Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000885.1 Hibiscus syriacus cultivar Beakdansim tig00001728_pilon, 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: 1639497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1270917 original size:21 final size:20
Alignment explanation
Indices: 1270893--1271149 Score: 68
Period size: 21 Copynumber: 13.4 Consensus size: 20
1270883 AATGATTTGA
1270893 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
1270914 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * *
1270932 TATTAATATTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
1270953 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
1270974 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
*
1270992 TATTAAT-TTT--TAATGAT
1 TAGTAATATTTAGTAATGAT
*
1271009 T--T--GA--TAGTAATGAT
1 TAGTAATATTTAGTAATGAT
* * *
1271023 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * * *
1271041 TATTAATTTTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
1271062 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
1271083 TAGTAATA-ATA-AAATTAT
1 TAGTAATATTTAGTAATGAT
* * *
1271101 TATTAATATTTAATATTTGA-
1 TAGTAATATTTAGTA-ATGAT
*
1271121 TATTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
1271142 TAGTAATA
1 TAGTAATA
1271150 ATGAAATTAT
Statistics
Matches: 165, Mismatches: 45, Indels: 53
0.63 0.17 0.20
Matches are distributed among these distances:
12 1 0.01
14 8 0.05
15 1 0.01
16 1 0.01
17 6 0.04
18 51 0.31
19 9 0.05
20 21 0.13
21 52 0.32
22 15 0.09
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:1270954 original size:169 final size:169
Alignment explanation
Indices: 1270675--1271642 Score: 1613
Period size: 169 Copynumber: 5.8 Consensus size: 169
1270665 TTATAAGATT
* * *
1270675 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGAGTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
1270740 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
*
1270805 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTAA
131 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1270844 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
*
1270909 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
1270974 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
131 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1271013 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
*
1271078 ATGATTAGTAATAATAAAATTATTATTAATATTTAAT-ATTTGATATTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
1271142 TAGTAATAATGAAATTATTATTAATTTTT-ATGATTTGA
131 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
1271180 TAGTAATGATTAGTAATAATGAAATTATTATTAAATTTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
*
1271245 ATGATTAGTATTAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
*
1271310 TAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
131 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
1271349 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGTTTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
*
1271414 ATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA--TAGTAATGAT
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
1271468 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATACTAATGA
131 TAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
* *
1271516 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGT
1 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGT
* *
1271581 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAAT
65 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
1271643 AATAATTTAT
Statistics
Matches: 756, Mismatches: 21, Indels: 35
0.93 0.03 0.04
Matches are distributed among these distances:
158 38 0.05
159 1 0.00
160 3 0.00
161 1 0.00
162 3 0.00
163 4 0.01
164 2 0.00
165 2 0.00
166 1 0.00
167 111 0.15
168 205 0.27
169 369 0.49
171 1 0.00
172 1 0.00
173 2 0.00
175 2 0.00
177 3 0.00
178 7 0.01
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (169 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:1271018 original size:39 final size:45
Alignment explanation
Indices: 1270969--1271523 Score: 210
Period size: 49 Copynumber: 10.3 Consensus size: 45
1270959 TGATTTAGTA
1270969 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGT
1 ATGATTAGTAATAATGAAATTATTATTAATTTTTAA-GA-TTGATA-T
1271017 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGT
1 -ATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A---G--A-T--TGA--TA-T
* * *
1271077 AATGATTAGTAATAATAAAATTATTATTAATATTTAATATTTGATATT
1 -ATGATTAGTAATAATGAAATTATTATTAATTTTTAAGA-TTGATA-T
*
1271125 AATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTATGATTTGATAGT
1 -ATG-----------ATTAGTAATAATGAAATTATTATTAATTTTTAAGA-TTGATA-T
*
1271184 AATGATTAGTAATAATGAAATTATTATTAAATTTTAATGATTTGATAGT
1 -ATGATTAGTAATAATGAAATTATTATTAATTTTTAA-GA-TTGATA-T
*
1271233 AATGATTTAGTAATGATTAGTATTAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 -ATGA--T--T-A-G--TA--A-TAATGAAATTATTATTAATTTTTAA-GA-T---------TGA
1271298 TTTAGT
43 --TA-T
*
1271304 AATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGT
1 -ATGATTAGTAATAATGAAATTATTATTAATTTTTAA-GA-TTGATA-T
1271353 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGTTTTGATAGTAATGATTTAGT
1 -ATGATTAGTAATAATGAAATTATTATTAATTTTTAA------G--A-T--TGA--TA-T
1271413 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGT
1 -ATGATTAGTAATAATGAAATTATTATTAATTTTTAA-GA-TTGATA-T
1271462 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATACT
1 -ATGATTAGTAATAATGAAATTATTATTAATTTTTAA-GA-TTGATA-T
1271511 AATGATTAGTAAT
1 -ATGATTAGTAAT
1271524 GATTAGTAAT
Statistics
Matches: 429, Mismatches: 21, Indels: 112
0.76 0.04 0.20
Matches are distributed among these distances:
48 38 0.09
49 155 0.36
50 4 0.01
51 7 0.02
52 3 0.01
53 3 0.01
54 5 0.01
55 3 0.01
56 4 0.01
57 3 0.01
58 6 0.01
59 45 0.10
60 134 0.31
61 1 0.00
63 2 0.00
65 1 0.00
66 1 0.00
67 1 0.00
69 4 0.01
71 9 0.02
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (45 bp):
ATGATTAGTAATAATGAAATTATTATTAATTTTTAAGATTGATAT
Found at i:1271465 original size:445 final size:444
Alignment explanation
Indices: 1270671--1271695 Score: 1634
Period size: 445 Copynumber: 2.3 Consensus size: 444
1270661 GTATTTATAA
* *
1270671 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGAGTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATGAT--T--TGA--T
1270736 AGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
55 AGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
*
1270801 TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTAATAGTAATGATTAGTAATAATGA
120 TGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTAATAGTAATGATTAGTAATAATGA
* * * *
1270866 AATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTA
185 AATTAATATAAATTATTAATAATTT-ATA-TAATGATTTAGTAATGATTAGTAATAATGAAATTA
1270931 TTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATT
248 TTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATT
1270996 AATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG
313 AATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG
*
1271061 ATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAAT-ATTTGATATT
378 ATACTAATGA-TTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATATT
1271125 AAT
442 AAT
1271128 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-ATGATTTGATAGTAATGATTA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
* *
1271192 GTAATAATGAAATTATTATTAA-ATTTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAT
66 GTAATAATGAAATTATTATTAATA-TTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAA
* * * *
1271256 TAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAA-TAAT
130 TAATGAAATTATTATTAATATTTAATGATTTAATAGTAATGA-TTAGTAAT-AAT-GAAATTAAT
*
1271320 A-AAATTATTATTAATTT-T-TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTA
192 ATAAATTATTAATAATTTATATAATGA-TT--TAGTAATGATTAGTAATAATGAAATTATTATTA
* *
1271382 ATTTTTAATGTTTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT
254 ATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT
1271447 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATACTA
319 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATACTA
*
1271512 ATGATTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
384 ATGATTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATATTAAT
1271573 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
*
1271638 GTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATT
66 GTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATT
1271696 TGATAGTAAT
Statistics
Matches: 538, Mismatches: 20, Indels: 32
0.91 0.03 0.05
Matches are distributed among these distances:
442 6 0.01
443 2 0.00
444 44 0.08
445 377 0.70
446 50 0.09
447 9 0.02
448 3 0.01
449 1 0.00
451 4 0.01
454 1 0.00
456 3 0.01
457 38 0.07
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (444 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
GTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAAT
AATGAAATTATTATTAATATTTAATGATTTAATAGTAATGATTAGTAATAATGAAATTAATATAA
ATTATTAATAATTTATATAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTA
ATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGAT
TTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATACTAATGATTA
GTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATATTAAT
Found at i:1271679 original size:14 final size:14
Alignment explanation
Indices: 1271663--1271710 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1271653 TATTAATATT
*
1271663 TAATGATTTGATAT
1 TAATGATTTGATAG
1271677 TAATGA-TT--TAG
1 TAATGATTTGATAG
1271688 TAATGATTTGATAG
1 TAATGATTTGATAG
1271702 TAATGATTT
1 TAATGATTT
1271711 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:1271696 original size:119 final size:118
Alignment explanation
Indices: 1271458--1271695 Score: 327
Period size: 119 Copynumber: 2.1 Consensus size: 118
1271448 AATGATTTGA
1271458 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATACTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATACTAATGATTAGTAA
* * * *
1271523 TGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATT
66 TAATAAGTAATAATGAAATTATGATTAATATTTAATGATTT-ATAGTAATGATT
*
1271577 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATACTAATGATTAGTAA
*
1271642 TAATAA-T--T--T---A-T-T-ATTAATATTTAATGATTTGATATTAATGATT
66 TAATAAGTAATAATGAAATTATGATTAATATTTAATGATTT-ATAGTAATGATT
1271685 TAGTAATGATT
1 TAGTAATGATT
1271696 TGATAGTAAT
Statistics
Matches: 116, Mismatches: 3, Indels: 11
0.89 0.02 0.08
Matches are distributed among these distances:
108 42 0.36
109 1 0.01
110 1 0.01
111 1 0.01
114 1 0.01
116 1 0.01
118 1 0.01
119 68 0.59
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (118 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATACTAATGATTAGTAA
