Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, 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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 108 of 131
Found at i:19211571 original size:22 final size:22
Alignment explanation
Indices: 19211526--19211779 Score: 147
Period size: 22 Copynumber: 11.5 Consensus size: 22
19211516 TAAATTAGCT
* *
19211526 AATCATTGATAACTTTGTAATA
1 AATCATTGATAACTTAGTAGTA
* *
19211548 AATCATTGATAAATTAATAGTA
1 AATCATTGATAACTTAGTAGTA
* **
19211570 AATTAGTT-ATAACTTTA-TAACA
1 AATCA-TTGATAAC-TTAGTAGTA
*
19211592 AATTATT-AGTAACTTAGTAGTA
1 AATCATTGA-TAACTTAGTAGTA
* ** * *
19211614 AATTATCAATGATTTAGTAGTA
1 AATCATTGATAACTTAGTAGTA
* * * *
19211636 AATTAGTCATAATTTAGTAGTA
1 AATCATTGATAACTTAGTAGTA
* * * *
19211658 AATTATTCATAAATTAGTCGTA
1 AATCATTGATAACTTAGTAGTA
* *
19211680 AATCAAT-ACTAACTTACTAGTA
1 AATCATTGA-TAACTTAGTAGTA
* *
19211702 AATCATTGATAATTTAGTAATA
1 AATCATTGATAACTTAGTAGTA
* * * *
19211724 TATCAATGACAATTTAGTAGTA
1 AATCATTGATAACTTAGTAGTA
* * * *
19211746 AATCAATGATAACTTAATTGTC
1 AATCATTGATAACTTAGTAGTA
19211768 AATCATTGATAA
1 AATCATTGATAA
19211780 ACTTTTTTAT
Statistics
Matches: 185, Mismatches: 40, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
21 7 0.04
22 171 0.92
23 7 0.04
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (22 bp):
AATCATTGATAACTTAGTAGTA
Found at i:19211614 original size:11 final size:11
Alignment explanation
Indices: 19211591--19211682 Score: 64
Period size: 11 Copynumber: 8.4 Consensus size: 11
19211581 ACTTTATAAC
*
19211591 AAATTATTAGT
1 AAATTAGTAGT
*
19211602 AACTTAGTAGT
1 AAATTAGTAGT
*
19211613 AAATTA-TCAAT
1 AAATTAGT-AGT
* *
19211624 GATTTAGTAGT
1 AAATTAGTAGT
19211635 AAATTAGTCA-T
1 AAATTAGT-AGT
*
19211646 AATTTAGTAGT
1 AAATTAGTAGT
*
19211657 AAATTATTCA-T
1 AAATTAGT-AGT
*
19211668 AAATTAGTCGT
1 AAATTAGTAGT
19211679 AAAT
1 AAAT
19211683 CAATACTAAC
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
10 2 0.03
11 56 0.92
12 3 0.05
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (11 bp):
AAATTAGTAGT
Found at i:19212115 original size:21 final size:21
Alignment explanation
Indices: 19212072--19212121 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
19212062 AAATTACTAG
* *
19212072 AATTATATCAATGGTTACTAA
1 AATTATATCAATAGTTACCAA
19212093 AATTATATC-ATAAGTTACCAA
1 AATTATATCAAT-AGTTACCAA
19212114 AATTATAT
1 AATTATAT
19212122 AGACAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (21 bp):
AATTATATCAATAGTTACCAA
Found at i:19212135 original size:21 final size:21
Alignment explanation
Indices: 19212091--19212158 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
19212081 AATGGTTACT
* * * *
19212091 AAAATTATATCATAAGTTACC
1 AAAATTATATAAAAAATTATC
* *
19212112 AAAATTATATAGACAATTATC
1 AAAATTATATAAAAAATTATC
*
19212133 AAAATTTTATAAAAAATTATC
1 AAAATTATATAAAAAATTATC
19212154 AAAAT
1 AAAAT
19212159 CAAAATTATA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (21 bp):
AAAATTATATAAAAAATTATC
Found at i:19212174 original size:27 final size:27
Alignment explanation
Indices: 19212130--19212183 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
19212120 ATAGACAATT
*
19212130 ATCAAAATTTTATAAAAAATTATCAAA
1 ATCAAAATTATATAAAAAATTATCAAA
* *
19212157 ATCAAAATTATATCAAAAGTTATCAAA
1 ATCAAAATTATATAAAAAATTATCAAA
19212184 TTTTACTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.31
Consensus pattern (27 bp):
ATCAAAATTATATAAAAAATTATCAAA
Found at i:19214148 original size:59 final size:58
Alignment explanation
Indices: 19214060--19214261 Score: 221
Period size: 60 Copynumber: 3.4 Consensus size: 58
19214050 AAATGTTTAC
* * * * * * *
19214060 TTTTAAGAAAATTTGATACTTTCAACTTTTCTTTAAAAACCTTTTTTAAAAATTCTTATT
1 TTTTAAGAAAAATTAATA-TTTCATCTTTTCTTAAAAAACATTTTTTAGAGATTCTTA-T
19214120 TTTTAAGAAAAATTAATATTTCATCTTTTCTTCAAAAAAACATTTTTT-GAGATTCTTAT
1 TTTTAAGAAAAATTAATATTTCATCTTTTCTT--AAAAAACATTTTTTAGAGATTCTTAT
* * *
19214179 TTTTAAGAAAAATTGATATTTCAAT-TTTTCCTCAAAAAA-ATTATTTTATGAGATTTTTAT
1 TTTTAAGAAAAATTAATATTTC-ATCTTTT-CTTAAAAAACATT-TTTTA-GAGATTCTTAT
19214239 TTTTAAGAAAAATTAATATTTCA
1 TTTTAAGAAAAATTAATATTTCA
19214262 ACGTTTAAGG
Statistics
Matches: 124, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
57 3 0.02
58 10 0.08
59 40 0.32
60 59 0.48
61 12 0.10
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (58 bp):
TTTTAAGAAAAATTAATATTTCATCTTTTCTTAAAAAACATTTTTTAGAGATTCTTAT
Found at i:19214183 original size:119 final size:119
Alignment explanation
Indices: 19214042--19214261 Score: 293
Period size: 119 Copynumber: 1.8 Consensus size: 119
19214032 GCATATTATT
* * * **
19214042 ATTTTTTGAAATGTTTACTTTTAAGAAAATTTGATACTTTCAACTTTTCTTTAAAAACCTT-TTT
1 ATTTTTTGAAATGTTTACTTTTAAGAAAAATTGATA-TTTCAACTTTTCCTCAAAAAAATTATTT
19214106 TA-AAAATTCTTATTTTTTAAGAAAAATTAATATTTCATCTTTTCTTCAAAAAAAC
65 TATAAAATTCTTA-TTTTTAAGAAAAATTAATATTTCATCTTTTCTTCAAAAAAAC
* * *
19214161 ATTTTTTGAGAT-TCTTATTTTTAAGAAAAATTGATATTTCAATTTTTCCTCAAAAAAATTATTT
1 ATTTTTTGAAATGT-TTACTTTTAAGAAAAATTGATATTTCAACTTTTCCTCAAAAAAATTATTT
* * *
19214225 TATGAGATTTTTATTTTTAAGAAAAATTAATATTTCA
65 TATAAAATTCTTATTTTTAAGAAAAATTAATATTTCA
19214262 ACGTTTAAGG
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
118 20 0.23
119 60 0.69
120 7 0.08
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (119 bp):
ATTTTTTGAAATGTTTACTTTTAAGAAAAATTGATATTTCAACTTTTCCTCAAAAAAATTATTTT
ATAAAATTCTTATTTTTAAGAAAAATTAATATTTCATCTTTTCTTCAAAAAAAC
Found at i:19215421 original size:21 final size:21
Alignment explanation
Indices: 19215396--19215435 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
19215386 ATCTGATAAT
19215396 ATAAAAA-CTAAAGATAAATCA
1 ATAAAAATC-AAAGATAAATCA
19215417 ATAAAAATCAAAGATAAAT
1 ATAAAAATCAAAGATAAAT
19215436 AAAATACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (21 bp):
ATAAAAATCAAAGATAAATCA
Found at i:19215468 original size:22 final size:23
Alignment explanation
Indices: 19215416--19215473 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
19215406 AAGATAAATC
* *
19215416 AATAAAAATCAA-AGATAAATAA
1 AATAATAATCAACAAATAAATAA
*
19215438 AATACTAAT-AACAAATAAAT-A
1 AATAATAATCAACAAATAAATAA
19215459 AATGAATAATCAACA
1 AAT-AATAATCAACA
19215474 TTATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 6 0.21
22 19 0.66
23 4 0.14
ACGTcount: A:0.67, C:0.09, G:0.03, T:0.21
Consensus pattern (23 bp):
AATAATAATCAACAAATAAATAA
Found at i:19216938 original size:25 final size:24
Alignment explanation
Indices: 19216910--19216963 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
19216900 TAAGTTCTTC
19216910 TTTTATTTT-TTTTCATTCATTTTTT
1 TTTTATTTTCTTTT-ATTC-TTTTTT
*
19216935 TTTTATTTTCTTTTTTTCTTTTTT
1 TTTTATTTTCTTTTATTCTTTTTT
19216959 TTTTA
1 TTTTA
19216964 AACGTAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 11 0.41
25 12 0.44
26 4 0.15
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTATTTTCTTTTATTCTTTTTT
Found at i:19216948 original size:13 final size:12
Alignment explanation
Indices: 19216910--19216962 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
19216900 TAAGTTCTTC
19216910 TTTTATTTTTTT
1 TTTTATTTTTTT
*
19216922 TCATTCA-TTTTTT
1 T--TTTATTTTTTT
19216935 TTTTATTTTCTTT
1 TTTTATTTT-TTT
*
19216948 TTTTCTTTTTTT
1 TTTTATTTTTTT
19216960 TTT
1 TTT
19216963 AAACGTAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 3 0.09
12 10 0.29
13 18 0.53
14 3 0.09
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTTTT
Found at i:19231265 original size:24 final size:24
Alignment explanation
Indices: 19231237--19231292 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
19231227 TATACTTTGA
19231237 AAAATATAGTATTTATTTAGTAAC
1 AAAATATAGTATTTATTTAGTAAC
19231261 AAAATATAGTATTTATTTAGTAAC
1 AAAATATAGTATTTATTTAGTAAC
19231285 AAAATATA
1 AAAATATA
19231293 AAACTTAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (24 bp):
AAAATATAGTATTTATTTAGTAAC
Found at i:19234533 original size:59 final size:58
Alignment explanation
Indices: 19234414--19234733 Score: 326
Period size: 59 Copynumber: 5.5 Consensus size: 58
19234404 ATATTATTAG
* * ** **
19234414 TTTTGAAATATTTACTTTTAAGAAAAATTGATACTTTCAAAGTTT-TCTCAACAAATTTT
1 TTTTGAAATTTTTATTTTTAAGAAAAATTGATA-TTTCAACTTTTCTCTCAA-AAAAATT
** * * *
19234473 TTTTTTAATTTTGATTTTTAAGAAAAATTGA-ATTTCAATTTTTCTCTTAAAAAACATT
1 TTTTGAAATTTTTATTTTTAAGAAAAATTGATATTTCAACTTTTCTCTCAAAAAA-ATT
* * * * * *
19234531 TTTTGAAATTCTTATTCTCAAGAAAAATTAATGTTTTAACTTTTC-CTCAAAAAAATATT
1 TTTTGAAATTTTTATTTTTAAGAAAAATTGATATTTCAACTTTTCTCTC-AAAAAA-ATT
* *
19234590 TTTTAAAATTTTTATTTTTAAGAAAAATTGATATTTTAACTTTTCT-TCAAAAAAATT
1 TTTTGAAATTTTTATTTTTAAGAAAAATTGATATTTCAACTTTTCTCTCAAAAAAATT
* * *
19234647 TTTTGAAATTTTTAATTTTAAGAAAAATTGATATTTAAACATTT-TCTCAAAAAAATACT
1 TTTTGAAATTTTTATTTTTAAGAAAAATTGATATTTCAACTTTTCTCTCAAAAAAAT--T
* *
19234706 TTCTGAAATTTTTATTTTTAAGGAAAAT
1 TTTTGAAATTTTTATTTTTAAGAAAAAT
19234734 ATTTTTATTT
Statistics
Matches: 218, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
56 1 0.00
57 65 0.30
58 40 0.18
59 112 0.51
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (58 bp):
