Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015577.1 Corchorus capsularis cultivar CVL-1 contig15598, 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: 26400
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Found at i:1484 original size:20 final size:20
Alignment explanation
Indices: 1459--1506 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1449 TCGTGAGTGA
*
1459 TGCTTTGGGTGTTTCTGTGT
1 TGCTTTGAGTGTTTCTGTGT
1479 TGCTTTGAGTGTTTCTGTGT
1 TGCTTTGAGTGTTTCTGTGT
1499 TGCTTTGA
1 TGCTTTGA
1507 ACTCTTATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.04, C:0.10, G:0.31, T:0.54
Consensus pattern (20 bp):
TGCTTTGAGTGTTTCTGTGT
Found at i:3707 original size:20 final size:21
Alignment explanation
Indices: 3663--3708 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3653 CTTTAGGGAG
* *
3663 CTTTATTGTAATGATTTAGCC
1 CTTTACTGTAATGATATAGCC
*
3684 CTTTACTGTAATGCTATA-CC
1 CTTTACTGTAATGATATAGCC
3704 CTTTA
1 CTTTA
3709 TGACTTGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.46
Consensus pattern (21 bp):
CTTTACTGTAATGATATAGCC
Found at i:16076 original size:29 final size:31
Alignment explanation
Indices: 16044--16112 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
16034 ATGCAATTTG
16044 GGATATAACGTTA-CAAAA-CAAGCAATTAA
1 GGATATAACGTTACCAAAAGCAAGCAATTAA
**
16073 GGATATAACGTTACCAAAAGTGAGCAATTAA
1 GGATATAACGTTACCAAAAGCAAGCAATTAA
16104 GGATATAAC
1 GGATATAAC
16113 CCGTTAGAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 13 0.36
30 5 0.14
31 18 0.50
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (31 bp):
GGATATAACGTTACCAAAAGCAAGCAATTAA
Found at i:16267 original size:31 final size:31
Alignment explanation
Indices: 16229--16309 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
16219 CCCTAACTGA
*
16229 TTATATCCTTAATTGCTTGAAATCGAAAACC
1 TTATATCCTTAATTGCTTGAAATCAAAAACC
* *
16260 TTATATCCTTAATTGCTCGAAATCAAAAACG
1 TTATATCCTTAATTGCTTGAAATCAAAAACC
*
16291 TTATATCCTTAATTCCTTG
1 TTATATCCTTAATTGCTTG
16310 TTTTGTAACG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATCAAAAACC
Found at i:16414 original size:3 final size:3
Alignment explanation
Indices: 16406--16449 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
16396 CCCGTATTTT
* *
16406 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ACA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
16450 CCTAATTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:17416 original size:31 final size:31
Alignment explanation
Indices: 17365--17506 Score: 94
Period size: 31 Copynumber: 4.7 Consensus size: 31
17355 TATAGATAAG
* * *
17365 CGCAATCAATTTA-GATATAACGTTTTCTAC
1 CGCAAGCAATTAAGGATATAACGTTTTCTAT
* *
17395 CGCAAGCAATTAAGGATATAACG-TTAC-AA
1 CGCAAGCAATTAAGGATATAACGTTTTCTAT
** * * *
17424 AACATGCAATTTAGGATATAATGTTTT-TGAT
1 CGCAAGCAATTAAGGATATAACGTTTTCT-AT
** * *
17455 TTCGAGCAATTAAGGATATAACGTTTTCGAT
1 CGCAAGCAATTAAGGATATAACGTTTTCTAT