TAATAAGTAATAATGAAATTATGATTAATATTTAATGATTTATAGTAATGATT
Found at i:1271707 original size:109 final size:109
Alignment explanation
Indices: 1270735--1271695 Score: 1120
Period size: 109 Copynumber: 8.7 Consensus size: 109
1270725 AGTAATGATT
1270735 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
*
1270800 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTAA
66 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* *
1270844 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
*
1270909 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
66 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* * * * * * *
1270953 TAGTAATGATT--TAGTAATG--ATTAGTAATAATGAAATT-ATTA-TTAATTTTTAATGATTTG
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT--ATTTAATGATTTGA-TATTAATGA-TT-
1271012 ATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
61 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
*
1271071 TTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAAT-ATTTGATATTAATGATTTAG
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAG
1271135 TAATGATTAGTAATAATGAAATTATTATTAATTTTT-ATGATTTGA
64 TAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
1271180 TAGTAATGATTAGTAATAATGAAATTATTATTAA-ATTTTAATGATTTGATAGTAATGATTTAGT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATA-TTTAATGATTTGATATTAATGATTTAGT
* *
1271244 AATGATTAGTATTAATGAAATTATTATTAATATTTAATGATTTGA
65 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* * * * * * * *
1271289 TATTAATGATT--TAGTAATG--ATTAGTAATAATA--AAATTATTATTAATTTTTAATGATTTG
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGA-T-TTGA-TATTAATGA-TT-
*
1271348 ATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGTTTTGA
61 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* * * * * * *
1271398 TAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTA-TTAAT-TTTTAATGATT--TGA-
1 TAGTAATGA-TTAGTAAT-AAT-GAAATTAT--TATTAATATTTAATGATTTGAT-ATTAATGAT
1271458 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATACTAATGA
60 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
1271516 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGT
1 -TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGT
1271581 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
65 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
1271626 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1271690 ATGATT
66 ATGATT
1271696 TGATAGTAAT
Statistics
Matches: 735, Mismatches: 57, Indels: 121
0.81 0.06 0.13
Matches are distributed among these distances:
103 4 0.01
104 1 0.00
105 25 0.03
106 19 0.03
107 59 0.08
108 102 0.14
109 289 0.39
110 7 0.01
111 1 0.00
112 6 0.01
113 6 0.01
114 21 0.03
115 10 0.01
116 23 0.03
117 6 0.01
118 20 0.03
119 90 0.12
120 11 0.01
121 2 0.00
122 18 0.02
123 5 0.01
124 10 0.01
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (109 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:1272728 original size:23 final size:23
Alignment explanation
Indices: 1272702--1272749 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1272692 TAAAATTACA
*
1272702 AAAACAATAAAATTTATTTAAAT
1 AAAACAATAAAATTAATTTAAAT
* * *
1272725 AAAATAATATAGTTAATTTAAAT
1 AAAACAATAAAATTAATTTAAAT
1272748 AA
1 AA
1272750 TAATTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAACAATAAAATTAATTTAAAT
Found at i:1273938 original size:8 final size:8
Alignment explanation
Indices: 1273925--1273959 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
1273915 AACTTTAATA
1273925 TAATAAAC
1 TAATAAAC
1273933 TAATAAAC
1 TAATAAAC
1273941 TAATAAAC
1 TAATAAAC
*
1273949 TAACAAAC
1 TAATAAAC
1273957 TAA
1 TAA
1273960 ACTTTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (8 bp):
TAATAAAC
Found at i:1274211 original size:39 final size:40
Alignment explanation
Indices: 1274142--1274248 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 40
1274132 TTTAACTACC
*
1274142 ACAAACTAATTAAATAATTTTTTATA-TAACTAACGACTAACAAA
1 ACAAACTAATTAAATAATTTTTTA-ACT-A-T-ACAACTAAC-AA
* * *
1274186 ACAAACTAATT-AATTATTTTTTAACTATATAACTATCAA
1 ACAAACTAATTAAATAATTTTTTAACTATACAACTAACAA
*
1274225 ACATACTAATTAAATAATTTTTTA
1 ACAAACTAATTAAATAATTTTTTA
1274249 TTTATGTATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
39 12 0.22
40 17 0.31
41 1 0.02
42 2 0.04
43 12 0.22
44 11 0.20
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (40 bp):
ACAAACTAATTAAATAATTTTTTAACTATACAACTAACAA
Found at i:1274297 original size:22 final size:21
Alignment explanation
Indices: 1274259--1274299 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1274249 TTTATGTATA
*
1274259 ATATAACTTAAACTAACAATC
1 ATATAACCTAAACTAACAATC
*
1274280 ATATAACCCTAAATTAACAA
1 ATATAA-CCTAAACTAACAA
1274300 ACTAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
ATATAACCTAAACTAACAATC
Found at i:1274437 original size:13 final size:13
Alignment explanation
Indices: 1274398--1274444 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1274388 CTCACAAGAG
1274398 CCTTATCTCCCTTT
1 CCTT-TCTCCCTTT
* *
1274412 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
1274426 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
1274439 -CTTTCT
1 CCTTTCT
1274445 TTCTCGGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 12 0.43
15 1 0.04
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:1274502 original size:26 final size:28
Alignment explanation
Indices: 1274439--1274502 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 28
1274429 TTCTCCCTTT
*
1274439 CTTTCTTTCTCGGCTGCAATTTCTTCTCC
1 CTTTCTTTCTC-GCTGCAATCTCTTCTCC
1274468 CTTTC-TTCT-GCTGCAATCTCTTCT-C
1 CTTTCTTTCTCGCTGCAATCTCTTCTCC
1274493 CTTTCTTTCT
1 CTTTCTTTCT
1274503 TTTATGTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 6 0.18
26 18 0.55
28 4 0.12
29 5 0.15
ACGTcount: A:0.06, C:0.34, G:0.08, T:0.52
Consensus pattern (28 bp):
CTTTCTTTCTCGCTGCAATCTCTTCTCC
Found at i:1274789 original size:29 final size:29
Alignment explanation
Indices: 1274748--1274821 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
1274738 CTTGGTCACC
*
1274748 GGGATTGCTTGGCGACCTACAAGGTCGCT
1 GGGAGTGCTTGGCGACCTACAAGGTCGCT
* ***
1274777 GGGAGTGCATGGCGACCTTGTAGGTCGCT
1 GGGAGTGCTTGGCGACCTACAAGGTCGCT
1274806 GGGAGTGCTTGGCGAC
1 GGGAGTGCTTGGCGAC
1274822 TTATGGTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.15, C:0.22, G:0.41, T:0.23
Consensus pattern (29 bp):
GGGAGTGCTTGGCGACCTACAAGGTCGCT
Found at i:1275826 original size:2 final size:2
Alignment explanation
Indices: 1275819--1275885 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1275809 AATTTAAATG
1275819 AT AT AT AT AT AT AT AT AT AT AT AT 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
1275861 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 A
1275886 CTTTTAACCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1279023 original size:3 final size:3
Alignment explanation
Indices: 1279015--1279062 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
1279005 TCTTAAAAAA
* *
1279015 TAT TAT TAT TAT CAT TAT T-T TAT TGT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1279062 T
1 T
1279063 TTAATTTACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1284566 original size:64 final size:63
Alignment explanation
Indices: 1284379--1284567 Score: 166
Period size: 74 Copynumber: 2.8 Consensus size: 63
1284369 AGAACTGAAA
* *
1284379 CAAAAGTGTTCTAAAGAGTCTAGCAATTAACTATGCTAGTTGTGTTATTTTGTTCGCCTGCGAT
1 CAAAA-TGTTCTAAAGAGTCTAGTAATTAACTATGCTAGTTGTGTCATTTTGTTCGCCTGCGAT
* ** *
1284443 CAAAATGTTAAACTAAGAAAGAGGGGC-ATGTCCTAATTTTC-ATGATGAGTTGTGTCATTTTGT
1 CAAAATGTT---CT---AAAGA--GTCTA-G---TAATTAACTATGCT-AGTTGTGTCATTTTGT
1284506 TCGCCTGCGAT
53 TCGCCTGCGAT
*
1284517 CAAAATTGTTCTAAAGAGTCTAGTAATTGACTATGCTAGTTGTGTCATTTT
1 CAAAA-TGTTCTAAAGAGTCTAGTAATTAACTATGCTAGTTGTGTCATTTT
1284568 CTTCTAAAGG
Statistics
Matches: 99, Mismatches: 10, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
63 4 0.04
64 25 0.25
65 4 0.04
66 2 0.02
67 3 0.03
68 1 0.01
69 10 0.10
70 1 0.01
71 3 0.03
72 2 0.02
73 4 0.04
74 36 0.36
75 4 0.04
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (63 bp):
CAAAATGTTCTAAAGAGTCTAGTAATTAACTATGCTAGTTGTGTCATTTTGTTCGCCTGCGAT
Found at i:1284709 original size:37 final size:36
Alignment explanation
Indices: 1284668--1284774 Score: 151
Period size: 36 Copynumber: 2.9 Consensus size: 36
1284658 ACAATTTTTC
* *
1284668 CTAAAAATAAATTTTGTCTGGCTTGAGACAGTTTTAT
1 CTAAAAACAAATTTTGTCTCGCTTGAGACA-TTTTAT
* *
1284705 CTAAAAACAAATTTTGTCTCGCTTGAGACAATTTCT
1 CTAAAAACAAATTTTGTCTCGCTTGAGACATTTTAT
* *
1284741 CTCAAAACAAATTTTGCCTCGCTTGAGACATTTT
1 CTAAAAACAAATTTTGTCTCGCTTGAGACATTTT
1284775 TCCTTTGAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 35 0.56
37 28 0.44
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (36 bp):
CTAAAAACAAATTTTGTCTCGCTTGAGACATTTTAT
Found at i:1284755 original size:36 final size:36
Alignment explanation
Indices: 1284656--1284770 Score: 149
Period size: 37 Copynumber: 3.1 Consensus size: 36
1284646 GTCTTGCTAT
* * *
1284656 AGACAATTTTTCCTAAAAATAAATTTTGTCTGGCTTG
1 AGACAATTTCT-CTAAAAACAAATTTTGTCTCGCTTG
* *
1284693 AGACAGTTTTATCTAAAAACAAATTTTGTCTCGCTTG
1 AGACA-ATTTCTCTAAAAACAAATTTTGTCTCGCTTG
* *
1284730 AGACAATTTCTCTCAAAACAAATTTTGCCTCGCTTG
1 AGACAATTTCTCTAAAAACAAATTTTGTCTCGCTTG
1284766 AGACA
1 AGACA
1284771 TTTTTCCTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 32 0.46
37 33 0.48
38 4 0.06
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (36 bp):
AGACAATTTCTCTAAAAACAAATTTTGTCTCGCTTG
Found at i:1284852 original size:102 final size:99
Alignment explanation
Indices: 1284721--1284919 Score: 238
Period size: 102 Copynumber: 2.0 Consensus size: 99
1284711 ACAAATTTTG
* * * * *
1284721 TCTCGCTTGAGACAATTTCTCTCAAAACAAATTTTGCCTCGCTTGAGACATTTTTCCTTTGAGAT
1 TCTCACTTGAGACAATTTCTCTCAAAACAAATTTTACCTCACTTGAGACAGTCTTCC-TT-A-A-
* *
1284786 ACAAAT-TTCGAGTTTGTTTCACTTGAAACAAAGTTGA
62 AAAAATCTTCGAGTATGTTTCACTTGAAACAAAGTTGA
** * *
1284823 TCTCACTTGAGATTATTTTTCTCAAAACAAATTTTATCTCACTTGAGACAGTCTTCCTTAAAAAA
1 TCTCACTTGAGACAATTTCTCTCAAAACAAATTTTACCTCACTTGAGACAGTCTTCCTTAAAAAA
* *
1284888 ATCTTTGAGTATGTTTCCCTTGAAACAAAGTT
66 ATCTTCGAGTATGTTTCACTTGAAACAAAGTT
1284920 TTGTCTCTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
98 5 0.06
99 27 0.33
100 1 0.01
101 2 0.02
102 48 0.58
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (99 bp):
TCTCACTTGAGACAATTTCTCTCAAAACAAATTTTACCTCACTTGAGACAGTCTTCCTTAAAAAA
ATCTTCGAGTATGTTTCACTTGAAACAAAGTTGA
Found at i:1284947 original size:37 final size:36
Alignment explanation
Indices: 1284900--1285020 Score: 119
Period size: 37 Copynumber: 3.5 Consensus size: 36
1284890 CTTTGAGTAT
1284900 GTTTCCCTTGAAACAAAGTTTTGTCTCTTTGGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTTT-GAGACA
* ** * *
