Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 54 of 89
Found at i:12303962 original size:36 final size:36
Alignment explanation
Indices: 12303921--12304008 Score: 88
Period size: 36 Copynumber: 2.5 Consensus size: 36
12303911 ATTATTTAAT
* ** *
12303921 TTAAATCATTAAAATTAAATAATTATTGTTAAATAG
1 TTAAATAATTAAAATTAAATAATTAAAGTTAAATAA
** * *
12303957 TTAAATAATTATTATTAAATCATTAAAGTTAAGTAA
1 TTAAATAATTAAAATTAAATAATTAAAGTTAAATAA
*
12303993 TT-AATTATTAAAATTA
1 TTAAATAATTAAAATTA
12304009 TAAAGTTAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
35 11 0.27
36 30 0.73
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (36 bp):
TTAAATAATTAAAATTAAATAATTAAAGTTAAATAA
Found at i:12303973 original size:64 final size:64
Alignment explanation
Indices: 12303891--12304153 Score: 255
Period size: 64 Copynumber: 4.0 Consensus size: 64
12303881 AAATCATTAA
* * * *
12303891 AGTTAAGTAATGATTATTAAATTATTTAATTTAAATCATTAAAATTAAATAATTATTGTTAAAT
1 AGTTAAATAATTATTATTAAATCATTTAATTTAAATCATTAAAATTAAATAATTATTATTAAAT
* * *
12303955 AGTTAAATAATTATTATTAAATCATTAAAGTTAAGTAATTAATTATTAAAATTATAA-AGTTAAA
1 AGTTAAATAATTATTATTAAATCATTTAA-TT---T-A--AATCATTAAAATTA-AATAATT--A
*
12304019 TCATT-AA-
56 TTATTAAAT
* * * * *
12304026 AGTTAAGTAATGATTATTAAATTATTTAATTTAAATCATTAAAGTTAAATAATTATTATGAAAT
1 AGTTAAATAATTATTATTAAATCATTTAATTTAAATCATTAAAATTAAATAATTATTATTAAAT
* * *
12304090 AGTTAAACAATTATTATTAAATCA-TTAATGTTAAATCATTAAAGTTAAGTAATTATTATTAAAT
1 AGTTAAATAATTATTATTAAATCATTTAAT-TTAAATCATTAAAATTAAATAATTATTATTAAAT
12304154 CATTAAAGTT
Statistics
Matches: 162, Mismatches: 23, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
62 4 0.02
63 9 0.06
64 92 0.57
65 2 0.01
66 1 0.01
67 1 0.01
68 1 0.01
69 1 0.01
70 2 0.01
71 41 0.25
72 4 0.02
73 4 0.02
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (64 bp):
AGTTAAATAATTATTATTAAATCATTTAATTTAAATCATTAAAATTAAATAATTATTATTAAAT
Found at i:12304117 original size:22 final size:22
Alignment explanation
Indices: 12304068--12304111 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12304058 AAATCATTAA
*
12304068 AGTTAAATAATTATTATGAAAT
1 AGTTAAACAATTATTATGAAAT
*
12304090 AGTTAAACAATTATTATTAAAT
1 AGTTAAACAATTATTATGAAAT
12304112 CATTAATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (22 bp):
AGTTAAACAATTATTATGAAAT
Found at i:12304136 original size:42 final size:41
Alignment explanation
Indices: 12304090--12304277 Score: 236
Period size: 42 Copynumber: 4.5 Consensus size: 41
12304080 ATTATGAAAT
* *
12304090 AGTTAAACAATTATTATTAAATCATTAATGTTAAATCATTAA
1 AGTTAAATAATAATTATTAAATCATTAAT-TTAAATCATTAA
* * *
12304132 AGTTAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAA
1 AGTTAAATAATAATTATTAAATCATT-AATTTAAATCATTAA
* * *
12304174 AGTTAAGTAATGATTATTAAATTATTTAATTTAAATCATTAA
1 AGTTAAATAATAATTATTAAATCA-TTAATTTAAATCATTAA
*
12304216 AGTT-AATAATAATTATTAAAT-TTTAAATTTAAATCATTAA
1 AGTTAAATAATAATTATTAAATCATT-AATTTAAATCATTAA
*
12304256 ATTTAAATAATAATTATTAAAT
1 AGTTAAATAATAATTATTAAAT
12304278 ATGTACTTTT
Statistics
Matches: 132, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
39 2 0.02
40 18 0.14
41 32 0.24
42 76 0.58
43 4 0.03
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (41 bp):
AGTTAAATAATAATTATTAAATCATTAATTTAAATCATTAA
Found at i:12304142 original size:106 final size:107
Alignment explanation
Indices: 12303991--12304195 Score: 306
Period size: 106 Copynumber: 1.9 Consensus size: 107
12303981 AAAGTTAAGT
* * * *
12303991 AATTAATTATTAAAATTATAAAGTTAAATCATTAAAGTTAAGTAATGATTATTAAATTATTTAAT
1 AATTAATTATTAAAATCATAAAGTTAAATCATTAAAGTTAAGTAATGATTATTAAATCATTAAAG
*
12304056 TTAAATCATTAAAGTTAAATAATTATTATGAAATAGTTAAAC
66 TTAAATCATTAAAGTTAAATAATGATTATGAAATAGTTAAAC
* *
12304098 AATT-ATTATT-AAATCATTAATGTTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAA
1 AATTAATTATTAAAATCA-TAAAGTTAAATCATTAAAGTTAAGTAATGATTATTAAATCATTAAA
* *
12304161 GTTAAATCATTAAAGTTAAGTAATGATTATTAAAT
65 GTTAAATCATTAAAGTTAAATAATGATTATGAAAT
12304196 TATTTAATTT
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
105 5 0.06
106 79 0.90
107 4 0.05
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (107 bp):
AATTAATTATTAAAATCATAAAGTTAAATCATTAAAGTTAAGTAATGATTATTAAATCATTAAAG
TTAAATCATTAAAGTTAAATAATGATTATGAAATAGTTAAAC
Found at i:12304275 original size:14 final size:13
Alignment explanation
Indices: 12304201--12304278 Score: 50
Period size: 14 Copynumber: 5.8 Consensus size: 13
12304191 TAAATTATTT
*
12304201 AATTTAAATCATTA
1 AATTTAAAT-AATA
*
12304215 AAGTT-AATAATA
1 AATTTAAATAATA
* **
12304227 ATTATTAAATTTTA
1 AAT-TTAAATAATA
*
12304241 AATTTAAATCATTA
1 AATTTAAAT-AATA
12304255 AATTTAAATAATA
1 AATTTAAATAATA
*
12304268 ATTATTAAATA
1 AAT-TTAAATA
12304279 TGTACTTTTG
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
12 4 0.08
13 16 0.32
14 30 0.60
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (13 bp):
AATTTAAATAATA
Found at i:12306934 original size:14 final size:14
Alignment explanation
Indices: 12306917--12307375 Score: 104
Period size: 14 Copynumber: 33.4 Consensus size: 14
12306907 AATCATTATT
12306917 ATTTAAATTTAATG
1 ATTTAAATTTAATG
*
12306931 ATTTAAATTTAA-A
1 ATTTAAATTTAATG
* *
12306944 ATTTTAATAATT-ATT
1 A-TTTAA-ATTTAATG
*
12306959 ATTTAACTTTAATG
1 ATTTAAATTTAATG
* *
12306973 ATTTAAATTAAATA
1 ATTTAAATTTAATG
* * *
12306987 ATTT-AATAATCATT
1 ATTTAAAT-TTAATG
* *
12307001 ACTTAACTTTAATG
1 ATTTAAATTTAATG
*
12307015 ATTTAACTTTAATG
1 ATTTAAATTTAATG
* *
12307029 ATTT-AATAATAATT
1 ATTTAAAT-TTAATG
* *
12307043 ACTTAACTTTAATG
1 ATTTAAATTTAATG
12307057 ATTTAACA-TTAATG
1 ATTTAA-ATTTAATG
12307071 ATTT-AA--TAAT-
1 ATTTAAATTTAATG
* *
12307081 AATT--GTTTAACT-
1 ATTTAAATTTAA-TG
*
12307093 ATTTCATAA--TAATT
1 ATTT-A-AATTTAATG
*
12307107 ATTTAACTTTAATG
1 ATTTAAATTTAATG
* * *
12307121 ATTTGAATTAAATA
1 ATTTAAATTTAATG
* * *
12307135 ATTT-AATAATCATT
1 ATTTAAAT-TTAATG
* *
12307149 ACTTAACTTTAATG
1 ATTTAAATTTAATG
* *
12307163 ATTTAACTTTAATA
1 ATTTAAATTTAATG
* *
12307177 ATTT-AATAATAATT
1 ATTTAAAT-TTAATG
* *
12307191 ACTTAACTTTAATG
1 ATTTAAATTTAATG
12307205 A-TT--ATTTAACT-
1 ATTTAAATTTAA-TG
* *
12307216 ATTT-AATAATAATT
1 ATTTAAAT-TTAATG
*
12307230 ATTTAACTTTAATG
1 ATTTAAATTTAATG
* *
12307244 ATTTAAATTAAATA
1 ATTTAAATTTAATG
* * *
12307258 ATTT-AATAATCATT
1 ATTTAAAT-TTAATG
* *
12307272 ACTTAACTTTAATG
1 ATTTAAATTTAATG
* *
12307286 ATTCCATAA--TAATT
1 ATT-TA-AATTTAATG
* *
12307300 ACTTAACTTTAATG
1 ATTTAAATTTAATG
* *
12307314 ATTTAACTTTAATA
1 ATTTAAATTTAATG
* *
12307328 ATTT-AATAATAATT
1 ATTTAAAT-TTAATG
*
12307342 ATTTAACTTTAATG
1 ATTTAAATTTAATG
* *
12307356 ATTTAACTTTAATA
1 ATTTAAATTTAATG
12307370 ATTTAA
1 ATTTAA
12307376 TAATAGTAAA
Statistics
Matches: 318, Mismatches: 90, Indels: 74
0.66 0.19 0.15
Matches are distributed among these distances:
10 3 0.01
11 13 0.04
12 10 0.03
13 27 0.08
14 245 0.77
15 19 0.06
16 1 0.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (14 bp):
ATTTAAATTTAATG
Found at i:12307081 original size:42 final size:42
Alignment explanation
Indices: 12306903--12307380 Score: 366
Period size: 42 Copynumber: 11.3 Consensus size: 42
12306893 TCGAGTACAT
* * * * *
12306903 ATTTAATCATTATTATTTAAATTTAATGATTTAAATTTAA-A
1 ATTTAATAATAATTATTTAACTTTAATGATTTAACTTTAATG
* * * *
12306944 ATTTTAATAATTATTATTTAACTTTAATGATTTAAATTAAATA
1 A-TTTAATAATAATTATTTAACTTTAATGATTTAACTTTAATG
* *
12306987 ATTTAATAATCATTACTTAACTTTAATGATTTAACTTTAATG
1 ATTTAATAATAATTATTTAACTTTAATGATTTAACTTTAATG
* *
12307029 ATTTAATAATAATTACTTAACTTTAATGATTTAACATTAATG
1 ATTTAATAATAATTATTTAACTTTAATGATTTAACTTTAATG
* *
12307071 ATTTAATAATAATTGTTTAACTATTTCATAATAATTATTTAACTTTAATG
1 ATTTAATAATAATTATTTAAC----T--T--TAATGATTTAACTTTAATG
* * * * * *
12307121 ATTTGAATTA-AATAATTTAA-TAATCATTACTTAACTTTAATG
1 ATTT-AATAATAATTATTTAACT-TTAATGATTTAACTTTAATG
* * * * *
12307163 ATTTAACT-TTAATAATTTAA-TAATAATTACTTAACTTTAATG
1 ATTTAA-TAATAATTATTTAACT-TTAATGATTTAACTTTAATG
* * * *
12307205 A-TT-AT-TTAACTATTTAA-TAATAATTATTTAACTTTAATG
1 ATTTAATAATAATTATTTAACT-TTAATGATTTAACTTTAATG
* * * * * *
12307244 ATTTAA-ATTAAATAATTTAA-TAATCATTACTTAACTTTAATG
1 ATTTAATAAT-AATTATTTAACT-TTAATGATTTAACTTTAATG
** * *
12307286 ATTCCATAATAATTACTTAACTTTAATGATTTAACTTTAATA
1 ATTTAATAATAATTATTTAACTTTAATGATTTAACTTTAATG
*
12307328 ATTTAATAATAATTATTTAACTTTAATGATTTAACTTTAATA
1 ATTTAATAATAATTATTTAACTTTAATGATTTAACTTTAATG
12307370 ATTTAATAATA
1 ATTTAATAATA
12307381 GTAAAGATAT
Statistics
Matches: 376, Mismatches: 42, Indels: 37
0.83 0.09 0.08
Matches are distributed among these distances:
39 33 0.09
40 3 0.01
41 8 0.02
42 290 0.77
43 5 0.01
44 1 0.00
45 1 0.00
46 1 0.00
48 1 0.00
50 29 0.08
51 4 0.01
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (42 bp):
ATTTAATAATAATTATTTAACTTTAATGATTTAACTTTAATG
Found at i:12307123 original size:106 final size:106
Alignment explanation
Indices: 12306987--12307190 Score: 320
Period size: 106 Copynumber: 1.9 Consensus size: 106
12306977 AAATTAAATA
* * *
12306987 ATTTAATAATCATTACTTAACTTTAATGATTT-AACTTTAATGATTTAATAATAATTACTTAACT
1 ATTTAATAATAATTACTTAACTTTAATGATTTGAA-TTAAATAATTTAATAATAATTACTTAACT
*
12307051 TTAATGATTTAACATTAATGATTTAATAATAATTGTTTAACT
65 TTAATGATTTAACATTAATAATTTAATAATAATTGTTTAACT
* * *
12307093 ATTTCATAATAATTATTTAACTTTAATGATTTGAATTAAATAATTTAATAATCATTACTTAACTT
1 ATTTAATAATAATTACTTAACTTTAATGATTTGAATTAAATAATTTAATAATAATTACTTAACTT
*
12307158 TAATGATTTAACTTTAATAATTTAATAATAATT
66 TAATGATTTAACATTAATAATTTAATAATAATT
12307191 ACTTAACTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
106 87 0.98
107 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.48
Consensus pattern (106 bp):
ATTTAATAATAATTACTTAACTTTAATGATTTGAATTAAATAATTTAATAATAATTACTTAACTT
TAATGATTTAACATTAATAATTTAATAATAATTGTTTAACT
Found at i:12307221 original size:25 final size:22
Alignment explanation
Indices: 12307071--12307237 Score: 101
Period size: 22 Copynumber: 8.0 Consensus size: 22
12307061 AACATTAATG
*
12307071 ATTTAATAATAATTGTTTAACT
1 ATTTAATAATAATTATTTAACT
*
12307093 ATTTCATAATAATTATTTAAC-
1 ATTTAATAATAATTATTTAACT
* * *
12307114 -TTTAATGAT--TTGAATTAAAT
1 ATTTAATAATAATT-ATTTAACT
* *
12307134 AATTTAATAATCATTACTTAAC-
1 -ATTTAATAATAATTATTTAACT
*
12307156 -TTTAATGAT--TTAACTTTAA-T
1 ATTTAATAATAATT-A-TTTAACT
*
12307176 AATTTAATAATAATTACTTAAC-
1 -ATTTAATAATAATTATTTAACT
*
12307198 --TT--TAATGATTATTTAACT
1 ATTTAATAATAATTATTTAACT
12307216 ATTTAATAATAATTATTTAACT
1 ATTTAATAATAATTATTTAACT
12307238 TTAATGATTT
Statistics
Matches: 110, Mismatches: 16, Indels: 38
0.67 0.10 0.23