** *
17486 TTCAAGCACTTAAGGATATAA
1 CGCAAGCAATTAAGGATATAA
17507 TCAGTTAGGG
Statistics
Matches: 87, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
29 19 0.22
30 16 0.18
31 52 0.60
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (31 bp):
CGCAAGCAATTAAGGATATAACGTTTTCTAT
Found at i:17698 original size:29 final size:31
Alignment explanation
Indices: 17625--17691 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
17615 TCTAACGGAC
17625 TATATCCTTAATTGTTCGATTTTCGTAACGT
1 TATATCCTTAATTGTTCGATTTTCGTAACGT
*
17656 TATATCCTTAATTGTTTG-TTTT-GTAACGT
1 TATATCCTTAATTGTTCGATTTTCGTAACGT
17685 TATATCC
1 TATATCC
17692 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (31 bp):
TATATCCTTAATTGTTCGATTTTCGTAACGT
Found at i:21750 original size:36 final size:36
Alignment explanation
Indices: 21703--21821 Score: 140
Period size: 36 Copynumber: 3.4 Consensus size: 36
21693 TCTTTTCTGG
* *
21703 ATTAAGCTCTTTATTGACCTCACTTAATTACCTTGA
1 ATTAAGTTCTTTATTGACCTCACTTAATTACCCTGA
* *
21739 ATTAAGTTCTTTATT---CT-TCTTAATTACCCTCA
1 ATTAAGTTCTTTATTGACCTCACTTAATTACCCTGA
* *
21771 ATTAAG-CCTTTTATTGACTTCACTTAATTACCCTGA
1 ATTAAGTTC-TTTATTGACCTCACTTAATTACCCTGA
21807 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
21822 TTACTTAATT
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
31 1 0.01
32 24 0.35
33 2 0.03
35 1 0.01
36 39 0.57
37 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACCTCACTTAATTACCCTGA
Found at i:21766 original size:32 final size:33
Alignment explanation
Indices: 21724--21831 Score: 132
Period size: 32 Copynumber: 3.2 Consensus size: 33
21714 TATTGACCTC
*
21724 ACTTAATTACCTTGAATTAAGTTCTTTATTCTT
1 ACTTAATTACCCTGAATTAAGTTCTTTATTCTT
* *
21757 -CTTAATTACCCTCAATTAAG-CCTTTTATTGACTT
1 ACTTAATTACCCTGAATTAAGTTC-TTTATT--CTT
21791 CACTTAATTACCCTGAATTAAGTTCTTTATT-TT
1 -ACTTAATTACCCTGAATTAAGTTCTTTATTCTT
21824 ACTTAATT
1 ACTTAATT
21832 TCCTTTCCTG
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
31 1 0.02
32 32 0.50
33 2 0.03
34 3 0.05
36 25 0.39
37 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.48
Consensus pattern (33 bp):
ACTTAATTACCCTGAATTAAGTTCTTTATTCTT
Found at i:21788 original size:68 final size:68
Alignment explanation
Indices: 21703--21831 Score: 208
Period size: 68 Copynumber: 1.9 Consensus size: 68
21693 TCTTTTCTGG
*
21703 ATTAAGCTCTTTATTGACCTCACTTAATTACCTTGAATTAAGTTCTTTATTCTT-CTTAATTACC
1 ATTAAGCTCTTTATTGACCTCACTTAATTACCCTGAATTAAGTTCTTTATT-TTACTTAATTACC
21767 CTCA
65 CTCA
*
21771 ATTAAGC-CTTTTATTGACTTCACTTAATTACCCTGAATTAAGTTCTTTATTTTACTTAATT
1 ATTAAGCTC-TTTATTGACCTCACTTAATTACCCTGAATTAAGTTCTTTATTTTACTTAATT
21832 TCCTTTCCTG
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
67 3 0.05
68 54 0.95
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.47
Consensus pattern (68 bp):
ATTAAGCTCTTTATTGACCTCACTTAATTACCCTGAATTAAGTTCTTTATTTTACTTAATTACCC
TCA