1284937 GTTTCTCTTGAAACAAA------AATCTTTGAGTCT
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTTTGAGACA
1284967 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCT-TTGAGACA
**
1285004 GTTTTTCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
1285021 AATCTTTGAG
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
30 20 0.31
31 5 0.08
36 3 0.05
37 37 0.57
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAAGTTTTGTCTCTTTGAGACA
Found at i:1284959 original size:67 final size:67
Alignment explanation
Indices: 1284847--1285087 Score: 332
Period size: 67 Copynumber: 3.7 Consensus size: 67
1284837 ATTTTTCTCA
* *
1284847 AAACAAA-TTTTATCTCACTTGAGACAGTCTTC-CTT--AA-AAAAATCTTTGAGTATGTTTCCC
1 AAACAAAGTTTTGTCTCTCTTGAGACAGT-TTCTCTTGAAACAAAAATCTTTGAGTATGTTTCCC
1284907 TTG
65 TTG
*
1284910 AAACAAAGTTTTGTCTCT-TTGGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCC
1 AAACAAAGTTTTGTCTCTCTT-GAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTATGTTTCCC
1284974 TTG
65 TTG
* * *
1284977 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGAAACAAAAATCTTTGAGTTTGTTTCCCA
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTATGTTTCCCT
1285042 TG
66 TG
* * * *
1285044 AAACAAAATTTTGTCTCTCTTGAGATAATTTCTCTTGACACAAA
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1285088 TCGCTAAAGA
Statistics
Matches: 160, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
63 12 0.08
64 19 0.12
66 2 0.01
67 125 0.78
68 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (67 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTATGTTTCCCT
TG
Found at i:1284977 original size:30 final size:30
Alignment explanation
Indices: 1284937--1285051 Score: 86
Period size: 30 Copynumber: 3.6 Consensus size: 30
1284927 TTTGGAGACA
*
1284937 GTTTCTCTTGAAACAAAAATCTTTGAGTCT
1 GTTTCCCTTGAAACAAAAATCTTTGAGTCT
** * *
1284967 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA------AATCT-TTGAGTCT
** *
1285004 GTTTTTCTTGAAACAAAAATCTTTGAGTTT
1 GTTTCCCTTGAAACAAAAATCTTTGAGTCT
*
1285034 GTTTCCCATGAAACAAAA
1 GTTTCCCTTGAAACAAAA
1285052 TTTTGTCTCT
Statistics
Matches: 63, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
30 36 0.57
31 3 0.05
36 3 0.05
37 21 0.33
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (30 bp):
GTTTCCCTTGAAACAAAAATCTTTGAGTCT
Found at i:1285641 original size:3 final size:3
Alignment explanation
Indices: 1285633--1285673 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1285623 GGTCTTAAAA
* *
1285633 ATT ATT ATT ATT ATC GTT ATT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1285674 TTAATTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1285659 original size:20 final size:20
Alignment explanation
Indices: 1285634--1285676 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1285624 GTCTTAAAAA
*
1285634 TTATTATTATTATCGTTATT
1 TTATTATTATTATCATTATT
*
1285654 TTATTATTATTATTATTATT
1 TTATTATTATTATCATTATT
1285674 TTA
1 TTA
1285677 ATTTACAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATTATTATTATCATTATT
Found at i:1285669 original size:17 final size:17
Alignment explanation
Indices: 1285637--1285670 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1285627 TTAAAAATTA
*
1285637 TTATTATTATCGTTATT
1 TTATTATTATCATTATT
*
1285654 TTATTATTATTATTATT
1 TTATTATTATCATTATT
1285671 ATTTTAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATTATTATCATTATT
Found at i:1288310 original size:100 final size:103
Alignment explanation
Indices: 1288197--1288398 Score: 322
Period size: 100 Copynumber: 2.0 Consensus size: 103
1288187 TGTAACTTTA
* *
1288197 TTTTTTAAGCATACTTTAAGCGGAGTCAA-TTCATCACACTACCATCCCACACTCTAAGTGAAAG
1 TTTTTTAAGCATACGTTAAGCGGAGTCAACCT-ATCACACTACCATCCCACACTCTAAGTGAAAG
*
1288261 GGAGTATACCTTCCACCC-CGAGCTAGTCA-GTAGAGTT
65 GGAGCATACCTTCCACCCTCGAGCTAGTCAGGTAGAGTT
* *
1288298 TTTTTTAA-CATACGTTAAGGGGAGTCAACCTATCACACTACCATCCCACACTCTAAGTGAAATG
1 TTTTTTAAGCATACGTTAAGCGGAGTCAACCTATCACACTACCATCCCACACTCTAAGTGAAAGG
1288362 GAGCATACCTTCCACCCTCGAGCTAGTCAGGTAGAGT
66 GAGCATACCTTCCACCCTCGAGCTAGTCAGGTAGAGT
1288399 CATCCCATGA
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
100 66 0.71
101 20 0.22
102 7 0.08
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (103 bp):
TTTTTTAAGCATACGTTAAGCGGAGTCAACCTATCACACTACCATCCCACACTCTAAGTGAAAGG
GAGCATACCTTCCACCCTCGAGCTAGTCAGGTAGAGTT
Found at i:1293225 original size:20 final size:20
Alignment explanation
Indices: 1293200--1293250 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1293190 TCCTAAATGG
1293200 AACTATATGCAACAATATGA
1 AACTATATGCAACAATATGA
*
1293220 AACTATATGCAACAATATGC
1 AACTATATGCAACAATATGA
1293240 AACTATATGCA
1 AACTATATGCA
1293251 TCAGTTGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.25
Consensus pattern (20 bp):
AACTATATGCAACAATATGA
Found at i:1293227 original size:10 final size:10
Alignment explanation
Indices: 1293200--1293250 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
1293190 TCCTAAATGG
1293200 AACTATATGC
1 AACTATATGC
* *
1293210 AACAATATGA
1 AACTATATGC
1293220 AACTATATGC
1 AACTATATGC
*
1293230 AACAATATGC
1 AACTATATGC
1293240 AACTATATGC
1 AACTATATGC
1293250 A
1 A
1293251 TCAGTTGAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.25
Consensus pattern (10 bp):
AACTATATGC
Found at i:1294839 original size:13 final size:13
Alignment explanation
Indices: 1294823--1294866 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1294813 AATTCTATAT
1294823 TCTTCTTGTTCAC
1 TCTTCTTGTTCAC
** *
1294836 TCTTCTTCCTCAT
1 TCTTCTTGTTCAC
*
1294849 TCTTCATGTTCAC
1 TCTTCTTGTTCAC
1294862 TCTTC
1 TCTTC
1294867 ACACACTCTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.09, C:0.34, G:0.05, T:0.52
Consensus pattern (13 bp):
TCTTCTTGTTCAC
Found at i:1296071 original size:27 final size:27
Alignment explanation
Indices: 1296035--1296119 Score: 143
Period size: 27 Copynumber: 3.1 Consensus size: 27
1296025 AACTTTGACA
* *
1296035 AACTTTAGAATTTCAAATGTTGAGATT
1 AACTTGAGAATTTCAAATGTTGAAATT
*
1296062 AACTTGAGAATTTCAAATGTTGATATT
1 AACTTGAGAATTTCAAATGTTGAAATT
1296089 AACTTGAGAATTTCAAATGTTGAAATT
1 AACTTGAGAATTTCAAATGTTGAAATT
1296116 AACT
1 AACT
1296120 CATTTGACAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (27 bp):
AACTTGAGAATTTCAAATGTTGAAATT
Found at i:1298965 original size:37 final size:36
Alignment explanation
Indices: 1298910--1299015 Score: 133
Period size: 36 Copynumber: 2.9 Consensus size: 36
1298900 GTTTCTCTCG
* *
1298910 AAACAAAGTGTCGTCTCGCTAGAGACAATTTTTCTTAA
1 AAACAAA-TTTCGTCTCGCTTGAGACAATTTTTC-TAA
* * *
1298948 AAACAAATTTTGTCTCGCTTGAGACAATTTCTCTCA
1 AAACAAATTTCGTCTCGCTTGAGACAATTTTTCTAA
*
1298984 AAACAAATTTCATCTCGCTTGAGAC-ATTTTTC
1 AAACAAATTTCGTCTCGCTTGAGACAATTTTTC
1299016 CTTTGAGATA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
35 6 0.10
36 25 0.42
37 22 0.37
38 7 0.12
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (36 bp):
AAACAAATTTCGTCTCGCTTGAGACAATTTTTCTAA
Found at i:1299000 original size:36 final size:36
Alignment explanation
Indices: 1298901--1299009 Score: 137
Period size: 37 Copynumber: 3.0 Consensus size: 36
1298891 TTTGATGTAG
* * *
1298901 TTTCTCTCGAAACAAAGTGTCGTCTCGCTAGAGACAA
1 TTTCTCTCAAAACAAA-TTTCGTCTCGCTTGAGACAA
* * *
1298938 TTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAA
1 TTTCTC-TCAAAACAAATTTCGTCTCGCTTGAGACAA
*
1298975 TTTCTCTCAAAACAAATTTCATCTCGCTTGAGACA
1 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACA
1299010 TTTTTCCTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
36 26 0.43
37 27 0.44
38 8 0.13
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (36 bp):
TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAA
Found at i:1299133 original size:36 final size:36
Alignment explanation
Indices: 1299062--1299133 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
1299052 ATAAAGTTGA
* *
1299062 TCTCACTTGAGATTATTTTTCTCAAAACAAACTTTG
1 TCTCACTTGAGATTATCTTCCTCAAAACAAACTTTG
*
1299098 TCTCACTTGAGA-TAGTCTTCCTTAAAA-AAATCTTTG
1 TCTCACTTGAGATTA-TCTTCCTCAAAACAAA-CTTTG
1299134 AGTCTGTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (36 bp):
TCTCACTTGAGATTATCTTCCTCAAAACAAACTTTG
Found at i:1299209 original size:67 final size:63
Alignment explanation
Indices: 1299086--1299362 Score: 231
Period size: 67 Copynumber: 4.4 Consensus size: 63
1299076 ATTTTTCTCA
* * * *
1299086 AAACAAACTTTGTCTCACTTGAGATAGTCTTCCTTAAAAAAATCTTTGAGTCTGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAATCTTCCTTAAAAAAATCTTTGAGTCTGTTTCCCTTG
*
1299149 AAACAAAGTTTTGTCTCTCTTGAGACAAT-TTCTCTTGAAACAAAACTCTTTGAGTCTGTTTTCC
1 AAACAAA-TTTTGTCTCTCTTGAGACAATCTTC-CTT-AAA-AAAA-TCTTTGAGTCTGTTTCCC
1299213 TTG
61 TTG
* * * *
1299216 AAACAAATTTTTGTATCTGTTGAG---A-----C----AAAAATCATTGAGTATGTTTCCCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAATCTTCCTTAAAAAAATCTTTGAGTCTGTTTCCCTTG
* *
1299268 AAACAAAGTTTTGTCTCTCTTGAGACAGT-TTCTCTTGAAACAAAAATCTTTGAGTATGTTTCCC
1 AAACAAA-TTTTGTCTCTCTTGAGACAATCTTC-CTT--AA-AAAAATCTTTGAGTCTGTTTCCC
1299332 TTG
61 TTG
*
1299335 AAACAAAATTTTTTTCTCTCTTGAGACA
1 AAAC-AAA-TTTTGTCTCTCTTGAGACA
1299363 GTTTCTCTTG
Statistics
Matches: 175, Mismatches: 18, Indels: 37
0.76 0.08 0.16
Matches are distributed among these distances:
52 39 0.22
53 4 0.02
54 1 0.01
59 1 0.01
60 1 0.01
63 10 0.06
64 21 0.12
65 3 0.02
66 4 0.02
67 70 0.40
68 21 0.12
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (63 bp):
AAACAAATTTTGTCTCTCTTGAGACAATCTTCCTTAAAAAAATCTTTGAGTCTGTTTCCCTTG
Found at i:1299254 original size:52 final size:52
Alignment explanation
Indices: 1299179--1299294 Score: 160
Period size: 52 Copynumber: 2.2 Consensus size: 52
1299169 TGAGACAATT
* * * * * *
1299179 TCTCTTGAAACAAAACTCTTTGAGTCTGTTTTCCTTGAAACAAATTTTTGTA
1 TCTCTTGAGACAAAAATCATTGAGTATGTTTCCCTTGAAACAAAGTTTTGTA
* *
1299231 TCTGTTGAGACAAAAATCATTGAGTATGTTTCCCTTGAAACAAAGTTTTGTC
1 TCTCTTGAGACAAAAATCATTGAGTATGTTTCCCTTGAAACAAAGTTTTGTA
1299283 TCTCTTGAGACA
1 TCTCTTGAGACA
1299295 GTTTCTCTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (52 bp):
TCTCTTGAGACAAAAATCATTGAGTATGTTTCCCTTGAAACAAAGTTTTGTA
Found at i:1299271 original size:119 final size:120
Alignment explanation
Indices: 1299123--1299362 Score: 392
Period size: 119 Copynumber: 2.0 Consensus size: 120
1299113 TCTTCCTTAA
* *
1299123 AAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAA
1 AAAAATCATTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAA
* * * *
1299188 ACAAAACTCTTTGAGTCTGTTTTCCTTGAAAC-AAATTTTTGTATCTGTTGAGAC
66 ACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAATTTTTGTATCTCTTGAGAC
*
1299242 AAAAATCATTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
1 AAAAATCATTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAA
* *
1299307 ACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAATTTTTTTCTCTCTTGAGAC
66 ACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAATTTTTGTATCTCTTGAGAC
1299362 A
1 A
1299363 GTTTCTCTTG
Statistics
Matches: 111, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
119 91 0.82
120 20 0.18
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (120 bp):
AAAAATCATTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAA
ACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAATTTTTGTATCTCTTGAGAC
Found at i:1299714 original size:134 final size:131
Alignment explanation
Indices: 1299402--1299737 Score: 341
Period size: 131 Copynumber: 2.5 Consensus size: 131
1299392 GCCAGCCGTC
* **
1299402 CTCATCACGTAGGAACCGTGTCATCCCCCGACCAAACCTCCTCATCACGTAGGATCCGTGTCAAA
1 CTCATCACGTAGGAACCGTGTCATCCCCCGACCAAACCTCCTCATCACGTAGGAGCCGTGTCACC
* * * * * * *
1299467 CTTAGATAACCAGCCATCCACATCATGTAGGAACCGTGTAATCATCCCTAAAGATGGTCTACCAT
66 CTTAGATAACCAACCATCCACATCACGTAGGAACCATGTAAACATCCCTAAAGATCGACCACCAT
1299532 T
131 T
** * * * * * *
1299533 CTCATTGCATAGGAATCGTGTCATTCACCGACCAGACCTCCTCATCACGTATGAGCCGTGTCACC
1 CTCATCACGTAGGAACCGTGTCATCCCCCGACCAAACCTCCTCATCACGTAGGAGCCGTGTCACC
* * * * * ** *
1299598 CCTAGATAACTAATCTTCCTCATTGCGTAGGAACCATGTTACAACATTCCCTAAATA-CGACCAG
66 CTTAGATAACCAACCATCCACATCACGTAGGAACCATG-TA-AACA-TCCCTAAAGATCGACCA-
*
1299662 TCATT
127 CCATT
* * * * *
1299667 CTCATCACGTAGGAACCGTGACATCCCCCGACCATATCTCTTCATCACATAGGAGCCGTGTCACC
1 CTCATCACGTAGGAACCGTGTCATCCCCCGACCAAACCTCCTCATCACGTAGGAGCCGTGTCACC
1299732 CTTAGA
66 CTTAGA
1299738 CGACCAGAGC
Statistics
Matches: 161, Mismatches: 40, Indels: 5
0.78 0.19 0.02
Matches are distributed among these distances:
131 82 0.51
132 2 0.01
133 6 0.04
134 71 0.44
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (131 bp):
CTCATCACGTAGGAACCGTGTCATCCCCCGACCAAACCTCCTCATCACGTAGGAGCCGTGTCACC
CTTAGATAACCAACCATCCACATCACGTAGGAACCATGTAAACATCCCTAAAGATCGACCACCAT
T
Found at i:1299933 original size:3 final size:3
Alignment explanation
Indices: 1299925--1299965 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1299915 AAAAAATATG
* *
1299925 ATT ATT ATT ATT ATC GTT ATT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1299966 TTAATTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1299951 original size:20 final size:20
Alignment explanation
Indices: 1299926--1299968 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1299916 AAAAATATGA
*
1299926 TTATTATTATTATCGTTATT
1 TTATTATTATTATCATTATT
*
1299946 TTATTATTATTATTATTATT
1 TTATTATTATTATCATTATT
1299966 TTA
1 TTA
1299969 ATTTACAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATTATTATTATCATTATT
Found at i:1299961 original size:17 final size:17
Alignment explanation
Indices: 1299929--1299962 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1299919 AATATGATTA
*
1299929 TTATTATTATCGTTATT
1 TTATTATTATCATTATT
*
1299946 TTATTATTATTATTATT
1 TTATTATTATCATTATT
1299963 ATTTTAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATTATTATCATTATT
Found at i:1303441 original size:16 final size:16
Alignment explanation
Indices: 1303420--1303497 Score: 61
Period size: 16 Copynumber: 5.6 Consensus size: 16
1303410 TTTGATAAAC
1303420 TTGAGAATTTCAAATG
1 TTGAGAATTTCAAATG
*
1303436 TTGAG-A-TT--AA-C
1 TTGAGAATTTCAAATG
1303447 TTGAGAATTTCAAATG
1 TTGAGAATTTCAAATG
*
1303463 TTGAG-A-TT--AA-C
1 TTGAGAATTTCAAATG
1303474 TTGAGAATTTCAAATG
1 TTGAGAATTTCAAATG
1303490 TTGA-AATT
1 TTGAGAATT
1303498 AACTCATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 21
0.66 0.05 0.29
Matches are distributed among these distances:
11 10 0.21
12 6 0.12
13 4 0.08
14 4 0.08
15 10 0.21
16 14 0.29
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.38
Consensus pattern (16 bp):
TTGAGAATTTCAAATG
Found at i:1303451 original size:27 final size:27
Alignment explanation
Indices: 1303417--1303501 Score: 161
Period size: 27 Copynumber: 3.1 Consensus size: 27
1303407 AACTTTGATA
1303417 AACTTGAGAATTTCAAATGTTGAGATT
1 AACTTGAGAATTTCAAATGTTGAGATT
1303444 AACTTGAGAATTTCAAATGTTGAGATT
1 AACTTGAGAATTTCAAATGTTGAGATT
*
1303471 AACTTGAGAATTTCAAATGTTGAAATT
1 AACTTGAGAATTTCAAATGTTGAGATT
1303498 AACT
1 AACT
1303502 CATTTAACTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.36
Consensus pattern (27 bp):
AACTTGAGAATTTCAAATGTTGAGATT
Found at i:1305841 original size:23 final size:22
Alignment explanation
Indices: 1305811--1305884 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 22
1305801 ACAAATTAAA
1305811 AAAAATAAAAATTCAGAGTTTAC
1 AAAAAT-AAAATTCAGAGTTTAC
*
1305834 AAAAATAAAA-TCAAAG--TAC
1 AAAAATAAAATTCAGAGTTTAC
**
1305853 AATCAT-AAATTCAGAGTTTAC
1 AAAAATAAAATTCAGAGTTTAC
1305874 AAAAATAAAAT
1 AAAAATAAAAT
1305885 CAAAGTACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
18 3 0.07
19 12 0.29
21 12 0.29
22 8 0.20
23 6 0.15
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.24
Consensus pattern (22 bp):
AAAAATAAAATTCAGAGTTTAC
Found at i:1305860 original size:19 final size:19
Alignment explanation
Indices: 1305838--1305901 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
1305828 GTTTACAAAA
1305838 ATAAAATCAAAGTACAATC
1 ATAAAATCAAAGTACAATC
* * **
1305857 ATAAATTCAGAGTTTACAAAA
1 ATAAAATCAAAG--TACAATC
1305878 ATAAAATCAAAGTACAATC
1 ATAAAATCAAAGTACAATC
1305897 ATAAA
1 ATAAA
1305902 TTCATAAGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 20 0.57
21 15 0.43
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.23
Consensus pattern (19 bp):
ATAAAATCAAAGTACAATC
Found at i:1305872 original size:40 final size:40
Alignment explanation
Indices: 1305819--1305905 Score: 174
Period size: 40 Copynumber: 2.2 Consensus size: 40
1305809 AAAAAAATAA
1305819 AAATTCAGAGTTTACAAAAATAAAATCAAAGTACAATCAT
1 AAATTCAGAGTTTACAAAAATAAAATCAAAGTACAATCAT
1305859 AAATTCAGAGTTTACAAAAATAAAATCAAAGTACAATCAT
1 AAATTCAGAGTTTACAAAAATAAAATCAAAGTACAATCAT
1305899 AAATTCA
1 AAATTCA
1305906 TAAGATATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (40 bp):
AAATTCAGAGTTTACAAAAATAAAATCAAAGTACAATCAT
Found at i:1305875 original size:21 final size:19
Alignment explanation
Indices: 1305831--1305905 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
1305821 ATTCAGAGTT
*
1305831 TACAAAAATAAAATCAAAG
1 TACAAAAATAAATTCAAAG
** *
1305850 TACAATCATAAATTCAGAG
1 TACAAAAATAAATTCAAAG
*
1305869 TTTACAAAAATAAAATCAAAG
1 --TACAAAAATAAATTCAAAG
**
1305890 TACAATCATAAATTCA
1 TACAAAAATAAATTCA
1305906 TAAGATATAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 28 0.65
21 15 0.35
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.24
Consensus pattern (19 bp):
TACAAAAATAAATTCAAAG
Found at i:1308439 original size:46 final size:46
Alignment explanation
Indices: 1308367--1308655 Score: 409
Period size: 46 Copynumber: 6.3 Consensus size: 46
1308357 TTATTCATTA
* * * *
1308367 ATTTCATTTATGGCAACCTTTTATGCCTTAACGCATCATTTCATGC
1 ATTTCTTTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* * *
1308413 ATTTCCTTTAAGGTAT-CTTCTCATGCCTTAATGCATCATTTCATGC
1 ATTTCTTTTATGGCATCCTT-TCATGCCTTAATGCATCATTTCATGC
*
1308459 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCTTTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* * * * *
1308505 ATTTATTTTATGACATCCTTTCATGCTTTAATGTATCCTTTCATGC
1 ATTTCTTTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* * *
1308551 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCTTTTCATGT
1 ATTTCTTTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
*
1308597 ATTTCTTTTATGGCATCATTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCTTTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1308643 ATTTCTTTTATGG
1 ATTTCTTTTATGG
1308656 ATTCGTTTTA
Statistics
Matches: 215, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
45 3 0.01
46 209 0.97
47 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.46
Consensus pattern (46 bp):
ATTTCTTTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:1308460 original size:12 final size:12
Alignment explanation
Indices: 1308443--1308530 Score: 51
Period size: 12 Copynumber: 7.3 Consensus size: 12
1308433 TCATGCCTTA
1308443 ATGCATCATTTC
1 ATGCATCATTTC
1308455 ATGCATTTCATTT-
1 ATGCA--TCATTTC
*
1308468 ATGGCATCCTTTC
1 AT-GCATCATTTC
*
1308481 ATGC--C--TTA
1 ATGCATCATTTC
1308489 ATGCATCATTTC
1 ATGCATCATTTC
* *
1308501 ATGCATTTATTTT
1 ATGCA-TCATTTC
*
1308514 ATGACATCCTTTC
1 ATG-CATCATTTC
1308527 ATGC
1 ATGC
1308531 TTTAATGTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
8 6 0.10
10 2 0.03
12 20 0.34
13 19 0.33
14 11 0.19
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (12 bp):
ATGCATCATTTC
Found at i:1315321 original size:46 final size:46
Alignment explanation
Indices: 1315271--1315408 Score: 213
Period size: 46 Copynumber: 3.0 Consensus size: 46
1315261 TTTTTCATTA
*
1315271 ATTTCATTTATGGCATCTTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
1315317 ATTTCCTTTATGGTATCCTCTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
1315363 ATTTCATTTATGGCATCCTTTCATTCCTTAATACATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1315409 CTGAATACAT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:1315334 original size:26 final size:26
Alignment explanation
Indices: 1315303--1315386 Score: 81
Period size: 26 Copynumber: 3.5 Consensus size: 26
1315293 ATGCCTTAAT
1315303 GCATCCTTTCATGCATTTCCTTTATG
1 GCATCCTTTCATGCATTTCCTTTATG
* * *
1315329 GTATCC--TC-T-CA-TGCCTTAAT-
1 GCATCCTTTCATGCATTTCCTTTATG
* *
1315349 GCATCATTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCCTTTATG
1315375 GCATCCTTTCAT
1 GCATCCTTTCAT
1315387 TCCTTAATAC
Statistics
Matches: 43, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
20 4 0.09
21 7 0.16
22 4 0.09
23 2 0.05
24 4 0.09
25 6 0.14
26 16 0.37
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.44
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTCCTTTATG
Found at i:1315401 original size:66 final size:66
Alignment explanation
Indices: 1315331--1315474 Score: 200
Period size: 66 Copynumber: 2.2 Consensus size: 66
1315321 CCTTTATGGT
* * * *
1315331 ATCCTCTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTCATTCCT-TAAT
1 ATCCTTTCATGCCTGAATACATCATTTCATGCATTTCATTTATGGAATCCTTTCA-TCCTGTAAT
1315395 AC
65 AC
* * *
1315397 ATCCTTTCATGCCTGAATACATCCTTTCATGCATTTCTTTTATGGAATCCTTTCATCCTGTAATG
1 ATCCTTTCATGCCTGAATACATCATTTCATGCATTTCATTTATGGAATCCTTTCATCCTGTAATA
1315462 C
66 C
*
1315463 ATTCTTTCATGC
1 ATCCTTTCATGC
1315475 ATTTCATTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 4 0.06
66 65 0.94
ACGTcount: A:0.22, C:0.26, G:0.09, T:0.43
Consensus pattern (66 bp):
ATCCTTTCATGCCTGAATACATCATTTCATGCATTTCATTTATGGAATCCTTTCATCCTGTAATA
C
Found at i:1315420 original size:112 final size:112
Alignment explanation
Indices: 1315284--1315519 Score: 368
Period size: 112 Copynumber: 2.1 Consensus size: 112
1315274 TCATTTATGG
* * * *
1315284 CATCTTTTCATGCCTTAATGCATCCTTTCATGCATTTCCTTTATGGTATCCTCTCATGCCT-TAA