Matches are distributed among these distances:
17 13 0.12
18 4 0.04
19 8 0.07
20 21 0.19
22 54 0.49
23 6 0.05
24 4 0.04
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.49
Consensus pattern (22 bp):
ATTTAATAATAATTATTTAACT
Found at i:12307243 original size:81 final size:83
Alignment explanation
Indices: 12307093--12307288 Score: 288
Period size: 81 Copynumber: 2.4 Consensus size: 83
12307083 TTGTTTAACT
* * *
12307093 ATTTCATAATAATTATTTAACTTTAATGATTTGAATTAAATAATTTAATAATCATTACTTAACTT
1 ATTTAATAATAATTACTTAACTTTAATGA-TTGAATTAAATAATTTAATAATAATTACTTAACTT
* *
12307158 TAATGATTTAACTTTAATA
65 TAATGATTTAAATTAAATA
* * *
12307177 ATTTAATAATAATTACTTAACTTTAATGATT-ATTTAACT-ATTTAATAATAATTATTTAACTTT
1 ATTTAATAATAATTACTTAACTTTAATGATTGAATTAAATAATTTAATAATAATTACTTAACTTT
12307240 AATGATTTAAATTAAATA
66 AATGATTTAAATTAAATA
*
12307258 ATTTAATAATCATTACTTAACTTTAATGATT
1 ATTTAATAATAATTACTTAACTTTAATGATT
12307289 CCATAATAAT
Statistics
Matches: 103, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
81 68 0.66
82 6 0.06
83 2 0.02
84 27 0.26
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (83 bp):
ATTTAATAATAATTACTTAACTTTAATGATTGAATTAAATAATTTAATAATAATTACTTAACTTT
AATGATTTAAATTAAATA
Found at i:12307306 original size:70 final size:70
Alignment explanation
Indices: 12307221--12307358 Score: 231
Period size: 70 Copynumber: 2.0 Consensus size: 70
12307211 TAACTATTTA
* *
12307221 ATAATAATTATTTAACTTTAATGATTTAAATTAAATAATTTAATAATCATTACTTAACTTTAATG
1 ATAATAATTACTTAACTTTAATGATTTAAATTAAATAATTTAATAATAATTACTTAACTTTAATG
12307286 ATTCC
66 ATTCC
* * *
12307291 ATAATAATTACTTAACTTTAATGATTTAACTTTAATAATTTAATAATAATTATTTAACTTTAATG
1 ATAATAATTACTTAACTTTAATGATTTAAATTAAATAATTTAATAATAATTACTTAACTTTAATG
12307356 ATT
66 ATT
12307359 TAACTTTAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (70 bp):
ATAATAATTACTTAACTTTAATGATTTAAATTAAATAATTTAATAATAATTACTTAACTTTAATG
ATTCC
Found at i:12307326 original size:28 final size:27
Alignment explanation
Indices: 12306914--12307376 Score: 191
Period size: 28 Copynumber: 16.9 Consensus size: 27
12306904 TTTAATCATT
*
12306914 ATTATTTAAATTTAATGATTTAAATTTA
1 ATTATTTAACTTTAATGATTT-AATTTA
* *
12306942 A-AATTTTAA-TAATT-ATTATTTAACTTTA
1 ATTA-TTTAACT--TTAATGATTTAA-TTTA
* * * * * *
12306970 ATGATTTAAATTAAATAATTTAATAATC
1 ATTATTTAACTTTAATGATTTAAT-TTA
*
12306998 ATTACTTAACTTTAATGATTTAACTTTA
1 ATTATTTAACTTTAATGATTTAA-TTTA
* * * *
12307026 ATGATTTAA-TAATAATTACTTAACTTTA
1 ATTATTTAACT-TTAATGATTTAA-TTTA
* * *
12307054 ATGATTTAACATTAATGATTTAATAATA
1 ATTATTTAACTTTAATGATTTAAT-TTA
* *
12307082 ATTGTTTAACTATT--TCA--TAA--TA
1 ATTATTTAACT-TTAATGATTTAATTTA
*
12307104 ATTATTTAACTTTAATGATTTGAATTAA
1 ATTATTTAACTTTAATGATTT-AATTTA
* * * * *
12307132 ATAATTTAA-TAATCATTACTTAACTTTA
1 ATTATTTAACT-TTAATGATTTAA-TTTA
* * *
12307160 ATGATTTAACTTTAATAATTTAATAATA
1 ATTATTTAACTTTAATGATTTAAT-TTA
*
12307188 ATTACTTAACTTTAATGA-TT-ATTTA
1 ATTATTTAACTTTAATGATTTAATTTA
* * *
12307213 ACTATTTAA-TAATAATTATTTAACTTTA
1 ATTATTTAACT-TTAATGATTTAA-TTTA
* * * * * *
12307241 ATGATTTAAATTAAATAATTTAATAATC
1 ATTATTTAACTTTAATGATTTAAT-TTA
* ** *
12307269 ATTACTTAACTTTAATGATTCCATAATA
1 ATTATTTAACTTTAATGATTTAAT-TTA
*
12307297 ATTACTTAACTTTAATGATTTAACTTTA
1 ATTATTTAACTTTAATGATTTAA-TTTA
* * *
12307325 ATAATTTAA-TAATAATTATTTAACTTTA
1 ATTATTTAACT-TTAATGATTTAA-TTTA
* *
12307353 ATGATTTAACTTTAATAATTTAAT
1 ATTATTTAACTTTAATGATTTAAT
12307377 AATAGTAAAG
Statistics
Matches: 326, Mismatches: 76, Indels: 67
0.70 0.16 0.14
Matches are distributed among these distances:
21 2 0.01
22 12 0.04
23 2 0.01
24 1 0.00
25 18 0.06
26 6 0.02
27 20 0.06
28 254 0.78
29 11 0.03
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (27 bp):
ATTATTTAACTTTAATGATTTAATTTA
Found at i:12309437 original size:13 final size:13
Alignment explanation
Indices: 12309419--12309443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12309409 AAAAATAAAA
12309419 ATAAACTTCAAAG
1 ATAAACTTCAAAG
12309432 ATAAACTTCAAA
1 ATAAACTTCAAA
12309444 TAATTAACTA
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:0.16, G:0.04, T:0.24
Consensus pattern (13 bp):
ATAAACTTCAAAG
Found at i:12309727 original size:13 final size:13
Alignment explanation
Indices: 12309709--12309734 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12309699 GTAATGTAAT
12309709 AACATATAATCAC
1 AACATATAATCAC
12309722 AACATATAATCAC
1 AACATATAATCAC
12309735 TAAACCTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
AACATATAATCAC
Found at i:12310142 original size:20 final size:20
Alignment explanation
Indices: 12310117--12310160 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
12310107 ATCTTTATCA
* *
12310117 GCTCACCCCATGAATTCCCT
1 GCTCACCACATGAATACCCT
*
12310137 GCTCACCACGTGAATACCCT
1 GCTCACCACATGAATACCCT
12310157 GCTC
1 GCTC
12310161 CAGCCCTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.43, G:0.14, T:0.23
Consensus pattern (20 bp):
GCTCACCACATGAATACCCT
Found at i:12311980 original size:4 final size:4
Alignment explanation
Indices: 12311946--12312053 Score: 51
Period size: 4 Copynumber: 25.8 Consensus size: 4
12311936 GATAATAATA
** * * *
12311946 AAAT AAAT AGAAT GGAT AAAT AGAG AAAT AAAT AAAT AAAT AAACA AAAT
1 AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT
* * *
12311996 AAACA AAAT AAA- AAAC AAA- ACA- AAAT GAAAT GAAAT AAAAT AAAAT
1 AAA-T AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT -AAAT -AAAT
12312042 AAAAT AAAT AAA
1 -AAAT AAAT AAA
12312054 AACCTAAATA
Statistics
Matches: 83, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
3 7 0.08
4 44 0.53
5 32 0.39
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:12312026 original size:5 final size:5
Alignment explanation
Indices: 12311971--12312054 Score: 54
Period size: 5 Copynumber: 17.6 Consensus size: 5
12311961 ATAAATAGAG
* * * *
12311971 AAAT- AAAT- AAAT- AAAT- AAACA AAATA AACA-A AATAAA AAACA AAACA
1 AAATA AAATA AAATA AAATA AAATA AAATA AA-ATA AA-ATA AAATA AAATA
* *
12312018 AAATG AAATG AAATA AAATA AAATA AAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
12312055 ACCTAAATAT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
4 19 0.28
5 46 0.67
6 4 0.06
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:12312054 original size:9 final size:9
Alignment explanation
Indices: 12311971--12312054 Score: 63
Period size: 9 Copynumber: 9.3 Consensus size: 9
12311961 ATAAATAGAG
12311971 AAATAAAT-
1 AAATAAATA
12311979 AAATAAATA
1 AAATAAATA
12311988 AACA-AAATA
1 AA-ATAAATA
12311997 AACA-AAATA
1 AA-ATAAATA
12312006 AAA-AACA-A
1 AAATAA-ATA
*
12312014 AACA-AAATG
1 AA-ATAAATA
12312023 AAATGAAATA
1 AAAT-AAATA
12312033 AAATAAAATA
1 AAAT-AAATA
12312043 AAATAAATA
1 AAATAAATA
12312052 AAA
1 AAA
12312055 ACCTAAATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
8 16 0.24
9 32 0.48
10 18 0.27
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.15
Consensus pattern (9 bp):
AAATAAATA
Found at i:12313187 original size:3 final size:3
Alignment explanation
Indices: 12313158--12313206 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
12313148 CAAAAATCTG
* *
12313158 TAA TAA -AA TAAA TAA AAA TAT TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
12313204 TAA
1 TAA
12313207 ATATTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.79
4 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:12313198 original size:13 final size:13
Alignment explanation
Indices: 12313158--12313209 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
12313148 CAAAAATCTG
12313158 TAATAA-AATAAA
1 TAATAATAATAAA
* *
12313170 TAAAAAT-ATTAA
1 TAATAATAATAAA
12313182 TAATAATAATAAA
1 TAATAATAATAAA
12313195 TAATAATAATAAA
1 TAATAATAATAAA
12313208 TA
1 TA
12313210 TTTTTTTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 15 0.44
13 19 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:12313624 original size:36 final size:36
Alignment explanation
Indices: 12313577--12314352 Score: 342
Period size: 36 Copynumber: 22.1 Consensus size: 36
12313567 TTTTTCAAGG
12313577 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGA
* *
12313613 GAAACTGTCTCAAGAGAGACAAAGACAAAATTCGTTTCAAGA
1 GAAACTGTCTC-A-AGAG----AGACAAAATTTGTTTAAAGA
* * *
12313655 GAAAATGTCTCAAGAGAGACAAAACTTAGTTCCAAA-A
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TAAAGA
*
12313692 GAAACTGTCTCAAG-GCAGACAAAATTTGTTTAATGTA
1 GAAACTGTCTCAAGAG-AGACAAAATTTGTTTAAAG-A
* * * *
12313729 -AAACATAT-TC-A-A-AG----ATTTTATTTCAAGA
1 GAAAC-TGTCTCAAGAGAGACAAAATTTGTTTAAAGA
* *
12313757 GAAACTGTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAGG
1 GAAACTGTCTC-A-AGAG----AGACAAAATTTGTTTAAAGA
* *
12313799 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA-A
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TAAAGA
* * * *
12313836 GAAACTGTCTTAAGGGAGACGAAATTTGTTTAATGTA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAG-A
* * * * *
12313873 -AAACATAT-TC-A-A-AG----ATTTTATTTCAAGG
1 GAAAC-TGTCTCAAGAGAGACAAAATTTGTTTAAAGA
* *
12313901 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA-A
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TAAAGA
* * * *
12313938 GAAACTGTCTTAAGGGAGACGAAATTTGTTTAATGTA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAG-A
* * * * *
12313975 -AAACATAT-TC-A-A-AG----ATTTTATTTCAAGG
1 GAAAC-TGTCTCAAGAGAGACAAAATTTGTTTAAAGA
* * *
12314003 GAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGA
* *
12314039 GAAACTGTC-CAAGAGAGTCAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGA
* * *
12314074 GAAACTGTCTTAAGAGAGTCAAAATTTGTTTAATGTA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAG-A
* * * * *
12314111 -AAACATAT-TC-A-A-AG----ATTTTATTTCAAGG
1 GAAAC-TGTCTCAAGAGAGACAAAATTTGTTTAAAGA
* *
12314139 GAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAG-
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGA
**
12314174 GAAAACTGTCTCAAGAGAGACAAAAAATGTTTAAAGA
1 G-AAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGA
* * *
12314211 GAAACTGTCTCAAGAGAGACAAAACATAGTTCCAAA-A
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TAAAGA
* * *
12314248 GAAACTGTCTCAAGGGAGACGAAATTTGTTTAATGTA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAG-A
* * * *
12314285 -AAACATAT-TC-A-A-AG----ATTTTGTTTTAAGG
1 GAAAC-TGTCTCAAGAGAGACAAAATTTGTTTAAAGA
*
12314313 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGA
12314349 GAAA
1 GAAA
12314353 TAATCTCAAA
Statistics
Matches: 554, Mismatches: 102, Indels: 168
0.67 0.12 0.20
