Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009970.1 Corchorus capsularis cultivar CVL-1 contig09991, 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: 20651
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:567 original size:13 final size:13
Alignment explanation
Indices: 549--575 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
539 CTGACATCAA
549 GAAGAAGAAGACC
1 GAAGAAGAAGACC
562 GAAGAAGAAGACC
1 GAAGAAGAAGACC
575 G
1 G
576 TTTTTAACGA
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:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGACC
Found at i:3576 original size:31 final size:31
Alignment explanation
Indices: 3541--3606 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3531 GAGGACTCAG
* * *
3541 TTGACCCAATTTTGTGAGTATAGTGAATAAA
1 TTGACCCAATCTTATGAGTATAGGGAATAAA
* *
3572 TTGACCCAATCTTATGGGTATAGGGACTAAA
1 TTGACCCAATCTTATGAGTATAGGGAATAAA
3603 TTGA
1 TTGA
3607 TTACTTTACG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (31 bp):
TTGACCCAATCTTATGAGTATAGGGAATAAA
Found at i:3957 original size:60 final size:60
Alignment explanation
Indices: 3889--4052 Score: 233
Period size: 60 Copynumber: 2.7 Consensus size: 60
3879 GCTAATTGCT
** *
3889 CAAATAAGGGTATAACGTT-TGCTAAAATGCTCAAATAAGGGCCTGGTCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CTAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
* * * *
3949 CAAATAAGGGCCTAACATTATCAAAAATGCTCAATTAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCTAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
4009 CAAATAAGGGCCTAACGTTAT-TGAAAATGCTCAAATAAGGGCCT
1 CAAATAAGGGCCTAACGTTATCT-AAAATGCTCAAATAAGGGCCT
4053 AACGTTATCG
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
60 90 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCTAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:3991 original size:31 final size:31
Alignment explanation
Indices: 3949--4080 Score: 137
Period size: 31 Copynumber: 4.3 Consensus size: 31
3939 TTAATTTGGC
* *
3949 CAAATAAGGGCCTAACATTATCAAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * * **
3980 CAATTAAGGGCCCGATC-TT-T-TAATTTGGC-
1 CAAATAAGGG-CCTAACGTTATCGAAAAT-GCT
*
4009 CAAATAAGGGCCTAACGTTATTGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
4040 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
4071 CAAATAAGGG
1 CAAATAAGGG
4081 TCTGATTTCT
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
28 4 0.05
29 14 0.17
30 6 0.07
31 54 0.66
32 4 0.05
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:4020 original size:29 final size:29
Alignment explanation
Indices: 3920--4020 Score: 80
Period size: 29 Copynumber: 3.4 Consensus size: 29
3910 CTAAAATGCT
* *
3920 CAAATAAGGGCCTGGTCTTTTAATTTGGC
1 CAAATAAGGGCCCGATCTTTTAATTTGGC
* * * **
3949 CAAATAAGGG-CCTAACATTATCAAAAAT-GC
1 CAAATAAGGGCCCGATC-TT-T-TAATTTGGC
*
3979 TCAATTAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTTGGC
4009 CAAATAAGGGCC
1 CAAATAAGGGCC
4021 TAACGTTATT
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
28 2 0.04
29 26 0.50
30 6 0.12
31 14 0.27
32 4 0.08
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:4184 original size:60 final size:60
Alignment explanation
Indices: 4114--4272 Score: 243
Period size: 60 Copynumber: 2.7 Consensus size: 60
4104 ATGAGATAGA
* *
4114 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGG-CTAAATTCAAAGACCGGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTC-AAATTAAAAGACCAGG
* * *
4174 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCTCTTATTTGGTCAAATTAAAAGATCATG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTCAAATTAAAAGACCAGG
4234 CCCTTATTTGAGCATTTTGGCAAA--TTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
4273 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
58 14 0.15
60 77 0.84
61 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTCAAATTAAAAGACCAGG
Found at i:4265 original size:29 final size:29
Alignment explanation
Indices: 4114--4276 Score: 104
Period size: 29 Copynumber: 5.5 Consensus size: 29
4104 ATGAGATAGA
4114 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTTGGCAAA--TTAGG
** *
4145 CCCTTATTTG-GCTAAATT--CAAA-GACCGGG
1 CCCTTATTTGAGC-ATTTTGGCAAATTA---GG
4174 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTTGGCAAA--TTAGG
* ** ** * *
4205 CTCTTATTTG-GTCAAATT-AAAAGATCATG
1 CCCTTATTTGAG-CATTTTGGCAA-ATTAGG
4234 CCCTTATTTGAGCATTTTGGCAAATTAGG
1 CCCTTATTTGAGCATTTTGGCAAATTAGG
4263 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
4277 ATTAGCCTAC
Statistics
Matches: 98, Mismatches: 20, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
26 1 0.01
29 53 0.54
30 10 0.10
31 33 0.34
34 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGGCAAATTAGG
Found at i:4680 original size:20 final size:19
Alignment explanation
Indices: 4652--4693 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
4642 TTTATAAACA
* *
4652 AAAAGTTAACTTAATTAGT
1 AAAAGTTAAATTAATTAAT
4671 AAAAGATTAAATTAATTAAT
1 AAAAG-TTAAATTAATTAAT
4691 AAA
1 AAA
4694 CTTCCCAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAAGTTAAATTAATTAAT
Found at i:8379 original size:13 final size:13
Alignment explanation
Indices: 8361--8388 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8351 TTGATGAAAC
8361 ATCTATACTAATT
1 ATCTATACTAATT
8374 ATCTATACTAATT
1 ATCTATACTAATT
8387 AT
1 AT
8389 AATGTGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.46
Consensus pattern (13 bp):
ATCTATACTAATT
Found at i:11360 original size:1 final size:1
Alignment explanation
Indices: 11354--11385 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
11344 CTATTACCTC
11354 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11386 CTCTTCACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13816 original size:35 final size:37
Alignment explanation
Indices: 13770--13844 Score: 109
Period size: 40 Copynumber: 2.0 Consensus size: 37
13760 AATCTTAGTA
13770 AATATATCAAAATTG-A-TAATTCAATTAGTAAGTGT
1 AATATATCAAAATTGTATTAATTCAATTAGTAAGTGT
13805 AATATATCAAAATTGTTAATTTAATTCAATTAGTAAGTGT
1 AATATATCAAAATTG-T-A-TTAATTCAATTAGTAAGTGT
13845 GTCATACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
35 15 0.43
38 1 0.03
40 19 0.54
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (37 bp):
AATATATCAAAATTGTATTAATTCAATTAGTAAGTGT
Done.