1 CATCCTTTCATGCCTGAATACATCCTTTCATGCATTTCCTTTATGGAATCCTCTCAT-CCTGTAA
*
1315348 TGCA-TCATTTCATGCATTTCATTTATGGCATCCTTTCATTCCTTAATA
65 TGCATTC-TTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATA
* *
1315396 CATCCTTTCATGCCTGAATACATCCTTTCATGCATTTCTTTTATGGAATCCTTTCATCCTGTAAT
1 CATCCTTTCATGCCTGAATACATCCTTTCATGCATTTCCTTTATGGAATCCTCTCATCCTGTAAT
*
1315461 GCATTCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
66 GCATTCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATA
1315508 CATCCTTTCATG
1 CATCCTTTCATG
1315520 TATTTCTTTT
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
111 3 0.03
112 109 0.96
113 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.10, T:0.44
Consensus pattern (112 bp):
CATCCTTTCATGCCTGAATACATCCTTTCATGCATTTCCTTTATGGAATCCTCTCATCCTGTAAT
GCATTCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATA
Found at i:1315446 original size:26 final size:26
Alignment explanation
Indices: 1315416--1315579 Score: 130
Period size: 20 Copynumber: 7.0 Consensus size: 26
1315406 TGCCTGAATA
1315416 CATCCTTTCATGCATTTCTTTTATGG
1 CATCCTTTCATGCATTTCTTTTATGG
* * *
1315442 AATCCTTTCAT-C----CTGTAAT-G
1 CATCCTTTCATGCATTTCTTTTATGG
* *
1315462 CATTCTTTCATGCATTTCATTTATGG
1 CATCCTTTCATGCATTTCTTTTATGG
*
1315488 CATCCTTTCATGC----C-TTAAT-G
1 CATCCTTTCATGCATTTCTTTTATGG
*
1315508 CATCCTTTCATGTATTTCTTTTATGG
1 CATCCTTTCATGCATTTCTTTTATGG
*
1315534 CATCCTTTCATGC----C-TTAAT-G
1 CATCCTTTCATGCATTTCTTTTATGG
1315554 CATCCTTTCATGCATTTCTTTTATGG
1 CATCCTTTCATGCATTTCTTTTATGG
1315580 ATTCATTTTA
Statistics
Matches: 105, Mismatches: 15, Indels: 36
0.67 0.10 0.23
Matches are distributed among these distances:
20 37 0.35
21 14 0.13
22 2 0.02
24 2 0.02
25 13 0.12
26 37 0.35
ACGTcount: A:0.18, C:0.24, G:0.11, T:0.47
Consensus pattern (26 bp):
CATCCTTTCATGCATTTCTTTTATGG
Found at i:1315447 original size:46 final size:46
Alignment explanation
Indices: 1315397--1315580 Score: 280
Period size: 46 Copynumber: 4.0 Consensus size: 46
1315387 TCCTTAATAC
*
1315397 ATCCTTTCATGCCTGAATACATCCTTTCATGCATTTCTTTTATGGA
1 ATCCTTTCATGCCTGAATGCATCCTTTCATGCATTTCTTTTATGGA
* * *
1315443 ATCCTTTCAT-CCTGTAATGCATTCTTTCATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTG-AATGCATCCTTTCATGCATTTCTTTTATGGA
* * *
1315489 ATCCTTTCATGCCTTAATGCATCCTTTCATGTATTTCTTTTATGGC
1 ATCCTTTCATGCCTGAATGCATCCTTTCATGCATTTCTTTTATGGA
*
1315535 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCTTTTATGGA
1 ATCCTTTCATGCCTGAATGCATCCTTTCATGCATTTCTTTTATGGA
1315581 TTCATTTTAG
Statistics
Matches: 126, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 4 0.03
46 119 0.94
47 3 0.02
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.46
Consensus pattern (46 bp):
ATCCTTTCATGCCTGAATGCATCCTTTCATGCATTTCTTTTATGGA
Found at i:1315551 original size:158 final size:158
Alignment explanation
Indices: 1315271--1315566 Score: 468
Period size: 158 Copynumber: 1.9 Consensus size: 158
1315261 TTTTTCATTA
* * * *
1315271 ATTTCATTTATGGCATCTTTTCATGCCTTAATGCATCCTTTCATGCATTTCCTTTATGGTATCCT
1 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCT
*
1315336 CTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTCATTCCTTAATACATCC
66 CTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATACATCC
1315401 TTTCATGCCTGAATACATCCTTTCATGC
131 TTTCATGCCTGAATACATCCTTTCATGC
* *
1315429 ATTTCTTTTATGGAATCCTTTCAT-CCTGTAATGCATTCTTTCATGCATTTCATTTATGGCATCC
1 ATTTCATTTATGGAATCCTTTCATGCCT-TAATGCATCCTTTCATGCATTTCATTTATGGCATCC
* * * * *
1315493 TTTCATGCCTTAATGCATCCTTTCATGTATTTCTTTTATGGCATCCTTTCATGCCTTAATGCATC
65 TCTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATACATC
1315558 CTTTCATGC
130 CTTTCATGC
1315567 ATTTCTTTTA
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
157 3 0.02
158 122 0.98
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (158 bp):
ATTTCATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCT
CTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATACATCC
TTTCATGCCTGAATACATCCTTTCATGC
Found at i:1316067 original size:22 final size:21
Alignment explanation
Indices: 1315975--1316068 Score: 56
Period size: 22 Copynumber: 4.5 Consensus size: 21
1315965 AGACCCAATA
*
1315975 GTATCGATACCCCTAC-C-ATG
1 GTATCGATA-CTCTACTCTATG
1315995 GTATCGATACTTCTA-TACTATG
1 GTATCGATAC-TCTACT-CTATG
* *
1316017 GTACCGATAC-CTTTCTCTCA--
1 GTATCGATACTC-TACTCT-ATG
*
1316037 GTATTGATACTACTACTCTATG
1 GTATCGATACT-CTACTCTATG
1316059 GTATCGATAC
1 GTATCGATAC
1316069 CATTTTGGCA
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
19 1 0.02
20 22 0.39
21 9 0.16
22 24 0.43
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (21 bp):
GTATCGATACTCTACTCTATG
Found at i:1322091 original size:26 final size:25
Alignment explanation
Indices: 1322031--1322250 Score: 124
Period size: 20 Copynumber: 9.4 Consensus size: 25
1322021 TTAATTTCAT
*
1322031 TTTCATTTATGGCATCCTCTCATGC-
1 TTTC-TTTATGGCATCCTTTCATGCA
* *
1322056 ---CTTAAT-GCATCTTTTCATGCA
1 TTTCTTTATGGCATCCTTTCATGCA
*
1322077 TTTCATTTATGGCATCCTTTCATGTA
1 TTTC-TTTATGGCATCCTTTCATGCA
1322103 TTT-TTTATGGCAT-CTTT--T-C-
1 TTTCTTTATGGCATCCTTTCATGCA
*
1322122 TTGTCTTAAT-GCATCCTTTCATGCA
1 TT-TCTTTATGGCATCCTTTCATGCA
1322147 TTTCATTTATGGCATCCTTTCATGC-
1 TTTC-TTTATGGCATCCTTTCATGCA
* * * *
1322172 ---CTTAAT-GCATCCTTTTATTCT
1 TTTCTTTATGGCATCCTTTCATGCA
* *
1322193 TTTCATTTATGGAATCATTTCATGC-
1 TTTC-TTTATGGCATCCTTTCATGCA
*
1322218 ---CTTAAT-GCATCCTTTCATGCA
1 TTTCTTTATGGCATCCTTTCATGCA
1322239 TTTCTTTTATGG
1 TTTC-TTTATGG
1322251 ATTCGTTTTA
Statistics
Matches: 147, Mismatches: 21, Indels: 53
0.67 0.10 0.24
Matches are distributed among these distances:
19 2 0.01
20 41 0.28
21 21 0.14
22 3 0.02
23 5 0.03
24 16 0.11
25 18 0.12
26 41 0.28
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (25 bp):
TTTCTTTATGGCATCCTTTCATGCA
Found at i:1322130 original size:70 final size:70
Alignment explanation
Indices: 1322036--1322170 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 70
1322026 TTCATTTTCA
*
1322036 TTTATGGCATCCTCTCATGCCTTAATGCATCTTTTCATGCATTTCATTTATGGCATCCTTTCATG
1 TTTATGGCATCCTCTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG
1322101 TATTT
66 TATTT
* * * *
1322106 TTTATGGCATCTTTTCTTGTCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG
1 TTTATGGCATCCTCTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG
1322171 CCTTAATGCA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.48
Consensus pattern (70 bp):
TTTATGGCATCCTCTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG
TATTT
Found at i:1322176 original size:46 final size:46
Alignment explanation
Indices: 1322088--1322250 Score: 222
Period size: 46 Copynumber: 3.6 Consensus size: 46
1322078 TTCATTTATG
* * * *
1322088 GCATCCTTTCATGTATTT--TTTATGGCATCTTTTCTTGTCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAAT
*
1322132 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAAT
* * * *
1322178 GCATCCTTTTATTCTTTTCATTTATGGAATCATTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAAT
*
1322224 GCATCCTTTCATGCATTTCTTTTATGG
1 GCATCCTTTCATGCATTTCATTTATGG
1322251 ATTCGTTTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 17 0.16
46 87 0.84
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.49
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAAT
Found at i:1322193 original size:70 final size:68
Alignment explanation
Indices: 1322056--1322187 Score: 187
Period size: 70 Copynumber: 1.9 Consensus size: 68
1322046 CCTCTCATGC
* ** *
1322056 CTTAATGCATCTTTTCATGCATTTCATTTATGGCATCCTTTCATGTATTTTTTATGGCATCTTTT
1 CTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG--TCCTTAATGGCATCTTTT
1322121 CTTGT
64 CTTGT
1322126 CTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG-CCTTAAT-GCATCCTTTT
1 CTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGTCCTTAATGGCAT-CTTTT
1322188 ATTCTTTTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
66 4 0.07
67 9 0.16
70 44 0.77
ACGTcount: A:0.18, C:0.22, G:0.11, T:0.49
Consensus pattern (68 bp):
CTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGTCCTTAATGGCATCTTTTCT
TGT
Found at i:1325310 original size:16 final size:17
Alignment explanation
Indices: 1325289--1325323 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1325279 CTGATTTCTA
1325289 TTATACAATATATA-TT
1 TTATACAATATATAGTT
1325305 TTATACAATATATAGTT
1 TTATACAATATATAGTT
1325322 TT
1 TT
1325324 GAAAACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (17 bp):
TTATACAATATATAGTT
Found at i:1325358 original size:20 final size:21
Alignment explanation
Indices: 1325313--1325365 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1325303 TTTTATACAA
*
1325313 TATATAGTTTTGAAAACATAT
1 TATATAGTTTTTAAAACATAT
* *
1325334 AATATAGTTTTTTAAA-ATAT
1 TATATAGTTTTTAAAACATAT
1325354 TATATAGTTTTT
1 TATATAGTTTTT
1325366 CAAGAAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.51
Consensus pattern (21 bp):
TATATAGTTTTTAAAACATAT
Found at i:1325376 original size:19 final size:20
Alignment explanation
Indices: 1325313--1325378 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1325303 TTTTATACAA
**
1325313 TATATAGTTTTGAAAACATA-
1 TATATAGTTTTTCAAA-ATAG
* *
1325333 TAATATAGTTTTTTAAAATAT
1 T-ATATAGTTTTTCAAAATAG
*
1325354 TATATAGTTTTTCAAGA-AG
1 TATATAGTTTTTCAAAATAG
1325373 TATATA
1 TATATA
1325379 AATATATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 7 0.18
20 18 0.46
21 14 0.36
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (20 bp):
TATATAGTTTTTCAAAATAG
Found at i:1325413 original size:29 final size:29
Alignment explanation
Indices: 1325348--1325407 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1325338 TAGTTTTTTA
* *
1325348 AAATATTATATAGTTTTTCAAGAAGTATAT
1 AAATA-TATATAATTTTTCAAGAAATATAT
*
1325378 AAATATATATAATTTTTGAA-AAATATAT
1 AAATATATATAATTTTTCAAGAAATATAT
1325406 AA
1 AA
1325408 TGTATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 9 0.33
29 13 0.48
30 5 0.19
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.42
Consensus pattern (29 bp):
AAATATATATAATTTTTCAAGAAATATAT
Found at i:1325486 original size:18 final size:19
Alignment explanation
Indices: 1325452--1325494 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
1325442 TAATATATAT
1325452 TATATAGTTTTTGAAAATA
1 TATATAGTTTTTGAAAATA
1325471 TATATAGTTTTT-AAAATA
1 TATATAGTTTTTGAAAATA
1325489 TATATA
1 TATATA
1325495 ATATGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (19 bp):
TATATAGTTTTTGAAAATA
Found at i:1325493 original size:22 final size:21
Alignment explanation
Indices: 1325443--1325503 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 21
1325433 CTGAAAATAT
*
1325443 AATATATATTATATAGTTTTTG
1 AATATATA-TATATAGTTTTTA
1325465 AA-A-ATATATATAGTTTTTA
1 AATATATATATATAGTTTTTA
1325484 AA-ATATATATAATATGTTTT
1 AATATATATAT-ATA-GTTTT
1325504 ATATTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 15 0.43
