Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 142 of 199
Found at i:42693647 original size:55 final size:55
Alignment explanation
Indices: 42693586--42693693 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
42693576 TCCTAAAATT
* *
42693586 CAATTTAGATTCTAATATAAAATCCTAAATTCTAAAATATAATCTTTTTTAAAGA
1 CAATTTAGATTCTAATAAAAAATCCTAAAGTCTAAAATATAATCTTTTTTAAAGA
* *
42693641 CAATTTAGATTCTAATAAAAAATCCTAAAGTCTAAAATCTATTCTTTTTTAAA
1 CAATTTAGATTCTAATAAAAAATCCTAAAGTCTAAAATATAATCTTTTTTAAA
42693694 AGAAAAGCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (55 bp):
CAATTTAGATTCTAATAAAAAATCCTAAAGTCTAAAATATAATCTTTTTTAAAGA
Found at i:42699522 original size:13 final size:13
Alignment explanation
Indices: 42699504--42699528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42699494 AAGCTACTAT
42699504 AAAATCTTAAATA
1 AAAATCTTAAATA
42699517 AAAATCTTAAAT
1 AAAATCTTAAAT
42699529 TCTAAAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATCTTAAATA
Found at i:42699664 original size:73 final size:72
Alignment explanation
Indices: 42699513--42699982 Score: 404
Period size: 73 Copynumber: 6.5 Consensus size: 72
42699503 TAAAATCTTA
* * * *
42699513 AATA-AAAATCTTAAATTCTAAAATTTAATTCTAATAT-AAATATAAATTCCTAAAAGTC-AATT
1 AATATAAAATCCTAAAGTCTAAAATCTAATTCTAATATAAAATATAAAATCCTAAAA-TCTAATT
*
42699575 TAAATTCT
65 AAAATTCT
* **
42699583 AATATAAAATCCTAAAGTATAAAATCT-ATTCTAATATAAAAATATAAAATCCTAGCATCTAATT
1 AATATAAAATCCTAAAGTCTAAAATCTAATTCTAATAT-AAAATATAAAATCCTAAAATCTAATT
42699647 AAAAATTCT
65 -AAAATTCT
* * * *
42699656 ACTATAAAAATCTTAAATTCTAAAATATAATTCTAATAT-AAATATAAAATCCTAAAATCTAACT
1 AATAT-AAAATCCTAAAGTCTAAAATCTAATTCTAATATAAAATATAAAATCCTAAAATCTAA-T
42699720 T-AAATTCT
64 TAAAATTCT
* * * * * * **
42699728 AATATAAATGTCCTAAAGTCTAGAATAT-ATTCTAATATAAAAAAATGAAACCCTAGCATCTAAT
1 AATATAAA-ATCCTAAAGTCTAAAATCTAATTCTAATAT-AAAATATAAAATCCTAAAATCTAA-
42699792 TTAAAA-TCT
63 TTAAAATTCT
* * * * * * * *
42699801 ACTAGAAAATCTTAAATTCTAAAATTTAATTCTAATAT-AAATAAAAAATTCTAAAATCTAGCTT
1 AATATAAAATCCTAAAGTCTAAAATCTAATTCTAATATAAAATATAAAATCCTAAAATCTA-ATT
42699865 -AAATTCT
65 AAAATTCT
* * * * *
42699872 AATATAAAAATCCTAAGGTCTAGATTCT-ATTCTAATATACAAATATGAAATCCTATAATCTAAT
1 AATAT-AAAATCCTAAAGTCTAAAATCTAATTCTAATATA-AAATATAAAATCCTAAAATCTAAT
*
42699936 TAAAAAATCT
64 T-AAAATTCT
* * * * *
42699946 ACTATAAACTCTTAAATTCCAAAATCTAATTCTAATA
1 AATATAAAATCCTAAAGTCTAAAATCTAATTCTAATA
42699983 AAATCTAACT
Statistics
Matches: 316, Mismatches: 63, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
70 17 0.05
71 66 0.21
72 77 0.24
73 104 0.33
74 42 0.13
75 10 0.03
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (72 bp):
AATATAAAATCCTAAAGTCTAAAATCTAATTCTAATATAAAATATAAAATCCTAAAATCTAATTA
AAATTCT
Found at i:42699687 original size:41 final size:41
Alignment explanation
Indices: 42699583--42699735 Score: 98
Period size: 41 Copynumber: 4.0 Consensus size: 41
42699573 TTTAAATTCT
* **
42699583 AATATAAAATCCTAAAGTATAA--AATCTATTCTAATATAAA
1 AATATAAAATCCTAAAATATAATTAA-AAATTCTAATATAAA
** * *
42699623 AATATAAAATCCTAGCATCTAATTAAAAATTCTACTATAAA
1 AATATAAAATCCTAAAATATAATTAAAAATTCTAATATAAA
* * *
42699664 AATCTTAAATTCT-AAA-AT-A-T---AATTCTAATAT--A
1 AATATAAAATCCTAAAATATAATTAAAAATTCTAATATAAA
*
42699696 AATATAAAATCCTAAAATCTAACTT--AAATTCTAATATAAA
1 AATATAAAATCCTAAAATATAA-TTAAAAATTCTAATATAAA
42699736 TGTCCTAAAG
Statistics
Matches: 85, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
32 11 0.13
33 3 0.04
34 11 0.13
35 1 0.01
37 2 0.02
38 12 0.14
39 1 0.01
40 20 0.24
41 22 0.26
42 2 0.02
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (41 bp):
AATATAAAATCCTAAAATATAATTAAAAATTCTAATATAAA
Found at i:42699723 original size:145 final size:145
Alignment explanation
Indices: 42699514--42700123 Score: 690
Period size: 144 Copynumber: 4.3 Consensus size: 145
42699504 AAAATCTTAA
* * *
42699514 ATAAAAATCTTAAATTCTAAAATTTAATTCTAATATAAATATAAATTCCTAAAAGTC-AATTTAA
1 ATAAAAATCTTAAATTCTAAAATATAATTCTAATATAAATATAAAATCCTAAAA-TCTAACTTAA
* * * *
42699578 ATTCTAATATAAAATCCTAAAGTATAAAATCTATTCTAATATAAAAATATAAAATCCTAGCATCT
65 ATTCTAATATAAAATCCTAAAGTCTAGAATCTATTCTAATATAAAAATATGAAATCCTAGAATCT
*
42699643 AATTAAAAATTCTACT
130 AATTAAAAAATCTACT
42699659 ATAAAAATCTTAAATTCTAAAATATAATTCTAATATAAATATAAAATCCTAAAATCTAACTTAAA
1 ATAAAAATCTTAAATTCTAAAATATAATTCTAATATAAATATAAAATCCTAAAATCTAACTTAAA
* * * * *
42699724 TTCTAATATAAATGTCCTAAAGTCTAGAATATATTCTAATATAAAAAAATGAAACCCTAGCATCT
66 TTCTAATATAAA-ATCCTAAAGTCTAGAATCTATTCTAATATAAAAATATGAAATCCTAGAATCT
*
42699789 AATT-TAAAATCTACT
130 AATTAAAAAATCTACT
* * * * *
42699804 A-GAAAATCTTAAATTCTAAAATTTAATTCTAATATAAATAAAAAATTCTAAAATCTAGCTTAAA
1 ATAAAAATCTTAAATTCTAAAATATAATTCTAATATAAATATAAAATCCTAAAATCTAACTTAAA
* * * *
42699868 TTCTAATATAAAAATCCTAAGGTCTAGATTCTATTCTAATATACAAATATGAAATCCTATAATCT
66 TTCTAATAT-AAAATCCTAAAGTCTAGAATCTATTCTAATATAAAAATATGAAATCCTAGAATCT
42699933 AATTAAAAAATCTACT
130 AATTAAAAAATCTACT
* * *
42699949 AT-AAACTCTTAAATTC---CA-A-AA-TCT-A-AT---TCT--AA---TAAAATCTAACTTAAA
1 ATAAAAATCTTAAATTCTAAAATATAATTCTAATATAAATATAAAATCCTAAAATCTAACTTAAA
* *
42699997 TT-TCAATATAAAACTCC-GAAGATCTACAATCTATTCTAATATAAAAATATGAAATCCTAGAAT
66 TTCT-AATATAAAA-TCCTAAAG-TCTAGAATCTATTCTAATATAAAAATATGAAATCCTAGAAT
* * *
42700060 CCATTTAAAAGAAACTACT
128 CTAATTAAAA-AATCTACT
* *
42700079 A-CAAAATCTTAAATTCTAAAAATCTAATTCTAATATAAATATAAA
1 ATAAAAATCTTAAATTCT-AAAATATAATTCTAATATAAATATAAA
42700124 TATAAATATA
Statistics
Matches: 395, Mismatches: 46, Indels: 49
0.81 0.09 0.10
Matches are distributed among these distances:
128 7 0.02
129 70 0.18
130 21 0.05
132 2 0.01
134 2 0.01
136 2 0.01
137 5 0.01
138 2 0.01
139 5 0.01
140 2 0.01
142 3 0.01
144 117 0.30
145 108 0.27
146 49 0.12
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (145 bp):
ATAAAAATCTTAAATTCTAAAATATAATTCTAATATAAATATAAAATCCTAAAATCTAACTTAAA
TTCTAATATAAAATCCTAAAGTCTAGAATCTATTCTAATATAAAAATATGAAATCCTAGAATCTA
ATTAAAAAATCTACT
Found at i:42699894 original size:33 final size:33
Alignment explanation
Indices: 42699840--42699915 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
42699830 TTCTAATATA
* *
42699840 AATA-AAAAATTCTAAAATCTAGCTTAAATTCT
1 AATATAAAAATCCTAAAATCTAGATTAAATTCT
** **
42699872 AATATAAAAATCCTAAGGTCTAGATTCTATTCT
1 AATATAAAAATCCTAAAATCTAGATTAAATTCT
*
42699905 AATATACAAAT
1 AATATAAAAAT
42699916 ATGAAATCCT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (33 bp):
AATATAAAAATCCTAAAATCTAGATTAAATTCT
Found at i:42699997 original size:129 final size:129
Alignment explanation
Indices: 42699852--42700217 Score: 406
Period size: 129 Copynumber: 2.9 Consensus size: 129
42699842 TAAAAAATTC
* * *
42699852 TAAAATCTAGCTTAAATTCTAATATAAAAATCCTAAGGTCTAGATTCTATTCTAATATACAAATA
1 TAAAATCTAACTTAAATT-TAATATAAAAATCCTAAGATCTAGATTCTATTCTAATATAAAAATA
* * *
42699917 TGAAATCCTATAATCTAATTAAAAAATCTACTATAAACTCTTAAATTC-CAAAATCTAATTCTAA
65 TGAAATCCTACAATCTAATTAAAAAATCTACTATAAAATCTTAAATTCTAAAAATCTAATTCTAA
* * * *
42699981 TAAAATCTAACTTAAATTTCAATATAAAACTCCGAAGATCTACAATCTATTCTAATATAAAAATA
1 TAAAATCTAACTTAAATTT-AATATAAAAATCCTAAGATCTAGATTCTATTCTAATATAAAAATA
* * * * *
42700046 TGAAATCCTAGAATCCATTTAAAAGAAACTACTACAAAATCTTAAATTCTAAAAATCTAATTCTA
65 TGAAATCCTACAATCTAATTAAAA-AATCTACTATAAAATCTTAAATTCTAAAAATCTAATTCTA
42700111 A
129 A
* * * **
42700112 TATAAA--T-A--TAAATATAA-ATATAAAATCCTAAAATCTAGCTTAAATTCTAATATAAAAAT
1 TA-AAATCTAACTTAAATTTAATATA-AAAATCCTAAGATCTAGATTCTATTCTAATATAAAAAT
* * * *
42700171 AT-AGCATCTTACAATCTAATTAAAAAATCTACCATAAAATCTGAAAT
64 ATGA-AATCCTACAATCTAATTAAAAAATCTACTATAAAATCTTAAAT
42700218 AAAAATCTAA
Statistics
Matches: 199, Mismatches: 32, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
125 22 0.11
126 50 0.25
127 6 0.03
128 1 0.01
129 78 0.39
130 22 0.11
131 17 0.09
132 3 0.02
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.33
Consensus pattern (129 bp):
TAAAATCTAACTTAAATTTAATATAAAAATCCTAAGATCTAGATTCTATTCTAATATAAAAATAT
GAAATCCTACAATCTAATTAAAAAATCTACTATAAAATCTTAAATTCTAAAAATCTAATTCTAA
Found at i:42700119 original size:6 final size:6
Alignment explanation
Indices: 42700110--42700135 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42700100 ATCTAATTCT
42700110 AATATA AATATA AATATA AATATA AA
1 AATATA AATATA AATATA AATATA AA
42700136 ATCCTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:42700170 original size:25 final size:24
Alignment explanation
Indices: 42700141--42700226 Score: 59
Period size: 25 Copynumber: 3.3 Consensus size: 24
42700131 ATAAAATCCT
42700141 AAAATCTAGCTTAAATTCTAATATA
1 AAAATCTAGCTTAAA-TCTAATATA
*
42700166 AAAATATAGCATCTTACAATCTAAT-TAA
1 AAAATCTAG---CTTA-AATCTAATAT-A
* *
42700194 AAAATCTACCATAAAATCTGAA-ATA
1 AAAATCTAGC-TTAAATCT-AATATA
42700219 AAAATCTA
1 AAAATCTA
42700227 AAATTCTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
25 23 0.47
26 5 0.10
27 1 0.02
28 18 0.37
29 2 0.04
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.30
Consensus pattern (24 bp):
AAAATCTAGCTTAAATCTAATATA
Found at i:42702863 original size:26 final size:26
Alignment explanation
Indices: 42702825--42702876 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
42702815 AACATGGGAC
* *
42702825 ATAAGAAATTAACATTGGAATATAAA
1 ATAAGAAACTAACATTAGAATATAAA
42702851 ATAAGAAACTAACATTAGAATATAAA
1 ATAAGAAACTAACATTAGAATATAAA
