Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011725.1 Corchorus capsularis cultivar CVL-1 contig11746, 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: 26372
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Found at i:4178 original size:87 final size:86
Alignment explanation
Indices: 3986--4192 Score: 222
Period size: 87 Copynumber: 2.4 Consensus size: 86
3976 GCACAAAATC
* * * * *
3986 CTCCACCAAATCAGTTTCCAAAGATTTTGCATCATTACTAACTAAAACTCCATTAGGAAGATCAA
1 CTCCACCATATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGATCAA
4051 TGAAATTTGAATTCAAATTAT
66 TGAAATTTGAATTCAAATTAT
* * * * *
4072 CTTCTACAATAAT-ACTTTCCAAAGATTTTGCACCATAACCACCCATAACTCCATTAGGAAGATC
1 C-TCCACCAT-ATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGAT-
*
4136 ACAAT-CAA-TTGAATTCAAATTATT
63 -CAATGAAATTTGAATTCAAATTA-T
* * *
4160 CTCCACCCTATCAGTTTCCACAGAATTTGCACC
1 CTCCACCATATCAGTTTCCAAAGATTTTGCACC
4193 TAAAAATCCT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
86 3 0.03
87 85 0.87
88 6 0.06
89 4 0.04
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (86 bp):
CTCCACCATATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGATCAA
TGAAATTTGAATTCAAATTAT
Found at i:9930 original size:13 final size:13
Alignment explanation
Indices: 9885--9931 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
9875 ATCATTTTTA
9885 CTCTTTTCTTATT
1 CTCTTTTCTTATT
*
9898 CT-TTTTACTAATT
1 CTCTTTT-CTTATT
*
9911 ACTCTTTTCTTACT
1 -CTCTTTTCTTATT
9925 CTCTTTT
1 CTCTTTT
9932 ATTGATTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 14 0.50
14 6 0.21
15 4 0.14
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.64
Consensus pattern (13 bp):
CTCTTTTCTTATT
Found at i:10016 original size:21 final size:21
Alignment explanation
Indices: 9992--10171 Score: 146
Period size: 21 Copynumber: 8.8 Consensus size: 21
9982 ACTCTTTGAA
* *
9992 TTACTGATCACCTTTTACTCT
1 TTACTGATTACATTTTACTCT
10013 TTACTGATTACTATTTTACTC-
1 TTACTGATTAC-ATTTTACTCT
* *
10034 TTACTAATTACCATTTTGCTC-
1 TTACTGATTA-CATTTTACTCT
10055 TTACTGATTACGATTTTACTC-
1 TTACTGATTAC-ATTTTACTCT
*
10076 TTACTGATTACGTTTTA----
1 TTACTGATTACATTTTACTCT
10093 -T--TGATTACTATTTTACTCT
1 TTACTGATTAC-ATTTTACTCT
* * * *
10112 TTACTAATTACCTTCTCACTTT
1 TTACTGATTACATT-TTACTCT
10134 TTACTGATTACTATTTTACTCT
1 TTACTGATTAC-ATTTTACTCT
*
10156 TTACTGATTACTTTTT
1 TTACTGATTACATTTT
10172 TTAACCTAGG
Statistics
Matches: 129, Mismatches: 17, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.05
15 5 0.04
16 1 0.01
20 7 0.05
21 61 0.47
22 46 0.36
23 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (21 bp):
TTACTGATTACATTTTACTCT
Found at i:10114 original size:22 final size:22
Alignment explanation
Indices: 10089--10172 Score: 98
Period size: 22 Copynumber: 3.8 Consensus size: 22
10079 CTGATTACGT
*
10089 TTTATTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* * * *
10111 TTTACTAATTACCT-TCTCACTT
1 TTTACTGATTA-CTATTTTACTC
10133 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
*
10155 TTTACTGATTACTTTTTT
1 TTTACTGATTACTATTTT
10173 TAACCTAGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 2 0.04
22 46 0.92
23 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:10115 original size:15 final size:15
Alignment explanation
Indices: 10097--10160 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
10087 GTTTTATTGA
10097 TTACTATTTTACTCT
1 TTACTATTTTACTCT
*
10112 TTACTA-ATTAC-CT
1 TTACTATTTTACTCT