Found at i:21947 original size:37 final size:36
Alignment explanation
Indices: 21869--22074 Score: 186
Period size: 37 Copynumber: 5.6 Consensus size: 36
21859 TTTTACTTAA
* * *
21869 TTTCCTTGAAATTAAGTCAGTC-TTTCCTTTACCTAA
1 TTTCCTTGAAACTAAGTCAGTCTTTTTC-TTACCTAG
*
21905 TTTCCTTGAAATTAAGTCAGGGT-TTTTTCTTACCTAG
1 TTTCCTTGAAACTAAGTCA--GTCTTTTTCTTACCTAG
* *
21942 TTTCCTTGAAACTAAG-CAAATCTGTTTTTTTACCTAG
1 TTTCCTTGAAACTAAGTC-AGTCT-TTTTCTTACCTAG
* *
21979 TTTCCTTGAAACTAAGCCAGTCTCTTTTTTTTACCTAG
1 TTTCCTTGAAACTAAGTCAG--TCTTTTTCTTACCTAG
* * * *
22017 TTTCCTTGAAACTAAGCCAGTCCTTTT-TTACTTAA
1 TTTCCTTGAAACTAAGTCAGTCTTTTTCTTACCTAG
* * *
22052 TTCCCTTGAAATTAAGACAGTCT
1 TTTCCTTGAAACTAAGTCAGTCT
22075 AACTTTACCT
Statistics
Matches: 148, Mismatches: 13, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
35 26 0.18
36 27 0.18
37 52 0.35
38 40 0.27
39 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTCCTTGAAACTAAGTCAGTCTTTTTCTTACCTAG
Found at i:22017 original size:38 final size:38
Alignment explanation
Indices: 21858--22045 Score: 206
Period size: 37 Copynumber: 5.1 Consensus size: 38
21848 AGCCTGTGTC
* * * *
21858 TTTTTACTTAATTTCCTTGAAATTAAGTCAG--TCTTT
1 TTTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTCTTT
** * * * **
21894 CCTTTACCTAATTTCCTTGAAATTAAGTCAGGGT-TTT
1 TTTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTCTTT
* * * *
21931 TTCTTACCTAGTTTCCTTGAAACTAAGCAAATCT-GTT
1 TTTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTCTTT
21968 TTTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTCTTT
1 TTTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTCTTT
22006 TTTTTACCTAGTTTCCTTGAAACTAAGCCAGTC-CTTT
1 TTTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTCTTT
22043 TTT
1 TTT
22046 ACTTAATTCC
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
36 28 0.21
37 67 0.51
38 36 0.27
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (38 bp):
TTTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTCTTT
Found at i:22022 original size:75 final size:74
Alignment explanation
Indices: 21896--22067 Score: 213
Period size: 75 Copynumber: 2.3 Consensus size: 74
21886 CAGTCTTTCC
* * *
21896 TTTACCTAATTTCCTTGAAATTAAGTCAGGGTTTTTTCTTACCTAGTTTCCTTGAAACTAAGCAA
1 TTTACCTAATTTCCTTGAAACTAAGCCAGGCTTTTTTCTTACCTAGTTTCCTTGAAACTAAGCAA
21961 ATCTGTTTT
66 ATCTGTTTT
* * * *
21970 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTCTTTTTTTTACCTAGTTTCCTTGAAACTAAGCC
1 TTTACCTAATTTCCTTGAAACTAAGCCAGGCT-TTTTTCTTACCTAGTTTCCTTGAAACTAAGCA
* *
22035 AGTC--CTTT
65 AATCTGTTTT
* * *
22043 TTTACTTAATTCCCTTGAAATTAAG
1 TTTACCTAATTTCCTTGAAACTAAG
22068 ACAGTCTAAC
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
73 24 0.29
74 27 0.32
75 33 0.39
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (74 bp):
TTTACCTAATTTCCTTGAAACTAAGCCAGGCTTTTTTCTTACCTAGTTTCCTTGAAACTAAGCAA
ATCTGTTTT
Found at i:22060 original size:110 final size:109