42702877 CCAAATCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.60, C:0.06, G:0.10, T:0.25
Consensus pattern (26 bp):
ATAAGAAACTAACATTAGAATATAAA
Found at i:42703898 original size:16 final size:15
Alignment explanation
Indices: 42703877--42703906 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42703867 AACATTTATT
42703877 AAAATAAATATAATTA
1 AAAATAAATA-AATTA
42703893 AAAATAAATAAATT
1 AAAATAAATAAATT
42703907 TACAACAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAATAAATTA
Found at i:42714339 original size:21 final size:22
Alignment explanation
Indices: 42714315--42714361 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
42714305 CTCTGCTCAA
*
42714315 ACTCCACCTGATGCGGAGTAC-
1 ACTCCACCTGATGCGAAGTACT
*
42714336 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGATGCGAAGTACT
42714358 ACTC
1 ACTC
42714362 ACTCCTTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGATGCGAAGTACT
Found at i:42724028 original size:14 final size:15
Alignment explanation
Indices: 42724009--42724037 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42723999 AAGATTAGTT
42724009 TGTAATTAT-TTTTA
1 TGTAATTATATTTTA
42724023 TGTAATTATATTTTA
1 TGTAATTATATTTTA
42724038 CATTGATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
TGTAATTATATTTTA
Found at i:42738307 original size:19 final size:19
Alignment explanation
Indices: 42738285--42738322 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
42738275 TCAATCATCC
42738285 CTCATCTCATCA-TCTCTCA
1 CTCAT-TCATCATTCTCTCA
42738304 CTCATTCATCATTCTCTCA
1 CTCATTCATCATTCTCTCA
42738323 ACTCTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (19 bp):
CTCATTCATCATTCTCTCA
Found at i:42738444 original size:13 final size:13
Alignment explanation
Indices: 42738422--42738457 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
42738412 AGAGCCATCA
42738422 GCAAAGAAGCAAC
1 GCAAAGAAGCAAC
*
42738435 GCAGAGAAGCAAC
1 GCAAAGAAGCAAC
42738448 GCAAAGAAGC
1 GCAAAGAAGC
42738458 GAAGGAGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.50, C:0.22, G:0.28, T:0.00
Consensus pattern (13 bp):
GCAAAGAAGCAAC
Found at i:42754800 original size:39 final size:39
Alignment explanation
Indices: 42754733--42754873 Score: 158
Period size: 39 Copynumber: 3.6 Consensus size: 39
42754723 CATATTCAAT
* * *
42754733 TTTAAGCATATATC-CTATTACACATATAATCACCTAACA
1 TTTAAGCATATATCAC-AATACTCATATAATCACATAACA
* * * **
42754772 CTCAAGCATATATCACAATACTCGTATAAAAACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
42754811 TTTAAGCATATATCACAGTACTCATATAATCATATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
42754850 TTTAAGCATAAATCAGAATACTCA
1 TTTAAGCATATATCACAATACTCA
42754874 AAAACATGTT
Statistics
Matches: 83, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
39 82 0.99
40 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:42757931 original size:28 final size:28
Alignment explanation
Indices: 42757888--42757942 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
42757878 GGGCATGTCA
*
42757888 AGTACTTTTTAACGGTGTTACAGTATCT
1 AGTACTTTGTAACGGTGTTACAGTATCT
*
42757916 AGTACTTTGTATCGGTGTTACAGTATC
1 AGTACTTTGTAACGGTGTTACAGTATC
42757943 AGACACTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (28 bp):
AGTACTTTGTAACGGTGTTACAGTATCT
Found at i:42757959 original size:28 final size:28
Alignment explanation
Indices: 42757900--42757963 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
42757890 TACTTTTTAA
* * *
42757900 CGGTGTTACAGTATCTAGTACTTTGTAT
1 CGGTGTTACAGTATCTAGCACTCTGTAC
*
42757928 CGGTGTTACAGTATC-AGACACTCTGTGC
1 CGGTGTTACAGTATCTAG-CACTCTGTAC
42757956 CGGTGTTA
1 CGGTGTTA
42757964 TATTTATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (28 bp):
CGGTGTTACAGTATCTAGCACTCTGTAC
Found at i:42767669 original size:18 final size:17
Alignment explanation
Indices: 42767625--42767669 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
42767615 GTCTCAGATC
*
42767625 AAAAAATAATTAAAATT
1 AAAAAATATTTAAAATT
42767642 ATAAAAATATTTCAAAATT
1 A-AAAAATATTT-AAAATT
42767661 AAAAAATAT
1 AAAAAATAT
42767670 ATAAGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 17 0.68
19 7 0.28
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAAATATTTAAAATT
Found at i:42767678 original size:18 final size:17
Alignment explanation
Indices: 42767625--42767678 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
42767615 GTCTCAGATC
42767625 AAAAAATA-ATTAAAATT
1 AAAAAATATA-TAAAATT
*
42767642 ATAAAAATATTTCAAAATT
1 A-AAAAATATAT-AAAATT
42767661 AAAAAATATATAAGAATT
1 AAAAAATATATAA-AATT
42767679 TCATAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 3 0.10
18 21 0.68
19 7 0.23
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAAAATATATAAAATT
Found at i:42769547 original size:14 final size:15
Alignment explanation
Indices: 42769512--42769547 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
42769502 ACCACATACC
*
42769512 AAACAACTCACATAT
1 AAACAAATCACATAT
42769527 AAACAAATCACATAT
1 AAACAAATCACATAT
42769542 -AACAAA
1 AAACAAA
42769548 CCGCATATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.61, C:0.22, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACAAATCACATAT
Found at i:42769554 original size:14 final size:15
Alignment explanation
Indices: 42769501--42769555 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
42769491 CACATCGATT
*
42769501 AACCACATACCAAAC-
1 AACCACATA-TAAACA
42769516 AACTCACATATAAACA
1 AAC-CACATATAAACA
*
42769532 AATCACATAT-AACA
1 AACCACATATAAACA
*
42769546 AACCGCATAT
1 AACCACATAT
42769556 CATCGGCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 12 0.35
15 14 0.41
16 8 0.24
ACGTcount: A:0.53, C:0.29, G:0.02, T:0.16
Consensus pattern (15 bp):
AACCACATATAAACA
Found at i:42770359 original size:26 final size:26
Alignment explanation
Indices: 42770319--42770378 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
42770309 TCGCATATAT
*
42770319 ATATATATATATATATAGCAGTTCGC
1 ATATATATATATATACAGCAGTTCGC
* * *
42770345 ATATGTATATTTATACATCAGTTCGC
1 ATATATATATATATACAGCAGTTCGC
*
42770371 ATTTATAT
1 ATATATAT
42770379 GGTTAACAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (26 bp):
ATATATATATATATACAGCAGTTCGC
Found at i:42772726 original size:17 final size:16
Alignment explanation
Indices: 42772706--42772739 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42772696 GACTTTTATT
42772706 ATCAAGTATATATAGAA
1 ATCAAGTA-ATATAGAA
*
42772723 ATCATGTAATATAGAA
1 ATCAAGTAATATAGAA
42772739 A
1 A
42772740 GTATGGTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (16 bp):
ATCAAGTAATATAGAA
Found at i:42777811 original size:22 final size:23
Alignment explanation
Indices: 42777765--42777837 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
42777755 GTGTAACACC
* *
42777765 CTAACTCGTATCCGATGCTGGAA
1 CTAACCCGTATCTGATGCTGGAA
42777788 CTAACCCGTATCTGATG-TGGAA
1 CTAACCCGTATCTGATGCTGGAA
*
42777810 CTAACCCGTATCTGATGCCGGAA
1 CTAACCCGTATCTGATGCTGGAA
42777833 CTAAC
1 CTAAC
42777838 AATGTCAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 22 0.48
23 24 0.52
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (23 bp):
CTAACCCGTATCTGATGCTGGAA
Found at i:42783500 original size:101 final size:102
Alignment explanation
Indices: 42783383--42783565 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 102
42783373 AAAGTGATGG
* *
42783383 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCT-GA-A-TGATAGGTCACATGTGTAG
1 TCACGTGTATAGTACTATGTGCAGGCTACTACGTGTA-CTGGATAGTGAT-GGTCACATGTGTAG
*
42783445 TACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
64 AACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
*
42783484 TCACGTGTATAGTACTATGTGCAGGCTACTACGTGTATTGGATAGTGATGGTCACATGTGTAGAA
1 TCACGTGTATAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTGATGGTCACATGTGTAGAA
42783549 CTATGTGCAGGCTACTA
66 CTATGTGCAGGCTACTA
42783566 AGTGAACCGG
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
100 1 0.01
101 37 0.49
102 33 0.44
103 4 0.05
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACGTGTATAGTACTATGTGCAGGCTACTACGTGTACTGGATAGTGATGGTCACATGTGTAGAA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:42783527 original size:51 final size:49
Alignment explanation
Indices: 42783380--42783565 Score: 212
Period size: 51 Copynumber: 3.7 Consensus size: 49
42783370 GTGAAAGTGA
* *
42783380 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCTGAAT-GAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTA-CTGGATAG-T
* * *
42783430 AGGTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGATAG-T
* * * * *
42783480 TCGATCACGTGTATAGTACTATGTGCAGGCTACTACGTGTATTGGATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGATAGT
*
42783530 GATGGTCACATGTGTAGAACTATGTGCAGGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
42783566 AGTGAACCGG
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
49 4 0.04
50 40 0.35
51 69 0.61
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGATAGT
Found at i:42783575 original size:102 final size:101
Alignment explanation
Indices: 42783383--42783575 Score: 282
Period size: 102 Copynumber: 1.9 Consensus size: 101
42783373 AAAGTGATGG
* * *
42783383 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCTGAATGATAGGTCACATGTGTAGTAC
1 TCACGTGTATAGTACTATGTGCAGGCTACTACGTGTACCTGAATGATAGGTCACATGTGTAGAAC