**
10125 TCTCACT-TTTTACTGA
1 T-T-ACTATTTTACTCT
10141 TTACTATTTTACTCT
1 TTACTATTTTACTCT
10156 TTACT
1 TTACT
10161 GATTACTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
13 3 0.08
14 8 0.21
15 26 0.68
16 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.02, T:0.55
Consensus pattern (15 bp):
TTACTATTTTACTCT
Found at i:10593 original size:13 final size:13
Alignment explanation
Indices: 10548--10594 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
10538 ATCATTTTTA
10548 CTCTTTTCTTATT
1 CTCTTTTCTTATT
*
10561 CT-TTTTACTAATT
1 CTCTTTT-CTTATT
*
10574 ACTCTTTTCTTACT
1 -CTCTTTTCTTATT
10588 CTCTTTT
1 CTCTTTT
10595 ATTGATTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 14 0.50
14 6 0.21
15 4 0.14
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.64
Consensus pattern (13 bp):
CTCTTTTCTTATT
Found at i:10679 original size:21 final size:21
Alignment explanation
Indices: 10655--10755 Score: 91
Period size: 21 Copynumber: 4.8 Consensus size: 21
10645 ACTCTTTGAA
*
10655 TTACTGATCACCTTTTACTCT
1 TTACTGATTACCTTTTACTCT
* *
10676 TTACTTATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
* *
10697 TTACTAATTACCATTTTGCTC-
1 TTACTGATTACC-TTTTACTCT
*
10718 TTACTGATTACGATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
*
10739 TTACTGATTACGTTTTA
1 TTACTGATTACCTTTTA
10756 TTGATTACTA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
20 5 0.07
21 54 0.81
22 8 0.12
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (21 bp):
TTACTGATTACCTTTTACTCT
Found at i:10722 original size:42 final size:43
Alignment explanation
Indices: 10667--10835 Score: 133
Period size: 44 Copynumber: 4.1 Consensus size: 43
10657 ACTGATCACC
* *
10667 TTTTACTCTTTACTTATTACTATTTTACTCTTACTAATTACCA
1 TTTTACTCTTTACTGATTACGATTTTACTCTTACTAATTACCA
* * *
10710 TTTTGCTC-TTACTGATTACGATTTTACTCTTACTGATTA-CG
1 TTTTACTCTTTACTGATTACGATTTTACTCTTACTAATTACCA
* *
10751 TTTTA-----T--TGATTACTATTTTACTCTTTACTGATTACC-
1 TTTTACTCTTTACTGATTACGATTTTACTC-TTACTAATTACCA
* * * * *
10787 TTCTCACTTTTTACTGATTACTATTTTACTCTTTACTGATTACCT
1 TT-TTACTCTTTACTGATTACGATTTTACTC-TTACTAATTACCA
10832 TTTT
1 TTTT
10836 CTACCTTCTT
Statistics
Matches: 106, Mismatches: 9, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
35 16 0.15
36 12 0.11
37 4 0.04
41 5 0.05
42 29 0.27
43 7 0.07
44 31 0.29
45 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (43 bp):
TTTTACTCTTTACTGATTACGATTTTACTCTTACTAATTACCA
Found at i:10763 original size:21 final size:21
Alignment explanation
Indices: 10654--10829 Score: 82
Period size: 21 Copynumber: 8.6 Consensus size: 21
10644 TACTCTTTGA
* *
10654 ATTACTGATCAC-CTTTTACT
1 ATTACTGATTACGATTTTACT
* * *
10674 CTTTACTTATTACTATTTTACT
1 -ATTACTGATTACGATTTTACT
* * * *
10696 CTTACTAATTACCATTTTGCT
1 ATTACTGATTACGATTTTACT
*
10717 CTTACTGATTACGATTTTACT
1 ATTACTGATTACGATTTTACT
*
10738 CTTACTGATTACG--TTT--T
1 ATTACTGATTACGATTTTACT
*
10755 A-T--TGATTACTATTTTACT
1 ATTACTGATTACGATTTTACT
* * *
10773 CTTTACTGATTAC-CTTCTCACTT
1 -ATTACTGATTACGATT-TTAC-T
* *
10796 TTTACTGATTACTATTTTACT
1 ATTACTGATTACGATTTTACT
*
10817 CTTTACTGATTAC
1 -ATTACTGATTAC
10830 CTTTTTCTAC
Statistics
Matches: 124, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
14 7 0.06
16 4 0.03
17 1 0.01
18 1 0.01
19 3 0.02
20 1 0.01
21 60 0.48
22 44 0.35
23 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (21 bp):
ATTACTGATTACGATTTTACT
Found at i:10769 original size:663 final size:662
Alignment explanation