20 9 0.26
21 4 0.11
22 7 0.20
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
AATATATATATATAGTTTTTA
Found at i:1325533 original size:22 final size:21
Alignment explanation
Indices: 1325506--1325559 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1325496 TATGTTTTAT
1325506 ATTTTTATTT-TCTTTTTTATTC
1 ATTTTTATTTAT-TTTTTT-TTC
*
1325528 ATTTTTATTTATTTTTTTTTT
1 ATTTTTATTTATTTTTTTTTC
*
1325549 GTTTTTATTTA
1 ATTTTTATTTA
1325560 ATTCCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 16 0.55
23 1 0.03
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.80
Consensus pattern (21 bp):
ATTTTTATTTATTTTTTTTTC
Found at i:1325542 original size:21 final size:21
Alignment explanation
Indices: 1325506--1325559 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1325496 TATGTTTTAT
*
1325506 ATTTTTATTTTCTTTTTTATTC
1 ATTTTTA-TTTATTTTTTATTC
* *
1325528 ATTTTTATTTATTTTTTTTTT
1 ATTTTTATTTATTTTTTATTC
*
1325549 GTTTTTATTTA
1 ATTTTTATTTA
1325560 ATTCCATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.80
Consensus pattern (21 bp):
ATTTTTATTTATTTTTTATTC
Found at i:1325553 original size:11 final size:11
Alignment explanation
Indices: 1325501--1325559 Score: 52
Period size: 10 Copynumber: 5.4 Consensus size: 11
1325491 TATAATATGT
1325501 TTTATATTTTTA
1 TTTAT-TTTTTA
*
1325513 TTTTCTTTTTTA
1 -TTTATTTTTTA
*
1325525 TTCA-TTTTTA
1 TTTATTTTTTA
1325535 TTTATTTTTT-
1 TTTATTTTTTA
1325545 TTT-TGTTTTTA
1 TTTAT-TTTTTA
1325556 TTTA
1 TTTA
1325560 ATTCCATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
9 1 0.03
10 17 0.45
11 10 0.26
12 6 0.16
13 4 0.11
ACGTcount: A:0.15, C:0.03, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:1327791 original size:5 final size:5
Alignment explanation
Indices: 1327783--1327932 Score: 63
Period size: 5 Copynumber: 28.2 Consensus size: 5
1327773 TATTATTTTA
* * *
1327783 TATTT TATTT TATTA TATTAT ATCTTT TATTT TATTT TACTT TA-TT T-TTT
1 TATTT TATTT TATTT TATT-T -TATTT TATTT TATTT TATTT TATTT TATTT
* * * * * **
1327833 TCTTT TATTG TATTT TCTTT AAAATTT AACACT T-TTT TATTT TATTT
1 TATTT TATTT TATTT TATTT --TATTT TA-TTT TATTT TATTT TATTT
* *
1327880 TGTTT TATCTT TATTT TCCCACTTTT TATTT TATTT TGTTT TATTTT TATTT
1 TATTT TAT-TT TATTT T---A--TTT TATTT TATTT TATTT TA-TTT TATTT
1327932 T
1 T
1327933 CTCTTTTAAC
Statistics
Matches: 110, Mismatches: 20, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
4 8 0.07
5 78 0.71
6 12 0.11
7 7 0.06
8 1 0.01
10 4 0.04
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.71
Consensus pattern (5 bp):
TATTT
Found at i:1327791 original size:15 final size:15
Alignment explanation
Indices: 1327771--1327848 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
1327761 ACTACTATTA
1327771 TTTATTATT-TTATAT
1 TTTATT-TTATTATAT
1327786 TTTATTTTATTATAT
1 TTTATTTTATTATAT
* *
1327801 TATATCTTTTATTTTAT
1 T-T-TATTTTATTATAT
*
1327818 TTTACTTTATT-T-T
1 TTTATTTTATTATAT
* *
1327831 TTTCTTTTATTGTAT
1 TTTATTTTATTATAT
1327846 TTT
1 TTT
1327849 CTTTAAAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 10 0.19
14 4 0.08
15 24 0.46
16 2 0.04
17 12 0.23
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (15 bp):
TTTATTTTATTATAT
Found at i:1327801 original size:22 final size:22
Alignment explanation
Indices: 1327776--1327848 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
1327766 TATTATTTAT
1327776 TATTTTATATTTTATTTTATTA
1 TATTTTATATTTTATTTTATTA
* * *
1327798 TATTATATCTTTTATTTTATTT
1 TATTTTATATTTTATTTTATTA
* * * *
1327820 TACTTTATTTTTTTCTTTTATTG
1 TATTTTA-TATTTTATTTTATTA
1327843 TATTTT
1 TATTTT
1327849 CTTTAAAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 24 0.59
23 17 0.41
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (22 bp):
TATTTTATATTTTATTTTATTA
Found at i:1327813 original size:27 final size:27
Alignment explanation
Indices: 1327766--1327848 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 27
1327756 TCTTAACTAC
1327766 TATTAT-TTATTAT-TTTATATTTTATTT
1 TATTATATTA-TATCTTT-TATTTTATTT
1327793 TATTATATTATATCTTTTATTTTATTT
1 TATTATATTATATCTTTTATTTTATTT
* * *
1327820 TACTT-TATTTTTTTCTTTTATTGTATTT
1 TA-TTATA-TTATATCTTTTATTTTATTT
1327848 T
1 T
1327849 CTTTAAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 23 0.47
28 26 0.53
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (27 bp):
TATTATATTATATCTTTTATTTTATTT
Found at i:1327838 original size:18 final size:18
Alignment explanation
Indices: 1327812--1327853 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1327802 ATATCTTTTA
1327812 TTTTATTTTACTT-TATTT
1 TTTTATTTTA-TTGTATTT
*
1327830 TTTTCTTTTATTGTATTT
1 TTTTATTTTATTGTATTT
1327848 TCTTTA
1 T-TTTA
1327854 AAATTTAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 15 0.75
19 3 0.15
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTATTTTATTGTATTT
Found at i:1328517 original size:18 final size:19
Alignment explanation
Indices: 1328482--1328519 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1328472 AATAACAAGT
*
1328482 TTAAATTTTAATTTATTTA
1 TTAAATTCTAATTTATTTA
1328501 TTAAATTCTAA-TTATTTA
1 TTAAATTCTAATTTATTTA
1328519 T
1 T
1328520 CTTTTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAAATTCTAATTTATTTA
Found at i:1333791 original size:101 final size:98
Alignment explanation
Indices: 1333609--1333808 Score: 296
Period size: 101 Copynumber: 2.0 Consensus size: 98
1333599 ACTTCAACTC
1333609 TTTTTTTAAGCATACTTTAAGGGGAGTCTCATCACACTACCATCCCACACTCTAAGTGAAAGAAA
1 TTTTTTTAAGCATACTTTAAGGGGAGTCTCATCACACTACCATCCCACACTCTAAGTGAAAGAAA
1333674 CATACATTCCACCCCTGAGCTAGTCAAGTAGAG
66 CATACATTCCACCCCTGAGCTAGTCAAGTAGAG
1333707 TTTTTATTAAGCATACTTTAA-GGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAA
1 TTTTT-TTAAGCATACTTTAAGGGGAGT---CTCATCACACTACCATCCCACACTCTAAGTGAAA
* * * * *
1333771 GGGAGCATACCTTTCA-CCCTGAGCTAGTCAGGTAGAG
62 -GAAACATACATTCCACCCCTGAGCTAGTCAAGTAGAG
1333808 T
1 T
1333809 CATCCCGTGA
Statistics
Matches: 92, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
98 11 0.12
99 15 0.16
101 55 0.60
102 11 0.12
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (98 bp):
TTTTTTTAAGCATACTTTAAGGGGAGTCTCATCACACTACCATCCCACACTCTAAGTGAAAGAAA
CATACATTCCACCCCTGAGCTAGTCAAGTAGAG
Found at i:1336606 original size:105 final size:103
Alignment explanation
Indices: 1336466--1336675 Score: 384
Period size: 105 Copynumber: 2.0 Consensus size: 103
1336456 TACAACCACA
1336466 CAACACCTAAATGATAAAACAAAATAGCAAATAAATCCATAAAAAATAATAAAGAAACAAGATAA
1 CAACACCTAAATGATAAAACAAAATAGCAAATAAATCCATAAAAAATAATAAAGAAACAAGATAA
1336531 TGCTATAACAAAACTTTTAAAAACACCAATTGCCAATC
66 TGCTATAACAAAACTTTTAAAAACACCAATTGCCAATC
* *
1336569 CAACACCTAAAATGGTAAAACAAAAATAGCGAATAAATCCATAAAAAATAATAAAGAAACAAGAT
1 CAACACCT-AAATGATAAAAC-AAAATAGCAAATAAATCCATAAAAAATAATAAAGAAACAAGAT
1336634 AATGCTATAACAAAACTTTTAAAAACACCAATTGCCAATC
64 AATGCTATAACAAAACTTTTAAAAACACCAATTGCCAATC
1336674 CA
1 CA
1336676 CGGCAACGGC
Statistics
Matches: 103, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
103 8 0.08
104 11 0.11
105 84 0.82
ACGTcount: A:0.57, C:0.18, G:0.07, T:0.19
Consensus pattern (103 bp):
CAACACCTAAATGATAAAACAAAATAGCAAATAAATCCATAAAAAATAATAAAGAAACAAGATAA
TGCTATAACAAAACTTTTAAAAACACCAATTGCCAATC
Found at i:1343087 original size:270 final size:269
Alignment explanation
Indices: 1342606--1343208 Score: 861
Period size: 270 Copynumber: 2.2 Consensus size: 269
1342596 ATTCAAAATA
* *
1342606 TCAACTTCACAACGAATGAGCCACCTATGATTTTGACTTCACAACGAAGGATATCATACCCAATA
1 TCAACTTCACAACGAAGGAGCCACCTATGATTTTGACTTCACAA-GAAGGATATCATACCCAAAA
* * * *
1342671 TATTGACCCAATTTTACAAAGAATGAGTCATCTGTAACACAACAATAAAAAACCAGTTTCATACC
65 GATTGACCCAACTTCACAAAGAATGAATCATCTGTAACACAACAATAAAAAACCAGTTTCATACC
** *
1342736 AAAGTCTTCAGGTCAAATTCCAGCTTCACGACGAAGTATATTAGGCTAAAAAACGATCCGAGAGT
130 AAAGTCTTCAGGTCAAATTCCAGCCCCACGACGAAGTATATTAGGCTAAAAAACGATCCGAGAGC
* * *
1342801 GACTTTCCAATGCTTTGAGCCCGATTTCAACTTCACGACGAAGGATATCGTGCTCAGGATTTTTC
195 GACTTTCCAATGCTTTGAGACCGATTTCAACTTCACAACGAAGGATATCGTGCTCAGGAATTTTC
1342866 AGTTCAAAGC
260 AGTTCAAAGC
* * *
1342876 TCAACTTCACAATGAAGGAGCCACCTACGATTTTGACTTCACAATGAAGGATATCATATCCAAAA
1 TCAACTTCACAACGAAGGAGCCACCTATGATTTTGACTTCACAA-GAAGGATATCATACCCAAAA
* * *
1342941 GATTGATCCAACTTCACGAAGAATGAATCATCTGTAACA-AGACAATGAAAAACCAGTTTCATAC
65 GATTGACCCAACTTCACAAAGAATGAATCATCTGTAACACA-ACAATAAAAAACCAGTTTCATAC
* * * *
1343005 CAAAGTCTTCAGGTCAAATTTCAGCCCCACGACGAAGTATATTGGGCTAAAAGATGATCC-AGGA
129 CAAAGTCTTCAGGTCAAATTCCAGCCCCACGACGAAGTATATTAGGCTAAAAAACGATCCGA-GA
* * *
1343069 GCGACTTTCCAATGCTTTGAGACCGTTTTCAACTTTACAACTAAGGATATCGTGCTCAGGAATTT
193 GCGACTTTCCAATGCTTTGAGACCGATTTCAACTTCACAACGAAGGATATCGTGCTCAGGAATTT
1343134 TCAGTTCAAAGC
258 TCAGTTCAAAGC
* * ** *
1343146 TCAAATTCACAACGAAGGAGTCA-CTCATGATTTCAACTTCACTAAGAAGGATATTATACCCAA
1 TCAACTTCACAACGAAGGAGCCACCT-ATGATTTTGACTTCAC-AAGAAGGATATCATACCCAA
1343209 TGGTTCGACT
Statistics
Matches: 295, Mismatches: 34, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
269 4 0.01
270 289 0.98
271 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (269 bp):
TCAACTTCACAACGAAGGAGCCACCTATGATTTTGACTTCACAAGAAGGATATCATACCCAAAAG
ATTGACCCAACTTCACAAAGAATGAATCATCTGTAACACAACAATAAAAAACCAGTTTCATACCA
AAGTCTTCAGGTCAAATTCCAGCCCCACGACGAAGTATATTAGGCTAAAAAACGATCCGAGAGCG
ACTTTCCAATGCTTTGAGACCGATTTCAACTTCACAACGAAGGATATCGTGCTCAGGAATTTTCA
GTTCAAAGC
Found at i:1344343 original size:4 final size:4
Alignment explanation
Indices: 1344334--1344367 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
1344324 TCTCTTTAGA
*
1344334 TTAT TTAT TTAT TTAT TTATT TTAT TTAA TTAT T
1 TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTAT T
1344368 ATCTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:1344357 original size:17 final size:18
Alignment explanation
Indices: 1344337--1344378 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
1344327 CTTTAGATTA
*
1344337 TTTATTTATTTATT-TAT
1 TTTATTTAATTATTATAT
*
1344354 TTTATTTAATTATTATCT
1 TTTATTTAATTATTATAT
1344372 TTTATTT
1 TTTATTT
1344379 TAAAAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:1344458 original size:22 final size:22
Alignment explanation
Indices: 1344419--1344468 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1344409 TCTTTACTGC
*
1344419 TATTTT-TATTATTTTATCTTT
1 TATTTTATATTATTATATCTTT
*
1344440 TATTTTATTTTATTATATCTTT
1 TATTTTATATTATTATATCTTT
*
1344462 TGTTTTA
1 TATTTTA
1344469 CCCTAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (22 bp):
TATTTTATATTATTATATCTTT
Found at i:1344555 original size:38 final size:39
Alignment explanation
Indices: 1344505--1344579 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 39
1344495 TTATTTAAAA
*
1344505 TTTAACACTTTTTTAT-TTTGTTTTATTTTTATTTTCTCT
1 TTTAACACTTTTTTATATTT-TATTATTTTTATTTTCTCT
*
1344544 TTTAACA-TTTTTTATATTTTATTATTTTTCTTTTCT