* *
42783448 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTAAGCGAACCGGATAGCTTCGA
*
42783484 TCACGTGTATAGTACTATGTGCAGGCTACTACGTGTA-TTGGATAGTGAT-GGTCACATGTGTAG
1 TCACGTGTATAGTACTATGTGCAGGCTACTACGTGTACCT-GA-A-TGATAGGTCACATGTGTAG
*
42783547 AACTATGTGCAGGCTACTAAGTGAACCGG
63 AACTATGTGCAGGCTACTAAGCGAACCGG
42783576 TATCATTAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
100 1 0.01
101 37 0.45
102 40 0.49
103 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACGTGTATAGTACTATGTGCAGGCTACTACGTGTACCTGAATGATAGGTCACATGTGTAGAAC
TATGTGCAGGCTACTAAGCGAACCGGATAGCTTCGA
Found at i:42783643 original size:46 final size:43
Alignment explanation
Indices: 42783571--42783669 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
42783561 TACTAAGTGA
*
42783571 ACCGGTATCATTAATTATAAGGTGGTTGCTGTGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTGTGTGCTGAAT-CC
* *
42783614 ACCGGATATCATTGATTACAAAGGGTGGTTGGTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTGTGTGCTGAATCC
42783660 ACCGTGTATC
1 ACCG-GTATC
42783670 TGTTATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 11 0.23
45 2 0.04
46 27 0.56
47 3 0.06
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTGTGTGCTGAATCC
Found at i:42783814 original size:16 final size:16
Alignment explanation
Indices: 42783793--42783824 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42783783 TAATTGAAAG
*
42783793 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
42783809 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
42783825 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:42788430 original size:10 final size:10
Alignment explanation
Indices: 42788415--42788442 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
42788405 CTTTAATTAT
42788415 AAAAAGATAA
1 AAAAAGATAA
42788425 AAAAAGATAA
1 AAAAAGATAA
42788435 AAAAAGAT
1 AAAAAGAT
42788443 TATCATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
AAAAAGATAA
Found at i:42794270 original size:17 final size:18
Alignment explanation
Indices: 42794245--42794278 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42794235 GAAGCTTTGG
*
42794245 TTATTCTTTAAA-AAGCC
1 TTATGCTTTAAACAAGCC
42794262 TTATGCTTTAAACAAGC
1 TTATGCTTTAAACAAGC
42794279 AACCAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (18 bp):
TTATGCTTTAAACAAGCC
Found at i:42818763 original size:24 final size:24
Alignment explanation
Indices: 42818662--42818769 Score: 99
Period size: 24 Copynumber: 4.5 Consensus size: 24
42818652 CCTCGAGATA
* * * *
42818662 AAATGATTGATTTGCCTTTGATGT
1 AAATGACTGATTTGTCTGTGATTT
* * * * *
42818686 AAATGAATGGTTTGTCCGAGATGT
1 AAATGACTGATTTGTCTGTGATTT
* *
42818710 AAATGACTAATTTTTCTGTGATTT
1 AAATGACTGATTTGTCTGTGATTT
42818734 AAATGACTGATTTGTCTGTGATTT
1 AAATGACTGATTTGTCTGTGATTT
**
42818758 GTATGACTGATT
1 AAATGACTGATT
42818770 CTGTGTATGG
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (24 bp):
AAATGACTGATTTGTCTGTGATTT
Found at i:42818876 original size:27 final size:27
Alignment explanation
Indices: 42818838--42818897 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
42818828 GGAAGTACTA
*
42818838 TACTGGTAGCTTTGCCACA-ATCACTGT
1 TACTGGTAGCTTGGCCACATAT-ACTGT
* *
42818865 TACTGGTGGCTTGGCCATATATACTGT
1 TACTGGTAGCTTGGCCACATATACTGT
42818892 TACTGG
1 TACTGG
42818898 CAGTTTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (27 bp):
TACTGGTAGCTTGGCCACATATACTGT
Found at i:42818923 original size:26 final size:26
Alignment explanation
Indices: 42818885--42818938 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
42818875 TTGGCCATAT
*
42818885 ATACTGTTACTGGCAGTTTTGTTGCG
1 ATACTGTTACTGGCAGCTTTGTTGCG
*
42818911 ATACTGTTGCTGGCAGCTTTGTTGCG
1 ATACTGTTACTGGCAGCTTTGTTGCG
42818937 AT
1 AT
42818939 GCTATTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.17, G:0.28, T:0.41
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGTTGCG
Found at i:42818950 original size:26 final size:26
Alignment explanation
Indices: 42818895--42818950 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
42818885 ATACTGTTAC
* * *
42818895 TGGCAGTTTTGTTGCGATACTGTTGC
1 TGGCAGCTTTGTTGCGATACTATTGA
* *
42818921 TGGCAGCTTTGTTGCGATGCTATTTA
1 TGGCAGCTTTGTTGCGATACTATTGA
42818947 TGGC
1 TGGC
42818951 TTTGTACCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.12, C:0.16, G:0.30, T:0.41
Consensus pattern (26 bp):
TGGCAGCTTTGTTGCGATACTATTGA
Found at i:42818982 original size:32 final size:32
Alignment explanation
Indices: 42818940--42819128 Score: 220
Period size: 32 Copynumber: 5.9 Consensus size: 32
42818930 TGTTGCGATG
*
42818940 CTATTTATGGCTTTGTACCGATCATATTACTA
1 CTATTGATGGCTTTGTACCGATCATATTACTA
* *
42818972 CTATTGATGGCTTTGTGCCGATCATACTACTA
1 CTATTGATGGCTTTGTACCGATCATATTACTA
* * * *
42819004 TTATTGATGGCTGTGTACCGATCATAGTATTA
1 CTATTGATGGCTTTGTACCGATCATATTACTA
* *
42819036 CTACTT-ATGGCTTTGTGCCGATCATACTACTA
1 CTA-TTGATGGCTTTGTACCGATCATATTACTA
* *
42819068 TTACTGATGG-TTGTGTACCGATCATATTACTA
1 CTATTGATGGCTT-TGTACCGATCATATTACTA
* * *
42819100 CTACTGATGGCTTTGTGCCAATCATATTA
1 CTATTGATGGCTTTGTACCGATCATATTA
42819129 TTGTACTTAT
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
31 3 0.02
32 126 0.95
33 4 0.03
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (32 bp):
CTATTGATGGCTTTGTACCGATCATATTACTA
Found at i:42819047 original size:64 final size:64
Alignment explanation
Indices: 42818941--42819125 Score: 282
Period size: 64 Copynumber: 2.9 Consensus size: 64
42818931 GTTGCGATGC
* *
42818941 TATTTATGGCTTTGTACCGATCATATTACTACTA-TTGATGGCTTTGTGCCGATCATACTACTAT
1 TATTGATGGCTGTGTACCGATCATATTACTACTACTT-ATGGCTTTGTGCCGATCATACTACTAT
* *
42819005 TATTGATGGCTGTGTACCGATCATAGTATTACTACTTATGGCTTTGTGCCGATCATACTACTAT
1 TATTGATGGCTGTGTACCGATCATATTACTACTACTTATGGCTTTGTGCCGATCATACTACTAT
* * * *
42819069 TACTGATGGTTGTGTACCGATCATATTACTACTACTGATGGCTTTGTGCCAATCATA
1 TATTGATGGCTGTGTACCGATCATATTACTACTACTTATGGCTTTGTGCCGATCATA
42819126 TTATTGTACT
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
64 108 0.98
65 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (64 bp):
TATTGATGGCTGTGTACCGATCATATTACTACTACTTATGGCTTTGTGCCGATCATACTACTAT
Found at i:42819108 original size:96 final size:95
Alignment explanation
Indices: 42818944--42819143 Score: 258
Period size: 96 Copynumber: 2.1 Consensus size: 95
42818934 GCGATGCTAT
* * * * *
42818944 TTATGGCTTTGTACCGATCATATTACTACTATTGATGGCTTTGTGCCGATCATACTACTATTATT
1 TTATGGCTTTGTACCGATCATACTACTACTACTGATGGCTTTGTACCGATCATACTACTACTACT
*
42819009 GATGGCTGTGTACCGATCATAGTATTACTAC
66 GATGGCTGTGTACCAATCATAGTATT-CTAC
* * *
42819040 TTATGGCTTTGTGCCGATCATACTACTATTACTGATGG-TTGTGTACCGATCATATTACTACTAC
1 TTATGGCTTTGTACCGATCATACTACTACTACTGATGGCTT-TGTACCGATCATACTACTACTAC
* * * *
42819104 TGATGGCTTTGTGCCAATCATATTATTGTAC
65 TGATGGCTGTGTACCAATCATAGTATTCTAC
42819135 TTATGGCTT
1 TTATGGCTT
42819144 GTAGCCATTC
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
95 14 0.16
96 76 0.84
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (95 bp):
TTATGGCTTTGTACCGATCATACTACTACTACTGATGGCTTTGTACCGATCATACTACTACTACT
GATGGCTGTGTACCAATCATAGTATTCTAC
Found at i:42824827 original size:24 final size:21
Alignment explanation
Indices: 42824744--42824841 Score: 121
Period size: 21 Copynumber: 4.7 Consensus size: 21
42824734 TCTTCAAGGA
*
42824744 TATGTAATCTTAGATATGA--
1 TATGCAATCTTAGATATGATT
*
42824763 TATGCAATCTTAGATATGATA
1 TATGCAATCTTAGATATGATT
42824784 TATGCAATCTTAGATATGATT
1 TATGCAATCTTAGATATGATT
42824805 TATGCAATCTTAGAAGATATGATT
1 TATGCAATCTT---AGATATGATT
*
42824829 T-TGTAATCTTAGA
1 TATGCAATCTTAGA
42824842 GATTTAATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
19 18 0.25
20 3 0.04
21 31 0.44
23 8 0.11
24 11 0.15
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (21 bp):
TATGCAATCTTAGATATGATT
Found at i:42825327 original size:17 final size:17
Alignment explanation
Indices: 42825305--42825339 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42825295 TATATACATA
42825305 TATATACATT-TACATTT
1 TATATAC-TTATACATTT
42825322 TATATACTTATACATTT
1 TATATACTTATACATTT
42825339 T
1 T
42825340 TTATTTCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATACTTATACATTT
Found at i:42825405 original size:2 final size:2
Alignment explanation
Indices: 42825364--42825394 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42825354 TTATATGCAC
42825364 AT AT 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 AT AT A
42825395 CTTTTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42825533 original size:31 final size:30
Alignment explanation
Indices: 42825497--42825602 Score: 89
Period size: 30 Copynumber: 3.6 Consensus size: 30
42825487 ATTAATTTTA
42825497 ATATATGTAATTATTATTTGTTTAT-ATATAT
1 ATATATGTAATTA-TATTT-TTTATAATATAT
* *
42825528 ATATATGTAATTATCTTTTTTATAATCTAT
1 ATATATGTAATTATATTTTTTATAATATAT
* *
42825558 ATCTATGT-ATATAAATTTTTT-T-ATATAT
1 ATATATGTAAT-TATATTTTTTATAATATAT
* *
42825586 GTACATGT-A-TATATTTT
1 ATATATGTAATTATATTTT
42825603 GTACCATTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
26 7 0.11
28 11 0.17
29 8 0.13
30 24 0.38
31 13 0.21
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.57
Consensus pattern (30 bp):
ATATATGTAATTATATTTTTTATAATATAT
Found at i:42825565 original size:30 final size:31
Alignment explanation