TTTTGAAATTTTTATTTTTAAGAAAAATTGATATTTCAACTTTTCTCTCAAAAAAATT
Found at i:19234625 original size:25 final size:25
Alignment explanation
Indices: 19234597--19234682 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 25
19234587 ATTTTTTAAA
19234597 ATTTTTATTTTTAAGAAAAATTGAT
1 ATTTTTATTTTTAAGAAAAATTGAT
* *
19234622 ATTTTAACTTTTCTTCAA-AAAAATTTTTTGAA
1 ATTTTTA--TTT-TT-AAGAAAAA----TTGAT
*
19234654 ATTTTTAATTTTAAGAAAAATTGAT
1 ATTTTTATTTTTAAGAAAAATTGAT
19234679 ATTT
1 ATTT
19234683 AAACATTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 18
0.67 0.07 0.26
Matches are distributed among these distances:
25 14 0.30
27 3 0.06
28 9 0.19
29 9 0.19
30 2 0.04
32 10 0.21
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (25 bp):
ATTTTTATTTTTAAGAAAAATTGAT
Found at i:19234716 original size:116 final size:116
Alignment explanation
Indices: 19234414--19234733 Score: 378
Period size: 116 Copynumber: 2.7 Consensus size: 116
19234404 ATATTATTAG
* * * * * *
19234414 TTTTGAAATATTTACTTTTAAGAAAAATTGATACTTTCAAAGTTTTCTC-AACAAATTTTTTTTT
1 TTTTGAAATTTTTAATTTTAAGAAAAATTGATA-TTT-AAACTTTTCTCAAAAAAATATTTTTTA
* * * *
19234478 TAATTTTGATTTTTAAGAAAAATTGAATTTCAATTTTTCTCTTAAAAAACATT
64 AAATTTTTATTTTTAAGAAAAATTGAATTTCAACTTTTCTCTCAAAAAACATT
* * * * *
19234531 TTTTGAAATTCTT-ATTCTCAAGAAAAATTAATGTTTTAACTTTTCCTCAAAAAAATATTTTTTA
1 TTTTGAAATTTTTAATT-TTAAGAAAAATTGATATTTAAACTTTT-CTCAAAAAAATATTTTTTA
*
19234595 AAATTTTTATTTTTAAGAAAAATTGATATTTTAACTTTTCT-TCAAAAAA-ATT
64 AAATTTTTATTTTTAAGAAAAATTGA-ATTTCAACTTTTCTCTCAAAAAACATT
* * *
19234647 TTTTGAAATTTTTAATTTTAAGAAAAATTGATATTTAAACATTTTCTCAAAAAAATACTTTCTGA
1 TTTTGAAATTTTTAATTTTAAGAAAAATTGATATTTAAAC-TTTTCTCAAAAAAATATTTTTTAA
*
19234712 AATTTTTATTTTTAAGGAAAAT
65 AATTTTTATTTTTAAGAAAAAT
19234734 ATTTTTATTT
Statistics
Matches: 172, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
115 6 0.03
116 80 0.47
117 74 0.43
118 12 0.07
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (116 bp):
TTTTGAAATTTTTAATTTTAAGAAAAATTGATATTTAAACTTTTCTCAAAAAAATATTTTTTAAA
ATTTTTATTTTTAAGAAAAATTGAATTTCAACTTTTCTCTCAAAAAACATT
Found at i:19234752 original size:20 final size:21
Alignment explanation
Indices: 19234713--19234756 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
19234703 ACTTTCTGAA
*
19234713 ATTTTTATTTTTAAGGAAAAT
1 ATTTTTATTTTTAAGAAAAAT
19234734 ATTTTTATTTTTAA-AAAAAT
1 ATTTTTATTTTTAAGAAAAAT
19234754 ATT
1 ATT
19234757 GGAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
ATTTTTATTTTTAAGAAAAAT
Found at i:19235866 original size:21 final size:21
Alignment explanation
Indices: 19235827--19235866 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19235817 ATCTGATAAT
*
19235827 ATAAAAACCAAAGATAAATCA
1 ATAAAAACCAAAGACAAATCA
* *
19235848 ATAAAAATCAAGGACAAAT
1 ATAAAAACCAAAGACAAAT
19235867 AAAAAATAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (21 bp):
ATAAAAACCAAAGACAAATCA
Found at i:19235881 original size:17 final size:19
Alignment explanation
Indices: 19235861--19235897 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
19235851 AAAATCAAGG
19235861 ACAAATAAA-AAAT-AATA
1 ACAAATAAATAAATGAATA
19235878 ACAAATAAATAAATGAATA
1 ACAAATAAATAAATGAATA
19235897 A
1 A
19235898 TCAACATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 4 0.22
19 5 0.28
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (19 bp):
ACAAATAAATAAATGAATA
Found at i:19237174 original size:28 final size:28
Alignment explanation
Indices: 19237118--19237175 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
19237108 ACGTAAGTTA
*
19237118 TTTAAATTCTTTTTAATTTTTAATTTAT
1 TTTAAATTCTTTTTAATTTTTAATATAT
* *
19237146 TTTAAATT-TTTTTTATTTTATTATATAT
1 TTTAAATTCTTTTTAATTTT-TAATATAT
19237174 TT
1 TT
19237176 AATTAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTAAATTCTTTTTAATTTTTAATATAT
Found at i:19237175 original size:21 final size:21
Alignment explanation
Indices: 19237134--19237175 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19237124 TTCTTTTTAA
*
19237134 TTTTTAATTTATTTTAAATTT
1 TTTTTAATTTATTATAAATTT
* *
19237155 TTTTTATTTTATTATATATTT
1 TTTTTAATTTATTATAAATTT
19237176 AATTAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTAATTTATTATAAATTT
Found at i:19237176 original size:27 final size:29
Alignment explanation
Indices: 19237116--19237177 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
19237106 AAACGTAAGT
19237116 TATTTAAATTCTTTTTAATTTTTAATTTA
1 TATTTAAATTCTTTTTAATTTTTAATTTA
*
19237145 T-TTTAAATT-TTTTTTA-TTTT-ATTATA
1 TATTTAAATTCTTTTTAATTTTTAATT-TA
19237171 TATTTAA
1 TATTTAA
19237178 TTAAAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 3 0.10
26 7 0.23
27 11 0.37
28 8 0.27
29 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
TATTTAAATTCTTTTTAATTTTTAATTTA
Found at i:19238077 original size:13 final size:13
Alignment explanation
Indices: 19238059--19238083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19238049 GAATGACGGC
19238059 AACTATTTCTTTG
1 AACTATTTCTTTG
19238072 AACTATTTCTTT
1 AACTATTTCTTT
19238084 TAGTAAAGTT
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:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (13 bp):
AACTATTTCTTTG
Found at i:19238300 original size:12 final size:12
Alignment explanation
Indices: 19238283--19238307 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19238273 AATTATTGAT
19238283 AATTACAAAAAG
1 AATTACAAAAAG
19238295 AATTACAAAAAG
1 AATTACAAAAAG
19238307 A
1 A
19238308 TCGTGTGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (12 bp):
AATTACAAAAAG
Found at i:19240517 original size:16 final size:16
Alignment explanation
Indices: 19240496--19240528 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19240486 ATGGACTTAA
19240496 ACAGGCCCCACGAGCT
1 ACAGGCCCCACGAGCT
19240512 ACAGGCCCCACGAGCT
1 ACAGGCCCCACGAGCT
19240528 A
1 A
19240529 GGGATAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.42, G:0.24, T:0.06
Consensus pattern (16 bp):
ACAGGCCCCACGAGCT
Found at i:19241447 original size:21 final size:21
Alignment explanation
Indices: 19241421--19241465 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
19241411 AAAAGATCCC
19241421 TCAAAATCAGTCA-CTAGTCCA
1 TCAAAATCAGTCATC-AGTCCA
*
19241442 TCAAAATCAGTTATCAGTCCA
1 TCAAAATCAGTCATCAGTCCA
19241463 TCA
1 TCA
19241466 CATTTGCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.38, C:0.27, G:0.09, T:0.27
Consensus pattern (21 bp):
TCAAAATCAGTCATCAGTCCA
Found at i:19242489 original size:22 final size:22
Alignment explanation
Indices: 19242461--19242504 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
19242451 GTTACCAAGA
19242461 AAGTCTCTAAAAACTCCACTCG
1 AAGTCTCTAAAAACTCCACTCG
19242483 AAGTCTCTAAAAACTCCACTCG
1 AAGTCTCTAAAAACTCCACTCG
19242505 CCCCTGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.09, T:0.23
Consensus pattern (22 bp):
AAGTCTCTAAAAACTCCACTCG
Found at i:19247088 original size:29 final size:29
Alignment explanation
Indices: 19247046--19247103 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
19247036 GAATTCGAAA
19247046 TTGGGTCTTCTCGATTGACCCTAGCTTTT
1 TTGGGTCTTCTCGATTGACCCTAGCTTTT
19247075 TTGGGTCTTCTCGATTGACCCTAGCTTTT
1 TTGGGTCTTCTCGATTGACCCTAGCTTTT
19247104 CCTTTATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (29 bp):
TTGGGTCTTCTCGATTGACCCTAGCTTTT
Found at i:19250287 original size:140 final size:140
Alignment explanation
Indices: 19250035--19250316 Score: 537
Period size: 140 Copynumber: 2.0 Consensus size: 140
19250025 TCTGGCATCT
*
19250035 TAGGTTCTTTATTTTCGATACAAGTTGGGCGGAGTTAACGTACCTGCACCGATGATATCGAGGCT
1 TAGGTTCTTTATTTTCGATACAAGTTGGGCCGAGTTAACGTACCTGCACCGATGATATCGAGGCT
19250100 TGATTGTAAGAACCCAATCAGCCTGGCCCCTGTCTATATATTTAACCTATTCCGCTCCGCAAGAC
66 TGATTGTAAGAACCCAATCAGCCTGGCCCCTGTCTATATATTTAACCTATTCCGCTCCGCAAGAC
19250165 CGCAACCAAG
131 CGCAACCAAG
* *
19250175 TAGGTTCTTTATTTTCGATACAAGTTGGGCCGAGTTGACGTACCTGCACCGATGATATCGAGGTT
1 TAGGTTCTTTATTTTCGATACAAGTTGGGCCGAGTTAACGTACCTGCACCGATGATATCGAGGCT
19250240 TGATTGTAAGAACCCAATCAGCCTGGCCCCTGTCTATATATTTAACCTATTCCGCTCCGCAAGAC
66 TGATTGTAAGAACCCAATCAGCCTGGCCCCTGTCTATATATTTAACCTATTCCGCTCCGCAAGAC
19250305 CGCAACCAAG
131 CGCAACCAAG
19250315 TA
1 TA
19250317 ATATATATAT
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (140 bp):
TAGGTTCTTTATTTTCGATACAAGTTGGGCCGAGTTAACGTACCTGCACCGATGATATCGAGGCT
TGATTGTAAGAACCCAATCAGCCTGGCCCCTGTCTATATATTTAACCTATTCCGCTCCGCAAGAC
CGCAACCAAG
Found at i:19250662 original size:25 final size:25
Alignment explanation
Indices: 19250634--19250719 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
19250624 AATAAAATTT
*
19250634 AATTCAAATATAATTATTTTTAAAA
1 AATTTAAATATAATTATTTTTAAAA
* **
19250659 AATTTAAATTTAAATTAAATTT-AAA
1 AATTTAAATAT-AATTATTTTTAAAA
* *
19250684 AATTTATAATATTATATATTATTAAAA
1 AATTTA-AATATAAT-TATTTTTAAAA
*
19250711 AAATTAAAT
1 AATTTAAAT
19250720 CAAATCCTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
25 20 0.43
26 19 0.40
27 8 0.17
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTTAAATATAATTATTTTTAAAA
Found at i:19255847 original size:3 final size:3
Alignment explanation
