Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005909.1 Corchorus capsularis cultivar CVL-1 contig05927, 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: 6348
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:2063 original size:20 final size:20
Alignment explanation
Indices: 2038--2076 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2028 AAAAAGAGCA
2038 CCAATTTGCAAATCAAATGT
1 CCAATTTGCAAATCAAATGT
*
2058 CCAATTTGTAAATCAAATG
1 CCAATTTGCAAATCAAATG
2077 CCTTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
CCAATTTGCAAATCAAATGT
Found at i:2170 original size:18 final size:18
Alignment explanation
Indices: 2133--2170 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2123 AATGTAAATG
*
2133 TTTCTTTTCTTTTTTCTT
1 TTTCTTTTCTTTTTTATT
2151 TTTCTTTT-TTTTTGTATT
1 TTTCTTTTCTTTTT-TATT
2169 TT
1 TT
2171 GTATTTTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (18 bp):
TTTCTTTTCTTTTTTATT
Found at i:2704 original size:26 final size:27
Alignment explanation
Indices: 2641--2731 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
2631 AAGTAGACTT
* * *
2641 AAAATGACCAAAATGCCCCTGGTGCCG
1 AAAATGACCAAAATGACCCTAGTGCCA
*
2668 AAAATGACCAAAATGACCTTAGTG-CA
1 AAAATGACCAAAATGACCCTAGTGCCA
**
2694 AAAATGACCAAAATCCCCCTAG-GACTCA
1 AAAATGACCAAAATGACCCTAGTG-C-CA
2722 AAAATGACCA
1 AAAATGACCA
2732 CAATAGCCCA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
25 1 0.02
26 20 0.37
27 21 0.39
28 12 0.22
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATGACCAAAATGACCCTAGTGCCA
Found at i:3181 original size:19 final size:19
Alignment explanation
Indices: 3157--3331 Score: 89
Period size: 19 Copynumber: 9.3 Consensus size: 19
3147 AAGTTGTGAA
*
3157 TTGAAATACTGAAAAGTTG
1 TTGAAATGCTGAAAAGTTG
**
3176 TTGAAATGCTGTGAAGTTG
1 TTGAAATGCTGAAAAGTTG
3195 -T-AAAT--TGAAAAGTTG
1 TTGAAATGCTGAAAAGTTG
*
3210 TTGAAATGCTGTAAAGTTG
1 TTGAAATGCTGAAAAGTTG
*
3229 TAAATTCTGAAAAGCTGAATAA-TT-
1 -----T-TGAAATGCTGAA-AAGTTG
3253 TT-AAAT--TGAAAAGTTG
1 TTGAAATGCTGAAAAGTTG
* *
3269 TTGAAAAGCCGAAAAGTTG
1 TTGAAATGCTGAAAAGTTG
** *
3288 TTGAAAACCTGTAAAGTTG
1 TTGAAATGCTGAAAAGTTG
* * * *
3307 ATGAAAAGCAGTAAAGTTG
1 TTGAAATGCTGAAAAGTTG
*
3326 ATGAAA
1 TTGAAA
3332 AACTGTGAAG
Statistics
Matches: 123, Mismatches: 17, Indels: 32
0.72 0.10 0.19
Matches are distributed among these distances:
14 2 0.02
15 14 0.11
16 3 0.02
17 14 0.11
18 2 0.02
19 73 0.59
24 1 0.01
25 12 0.10
26 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (19 bp):
TTGAAATGCTGAAAAGTTG
Found at i:3204 original size:34 final size:34
Alignment explanation
Indices: 3166--3234 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
3156 ATTGAAATAC
*
3166 TGAAAAGTTGTTGAAATGCTGTGAAGTTGTAAAT
1 TGAAAAGTTGTTGAAATGCTGTAAAGTTGTAAAT
3200 TGAAAAGTTGTTGAAATGCTGTAAAGTTGTAAAT
1 TGAAAAGTTGTTGAAATGCTGTAAAGTTGTAAAT
3234 T
1 T
3235 CTGAAAAGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (34 bp):
TGAAAAGTTGTTGAAATGCTGTAAAGTTGTAAAT
Found at i:3312 original size:38 final size:38
Alignment explanation
Indices: 3262--3352 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
3252 TTTAAATTGA
* * * *
3262 AAAGTTGTTGAAAAGCCGAAAAGTTGTTGAAAACCTGT
1 AAAGTTGATGAAAAGCAGAAAAGTTGATGAAAAACTGT
*
3300 AAAGTTGATGAAAAGCAGTAAAGTTGATGAAAAACTGT
1 AAAGTTGATGAAAAGCAGAAAAGTTGATGAAAAACTGT
*
3338 GAAGTT-ATTGAAAAG
1 AAAGTTGA-TGAAAAG
3353 TTGAAAAGCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 1 0.02
38 45 0.98
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.25
Consensus pattern (38 bp):
AAAGTTGATGAAAAGCAGAAAAGTTGATGAAAAACTGT
Found at i:3351 original size:19 final size:19
Alignment explanation
Indices: 3262--3343 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
3252 TTTAAATTGA
* * * *
3262 AAAGTTGTTGAAAAGCCGA
1 AAAGTTGATGAAAAACTGT