Indices: 42825497--42825566 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
42825487 ATTAATTTTA
42825497 ATATATGTAATTATTATTTGTTTATATATAT
1 ATATATGTAATTATTATTTGTTTATATATAT
* *
42825528 ATATATGTAATTA-TCTTT-TTTATAATCTAT
1 ATATATGTAATTATTATTTGTTTAT-ATATAT
*
42825558 ATCTATGTA
1 ATATATGTA
42825567 TATAAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 5 0.14
30 17 0.49
31 13 0.37
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (31 bp):
ATATATGTAATTATTATTTGTTTATATATAT
Found at i:42830885 original size:44 final size:44
Alignment explanation
Indices: 42830837--42831068 Score: 146
Period size: 44 Copynumber: 5.3 Consensus size: 44
42830827 AGACACCAAC
*
42830837 CTTGCCTCCCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* **** * * ** * *
42830881 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACA-CTAG-T
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGC-AGAT
42830925 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* **** * * * ** * * * *
42830969 CTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACATCAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
* *
42831013 CTTGCCTCCCTGGGTTGCAGCGGAGTAGGTTAAAAATAGTAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* *
42831057 CTTACCTTCCTG
1 CTTGCCTCCCTG
42831069 CACCGATAGC
Statistics
Matches: 127, Mismatches: 55, Indels: 12
0.65 0.28 0.06
Matches are distributed among these distances:
43 32 0.25
44 62 0.49
45 33 0.26
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.23
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:42831113 original size:88 final size:88
Alignment explanation
Indices: 42830779--42831101 Score: 484
Period size: 88 Copynumber: 3.7 Consensus size: 88
42830769 AGCAGATCAG
* * * * *
42830779 TAAAGATAACAGATCTTGCCTTCATGCACTGACAGTGAAGCAGATCGAAGACACCAACCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
*
42830844 CCCTGGGTTGTAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* **
42830867 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGTCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
42830932 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * *
42830955 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACATCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
*
42831020 CCCTGGGTTGCAGCGGAGTAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * * *
42831043 TAAAAATAGTAGATCTTACCTTCCTGCACCGATAGCGAAGCAGATCGATGACCCCAACC
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACC
42831102 CTATCTCCCT
Statistics
Matches: 213, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 213 1.00
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCT
CCCTGGGTTGCAGCGGAGCAGGT
Found at i:42831638 original size:44 final size:43
Alignment explanation
Indices: 42831542--42831653 Score: 127
Period size: 44 Copynumber: 2.6 Consensus size: 43
42831532 GAAGATAGCG
* * * **
42831542 AATCTTATCTCCTGAAGTTGTAGTGGAGCATATTAAAGTCAAT
1 AATCTTATCTCCTGAAGTTGCAGTGAAGCAGATTAAAACCAAT
* *
42831585 AATCCTATCTCCATGAAGTTACAGTGAAGCAGATTAAAACCACAT
1 AATCTTATCTCC-TGAAGTTGCAGTGAAGCAGATTAAAACCA-AT
42831630 -ATCTTATCTCTCTGAAGTTGCAGT
1 AATCTTATCTC-CTGAAGTTGCAGT
42831654 AGAGTAGATC
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
43 11 0.19
44 43 0.75
45 3 0.05
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (43 bp):
AATCTTATCTCCTGAAGTTGCAGTGAAGCAGATTAAAACCAAT
Found at i:42832122 original size:21 final size:21
Alignment explanation
Indices: 42832097--42832153 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
42832087 TTCTTCAAGG
*
42832097 ATATGTAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
42832118 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
42832139 TTATGCAATCTTAGA
1 ATATGCAATCTTAGA
42832154 AGATATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:42832175 original size:23 final size:24
Alignment explanation
Indices: 42832109--42832176 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 24
42832099 ATGTAATCTT
*
42832109 AGATATGATATATGCAATCTT---
1 AGATATGATTTATGCAATCTTAGA
42832130 AGATATGATTTATGCAATCTTAGA
1 AGATATGATTTATGCAATCTTAGA
*
42832154 AGATATGATTTA-GTAATCTTAGA
1 AGATATGATTTATGCAATCTTAGA
42832177 GATTTAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.48
23 10 0.24
24 12 0.29
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (24 bp):
AGATATGATTTATGCAATCTTAGA
Found at i:42832458 original size:3 final size:3
Alignment explanation
Indices: 42832450--42832547 Score: 67
Period size: 3 Copynumber: 32.0 Consensus size: 3
42832440 TCTTTTTTAT
* * *
42832450 TTA TTA TTA TTTA TTTA TTA TTTA TTT TTA TTA -AA TT- TTA TT- TTC
1 TTA TTA TTA -TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * **
42832495 TTG TTA TTAA GTTA TTA TTA TTA TTG TTA TTA TTA CCA TTA TTA TTA
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42832542 TTA TTA
1 TTA TTA
42832548 CTATATATAC
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
2 5 0.07
3 57 0.75
4 12 0.16
5 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:42832463 original size:7 final size:7
Alignment explanation
Indices: 42832446--42832482 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
42832436 TTAGTCTTTT
42832446 TTATTTA
1 TTATTTA
42832453 TTA-TTA
1 TTATTTA
42832459 TTTATTTA
1 -TTATTTA
42832467 TTATTTA
1 TTATTTA
42832474 TT-TTTA
1 TTATTTA
42832480 TTA
1 TTA
42832483 AATTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 9 0.33
7 15 0.56
8 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:42832702 original size:17 final size:17
Alignment explanation
Indices: 42832671--42832714 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
42832661 CATAACTTTT
*
42832671 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
42832687 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
42832704 ATATACATTTT
1 ATATACATTTT
42832715 TATTTCCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:42832825 original size:22 final size:22
Alignment explanation
Indices: 42832800--42832842 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42832790 GTATGTTTTC
42832800 TTATAT-TATTCTTCATAAATTT
1 TTATATATATTCTTC-TAAATTT
*
42832822 TTATATATATTTTTCTAAATT
1 TTATATATATTCTTCTAAATT
42832843 AATTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATATATTCTTCTAAATTT
Found at i:42832866 original size:19 final size:21
Alignment explanation
Indices: 42832842--42832880 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
42832832 TTTTCTAAAT
42832842 TAATTAAT-TTTA-ATATATG
1 TAATTAATATTTATATATATG
*
42832861 TAATTATTATTTATATATAT
1 TAATTAATATTTATATATAT
42832881 ATATGTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TAATTAATATTTATATATATG
Found at i:42832932 original size:30 final size:30
Alignment explanation
Indices: 42832854--42832917 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 30
42832844 ATTAATTTTA
*
42832854 ATATATGTAATTA--TTATTTAT-A--TAT
1 ATATATGTAATTATCTTTTTTATAATCTAT
42832879 ATATATGTAATTATCTTTTTTATAATCTAT
1 ATATATGTAATTATCTTTTTTATAATCTAT
42832909 ATATATGTA
1 ATATATGTA
42832918 TATACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 13 0.39
27 7 0.21
28 1 0.03
30 12 0.36
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (30 bp):
ATATATGTAATTATCTTTTTTATAATCTAT
Found at i:42846418 original size:47 final size:47
Alignment explanation
Indices: 42846345--42846439 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
42846335 TTTGTGTCTA
*
42846345 AATAAGCTCAAAAACACTCTTTAAAGAGAAAAATCTATCAAAATAGT
1 AATAAGCTCAAAAACACTCTTCAAAGAGAAAAATCTATCAAAATAGT
42846392 AATAAGCTCAAAAACACTCTTCAAAGAGAAAAATCTATCAAAATAGT
1 AATAAGCTCAAAAACACTCTTCAAAGAGAAAAATCTATCAAAATAGT
42846439 A
1 A
42846440 TTTTTCTACA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.54, C:0.16, G:0.08, T:0.22
Consensus pattern (47 bp):
AATAAGCTCAAAAACACTCTTCAAAGAGAAAAATCTATCAAAATAGT
Found at i:42856449 original size:2 final size:2
Alignment explanation
Indices: 42856442--42856466 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42856432 CTTCTAGAAT
42856442 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
42856467 ATTTGACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:42856887 original size:23 final size:23
Alignment explanation
Indices: 42856839--42856889 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
42856829 ACCTACTTTT
* **
42856839 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGACA
42856862 TTACAGTAGTAATTTTCGGGACA
1 TTACAGTAGTAATTTTCGGGACA
42856885 TTACA
1 TTACA
42856890 TTTCTCCCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGACA
Found at i:42858535 original size:50 final size:53
Alignment explanation
Indices: 42858481--42858611 Score: 169
Period size: 50 Copynumber: 2.5 Consensus size: 53
42858471 TGGTGCCCAT
* * *
42858481 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCT-CT-TCTC-GATGCCAAC
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTGATATCTCAAATGCCAAC
* *
42858531 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTGATAATCTCAATAATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTGAT-ATCTC-A-AATGCCAAC
42858587 GCCATGTCCCAGACATGGTCTTACA
1 GCCATGTCCCAGACATGGTCTTACA
42858612 CTGGCTCACA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
50 33 0.47
51 1 0.01
53 4 0.06
56 32 0.46
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.25
