATAA
1 TATATAATAATAA
21273 TATATAATAATAA
1 TATATAATAATAA
21286 T
1 T
21287 GAAATAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATAATAATAA
Found at i:32932 original size:34 final size:34
Alignment explanation
Indices: 32893--32961 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
32883 TTTCTAACAG
32893 TGCTTCTTGTTTATAAAGTGGTAGAAAATTTAGC
1 TGCTTCTTGTTTATAAAGTGGTAGAAAATTTAGC
32927 TGCTTCTTGTTTATAAAGTGGTAGAAAATTTAGC
1 TGCTTCTTGTTTATAAAGTGGTAGAAAATTTAGC
32961 T
1 T
32962 TAGAGGGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (34 bp):
TGCTTCTTGTTTATAAAGTGGTAGAAAATTTAGC
Done.