Indices: 9505--10835 Score: 2563
Period size: 663 Copynumber: 2.0 Consensus size: 662
9495 CCACTAATCT
9505 TTTTTTTAACCTAGGTGTGATTAGCCACCTATCTGATTATTAAGTCTAATGTTAACCTAAGCTTG
1 TTTTTTTAACCTAGGTGTGATTAGCCACCTATCTGATTATTAAGTCTAATGTTAACCTAAGCTTG
9570 GCAAAGGTAACACTAAACCTAATAAACGGTCTTCTAACCAGAGTCTGAGGTTCGAGAGTCGGGTA
66 GCAAAGGTAACACTAAACCTAATAAACGGTCTTCTAACCAGAGTCTGAGGTTCGAGAGTCGGGTA
9635 CGCGTAGGGAAGGATTAGCACCCCCACGACGCCCGTCAAAAGACGGCACTGACTAGTTTAGACCT
131 CGCGTAGGGAAGGATTAGCACCCCCACGACGCCCGTCAAAAGACGGCACTGACTAGTTTAGACCT
* *
9700 AACTGTGGGTTTCCATATTTGGTTGTTTTCTATCTTTAAGTATATTCATGCCATTTGACTCTTTT
196 AACTATGGGTTTCCATATTTGGTTGTTTTCCATCTTTAAGTATATTCATGCCATTTGACTCTTTT
9765 ATACTAACTAAATTACTAACTAACATACTCTTCTCTCATTTTTATTAACTACCATTTTTTACTAA
261 ATACTAACTAAATTACTAACTAACATACTCTTCTCTCATTTTTATTAACTACCATTTTTTACTAA
*
9830 TTATCCTCTTCTCACTGATTACCTTTTTTTACTTTTCCTACTTTTATCATTTTTACTCTTTTCTT
326 TTATCCTCTTCTCACTGATTACCATTTTTTACTTTTCCTACTTTTATCATTTTTACTCTTTTCTT
9895 ATTCTTTTTACTAATTACTCTTTTCTTACTCTCTTTTATTGATTACCACTTTTTACTCTTCTTTT
391 ATTCTTTTTACTAATTACTCTTTTCTTACTCTCTTTTATTGATTACCACTTTTTACTCTTCTTTT
9960 TTGTTATACTGACTACCATTTTACTCTTTGAATTACTGATCACCTTTTACTCTTTACTGATTACT
456 TTGTTATACTGACTACCATTTTACTCTTTGAATTACTGATCACCTTTTACTCTTTACTGATTACT
10025 ATTTTACTCTTACTAATTACCATTTTGCTCTTACTGATTACGATTTTACTCTTACTGATTACGTT
521 ATTTTACTCTTACTAATTACCATTTTGCTCTTACTGATTACGATTTTACTCTTACTGATTACGTT
10090 TTATTGATTACTATTTTACTCTTTACTAATTACCTTCTCACTTTTTACTGATTACTATTTTACTC
586 TTATTGATTACTATTTTACTCTTTACTAATTACCTTCTCACTTTTTACTGATTACTATTTTACTC
10155 TTTACTGATTAC
651 TTTACTGATTAC
10167 TTTTTTTAACCTAGGTGTGATTAGCCACCTATCTGATTATTAAGTCTAATGTTAACCTAAGCTTG
1 TTTTTTTAACCTAGGTGTGATTAGCCACCTATCTGATTATTAAGTCTAATGTTAACCTAAGCTTG
* *
10232 GCGAAGGTAACACTAAACCTAATAAAACGGTCTTCTAACCAGAGTCTGAGGTTCGGGAGTCGGGT
66 GCAAAGGTAACACTAAACCTAAT-AAACGGTCTTCTAACCAGAGTCTGAGGTTCGAGAGTCGGGT
*
10297 ACGCGTAGGGAAGGATTAGCACCCTCACGACGCCCGTCAAAAGACGGCACTGACTAGTTTAGACC
130 ACGCGTAGGGAAGGATTAGCACCCCCACGACGCCCGTCAAAAGACGGCACTGACTAGTTTAGACC
10362 TAACTATGGGTTTCCATATTTGGTTGTTTTCCATCTTTAAGTATATTCATGCCATTTGACTCTTT
195 TAACTATGGGTTTCCATATTTGGTTGTTTTCCATCTTTAAGTATATTCATGCCATTTGACTCTTT
*
10427 TATACTAACTAAATTACTAACTAACATACTCTTCTCTCCTTTTTATTAACTACCATTTTTTACTA
260 TATACTAACTAAATTACTAACTAACATACTCTTCTCTCATTTTTATTAACTACCATTTTTTACTA
10492 ATTATCCTCTTCTCACTGATTACCATTTTTTACTTTTCCTACTTTTATCATTTTTACTCTTTTCT
325 ATTATCCTCTTCTCACTGATTACCATTTTTTACTTTTCCTACTTTTATCATTTTTACTCTTTTCT
10557 TATTCTTTTTACTAATTACTCTTTTCTTACTCTCTTTTATTGATTACCACTTTTTACTCTTCTTT
390 TATTCTTTTTACTAATTACTCTTTTCTTACTCTCTTTTATTGATTACCACTTTTTACTCTTCTTT
*
10622 TTTGTTATACTGACTACCATTTTACTCTTTGAATTACTGATCACCTTTTACTCTTTACTTATTAC
455 TTTGTTATACTGACTACCATTTTACTCTTTGAATTACTGATCACCTTTTACTCTTTACTGATTAC
10687 TATTTTACTCTTACTAATTACCATTTTGCTCTTACTGATTACGATTTTACTCTTACTGATTACGT
520 TATTTTACTCTTACTAATTACCATTTTGCTCTTACTGATTACGATTTTACTCTTACTGATTACGT
*
10752 TTTATTGATTACTATTTTACTCTTTACTGATTACCTTCTCACTTTTTACTGATTACTATTTTACT
585 TTTATTGATTACTATTTTACTCTTTACTAATTACCTTCTCACTTTTTACTGATTACTATTTTACT
10817 CTTTACTGATTAC
650 CTTTACTGATTAC
*
10830 CTTTTT
1 TTTTTT
10836 CTACCTTCTT
Statistics
Matches: 658, Mismatches: 10, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
662 87 0.13
663 571 0.87
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (662 bp):
TTTTTTTAACCTAGGTGTGATTAGCCACCTATCTGATTATTAAGTCTAATGTTAACCTAAGCTTG
GCAAAGGTAACACTAAACCTAATAAACGGTCTTCTAACCAGAGTCTGAGGTTCGAGAGTCGGGTA