Matches are distributed among these distances:
28 10 0.02
29 75 0.14
30 4 0.01
31 4 0.01
32 9 0.02
33 11 0.02
34 1 0.00
35 46 0.08
36 197 0.36
37 122 0.22
38 15 0.03
40 8 0.01
41 2 0.00
42 50 0.09
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.27
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGA
Found at i:12313644 original size:42 final size:42
Alignment explanation
Indices: 12313593--12313677 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
12313583 GTCTCAAGAG
* *
12313593 AGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGAGAGACAA
1 AGACAAAATTCGTTTAAAGAGAAAATGTCTCAAGAGAGACAA
*
12313635 AGACAAAATTCGTTTCAAGAGAAAATGTCTCAAGAGAGACAA
1 AGACAAAATTCGTTTAAAGAGAAAATGTCTCAAGAGAGACAA
12313677 A
1 A
12313678 ACTTAGTTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (42 bp):
AGACAAAATTCGTTTAAAGAGAAAATGTCTCAAGAGAGACAA
Found at i:12313777 original size:65 final size:66
Alignment explanation
Indices: 12313691--12313924 Score: 190
Period size: 65 Copynumber: 3.4 Consensus size: 66
12313681 TAGTTCCAAA
*
12313691 AGAAACTGTCTCAAG-GCAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAA
1 AGAAACTGTCTCAAGAGAAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAA
12313755 G
66 G
** *
12313756 AGAAACTGTCTCAAGAGAGACAAAGACAAAATTTGTTTCAA-GGGAAAC-TGTCTCAAGAGAGAC
1 AGAAACTGTCTC-A-AGAG---AAGACAAAATTTGTTT-AATGTAAAACATAT-TC-A-A-AG--
** * *
12313819 AAAACTTAGTTCCAAA
54 --ATTTTA-TTTCAAG
* * *
12313835 AGAAACTGTCTTAAG-GGAGACGAAATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAA
1 AGAAACTGTCTCAAGAGAAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAA
12313899 G
66 G
*
12313900 GGAAACTGTCTCAAGAG-AGACAAAA
1 AGAAACTGTCTCAAGAGAAGACAAAA
12313925 CTTAGTTCCA
Statistics
Matches: 129, Mismatches: 21, Indels: 38
0.69 0.11 0.20
Matches are distributed among these distances:
65 37 0.29
66 6 0.05
67 2 0.02
68 1 0.01
70 4 0.03
71 23 0.18
72 6 0.05
73 22 0.17
74 4 0.03
76 1 0.01
77 2 0.02
78 5 0.04
79 16 0.12
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (66 bp):
AGAAACTGTCTCAAGAGAAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAA
G
Found at i:12313785 original size:144 final size:144
Alignment explanation
Indices: 12313609--12313923 Score: 567
Period size: 144 Copynumber: 2.2 Consensus size: 144
12313599 AATTTGTTTA
12313609 AAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATTCGTTTCAAGAGAAAATGTCTCAAGAGAGA
1 AAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATTCGTTTCAAGAGAAAATGTCTCAAGAGAGA
12313674 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGCAGACAAAATTTGTTTAATGTAAAACATATTC
66 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGCAGACAAAATTTGTTTAATGTAAAACATATTC
12313739 AAAGATTTTATTTC
131 AAAGATTTTATTTC
* * *
12313753 AAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 AAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATTCGTTTCAAGAGAAAATGTCTCAAGAGAGA
* * *
12313818 CAAAACTTAGTTCCAAAAGAAACTGTCTTAAGGGAGACGAAATTTGTTTAATGTAAAACATATTC
66 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGCAGACAAAATTTGTTTAATGTAAAACATATTC
12313883 AAAGATTTTATTTC
131 AAAGATTTTATTTC
*
12313897 AAGGGAAACTGTCTCAAGAGAGACAAA
1 AAGAGAAACTGTCTCAAGAGAGACAAA
12313924 ACTTAGTTCC
Statistics
Matches: 164, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
144 164 1.00
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (144 bp):
AAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATTCGTTTCAAGAGAAAATGTCTCAAGAGAGA
CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGCAGACAAAATTTGTTTAATGTAAAACATATTC
AAAGATTTTATTTC
Found at i:12313840 original size:37 final size:39
Alignment explanation
Indices: 12313756--12313855 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 39
12313746 TTATTTCAAG
* * *
12313756 AGAAACTGTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAGAC---ATTAGTTCCAAA
*
12313798 GGAAACTGTCTCAAGAGAGACAAA-AC-TTAGTTCCAAA
1 AGAAACTGTCTCAAGAGAGACAAAGACATTAGTTCCAAA
* *
12313835 AGAAACTGTCTTAAGGGAGAC
1 AGAAACTGTCTCAAGAGAGAC
12313856 GAAATTTGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 26 0.51
41 2 0.04
42 23 0.45
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (39 bp):
AGAAACTGTCTCAAGAGAGACAAAGACATTAGTTCCAAA
Found at i:12313914 original size:102 final size:102
Alignment explanation
Indices: 12313791--12314026 Score: 463
Period size: 102 Copynumber: 2.3 Consensus size: 102
12313781 ACAAAATTTG
12313791 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTTAAGGGAGAC
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTTAAGGGAGAC
12313856 GAAATTTGTTTAATGTAAAACATATTCAAAGATTTTA
66 GAAATTTGTTTAATGTAAAACATATTCAAAGATTTTA
12313893 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTTAAGGGAGAC
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTTAAGGGAGAC
12313958 GAAATTTGTTTAATGTAAAACATATTCAAAGATTTTA
66 GAAATTTGTTTAATGTAAAACATATTCAAAGATTTTA
*
12313995 TTTCAAGGGAAACTGTCTTAAGAGAGACAAAA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
12314027 TTTGTTTCAA
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 133 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.28
Consensus pattern (102 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTTAAGGGAGAC
GAAATTTGTTTAATGTAAAACATATTCAAAGATTTTA
Found at i:12314158 original size:136 final size:137
Alignment explanation
Indices: 12313893--12314234 Score: 542
Period size: 136 Copynumber: 2.5 Consensus size: 137
12313883 AAAGATTTTA
* * * *
12313893 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTTAAGGGAGAC
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTTAAGAGAGAC
* * *
12313958 GAAATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAAGGGAAACTGTCTTAAGAGAGAC
65 AAAATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAAGGGAAACAGTCTCAAGAGAGAC
12314023 AAAATTTG
130 AAAATTTG
* *
12314031 TTTCAAGGGAAACTGTC-CAAGAGAGTCAAAATTTGTTTCAAGAGAAACTGTCTTAAGAGAGTCA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTTAAGAGAGACA
12314095 AAATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAAGGGAAACAGTCTCAAGAGAGACA
66 AAATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAAGGGAAACAGTCTCAAGAGAGACA
12314160 AAATTTG
131 AAATTTG
* ** * *
12314167 TTTCAAGGAAAACTGTCTCAAGAGAGACAAAAAATGTTTAAAGAGAAACTGTCTCAAGAGAGACA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTTAAGAGAGACA
12314232 AAA
66 AAA
12314235 CATAGTTCCA
Statistics
Matches: 187, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
136 113 0.60
137 57 0.30
138 17 0.09
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (137 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTTAAGAGAGACA
AAATTTGTTTAATGTAAAACATATTCAAAGATTTTATTTCAAGGGAAACAGTCTCAAGAGAGACA
AAATTTG
Found at i:12314296 original size:174 final size:172
Alignment explanation
Indices: 12313995--12314352 Score: 527
Period size: 174 Copynumber: 2.1 Consensus size: 172
12313985 AAAGATTTTA
* * ** * * *
12313995 TTTCAAGGGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCCAAGAGAGTCAA
1 TTTCAAGGAAAACTGTCTCAAGAGAGACAAAAAATGTTTAAAGAGAAACTGTCCAAGAGAGACAA
* * * * * *
12314060 AATTTGTTTCAAGAGAAACTGTCTTAAGAGAGTCAAAATTTGTTTAATGTAAAACATATTCAAAG
66 AAATAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAATGTAAAACATATTCAAAG
12314125 ATTTTATTTCAAGGGAAACAGTCTCAAGAGAGACAAAATTTG
131 ATTTTATTTCAAGGGAAACAGTCTCAAGAGAGACAAAATTTG
12314167 TTTCAAGGAAAACTGTCTCAAGAGAGACAAAAAATGTTTAAAGAGAAACTGTCTCAAGAGAGACA
1 TTTCAAGGAAAACTGTCTCAAGAGAGACAAAAAATGTTTAAAGAGAAACTGTC-CAAGAGAGACA
* *
12314232 AAACATAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTAATGTAAAACATATTCAA
65 AAA-ATAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAATGTAAAACATATTCAA
* * *
12314297 AGATTTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
129 AGATTTTATTTCAAGGGAAACAGTCTCAAGAGAGACAAAATTTG
12314341 TTTCAAGAGAAA
1 TTTCAAG-GAAA
12314353 TAATCTCAAA
Statistics
Matches: 165, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
172 47 0.28
173 13 0.08
174 101 0.61
175 4 0.02
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (172 bp):
TTTCAAGGAAAACTGTCTCAAGAGAGACAAAAAATGTTTAAAGAGAAACTGTCCAAGAGAGACAA
AAATAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAATGTAAAACATATTCAAAG
ATTTTATTTCAAGGGAAACAGTCTCAAGAGAGACAAAATTTG
Found at i:12314609 original size:124 final size:124
Alignment explanation
Indices: 12314389--12314629 Score: 356
Period size: 124 Copynumber: 1.9 Consensus size: 124
12314379 CTTGTTCCTG
* * * *
12314389 AAGATGAATGTTGCTGGTGGGTACGATTCCCTTCGTCGTGATGTTGAAACCGTGGATGGCCCCTT
1 AAGATGAATGATGCTGGTGGGCACGATTCCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCCTT
* * *
12314454 CGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCAAATCTA
66 CGTCGTGAAGTTGAGCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCAAATCTA
* * * * *
12314513 AAGATGAATGATGCTTGTGTGCATGATTCCCTTCGTCGTTAAGTTGAAACCATGGATGTCCCCTT
1 AAGATGAATGATGCTGGTGGGCACGATTCCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCCTT
* *
12314578 TGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCATCGTGAAGTTGAAATC
66 CGTCGTGAAGTTGAGCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATC
12314630 CAAGCTTGTA
Statistics
Matches: 103, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
124 103 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (124 bp):
AAGATGAATGATGCTGGTGGGCACGATTCCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCCTT
CGTCGTGAAGTTGAGCCTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCAAATCTA
Found at i:12314796 original size:44 final size:44
Alignment explanation
Indices: 12314733--12314846 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 44
12314723 CTTTGAATTG
* * *
12314733 GATATCGTTCGTCGTGAAGTTGAAATCCAAT-CTAGAGTTGACAC
1 GATATCCTTCGTTGTGAAGTTGAAATCC-ATGCTAGAGTGGACAC
* * * *
12314777 GATATCCTTCGTTGTGAAGTTGAAAT-CATGGTTGTGTGGGCAC
1 GATATCCTTCGTTGTGAAGTTGAAATCCATGCTAGAGTGGACAC
* *
12314820 GATATCCTTCGTTGTGGAGTTCAAATC
1 GATATCCTTCGTTGTGAAGTTGAAATC
12314847 GTGGATTCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 2 0.03
43 33 0.56
44 24 0.41
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (44 bp):
GATATCCTTCGTTGTGAAGTTGAAATCCATGCTAGAGTGGACAC
Found at i:12314832 original size:43 final size:43
Alignment explanation
Indices: 12314774--12314895 Score: 156
Period size: 43 Copynumber: 2.8 Consensus size: 43
12314764 CTAGAGTTGA
* * **
12314774 CACGATATCCTTCGTTGTGAAGTTGAAATCATGG-TTGTGTGGG
1 CACGATATCCTTCGTTGTGGAGTTAAAATCATGGATT-CATGGG
* *