Alignment explanation
Indices: 21858--22067 Score: 244
Period size: 110 Copynumber: 1.9 Consensus size: 109
21848 AGCCTGTGTC
* * * * *
21858 TTTTTACTTAATTTCCTTGAAATTAAGTCAGTCTTTCCTTTACCTAATTTCCTTGAAATTAAGTC
1 TTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTCCTTTACCTAATTTCCTTGAAACTAAGCC
* * *
21923 AGGGTTTTTTCTTACCTAGTTTCCTTGAAACTAAGCAAATCTGTT
66 A-GGTCTTTTCTTACCTAATTCCCTTGAAACTAAGCAAATCTGTT
* ** *
21968 TTTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTCTTTTTTTTACCTAGTTTCCTTGAAACTAAG
1 TTTTTACCTAATTTCCTTGAAACTAAGCCAG--TCTTTCCTTTACCTAATTTCCTTGAAACTAAG
* *
22033 CCA-GTCCTTTT-TTACTTAATTCCCTTGAAATTAAG
64 CCAGGT-CTTTTCTTACCTAATTCCCTTGAAACTAAG
22068 ACAGTCTAAC
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
110 49 0.59
111 4 0.05
112 30 0.36
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (109 bp):
TTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTCCTTTACCTAATTTCCTTGAAACTAAGCC
AGGTCTTTTCTTACCTAATTCCCTTGAAACTAAGCAAATCTGTT
Found at i:22128 original size:11 final size:11
Alignment explanation
Indices: 22114--22210 Score: 77
Period size: 11 Copynumber: 8.6 Consensus size: 11
22104 CAGTTTTTTA
22114 TCAGTCTAATT
1 TCAGTCTAATT
**
22125 TCAGTCTTCTT
1 TCAGTCTAATT
* *
22136 TCAATCTGATT
1 TCAGTCTAATT
*
22147 TCAGTTTAATT
1 TCAGTCTAATT
**
22158 ATCAGTCTTTTT
1 -TCAGTCTAATT
22170 TCAGTCTAATT
1 TCAGTCTAATT
***
22181 TCAGTCTTCCT
1 TCAGTCTAATT
*
22192 TCAGTTTAATT
1 TCAGTCTAATT
22203 ATCAGTCT
1 -TCAGTCT
22211 TTTTTCAATC
Statistics
Matches: 63, Mismatches: 21, Indels: 3
0.72 0.24 0.03
Matches are distributed among these distances:
11 49 0.78
12 14 0.22
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (11 bp):
TCAGTCTAATT
Found at i:22163 original size:45 final size:45
Alignment explanation
Indices: 22111--22226 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
22101 AGCCAGTTTT
** *
22111 TTATCAGTCTAATTTCAGTCTTCTTTCAATCTGATTTCAGTTTAA
1 TTATCAGTCTTTTTTCAGTCTTCTTTCAATCTGACTTCAGTTTAA
** * **
22156 TTATCAGTCTTTTTTCAGTCTAATTTCAGTCTTCCTTCAGTTTAA
1 TTATCAGTCTTTTTTCAGTCTTCTTTCAATCTGACTTCAGTTTAA
*
22201 TTATCAGTCTTTTTTCAATCTTCTTT
1 TTATCAGTCTTTTTTCAGTCTTCTTT
22227 TCAGTCTTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.53
Consensus pattern (45 bp):
TTATCAGTCTTTTTTCAGTCTTCTTTCAATCTGACTTCAGTTTAA
Found at i:22179 original size:23 final size:23
Alignment explanation
Indices: 22145--22237 Score: 107
Period size: 23 Copynumber: 4.1 Consensus size: 23
22135 TTCAATCTGA
*
22145 TTTCAGTTTAATTATCAGTCTTT
1 TTTCAGTCTAATTATCAGTCTTT
*
22168 TTTCAGTCTAATT-TCAGTCTTC
1 TTTCAGTCTAATTATCAGTCTTT
* *
22190 CTTCAGTTTAATTATCAGTCTTT
1 TTTCAGTCTAATTATCAGTCTTT
* ** *
22213 TTTCAATCTTCTTTTCAGTCTTT
1 TTTCAGTCTAATTATCAGTCTTT
22236 TT
1 TT
22238 CTTTACCTAG
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 19 0.33
23 39 0.67
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTCAGTCTAATTATCAGTCTTT
Done.