CGCGTAGGGAAGGATTAGCACCCCCACGACGCCCGTCAAAAGACGGCACTGACTAGTTTAGACCT
AACTATGGGTTTCCATATTTGGTTGTTTTCCATCTTTAAGTATATTCATGCCATTTGACTCTTTT
ATACTAACTAAATTACTAACTAACATACTCTTCTCTCATTTTTATTAACTACCATTTTTTACTAA
TTATCCTCTTCTCACTGATTACCATTTTTTACTTTTCCTACTTTTATCATTTTTACTCTTTTCTT
ATTCTTTTTACTAATTACTCTTTTCTTACTCTCTTTTATTGATTACCACTTTTTACTCTTCTTTT
TTGTTATACTGACTACCATTTTACTCTTTGAATTACTGATCACCTTTTACTCTTTACTGATTACT
ATTTTACTCTTACTAATTACCATTTTGCTCTTACTGATTACGATTTTACTCTTACTGATTACGTT
TTATTGATTACTATTTTACTCTTTACTAATTACCTTCTCACTTTTTACTGATTACTATTTTACTC
TTTACTGATTAC
Found at i:10835 original size:22 final size:22
Alignment explanation
Indices: 10752--10829 Score: 104
Period size: 22 Copynumber: 3.5 Consensus size: 22
10742 CTGATTACGT
*
10752 TTTATTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* * *
10774 TTTACTGATTACCT-TCTCACTT
1 TTTACTGATTA-CTATTTTACTC
10796 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
10818 TTTACTGATTAC
1 TTTACTGATTAC
10830 CTTTTTCTAC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 2 0.04
22 43 0.91
23 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:10848 original size:29 final size:26
Alignment explanation
Indices: 10772--10949 Score: 115
Period size: 29 Copynumber: 6.8 Consensus size: 26
10762 ACTATTTTAC
*
10772 TCTTTACTGATTACC--TTCT-CACT
1 TCTTTACTGATTACCTTTTCTACTCT
10795 T-TTTACTGATTA-CTATTT-TA--C-
1 TCTTTACTGATTACCT-TTTCTACTCT
10816 TCTTTACTGATTACCTTTTTCTACCTTCT
1 TCTTTACTGATTACC-TTTTCTA-C-TCT
* *
10845 TCTTTTACTAACTACCTTTTCTTACTCT
1 TC-TTTACTGATTACCTTTTC-TACTCT
* * *
10873 T-TTTATTGATTACCATTTCTACTTTT
1 TCTTTACTGATTACCTTTTCTAC-TCT
*
10899 TTTTTACTGATTACCCTTTTCTTACTCT
1 TCTTTACTGATTA-CCTTTTC-TACTCT
*
10927 GTTTTTACTGATTACCCTTTTCT
1 -TCTTTACTGATTA-CCTTTTCT
10950 TTTCTCTTTT
Statistics
Matches: 125, Mismatches: 10, Indels: 35
0.74 0.06 0.21
Matches are distributed among these distances:
21 2 0.02
22 23 0.18
23 6 0.05
24 5 0.04
25 3 0.02
26 17 0.14
27 10 0.08
28 14 0.11
29 32 0.26
30 13 0.10
ACGTcount: A:0.17, C:0.24, G:0.04, T:0.56
Consensus pattern (26 bp):
TCTTTACTGATTACCTTTTCTACTCT
Found at i:10933 original size:56 final size:53
Alignment explanation
Indices: 10794--10964 Score: 156
Period size: 56 Copynumber: 3.2 Consensus size: 53
10784 ACCTTCTCAC
* * *
10794 TTTTTACTGATTA-CTATT-TTACTC--TTTACTGATTACCTTTTTCTACCTTCTT
1 TTTTTACTGACTACCTTTTCTTACTCTTTTTACTGATTACC-ATTTCTA-CTT-TT
* * *
10846 CTTTTACTAACTACCTTTTCTTACTCTTTTTATTGATTACCATTTCTACTTTT
1 TTTTTACTGACTACCTTTTCTTACTCTTTTTACTGATTACCATTTCTACTTTT
* *
10899 TTTTTACTGATTACCCTTTTCTTACTCTGTTTTTACTGATTACCCTTT-T-CTTTT
1 TTTTTACTGACTA-CCTTTTCTTACTC--TTTTTACTGATTACCATTTCTACTTTT
10953 CTCTTTTACTGA
1 -T-TTTTACTGA
10965 ATACTATTTC
Statistics
Matches: 99, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
52 10 0.10
53 16 0.16
54 27 0.27
55 8 0.08
56 38 0.38
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.57
Consensus pattern (53 bp):
TTTTTACTGACTACCTTTTCTTACTCTTTTTACTGATTACCATTTCTACTTTT
Found at i:10950 original size:29 final size:28
Alignment explanation
Indices: 10818--10964 Score: 135
Period size: 29 Copynumber: 5.3 Consensus size: 28
10808 TATTTTACTC
*
10818 TTTACTGATTACCTTTTTC-TACCTTCTTCT
1 TTTACTGATTACCCTTTTCTTA-C-TCTT-T
* *
10848 TTTACTAACTA-CCTTTTCTTACTC-TT
1 TTTACTGATTACCCTTTTCTTACTCTTT
* * *
10874 TTTATTGATTA-CCATTTC-TACTTTTTT
1 TTTACTGATTACCCTTTTCTTAC-TCTTT
10901 TTTACTGATTACCCTTTTCTTACTCTGTT