12314817 CACGATATCCTTCGTTGTGGAGTTCAAATCGTGGATTCATGGG
1 CACGATATCCTTCGTTGTGGAGTTAAAATCATGGATTCATGGG
* *
12314860 TACGATATCCTTCGTCGTGGAGTTAAAATCATGGAT
1 CACGATATCCTTCGTTGTGGAGTTAAAATCATGGAT
12314896 GGCCCCTTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 67 0.97
44 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
CACGATATCCTTCGTTGTGGAGTTAAAATCATGGATTCATGGG
Found at i:12316511 original size:23 final size:21
Alignment explanation
Indices: 12316485--12316531 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
12316475 CTTTTGCTTT
*
12316485 TTTATTTTCTCTTTGCTTTTTTC
1 TTTATTTTCTCTCT--TTTTTTC
*
12316508 TTTATTTTTTCTCTTTTTTTC
1 TTTATTTTCTCTCTTTTTTTC
12316529 TTT
1 TTT
12316532 TTGTTCTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
23 12 0.55
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTATTTTCTCTCTTTTTTTC
Found at i:12318946 original size:64 final size:65
Alignment explanation
Indices: 12318810--12318970 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 65
12318800 ATTGTTCAGT
* * *
12318810 GTGTATCGATTCACAGGAAGTGCATCGATGCA-CCCATTAAAAATGGAAACATCGAATGCAGTTA
1 GTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAATGCAGTTA
* *
12318874 GTGCATCGATGCATAAGG-AGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTG-A-
1 GTGTATCGATGCAT-AGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAA--TGCAG
*
12318935 TTG
63 TTA
* * *
12318938 GTGTATCGATGCATGGGTAGTACATCGATGCAC
1 GTGTATCGATGCATAGGAAGTGCATCGATGCAC
12318971 ATGTTAAAGA
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 2 0.02
64 70 0.84
65 9 0.11
66 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (65 bp):
GTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAATGCAGTTA
Found at i:12318987 original size:24 final size:24
Alignment explanation
Indices: 12318960--12319038 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
12318950 ATGGGTAGTA
12318960 CATCGATGCACATGTTAAAGAATG
1 CATCGATGCACATGTTAAAGAATG
12318984 CATCGATGCACATGTTAAAGAATG
1 CATCGATGCACATGTTAAAGAATG
12319008 CATCGATGCAC-TG-T--AGAATG
1 CATCGATGCACATGTTAAAGAATG
*
12319028 TATCGATGCAC
1 CATCGATGCAC
12319039 TTCAAGAGGA
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
20 16 0.30
22 1 0.02
23 2 0.04
24 35 0.65
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (24 bp):
CATCGATGCACATGTTAAAGAATG
Found at i:12319349 original size:18 final size:16
Alignment explanation
Indices: 12319328--12319367 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
12319318 TGATTATACG
12319328 TATATGAATGACATGAAT
1 TATATGAATG-CATG-AT
*
12319346 TATATGTATGCATGAT
1 TATATGAATGCATGAT
12319362 TATATG
1 TATATG
12319368 TGTTAACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (16 bp):
TATATGAATGCATGAT
Found at i:12319365 original size:16 final size:18
Alignment explanation
Indices: 12319328--12319368 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
12319318 TGATTATACG
*
12319328 TATATGAATGACATGAAT
1 TATATGTATGACATGAAT
12319346 TATATGTATG-CATG-AT
1 TATATGTATGACATGAAT
12319362 TATATGT
1 TATATGT
12319369 GTTAACATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 9 0.41
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (18 bp):
TATATGTATGACATGAAT
Found at i:12319891 original size:32 final size:34
Alignment explanation
Indices: 12319816--12319896 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 34
12319806 ATGTATGTGA
* *
12319816 TATATATATAT-ATATATGTTTTGTGATATGAAT
1 TATATGTATATGATATATGTTGTGTGATATGAAT
*
12319849 TATATG-ATATGATATATG-TGTGTGTTAATG-AT
1 TATATGTATATGATATATGTTGTGTGAT-ATGAAT
*
12319881 TAT-TGTATATGTTATA
1 TATATGTATATGATATA
12319897 AGATATATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 2 0.05
32 24 0.59
33 15 0.37
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (34 bp):
TATATGTATATGATATATGTTGTGTGATATGAAT
Found at i:12321732 original size:5 final size:5
Alignment explanation
Indices: 12321722--12321769 Score: 89
Period size: 5 Copynumber: 9.8 Consensus size: 5
12321712 AATAAATAAA
12321722 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
12321770 AGCTAAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.10
5 38 0.90
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:12323882 original size:33 final size:33
Alignment explanation
Indices: 12323840--12323903 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
12323830 TCTAAAATCC
*
12323840 TATAAGTCAACAAACAACATATGAACTTTATCA
1 TATAAGTCAAAAAACAACATATGAACTTTATCA
12323873 TATAAGTCAAAAAACAACATATGAACTTTAT
1 TATAAGTCAAAAAACAACATATGAACTTTAT
12323904 GCCAATTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (33 bp):
TATAAGTCAAAAAACAACATATGAACTTTATCA
Found at i:12327010 original size:15 final size:15
Alignment explanation
Indices: 12326987--12327019 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12326977 CGTAAGACTC
12326987 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
12327002 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
12327017 CTA
1 CTA
12327020 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:12327146 original size:29 final size:29
Alignment explanation
Indices: 12327104--12327177 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
12327094 TTTCATATGT
12327104 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
12327132 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
12327161 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
12327178 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:12327611 original size:64 final size:64
Alignment explanation
Indices: 12327524--12327684 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 64
12327514 TAATGAAGGT
* * * **
12327524 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGT-GTCATTATTAATGGG
* * * * ** *
12327588 ATGCATCGATGTACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTGTCATTATTAATGGG
12327652 ATGCATCGATGCACTACTGATGCATCGATGCAC
1 ATGCATCGATGCACTACTGATGCATCGATGCAC
12327685 TACTTATGCA
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
63 1 0.01
64 80 0.99
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTGTCATTATTAATGGG
Found at i:12327673 original size:19 final size:19
Alignment explanation
Indices: 12327651--12327702 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
12327641 TTATTAATGG
12327651 GATGCATCGATGCACTACT
1 GATGCATCGATGCACTACT
12327670 GATGCATCGATGCACTACT
1 GATGCATCGATGCACTACT
*
12327689 TATGCATCGATGCA
1 GATGCATCGATGCA
12327703 TGAATTGCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (19 bp):
GATGCATCGATGCACTACT
Found at i:12327740 original size:83 final size:83
Alignment explanation
Indices: 12327587--12327748 Score: 220
Period size: 83 Copynumber: 2.0 Consensus size: 83
12327577 TTATTGTTGG
* * * *
12327587 GATGCATCGATGTACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
*
12327652 ATGCATCGATGCACTACT
66 ATGCATCGAAGCACTACT
** *
12327670 GATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGA
12327733 GAGTGCATCGAAGCAC
65 GA-TGCATCGAAGCAC
12327749 ATTCAAACAA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
82 2 0.03
83 62 0.90
84 5 0.07
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (83 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
ATGCATCGAAGCACTACT
Found at i:12333914 original size:15 final size:15
Alignment explanation
Indices: 12333894--12333941 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
12333884 ATTAGGACTC
12333894 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
12333909 CTACATCTCGAAGGA
1 CTACATCCCGAAGGA
*
12333924 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
12333939 CTA
1 CTA
12333942 TTATACCCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:12334057 original size:28 final size:28
Alignment explanation
Indices: 12334025--12334097 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
12334015 TTTCATATGT
12334025 TCATGTACTCATGTCATTTCTCTTGTGA
1 TCATGTACTCATGTCATTTCTCTTGTGA
12334053 TCATGTACTCATGTCATTTCTCTTGTGA
1 TCATGTACTCATGTCATTTCTCTTGTGA
12334081 TCATGTAGCTCATGTCA
1 TCATGTA-CTCATGTCA
12334098 CTTCATATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 35 0.80
29 9 0.20
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (28 bp):
TCATGTACTCATGTCATTTCTCTTGTGA
Found at i:12334554 original size:64 final size:64
Alignment explanation
Indices: 12334444--12334669 Score: 188
Period size: 64 Copynumber: 3.5 Consensus size: 64
12334434 TAATGAAGGT
* * * ** ** * **
12334444 ATGCATCGAATGCACTACTGATGCATCGGTACATAAAAGGTATTCGATGTAGT-ATTATTGCTGG
1 ATGCATCG-ATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-GTCATTATTAATGG
12334508 G
64 G
* * * *
12334509 ATGCATCGATGTACTCCTTATGCATTGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTGTCATTATTAATGGG
** * * **
12334573 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-GTCATTATTAATGGG
** *
12334636 AGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
12334670 ATTCAAACAA
Statistics
Matches: 132, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
63 3 0.02
64 116 0.88
65 13 0.10
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTGTCATTATTAATGGG
Found at i:12338268 original size:30 final size:30
Alignment explanation
Indices: 12338220--12338293 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
12338210 GAAAATGTAC
* *
12338220 TTCATTTTACAT-AAACAATTTTCAGATAA
1 TTCATTTTACGTAAAACAATTTTAAGATAA
* * *
12338249 TTTATTTTATGTAAAACAATTTTAAGGTAA
1 TTCATTTTACGTAAAACAATTTTAAGATAA
12338279 TTCATTTTACGTAAA
1 TTCATTTTACGTAAA
12338294 TTATTTCTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 9 0.24
30 28 0.76
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (30 bp):
TTCATTTTACGTAAAACAATTTTAAGATAA
Found at i:12340649 original size:231 final size:231
Alignment explanation
Indices: 12340246--12340712 Score: 835
Period size: 231 Copynumber: 2.0 Consensus size: 231
12340236 TTAAAATAAG
12340246 ATAAATTTAAATAAAGTTAGTATTTCAACTTAATGGTGACACACGACACGACACGTGGTATCAAT
1 ATAAATTTAAATAAAGTTAGTATTTCAACTTAATGGTGACACACGACACGACACGTGGTATCAAT
12340311 GACATGTGACATCATTCAATTGGAGGATTAAATTTATTTTTAATTTATTAAAAGTTTGACTAAAT
66 GACATGTGACATCATTCAATTGGAGGATTAAATTTATTTTTAATTTATTAAAAGTTTGACTAAAT
* *
12340376 TGGGAGAATATGTAAATAATAGAGACAAAATATGTGATTATACCAAAATATTTAATGACAATTAA
131 TGGGAGAATATGTAAATAACAGAGACAAAATATGTGATTATACCAAAATATTTAACGACAATTAA
*
12340441 ATAATGATGATCACATCTTAATTAAATATTAATTAA
196 ATAATGATGACCACATCTTAATTAAATATTAATTAA
*
12340477 ATAAATTTAAATAAAGTTAGTCTTTCAACTTAATGGTGACACACGACACGACACGTGGTATCAAT