Indices: 19255839--19255887 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
19255829 CATGTTATAA
19255839 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19255887 A
1 A
19255888 GGATCCTCGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:19267269 original size:30 final size:30
Alignment explanation
Indices: 19267179--19267295 Score: 92
Period size: 30 Copynumber: 3.8 Consensus size: 30
19267169 TGTTTAAATA
* * * * *
19267179 TAAATTAAAAATTAAAATTTTATGTGGATA
1 TAAATTAAAATTTAAAAATTTATTTGAATG
* ** *
19267209 TAAATTAAAAGTTAAATGCTTTTAATTTGAACG
1 TAAATTAAAATTTAAA--AATTT-ATTTGAATG
19267242 TAAATTAAAATTTAAAAATTTATTTGAATG
1 TAAATTAAAATTTAAAAATTTATTTGAATG
* * *
19267272 -CAATAAAAATATAAAAATTTATTT
1 TAAATTAAAATTTAAAAATTTATTT
19267296 AAATAAAGTG
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
29 21 0.30
30 23 0.32
31 3 0.04
32 4 0.06
33 20 0.28
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.40
Consensus pattern (30 bp):
TAAATTAAAATTTAAAAATTTATTTGAATG
Found at i:19268493 original size:62 final size:60
Alignment explanation
Indices: 19268416--19268545 Score: 163
Period size: 60 Copynumber: 2.1 Consensus size: 60
19268406 GAATAGTTTA
*
19268416 ATATGCAATTGAGAGA-TTCACAAATTTAATCAAGTTTTTTATTTTTTTAACATATTTAATAT
1 ATATACAATTGAGAGACTT-ACAAATTTAATCAAG-TTTTTA-TTTTTTAACATATTTAATAT
* ** * * *
19268478 ATATACAATTTAGAGACTTGTAAATTTAATTAAGTTTTTATTTTTTAATATATTTATTAT
1 ATATACAATTGAGAGACTTACAAATTTAATCAAGTTTTTATTTTTTAACATATTTAATAT
19268538 ATATACAA
1 ATATACAA
19268546 GTAAATAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
60 26 0.43
61 6 0.10
62 26 0.43
63 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.48
Consensus pattern (60 bp):
ATATACAATTGAGAGACTTACAAATTTAATCAAGTTTTTATTTTTTAACATATTTAATAT
Found at i:19268799 original size:2 final size:2
Alignment explanation
Indices: 19268794--19268829 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
19268784 ATATCTATCC
19268794 AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19268830 TTGAAGATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19274432 original size:23 final size:23
Alignment explanation
Indices: 19274406--19274456 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
19274396 ATATTAATTT
19274406 TAATAAATTAA-TAAATTATTTAA
1 TAATAAA-TAATTAAATTATTTAA
* * *
19274429 TAATAGATAATTAATTTGTTTAA
1 TAATAAATAATTAAATTATTTAA
19274452 TAATA
1 TAATA
19274457 TGATATATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TAATAAATAATTAAATTATTTAA
Found at i:19274549 original size:19 final size:18
Alignment explanation
Indices: 19274520--19274556 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
19274510 TTTTTTCTCA
19274520 TAATTATTATAATATAAT
1 TAATTATTATAATATAAT
*
19274538 TAATTAATTATAATTTAAT
1 TAATT-ATTATAATATAAT
19274557 ATTATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTATTATAATATAAT
Found at i:19276631 original size:10 final size:9
Alignment explanation
Indices: 19276606--19276632 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
19276596 TGTTTGATGA
19276606 TTTAAAAAT
1 TTTAAAAAT
19276615 TTTAAAAAT
1 TTTAAAAAT
19276624 TTTAAAAAT
1 TTTAAAAAT
19276633 AATAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:19277432 original size:2 final size:2
Alignment explanation
Indices: 19277425--19277450 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19277415 TGTTTATCAT
19277425 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
19277451 CACACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19278530 original size:14 final size:14
Alignment explanation
Indices: 19278490--19278532 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
19278480 TAAAAATGAA
19278490 AAAAAATAAAAAGAGT
1 AAAAAA-AAAAA-AGT
* *
19278506 AAATAAGAAAAAGT
1 AAAAAAAAAAAAGT
19278520 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
19278533 GTTTGATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 14 0.61
15 4 0.17
16 5 0.22
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (14 bp):
AAAAAAAAAAAAGT
Found at i:19278809 original size:15 final size:16
Alignment explanation
Indices: 19278791--19278820 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19278781 ATTTTTTATT
19278791 TAAAAAGAA-AAAAAA
1 TAAAAAGAATAAAAAA
19278806 TAAAAAGAATAAAAA
1 TAAAAAGAATAAAAA
19278821 GCAAAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (16 bp):
TAAAAAGAATAAAAAA
Found at i:19284645 original size:22 final size:22
Alignment explanation
Indices: 19284619--19284662 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19284609 TGTATATTTA
*
19284619 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
19284641 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
19284663 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:19291823 original size:44 final size:42
Alignment explanation
Indices: 19291724--19291827 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 42
19291714 AAATTGATAC
* * *
19291724 ACATGAAAAATTAAAATCTACAAAATAAACAAATAGATTAAT
1 ACATGAAAAATCATAAGCTACAAAATAAACAAATAGATTAAT
* * *
19291766 ACATAAAATAAATCATAAGCTACAAAATAAACAGATAGGTTAGTAT
1 ACAT-GAA-AAATCATAAGCTACAAAATAAACAAATAGATTA--AT
19291812 ACATGAAAAATCATAA
1 ACATGAAAAATCATAA
19291828 TAATGAAACC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
42 4 0.08
43 2 0.04
44 37 0.73
45 2 0.04
46 6 0.12
ACGTcount: A:0.59, C:0.11, G:0.08, T:0.23
Consensus pattern (42 bp):
ACATGAAAAATCATAAGCTACAAAATAAACAAATAGATTAAT
Found at i:19292327 original size:20 final size:20
Alignment explanation
Indices: 19292299--19292382 Score: 132
Period size: 20 Copynumber: 4.2 Consensus size: 20
19292289 AATAAAAACT
* *
19292299 TCATGCAAATATATTAATGA
1 TCATACAAATATATTAATAA
19292319 TCATACAAATATATTAATAA
1 TCATACAAATATATTAATAA
*
19292339 TCATGCAAATATATTAATAA
1 TCATACAAATATATTAATAA
*
19292359 TCATACAATTATATTAATAA
1 TCATACAAATATATTAATAA
19292379 TCAT
1 TCAT
19292383 GTAAGCAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.37
Consensus pattern (20 bp):
TCATACAAATATATTAATAA
Found at i:19292344 original size:40 final size:40
Alignment explanation
Indices: 19292299--19292383 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
19292289 AATAAAAACT
*
19292299 TCATGCAAATATATTAATGATCATACAAATATATTAATAA
1 TCATGCAAATATATTAATAATCATACAAATATATTAATAA
*
19292339 TCATGCAAATATATTAATAATCATACAATTATATTAATAA
1 TCATGCAAATATATTAATAATCATACAAATATATTAATAA
19292379 TCATG
1 TCATG
19292384 TAAGCAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (40 bp):
TCATGCAAATATATTAATAATCATACAAATATATTAATAA
Found at i:19292395 original size:40 final size:40
Alignment explanation
Indices: 19292299--19292436 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
19292289 AATAAAAACT
* * *
19292299 TCATGCAAATATATTAATGATCATACAAATATATTAATAA
1 TCATGCAAACAAATTAATAATCATACAAATATATTAATAA
* * *
19292339 TCATGCAAATATATTAATAATCATACAATTATATTAATAA
1 TCATGCAAACAAATTAATAATCATACAAATATATTAATAA
* * * * * *
19292379 TCATGTAAGCAAATTAA-ATTCTTGCAAATGTATATTAATTAT
1 TCATGCAAACAAATTAATAATCATACAAA--TATATTAA-TAA
*
19292421 TCATGCAAATAAATTA
1 TCATGCAAACAAATTA
19292437 GAAACCATAC
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 7 0.09
40 51 0.63
41 8 0.10
42 15 0.19
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (40 bp):
TCATGCAAACAAATTAATAATCATACAAATATATTAATAA
Found at i:19292556 original size:62 final size:60
Alignment explanation
Indices: 19292459--19292595 Score: 142
Period size: 62 Copynumber: 2.3 Consensus size: 60
19292449 GTAGACATCT
* * * *
19292459 TGCAAAA-ATA-ACTATTCATGCAAAAATATATAATAAATCATACAGTT-A-AT-AAATAATCA
1 TGCAAAATATATATTATTCATGCAAAAAAAAATAATAAAT--TA-AATTCATATCAAAT-ATCA
19292518 TGC-AAATATATATTATTCATGCAAAAAAAAATGCAATAAATTAAATTCATATCAAATATCA
1 TGCAAAATATATATTATTCATGCAAAAAAAAAT--AATAAATTAAATTCATATCAAATATCA
19292579 TGCAAAATATATATTAT
1 TGCAAAATATATATTAT
19292596 AATTATTCGA
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
58 3 0.05
59 9 0.14
60 21 0.32
61 9 0.14
62 24 0.36
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (60 bp):
TGCAAAATATATATTATTCATGCAAAAAAAAATAATAAATTAAATTCATATCAAATATCA
Found at i:19293937 original size:6 final size:6
Alignment explanation
Indices: 19293888--19293964 Score: 57
Period size: 6 Copynumber: 13.0 Consensus size: 6
19293878 AAATTGAACC
* * * * * *
19293888 AAAAAT AAAA-T AAAATA AAAATT GACATT AACATT AACATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
* * * *
19293935 AAAATT GAAATC AAAATC AAAATC AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT
19293965 TTTGGGCTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
5 5 0.08
6 55 0.92
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.26
Consensus pattern (6 bp):
AAAATT
Found at i:19295104 original size:40 final size:40
Alignment explanation
Indices: 19295044--19295187 Score: 139
Period size: 40 Copynumber: 3.6 Consensus size: 40
19295034 AAAGTGTTAC
* * * *
19295044 ATTTTTGAATGATTTTCAAGATCTCTAGG-CTAAATCTTTG
1 ATTTTTTAATGATTTTCAAGACCT-TAGGACAAAATCTTAG
* *
19295084 ATTTTTTAATGATTTCCAAGACCTTTGGACAAAATCTTAG
1 ATTTTTTAATGATTTTCAAGACCTTAGGACAAAATCTTAG
* * * * * *
19295124 ATATTTTAACGATTTTCAAGACCATCAGG-TAAAATTTTAA