1 TTTACTGATTACCCTTTTCTTACTCT-TT
* *
10930 TTTACTGATTACCCTTTTCTT-TTCTCT
1 TTTACTGATTACCCTTTTCTTACTCTTT
10957 TTTACTGA
1 TTTACTGA
10965 ATACTATTTC
Statistics
Matches: 98, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.03
26 16 0.16
27 22 0.22
28 13 0.13
29 33 0.34
30 11 0.11
ACGTcount: A:0.16, C:0.23, G:0.04, T:0.57
Consensus pattern (28 bp):
TTTACTGATTACCCTTTTCTTACTCTTT
Found at i:10960 original size:83 final size:83
Alignment explanation
Indices: 10818--10975 Score: 189
Period size: 83 Copynumber: 1.9 Consensus size: 83
10808 TATTTTACTC
* * *
10818 TTTACTGATTACCTTTTTCTACCTTCTTCTTTTACTAACTACCTTTTCTTACTCTTTTTATTGAT
1 TTTACTGATTACCCTTTTCTACCTTCTTCTTTTACTAACTACCTTTTCTTACTCTTTTTACTGAA
10883 TACCATTTCTACTTTTTT
66 TACCATTTCTACTTTTTT
* * *
10901 TTTACTGATTACCCTTTTCTTA-C-TCTGT-TTTTACTGATTACCCTTTTCTT-TTCTCTTTTAC
1 TTTACTGATTACCCTTTTC-TACCTTCT-TCTTTTACTAACTA-CCTTTTCTTACTCT-TTTTAC
*
10962 TGAATACTATTTCT
62 TGAATACCATTTCT
10976 TTTACTTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
82 16 0.25
83 46 0.72
84 2 0.03
ACGTcount: A:0.16, C:0.23, G:0.04, T:0.57
Consensus pattern (83 bp):
TTTACTGATTACCCTTTTCTACCTTCTTCTTTTACTAACTACCTTTTCTTACTCTTTTTACTGAA
TACCATTTCTACTTTTTT
Found at i:10985 original size:83 final size:83
Alignment explanation
Indices: 10810--10986 Score: 179
Period size: 83 Copynumber: 2.1 Consensus size: 83
10800 CTGATTACTA
* *
10810 TTTTAC-TCTTTACTGATTACCTTTTTCTACCTTCTTCTTTTACTAACTACCTTTTCTTACTCTT
1 TTTTACTTTTTTACTGATTACCCTTTTCTACCTTCTTCTTTTACTAACTACCTTTTCTTACTCTT
* *
10874 TTTATTGATTACCATTTC
66 TTTACTGAATACCATTTC
* *
10892 TACTTT--TTTTTTACTGATTACCCTTTTCTTA-C-TCTGT-TTTTACTGATTACCCTTTTCTT-
1 T--TTTACTTTTTTACTGATTACCCTTTTC-TACCTTCT-TCTTTTACTAACTA-CCTTTTCTTA
* *
10951 TTCTCTTTTACTGAATACTATTTC
61 CTCT-TTTTACTGAATACCATTTC
10975 TTTTACTTTTTT
1 TTTTACTTTTTT
10987 TTCTTTACTG
Statistics
Matches: 78, Mismatches: 8, Indels: 17
0.76 0.08 0.17
Matches are distributed among these distances:
81 3 0.04
82 17 0.22
83 53 0.68
84 5 0.06
ACGTcount: A:0.16, C:0.22, G:0.03, T:0.59
Consensus pattern (83 bp):
TTTTACTTTTTTACTGATTACCCTTTTCTACCTTCTTCTTTTACTAACTACCTTTTCTTACTCTT
TTTACTGAATACCATTTC
Found at i:10986 original size:27 final size:26
Alignment explanation
Indices: 10818--10986 Score: 94
Period size: 27 Copynumber: 6.1 Consensus size: 26
10808 TATTTTACTC
* *
10818 TTTACTGATTACCTTTTTCTACCTTCTTCT
1 TTTACTGAATACC-TTTTCT--TTTCTT-T
*
10848 TTTACT-AACTACCTTTTC-TTACTCTT
1 TTTACTGAA-TACCTTTTCTTTTCT-TT
* * *
10874 TTTATTGATTACCATTTCTACTTT-TTT
1 TTTACTGAATACCTTTTCT--TTTCTTT
* *
10901 TTTACTGATTACCCTTTTCTTACTCTGTT
1 TTTACTGAATA-CCTTTTCTT-TTCT-TT
* *
10930 TTTACTGATTACCCTTTTCTTTTCTCT
1 TTTACTGAATA-CCTTTTCTTTTCTTT
10957 TTTACTGAATA-CTATTTCTTTTACTTT
1 TTTACTGAATACCT-TTTCTTTT-CTTT
10984 TTT
1 TTT
10987 TTCTTTACTG
Statistics
Matches: 113, Mismatches: 14, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
25 2 0.02
26 26 0.23
27 32 0.28
28 12 0.11
29 31 0.27
30 10 0.09
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTACTGAATACCTTTTCTTTTCTTT
Found at i:10988 original size:56 final size:54
Alignment explanation
Indices: 10818--10988 Score: 129
Period size: 56 Copynumber: 3.1 Consensus size: 54
10808 TATTTTACTC
* *
10818 TTTACTGATTACCTTTTTCTACCTTCTTCTTTTACT-AACTACCTTTTC-TTAC-TCTT
1 TTTACTGATTACCATTTTCT--TTTC-TCTTTTACTGAA-TA-CTTTTCTTTACTTCTT
* * *
10874 TTTATTGATTACCATTTCTACTTTT-T-TTTTACTGATTACCCTTTTC-TTACTCTGTT