1 ATAAATTTAAATAAAGTTAGTATTTCAACTTAATGGTGACACACGACACGACACGTGGTATCAAT
* * *
12340542 GACATGTGGCATCATTCAATTGTAGGATTAAATTTATTTTTAATTTATTAAAAGTTTGACTACAT
66 GACATGTGACATCATTCAATTGGAGGATTAAATTTATTTTTAATTTATTAAAAGTTTGACTAAAT
* *
12340607 TGGGAGAATATGTAAATAACAGAGACAAAATATGTGATTATACTAAAATATTTAACGACATTTAA
131 TGGGAGAATATGTAAATAACAGAGACAAAATATGTGATTATACCAAAATATTTAACGACAATTAA
* *
12340672 ATAGTGATGACCATATCTTAATTAAATATTAATTAA
196 ATAATGATGACCACATCTTAATTAAATATTAATTAA
12340708 ATAAA
1 ATAAA
12340713 AACGAATGTG
Statistics
Matches: 225, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
231 225 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (231 bp):
ATAAATTTAAATAAAGTTAGTATTTCAACTTAATGGTGACACACGACACGACACGTGGTATCAAT
GACATGTGACATCATTCAATTGGAGGATTAAATTTATTTTTAATTTATTAAAAGTTTGACTAAAT
TGGGAGAATATGTAAATAACAGAGACAAAATATGTGATTATACCAAAATATTTAACGACAATTAA
ATAATGATGACCACATCTTAATTAAATATTAATTAA
Found at i:12341980 original size:11 final size:11
Alignment explanation
Indices: 12341964--12341990 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12341954 ATTTATTATA
12341964 GTGACTAAAAC
1 GTGACTAAAAC
12341975 GTGACTAAAAC
1 GTGACTAAAAC
12341986 GTGAC
1 GTGAC
12341991 GAGTTCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (11 bp):
GTGACTAAAAC
Found at i:12346813 original size:229 final size:233
Alignment explanation
Indices: 12346359--12346820 Score: 754
Period size: 229 Copynumber: 2.0 Consensus size: 233
12346349 TAGTTCAACA
12346359 TTATGAGTATTTTTGTCTTAAAATGAAATGTTAGAGGTTAAAATACTCAAAAAAAAAGAAGTCAA
1 TTATGAGTATTTTTGTCTTAAAATGAAATGTTAGAGGTTAAAATACTCAAAAAAAAAGAAGTCAA
12346424 AATAACTATTTAATCAAGTGTTATGAGTATTTATTGGCATTATACCTTTATATAATTCTAAGAAG
66 AATAACTATTTAATCAAGTGTTATGAGTATTTATTGGCATTATACCTTTATATAATTCT-A-AAG
* * *
12346489 TTAGTTCCTCCACTTTGATTTTTCATAATTTAATTCTCATGCTTTACGGAAACGAATAAATTAAT
129 TTAGTTCCTCCACTTTGATTTATCATAATTTAATTCTCATGCCTTACGGAAACGAAGAAATTAAT
* **
12346554 TTAATTATGTAATAATATTAAATTTTATTTTTATTCAATG
194 TCAATTATGTAATAATATTAAACCTTATTTTTATTCAATG
* *
12346594 TTATGAGTCTTTTTGTCTTAAAATGAAATG-TAG-GAGTTAAAATACT-AAAAAAAGAG-AGTCA
1 TTATGAGTATTTTTGTCTTAAAATGAAATGTTAGAG-GTTAAAATACTCAAAAAAAAAGAAGTCA
*
12346655 AAATAACTATTTGATCAAGTGTTATGAGTATTTATTGGCATTATACCTTTATATAATTCT-AAGT
65 AAATAACTATTTAATCAAGTGTTATGAGTATTTATTGGCATTATACCTTTATATAATTCTAAAGT
*
12346719 TAGTTCCTCCACTTTGATTTATCGTAATTTAATTCTCATGCCTTACGGAAACGAAGAAATTAATT
130 TAGTTCCTCCACTTTGATTTATCATAATTTAATTCTCATGCCTTACGGAAACGAAGAAATTAATT
* *
12346784 CAATTATTTAATAATGTTAAACCTTATTTTTATTCAA
195 CAATTATGTAATAATATTAAACCTTATTTTTATTCAA
12346821 CGATTATATG
Statistics
Matches: 214, Mismatches: 12, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
229 97 0.45
232 64 0.30
233 10 0.05
234 14 0.07
235 29 0.14
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (233 bp):
TTATGAGTATTTTTGTCTTAAAATGAAATGTTAGAGGTTAAAATACTCAAAAAAAAAGAAGTCAA
AATAACTATTTAATCAAGTGTTATGAGTATTTATTGGCATTATACCTTTATATAATTCTAAAGTT
AGTTCCTCCACTTTGATTTATCATAATTTAATTCTCATGCCTTACGGAAACGAAGAAATTAATTC
AATTATGTAATAATATTAAACCTTATTTTTATTCAATG
Found at i:12347484 original size:3 final size:3
Alignment explanation
Indices: 12347476--12347509 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
12347466 TACTTTGTAT
*
12347476 ACA ACA ACA ACA ACA ACA ACA ACA ACA CCA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
12347510 AACCCTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:12347655 original size:4 final size:4
Alignment explanation
Indices: 12347646--12347680 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
12347636 CAATGCATGT
12347646 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
12347681 CATAGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:12347709 original size:13 final size:13
Alignment explanation
Indices: 12347691--12347715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12347681 CATAGTTGAA
12347691 CAGTCTTCATATG
1 CAGTCTTCATATG
12347704 CAGTCTTCATAT
1 CAGTCTTCATAT
12347716 ACGCGTCTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:12353524 original size:20 final size:20
Alignment explanation
Indices: 12353501--12353538 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12353491 ATACCACAGT
12353501 ACTAGTCTCCATAACGAAGA
1 ACTAGTCTCCATAACGAAGA
*
12353521 ACTAGTCTCCATACCGAA
1 ACTAGTCTCCATAACGAA
12353539 AGACTGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (20 bp):
ACTAGTCTCCATAACGAAGA
Found at i:12353573 original size:20 final size:20
Alignment explanation
Indices: 12353528--12353578 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
12353518 AGAACTAGTC
12353528 TCCATACCGAAAGACTGATA
1 TCCATACCGAAAGACTGATA
* * *
12353548 TTCATACTG-AAGATTGAGTA
1 TCCATACCGAAAGACTGA-TA
*
12353568 TCCATATCGAA
1 TCCATACCGAA
12353579 GGCTTAATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
19 7 0.30
20 15 0.65
21 1 0.04
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (20 bp):
TCCATACCGAAAGACTGATA
Found at i:12365230 original size:45 final size:45
Alignment explanation
Indices: 12365166--12365467 Score: 410
Period size: 45 Copynumber: 6.7 Consensus size: 45
12365156 AACGAATGAA
*
12365166 CAAAAGAATAATACATATGGGTGCATTATCAGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGC
* ** *
12365211 CAAAAGAATAATGTATATGGGTTTATTATCAACATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGC
* * ** *
12365256 CAAAAGAATAATACATATGAGTGCATTATTGGCATGAAAGAATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGC
* * *
12365301 CAAAAGAATAATACATATGGGTGCACTATCGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGC
*
12365346 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGC
* *
12365391 CAAAAGAATAATGGATATAGGTGCATTATCAGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGC
* *
12365436 C-ATAG-CTGAAATGCATATGGGTGCATTATCAG
1 CAAAAGAAT--AATGCATATGGGTGCATTATCAG
12365468 TATAAAAGTA
Statistics
Matches: 228, Mismatches: 27, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
43 1 0.00
44 3 0.01
45 224 0.98
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (45 bp):
CAAAAGAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGC
Found at i:12371477 original size:20 final size:20
Alignment explanation
Indices: 12371452--12371489 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12371442 TAATTCAATC
12371452 AGTATCGATACCGAAGGGGG
1 AGTATCGATACCGAAGGGGG
12371472 AGTATCGATACCGAAGGG
1 AGTATCGATACCGAAGGG
12371490 AAGGTATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.37, T:0.16
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGGG
Found at i:12371550 original size:19 final size:20
Alignment explanation
Indices: 12371526--12371597 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 20
12371516 ATGAAAAAAT
*
12371526 GGTATCGATACCATAATA-G
1 GGTATCGATACCATAGTAGG
*
12371545 GGTATCGGTACCATAGTATGG
1 GGTATCGATACCATAGTA-GG
* * *
12371566 TAGTATTGATACCATGGTAGG
1 -GGTATCGATACCATAGTAGG
12371587 GGTATCGATAC
1 GGTATCGATAC
12371598 TGAGGAGCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 16 0.38
20 9 0.21
21 3 0.07
22 14 0.33
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (20 bp):
GGTATCGATACCATAGTAGG
Found at i:12372894 original size:19 final size:20
Alignment explanation
Indices: 12372851--12372898 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
12372841 ATGCCTGCAA
* *
12372851 TATCGATACTGACCCTTGGG
1 TATCGATACTCACCCTTGAG
*
12372871 TATCGATATTCACCC-TGAG
1 TATCGATACTCACCCTTGAG
12372890 TATCGATAC
1 TATCGATAC
12372899 CAAAAATAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (20 bp):
TATCGATACTCACCCTTGAG
Found at i:12373101 original size:21 final size:21
Alignment explanation
Indices: 12373075--12373126 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
12373065 CCAGACATCA
*
12373075 AGTATCGATACTCTTTGAGGT
1 AGTATCGATACTCCTTGAGGT
12373096 AGTATCGATACTCCTTGAGGT
1 AGTATCGATACTCCTTGAGGT
12373117 AGTATCGATA
1 AGTATCGATA
12373127 TTACGCTCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (21 bp):
AGTATCGATACTCCTTGAGGT
Found at i:12377837 original size:21 final size:21
Alignment explanation
Indices: 12377788--12377837 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
12377778 TTGTTGGAAC
*
12377788 ATGGGGTTTAGAAACCAGATA
1 ATGGGGTTTAGAAACCAGACA
*
12377809 AT-GGGTTTTGAAACCA-AGCA
1 ATGGGGTTTAGAAACCAGA-CA
12377829 ATGGGGTTT
1 ATGGGGTTT
12377838 CCAAACTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.04
20 16 0.64
21 8 0.32
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (21 bp):
ATGGGGTTTAGAAACCAGACA
Found at i:12380701 original size:30 final size:30
Alignment explanation
Indices: 12380661--12380769 Score: 182
Period size: 30 Copynumber: 3.6 Consensus size: 30
12380651 TCAATATCAT
*
12380661 ATCAATTGATTTCGGGTCGGATCAAATGGA
1 ATCAATTGATTTCGGGTCGGATCAAATTGA
*
12380691 ATCGATTGATTTCGGGTCGGATCAAATTGA
1 ATCAATTGATTTCGGGTCGGATCAAATTGA
*
12380721 ATCAATTGATTTTGGGTCGGATCAAATTGA
1 ATCAATTGATTTCGGGTCGGATCAAATTGA
12380751 ATCAATTGATTTTCGGGTC
1 ATCAATTGA-TTTCGGGTC
12380770 ATATCATATC
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
30 65 0.89
31 8 0.11
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.35
Consensus pattern (30 bp):
ATCAATTGATTTCGGGTCGGATCAAATTGA
Found at i:12380786 original size:31 final size:31
Alignment explanation
Indices: 12380661--12380794 Score: 143
Period size: 30 Copynumber: 4.5 Consensus size: 31
12380651 TCAATATCAT
* *
12380661 ATCAATTGA-TTTCGGGTCGGATCAAATGGA
1 ATCAATTGATTTTCGGGTCAGATCAAATCGA
* * *
12380691 ATCGATTGA-TTTCGGGTCGGATCAAATTGA
1 ATCAATTGATTTTCGGGTCAGATCAAATCGA
* *
12380721 ATCAATTGATTTT-GGGTCGGATCAAATTGA
1 ATCAATTGATTTTCGGGTCAGATCAAATCGA
* *
12380751 ATCAATTGATTTTCGGGTCATATCATATCCG-
1 ATCAATTGATTTTCGGGTCAGATCAAAT-CGA
12380782 ATCAATT-ATTTTC
1 ATCAATTGATTTTC
12380795 AGTTAAGGTC
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
30 72 0.77
31 21 0.22
32 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (31 bp):
ATCAATTGATTTTCGGGTCAGATCAAATCGA
Found at i:12380793 original size:60 final size:60
Alignment explanation
Indices: 12380661--12380793 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 60
12380651 TCAATATCAT
* * * *
12380661 ATCAATTGATTTCGGGTCGGATCAAATGGAATCGATTGATTTCGGGTCGGATCAAATTGA
1 ATCAATTGATTTTGGGTCGGATCAAATGGAATCAATTGATTTCGGGTCAGATCAAATCGA
* * *
12380721 ATCAATTGATTTTGGGTCGGATCAAATTGAATCAATTGATTTTCGGGTCATATCATATCCG-
1 ATCAATTGATTTTGGGTCGGATCAAATGGAATCAATTGA-TTTCGGGTCAGATCAAAT-CGA
12380782 ATCAATT-ATTTT
1 ATCAATTGATTTT
12380794 CAGTTAAGGT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