1 ATTTTTTAATGATTTTCAAGACC-TTAGGACAAAATCTTAG
*
19295164 ATTTTTGAATGATTTTCAAGACCT
1 ATTTTTTAATGATTTTCAAGACCT
19295188 CCAAGAGAAT
Statistics
Matches: 85, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
39 4 0.05
40 78 0.92
41 3 0.04
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (40 bp):
ATTTTTTAATGATTTTCAAGACCTTAGGACAAAATCTTAG
Found at i:19295214 original size:39 final size:39
Alignment explanation
Indices: 19295114--19295210 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
19295104 ACCTTTGGAC
* * *
19295114 AAAATCTTAGATATTTTAACGATTTTCAAGACCATCAGGT
1 AAAATCTTAAAT-TTTTAATGATTTTCAAGACCATCAAGT
*
19295154 AAAATTTTAAATTTTTGAATGATTTTCAAGACC-TCCAAG-
1 AAAATCTTAAATTTTT-AATGATTTTCAAGACCAT-CAAGT
*
19295193 AGAATCTTAAATTTTTAA
1 AAAATCTTAAATTTTTAA
19295211 ATGAATTCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
38 2 0.04
39 19 0.39
40 28 0.57
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.38
Consensus pattern (39 bp):
AAAATCTTAAATTTTTAATGATTTTCAAGACCATCAAGT
Found at i:19295875 original size:50 final size:49
Alignment explanation
Indices: 19295810--19296025 Score: 163
Period size: 50 Copynumber: 4.3 Consensus size: 49
19295800 GCTTTTTATT
* *
19295810 TTTTTACAATTTCAAAGCCTCTATTTAGG-AGTAGCTTTTC-AAGTATGAGA
1 TTTTTA-AATTTCAAAGCCTCTATTTAGGAAG-ACCTTTACAAAG-ATGAGA
*
19295860 TTTTTAAACTTTCAAAGCCTCTGTTTAGGAAGACCTTTACAAAGATGAGA
1 TTTTTAAA-TTTCAAAGCCTCTATTTAGGAAGACCTTTACAAAGATGAGA
* * * * **
19295910 TTTTTAAAGTTTTAAAGCCTTTATTCA-GAATGAACCTTT-CAGAGACAAGA
1 TTTTTAAA-TTTCAAAGCCTCTATTTAGGAA-G-ACCTTTACAAAGATGAGA
* ** * * *
19295960 ATTTTAAAGTTTCAAAATCTCTATTTAGGTAA-AGCTTTTCAAAGATGATA
1 TTTTTAAA-TTTCAAAGCCTCTATTTAGG-AAGACCTTTACAAAGATGAGA
*
19296010 TTCTTAAAGTTTCAAA
1 TTTTTAAA-TTTCAAA
19296026 ATCTTTATTG
Statistics
Matches: 134, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
49 10 0.07
50 110 0.82
51 12 0.09
52 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (49 bp):
TTTTTAAATTTCAAAGCCTCTATTTAGGAAGACCTTTACAAAGATGAGA
Found at i:19296465 original size:20 final size:20
Alignment explanation
Indices: 19296437--19296479 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
19296427 TAAAGAGAGG
*
19296437 CAAGAAAAATAG-CAAAAAGT
1 CAAGAAAAAAAGTC-AAAAGT
*
19296457 CAAGGAAAAAAGTCAAAAGT
1 CAAGAAAAAAAGTCAAAAGT
19296477 CAA
1 CAA
19296480 CTTAAAGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.63, C:0.12, G:0.16, T:0.09
Consensus pattern (20 bp):
CAAGAAAAAAAGTCAAAAGT
Found at i:19296603 original size:7 final size:7
Alignment explanation
Indices: 19296587--19296656 Score: 69
Period size: 7 Copynumber: 10.7 Consensus size: 7
19296577 AGGTTCCCAA
*
19296587 AAACCTT
1 AAACCCT
19296594 AAACCCT
1 AAACCCT
*
19296601 AAACCTT
1 AAACCCT
*
19296608 AAAACC-
1 AAACCCT
19296614 AAACCCT
1 AAACCCT
19296621 AAACCCT
1 AAACCCT
19296628 AAA--CT
1 AAACCCT
*
19296633 AAACTCT
1 AAACCCT
19296640 AAA-CC-
1 AAACCCT
19296645 AAACCCT
1 AAACCCT
19296652 AAACC
1 AAACC
19296657 AAAAATCTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 8 0.15
6 8 0.15
7 36 0.69
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:19296636 original size:19 final size:20
Alignment explanation
Indices: 19296593--19296644 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
19296583 CCAAAAACCT
*
19296593 TAAACCCTAAACCTTAAAAC
1 TAAACCCTAAACCCTAAAAC
*
19296613 CAAACCCTAAACCCT-AAAC
1 TAAACCCTAAACCCTAAAAC
*
19296632 TAAACTCTAAACC
1 TAAACCCTAAACC
19296645 AAACCCTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAACCCTAAACCCTAAAAC
Found at i:19296656 original size:12 final size:12
Alignment explanation
Indices: 19296594--19296659 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 12
19296584 CAAAAACCTT
19296594 AAACCCTAAACC
1 AAACCCTAAACC
*
19296606 TTAAAACC-AAACCC
1 --AAACCCTAAA-CC
*
19296620 TAAACCCTAAACT
1 -AAACCCTAAACC
*
19296633 AAACTCTAAACC
1 AAACCCTAAACC
19296645 AAACCCTAAACC
1 AAACCCTAAACC
19296657 AAA
1 AAA
19296660 AATCTAACCA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
12 24 0.55
13 10 0.23
14 10 0.23
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.14
Consensus pattern (12 bp):
AAACCCTAAACC
Found at i:19298048 original size:19 final size:19
Alignment explanation
Indices: 19298021--19298060 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
19298011 AATTATACCC
*
19298021 ATCCTCATAATGTAATACT
1 ATCCCCATAATGTAATACT
19298040 ATCCCCATAATGTAATACT
1 ATCCCCATAATGTAATACT
19298059 AT
1 AT
19298061 TCCTATCCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (19 bp):
ATCCCCATAATGTAATACT
Found at i:19298856 original size:13 final size:13
Alignment explanation
Indices: 19298838--19298867 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19298828 ATTAAAGTTT
19298838 ATTTAAATAAAAA
1 ATTTAAATAAAAA
19298851 ATTTAAATAAAAA
1 ATTTAAATAAAAA
19298864 ATTT
1 ATTT
19298868 GCCTGTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAATAAAAA
Found at i:19298906 original size:15 final size:16
Alignment explanation
Indices: 19298882--19298916 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
19298872 GTGTAATTTG
19298882 TTTT-AAAGAATATT-
1 TTTTAAAAGAATATTA
19298896 TTTTAAAAGAATATTA
1 TTTTAAAAGAATATTA
19298912 TTTTA
1 TTTTA
19298917 TTTTAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 10 0.53
16 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
TTTTAAAAGAATATTA
Found at i:19298947 original size:14 final size:15
Alignment explanation
Indices: 19298920--19298951 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
19298910 TATTTTATTT
19298920 TAATTTATTATTATA
1 TAATTTATTATTATA
19298935 TAATTTA-TATTATA
1 TAATTTATTATTATA
19298949 TAA
1 TAA
19298952 AAGATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATTTATTATTATA
Found at i:19300104 original size:11 final size:11
Alignment explanation
Indices: 19300088--19300112 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19300078 AGAAAAACAT
19300088 AAAAAATTCTA
1 AAAAAATTCTA
19300099 AAAAAATTCTA
1 AAAAAATTCTA
19300110 AAA
1 AAA
19300113 TTTTTCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAAATTCTA
Found at i:19301682 original size:20 final size:20
Alignment explanation
Indices: 19301649--19301732 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
19301639 CATTTTAAAG
*
19301649 AATTTTTTAG--AATTTT-G
1 AATTTTTTAGAAAATTTTAA
*
19301666 AATTTGTTTTGAAAATTTTAA
1 AATTT-TTTAGAAAATTTTAA
*
19301687 AATTTTTTAGAAAATTTTAGC
1 AATTTTTTAGAAAATTTTA-A
*
19301708 AA-TATTTA-AAAATTTTTAA
1 AATTTTTTAGAAAA-TTTTAA
19301727 AATTTT
1 AATTTT
19301733 AAAATTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
17 5 0.09
18 4 0.08
19 6 0.11
20 31 0.58
21 7 0.13
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.52
Consensus pattern (20 bp):
AATTTTTTAGAAAATTTTAA
Found at i:19301705 original size:48 final size:45
Alignment explanation
Indices: 19301605--19301742 Score: 123
Period size: 48 Copynumber: 2.9 Consensus size: 45
19301595 TTTTGAATTT
* * ** **
19301605 TTTTAGAATTTTAGATTTTTCTAAAAATTTTTAACATTTTAAAGAATT
1 TTTTAGAATTTTA-ATTTTT-TTAAAA-TTTTAAAATTTTTTAGAAAA
19301653 TTTTAGAATTTTGAATTTGTTTTGAAAATTTTAAAATTTTTTAGAAAA
1 TTTTAGAATTTT-AATTT-TTTT-AAAATTTTAAAATTTTTTAGAAAA
**
19301701 TTTTAGCAATATTTAAAAATTTTTAAAATTTTAAAATTTTTT
1 TTTTAG-AAT-TTT-AATTTTTTTAAAATTTTAAAATTTTTT
19301743 TTGAAGTGAT
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
48 56 0.74
49 14 0.18
50 6 0.08
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (45 bp):
TTTTAGAATTTTAATTTTTTTAAAATTTTAAAATTTTTTAGAAAA
Found at i:19301742 original size:10 final size:9
Alignment explanation
Indices: 19301628--19301741 Score: 61
Period size: 9 Copynumber: 12.0 Consensus size: 9
19301618 GATTTTTCTA
19301628 AAAATTTTT
1 AAAATTTTT
* *
19301637 AACATTTTA
1 AAAATTTTT
19301646 AAGAATTTTTT
1 AA-AA-TTTTT
* *
19301657 AGAATTTTG
1 AAAATTTTT
**
19301666 AATTTGTTTT
1 AAAAT-TTTT
19301676 GAAAA-TTTT
1 -AAAATTTTT
19301685 AAAATTTTTT
1 AAAA-TTTTT
*
19301695 AGAAAATTTT
1 A-AAATTTTT
* *
19301705 AGCAATATTTA
1 A-AAAT-TTTT
19301716 AAAATTTTT
1 AAAATTTTT
19301725 AAAA-TTTT
1 AAAATTTTT
19301733 AAAATTTTT
1 AAAATTTTT
19301742 TTTGAAGTGA
Statistics
Matches: 78, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
8 12 0.15
9 30 0.38
10 22 0.28
11 14 0.18
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (9 bp):
AAAATTTTT
Found at i:19301743 original size:20 final size:20
Alignment explanation
Indices: 19301632--19301744 Score: 59
Period size: 20 Copynumber: 5.2 Consensus size: 20
19301622 TTTCTAAAAA
* *
19301632 TTTTTAACATTTTAAAGA-AT
1 TTTTTAAAATTTTAAA-ATTT
* *
19301652 TTTTTAGAATTTT-GAATTT
1 TTTTTAAAATTTTAAAATTT
*
19301671 GTTTTGAAAATTTTAAAATTT
1 -TTTTTAAAATTTTAAAATTT
**
19301692 TTTAGAAAATTTTAGCAATATTT
1 TTTTTAAAATTTTA--AA-ATTT
19301715 AAAAATTTTTAAAATTTTAAAATTT
1 -----TTTTTAAAATTTTAAAATTT
19301740 TTTTT
1 TTTTT
19301745 GAAGTGATTA
Statistics
Matches: 72, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
18 1 0.01
19 2 0.03
20 40 0.56
21 5 0.07
22 2 0.03
23 4 0.06
25 4 0.06
26 2 0.03
28 12 0.17
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTTAAAATTTTAAAATTT
Found at i:19302771 original size:1 final size:1
Alignment explanation
Indices: 19302765--19302795 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
19302755 TCATGATCTC
19302765 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19302796 ACATTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19304705 original size:65 final size:65
Alignment explanation
Indices: 19304624--19304757 Score: 250
Period size: 65 Copynumber: 2.1 Consensus size: 65
19304614 TCTTCTTTCT
*
19304624 TCATTTATTTCTTTTCATACTTTTCATATGATAATTAAACTATAGAATATAGATATTTTATGTTA
1 TCATTTATTTCTTTTCATACTTTTCATATGATAATTAAACTATAGAATATAGATATTTTATATTA
*
19304689 TCATTTATTTCTTTTCATTCTTTTCATATGATAATTAAACTATAGAATATAGATATTTTATATTA
1 TCATTTATTTCTTTTCATACTTTTCATATGATAATTAAACTATAGAATATAGATATTTTATATTA
19304754 TCAT
1 TCAT
19304758 ATTTGTTTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (65 bp):
TCATTTATTTCTTTTCATACTTTTCATATGATAATTAAACTATAGAATATAGATATTTTATATTA
Found at i:19306229 original size:2 final size:2
Alignment explanation
Indices: 19306216--19306258 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
19306206 TTTGCATCAG
* *
19306216 AT AT AT AA AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19306258 A
1 A
19306259 AAATTAATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19312819 original size:30 final size:30
Alignment explanation
Indices: 19312724--19312829 Score: 92
Period size: 30 Copynumber: 3.5 Consensus size: 30
19312714 TTATTGTAAT
* * * *
19312724 TAAATAATTTTTTAATTTTTAATTTACATC
1 TAAATAACTCTTTAATTTTTAATTTATATA
* * *
19312754 TAAATAATTCTTTAATTTTTAATATAT-TT
1 TAAATAACTCTTTAATTTTTAATTTATATA
*
19312783 TCAAATAAGCTC-TTAACTTTTAATTTATATA
1 T-AAATAA-CTCTTTAATTTTTAATTTATATA
19312814 TAAATAAACT-TTTAAT
1 TAAAT-AACTCTTTAAT
19312830 ATAAATCAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
29 2 0.03
30 54 0.87
31 6 0.10
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.52
Consensus pattern (30 bp):
TAAATAACTCTTTAATTTTTAATTTATATA
Found at i:19313396 original size:26 final size:26
Alignment explanation
Indices: 19313354--19313404 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
19313344 CTAAATACTA
*
19313354 AAAACTAAAACCCTAAACCCTAAACCC
1 AAAACTAAAACCATAAACCC-AAACCC
19313381 AAAA-TAAAACCATAAACCCAAACC
1 AAAACTAAAACCATAAACCCAAACC
19313405 TAACCTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 14 0.61
27 4 0.17
ACGTcount: A:0.57, C:0.33, G:0.00, T:0.10
Consensus pattern (26 bp):
AAAACTAAAACCATAAACCCAAACCC
Found at i:19313431 original size:20 final size:20
Alignment explanation
Indices: 19313406--19313445 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19313396 ACCCAAACCT
19313406 AACCTAAACCCGAAATCAAA
1 AACCTAAACCCGAAATCAAA
*
19313426 AACCTAAACCCTAAATCAAA
1 AACCTAAACCCGAAATCAAA
19313446 CCCTGAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.30, G:0.03, T:0.12
Consensus pattern (20 bp):
AACCTAAACCCGAAATCAAA
Found at i:19313456 original size:19 final size:19
Alignment explanation
Indices: 19313368--19313459 Score: 89
Period size: 19 Copynumber: 4.9 Consensus size: 19
19313358 CTAAAACCCT
* *
19313368 AAACCCTAAACCCAAAATA
1 AAACCCTAAACCCTAAATC
* *
19313387 AAACCATAAACCC-AAACC
1 AAACCCTAAACCCTAAATC
* *
19313405 TAA-CCTAAACCCGAAATC
1 AAACCCTAAACCCTAAATC
*
19313423 AAAAACCTAAACCCTAAATC
1 -AAACCCTAAACCCTAAATC
*
19313443 AAACCCTGAACCCTAAA
1 AAACCCTAAACCCTAAA
19313460 NNNNNNNNNN
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
17 8 0.13
18 9 0.15
19 29 0.48
20 14 0.23
ACGTcount: A:0.52, C:0.34, G:0.02, T:0.12
Consensus pattern (19 bp):
AAACCCTAAACCCTAAATC
Found at i:19321263 original size:26 final size:26
Alignment explanation
Indices: 19321221--19321271 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
19321211 CTAAATACTA
*
19321221 AAAACTAAAACCCTAAACCCTAAACCC
1 AAAACTAAAACCATAAACCC-AAACCC
19321248 AAAA-TAAAACCATAAACCCAAACC
1 AAAACTAAAACCATAAACCCAAACC
19321272 TAACCCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 14 0.61
27 4 0.17
ACGTcount: A:0.57, C:0.33, G:0.00, T:0.10
Consensus pattern (26 bp):
AAAACTAAAACCATAAACCCAAACCC
Found at i:19321281 original size:26 final size:26
Alignment explanation
Indices: 19321225--19321307 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 26
19321215 ATACTAAAAA
* *
19321225 CTAAAACCCTAAACCCTAAACCCAA-A
1 CTAAAACCCTAAACCC-AAACCTAACC
* *
19321251 ATAAAACCATAAACCCAAACCTAACC
1 CTAAAACCCTAAACCCAAACCTAACC
* * *
19321277 CT-AAACCCGAAATCAAAACCTAAACC
1 CTAAAACCCTAAACCCAAACCT-AACC
19321303 CTAAA
1 CTAAA
19321308 TCAAACCCTG
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
25 22 0.49
26 21 0.47
27 2 0.04
ACGTcount: A:0.52, C:0.35, G:0.01, T:0.12
Consensus pattern (26 bp):
CTAAAACCCTAAACCCAAACCTAACC
Found at i:19321323 original size:19 final size:19
Alignment explanation
Indices: 19321235--19321333 Score: 110
Period size: 19 Copynumber: 5.3 Consensus size: 19
19321225 CTAAAACCCT
* *
19321235 AAACCCTAAACCCAAAATA
1 AAACCCTAAACCCTAAATC
* *
19321254 AAACCATAAACCC-AAACC
1 AAACCCTAAACCCTAAATC
* *
19321272 TAACCCTAAACCCGAAATC
1 AAACCCTAAACCCTAAATC
*
19321291 AAAACCTAAACCCTAAATC
1 AAACCCTAAACCCTAAATC
* *
19321310 AAACCCTGAACCCTAAACC
1 AAACCCTAAACCCTAAATC
19321329 AAACC
1 AAACC
19321334 TTAGACCATA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
18 14 0.21
19 53 0.79
ACGTcount: A:0.51, C:0.36, G:0.02, T:0.11
Consensus pattern (19 bp):
AAACCCTAAACCCTAAATC
Found at i:19321412 original size:52 final size:53
Alignment explanation
Indices: 19321348--19321458 Score: 117
Period size: 52 Copynumber: 2.1 Consensus size: 53
19321338 ACCATAAATT
19321348 CCTAAA-CTCTAAA-CC-AAACCTTAACT-TTAAATA-CTAAAACCAAACCTTAAAC
1 CCTAAATCTCTAAATCCTAAACC--AACTCTTAAA-ACCT-AAACCAAACCTTAAAC
* * *
19321400 CCTAAATC-CTAAATCCTAAACCAAGTCTTAAAACCTAAACCTAACTTTAAAC
1 CCTAAATCTCTAAATCCTAAACCAACTCTTAAAACCTAAACCAAACCTTAAAC
19321452 CCTAAAT
1 CCTAAAT
19321459 GAAACTCTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
52 36 0.71
53 10 0.20
54 5 0.10
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (53 bp):
CCTAAATCTCTAAATCCTAAACCAACTCTTAAAACCTAAACCAAACCTTAAAC
Found at i:19321421 original size:33 final size:33
Alignment explanation
Indices: 19321375--19321443 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
19321365 ACCTTAACTT
*
19321375 TAAATACTAAAACCAAACCTTAAACCCTAAATCC
1 TAAATACTAAAACCAAACCTTAAAACCTAAA-CC
* **
19321409 TAAATCCT-AAACCAAGTCTTAAAACCTAAACC
1 TAAATACTAAAACCAAACCTTAAAACCTAAACC
19321441 TAA
1 TAA
19321444 CTTTAAACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 5 0.16
33 19 0.61
34 7 0.23
ACGTcount: A:0.49, C:0.28, G:0.01, T:0.22
Consensus pattern (33 bp):
TAAATACTAAAACCAAACCTTAAAACCTAAACC
Found at i:19321505 original size:19 final size:19
Alignment explanation
Indices: 19321260--19321513 Score: 87
Period size: 19 Copynumber: 13.9 Consensus size: 19
19321250 AATAAAACCA
* *
19321260 TAAACCC-AAACCTAACCC
1 TAAACCCTAAACCAAACTC
* *
19321278 TAAACCCGAAATCAAAAC-C
1 TAAACCCTAAA-CCAAACTC
* *
19321297 TAAACCCTAAATCAAACCC
1 TAAACCCTAAACCAAACTC
*
19321316 TGAACCCTAAACCAAAC-C
1 TAAACCCTAAACCAAACTC
* *
19321334 TTAGACCATAAATTCCTAAACTC
1 -TAAACCCTAAA--CC-AAACTC
* *
19321357 TAAA-CC-AAACCTTAACTT
1 TAAACCCTAAACC-AAACTC
**
19321375 TAAATACTAAAACCAAAC-C
1 TAAACCCT-AAACCAAACTC
*
19321394 TTAAACCCT--A--AATC-C
1 -TAAACCCTAAACCAAACTC
* *
19321409 TAAATCCTAAACC-AAGTC
1 TAAACCCTAAACCAAACTC
* * *
19321427 TTAAAACCTAAACCTAACTT
1 -TAAACCCTAAACCAAACTC
**
19321447 TAAACCCTAAATGAAACTC
1 TAAACCCTAAACCAAACTC
*
19321466 TAAACCCTATACCAAA---
1 TAAACCCTAAACCAAACTC
19321482 T----CCTAAACCAAACTC
1 TAAACCCTAAACCAAACTC
*
19321497 TAAACCCTAAACTAAAC
1 TAAACCCTAAACCAAAC
19321514 CTTAAATAAA
Statistics
Matches: 174, Mismatches: 36, Indels: 51
0.67 0.14 0.20
Matches are distributed among these distances:
12 10 0.06
14 7 0.04
15 5 0.03
16 2 0.01
17 2 0.01
18 24 0.14
19 89 0.51
20 19 0.11
21 8 0.05
22 7 0.04
23 1 0.01
ACGTcount: A:0.46, C:0.31, G:0.02, T:0.20
Consensus pattern (19 bp):
TAAACCCTAAACCAAACTC
Found at i:19321519 original size:7 final size:6
Alignment explanation
Indices: 19321232--19321515 Score: 70
Period size: 7 Copynumber: 44.5 Consensus size: 6
19321222 AAACTAAAAC
* * * *
19321232 CCTAAA CCCTAAA CCCAAA -ATAAAA CCATAAA CCCAAA CCTAAC CCTAAA
1 CCTAAA -CCTAAA CCTAAA CCT-AAA CC-TAAA CCTAAA CCTAAA CCTAAA
* * * * *
19321282 CCCGAAA TCAAAA CCTAAA CCCTAAA TC-AAA CCCTGAAC CCTAAA CC-AAA
1 -CCTAAA CCTAAA CCTAAA -CCTAAA CCTAAA -CCT-AAA CCTAAA CCTAAA
* * *
19321332 CCTTAGA CCATAAA TTCCTAAA CTCTAAA CC-AAA CCTTAA CTTTAAA
1 CC-TAAA CC-TAAA --CCTAAA C-CTAAA CCTAAA CCTAAA C-CTAAA
* *
19321379 TACTAAAA CC-AAA CCTTAAA CCCTAAA TCCTAAA TCCTAAA CC-AAGT
1 -CCT-AAA CCTAAA CC-TAAA -CCTAAA -CCTAAA -CCTAAA CCTAA-A
* * *
19321426 CTTAAAA CCTAAA CCT-AA CTTTAAA CCCTAAA --TGAAA CTCTAAA CCCTATA
1 CCT-AAA CCTAAA CCTAAA C-CTAAA -CCTAAA CCT-AAA C-CTAAA -CCTAAA
19321477 CC-AAA TCCTAAA CC-AAA CTCTAAA CCCTAAA -CTAAA CCT
1 CCTAAA -CCTAAA CCTAAA C-CTAAA -CCTAAA CCTAAA CCT
19321516 TAAATAAAGA
Statistics