1 TTTACTGATTACCATTT-T-CTTTTCTCTTTTACTGAATA--CTTTTCTTTACT-TCTT
* *
10930 TTTACTGATTACCCTTTTCTTTTCTCTTTTACTGAATACTATTTCTTTTACTTTTT
1 TTTACTGATTACCATTTTCTTTTCTCTTTTACTGAATACT-TTTC-TTTACTTCTT
10986 TTT
1 TTT
10989 CTTTACTGAT
Statistics
Matches: 95, Mismatches: 9, Indels: 22
0.75 0.07 0.17
Matches are distributed among these distances:
53 9 0.09
54 20 0.21
55 6 0.06
56 52 0.55
57 6 0.06
58 2 0.02
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.59
Consensus pattern (54 bp):
TTTACTGATTACCATTTTCTTTTCTCTTTTACTGAATACTTTTCTTTACTTCTT
Found at i:11064 original size:36 final size:34
Alignment explanation
Indices: 11019--11138 Score: 126
Period size: 29 Copynumber: 3.6 Consensus size: 34
11009 ACTTTACTAA
*
11019 TTAC-TTTACCATTTTACTATTTACTTATTACTC
1 TTACTTTTACCATTTTACTATTTACTGATTACTC
*
11052 TTAACTTCTTACCATTTTACTCTTTACTGATTA--C
1 TT-ACTT-TTACCATTTTACTATTTACTGATTACTC
*
11086 -T--TTTTACCATTTTACTATTTACCGATTACTC
1 TTACTTTTACCATTTTACTATTTACTGATTACTC
11117 TTTACTTTTTTACCATTTTACT
1 -TTAC--TTTTACCATTTTACT
11139 CTTTTTAACT
Statistics
Matches: 72, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
29 23 0.32
30 2 0.03
31 1 0.01
33 4 0.06
34 3 0.04
35 1 0.01
36 23 0.32
37 15 0.21
ACGTcount: A:0.23, C:0.22, G:0.02, T:0.54
Consensus pattern (34 bp):
TTACTTTTACCATTTTACTATTTACTGATTACTC
Found at i:11085 original size:22 final size:22
Alignment explanation
Indices: 11046--11142 Score: 69
Period size: 22 Copynumber: 4.4 Consensus size: 22
11036 TATTTACTTA
* *
11046 TTACTCTTAACTTCTTACCATT
1 TTACTCTTTACTTATTACCATT
* *
11068 TTACTCTTTACTGATTA-CTTT
1 TTACTCTTTACTTATTACCATT
11089 TTAC-CATTTTAC-TATTTACCGA--
1 TTACTC--TTTACTTA-TTACC-ATT
*
11111 TTACTCTTTACTTTTTTACCATT
1 TTACTCTTTAC-TTATTACCATT
11134 TTACTCTTT
1 TTACTCTTT
11143 TTAACTTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
20 1 0.02
21 14 0.24
22 31 0.53
23 12 0.21
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.55
Consensus pattern (22 bp):
TTACTCTTTACTTATTACCATT
Found at i:11221 original size:40 final size:40
Alignment explanation
Indices: 11166--11548 Score: 165
Period size: 40 Copynumber: 10.1 Consensus size: 40
11156 TAAATACCAT
**
11166 CTTTTGAC-CTTAATTACTGATTTACTGAC-TACTTCCTTTA
1 CTTTT-ACTCTTAATTACCAATTTACTG-CTTACTTCCTTTA
* *
11206 CTTTTACTCTTAATTACCAATTTACTGCTTCCTTCTTTTA
1 CTTTTACTCTTAATTACCAATTTACTGCTTACTTCCTTTA
* * *
11246 CTTTTACTC-CATTCTACTAA-TT--T-CTT-C-T--TTTA
1 CTTTTACTCTTAAT-TACCAATTTACTGCTTACTTCCTTTA
* * * * *
11278 CCTTGATTCTTAATTACCCATTTACTG---A-TTAC-TT-
1 CTTTTACTCTTAATTACCAATTTACTGCTTACTTCCTTTA
* * * ** *
11312 CTTTTACTC----TTGCCATTTTTCTAATTACTTCTTTTA
1 CTTTTACTCTTAATTACCAATTTACTGCTTACTTCCTTTA
* * *
11348 CTTTCT-CTCTTAATTATCAATTTACTGATTAATT--TTTA
1 CTTT-TACTCTTAATTACCAATTTACTGCTTACTTCCTTTA
** * * *
11386 CTTTTACTCTTAATTACTGATTGACTGATTACTTCTTTTA
1 CTTTTACTCTTAATTACCAATTTACTGCTTACTTCCTTTA
* * * *
11426 CTTCCT-CTCTTAATTATCAATTTACTGATTACTTTC-TTA
1 CTT-TTACTCTTAATTACCAATTTACTGCTTACTTCCTTTA
* * * * * *
11465 CTTTCACTTTTAGTTACCAATTTACCGATTAC-CCCTTTTA
1 CTTTTACTCTTAATTACCAATTTACTGCTTACTTCC-TTTA
* *
11505 CTTTTACTCTTAATTACCAAGTTACTACTTACTT-CTTGTA
1 CTTTTACTCTTAATTACCAATTTACTGCTTACTTCCTT-TA
11545 CTTT
1 CTTT
11549 CACCCCATTC
Statistics
Matches: 253, Mismatches: 58, Indels: 64
0.67 0.15 0.17
Matches are distributed among these distances:
30 9 0.04
32 14 0.06
33 5 0.02
34 10 0.04
35 6 0.02
36 10 0.04
37 3 0.01
38 32 0.13
39 37 0.15
40 126 0.50