Consensus pattern (53 bp):
GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTGATATCTCAAATGCCAAC
Found at i:42869467 original size:22 final size:22
Alignment explanation
Indices: 42869439--42869543 Score: 138
Period size: 22 Copynumber: 4.8 Consensus size: 22
42869429 TTTATTGTTC
*
42869439 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
42869461 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
42869483 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
42869505 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
42869527 AAACATGAGAGCTTAGT
1 AAACATGAGAGCTTAGT
42869544 GCAGTCTATT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:42874430 original size:40 final size:40
Alignment explanation
Indices: 42874386--42874475 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
42874376 GGCAGGTAAA
* * *
42874386 TGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTCTG
1 TGCATTCAGGGGTACCAAAGCACAAACAGGGGCACATCTG
* *
42874426 TGCATTCAGGGGTACCAAAGCACAAGCAGGGGCACATTTG
1 TGCATTCAGGGGTACCAAAGCACAAACAGGGGCACATCTG
42874466 TGCATTCAGG
1 TGCATTCAGG
42874476 CAATAATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (40 bp):
TGCATTCAGGGGTACCAAAGCACAAACAGGGGCACATCTG
Found at i:42885556 original size:19 final size:19
Alignment explanation
Indices: 42885534--42885571 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42885524 TCAATCATCC
42885534 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
42885553 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
42885572 ACTCTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:42905740 original size:8 final size:8
Alignment explanation
Indices: 42905708--42905736 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
42905698 TTTATTAGGT
42905708 TTTATTAA
1 TTTATTAA
42905716 TTTATTAA
1 TTTATTAA
42905724 TTTATT-A
1 TTTATTAA
42905731 TTTATT
1 TTTATT
42905737 TATTCCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTATTAA
Found at i:42917339 original size:5 final size:5
Alignment explanation
Indices: 42917331--42917356 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42917321 GAGATGGAAT
42917331 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
42917357 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:42917356 original size:26 final size:26
Alignment explanation
Indices: 42917305--42917356 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
42917295 TAAAGTTTTC
* * *
42917305 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
42917331 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
42917357 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:42917760 original size:19 final size:19
Alignment explanation
Indices: 42917726--42917774 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
42917716 CTAAACAATT
42917726 TAATAATATAAA--TAATA
1 TAATAATATAAATTTAATA
*
42917743 TAA-AATATGAAATTTAATT
1 TAATAATAT-AAATTTAATA
42917762 TAATAATATAAAT
1 TAATAATATAAAT
42917775 AAAATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 6 0.22
19 11 0.41
20 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAATAATATAAATTTAATA
Found at i:42918026 original size:30 final size:31
Alignment explanation
Indices: 42917987--42918046 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
42917977 GGAGGTGGGA
*
42917987 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* * *
42918018 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
42918047 TAAAAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:42918211 original size:30 final size:30
Alignment explanation
Indices: 42918157--42918218 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
42918147 GGAGGGGAGG
* * * *
42918157 GGAGTAAAAGTTTTGGGGGGAAAGTGAAAA
1 GGAGTAAAAGTTTTGAGAGAAAAGTAAAAA
42918187 GGAGTAAAAGTTTTGAGAGAAAAGTAAAAA
1 GGAGTAAAAGTTTTGAGAGAAAAGTAAAAA
42918217 GG
1 GG
42918219 TTTGGAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGAGAAAAGTAAAAA
Found at i:42918278 original size:9 final size:9
Alignment explanation
Indices: 42918260--42918296 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
42918250 TATAGTTTGA
42918260 TATTCGAAT
1 TATTCGAAT
*
42918269 TATTCAAAT
1 TATTCGAAT
*
42918278 TATTCGAGT
1 TATTCGAAT
42918287 TATTCGAAT
1 TATTCGAAT
42918296 T
1 T
42918297 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42918366 original size:9 final size:9
Alignment explanation
Indices: 42918349--42918379 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42918339 TCGAGTTGAT
42918349 TCGAATAAC
1 TCGAATAAC
*
42918358 TCGATTAAC
1 TCGAATAAC
42918367 TCGAATAAC
1 TCGAATAAC
42918376 TCGA
1 TCGA
42918380 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:42922910 original size:12 final size:12
Alignment explanation
Indices: 42922886--42922928 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
42922876 ATTTTTACGG
42922886 TTTAAAAAA-AT
1 TTTAAAAAATAT
42922897 TTTAAAAAATAT
1 TTTAAAAAATAT
* *
42922909 TTTTAAAATTA-
1 TTTAAAAAATAT
42922920 TTTAAAAAA
1 TTTAAAAAA
42922929 AGAGAGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTAAAAAATAT
Found at i:42922951 original size:11 final size:11
Alignment explanation
Indices: 42922935--42922963 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
42922925 AAAAAGAGAG
42922935 TTAAGAGGAAC
1 TTAAGAGGAAC
42922946 TTAAGAGGAAC
1 TTAAGAGGAAC
42922957 TTAAGAG
1 TTAAGAG
42922964 AATTTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.21
Consensus pattern (11 bp):
TTAAGAGGAAC
Found at i:42923729 original size:9 final size:9
Alignment explanation
Indices: 42923703--42923759 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
42923693 TTAAAGTTTA
42923703 TATAAAAAT
1 TATAAAAAT
*
42923712 TCTCAAAAAAT
1 TAT--AAAAAT
42923723 TATAAAAAT
1 TATAAAAAT
* *
42923732 AAGAAAAAT
1 TATAAAAAT
*
42923741 TCATAAAATT
1 T-ATAAAAAT
42923751 TATAAAAAT
1 TATAAAAAT
42923760 AAGTAGTAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 22 0.59
10 7 0.19
11 8 0.22
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (9 bp):
TATAAAAAT
Found at i:42930846 original size:13 final size:13
Alignment explanation
Indices: 42930828--42930883 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
42930818 TAGATTTTTC
42930828 CTAAATATTATCA
1 CTAAATATTATCA
*
42930841 CTAAATATTATTA
1 CTAAATATTATCA
*
42930854 CTAAATA--AT-T
1 CTAAATATTATCA
42930864 CTAAATATTATCA
1 CTAAATATTATCA
42930877 CTAAATA
1 CTAAATA
42930884 ATTCAAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 7 0.19
11 2 0.05
12 2 0.05
13 26 0.70
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:42930870 original size:23 final size:23
Alignment explanation
Indices: 42930841--42930892 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
42930831 AATATTATCA
*
42930841 CTAAATATTATTACTAAATAATT
1 CTAAATATTATCACTAAATAATT
42930864 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
42930887 CAAAAT
1 CTAAAT
42930893 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:42935560 original size:26 final size:26
Alignment explanation
Indices: 42935524--42935603 Score: 151
Period size: 26 Copynumber: 3.1 Consensus size: 26
42935514 AGAAATAAAC
42935524 GCCGCTAAAAGTCATGACCTATAGCG
1 GCCGCTAAAAGTCATGACCTATAGCG
42935550 GCCGCTAAAAGTCATGACCTATAGCG
1 GCCGCTAAAAGTCATGACCTATAGCG
*
42935576 GCCGCTAAAAGTCATGACCTTTAGCG
1 GCCGCTAAAAGTCATGACCTATAGCG
42935602 GC
1 GC
42935604 GCTTCTCCCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.20
Consensus pattern (26 bp):
GCCGCTAAAAGTCATGACCTATAGCG
Found at i:42935642 original size:43 final size:43
Alignment explanation
Indices: 42935587--42935859 Score: 343
Period size: 43 Copynumber: 6.4 Consensus size: 43
42935577 CCGCTAAAAG
* * *
42935587 TCATGACCTTTAGCGGCGCTTCTCCCACAAACGCCGCTATAGG
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * * *
42935630 TCATGACTTTTAGCGGCGC-TTTACTATAAACACCGCTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* ** * *
42935672 TCATGACTTTTAGCGGCGTTTTTTTCACGAACGCCACTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * * * *
42935715 TCATGACTTTTAGCGGCACTTCTCCAACAATCGCCGCTAGAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* *
42935758 TCATGACTTTTAGCGGCGCTTTTCCAACAAACGCTGCTATA-A
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
42935800 GTCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
1 -TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
*
42935844 TCATTACTTTTAGCGG
1 TCATGACTTTTAGCGG
42935860 TGCCTTTTTT
Statistics
Matches: 194, Mismatches: 33, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
42 36 0.19
43 157 0.81
44 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (43 bp):
TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
Found at i:42936241 original size:21 final size:21
Alignment explanation
Indices: 42936212--42936300 Score: 106
Period size: 21 Copynumber: 4.2 Consensus size: 21
42936202 TTCTTCTCTA
*
42936212 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCTGC
* * *
42936233 CTTTGCTTCTCTCGTTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
*
42936254 CTCTGCTTCCCTCACTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
* *
42936275 CTGTGCTTCCCTCGCTGTTGC
1 CTCTGCTTCCCTCGCTGCTGC
*
42936296 ATCTG
1 CTCTG
42936301 TTTTAAGTTG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.03, C:0.40, G:0.19, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCTGC
Found at i:42936405 original size:87 final size:87
Alignment explanation
Indices: 42936259--42936451 Score: 316
Period size: 87 Copynumber: 2.2 Consensus size: 87
42936249 GCTGCCTCTG
** *
42936259 CTTCCCTC-ACTGCTGCCTGTGCTTCCCTCGCTGTTGCATCTGTTTTAAGTTGTAGCTGGAGTTC
1 CTTCCCTCGA-TGCTGCCTCCGCTTCCCTCGCTGTTGCATCTGCTTTAAGTTGTAGCTGGAGTTC
42936323 TTCATATTTTCTTTGAACCTCAA
65 TTCATATTTTCTTTGAACCTCAA
*
42936346 CTTCCCTCGATGCTGCCTCCGCTTCCCTCGCTGTTGCATTTGCTTTAAGTTGTAGCTGGAGTTCT
1 CTTCCCTCGATGCTGCCTCCGCTTCCCTCGCTGTTGCATCTGCTTTAAGTTGTAGCTGGAGTTCT
*
42936411 TCATATTTTCTTTGAACCTCAG
66 TCATATTTTCTTTGAACCTCAA
*
42936433 CTTCTCTCGATGCTGCCTC
1 CTTCCCTCGATGCTGCCTC
42936452 TACTTTAAGT
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
87 98 0.99
88 1 0.01
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.40
Consensus pattern (87 bp):
CTTCCCTCGATGCTGCCTCCGCTTCCCTCGCTGTTGCATCTGCTTTAAGTTGTAGCTGGAGTTCT
TCATATTTTCTTTGAACCTCAA
Found at i:42939902 original size:36 final size:36
Alignment explanation
Indices: 42939855--42939924 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
42939845 ATTTTCCATT
*
42939855 GACATTCAAAATTATACCGATAATGTTCTTGCAATC
1 GACATTCAAAATTATACCGATAATGTTCTCGCAATC
*
42939891 GACATTCAAAATTGTACCGATAATGTTCTCGCAA
1 GACATTCAAAATTATACCGATAATGTTCTCGCAA
42939925 ACATTTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (36 bp):
GACATTCAAAATTATACCGATAATGTTCTCGCAATC
Found at i:42941803 original size:9 final size:9
Alignment explanation
Indices: 42941789--42942155 Score: 190
Period size: 9 Copynumber: 42.3 Consensus size: 9
42941779 ACTATAAATG
42941789 AGTTATGTA
1 AGTTATGTA
42941798 AGTTATGATA
1 AGTTATG-TA
* * *
42941808 TGATATAT-
1 AGTTATGTA
*
42941816 ATTTATGT-
1 AGTTATGTA
*
42941824 A-TTAGGTA
1 AGTTATGTA
*
42941832 AATTATGTA
1 AGTTATGTA
42941841 AGTTATGT-
1 AGTTATGTA
*
42941849 A-TTATATA
1 AGTTATGTA
42941857 AGTTATGTA
1 AGTTATGTA
42941866 AGTTATGT-
1 AGTTATGTA
42941874 A-TTATGTA
1 AGTTATGTA
** *
42941882 AGCAATATA
1 AGTTATGTA
*
42941891 GGTTATGT-
1 AGTTATGTA
42941899 A-TTATGTA
1 AGTTATGTA
42941907 AGTTATGT-
1 AGTTATGTA
*
42941915 A-TTATGCA
1 AGTTATGTA
*
42941923 TGTTATGTATA
1 AGTTATG--TA
*
42941934 ATATTAAT-TA
1 A-GTT-ATGTA
42941944 AGTTATGTA
1 AGTTATGTA
*
42941953 AGTTGTGT-
1 AGTTATGTA
* *
42941961 A-TAATGCA
1 AGTTATGTA
42941969 AGTTATGTA
1 AGTTATGTA
*
42941978 AGTAATGT-
1 AGTTATGTA
42941986 A-TTATGTA
1 AGTTATGTA
*
42941994 AGTTGTGT-
1 AGTTATGTA
* *
42942002 A-TAATGTT
1 AGTTATGTA
**
42942010 AGTTATCAA
1 AGTTATGTA
42942019 AGTTATGT-
1 AGTTATGTA
42942027 A-TTATGTA
1 AGTTATGTA
*
42942035 AGTTATTTA
1 AGTTATGTA
42942044 AGTTATGTA
1 AGTTATGTA
*
42942053 AGTTGTGT-
1 AGTTATGTA
42942061 A-TTATGTA
1 AGTTATGTA
*
42942069 AGTTGTGTA
1 AGTTATGTA
42942078 AGTTATGTA
1 AGTTATGTA
* *
42942087 GGCTATGT-
1 AGTTATGTA
42942095 A-TTATGTA
1 AGTTATGTA
42942103 AGTTAT-TA
1 AGTTATGTA
*
42942111 TGTTATTATGTA
1 AG---TTATGTA
42942123 AGTTATGTA
1 AGTTATGTA
*
42942132 AGTTTATATATA
1 AG--T-TATGTA
42942144 AGTTATGTA
1 AGTTATGTA
42942153 AGT
1 AGT
42942156 ATATCACTTT
Statistics
Matches: 266, Mismatches: 57, Indels: 70
0.68 0.15 0.18
Matches are distributed among these distances:
7 55 0.21
8 28 0.11
9 153 0.58
10 10 0.04
11 6 0.02
12 12 0.05
13 2 0.01
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.46
Consensus pattern (9 bp):
AGTTATGTA
Found at i:42941849 original size:25 final size:25
Alignment explanation
Indices: 42941818--42942131 Score: 164
Period size: 25 Copynumber: 12.3 Consensus size: 25
42941808 TGATATATAT
* *
42941818 TTATGTATTAGGTAAATTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
42941843 TTATGTATTATATAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
** * *
42941868 TTATGTATTATGTAAGCAATATAGG
1 TTATGTATTATGTAAGTTATGTAAG
42941893 TTATGTATTATGTAAGTTATGT-A-
1 TTATGTATTATGTAAGTTATGTAAG
* *
42941916 TTATGCATGTTATGTATAATATTAAT-TAAG
1 TTATG--TATTATG--TAA-GTT-ATGTAAG
* * *
42941946 TTATGTAAGTTGTGT-A-TAATGCAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
*
42941971 TTATGTAAGTAATGT-A-TTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* * * **
42941996 TTGTGTATAATGTTAGTTATCAAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
42942021 TTATGTATTATGTAAGTTATTTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
42942046 TTATGTAAGTTGTGT-A-TTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* * *
42942071 TTGTGTAAGTTATGTAGGCTATGTATTA-
1 TTATGT-A-TTATGTAAGTTATGTA--AG
* *
42942099 TGTAAGTTATTATGTTA-TTATGTAAG
1 T-TATG-TATTATGTAAGTTATGTAAG
42942125 TTATGTA
1 TTATGTA
42942132 AGTTTATATA
Statistics
Matches: 225, Mismatches: 42, Indels: 45
0.72 0.13 0.14
Matches are distributed among these distances:
23 11 0.05
24 6 0.03
25 155 0.69
26 3 0.01
27 21 0.09
28 12 0.05
29 7 0.03
30 10 0.04
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.46
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:42941852 original size:16 final size:16
Alignment explanation
Indices: 42941833--42942131 Score: 159
Period size: 16 Copynumber: 18.1 Consensus size: 16
42941823 TATTAGGTAA
42941833 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
42941849 ATTATATAAGTTATGT
1 ATTATGTAAGTTATGT
42941865 AAGTTATGT-A-TTATGT
1 -A-TTATGTAAGTTATGT
** * *
42941881 AAGCAATATAGGTTATGT
1 -A-TTATGTAAGTTATGT
42941899 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
* *
42941915 ATTATGCATGTTATGT
1 ATTATGTAAGTTATGT
*
42941931 ATAATAT-TAA-TTAAG-
1 AT--TATGTAAGTTATGT
*
42941946 -TTATGTAAGTTGTGT
1 ATTATGTAAGTTATGT
* *
42941961 ATAATGCAAGTTATGT
1 ATTATGTAAGTTATGT
*
42941977 AAGTAATGT-A-TTATGT
1 -A-TTATGTAAGTTATGT
* *
42941993 AAGTTGTGT-A-TAATGTT
1 -A-TTATGTAAGTTATG-T
**
42942010 AGTTATCAAAGTTATGT
1 A-TTATGTAAGTTATGT
*
42942027 ATTATGTAAGTTATTT
1 ATTATGTAAGTTATGT
*
42942043 AAGTTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGT
*
42942061 ATTATGTAAGTTGTGT
1 ATTATGTAAGTTATGT
* *
42942077 AAGTTATGTAGGCTATGT
1 -A-TTATGTAAGTTATGT
42942095 ATTATGTAAGTTATTATGTT
1 ATTATGTAAG---TTATG-T
42942115 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
42942131 A
1 A
42942132 AGTTTATATA
Statistics
Matches: 222, Mismatches: 38, Indels: 46
0.73 0.12 0.15
Matches are distributed among these distances:
12 3 0.01
13 3 0.01
14 4 0.02
16 130 0.59
17 19 0.09
18 48 0.22
19 4 0.02
20 11 0.05
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.46
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:42942119 original size:20 final size:19
Alignment explanation
Indices: 42942090--42942128 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
42942080 TTATGTAGGC
42942090 TATGTATTATGTAAGTTAT
1 TATGTATTATGTAAGTTAT
42942109 TATGTTATTATGTAAGTTAT
1 TATG-TATTATGTAAGTTAT
42942129 GTAAGTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
TATGTATTATGTAAGTTAT
Found at i:42944618 original size:21 final size:22
Alignment explanation
Indices: 42944589--42944635 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
42944579 GATTAAATAC
42944589 AAACACCT-AATCCTCAAACTCT
1 AAACACCTAAAT-CTCAAACTCT
*
42944611 AAAC-CCTAAATCTTAAACTCT
1 AAACACCTAAATCTCAAACTCT
42944632 AAAC
1 AAAC
42944636 GACCACACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (22 bp):
AAACACCTAAATCTCAAACTCT
Found at i:42945334 original size:114 final size:113
Alignment explanation
Indices: 42945163--42945681 Score: 469
Period size: 114 Copynumber: 4.6 Consensus size: 113
42945153 TAACAATTTT
* * *
42945163 GTGGCGTTTTTAAA-AACGCGCCACTAATGCCACTATATCTCAAAACCGAACGATGCGTTTTGGT
1 GTGGCG-TTTTAAATAA-GCGCCGCTAATACCACTATAGCTCAAAACCGAACGATGCGTTTTGGT
* *
42945227 TAACATTTTTGCGGCATTTTTAAAAAAGCACTGCTAATG-TTAGATATATA
64 TAACATTTTTGCGGCACTTTTAAAAAAGCGCTGCTAATGCTT-GATATATA
* * * *
42945277 GTGGTGTTTCTAAATAAGCGTCGCTAATGCCACAATAGCTCAAAACCGAACGATGCGTTTTGGTT
1 GTGGCGTTT-TAAATAAGCGCCGCTAATACCACTATAGCTCAAAACCGAACGATGCGTTTTGGTT
* * * *
42945342 AACATTTTTGCGGCGCTTTTAAACAAGCGCCGCTAATGCTTGATGTATA
65 AACATTTTTGCGGCACTTTTAAAAAAGCGCTGCTAATGCTTGATATATA
* * * * * * ** *
42945391 GTGGCGTTTTTATATAAGCGCCACTAATACCAGTACACCTCAAGATAGAACAATGCGTTTTGGTT
1 GTGGCG-TTTTAAATAAGCGCCGCTAATACCACTATAGCTCAAAACCGAACGATGCGTTTTGGTT
* ** * * * * * *
42945456 AATAACTTTGCGGCATTTTTACATAAGCGCTGGTAATGGTGTGCT-T-TA
65 AACATTTTTGCGGCACTTTTAAAAAAGCGCTGCTAATGCT-TGATATATA
* * * * * * * *
42945504 GTGGCGTTTATAAATAAGTGCCGCAAATATCACTATAGCTTAAGATCAAACGATACGTTTTGGTT
1 GTGGCGTTT-TAAATAAGCGCCGCTAATACCACTATAGCTCAAAACCGAACGATGCGTTTTGGTT
*
42945569 AACATTTTTGCGGCACTTTTAAACAAA-CGCCAG-TAATGCTTGATATATA
65 AACATTTTTGCGGCACTTTTAAA-AAAGCG-CTGCTAATGCTTGATATATA
* * * ** *
42945618 GTGACGTTTTAATATAAGCGCCACTAA-ACC-CGTATACCTCAAAATAGAACGATGCATTTTGGT
1 GTGGCGTTTTAA-ATAAGCGCCGCTAATACCAC-TATAGCTCAAAACCGAACGATGCGTTTTGGT
42945681 T
64 T
42945682 GTTGTGGCGC
Statistics
Matches: 324, Mismatches: 69, Indels: 25
0.78 0.17 0.06
Matches are distributed among these distances:
112 7 0.02
113 110 0.34
114 197 0.61
115 10 0.03
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (113 bp):
GTGGCGTTTTAAATAAGCGCCGCTAATACCACTATAGCTCAAAACCGAACGATGCGTTTTGGTTA
ACATTTTTGCGGCACTTTTAAAAAAGCGCTGCTAATGCTTGATATATA
Found at i:42945611 original size:227 final size:228
Alignment explanation
Indices: 42945163--42945681 Score: 627