Matches: 205, Mismatches: 35, Indels: 75
0.65 0.11 0.24
Matches are distributed among these distances:
4 1 0.00
5 37 0.18
6 58 0.28
7 89 0.43
8 18 0.09
9 2 0.01
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.19
Consensus pattern (6 bp):
CCTAAA
Found at i:19321519 original size:19 final size:19
Alignment explanation
Indices: 19321233--19321519 Score: 64
Period size: 19 Copynumber: 15.6 Consensus size: 19
19321223 AACTAAAACC
*
19321233 CTAAACCCTAAACCC-AAA
1 CTAAACCTTAAACCCTAAA
* *
19321251 ATAAAACCATAAACCC-AAA
1 CT-AAACCTTAAACCCTAAA
* *
19321270 CCT-AACCCTAAACCCGAAA
1 -CTAAACCTTAAACCCTAAA
*
19321289 TCAAAACC-TAAACCCTAAA
1 -CTAAACCTTAAACCCTAAA
* *
19321308 -TCAAACCCTGAACCCTAAA
1 CT-AAACCTTAAACCCTAAA
* * *
19321327 CCAAACCTTAGACCATAAA
1 CTAAACCTTAAACCCTAAA
19321346 TTCCTAAA-CTCTAAA-CC-AAA
1 ---CTAAACCT-TAAACCCTAAA
* * **
19321366 CCTTAACTTTAAATACTAAAA
1 -CTAAACCTTAAACCCT-AAA
*
19321387 CCAAACCTTAAACCCTAAA
1 CTAAACCTTAAACCCTAAA
*
19321406 -T---CC-TAAATCCTAAA
1 CTAAACCTTAAACCCTAAA
* ** *
19321420 CCAAGTCTTAAAACCTAAA
1 CTAAACCTTAAACCCTAAA
*
19321439 CCT-AACTTTAAACCCTAAA
1 -CTAAACCTTAAACCCTAAA
19321458 -TGAAA-CTCTAAACCCT--A
1 CT-AAACCT-TAAACCCTAAA
*
19321475 -T--ACC--AAATCCTAAA
1 CTAAACCTTAAACCCTAAA
*
19321489 CCAAA-CTCTAAACCCTAAA
1 CTAAACCT-TAAACCCTAAA
19321508 CTAAACCTTAAA
1 CTAAACCTTAAA
19321520 TAAAGAACCT
Statistics
Matches: 195, Mismatches: 40, Indels: 67
0.65 0.13 0.22
Matches are distributed among these distances:
12 6 0.03
14 12 0.06
15 3 0.02
16 1 0.01
17 4 0.02
18 28 0.14
19 106 0.54
20 22 0.11
21 6 0.03
22 7 0.04
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (19 bp):
CTAAACCTTAAACCCTAAA
Found at i:19323180 original size:15 final size:16
Alignment explanation
Indices: 19323148--19323182 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
19323138 GGGAAAAATG
19323148 TTTTTTAAAAAATTGAT
1 TTTTTTAAAAAA-TGAT
19323165 TTTTTTAAAAAA-GAT
1 TTTTTTAAAAAATGAT
19323180 TTT
1 TTT
19323183 CCAATCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
17 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTTTTAAAAAATGAT
Found at i:19329151 original size:17 final size:16
Alignment explanation
Indices: 19329124--19329165 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
19329114 AGCTATTTCA
19329124 TTTTG-ATTTTTGGTT
1 TTTTGAATTTTTGGTT
19329139 CTTTTGAATTTTTTGGTT
1 -TTTTGAA-TTTTTGGTT
*
19329157 TTTTTAATT
1 TTTTGAATT
19329166 CATCTTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 9 0.39
ACGTcount: A:0.12, C:0.02, G:0.14, T:0.71
Consensus pattern (16 bp):
TTTTGAATTTTTGGTT
Found at i:19329153 original size:18 final size:17
Alignment explanation
Indices: 19329130--19329165 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
19329120 TTCATTTTGA
19329130 TTTTTGGTTCTTTTGAAT
1 TTTTTGGTT-TTTTGAAT
*
19329148 TTTTTGGTTTTTTTAAT
1 TTTTTGGTTTTTTGAAT
19329165 T
1 T
19329166 CATCTTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.03, G:0.14, T:0.72
Consensus pattern (17 bp):
TTTTTGGTTTTTTGAAT
Found at i:19331139 original size:24 final size:24
Alignment explanation
Indices: 19331112--19331178 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
19331102 CGTTTTGTGA
*
19331112 AAAAAAAAAAGCCAAAAAATGGCT
1 AAAAAAAAAAGCAAAAAAATGGCT
*
19331136 AAAAAAAAAA-AAAACAAAATGGCT
1 AAAAAAAAAAGCAAA-AAAATGGCT
* *
19331160 AAACAAAAATGCAAAAAAA
1 AAAAAAAAAAGCAAAAAAA
19331179 AAAAAATTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.06
24 31 0.86
25 3 0.08
ACGTcount: A:0.73, C:0.10, G:0.09, T:0.07
Consensus pattern (24 bp):
AAAAAAAAAAGCAAAAAAATGGCT
Found at i:19333421 original size:14 final size:15
Alignment explanation
Indices: 19333398--19333440 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
19333388 AAAAGTGGAT
*
19333398 AGAAACAAAGA-AAA
1 AGAAAAAAAGAGAAA
19333412 AGAAAAAAAGAGAAA
1 AGAAAAAAAGAGAAA
*
19333427 AAACAAAAAAGAGA
1 AGA-AAAAAAGAGA
19333441 GAAAAGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 10 0.40
15 5 0.20
16 10 0.40
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAGAGAAA
Found at i:19333435 original size:24 final size:24
Alignment explanation
Indices: 19333408--19333458 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
19333398 AGAAACAAAG
19333408 AAAAAGA-AAAAAAGAGAAAAAACA
1 AAAAAGAGAAAAAAG-GAAAAAACA
* *
19333432 AAAAAGAGAGAAAAGGAAAAAATA
1 AAAAAGAGAAAAAAGGAAAAAACA
19333456 AAA
1 AAA
19333459 TGAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (24 bp):
AAAAAGAGAAAAAAGGAAAAAACA
Found at i:19333451 original size:17 final size:16
Alignment explanation
Indices: 19333406--19333453 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
19333396 ATAGAAACAA
19333406 AGAAAAAGAAAAAAAG
1 AGAAAAAGAAAAAAAG
19333422 AGAAAAA-ACAAAAAAG
1 AGAAAAAGA-AAAAAAG
19333438 AGAGAAAAGGAAAAAA
1 AGA-AAAA-GAAAAAA
19333454 TAAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 17 0.61
17 4 0.14
18 5 0.18
19 1 0.04
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAAAAAG
Found at i:19336504 original size:44 final size:42
Alignment explanation
Indices: 19336405--19336508 Score: 127
Period size: 44 Copynumber: 2.4 Consensus size: 42
19336395 AAATTGATAC
* * *
19336405 ACATGAAAAATTAAAATCTACAAAATAAACAAATAGATTAAT
1 ACATGAAAAATCATAAGCTACAAAATAAACAAATAGATTAAT
* *
19336447 ACATAAAATAAATCATAAGCTACAAAATAAACAAATAGGTTAGTAT
1 ACAT-GAA-AAATCATAAGCTACAAAATAAACAAATAGATTA--AT
19336493 ACATGAAAAATCATAA
1 ACATGAAAAATCATAA
19336509 TAATGAAACC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
42 4 0.08
43 2 0.04
44 38 0.73
45 2 0.04
46 6 0.12
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.23
Consensus pattern (42 bp):
ACATGAAAAATCATAAGCTACAAAATAAACAAATAGATTAAT
Found at i:19337024 original size:40 final size:40
Alignment explanation
Indices: 19336979--19337067 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
19336969 CAATAAAAAC
*
19336979 ATCATGCAAATATATTAATGATCATACAAATATATTAATA
1 ATCATGCAAATATATTAATAATCATACAAATATATTAATA
*
19337019 ATCATGCAAATATATTAATAATCATACAATTATATTAATA
1 ATCATGCAAATATATTAATAATCATACAAATATATTAATA
19337059 ATCATGCAA
1 ATCATGCAA
19337068 GCAAATTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.35
Consensus pattern (40 bp):
ATCATGCAAATATATTAATAATCATACAAATATATTAATA
Found at i:19337075 original size:20 final size:20
Alignment explanation
Indices: 19336979--19337117 Score: 145
Period size: 20 Copynumber: 6.8 Consensus size: 20
19336969 CAATAAAAAC
*
19336979 ATCATGCAAATATATTAATG
1 ATCATGCAAATATATTAATA
*
19336999 ATCATACAAATATATTAATA
1 ATCATGCAAATATATTAATA
19337019 ATCATGCAAATATATTAATA
1 ATCATGCAAATATATTAATA
* *
19337039 ATCATACAATTATATTAATA
1 ATCATGCAAATATATTAATA
** *
19337059 ATCATGCAAGCAAATTAA-A
1 ATCATGCAAATATATTAATA
* *
19337078 TTCTTGCAAATGTATATTAATTA
1 ATCATGCAAA--TATATTAA-TA
* *
19337101 TTCATGCAAATAAATTA
1 ATCATGCAAATATATTA
19337118 GAAACCATAC
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
19 8 0.08
20 69 0.70
21 12 0.12
23 10 0.10
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (20 bp):
ATCATGCAAATATATTAATA
Found at i:19338595 original size:6 final size:6
Alignment explanation
Indices: 19338546--19338616 Score: 54
Period size: 6 Copynumber: 12.0 Consensus size: 6
19338536 AAATTGAACC
* * * * * *
19338546 AAAAAT AAAA-T AAAATA AAAATT GACATT AACATT AACATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
* * *
19338593 AAAATT GAAATC AAAATC AAAATT
1 AAAATT AAAATT AAAATT AAAATT
19338617 TTTAGGCTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
5 5 0.09
6 49 0.91
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (6 bp):
AAAATT
Found at i:19339760 original size:40 final size:39
Alignment explanation
Indices: 19339684--19339920 Score: 136
Period size: 40 Copynumber: 5.9 Consensus size: 39
19339674 TGTAACACTT
* * * *
19339684 TCAGGCAAAGTGTTACATTTTTGAATGATTTCCAAGACC
1 TCAGGCAAAATCTTAAATTTTTGAATGATTTTCAAGACC
** *
19339723 TTTGGACAAAATCTTAGATATTTT-AATGATTTTCAAGACC
1 TCAGG-CAAAATCTTAAAT-TTTTGAATGATTTTCAAGACC
* *
19339763 ATCAGGTAAAATTTTAAATTTTTGAATGATTTTCAAGACC
1 -TCAGGCAAAATCTTAAATTTTTGAATGATTTTCAAGACC
* * * * * * *
19339803 TCCAAG-ATAATCTTAAATTTTTAAATGAATTCCAATACTT
1 T-CAGGCAAAATCTTAAATTTTTGAATGATTTTCAAGAC-C
** * * * * *
19339843 TTGGGCAGAATTTTAAAATTTTGAATGATTTCCAAGATCT
1 TCAGGCAAAATCTTAAATTTTTGAATGATTTTCAAGA-CC
* ** * * *
19339883 TTATACATAATTTTCAATTTTGTGAATGATTTTCAAGA
1 TCAGGCAAAATCTTAAATTTT-TGAATGATTTTCAAGA
19339921 TTTTCAAGCT
Statistics
Matches: 154, Mismatches: 35, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
39 35 0.23
40 96 0.62
41 23 0.15
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (39 bp):
TCAGGCAAAATCTTAAATTTTTGAATGATTTTCAAGACC
Found at i:19340642 original size:50 final size:50
Alignment explanation
Indices: 19340425--19340731 Score: 226
Period size: 50 Copynumber: 6.1 Consensus size: 50
19340415 GGCTTTTTAT
* * *
19340425 TTTTTAAAAGTTTCAAAGCCTCTATTTAGG-AGTAGTTTTTCAAATATGAGA
1 TTTTT-AAAGTTTCAAAGCCTCTATTTAGGAAG-AGCTTTTCAAAGATAAGA
* *
19340476 TTTTTAAACTTTCAAAGCCTCTGTTTAGGAAGA-CTTTTACAAAGATAAGA
1 TTTTTAAAGTTTCAAAGCCTCTATTTAGGAAGAGCTTTT-CAAAGATAAGA