41 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.51
Consensus pattern (40 bp):
CTTTTACTCTTAATTACCAATTTACTGCTTACTTCCTTTA
Found at i:11291 original size:72 final size:70
Alignment explanation
Indices: 11195--11459 Score: 205
Period size: 72 Copynumber: 3.6 Consensus size: 70
11185 ATTTACTGAC
* * * * * *
11195 TACTTCCTTTACTT-TTACTCTTAATTACCAATTTACTGCTTCCTTCTTTTACTTTTACTCCATT
1 TACTTCTTTTACTTGAT-CTCTTAATTACCAATTTACTGATTACTTCTTTTACTCTT--GCCATT
11259 CTACTAAT
63 CTACTAAT
* * *
11267 TTCTTCTTTTACCTTGAT-TCTTAATTACCCATTTACTGATTACTTCTTTTACTCTTGCCATTTT
1 TACTTCTTTTA-CTTGATCTCTTAATTACCAATTTACTGATTACTTCTTTTACTCTTGCCATTCT
*
11331 TCTAAT
65 ACTAAT
** * * *
11337 TACTTCTTTTACTTTCTCTCTTAATTATCAATTTACTGATTAATTTTTACTTTTACTCTT--AAT
1 TACTTCTTTTACTTGATCTCTTAATTACCAATTTACTGATT-A--CTT-CTTTTACTCTTGCCAT
*
11400 TACTGATTGACTGAT
62 T-C----T-ACTAAT
** *
11415 TACTTCTTTTACTTCCTCTCTTAATTATCAATTTACTGATTACTT
1 TACTTCTTTTACTTGATCTCTTAATTACCAATTTACTGATTACTT
11460 TCTTACTTTC
Statistics
Matches: 158, Mismatches: 22, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
69 4 0.03
70 42 0.27
71 1 0.01
72 46 0.29
73 5 0.03
74 12 0.08
75 2 0.01
77 2 0.01
78 44 0.28
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (70 bp):
TACTTCTTTTACTTGATCTCTTAATTACCAATTTACTGATTACTTCTTTTACTCTTGCCATTCTA
CTAAT
Found at i:11423 original size:78 final size:79
Alignment explanation
Indices: 11335--11530 Score: 252
Period size: 79 Copynumber: 2.5 Consensus size: 79
11325 CATTTTTCTA
*
11335 ATTACTTCTTTTACTTTCTCTCTTAATTATCAATTTACTGATTAATTT-TTACTTTTACTCTTAA
1 ATTACTTCTTTTACTTTCTCTCTTAATTATCAATTTACTGATTAATTTCTTACTTTCACTCTTAA
** *
11399 TTACTGATTGACTG
66 TTACCAATTGACCG
* * * *
11413 ATTACTTCTTTTACTTCCTCTCTTAATTATCAATTTACTGATTACTTTCTTACTTTCACTTTTAG
1 ATTACTTCTTTTACTTTCTCTCTTAATTATCAATTTACTGATTAATTTCTTACTTTCACTCTTAA
*
11478 TTACCAATTTACCG
66 TTACCAATTGACCG
** * *
11492 ATTACCCCTTTTACTTT-TACTCTTAATTACCAAGTTACT
1 ATTACTTCTTTTACTTTCT-CTCTTAATTATCAATTTACT
11531 ACTTACTTCT
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
78 47 0.46
79 55 0.54
ACGTcount: A:0.24, C:0.21, G:0.04, T:0.51
Consensus pattern (79 bp):
ATTACTTCTTTTACTTTCTCTCTTAATTATCAATTTACTGATTAATTTCTTACTTTCACTCTTAA
TTACCAATTGACCG
Found at i:11579 original size:32 final size:32
Alignment explanation
Indices: 11533--11924 Score: 541
Period size: 32 Copynumber: 12.2 Consensus size: 32
11523 AAGTTACTAC
* * * *
11533 TTACTTCTTGTACTTTCACCCCATTCTTCTGA
1 TTACTTCTTTTACTTTTACTCCATTCTACTGA
*
11565 TTTCTTCTTTTACTTTTACTCCATTCTACTGA
1 TTACTTCTTTTACTTTTACTCCATTCTACTGA
* * *
11597 TTATTTCTTTTACTCTTACTCCATTCTGCTGA
1 TTACTTCTTTTACTTTTACTCCATTCTACTGA
* *
11629 TTACTTTTTTTTACTTTTACTCCATTCTATTGA
1 TTAC-TTCTTTTACTTTTACTCCATTCTACTGA
* *
11662 TTACTTATTTTACTTTTACTCCATTTTACTGA
1 TTACTTCTTTTACTTTTACTCCATTCTACTGA
* * *
11694 TTATTTCTTTTACTTTTACTTCATTTTACTGA
1 TTACTTCTTTTACTTTTACTCCATTCTACTGA
* *
11726 TTACTTCCTCTTACTTTTACTCCATTTTACTGA
1 TTACTT-CTTTTACTTTTACTCCATTCTACTGA
* *
11759 CTACTTCTTTTACTTTTACTCCATTCTACTAA
1 TTACTTCTTTTACTTTTACTCCATTCTACTGA
*
11791 TTACTTCTTTTACTTTTACTCCATTCTACTAA
1 TTACTTCTTTTACTTTTACTCCATTCTACTGA
* * *
11823 TTAGTTCTTTTACTTTTGCTCAATTCTACTGA
1 TTACTTCTTTTACTTTTACTCCATTCTACTGA
*
11855 TTACTTCTTTTACTTTCACTCCATTCTACTGA
1 TTACTTCTTTTACTTTTACTCCATTCTACTGA
*
11887 TTACTTCTTTTACTTTCACTCCATTCTACTGA
1 TTACTTCTTTTACTTTTACTCCATTCTACTGA
11919 TTACTT
1 TTACTT
11925 TCTCTTTTAC
Statistics
Matches: 322, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