Period size: 227 Copynumber: 2.3 Consensus size: 228
42945153 TAACAATTTT
* * * * **
42945163 GTGGCGTTTTTA-AAAACGCGCCACTAATGCCACTATATCTCAAAACCGAACGATGCGTTTTGGT
1 GTGGCGTTTTTATATAA-GCGCCACTAATACCAGTATACCTCAAAATAGAACGATGCGTTTTGGT
** * *
42945227 TAACATTTTTGCGGCATTTTTAAAAAAGCACTGCTAATGTTAGATATATAGTGGTGTTTCTAAAT
65 TAACAACTTTGCGGCATTTTTAAAAAAGCACTGCTAATGTTAGATATATAGTGGCGTTTATAAAT
* * * * * *
42945292 AAGCGTCGCTAATGCCACAATAGCTCAAAACCGAACGATGCGTTTTGGTTAACATTTTTGCGGCG
130 AAGCGCCGCAAATACCACAATAGCTCAAAACCAAACGATACGTTTTGGTTAACATTTTTGCGGCA
* *
42945357 CTTTTAAACAAGCGCCGCTAATGCTTGATGTATA
195 CTTTTAAACAAACGCCGCTAATGCTTGATATATA
* * *
42945391 GTGGCGTTTTTATATAAGCGCCACTAATACCAGTACACCTCAAGATAGAACAATGCGTTTTGGTT
1 GTGGCGTTTTTATATAAGCGCCACTAATACCAGTATACCTCAAAATAGAACGATGCGTTTTGGTT
* * * * * *
42945456 AATAACTTTGCGGCATTTTTACATAAGCGCTGGTAATGGTGT-GCT-T-TAGTGGCGTTTATAAA
66 AACAACTTTGCGGCATTTTTAAAAAAGCACTGCTAAT-GT-TAGATATATAGTGGCGTTTATAAA
* * * * * *
42945518 TAAGTGCCGCAAATATCACTATAGCTTAAGATCAAACGATACGTTTTGGTTAACATTTTTGCGGC
129 TAAGCGCCGCAAATACCACAATAGCTCAAAACCAAACGATACGTTTTGGTTAACATTTTTGCGGC
42945583 ACTTTTAAACAAACGCCAG-TAATGCTTGATATATA
194 ACTTTTAAACAAACGCC-GCTAATGCTTGATATATA
* * * *
42945618 GTGACGTTTTAATATAAGCGCCACTAA-ACCCGTATACCTCAAAATAGAACGATGCATTTTGGTT
1 GTGGCGTTTTTATATAAGCGCCACTAATACCAGTATACCTCAAAATAGAACGATGCGTTTTGGTT
42945682 GTTGTGGCGC
Statistics
Matches: 247, Mismatches: 40, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
226 32 0.13
227 123 0.50
228 84 0.34
229 7 0.03
230 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (228 bp):
GTGGCGTTTTTATATAAGCGCCACTAATACCAGTATACCTCAAAATAGAACGATGCGTTTTGGTT
AACAACTTTGCGGCATTTTTAAAAAAGCACTGCTAATGTTAGATATATAGTGGCGTTTATAAATA
AGCGCCGCAAATACCACAATAGCTCAAAACCAAACGATACGTTTTGGTTAACATTTTTGCGGCAC
TTTTAAACAAACGCCGCTAATGCTTGATATATA
Found at i:42950144 original size:41 final size:41
Alignment explanation
Indices: 42950082--42950257 Score: 298
Period size: 41 Copynumber: 4.3 Consensus size: 41
42950072 AATTTAACAT
* *
42950082 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
42950123 ATTCATATCACCGGCATTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
42950164 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
42950205 ATTCAGATCACTGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
42950246 ATTCAGATCACC
1 ATTCAGATCACC
42950258 AATTCCAAAC
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 125 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:42950490 original size:41 final size:41
Alignment explanation
Indices: 42950429--42950523 Score: 181
Period size: 41 Copynumber: 2.3 Consensus size: 41
42950419 TTCGTTCCTT
*
42950429 TGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCC
1 TGATTCAGATCACCGACACTTAGCCTGCTAGGCTTATAGCC
42950470 TGATTCAGATCACCGACACTTAGCCTGCTAGGCTTATAGCC
1 TGATTCAGATCACCGACACTTAGCCTGCTAGGCTTATAGCC
42950511 TGATTCAGATCAC
1 TGATTCAGATCAC
42950524 AAATTTCAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (41 bp):
TGATTCAGATCACCGACACTTAGCCTGCTAGGCTTATAGCC
Found at i:42958142 original size:41 final size:41
Alignment explanation
Indices: 42958080--42958214 Score: 225
Period size: 41 Copynumber: 3.3 Consensus size: 41
42958070 AATTTAACAT
* *
42958080 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
42958121 ATTCATATCACCGGCATTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
42958162 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
42958203 ATTCAGATCACC
1 ATTCAGATCACC
42958215 AATTCCAAAC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:42969099 original size:12 final size:12
Alignment explanation
Indices: 42969050--42969092 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
42969040 ATGGTAAGCA
42969050 GTTATTTATTTT
1 GTTATTTATTTT
42969062 GTTATTTATTTT
1 GTTATTTATTTT
42969074 GTTATTTATTTT
1 GTTATTTATTTT
42969086 GTTATTT
1 GTTATTT
42969093 TTATTGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (12 bp):
GTTATTTATTTT
Found at i:42969895 original size:15 final size:15
Alignment explanation
Indices: 42969867--42969910 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
42969857 AATTATAATG
*
42969867 TAATGTTTTAAATA-
1 TAATGTTATAAATAT
42969881 TAATGTTAATAAATAT
1 TAATGTT-ATAAATAT
*
42969897 TTATGTTATAAATA
1 TAATGTTATAAATA
42969911 GATTAGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 7 0.27
15 13 0.50
16 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
TAATGTTATAAATAT
Found at i:42992626 original size:28 final size:27
Alignment explanation
Indices: 42992583--42992651 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
42992573 AAATAAAAAA
*
42992583 TTATCAAAATGT-TATAACTTTTTTTAT
1 TTATCAAAATATATATAA-TTTTTTTAT
42992610 TTATCAAAATATATATAATTTTTTTAT
1 TTATCAAAATATATATAATTTTTTTAT
*
42992637 TTACCAAAATATATA
1 TTATCAAAATATATA
42992652 AAAAAACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 34 0.87
28 5 0.13
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (27 bp):
TTATCAAAATATATATAATTTTTTTAT
Found at i:42992760 original size:27 final size:27
Alignment explanation
Indices: 42992730--42992796 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
42992720 AGGGAAGTAG
42992730 GTTGGCGGCACCAAACAAGGGAACCCT
1 GTTGGCGGCACCAAACAAGGGAACCCT
* * *
42992757 GTTGGCGGCACCGAACAAGGGATCCTT
1 GTTGGCGGCACCAAACAAGGGAACCCT
42992784 GTTGGCGGCACCA
1 GTTGGCGGCACCA
42992797 CCCTTGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.24, C:0.28, G:0.33, T:0.15
Consensus pattern (27 bp):
GTTGGCGGCACCAAACAAGGGAACCCT
Found at i:42992866 original size:18 final size:17
Alignment explanation
Indices: 42992843--42993016 Score: 78
Period size: 18 Copynumber: 10.0 Consensus size: 17
42992833 GAAGGAGAGG
42992843 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
42992861 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
42992878 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
42992894 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
** *
42992912 GGAAAGAAAAGGAAAGGGGA
1 GG-AAG-AAA-GAAAAAGAA
*
42992932 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
*
42992950 -G--GAAAGAAAAGGAAA
1 GGAAGAAAGAAAAAG-AA
42992965 GG-AGAAGAGAAAAA-AA
1 GGAAGAA-AGAAAAAGAA
* *
42992981 -AAAGAAAGAGAGAGAGAA
1 GGAAGAAAGA-A-AAAGAA
*
42992999 GGAAGGAAAAAAAAAGAA
1 GGAA-GAAAGAAAAAGAA
42993017 AATAAGGTAA
Statistics
Matches: 120, Mismatches: 19, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
14 9 0.08
15 14 0.12
16 12 0.10
17 10 0.08
18 35 0.29
19 23 0.19
20 17 0.14
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:42992876 original size:10 final size:10
Alignment explanation
Indices: 42992845--42992916 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
42992835 AGGAGAGGGG
*
42992845 AAGAAGAAGA
1 AAGAAAAAGA
42992855 AAGAAAGGAAGA
1 AAGAAA--AAGA
42992867 AAGAAAAAGA
1 AAGAAAAAGA
* *
42992877 AGGAAAAGGA
1 AAGAAAAAGA
42992887 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
42992901 AAGAAAAAGA
1 AAGAAAAAGA
*
42992911 AGGAAA
1 AAGAAA
42992917 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:42992876 original size:22 final size:23
Alignment explanation
Indices: 42992845--42992946 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
42992835 AGGAGAGGGG
*
42992845 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
42992867 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
42992889 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* ***
42992915 AAGAAAAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
42992939 AAGAAAAA
1 AAGAAAAA
42992947 TAAGGAAAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
22 12 0.20
23 10 0.17
24 32 0.53
25 5 0.08
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:42992882 original size:14 final size:13
Alignment explanation
Indices: 42992848--42992921 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 13
42992838 AGAGGGGAAG
42992848 AAGAAGAAAG-AA
1 AAGAAGAAAGAAA
*
42992860 AGGAAGAAAGAAA
1 AAGAAGAAAGAAA
42992873 AAGAAGGAAAAGGAAA
1 AAGAA-G-AAA-GAAA
42992889 GGAGAGGAAAGAAAGAAA
1 --A-A-G-AAGAAAGAAA
42992907 AAGAAGGAAAGAAA
1 AAGAA-GAAAGAAA
42992921 A
1 A
42992922 GGAAAGGGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
12 9 0.18
13 8 0.16
14 11 0.22
15 4 0.08
16 5 0.10
18 5 0.10
19 4 0.08
20 2 0.04
21 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAA
Found at i:42992903 original size:28 final size:28
Alignment explanation
Indices: 42992848--42992927 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
42992838 AGAGGGGAAG
42992848 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
42992873 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
42992907 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
42992928 GGGAGGAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 3 0.07
28 8 0.17
29 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 6 0.13
34 17 0.37
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:42992921 original size:38 final size:38
Alignment explanation
Indices: 42992863--42992986 Score: 170
Period size: 38 Copynumber: 3.4 Consensus size: 38
42992853 GAAAGAAAGG
42992863 AAGAAAGAAAAAGAA-G---GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
42992897 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
* *