* * * * * * *
19340526 TTTTTAAAGTTTTAAAGCCTTTATTCA-GAATGAACCTTTCAGAGACAAGA
1 TTTTTAAAGTTTCAAAGCCTCTATTTAGGAA-GAGCTTTTCAAAGATAAGA
* ** * *
19340576 ATTTTAAAGTTTCAAAATCTCTATTTAGGTAGAGCTTTTCAAAGATGAGA
1 TTTTTAAAGTTTCAAAGCCTCTATTTAGGAAGAGCTTTTCAAAGATAAGA
* ** * ** ** ** * * *
19340626 TTCTTAAAGTTTCAAAATCTTTATTGGGGGGGATTTTTTTTAAATATAAAA
1 TTTTTAAAGTTTCAAAGCCTCTATTTAGGAAGA-GCTTTTCAAAGATAAGA
* * * *
19340677 TTTTTAAAGTTTTAAAGCCTCTGTTAAGAAAGAGCCTTTT-AAAGATAAGA
1 TTTTTAAAGTTTCAAAGCCTCTATTTAGGAAGAG-CTTTTCAAAGATAAGA
19340727 TTTTT
1 TTTTT
19340732 TTCTCTTAAA
Statistics
Matches: 196, Mismatches: 53, Indels: 15
0.74 0.20 0.06
Matches are distributed among these distances:
49 7 0.04
50 139 0.71
51 50 0.26
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (50 bp):
TTTTTAAAGTTTCAAAGCCTCTATTTAGGAAGAGCTTTTCAAAGATAAGA
Found at i:19341225 original size:7 final size:7
Alignment explanation
Indices: 19341209--19341334 Score: 78
Period size: 7 Copynumber: 19.7 Consensus size: 7
19341199 GGGTTCCCAA
*
19341209 AAACCTT
1 AAACCCT
19341216 AAACCCT
1 AAACCCT
*
19341223 AAACCTT
1 AAACCCT
*
19341230 AAAACC-
1 AAACCCT
19341236 AAACCCT
1 AAACCCT
19341243 AAA---T
1 AAACCCT
*
19341247 AAACCTT
1 AAACCCT
*
19341254 AAACCTT
1 AAACCCT
19341261 AAA-CCT
1 AAACCCT
* *
19341267 TAATCC-
1 AAACCCT
*
19341273 AAGCCCT
1 AAACCCT
19341280 AAACCCT
1 AAACCCT
19341287 AAA-CC-
1 AAACCCT
*
19341292 AAGCCCT
1 AAACCCT
19341299 AAACCCT
1 AAACCCT
19341306 AAA--CT
1 AAACCCT
*
19341311 AAACTCT
1 AAACCCT
19341318 AAA-CC-
1 AAACCCT
19341323 AAACCCT
1 AAACCCT
19341330 AAACC
1 AAACC
19341335 AAAAATCTAA
Statistics
Matches: 93, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
4 4 0.04
5 10 0.11
6 19 0.20
7 60 0.65
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:19341251 original size:38 final size:37
Alignment explanation
Indices: 19341209--19341334 Score: 112
Period size: 38 Copynumber: 3.3 Consensus size: 37
19341199 GGGTTCCCAA
19341209 AAACCTTAAACCCTAAACCTTAAAACCAAACCCTAAAT
1 AAACCTTAAACCCTAAACCTT-AAACCAAACCCTAAAT
* * *
19341247 AAACCTTAAACCTTAAACCTTAATCCAAGCCCTAAACCCT
1 AAACCTTAAACCCTAAACCTTAAACCAAACCCTAAA---T
* * * * *
19341287 AAACC--AAGCCCTAAACCCTAAACTAAACTCTAAACC
1 AAACCTTAAACCCTAAACCTTAAACCAAACCCTAAA-T
*
19341323 AAACCCTAAACC
1 AAACCTTAAACC
19341335 AAAAATCTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
36 6 0.08
37 13 0.18
38 46 0.65
40 6 0.08
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.17
Consensus pattern (37 bp):
AAACCTTAAACCCTAAACCTTAAACCAAACCCTAAAT
Found at i:19341319 original size:19 final size:19
Alignment explanation
Indices: 19341216--19341322 Score: 94
Period size: 19 Copynumber: 5.6 Consensus size: 19
19341206 CAAAAACCTT
*
19341216 AAACCCTAAACCTTAAAACC
1 AAACCCTAAACCCT-AAACC
19341236 AAACCCTAAA---TAAACC
1 AAACCCTAAACCCTAAACC
* * *
19341252 TTAAACCTTAAACCTTAATCC
1 --AAACCCTAAACCCTAAACC
*
19341273 AAGCCCTAAACCCTAAACC
1 AAACCCTAAACCCTAAACC
* *
19341292 AAGCCCTAAACCCTAAACT
1 AAACCCTAAACCCTAAACC
*
19341311 AAACTCTAAACC
1 AAACCCTAAACC
19341323 AAACCCTAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
16 5 0.07
17 1 0.01
18 9 0.12
19 43 0.59
20 10 0.14
21 5 0.07
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.18
Consensus pattern (19 bp):
AAACCCTAAACCCTAAACC
Found at i:19341334 original size:12 final size:12
Alignment explanation
Indices: 19341231--19341337 Score: 67
Period size: 12 Copynumber: 8.7 Consensus size: 12
19341221 CTAAACCTTA
19341231 AAACCAAACCCT
1 AAACCAAACCCT
* *
19341243 AAA-TAAACCTT
1 AAACCAAACCCT
*
19341254 AAACCTTAAACCTT
1 AAACC--AAACCCT
* *
19341268 AATCCAAGCCCT
1 AAACCAAACCCT
19341280 AAACCCTAAA-CC-
1 AAA-CC-AAACCCT
*
19341292 AAGCCCTAAACCCT
1 AA-ACC-AAACCCT
* *
19341306 AAACTAAACTCT
1 AAACCAAACCCT
19341318 AAACCAAACCCT
1 AAACCAAACCCT
19341330 AAACCAAA
1 AAACCAAA
19341338 AATCTAACCA
Statistics
Matches: 73, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
11 9 0.12
12 42 0.58
13 7 0.10
14 15 0.21
ACGTcount: A:0.48, C:0.35, G:0.02, T:0.16
Consensus pattern (12 bp):
AAACCAAACCCT
Found at i:19341346 original size:24 final size:24
Alignment explanation
Indices: 19341299--19341349 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
19341289 ACCAAGCCCT
* *
19341299 AAACCCTAAACTAAACTCTAAACC
1 AAACCCTAAACAAAAATCTAAACC
19341323 AAACCCTAAACCAAAAATCT-AACC
1 AAACCCTAAA-CAAAAATCTAAACC
19341347 AAA
1 AAA
19341350 GCCTTTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.14
Consensus pattern (24 bp):
AAACCCTAAACAAAAATCTAAACC
Found at i:19343522 original size:13 final size:13
Alignment explanation
Indices: 19343504--19343533 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19343494 ATTAAAGTTT
19343504 ATTTAAATAAAAA
1 ATTTAAATAAAAA
19343517 ATTTAAATAAAAA
1 ATTTAAATAAAAA
19343530 ATTT
1 ATTT
19343534 GCTAGTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAATAAAAA
Found at i:19343565 original size:14 final size:14
Alignment explanation
Indices: 19343542--19343572 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19343532 TTGCTAGTGT
19343542 AATTTGTTTTAAAG
1 AATTTGTTTTAAAG
*
19343556 AATTTTTTTTAAAG
1 AATTTGTTTTAAAG
19343570 AAT
1 AAT
19343573 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (14 bp):
AATTTGTTTTAAAG
Found at i:19343612 original size:14 final size:15
Alignment explanation
Indices: 19343585--19343616 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
19343575 TATTTTATTT
19343585 TAATTTATTATTATA
1 TAATTTATTATTATA
19343600 TAATTTA-TATTATA
1 TAATTTATTATTATA
19343614 TAA
1 TAA
19343617 AAGATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATTTATTATTATA
Found at i:19345129 original size:230 final size:232
Alignment explanation
Indices: 19344680--19345150 Score: 901
Period size: 230 Copynumber: 2.0 Consensus size: 232
19344670 CATAAACATC
19344680 AAATAAAATATTGACACGTGTCAAAATGTCCAATTAGCTCCACATCATCAATGTCACGTCAACAC
1 AAATAAAATATTGACACGTGTCAAAATGTCCAATTAGCTCCACATCATCAATGTCACGTCAACAC
19344745 CAAAAGAAAAACATAAAAAATTCTAAAAATTTTCAAAATTAAAAAAAAAAATAGAAACATATGGG
66 CAAAAGAAAAACATAAAAAATTCTAAAAATTTTCAAAATT-AAAAAAAAAATAGAAACATATGGG
*
19344810 TTACATAGCACAATGGGTAGACATGCGGGTCACATAGATTACACACGGGTCTTGCAAAAATTTTT
130 TTACATAGCACAATGGGTAGACATACGGGTCACATAGATTACACACGGGTCTTGCAAAAATTTTT
19344875 CCTAAAATGACATTATTTTAAGTTTCTTTAACTAGCAA
195 CCTAAAATGACATTATTTTAAGTTTCTTTAACTAGCAA
19344913 AAATAAAATATTGACACGTGTCAAAATGTCCAATTAGCTCCACATCATCAATGTCACGTCAACAC
1 AAATAAAATATTGACACGTGTCAAAATGTCCAATTAGCTCCACATCATCAATGTCACGTCAACAC
19344978 CAAAAGAAAAACATAAAAAATTCTAAAAATTTTCAAAA-T-AAAAAAAAATAGAAACATATGGGT
66 CAAAAGAAAAACATAAAAAATTCTAAAAATTTTCAAAATTAAAAAAAAAATAGAAACATATGGGT
19345041 TACATAGCACAATGGGTAGACATACGGGTCACATAGATTACACACGGGTCTTGCAAAAATTTTTC
131 TACATAGCACAATGGGTAGACATACGGGTCACATAGATTACACACGGGTCTTGCAAAAATTTTTC
19345106 CTAAAATGACATTATTTTAAGTTTCTTTAACTAGCAA
196 CTAAAATGACATTATTTTAAGTTTCTTTAACTAGCAA
*
19345143 AAGTAAAA
1 AAATAAAA
19345151 ATTTTTATTT
Statistics
Matches: 236, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
230 132 0.56
232 1 0.00
233 103 0.44
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (232 bp):
AAATAAAATATTGACACGTGTCAAAATGTCCAATTAGCTCCACATCATCAATGTCACGTCAACAC
CAAAAGAAAAACATAAAAAATTCTAAAAATTTTCAAAATTAAAAAAAAAATAGAAACATATGGGT
TACATAGCACAATGGGTAGACATACGGGTCACATAGATTACACACGGGTCTTGCAAAAATTTTTC
CTAAAATGACATTATTTTAAGTTTCTTTAACTAGCAA
Found at i:19346556 original size:20 final size:20
Alignment explanation
Indices: 19346506--19346557 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
19346496 TTTTTTAGAA
*
19346506 TTTTAGATTTTTATAAAAAT
1 TTTTAGAATTTTATAAAAAT
*
19346526 TTTTA-ACATTTTA-AAGAATT
1 TTTTAGA-ATTTTATAA-AAAT
19346546 TTTTAGAATTTT
1 TTTTAGAATTTT
19346558 GAATTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 23 0.85
21 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTAGAATTTTATAAAAAT
Found at i:19346635 original size:10 final size:9
Alignment explanation
Indices: 19346521--19346634 Score: 61
Period size: 9 Copynumber: 12.0 Consensus size: 9
19346511 GATTTTTATA
19346521 AAAATTTTT
1 AAAATTTTT
* *
19346530 AACATTTTA
1 AAAATTTTT
19346539 AAGAATTTTTT
1 AA-AA-TTTTT
* *
19346550 AGAATTTTG
1 AAAATTTTT
**
19346559 AATTTGTTTT
1 AAAAT-TTTT
19346569 GAAAA-TTTT
1 -AAAATTTTT
19346578 AAAATTTTTT
1 AAAA-TTTTT
*
19346588 AAAAAATTTT
1 -AAAATTTTT
* *
19346598 AGCAATATTTA
1 A-AAAT-TTTT
19346609 AAAATTTTT
1 AAAATTTTT
19346618 AAAA-TTTT
1 AAAATTTTT
19346626 AAAATTTTT
1 AAAATTTTT
19346635 TTTGAAGTGA
Statistics
Matches: 77, Mismatches: 18, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
8 12 0.16
9 31 0.40
10 19 0.25
11 15 0.19
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (9 bp):
AAAATTTTT
Found at i:19346636 original size:20 final size:20
Alignment explanation
Indices: 19346525--19346637 Score: 59
Period size: 20 Copynumber: 5.2 Consensus size: 20
19346515 TTTATAAAAA
* *
19346525 TTTTTAACATTTTAAAGA-AT
1 TTTTTAAAATTTTAAA-ATTT
* *
19346545 TTTTTAGAATTTT-GAATTT
1 TTTTTAAAATTTTAAAATTT
*
19346564 GTTTTGAAAATTTTAAAATTT
1 -TTTTTAAAATTTTAAAATTT