1 TTTAACACTTTTTTATATTTTATTATTTTTATTTTCT
1344580 GAAATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 23 0.70
39 10 0.30
ACGTcount: A:0.17, C:0.09, G:0.01, T:0.72
Consensus pattern (39 bp):
TTTAACACTTTTTTATATTTTATTATTTTTATTTTCTCT
Found at i:1349981 original size:20 final size:20
Alignment explanation
Indices: 1349956--1350031 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
1349946 GGTATACAAA
1349956 TATTTTAAAAGAGATGGATC
1 TATTTTAAAAGAGATGGATC
** *
1349976 TATTTTTCAAGGGATGGATC
1 TATTTTAAAAGAGATGGATC
* *
1349996 TATTTTTCAACG-GATGGATC
1 TA-TTTTAAAAGAGATGGATC
1350016 -ATTTCTGAAAAGAGAT
1 TATTT-T-AAAAGAGAT
1350032 CGATATTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
18 3 0.07
19 2 0.05
20 30 0.68
21 9 0.20
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (20 bp):
TATTTTAAAAGAGATGGATC
Found at i:1352574 original size:20 final size:20
Alignment explanation
Indices: 1352529--1352583 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1352519 AAACTTTAGA
*
1352529 GAAAGTTTCAAAACTATGAT
1 GAAAGTTTCGAAACTATGAT
*
1352549 GCAAGTTTCGAAACTATTG-T
1 GAAAGTTTCGAAACTA-TGAT
*
1352569 GAAAGTATCGAAACT
1 GAAAGTTTCGAAACT
1352584 TCTAAACACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (20 bp):
GAAAGTTTCGAAACTATGAT
Found at i:1355184 original size:3 final size:3
Alignment explanation
Indices: 1355169--1355241 Score: 74
Period size: 3 Copynumber: 23.3 Consensus size: 3
1355159 AAACAAAATA
* ** *
1355169 AAT AAT GAT AAT AAT AAT GTT AAT AAT AAT AAT AAAT ATT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT A-AT AAT
*
1355216 AAT ATGT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT A
1355242 TATATTATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
3 50 0.88
4 7 0.12
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:1356302 original size:19 final size:19
Alignment explanation
Indices: 1356242--1356303 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
1356232 ACTTTCACAT
*
1356242 TTCATAA-TTCATTTC-TGA
1 TTCATAACTTAATTTCAT-A
* * *
1356260 TTCAGAACTTACTTTCAGA
1 TTCATAACTTAATTTCATA
1356279 TTCATAACTTAATTTCATA
1 TTCATAACTTAATTTCATA
1356298 TTCATA
1 TTCATA
1356304 GCTTCTTTTC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
18 6 0.17
19 29 0.83
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (19 bp):
TTCATAACTTAATTTCATA
Found at i:1356313 original size:19 final size:19
Alignment explanation
Indices: 1356259--1356320 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
1356249 TTCATTTCTG
* * *
1356259 ATTCAGAACTTACTTTCAG
1 ATTCATAACTTAATTTCAA
*
1356278 ATTCATAACTTAATTTCAT
1 ATTCATAACTTAATTTCAA
* **
1356297 ATTCATAGCTTCTTTTCAA
1 ATTCATAACTTAATTTCAA
1356316 ATTCA
1 ATTCA
1356321 AAGCCCAATG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
ATTCATAACTTAATTTCAA
Found at i:1357963 original size:21 final size:21
Alignment explanation
Indices: 1357939--1357987 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1357929 TTTCTCAATA
1357939 TTTGCCATTTAGTACTCAAAC
1 TTTGCCATTTAGTACTCAAAC
1357960 TTTGCCATTTAGTACTCAAAC
1 TTTGCCATTTAGTACTCAAAC
1357981 TTTGCCA
1 TTTGCCA
1357988 ACTTCCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (21 bp):
TTTGCCATTTAGTACTCAAAC
Found at i:1359219 original size:30 final size:30
Alignment explanation
Indices: 1359185--1359250 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1359175 CAAAACACCT
1359185 AACTTTTGAAAATTACAC-TTTTAGTCCCTA
1 AACTTTTGAAAATTAC-CTTTTTAGTCCCTA
*
1359215 AACTTTTGAAAATTACCTTTTTGGTCCCTA
1 AACTTTTGAAAATTACCTTTTTAGTCCCTA
1359245 AACTTT
1 AACTTT
1359251 CCAAACTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (30 bp):
AACTTTTGAAAATTACCTTTTTAGTCCCTA
Found at i:1362131 original size:20 final size:20
Alignment explanation
Indices: 1362078--1362133 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
1362068 TAGTATCGAT
1362078 AGGGTATCGATACCATAATA
1 AGGGTATCGATACCATAATA
* * **
1362098 GGGTAGTATAGATACCATGGTA
1 AGG--GTATCGATACCATAATA
1362120 AGGGTATCGATACC
1 AGGGTATCGATACC
1362134 TGGCAACATC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 12 0.43
22 16 0.57
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (20 bp):
AGGGTATCGATACCATAATA
Found at i:1362624 original size:55 final size:55
Alignment explanation
Indices: 1362553--1362791 Score: 388
Period size: 55 Copynumber: 4.3 Consensus size: 55
1362543 CTATGTGTAC
* * *
1362553 TACAAGCACTTTGTGTGCATATTTACGGAATTCATCATGAGTTGACGAATCACCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * *
1362608 TACAGGCACTTTGTGTGCATATTCACGAAATTTATCATGAGTTGATGAATCACCA
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
*
1362663 TATAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
*
1362718 CACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* *
1362773 TACAGACACTATGTGTGCA
1 TACAGGCACTTTGTGTGCA
1362792 GCCCACAAAA
Statistics
Matches: 169, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 169 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (55 bp):
TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
Found at i:1364089 original size:30 final size:30
Alignment explanation
Indices: 1363969--1364089 Score: 102
Period size: 30 Copynumber: 4.1 Consensus size: 30
1363959 ATAATAGATC
* * *
1363969 TAGCAAAAACATGAACTTAAAGGA-TTAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
* * * * *
1363998 TGGTAAAAACATAAACTCAAAAGGCTAAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
* * * *
1364028 TAGCTAAAACAGATATTTAAATGAC-ATAAA
1 TAGCAAAAACATAAACTTAAATGACTA-AAA
*
1364058 TAGCAAAAACATAAACTTAAGTGACTAAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
1364088 TA
1 TA
1364090 TAATAACAGA
Statistics
Matches: 68, Mismatches: 21, Indels: 5
0.72 0.22 0.05
Matches are distributed among these distances:
29 19 0.28
30 48 0.71
31 1 0.01
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (30 bp):
TAGCAAAAACATAAACTTAAATGACTAAAA
Found at i:1364743 original size:145 final size:145
Alignment explanation
Indices: 1364467--1364760 Score: 378
Period size: 145 Copynumber: 2.0 Consensus size: 145
1364457 TCAATATTTT
* * *
1364467 GAATGTCGATCGGAAATCTCGATCGTCGGCAAGAAGCCAAAAACCGTTCGGCTTATTTTCTTCGA
1 GAATGTCGATCGGAAACCCCGATCGTCGGCAAGAAGCCAAAAACCGTTCGGCTTATTATCTTCGA
** * * ** * * *
1364532 TCTGTTGTGATCCACTGTCCGATCGTCCTGAATTTTTAGTATGTTGCTTGTGCTGGTCTCGTGCA
66 TCCATTCTGATCCACTGTCCGATCGTCCTGAATTTTCAGTATGTTGCTTAAGATAGTCTCGCGCA
1364597 ACTTTTGACCGTTCA
131 ACTTTTGACCGTTCA
* * * *
1364612 GAATGTCGATTGGAGACCCCGATC-TCTGGCAAGAATCCAAAAACCGTTCTGCTTATTATCTTCG
1 GAATGTCGATCGGAAACCCCGATCGTC-GGCAAGAAGCCAAAAACCGTTCGGCTTATTATCTTCG
* *
1364676 ATCCATCTCTG-TCCACTGTCCGATCGTTCTGAATTTTCAGTATGTTG-TTCAAGATAGTCTTGC
65 ATCCAT-TCTGATCCACTGTCCGATCGTCCTGAATTTTCAGTATGTTGCTT-AAGATAGTCTCGC
1364739 GCAACTTTTGACCGTTCA
128 GCAACTTTTGACCGTTCA
1364757 GAAT
1 GAAT
1364761 ATTGATCAGA
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
144 4 0.03
145 121 0.95
146 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (145 bp):
GAATGTCGATCGGAAACCCCGATCGTCGGCAAGAAGCCAAAAACCGTTCGGCTTATTATCTTCGA
TCCATTCTGATCCACTGTCCGATCGTCCTGAATTTTCAGTATGTTGCTTAAGATAGTCTCGCGCA
ACTTTTGACCGTTCA
Found at i:1365496 original size:3 final size:3
Alignment explanation
Indices: 1365490--1365526 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1365480 GTTGTATTAT
* *
1365490 TAA TAA TAA TAA TAA TAA TAA TTA TTA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1365527 TTTTTGGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:1366198 original size:43 final size:43
Alignment explanation
Indices: 1366151--1366260 Score: 148
Period size: 43 Copynumber: 2.6 Consensus size: 43
1366141 GATTCCCTTT
* * **
1366151 GTCGTGAAGTTGAAACCGTGGATGTGTGGGCACGATATCCTCC
1 GTCGTGGAGTTGAAATCGTGGATGCATGGGCACGATATCCTCC
* * *
1366194 GTCGTGGAGTTGAAATCGTGGATCCATGGGTACGATATCCTCT
1 GTCGTGGAGTTGAAATCGTGGATGCATGGGCACGATATCCTCC
*
1366237 GTCGTGGAGTTAAAATCGTGGATG
1 GTCGTGGAGTTGAAATCGTGGATG
1366261 GCCTCTTCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (43 bp):
GTCGTGGAGTTGAAATCGTGGATGCATGGGCACGATATCCTCC
Found at i:1366552 original size:64 final size:64
Alignment explanation
Indices: 1366466--1366654 Score: 244
Period size: 64 Copynumber: 3.0 Consensus size: 64
1366456 ATTTCGTTTC
* * * * * *
1366466 GAGTTCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAATTGTTTGTT
1 GAGTACAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAATTGGAAAGTTGTTTGTT
*
1366530 GAGTACAATATCCTTCGCTGTGAAGTTAAAATTGA--CTG-A--AAGTTGGAAAGTTGTTTGTT
1 GAGTACAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAATTGGAAAGTTGTTTGTT
* * * *
1366589 GAGTCCAATATCCTTTGCCGTGAAGTTAAAATTGACTCTGAATGAAATTGGGAAGTTGTTTGTT
1 GAGTACAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAATTGGAAAGTTGTTTGTT
1366653 GA
1 GA
1366655 CAGACACTCA
Statistics
Matches: 108, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
59 48 0.44
61 4 0.04
62 4 0.04
64 52 0.48
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (64 bp):
GAGTACAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAATTGGAAAGTTGTTTGTT
Found at i:1366994 original size:32 final size:32
Alignment explanation
Indices: 1366919--1366994 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 32
1366909 TTCGTATCAG
* *
1366919 GATGTTGAATCCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
* * *
1366951 GATGTTGAATCTCGAAAGATTCCCCAACATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
1366983 GATGTTGAATCT
1 GATGTTGAATCT
1366995 TTAATGATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTC
Found at i:1371461 original size:30 final size:30
Alignment explanation
Indices: 1371394--1371481 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
1371384 ACTCAAAAGG
** * * *
1371394 CTAAAATAGCTAAAACAGATATTTAAATGA
1 CTAAAATAGAAAAAACAGAAACTTAAGTGA
1371424 C-ATAAATAGAAAAAACAGAAACTTAAGTGA
1 CTA-AAATAGAAAAAACAGAAACTTAAGTGA
* *
1371454 CTAAAATA-AAATAACAGAAACTAAAGTG
1 CTAAAATAGAAAAAACAGAAACTTAAGTG
1371482 TCAAAATCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
29 19 0.39
30 29 0.59
31 1 0.02
ACGTcount: A:0.58, C:0.10, G:0.11, T:0.20
Consensus pattern (30 bp):
CTAAAATAGAAAAAACAGAAACTTAAGTGA
Found at i:1371498 original size:29 final size:28
Alignment explanation
Indices: 1371433--1371498 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
1371423 ACATAAATAG
*
1371433 AAAAAACAGAAACTTAAGTGACTAAAAT
1 AAAAAACAGAAACTAAAGTGACTAAAAT
*
1371461 AAAATAACAGAAACTAAAGTGTC-AAAAT
1 AAAA-AACAGAAACTAAAGTGACTAAAAT
1371489 CAAGAAAACA
1 -AA-AAAACA
1371499 TATATATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 9 0.27
29 22 0.67
30 2 0.06
ACGTcount: A:0.62, C:0.12, G:0.11, T:0.15
Consensus pattern (28 bp):
AAAAAACAGAAACTAAAGTGACTAAAAT
Found at i:1384516 original size:95 final size:95
Alignment explanation
Indices: 1384330--1384519 Score: 238