60 41 0.64
61 22 0.34
62 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (60 bp):
ATCAATTGATTTTGGGTCGGATCAAATGGAATCAATTGATTTCGGGTCAGATCAAATCGA
Found at i:12381536 original size:31 final size:31
Alignment explanation
Indices: 12381442--12381543 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 31
12381432 ACAATGATTC
* *
12381442 TCATCCTTAAACTATGACTCTCATTCTAA-A
1 TCATCCTTAAACTATGAATCTCATTCTAATT
* * *
12381472 TCAGTCCTTAAACTTTTGAA---GATTCAAATT
1 TCA-TCCTTAAAC-TATGAATCTCATTCTAATT
*
12381502 TCATCCTCAAACTATGAATCTCATTCTAATT
1 TCATCCTTAAACTATGAATCTCATTCTAATT
12381533 TCATCCTTAAA
1 TCATCCTTAAA
12381544 TTTTTAGATC
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
28 5 0.09
29 14 0.25
30 6 0.11
31 27 0.48
32 4 0.07
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (31 bp):
TCATCCTTAAACTATGAATCTCATTCTAATT
Found at i:12387726 original size:9 final size:10
Alignment explanation
Indices: 12387686--12387726 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
12387676 AAAAATAAAA
12387686 TTTT-CGGTT
1 TTTTCCGGTT
12387695 TTTTCCGGTT
1 TTTTCCGGTT
*
12387705 TTTTCCCGTT
1 TTTTCCGGTT
*
12387715 TTTTTCGGTT
1 TTTTCCGGTT
12387725 TT
1 TT
12387727 CAACCGGTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 4 0.14
10 24 0.86
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.66
Consensus pattern (10 bp):
TTTTCCGGTT
Found at i:12388402 original size:14 final size:14
Alignment explanation
Indices: 12388385--12388442 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
12388375 TATTCATTTT
12388385 TTATTTATATTATA
1 TTATTTATATTATA
12388399 TTATTTATATTATA
1 TTATTTATATTATA
12388413 TATATCTTATA-TA-A
1 T-TAT-TTATATTATA
*
12388427 TTATATATATATATA
1 TTATTTATAT-TATA
12388442 T
1 T
12388443 ATGTATGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
12 4 0.11
13 3 0.08
14 19 0.50
15 7 0.18
16 5 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:12388416 original size:2 final size:2
Alignment explanation
Indices: 12388390--12388444 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
12388380 ATTTTTTATT
* *
12388390 TA TA T- TA TA T- TA TT TA TA T- TA TA TA TA TC T- TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12388427 T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
12388445 GTATGTATAC
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
1 6 0.14
2 38 0.86
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:12388422 original size:25 final size:25
Alignment explanation
Indices: 12388342--12388444 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 25
12388332 TTCCGTCCCC
*
12388342 TATA-TATATTTTTTA-ATTATATA
1 TATATTATATTATTTATATTATATA
* * * * * *
12388365 TTTTTTACTA-TATTCATTTTTTATT
1 TATATTA-TATTATTTATATTATATA
12388390 TATATTATATTATTTATATTATATA
1 TATATTATATTATTTATATTATATA
* *
12388415 TATCTTATA-TAATTATATATATATA
1 TATATTATATTATTTATAT-TATATA
12388440 TATAT
1 TATAT
12388445 GTATGTATAC
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
23 2 0.03
24 16 0.27
25 41 0.69
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATTATATTATTTATATTATATA
Found at i:12388667 original size:18 final size:17
Alignment explanation
Indices: 12388635--12388679 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
12388625 TGTACACATT
12388635 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
12388652 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
12388670 ATTTTTTTAC
1 ATTTTTTTAC
12388680 TCCATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:12388677 original size:17 final size:17
Alignment explanation
Indices: 12388633--12388679 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
12388623 TATGTACACA
12388633 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
12388650 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
12388668 TTATTTTTTTAC
1 TTATTTTTTTAC
12388680 TCCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:12388770 original size:26 final size:25
Alignment explanation
Indices: 12388741--12388805 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 25
12388731 TTTTCTTTAT
12388741 TTTTATTTTTTATTATTTTTTATGTG
1 TTTTATTTTTTATTATTTTTTAT-TG
* ** *
12388767 TTTTGTTATTTT-CCATTTTTTCTTG
1 TTTTATT-TTTTATTATTTTTTATTG
*
12388792 TTTTATTTATTATT
1 TTTTATTTTTTATT
12388806 CTCACGTTTG
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
24 3 0.10
25 8 0.28
26 14 0.48
27 4 0.14
ACGTcount: A:0.14, C:0.05, G:0.06, T:0.75
Consensus pattern (25 bp):
TTTTATTTTTTATTATTTTTTATTG
Found at i:12388775 original size:19 final size:17
Alignment explanation
Indices: 12388740--12388778 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
12388730 ATTTTCTTTA
12388740 TTTTTATTTTTTATTAT
1 TTTTTATTTTTTATTAT
*
12388757 TTTTTATGTGTTTTGTTAT
1 TTTTTAT-T-TTTTATTAT
12388776 TTT
1 TTT
12388779 CCATTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (17 bp):
TTTTTATTTTTTATTAT
Found at i:12391928 original size:26 final size:26
Alignment explanation
Indices: 12391897--12391954 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
12391887 ATTCAATCAG
*
12391897 AACAAAAAGAGAA-AAAAAGAGAAAA
1 AACAAAAAGAAAATAAAAAGAGAAAA
*
12391922 AAGCAAAGAGAAAATAAAAAGAGAAAA
1 AA-CAAAAAGAAAATAAAAAGAGAAAA
12391949 AACAAA
1 AACAAA
12391955 GGAAAATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 13 0.45
27 14 0.48
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.02
Consensus pattern (26 bp):
AACAAAAAGAAAATAAAAAGAGAAAA
Found at i:12391942 original size:13 final size:13
Alignment explanation
Indices: 12391897--12391960 Score: 71
Period size: 12 Copynumber: 5.0 Consensus size: 13
12391887 ATTCAATCAG
* *
12391897 AACAAAAAGAGAA
1 AACAAAGAGAAAA
12391910 AA-AAAGAGAAAA
1 AACAAAGAGAAAA
12391922 AAGCAAAGAGAAAA
1 AA-CAAAGAGAAAA
12391936 TAA-AAAGAGAAAA
1 -AACAAAGAGAAAA
12391949 AACAAAG-GAAAA
1 AACAAAGAGAAAA
12391961 TTGAAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
12 17 0.38
13 16 0.36
14 10 0.22
15 2 0.04
ACGTcount: A:0.77, C:0.05, G:0.17, T:0.02
Consensus pattern (13 bp):
AACAAAGAGAAAA
Found at i:12391946 original size:27 final size:25
Alignment explanation
Indices: 12391910--12391961 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
12391900 AAAAAGAGAA
12391910 AAAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAA-CAAAG-GAAAAT
12391937 AAAAAGAGAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAACAAAGGAAAAT
12391962 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (25 bp):
AAAAAGAGAAAAAACAAAGGAAAAT
Found at i:12391955 original size:26 final size:26
Alignment explanation
Indices: 12391897--12391961 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
12391887 ATTCAATCAG
* *
12391897 AACAAAAAGAGAA-AAAAAGAGAAAA
1 AACAAAGAGAAAATAAAAAGAGAAAA
12391922 AAGCAAAGAGAAAATAAAAAGAGAAAA
1 AA-CAAAGAGAAAATAAAAAGAGAAAA
12391949 AACAAAG-GAAAAT
1 AACAAAGAGAAAAT
12391962 TGAAGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
25 8 0.22
26 14 0.39
27 14 0.39
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (26 bp):
AACAAAGAGAAAATAAAAAGAGAAAA
Found at i:12392151 original size:69 final size:69
Alignment explanation
Indices: 12392033--12392170 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
12392023 TATTCAAACT
* *
12392033 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTTCACTCGAATATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
12392098 TCAA
66 TCAA
* *
12392102 ATGAGATTGATCAAGCACAATCATTTTTGAATCACTGAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
12392167 TCAA
66 TCAA
12392171 GAGAGAGACA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:12393055 original size:37 final size:37
Alignment explanation
Indices: 12393003--12393074 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
12392993 TAAAAAGAAG
* *
12393003 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAA
* *
12393040 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
12393075 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:12393143 original size:36 final size:36
Alignment explanation
Indices: 12393090--12393180 Score: 146
Period size: 36 Copynumber: 2.5 Consensus size: 36
12393080 ATTGAAAACA
*
12393090 TTTCCCTTGAAATAAATTACGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTACGTCTCTCTTGAGACAG
* **
12393126 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTACGTCTCTCTTGAGACAG
12393162 TTTCCCTTGAAACAAATTA
1 TTTCCCTTGAAACAAATTA
12393181 TTTGAGTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTACGTCTCTCTTGAGACAG
Found at i:12393200 original size:29 final size:29
Alignment explanation
Indices: 12393168--12393237 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
12393158 ACAGTTTCCC
*
12393168 TTGAAACAAATTATTTGAGTATGTTTTAT
1 TTGAAACAAATTATTTGAATATGTTTTAT
12393197 TTGAAACAAATTATTTGAATATGTTTTAT
1 TTGAAACAAATTATTTGAATATGTTTTAT
12393226 TTGAAACAAATT
1 TTGAAACAAATT
12393238 TCATCTCCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (29 bp):
TTGAAACAAATTATTTGAATATGTTTTAT
Found at i:12393227 original size:15 final size:15
Alignment explanation
Indices: 12393178--12393230 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
12393168 TTGAAACAAA
*
12393178 TTATTTGAGTATGTT
1 TTATTTGAATATGTT
****
12393193 TTATTTGAA-ACAAA
1 TTATTTGAATATGTT
12393207 TTATTTGAATATGTT
1 TTATTTGAATATGTT
12393222 TTATTTGAA
1 TTATTTGAA
12393231 ACAAATTTCA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (15 bp):
TTATTTGAATATGTT
Found at i:12393324 original size:36 final size:36
Alignment explanation
Indices: 12393226--12393344 Score: 141
Period size: 36 Copynumber: 3.3 Consensus size: 36
12393216 TATGTTTTAT
* * *
12393226 TTGAAACAAATTTCATCTCCCTTGAGATAGTTTATT-
1 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTT-TTC
* * *
12393262 TTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTTTC
1 TTGAAAC-AAATTTCGTCTCTCTTGAGACAGTTTTTC
**
12393299 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCC
1 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTTTC
12393335 TTGAAACAAA
1 TTGAAACAAA
12393345 ATCTTTGAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
36 43 0.61
37 27 0.39
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTTTC
Found at i:12393406 original size:65 final size:64
Alignment explanation
Indices: 12393302--12393475 Score: 206
Period size: 65 Copynumber: 2.6 Consensus size: 64
12393292 GTTTTTCTTG
* * **
12393302 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTC-CTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
