Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012276.1 Corchorus olitorius cultivar O-4 contig12309, 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: 22832
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Found at i:7374 original size:12 final size:12
Alignment explanation
Indices: 7357--7382 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7347 TGAATAGCCT
7357 ATCCACATAAGC
1 ATCCACATAAGC
7369 ATCCACATAAGC
1 ATCCACATAAGC
7381 AT
1 AT
7383 TTTCTCTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (12 bp):
ATCCACATAAGC
Found at i:7672 original size:31 final size:28
Alignment explanation
Indices: 7634--7797 Score: 98
Period size: 31 Copynumber: 5.5 Consensus size: 28
7624 AGGCTAATTA
7634 CTCAAATAAGGGCCTAACGTTTATCAAAATG
1 CTCAAATAAGGGCCTAAC-TTT-T-AAAATG
* * **
7665 CTCAAATAAGGGCCCGATCTTTTAATTTGG
1 CTCAAATAAGGG-CCTAACTTTTAAAAT-G
* *
7695 C-CAAATAAGGACCTAATGTTATTGAAAATG
1 CTCAAATAAGGGCCTAA-CTT-TT-AAAATG
* * **
7725 CTCAAATAAGGGCCCGATCTTTTAATTTGG
1 CTCAAATAAGGG-CCTAACTTTTAAAAT-G
*
7755 C-CAAATAAGGGCCTAACATTTGCCAAAATG
1 CTCAAATAAGGGCCTAAC-TTT--TAAAATG
7785 CTCAAATAAGGGC
1 CTCAAATAAGGGC
7798 TTGACATCAG
Statistics
Matches: 100, Mismatches: 21, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
28 7 0.07
29 30 0.30
30 13 0.13
31 43 0.43
32 7 0.07
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (28 bp):
CTCAAATAAGGGCCTAACTTTTAAAATG
Found at i:7701 original size:60 final size:60
Alignment explanation
Indices: 7636--7797 Score: 254
Period size: 60 Copynumber: 2.7 Consensus size: 60
7626 GCTAATTACT
7636 CAAATAAGGGCCTAACGTTTATCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTATCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* * *
7696 CAAATAAGGACCTAATG-TTATTGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTA-TCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* **
7756 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAACGTTTATCAAAATGCTCAAATAAGGGC
7798 TTGACATCAG
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
59 3 0.03
60 86 0.95
61 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTATCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:7764 original size:29 final size:29
Alignment explanation
Indices: 7667--7767 Score: 114
Period size: 29 Copynumber: 3.4 Consensus size: 29
7657 TCAAAATGCT
7667 CAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCCGATCTTTTAATTTGGC
* ** * **
7696 CAAATAAGGACCTAATGTTATTGAAAAT-GC
1 CAAATAAGGGCCCGATCTT-TT-AATTTGGC
7726 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTTGGC
7756 CAAATAAGGGCC
1 CAAATAAGGGCC
7768 TAACATTTGC
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
29 30 0.54
30 8 0.14
31 18 0.32
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:7880 original size:31 final size:30
Alignment explanation
Indices: 7838--8004 Score: 125
Period size: 31 Copynumber: 5.6 Consensus size: 30
7828 TTTCGATGCC
* *
7838 AGGCCCCTATTTGAGCATTTTGGAAAACGTT
1 AGGCCCTTATTTGAGCATTTT-AAAAACGTT
* **
7869 AGACCCTTATTTG-GCCAAATTAAAAGACCG--
1 AGGCCCTTATTTGAG-CATTTTAAAA-A-CGTT
**
7899 -GGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT-AAAAACGTT
* *
7929 AGGCCCTTATTTG-GCCA-ATT-AAAA-GATC
1 AGGCCCTTATTTGAG-CATTTTAAAAACG-TT
7957 AGGCCCTTATTTGAGCATTTTAACAAACGTT
1 AGGCCCTTATTTGAGCATTTTAA-AAACGTT
7988 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
8005 ATTAGCCCCC
Statistics
Matches: 106, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
27 1 0.01
28 21 0.20
29 19 0.18
30 11 0.10
31 51 0.48
32 3 0.03
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTAAAAACGTT
Found at i:7936 original size:60 final size:59
Alignment explanation
Indices: 7836--8008 Score: 258
Period size: 59 Copynumber: 2.9 Consensus size: 59
7826 ATTTTCGATG
* * *
7836 CCAGGCCCCTATTTGAGCATTTTGGAAAACGTTAGACCCTTATTTGGCCAAATTAAAAGA
1 CCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCC-AATTAAAAGA
*
7896 CCGGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAATTAAAAGA
1 CCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAATTAAAAGA
* **
7955 TCAGGCCCTTATTTGAGCATTTTAACAAACGTTAGGCCCTTATTTGAG-CAATTA
1 CCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG-GCCAATTA
8009 GCCCCCATTT
Statistics
Matches: 104, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
59 58 0.56
60 46 0.44
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (59 bp):
CCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAATTAAAAGA
Found at i:7968 original size:28 final size:28
Alignment explanation
Indices: 7872--7969 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 28
7862 AAACGTTAGA
* *
7872 CCCTTATTTGGCCAAATTAAAAGACCGGG
1 CCCTTATTTGGCC-AATTAAAAGATCAGG
* * *
7901 CCCTTATTTGAG-CATTTTGGCAAACG-TTAGG
1 CCCTTATTTG-GCCA-ATT---AAAAGATCAGG
7932 CCCTTATTTGGCCAATTAAAAGATCAGG
1 CCCTTATTTGGCCAATTAAAAGATCAGG
7960 CCCTTATTTG
1 CCCTTATTTG
7970 AGCATTTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
27 4 0.07
28 15 0.28
29 13 0.24
30 4 0.07
31 14 0.26
32 4 0.07
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (28 bp):
CCCTTATTTGGCCAATTAAAAGATCAGG
Found at i:8354 original size:24 final size:24
Alignment explanation
Indices: 8326--8371 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
8316 CCGACTATAA
8326 TATATAATATAATT-TTAAAAATAT
1 TATAT-ATATAATTATTAAAAATAT
*
8350 TATATATATTATTATTAAAAAT
1 TATATATATAATTATTAAAAAT
8372 TCAGAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATATATAATTATTAAAAATAT
Found at i:14369 original size:39 final size:39
Alignment explanation
Indices: 14282--14370 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 39
14272 ACTCCAAAGG
* * *
14282 CATTTGATTGAGGCTGCAATTGCTGATCCATATAATTGA
1 CATTAGATTGGGGCTGCAATTGCTGAACCATATAATTGA
* * * * *
14321 TATTGGATTGGGGTTGCAATTGCTGAACCATCA-CATTTA
1 CATTAGATTGGGGCTGCAATTGCTGAACCAT-ATAATTGA
14360 CATTAGATTGG
1 CATTAGATTGG
14371 AAATGCAGCT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
39 39 0.98
40 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (39 bp):
CATTAGATTGGGGCTGCAATTGCTGAACCATATAATTGA
Done.