**
19346585 TTTAAAAAATTTTAGCAATATTT
1 TTTTTAAAATTTTA--AA-ATTT
19346608 AAAAATTTTTAAAATTTTAAAATTT
1 -----TTTTTAAAATTTTAAAATTT
19346633 TTTTT
1 TTTTT
19346638 GAAGTGATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
18 1 0.01
19 2 0.03
20 39 0.55
21 5 0.07
22 2 0.03
23 4 0.06
25 4 0.06
26 2 0.03
28 12 0.17
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTTTAAAATTTTAAAATTT
Found at i:19349596 original size:65 final size:65
Alignment explanation
Indices: 19349492--19349621 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 65
19349482 CTTTCTTTAG
*
19349492 TTATTTCTTTTCATACTTTTCATATGATAACTAAACTATAGAATATAGATATTTTATGTTATCAT
1 TTATTTCTTTTCATACTTTTCATATGATAACTAAACTATAGAATATAGATATTTTATATTATCAT
* *
19349557 TTATTTCTTTTCATTCTTTTCATATGATAATTAAACTATAGAATATAGATATTTTATATTATCAT
1 TTATTTCTTTTCATACTTTTCATATGATAACTAAACTATAGAATATAGATATTTTATATTATCAT
19349622 ATTTGCTTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (65 bp):
TTATTTCTTTTCATACTTTTCATATGATAACTAAACTATAGAATATAGATATTTTATATTATCAT
Found at i:19355411 original size:49 final size:49
Alignment explanation
Indices: 19355356--19355453 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
19355346 GATTGGCATA
*
19355356 GGTGAATTTTTTTTATTTACCTCCTCAAAAGTAAGTATCTTAAAAAAAT
1 GGTGAATTTTTTTTATTTAACTCCTCAAAAGTAAGTATCTTAAAAAAAT
19355405 GGTGAATTTTTTTTATTTAACTCCTCAAAAGTAAGTATCTTAAAAAAAT
1 GGTGAATTTTTTTTATTTAACTCCTCAAAAGTAAGTATCTTAAAAAAAT
19355454 ATAGATTTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (49 bp):
GGTGAATTTTTTTTATTTAACTCCTCAAAAGTAAGTATCTTAAAAAAAT
Found at i:19357020 original size:25 final size:25
Alignment explanation
Indices: 19356973--19357029 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
19356963 TTTTTTATTA
* * *
19356973 AAATTCTTTTAATCGTAATTATAAT
1 AAATTTTTTTAATCATAACTATAAT
*
19356998 AATTTTTTTTAATCATAACTATAAT
1 AAATTTTTTTAATCATAACTATAAT
19357023 AAATTTT
1 AAATTTT
19357030 ATTATTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (25 bp):
AAATTTTTTTAATCATAACTATAAT
Found at i:19357433 original size:12 final size:12
Alignment explanation
Indices: 19357416--19357446 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19357406 AGAAAATTTC
19357416 AAAATTTAAAAG
1 AAAATTTAAAAG
19357428 AAAATTTAAAAG
1 AAAATTTAAAAG
*
19357440 AGAATTT
1 AAAATTT
19357447 GAGCCATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (12 bp):
AAAATTTAAAAG
Found at i:19357612 original size:20 final size:19
Alignment explanation
Indices: 19357566--19357613 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
19357556 TATTTAACTC
*
19357566 TAAAATATTTTTATATTAT
1 TAAAATATTTATATATTAT
*
19357585 TAATAATATTTATATATTTT
1 TAA-AATATTTATATATTAT
19357605 TATAAATAT
1 TA-AAATAT
19357614 AATGATACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 21 0.84
21 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAAAATATTTATATATTAT
Found at i:19368447 original size:7 final size:7
Alignment explanation
Indices: 19368435--19368468 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
19368425 ATGTGCTCGC
19368435 ACATGCA
1 ACATGCA
19368442 ACATGC-
1 ACATGCA
19368448 ACATGCA
1 ACATGCA
19368455 ACATGCA
1 ACATGCA
19368462 A-ATGCA
1 ACATGCA
19368468 A
1 A
19368469 ATACAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (7 bp):
ACATGCA
Found at i:19368451 original size:13 final size:13
Alignment explanation
Indices: 19368433--19368468 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
19368423 ACATGTGCTC
19368433 GCACATGCAACAT
1 GCACATGCAACAT
19368446 GCACATGCAACAT
1 GCACATGCAACAT
*
19368459 GCAAATGCAA
1 GCACATGCAA
19368469 ATACAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.42, C:0.28, G:0.17, T:0.14
Consensus pattern (13 bp):
GCACATGCAACAT
Found at i:19371296 original size:36 final size:36
Alignment explanation
Indices: 19371256--19371336 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
19371246 GCGACCTACT
19371256 CCTACTCCTACTCCTCCTCCGGTCTCTACGGGGCGA
1 CCTACTCCTACTCCTCCTCCGGTCTCTACGGGGCGA
* *
19371292 CCTACTCCTACTCTTCCTCCGGTCTCTACGTGGCGA
1 CCTACTCCTACTCCTCCTCCGGTCTCTACGGGGCGA
19371328 CCTACTCCT
1 CCTACTCCT
19371337 GCTTCTCCGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.11, C:0.44, G:0.16, T:0.28
Consensus pattern (36 bp):
CCTACTCCTACTCCTCCTCCGGTCTCTACGGGGCGA
Found at i:19374580 original size:10 final size:10
Alignment explanation
Indices: 19374556--19374585 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
19374546 TATTTTATCA
19374556 ATTAAAATA-
1 ATTAAAATAT
19374565 ATTAAAATAT
1 ATTAAAATAT
19374575 ATTAAAATAT
1 ATTAAAATAT
19374585 A
1 A
19374586 AAAGCTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:19382559 original size:18 final size:18
Alignment explanation
Indices: 19382522--19382558 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
19382512 ATTTAAGATT
*
19382522 AATTAATTAATTAATTAA
1 AATTAATTAAATAATTAA
19382540 AATTAA-TAAATAATTAA
1 AATTAATTAAATAATTAA
19382557 AA
1 AA
19382559 AAACCTAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAATTAAATAATTAA
Found at i:19384886 original size:24 final size:24
Alignment explanation
Indices: 19384842--19384887 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
19384832 AACCTTTTTT
*
19384842 TCATTTTTGATTTATTTTTAAATC
1 TCATTTTTGATTTATTCTTAAATC
*
19384866 TCATTTTTTATCTT-TTCTTAAA
1 TCATTTTTGAT-TTATTCTTAAA
19384888 AATAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (24 bp):
TCATTTTTGATTTATTCTTAAATC
Found at i:19392224 original size:12 final size:13
Alignment explanation
Indices: 19392207--19392236 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19392197 CTCAGATCAA
19392207 TTTTTC-TCTTTT
1 TTTTTCTTCTTTT
19392219 TTTTTCTTCTTTT
1 TTTTTCTTCTTTT
19392232 TTTTT
1 TTTTT
19392237 TGTTTCTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTCTTCTTTT
Found at i:19392243 original size:15 final size:15
Alignment explanation
Indices: 19392207--19392244 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
19392197 CTCAGATCAA
19392207 TTTTTCTCTTTTTTT
1 TTTTTCTCTTTTTTT
*
19392222 TTCTTCT-TTTTTTT
1 TTTTTCTCTTTTTTT
19392236 TTGTTTCTC
1 TT-TTTCTC
19392245 ACTCTAGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTCTCTTTTTTT
Found at i:19394830 original size:3 final size:3
Alignment explanation
Indices: 19394822--19394870 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
19394812 ACTTTTTTGC
19394822 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19394870 A
1 A
19394871 CTAATAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:19395117 original size:135 final size:134
Alignment explanation
Indices: 19394876--19395124 Score: 408
Period size: 135 Copynumber: 1.9 Consensus size: 134
19394866 TATTACTAAT
* * * *
19394876 AAAATGAAACCACTCCAAATGTCCCACCATCCTCATATTTTCCTTATTAAAATATTTGTTCTATC
1 AAAATGAAACCACTCCAAATGTCCCACCATCCTCACATTTTCCTTATCAAAACATTTGTTCCATC
* * *
19394941 ATGTTGGACTTTGGTGCCAAAAACTCTTCTTACCTTTTGACTAAAATAATAGAAGGCTAACCTTG
66 ATGTTAGACTTTGGTACCAAAAACTATTCTTACCTTTTGACTAAAATAATAGAAGGCTAACCTTG
19395006 TTAC
131 TTAC
*
19395010 AAAATGAAACCACTCCAAGATGTCCCACCATCCTTACATTTTCCTTATCAAAACATTTGTTCCAT
1 AAAATGAAACCACTCCAA-ATGTCCCACCATCCTCACATTTTCCTTATCAAAACATTTGTTCCAT
*
19395075 CATGTTAGACTTTGGTACCAAAAACTATTCTTACTTTTTGACTAAAATAA
65 CATGTTAGACTTTGGTACCAAAAACTATTCTTACCTTTTGACTAAAATAA
19395125 CTTAAGAATA
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
134 18 0.17
135 87 0.83
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (134 bp):
AAAATGAAACCACTCCAAATGTCCCACCATCCTCACATTTTCCTTATCAAAACATTTGTTCCATC
ATGTTAGACTTTGGTACCAAAAACTATTCTTACCTTTTGACTAAAATAATAGAAGGCTAACCTTG
TTAC
Found at i:19401550 original size:15 final size:16
Alignment explanation
Indices: 19401530--19401565 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
19401520 CATAATTAAA
19401530 AATAAT-TATAAAAAT
1 AATAATATATAAAAAT
*
19401545 AATAATATATAAAATT
1 AATAATATATAAAAAT
19401561 AATAA
1 AATAA
19401566 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATATATAAAAAT
Found at i:19401572 original size:16 final size:16
Alignment explanation
Indices: 19401537--19401586 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
19401527 AAAAATAATT
* * *
19401537 ATAAAAATAATAATAT
1 ATAAAATTAATAAAAA
19401553 ATAAAATTAATAAAAA
1 ATAAAATTAATAAAAA
19401569 ATAAAATGTTAATAAAAA
1 ATAAAA--TTAATAAAAA
19401587 TGATTAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 19 0.66
18 10 0.34
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
ATAAAATTAATAAAAA
Found at i:19401753 original size:30 final size:32
Alignment explanation
Indices: 19401689--19401761 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
19401679 AATAATTTTA
19401689 ATTTCTTTTTTACTAATTTTCATAATATAAAT
1 ATTTCTTTTTTACTAATTTTCATAATATAAAT
* * *
19401721 ATTTCCTTTTTATTAATTTT-AT-ATATAGAT
1 ATTTCTTTTTTACTAATTTTCATAATATAAAT
19401751 ATTTCTTTTTT
1 ATTTCTTTTTT
19401762 GTTATGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 17 0.46
31 2 0.05
32 18 0.49
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.62
Consensus pattern (32 bp):
ATTTCTTTTTTACTAATTTTCATAATATAAAT
Done.