* *
12393367 AAACAAATTTTATCTCCATTGAGACAGTTTCTCTTGAAACGCAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCC-TTGAGACAGTTTCTCTTGAAA--CAAAATCTTCAAATTTATTTCCCC
12393432 TA
63 TA
* * *
12393434 AAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACAA
1 AAAC-AAATTTTGTCT-CCTTGAGACAGTTTCTCTTGAAACAA
12393476 CAGATATCTT
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
64 1 0.01
65 37 0.39
67 34 0.36
68 20 0.21
69 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.36
Consensus pattern (64 bp):
AAACAAATTTTGTCTCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:12393472 original size:67 final size:67
Alignment explanation
Indices: 12393302--12393473 Score: 190
Period size: 67 Copynumber: 2.6 Consensus size: 67
12393292 GTTTTTCTTG
** * * **
12393302 AAACAAATTTCGTCTCTC-TTGAGACAGTTTCCCTTGAAA--CAAAATCTTTGAATTTATTTCCC
1 AAACAAATTTTATCTC-CATTGAGACAGTTTCTCATGAAACGCAAAATCTTCAAATTTATTTCCC
12393364 CTA
65 CTA
* *
12393367 AAACAAATTTTATCTCCATTGAGACAGTTTCTCTTGAAACGCAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTATCTCCATTGAGACAGTTTCTCATGAAACGCAAAATCTTCAAATTTATTTCCCC
12393432 TA
66 TA
* * * *
12393434 AAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAAC
1 AAAC-AAATTTTATCTCCATTGAGACAGTTTCTCATGAAAC
12393474 AACAGATATC
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 1 0.01
65 34 0.37
67 35 0.38
68 22 0.24
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTATCTCCATTGAGACAGTTTCTCATGAAACGCAAAATCTTCAAATTTATTTCCCC
TA
Found at i:12394391 original size:110 final size:108
Alignment explanation
Indices: 12394193--12394445 Score: 309
Period size: 110 Copynumber: 2.3 Consensus size: 108
12394183 GCTTTCCAGT
* *
12394193 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAAATTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* * * *
12394258 TAACGAAGGGGCGACTGATTGTCAACAAACAACTTT-TCAGTTTC
66 CAACGAAGGGGCGACAGACTGTCAACAAACAA-TTTCCCAG-TTC
* * * *
12394302 ATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTT
1 -TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTC
* *
12394367 ACAGCGAAGGGGCGGCCAG-CTGTCAACAAACAATTTCCCAGTTC
65 ACAACGAAGGGGC-GACAGACTGTCAACAAACAATTTCCCAGTTC
*
12394411 --CAGAGCCAATTTCAACTTCAC-GACGGAGGATATTG
1 TTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTG
12394446 GACTGGGAAC
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
105 1 0.01
106 31 0.25
109 6 0.05
110 85 0.67
111 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (108 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
CAACGAAGGGGCGACAGACTGTCAACAAACAATTTCCCAGTTC
Found at i:12395880 original size:2 final size:2
Alignment explanation
Indices: 12395873--12395919 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
12395863 TTGTTTTTAT
*
12395873 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
*
12395914 TG TA TA
1 TA TA TA
12395920 GATGTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12395974 original size:41 final size:40
Alignment explanation
Indices: 12395924--12396014 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 40
12395914 TGTATAGATG
* *
12395924 TATTA-ATTTTTCTCCATTTACTATATATATATTTTCTTAA
1 TATTATATTTTTATACATTT-CTATATATATATTTTCTTAA
* *
12395964 TATTATA-TTTTATACGTTTTTATATATATATTTTCTTAA
1 TATTATATTTTTATACATTTCTATATATATATTTTCTTAA
*
12396003 TATTTTATTTTT
1 TATTATATTTTT
12396015 GGTTTTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 25 0.57
40 18 0.41
41 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.63
Consensus pattern (40 bp):
TATTATATTTTTATACATTTCTATATATATATTTTCTTAA
Found at i:12396220 original size:18 final size:17
Alignment explanation
Indices: 12396175--12396222 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
12396165 TATGTACACA
12396175 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
12396192 TAATTTCTTTTACCTTTTT
1 TTATTT-TTTTACC-TTTT
12396211 TTATTTTTTTAC
1 TTATTTTTTTAC
12396223 GCCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.27
18 10 0.38
19 9 0.35
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:12396285 original size:10 final size:10
Alignment explanation
Indices: 12396265--12396299 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
12396255 GTTTTTTTAA
12396265 CATTTTA-TT
1 CATTTTATTT
12396274 CATTTTATTT
1 CATTTTATTT
12396284 CATTTTATTT
1 CATTTTATTT
*
12396294 TATTTT
1 CATTTT
12396300 TTACGTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (10 bp):
CATTTTATTT
Found at i:12396341 original size:26 final size:26
Alignment explanation
Indices: 12396286--12396347 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
12396276 TTTTATTTCA
12396286 TTTTA-TTT-TATTTTTTACGTGTTT
1 TTTTATTTTCTATTTTTTACGTGTTT
* *
12396310 TGTTATTTTCTATTTTTT-CTTGTTT
1 TTTTATTTTCTATTTTTTACGTGTTT
12396335 TATTTATTATTCT
1 T-TTTATT-TTCT
12396348 CACGTTTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 4 0.13
25 10 0.32
26 13 0.42
27 4 0.13
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.74
Consensus pattern (26 bp):
TTTTATTTTCTATTTTTTACGTGTTT
Found at i:12399834 original size:20 final size:20
Alignment explanation
Indices: 12399797--12399837 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12399787 AAGACACATA
* *
12399797 TAGGATCATGTAGATGCATT
1 TAGGAGCATATAGATGCATT
*
12399817 TAGGAGCATATAGCTGCATT
1 TAGGAGCATATAGATGCATT
12399837 T
1 T
12399838 GGTGGTTTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.34
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:12405637 original size:20 final size:19
Alignment explanation
Indices: 12405595--12405644 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
12405585 TGTATGCTTA
12405595 TTTTATTTTATTTTTTATG
1 TTTTATTTTATTTTTTATG
* * *
12405614 TTTTGTTTTTTTTTTCTATTT
1 TTTTATTTTATTTTT-TA-TG
12405635 TTTTATTTTA
1 TTTTATTTTA
12405645 ATTAGGTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 13 0.54
20 2 0.08
21 9 0.38
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTATTTTATTTTTTATG
Found at i:12409498 original size:24 final size:23
Alignment explanation
Indices: 12409451--12409498 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
12409441 AGAAAATTCC
**
12409451 AGCACTCAAAAGAAGAAATGGAA
1 AGCACTCAAAAGAAGAAAAAGAA
12409474 AGCACTCAAAAAGAAGAAAAAGAA
1 AGCACTC-AAAAGAAGAAAAAGAA
12409498 A
1 A
12409499 AGAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.62, C:0.12, G:0.19, T:0.06
Consensus pattern (23 bp):
AGCACTCAAAAGAAGAAAAAGAA
Found at i:12413377 original size:23 final size:23
Alignment explanation
Indices: 12413333--12413377 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12413323 GAAATTCCAG
* **
12413333 CACTCAAAAGAAGAAATGGAAAT
1 CACTCAAAAAAAGAAAAAGAAAT
12413356 CACTCAAAAAAAGAAAAAGAAA
1 CACTCAAAAAAAGAAAAAGAAA
12413378 AAGAAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.13, G:0.13, T:0.09
Consensus pattern (23 bp):
CACTCAAAAAAAGAAAAAGAAAT
Found at i:12417047 original size:19 final size:20
Alignment explanation
Indices: 12417005--12417047 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
12416995 AGAAAATTCC
12417005 AGCACTCAAAAGAAGAATGGAA
1 AGCACTCAAAAGAAGAA--GAA
12417027 AGCACTCAAAAGAAGAA-AA
1 AGCACTCAAAAGAAGAAGAA
12417046 AG
1 AG
12417048 AAAAGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
22 17 0.81
ACGTcount: A:0.58, C:0.14, G:0.21, T:0.07
Consensus pattern (20 bp):
AGCACTCAAAAGAAGAAGAA
Found at i:12426160 original size:24 final size:23
Alignment explanation
Indices: 12426113--12426160 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
12426103 AGAAAATTCC
**
12426113 AGCACTCAAAAGAAGAAATGGAA
1 AGCACTCAAAAGAAGAAAAAGAA
12426136 AGCACTCAAAAAGAAGAAAAAGAA
1 AGCACTC-AAAAGAAGAAAAAGAA
12426160 A
1 A
12426161 AGAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.62, C:0.12, G:0.19, T:0.06
Consensus pattern (23 bp):
AGCACTCAAAAGAAGAAAAAGAA
Found at i:12430048 original size:24 final size:23
Alignment explanation
Indices: 12430001--12430048 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
12429991 AGAAAATTCC
**
12430001 AGCACTCAAAAGAAGAAATGGAA
1 AGCACTCAAAAGAAGAAAAAGAA
12430024 AGCACTCAAAAAGAAGAAAAAGAA
1 AGCACTC-AAAAGAAGAAAAAGAA
12430048 A
1 A
12430049 AGAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.62, C:0.12, G:0.19, T:0.06
Consensus pattern (23 bp):
AGCACTCAAAAGAAGAAAAAGAA
Found at i:12443495 original size:511 final size:503
Alignment explanation
Indices: 12442251--12443766 Score: 2640
Period size: 511 Copynumber: 3.0 Consensus size: 503
12442241 AATAATGTCC
*
12442251 AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGAATGAGGAGCTTGGTTACGATCTAC
1 AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
* *
12442316 ACAAGAATCCATAATCACACATACAATATAAATTTTAGTATACTTTCTAACATTTATACAAAATA
66 ACAAGCATCCATAATCACACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
* *
12442381 ATAATGCTCAAAAGTACTATTATTTTCCAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
131 ATAATACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
* *
12442446 CTAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTTCCGATACCAATTT
196 CTAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTT
* * * * *
12442511 TAGTATCAATACCATTCTAGCATTTTATTTTTTATTACGATATCGATACCTTCCTCTT-GTAACT
261 CAGTATCAATACCATTCTAGCATTTCATTTTTGATTACGGTATCGATACCTTCCTCTTGGT-ATT
*
12442575 GATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTATTCATCCGAATCCTCT
325 GATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTGTTCATCCGAATCCTCT
* *
12442640 AATTTAAACTTATAGTATCGATAATGTTCTTCTTGTACTGATACCTTTACCAAGATCTTACCTCT
390 AATTTAACCTTATAGTATCGATAATGTTCTTCCTGTACTGATACCTTTACCAAGATCTTACCTCT
12442705 TTTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATCT
455 TTTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATCT
* *
12442754 AACTATTTGATAACTTTA-CCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
1 AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
*
12442818 ACAAGCATCCATAATCATACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
66 ACAAGCATCCATAATCACACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
12442883 ATAATACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
131 ATAATACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
*
12442948 CTGAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTT
196 CTAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTT
12443013 CAGTATCAATACCTTTCTAGCATTCTAGCATTTCATTTTTGATTACGGTATCGATACCTTCCTCT
261 CAGTATCAATA-----C---CATTCTAGCATTTCATTTTTGATTACGGTATCGATACCTTCCTCT