42992935 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGAAGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
42992973 GAA-AAA-AAAAAGAA
1 -AAGAAAGAAAAAGAA
42992987 AGAGAGAGAG
Statistics
Matches: 80, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
34 15 0.19
35 1 0.01
37 7 0.09
38 55 0.69
39 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
Found at i:42992923 original size:10 final size:10
Alignment explanation
Indices: 42992865--42992965 Score: 79
Period size: 10 Copynumber: 10.5 Consensus size: 10
42992855 AAGAAAGGAA
*
42992865 GAAAGAAAAA
1 GAAAGAAAAG
*
42992875 GAAGGAAAAG
1 GAAAGAAAAG
* *
42992885 GAAAGGAGAG
1 GAAAGAAAAG
42992895 GAAAG-AAA-
1 GAAAGAAAAG
42992903 GAAA-AAGAAG
1 GAAAGAA-AAG
42992913 GAAAGAAAAG
1 GAAAGAAAAG
***
42992923 GAAAGGGGAG
1 GAAAGAAAAG
42992933 GAAAG-AAA-
1 GAAAGAAAAG
42992941 GAAA-AATAAG
1 GAAAGAA-AAG
42992951 GAAAGAAAAG
1 GAAAGAAAAG
42992961 GAAAG
1 GAAAG
42992966 GAGAAGAGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
8 10 0.14
9 7 0.10
10 51 0.71
11 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:42994947 original size:28 final size:28
Alignment explanation
Indices: 42994916--42994972 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
42994906 AGTAAATAAA
42994916 AAATATATATAATATTTTGGTAAT-TTTT
1 AAATAT-TATAATATTTTGGTAATGTTTT
* * *
42994944 AAATATTTTATTATTTTTGTAATGTTTT
1 AAATATTATAATATTTTGGTAATGTTTT
42994972 A
1 A
42994973 TTATGGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (28 bp):
AAATATTATAATATTTTGGTAATGTTTT
Found at i:42995001 original size:13 final size:13
Alignment explanation
Indices: 42994983--42995008 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42994973 TTATGGGTTT
42994983 TATAAAAAAATAA
1 TATAAAAAAATAA
42994996 TATAAAAAAATAA
1 TATAAAAAAATAA
42995009 AAAATTGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TATAAAAAAATAA
Found at i:42995065 original size:30 final size:28
Alignment explanation
Indices: 42995017--42995083 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
42995007 AAAAAATTGT
42995017 CAAAATAT-TATAACTTTTTTTGTATTTAC
1 CAAAATATATATAA-TTTTTTT-TATTTAC
42995046 CAAAATATATATAATTTTTTTTATTTAC
1 CAAAATATATATAATTTTTTTTATTTAC
42995074 CAAAATATAT
1 CAAAATATAT
42995084 CAAAAAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
28 17 0.46
29 15 0.41
30 5 0.14
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.49
Consensus pattern (28 bp):
CAAAATATATATAATTTTTTTTATTTAC
Found at i:42995099 original size:9 final size:9
Alignment explanation
Indices: 42995085--42995119 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
42995075 AAAATATATC
*
42995085 AAAAAAAGT
1 AAAAAAAAT
*
42995094 AAAAAAAAC
1 AAAAAAAAT
42995103 AAAAAAAAT
1 AAAAAAAAT
42995112 AAAAAAAA
1 AAAAAAAA
42995120 ACAGAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.89, C:0.03, G:0.03, T:0.06
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:42995107 original size:19 final size:20
Alignment explanation
Indices: 42995085--42995130 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
42995075 AAAATATATC
42995085 AAAAAAAGT-AAAAAAAACA-
1 AAAAAAA-TAAAAAAAAACAG
42995104 AAAAAAATAAAAAAAAACAG
1 AAAAAAATAAAAAAAAACAG
42995124 AAAAAAA
1 AAAAAAA
42995131 CACACTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.04
19 17 0.68
20 7 0.28
ACGTcount: A:0.87, C:0.04, G:0.04, T:0.04
Consensus pattern (20 bp):
AAAAAAATAAAAAAAAACAG
Found at i:42995131 original size:10 final size:9
Alignment explanation
Indices: 42995084--42995132 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 9
42995074 CAAAATATAT
*
42995084 CAAAAAAAG
1 CAAAAAAAA
*
42995093 TAAAAAAAA
1 CAAAAAAAA
42995102 CAAAAAAAA
1 CAAAAAAAA
*
42995111 TAAAAAAAAA
1 -CAAAAAAAA
42995121 CAGAAAAAAA
1 CA-AAAAAAA
42995131 CA
1 CA
42995133 CACTAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.84, C:0.08, G:0.04, T:0.04
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:42996456 original size:17 final size:17
Alignment explanation
Indices: 42996434--42996470 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
42996424 ATGGGGTAAG
42996434 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
* *
42996451 ATGCTATTGTCATATTC
1 ATGCTATTCTAATATTC
42996468 ATG
1 ATG
42996471 ACATCTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:42997456 original size:14 final size:14
Alignment explanation
Indices: 42997437--42997469 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
42997427 TTTTTGTATC
42997437 AATTTAATTATTCT
1 AATTTAATTATTCT
42997451 AATTTAATTATTCT
1 AATTTAATTATTCT
42997465 AATTT
1 AATTT
42997470 TAGTTATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:42998841 original size:27 final size:27
Alignment explanation
Indices: 42998765--42998831 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
42998755 TTGGTAGGAC
*
42998765 TGGTGCCGCCAACAGGGATCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
42998792 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
42998819 TGGTGCCGCCAAC
1 TGGTGCCGCCAAC
42998832 CTGCTTCCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.13, C:0.31, G:0.30, T:0.25
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:42998887 original size:9 final size:9
Alignment explanation
Indices: 42998871--42998917 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 9
42998861 ATCAGTTCAG
42998871 GTTTTTTTCT
1 GTTTTTTT-T
42998881 GTTTTTTATT
1 GTTTTTT-TT
*
42998891 TTTTTTTTT
1 GTTTTTTTT
*
42998900 GTTTTTTGT
1 GTTTTTTTT
42998909 -TTTTTTTT
1 GTTTTTTTT
42998917 G
1 G
42998918 ATATATTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
8 7 0.23
9 9 0.29
10 14 0.45
11 1 0.03
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (9 bp):
GTTTTTTTT
Found at i:42998897 original size:20 final size:19
Alignment explanation
Indices: 42998872--42998916 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
42998862 TCAGTTCAGG
*
42998872 TTTTTTTCTGTTTTTTATT
1 TTTTTTTTTGTTTTTTATT
*
42998891 TTTTTTTTTGTTTTTTGTT
1 TTTTTTTTTGTTTTTTATT
42998910 TTTTTTT
1 TTTTTTT
42998917 GATATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTGTTTTTTATT
Found at i:42998948 original size:27 final size:28
Alignment explanation
Indices: 42998918--42998985 Score: 113
Period size: 27 Copynumber: 2.5 Consensus size: 28
42998908 TTTTTTTTTG
42998918 ATATATTTTGGTAAAT-AAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAATTAT
42998945 ATATATTTTGGTAAATAAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAATTAT
*
42998973 A-ACATTTTGGTAA
1 ATATATTTTGGTAA
42998986 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 27 0.69
28 12 0.31
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAATTAT
Found at i:43000447 original size:9 final size:9
Alignment explanation
Indices: 43000430--43000466 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43000420 TGCGTTTTCG
43000430 AATTCGAAT
1 AATTCGAAT
*
43000439 AACTCGAAT
1 AATTCGAAT
43000448 AATTCGAAT
1 AATTCGAAT
43000457 AATTCGAAT
1 AATTCGAAT
43000466 A
1 A
43000467 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:43001017 original size:17 final size:17
Alignment explanation
Indices: 43000997--43001043 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
43000987 CACATTTTAT
43000997 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
43001014 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTGA
43001032 A-TATTTATATTA
1 ATTATTTATATTA
43001044 AAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 14 0.52
18 8 0.30
19 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:43001391 original size:5 final size:5
Alignment explanation
Indices: 43001381--43001406 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
43001371 GAACAAATAT
43001381 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
43001407 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:43003418 original size:16 final size:16
Alignment explanation
Indices: 43003397--43003427 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43003387 GAGAAAAATA
*
43003397 AAAAGTTTTAGGGAAT
1 AAAAGTTTGAGGGAAT
43003413 AAAAGTTTGAGGGAA
1 AAAAGTTTGAGGGAA
43003428 AGTAAATAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (16 bp):
AAAAGTTTGAGGGAAT
Found at i:43003558 original size:30 final size:31
Alignment explanation
Indices: 43003513--43003572 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
43003503 GGAGGTGGGA
43003513 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
43003544 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
43003573 TAAAAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:43003795 original size:9 final size:9
Alignment explanation
Indices: 43003781--43003817 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43003771 TTTAGTTTGA
43003781 TATTCGAAT
1 TATTCGAAT
43003790 TATTCGAAT
1 TATTCGAAT
*
43003799 TATTCGAGT
1 TATTCGAAT
43003808 TATTCGAAT
1 TATTCGAAT
43003817 T
1 T
43003818 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43003888 original size:9 final size:9
Alignment explanation
Indices: 43003871--43003901 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43003861 TCGAGTTGAT
43003871 TCGAATAAC
1 TCGAATAAC
*
43003880 TCGATTAAC
1 TCGAATAAC
43003889 TCGAATAAC
1 TCGAATAAC
43003898 TCGA
1 TCGA
43003902 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Done.