32 265 0.82
33 57 0.18
ACGTcount: A:0.19, C:0.24, G:0.04, T:0.54
Consensus pattern (32 bp):
TTACTTCTTTTACTTTTACTCCATTCTACTGA
Found at i:11673 original size:97 final size:97
Alignment explanation
Indices: 11533--11936 Score: 542
Period size: 97 Copynumber: 4.2 Consensus size: 97
11523 AAGTTACTAC
* * * * *
11533 TTAC-TTCTTGTACTTTCACCCCATTCTTCTGATTTCTTCTTTTACTTTTACTCCATTCTACTGA
1 TTACTTTCTTTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGA
* * *
11597 TTATTTCTTTTACTCTTACTCCATTCTGCTGA
66 TTACTTCTTTTACTTTTACTCCATTCTACTGA
* * * *
11629 TTACTTTTTTTTACTTTTACTCCATTCTATTGATTACTTATTTTACTTTTACTCCATTTTACTGA
1 TTACTTTCTTTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGA
* * *
11694 TTATTTCTTTTACTTTTACTTCATTTTACTGA
66 TTACTTCTTTTACTTTTACTCCATTCTACTGA
* * * * *
11726 TTACTTCCTCTTACTTTTACTCCATTTTACTGACTACTTCTTTTACTTTTACTCCATTCTACTAA
1 TTACTTTCTTTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGA
*
11791 TTACTTCTTTTACTTTTACTCCATTCTACTAA
66 TTACTTCTTTTACTTTTACTCCATTCTACTGA
* * * *
11823 TTA-GTTCTTTTACTTTTGCTCAATTCTACTGATTACTTCTTTTACTTTCACTCCATTCTACTGA
1 TTACTTTCTTTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGA
*
11887 TTACTTCTTTTACTTTCACTCCATTCTACTGA
66 TTACTTCTTTTACTTTTACTCCATTCTACTGA
11919 TTACTTTCTCTTTTACTT
1 TTAC-TT-TCTTTTACTT
11937 CTTTAACTTA
Statistics
Matches: 266, Mismatches: 38, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
96 89 0.33
97 166 0.62
98 1 0.00
99 10 0.04
ACGTcount: A:0.18, C:0.24, G:0.03, T:0.54
Consensus pattern (97 bp):
TTACTTTCTTTTACTTTTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTACTGA
TTACTTCTTTTACTTTTACTCCATTCTACTGA
Found at i:12056 original size:51 final size:49
Alignment explanation
Indices: 11929--12074 Score: 141
Period size: 51 Copynumber: 2.9 Consensus size: 49
11919 TTACTTTCTC
* * * *
11929 TTTTACTTCTTTAACTTAATTACTTTGAATTAAACTAATCTACTGATTACT
1 TTTTACTT-TTTAGCTTAGTTACTCTGAATTAAACTAA-CTACTGACTACT
* * * * *
11980 TTTTCCTTCTTAGC-TCGATTGCTCTGAATTAAACTAACTACTTACTACCAT
1 TTTTACTTTTTAGCTTAG-TTACTCTGAATTAAACTAACTACTGACTA-C-T
* *
12031 TTTTGCTTTTTAGCTTAGTTACTCTGAATTAAACTAATTACTGA
1 TTTTACTTTTTAGCTTAGTTACTCTGAATTAAACTAACTACTGA
12075 TCACCTTCTC
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
49 9 0.12
50 22 0.29
51 43 0.57
52 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (49 bp):
TTTTACTTTTTAGCTTAGTTACTCTGAATTAAACTAACTACTGACTACT
Found at i:12968 original size:76 final size:76
Alignment explanation
Indices: 12837--12983 Score: 276
Period size: 76 Copynumber: 1.9 Consensus size: 76
12827 CTCAGATCCG
*
12837 GCCTTGGTTCTCTCCGAAACAACCCCTAACCCTTTGAATCTAGCCTATACTGAACCTACTTCCCA
1 GCCTTGGTTCTCTCCGAAACAACCCCTAACCCTTTGAATCTAGCCTATACCGAACCTACTTCCCA
12902 CTTCCGGTCCA
66 CTTCCGGTCCA
*
12913 GCCTTGGTTCTCTCCGAAACACCCCCTAACCCTTTGAATCTAGCCTATACCGAACCTACTTCCCA
1 GCCTTGGTTCTCTCCGAAACAACCCCTAACCCTTTGAATCTAGCCTATACCGAACCTACTTCCCA
12978 CTTCCG
66 CTTCCG
12984 ATCCGGTGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.22, C:0.39, G:0.12, T:0.27
Consensus pattern (76 bp):
GCCTTGGTTCTCTCCGAAACAACCCCTAACCCTTTGAATCTAGCCTATACCGAACCTACTTCCCA
CTTCCGGTCCA
Found at i:20667 original size:2 final size:2
Alignment explanation
Indices: 20625--20651 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20615 TTAGGTTATG
20625 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20652 CACATTTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.