Period size: 94 Copynumber: 2.0 Consensus size: 95
1384320 GATACCTATT
*
1384330 AGGTAGTATTGATACCATAGTAAAGGGTATCGATACCTAGAAACATCGAATCTAATTTTGGTATC
1 AGGTAGTATTGATACCATAGTAAAGGGTATCGATACCTAGAAACATCGAACCTAATTTTGGTATC
* *** * *
1384395 GATACCGGTAGGGGTATCGGTACCATAGTA
66 AATACCCAAAGGAGTATCAGTACCATAGTA
* * * * ** *
1384425 AGGTAGTATTGATACCATGGT-AAGGTTATCGATACCTGGCAACATTTAACCTATTTTTGGTATC
1 AGGTAGTATTGATACCATAGTAAAGGGTATCGATACCTAGAAACATCGAACCTAATTTTGGTATC
1384489 AATACCCAAACGGAGTATCAGTACCATAGTA
66 AATACCCAAA-GGAGTATCAGTACCATAGTA
1384520 TAGAAGTATC
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 42 0.52
95 38 0.47
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (95 bp):
AGGTAGTATTGATACCATAGTAAAGGGTATCGATACCTAGAAACATCGAACCTAATTTTGGTATC
AATACCCAAAGGAGTATCAGTACCATAGTA
Found at i:1384948 original size:55 final size:55
Alignment explanation
Indices: 1384878--1385142 Score: 370
Period size: 55 Copynumber: 4.8 Consensus size: 55
1384868 CTATGTGTAC
* *
1384878 TACAGGCACTCTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACATGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* *
1384933 TACAGGCACTTTGTGTGCATATTCACGGAATTTATCATGAGTTGATGAATCACCG
1 TACATGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * *
1384988 TGCATGCACTTTGTGTACATATTCACGGAATTCATCATGAGTTGATGAGTCACCG
1 TACATGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* **
1385043 TACATGCACTTTGTTTGCATATTCACATAATTCATCATGAGTTGATGAATCACCG
1 TACATGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * * ** * *
1385098 TACATGAAATATGTGTGCA-ACCCACGAAATTCATCATGGGTTGAT
1 TACATGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGAT
1385143 TAATTCTCGT
Statistics
Matches: 188, Mismatches: 22, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
54 21 0.11
55 167 0.89
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (55 bp):
TACATGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
Found at i:1398706 original size:29 final size:30
Alignment explanation
Indices: 1398673--1398729 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1398663 CAAGAAAATC
*
1398673 AGATTCTACC-TTTTCTACAAACCTTTTTT
1 AGATTCGACCTTTTTCTACAAACCTTTTTT
1398702 AGATTCGACCTTTTTCTACAAACCTTTT
1 AGATTCGACCTTTTTCTACAAACCTTTT
1398730 CAAAATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.46
Consensus pattern (30 bp):
AGATTCGACCTTTTTCTACAAACCTTTTTT
Found at i:1406371 original size:16 final size:16
Alignment explanation
Indices: 1406346--1406388 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1406336 AACGTCTTTT
1406346 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
1406362 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
1406379 ACAAAAATTT
1 AAAAAAATTT
1406389 GGTCTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:1408702 original size:3 final size:3
Alignment explanation
Indices: 1408694--1408749 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
1408684 TATGTAAAAT
* *
1408694 TAA TAA TAA TAGT TAA TAA TAA TAA -AA TAA TAA -AA AAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1408738 AAA TAA AAA TAA
1 TAA TAA TAA TAA
1408750 ATAAAAAAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:1408709 original size:13 final size:13
Alignment explanation
Indices: 1408693--1408717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1408683 ATATGTAAAA
1408693 TTAATAATAATAG
1 TTAATAATAATAG
1408706 TTAATAATAATA
1 TTAATAATAATA
1408718 AAATAATAAA
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
TTAATAATAATAG
Found at i:1408733 original size:19 final size:18
Alignment explanation
Indices: 1408711--1408757 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1408701 AATAGTTAAT
1408711 AATAATAAAATAATAAAAA
1 AATAATAAAATAA-AAAAA
*
1408730 AATAATAAAAATAAAAATA
1 AATAAT-AAAATAAAAAAA
1408749 AATAA-AAAA
1 AATAATAAAA
1408758 GACCCGGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.15
19 15 0.58
20 7 0.27
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
AATAATAAAATAAAAAAA
Found at i:1408757 original size:11 final size:12
Alignment explanation
Indices: 1408708--1408755 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
1408698 AATAATAGTT
1408708 AATAAT-AATAA
1 AATAATAAATAA
1408719 AATAATAAA-AA
1 AATAATAAATAA
1408730 AATAATAAA-AA
1 AATAATAAATAA
*
1408741 TAAAAATAAATAA
1 -AATAATAAATAA
1408754 AA
1 AA
1408756 AAGACCCGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
11 19 0.58
12 12 0.36
13 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AATAATAAATAA
Found at i:1419933 original size:20 final size:21
Alignment explanation
Indices: 1419900--1419938 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1419890 TCAAATTCAC
1419900 TTTTTAAAAGACTTTGAATTA
1 TTTTTAAAAGACTTTGAATTA
*
1419921 TTTTTGAAA-ACTTTGAAT
1 TTTTTAAAAGACTTTGAAT
1419939 AAATTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (21 bp):
TTTTTAAAAGACTTTGAATTA
Found at i:1421705 original size:18 final size:18
Alignment explanation
Indices: 1421682--1421717 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1421672 TCGTTTTTTT
*
1421682 TAAAAGATAAGAATTAAA
1 TAAAAGAAAAGAATTAAA
*
1421700 TAAAAGAAAATAATTAAA
1 TAAAAGAAAAGAATTAAA
1421718 CAAATAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (18 bp):
TAAAAGAAAAGAATTAAA
Found at i:1422164 original size:16 final size:16
Alignment explanation
Indices: 1422143--1422175 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1422133 ACAAGCTCAT
1422143 TTTGATTTGAAAACGA
1 TTTGATTTGAAAACGA
*
1422159 TTTGATTTTAAAACGA
1 TTTGATTTGAAAACGA
1422175 T
1 T
1422176 AGGTCAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (16 bp):
TTTGATTTGAAAACGA
Found at i:1422372 original size:20 final size:20
Alignment explanation
Indices: 1422349--1422386 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1422339 AAATAAAAAT
1422349 AAAAC-AAAGAAAAACTTTGA
1 AAAACAAAAG-AAAACTTTGA
*
1422369 AAAAGAAAAGAAAACTTT
1 AAAACAAAAGAAAACTTT
1422387 TATTAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.16
Consensus pattern (20 bp):
AAAACAAAAGAAAACTTTGA
Found at i:1425149 original size:24 final size:23
Alignment explanation
Indices: 1425105--1425149 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
1425095 AAAACGAAAC
*
1425105 ATAAAAAAATAAAAGTGAAATGT
1 ATAAAAAAATAAAAATGAAATGT
* *
1425128 ATAAAAATAGTAAAAATTAAAT
1 ATAAAAA-AATAAAAATGAAAT
1425150 ACACTAGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (23 bp):
ATAAAAAAATAAAAATGAAATGT
Found at i:1427219 original size:98 final size:96
Alignment explanation
Indices: 1427106--1427292 Score: 277
Period size: 98 Copynumber: 1.9 Consensus size: 96
1427096 CCCCTCCCCC
*
1427106 CTCTCTCTCTCTTACAGTTCGTTAGTAATTTAGGGAGGCCTCCTCGCCCACATAGAGTACCCCGA
1 CTCTCTCTCTCTTACAGTTCGTTAGTAATTTAAGGAGGCCTCCTCGCCCACATAGAGTA-CCCGA
1427171 AAAA-ATATTTTCACGTGTAGAGTATCCCTCTCT
65 AAAATAT-TTTTC-CGTGTAGAGTATCCCTCTCT
* * * * * *
1427204 CTCTCTTTCTCTTACAGTTCGTTAGTAATTTAAGGAGGCTTCCTTGCCCATATATAGTAGCCGAA
1 CTCTCTCTCTCTTACAGTTCGTTAGTAATTTAAGGAGGCCTCCTCGCCCACATAGAGTACCCGAA
1427269 AAATATTTTTCCGTGTAGAGTATC
66 AAATATTTTTCCGTGTAGAGTATC
1427293 ATTGTATTAT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 13 0.16
97 13 0.16
98 55 0.68
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.35
Consensus pattern (96 bp):
CTCTCTCTCTCTTACAGTTCGTTAGTAATTTAAGGAGGCCTCCTCGCCCACATAGAGTACCCGAA
AAATATTTTTCCGTGTAGAGTATCCCTCTCT
Found at i:1428540 original size:8 final size:8
Alignment explanation
Indices: 1428527--1428551 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1428517 TTTTAATCTC
1428527 ACTTTCTA
1 ACTTTCTA
1428535 ACTTTCTA
1 ACTTTCTA
1428543 ACTTTCTA
1 ACTTTCTA
1428551 A
1 A
1428552 TTGAGGCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (8 bp):
ACTTTCTA
Found at i:1428543 original size:118 final size:117
Alignment explanation
Indices: 1428320--1428532 Score: 295
Period size: 118 Copynumber: 1.8 Consensus size: 117
1428310 CTTGTTTTCA
* * *
1428320 ATCAATTTTTTACTTTTATAATTGAGGCCTCTAATTTTGTAATCTCACTTTTAACTTTATAATTG
1 ATCAATTTTCTACCTTTATAATTGAAGCCTCTAATTTTGTAATCTCACTTTTAACTTTATAATTG
** *
1428385 AGGCTTTTAAGTTTTTTCAATTTCACTTTCAAAGCCTCTAAGTTTTTTCAAT
66 AGGCCCTTAAGTTTTTTCAATCTCACTTTCAAAGCCTCTAAGTTTTTTCAAT
* * *
1428437 ATCAA-TTTCTACCTTTATAATTGAAG-CTCATAATTTTTTTAATCTCTCTTTTTAATTTTATAA
1 ATCAATTTTCTACCTTTATAATTGAAGCCTC-TAA-TTTTGTAATCTCAC-TTTTAACTTTATAA
*
1428500 TTGAGGCCCTTAAGTTTTTTTAATCTCACTTTC
63 TTGAGGCCCTTAAGTTTTTTCAATCTCACTTTC
1428533 TAACTTTCTA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
115 3 0.04
116 21 0.25
117 17 0.20
118 42 0.51
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (117 bp):
ATCAATTTTCTACCTTTATAATTGAAGCCTCTAATTTTGTAATCTCACTTTTAACTTTATAATTG
AGGCCCTTAAGTTTTTTCAATCTCACTTTCAAAGCCTCTAAGTTTTTTCAAT
Found at i:1428615 original size:43 final size:45
Alignment explanation
Indices: 1428568--1428664 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 45
1428558 CCCCTAAGAA
* *
1428568 TTTTCGATATCAA-TTATACCTTTATAATTGAGG-CTC-ATATTTT
1 TTTTCAATATCAATTTATACCTTTATAATTAAGGCCTCTA-ATTTT
* *
1428611 TTTTCAATCTCAATTTCTACCTTTATAATTAAGGCCTCTAATTTT
1 TTTTCAATATCAATTTATACCTTTATAATTAAGGCCTCTAATTTT
1428656 TTTTACAAT
1 TTTT-CAAT
1428665 TTTATAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
43 11 0.24
44 18 0.39
45 12 0.26
46 5 0.11
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.49
Consensus pattern (45 bp):
TTTTCAATATCAATTTATACCTTTATAATTAAGGCCTCTAATTTT
Found at i:1429342 original size:16 final size:16
Alignment explanation
Indices: 1429321--1429361 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
1429311 TTTTATATCA
1429321 CAAGTCATATTCAAAG
1 CAAGTCATATTCAAAG
1429337 CAAGTCATATTCAAAG
1 CAAGTCATATTCAAAG
1429353 CAAGTCATA
1 CAAGTCATA
1429362 ACATATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (16 bp):
CAAGTCATATTCAAAG
Found at i:1432541 original size:22 final size:21
Alignment explanation
Indices: 1432516--1432571 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
1432506 ATTATATTTA
1432516 TTTATATAATATATAGTCTTTT
1 TTTATATAATATATAGT-TTTT
* *
1432538 TTTA-AAACATGTATAGTTTTT
1 TTTATATA-ATATATAGTTTTT
*
1432559 TTAATAT-ATATAT
1 TTTATATAATATAT
1432572 TTAGTATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
20 5 0.19
21 9 0.33
22 13 0.48
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTATATAATATATAGTTTTT
Found at i:1432579 original size:13 final size:14
Alignment explanation
Indices: 1432558--1432598 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1432548 GTATAGTTTT
1432558 TTTAATATA-TATA
1 TTTAATATATTATA
*
1432571 TTTAGTATATTATA
1 TTTAATATATTATA
*
1432585 TTGAA-ATATTATA
1 TTTAATATATTATA
1432598 T
1 T
1432599 ATATATAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 17 0.71
14 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
TTTAATATATTATA
Done.