* *
3281 AAAGTTGTTGAAAACCTGT
1 AAAGTTGATGAAAAACTGT
* *
3300 AAAGTTGATGAAAAGCAGT
1 AAAGTTGATGAAAAACTGT
3319 AAAGTTGATGAAAAACTGT
1 AAAGTTGATGAAAAACTGT
*
3338 GAAGTT
1 AAAGTT
3344 ATTGAAAAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (19 bp):
AAAGTTGATGAAAAACTGT
Found at i:3636 original size:38 final size:38
Alignment explanation
Indices: 3411--3629 Score: 210
Period size: 38 Copynumber: 5.8 Consensus size: 38
3401 AGCAGCTGAA
* ** *
3411 AATTGCTGAAAGATGACCCATTTCGAGTCGATATTGAT
1 AATTGCTGAAAGACGACCTGTTTCCAGTCGATATTGAT
* *
3449 AGTTGTTGAAAGACGACCTGTTTCCAGTCGATATTGAT
1 AATTGCTGAAAGACGACCTGTTTCCAGTCGATATTGAT
* * *
3487 AACTGATGAAAGACGACCTGCTTCCAGTCGA-ACTTGAT
1 AATTGCTGAAAGACGACCTGTTTCCAGTCGATA-TTGAT
* * * * *
3525 AAGTGCTGAAAGAC-AGCATGTCTCCAATCGATCTTGAT
1 AATTGCTGAAAGACGA-CCTGTTTCCAGTCGATATTGAT
* * *
3563 AACTGCTGAAAGATGACATGTTTCCAGTCGACT-TTGAT
1 AATTGCTGAAAGACGACCTGTTTCCAGTCGA-TATTGAT
* **
3601 TATTGCTGAAAGATAACCTGTTTCCAGTC
1 AATTGCTGAAAGACGACCTGTTTCCAGTC
3630 AACTTTGGGA
Statistics
Matches: 151, Mismatches: 25, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
37 2 0.01
38 147 0.97
39 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (38 bp):
AATTGCTGAAAGACGACCTGTTTCCAGTCGATATTGAT
Found at i:3852 original size:21 final size:21
Alignment explanation
Indices: 3828--3895 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
3818 GCAATATTAA
3828 AATGCATGGTGATGCAATGCC
1 AATGCATGGTGATGCAATGCC
* * *
3849 AATGCTTGGTTAT-TAA----
1 AATGCATGGTGATGCAATGCC
3865 AATGCATGGTGATGCAATGCC
1 AATGCATGGTGATGCAATGCC
*
3886 AATGCTTGGT
1 AATGCATGGT
3896 AATATGAGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
16 11 0.31
17 2 0.06
20 2 0.06
21 20 0.57
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (21 bp):
AATGCATGGTGATGCAATGCC
Found at i:3872 original size:37 final size:37
Alignment explanation
Indices: 3822--3895 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3812 TTTGATGCAA
3822 TATTAAAATGCATGGTGATGCAATGCCAATGCTTGGT
1 TATTAAAATGCATGGTGATGCAATGCCAATGCTTGGT
3859 TATTAAAATGCATGGTGATGCAATGCCAATGCTTGGT
1 TATTAAAATGCATGGTGATGCAATGCCAATGCTTGGT
3896 AATATGAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (37 bp):
TATTAAAATGCATGGTGATGCAATGCCAATGCTTGGT
Found at i:4698 original size:14 final size:13
Alignment explanation
Indices: 4667--4729 Score: 69
Period size: 12 Copynumber: 4.9 Consensus size: 13
4657 CTAGAGCTGC
4667 TTTTC-TTTTTC-
1 TTTTCTTTTTTCT
*
4678 GTTTCTTTTTTCT
1 TTTTCTTTTTTCT
4691 CTTTTCTTTTTTCT
1 -TTTTCTTTTTTCT
*
4705 TTTTC-ATTTTCT
1 TTTTCTTTTTTCT
4717 TTTTCATTTTTTC
1 TTTTC-TTTTTTC
4730 ATCATTCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
11 4 0.09
12 17 0.40
13 5 0.12
14 17 0.40
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:4705 original size:12 final size:12
Alignment explanation
Indices: 4666--4729 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 12
4656 CCTAGAGCTG
4666 CTTTTC-TTTTT
1 CTTTTCTTTTTT
*
4677 CGTTTCTTTTTTCT
1 CTTTTC-TTTTT-T
4691 CTTTTCTTTTTT
1 CTTTTCTTTTTT
*
4703 CTTTT-TCATTTT
1 CTTTTCT-TTTTT
4715 CTTTTTCATTTTTT
1 C-TTTTC-TTTTTT
4729 C
1 C
4730 ATCATTCATT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
11 6 0.14
12 11 0.26
13 13 0.31
14 11 0.26
15 1 0.02
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.77
Consensus pattern (12 bp):
CTTTTCTTTTTT
Found at i:4805 original size:27 final size:27
Alignment explanation
Indices: 4767--4826 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
4757 AGAATCTTAA
4767 TTGACTCGAAAACTCTTTTCAAAAGTT
1 TTGACTCGAAAACTCTTTTCAAAAGTT
*
4794 TTGACTTGAAAACTCTTTTCAAAAGTT
1 TTGACTCGAAAACTCTTTTCAAAAGTT
4821 TTGACT
1 TTGACT
4827 AAACATTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.40
Consensus pattern (27 bp):
TTGACTCGAAAACTCTTTTCAAAAGTT
Done.