* *
12443078 TGGTATTGATACCTATACCTCATTATCGTTACTTTTTTAAATCGATATCGATACTGTTCATCCGA
318 TGGTATTGATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTGTTCATCCGA
* * *
12443143 ATCCTCTAATTTAACCTTATAGTATCGATAATGATCTTCCTATACTGATACCTTTACCAAGATAT
383 ATCCTCTAATTTAACCTTATAGTATCGATAATGTTCTTCCTGTACTGATACCTTTACCAAGATCT
*
12443208 TACCTCTTTTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATGT
448 TACCTCTTTTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATCT
12443264 AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
1 AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
12443329 ACAAGCATCCATAATCACACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
66 ACAAGCATCCATAATCACACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
*
12443394 ATAACACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
131 ATAATACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
12443459 CTAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTT
196 CTAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTT
*
12443524 CAGTATCAATACCATTCTAGTATTTCATTTTTGATTACGGTATCGATACCTTCCTCTTGGTATTG
261 CAGTATCAATACCATTCTAGCATTTCATTTTTGATTACGGTATCGATACCTTCCTCTTGGTATTG
* *
12443589 ATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTGTTCATCTGAATACTCTA
326 ATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTGTTCATCCGAATCCTCTA
* *
12443654 ATTTAACCTTATAGTATCGGTAATGTTCTTCCTGTACTGATACATTTACCAAGATCTTACCTCTT
391 ATTTAACCTTATAGTATCGATAATGTTCTTCCTGTACTGATACCTTTACCAAGATCTTACCTCTT
* *
12443719 TTACTTCGAGTTTTAAGTAAATTCCACCTAAATCTCTTACTCTTATCT
456 TTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATCT
12443767 CCAACCATAT
Statistics
Matches: 960, Mismatches: 43, Indels: 20
0.94 0.04 0.02
Matches are distributed among these distances:
502 242 0.25
503 234 0.24
506 1 0.00
507 1 0.00
510 231 0.24
511 251 0.26
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.40
Consensus pattern (503 bp):
AACTATTCGACAACTTTATCCTTGCCCTTTTTCTTCCTTGACTGAGGAGCTTGGTTACGATCTAC
ACAAGCATCCATAATCACACATACAATATAAATGTTAGTATACTTTCTAACATTTATACAAAATA
ATAATACTCAAAAGTACTATTATTTTCGAATTCTATTAAAATTCATCCTAACTTAACATTTCATA
CTAAATAGTATCGGTACCCCTCTTATAGTATCGATACTTCTCTTCTATGGTGCCGATACCCATTT
CAGTATCAATACCATTCTAGCATTTCATTTTTGATTACGGTATCGATACCTTCCTCTTGGTATTG
ATACCTATACCTCATTATCGATACTTTTTTAAATCGATATCGATATTGTTCATCCGAATCCTCTA
ATTTAACCTTATAGTATCGATAATGTTCTTCCTGTACTGATACCTTTACCAAGATCTTACCTCTT
TTACTTCGATTTTTACGTAAATTCCACCTAAATCTCTTACTCTTATCT
Found at i:12443998 original size:25 final size:23
Alignment explanation
Indices: 12443970--12444015 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
12443960 TCAATAACTG
12443970 ACCATATTTCATCAAATCACTAAAA
1 ACCAT-TTT-ATCAAATCACTAAAA
* *
12443995 ACCATTTTATTAAATCTCTAA
1 ACCATTTTATCAAATCACTAA
12444016 TAAATCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 3 0.16
25 5 0.26
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (23 bp):
ACCATTTTATCAAATCACTAAAA
Found at i:12456262 original size:6 final size:6
Alignment explanation
Indices: 12456260--12456328 Score: 68
Period size: 6 Copynumber: 11.5 Consensus size: 6
12456250 GGAAAAAGAA
* * * *
12456260 AAAAAG AAAAAG AAAGAG AAAAGG AAAAGG AAAAGG AAAAAGG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAAAG
* *
12456309 GAAAAG GAAAAG -AAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAA
12456329 GAAAAAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
5 5 0.09
6 45 0.80
7 6 0.11
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:12456279 original size:20 final size:20
Alignment explanation
Indices: 12456251--12456334 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
12456241 CCTAAAAATG
12456251 GAAAAAGAAAAAAAGAAAAA
1 GAAAAAGAAAAAAAGAAAAA
* *
12456271 GAAAGAGAAAAGGAAAAGGAAAAG
1 GAAAAAG-AAA--AAAA-GAAAAA
* *
12456295 GAAAAAG-GAAAAAGGAAAA
1 GAAAAAGAAAAAAAGAAAAA
*
12456314 GGAAAAGAAAAGAAAGAAAAA
1 GAAAAAGAAAA-AAAGAAAAA
12456335 AAATGAGAGG
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
19 10 0.20
20 12 0.24
21 11 0.22
22 1 0.02
23 4 0.08
24 11 0.22
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
GAAAAAGAAAAAAAGAAAAA
Found at i:12456286 original size:26 final size:27
Alignment explanation
Indices: 12456244--12456334 Score: 78
Period size: 27 Copynumber: 3.2 Consensus size: 27
12456234 TATTACGCCT
*
12456244 AAAAATGGAAAAAGAAAAAAAGAAAAAG
1 AAAAA-GGAAAAGGAAAAAAAGAAAAAG
*
12456272 AAAGA-GAAAAGGAAAAGGAAAAGGAAAAAGG
1 AAAAAGGAAAAGG-AAA--AAAA-GAAAAA-G
*
12456303 AAAAAGGAAAAGGAAAAGAAA-AGAAAG
1 AAAAAGGAAAAGGAAAA-AAAGAAAAAG
12456330 AAAAA
1 AAAAA
12456335 AAATGAGAGG
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
26 6 0.12
27 9 0.17
28 8 0.15
29 5 0.10
30 9 0.17
31 8 0.15
32 7 0.13
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (27 bp):
AAAAAGGAAAAGGAAAAAAAGAAAAAG
Found at i:12456287 original size:32 final size:31
Alignment explanation
Indices: 12456253--12456342 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 31
12456243 TAAAAATGGA
12456253 AAAAGAAAAAAAGAAAAAGAAAGAGAAAAGG
1 AAAAGAAAAAAAGAAAAAGAAAGAGAAAAGG
* * *
12456284 AAAAG-GAAAAGGAAAAAGGAAAAAGGAAAAGG
1 AAAAGAAAAAAAGAAAAA-GAAAGA-GAAAAGG
12456316 AAAAGAAAAGAAAGAAAAA-AAATGAGA
1 AAAAGAAAA-AAAGAAAAAGAAA-GAGA
12456343 GGTTCAAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
30 10 0.21
31 10 0.21
32 17 0.35
33 3 0.06
34 8 0.17
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.01
Consensus pattern (31 bp):
AAAAGAAAAAAAGAAAAAGAAAGAGAAAAGG
Found at i:12457159 original size:36 final size:33
Alignment explanation
Indices: 12457080--12457159 Score: 83
Period size: 36 Copynumber: 2.3 Consensus size: 33
12457070 AATCAAGGAG
*
12457080 AAAAAAAGAGGAGGTCTCGAACGAAACAGAAAA
1 AAAAAAAGAGGAGGTCTCGAACCAAACAGAAAA
12457113 AAAAACAAGAGGAGGAAT-TCGAAACCAAACA-AAAA
1 AAAAA-AAGAGGAGG--TCTCG-AACCAAACAGAAAA
12457148 AAGGAAAAAGAG
1 AA--AAAAAGAG
12457160 AGTGAAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
33 5 0.12
34 9 0.22
35 9 0.22
36 14 0.35
37 3 0.08
ACGTcount: A:0.61, C:0.11, G:0.23, T:0.05
Consensus pattern (33 bp):
AAAAAAAGAGGAGGTCTCGAACCAAACAGAAAA
Found at i:12458072 original size:2 final size:2
Alignment explanation
Indices: 12458065--12458126 Score: 115
Period size: 2 Copynumber: 30.5 Consensus size: 2
12458055 ATTGCTTCTT
12458065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12458107 TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA T-A TA T
12458127 TGATTTGATT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 57 0.97
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12469503 original size:18 final size:18
Alignment explanation
Indices: 12469475--12469524 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
12469465 CTTAAAAGTG
* *
12469475 AATTCGTTACAATTTGTGT
1 AATT-GTTACAATGTATGT
12469494 AATTGTTACAATGTATGT
1 AATTGTTACAATGTATGT
12469512 AATTGTTACAATG
1 AATTGTTACAATG
12469525 AACGAATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (18 bp):
AATTGTTACAATGTATGT
Found at i:12470129 original size:33 final size:33
Alignment explanation
Indices: 12470092--12470158 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
12470082 AAGGGACTTG
12470092 ACTCAAACTTGAAAATCAATCCACTAATGACTA
1 ACTCAAACTTGAAAATCAATCCACTAATGACTA
12470125 ACTCAAACTTGAAAATCAATCCACTAATGACTA
1 ACTCAAACTTGAAAATCAATCCACTAATGACTA
12470158 A
1 A
12470159 AAATTTTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (33 bp):
ACTCAAACTTGAAAATCAATCCACTAATGACTA
Found at i:12470475 original size:2 final size:2
Alignment explanation
Indices: 12470468--12470501 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12470458 AATTTAAATT
12470468 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12470502 TAATATTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12475259 original size:17 final size:17
Alignment explanation
Indices: 12475222--12475269 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
12475212 TAAAAGAAAG
*
12475222 TACAGTAAAAG-TAACAT
1 TACAGTAAAAGAT-ACAA
12475239 TACAGTAAAAGATACAA
1 TACAGTAAAAGATACAA
* *
12475256 TACAATAAGAGATA
1 TACAGTAAAAGATA
12475270 TAGTACAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.21
Consensus pattern (17 bp):
TACAGTAAAAGATACAA
Found at i:12475326 original size:38 final size:39
Alignment explanation
Indices: 12475252--12475328 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 39
12475242 AGTAAAAGAT
* * *
12475252 ACAATACAATAAGAGATATAGTACAATACAGTATATGAA
1 ACAACACAACAAGAGATATAGTACAATACAGGATATGAA
12475291 ACAACACAACAAGAGA-ATAGTACAATA-AGGGATATGAA
1 ACAACACAACAAGAGATATAGTACAATACA-GGATATGAA
12475329 TATAGATGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 1 0.03
38 19 0.56
39 14 0.41
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.18
Consensus pattern (39 bp):
ACAACACAACAAGAGATATAGTACAATACAGGATATGAA
Found at i:12480061 original size:45 final size:45
Alignment explanation
Indices: 12479966--12480129 Score: 242
Period size: 45 Copynumber: 3.7 Consensus size: 45
12479956 GATAAACATG
* *
12479966 AAAATAAGCTTACGAGCTTATCGAAT-AATGATAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * *
12480010 AAAATAAGCTTATGAGCTTATGGAGTAAATGGTAAGTATATTAGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
12480055 AAAATAAGCTTACGGGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
12480100 AGAATAAGCTTACGAGCTTATAGG-ATAAAT
1 AAAATAAGCTTACGAGCTTAT-GGAATAAAT
12480130 AATAAGAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
44 23 0.21
45 82 0.77
46 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:12482975 original size:15 final size:15
Alignment explanation
Indices: 12482969--12483027 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 15
12482959 AAAATAATAT
12482969 AAGAAAAAACAAAAA
1 AAGAAAAAACAAAAA
*
12482984 AAGAAAAAAAAAGAAAA
1 AAG-AAAAAACA-AAAA
*
12483001 AAGAAAATGAAGAAAAA
1 AAGAAAA--AACAAAAA
12483018 ATAGAAAAAA
1 A-AGAAAAAA
12483028 AGAAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 3 0.08
16 13 0.35
17 12 0.32
18 9 0.24
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (15 bp):
AAGAAAAAACAAAAA
Found at i:12482991 original size:9 final size:9
Alignment explanation
Indices: 12482979--12483037 Score: 68
Period size: 9 Copynumber: 6.8 Consensus size: 9
12482969 AAGAAAAAAC
12482979 AAAAAAAGA
1 AAAAAAAGA
12482988 AAAAAAA-A
1 AAAAAAAGA
*
12482996 GAAAAAAGA
1 AAAAAAAGA
**
12483005 AAATGAAGA
1 AAAAAAAGA
*
12483014 AAAAATAG-
1 AAAAAAAGA
12483022 AAAAAAAGA
1 AAAAAAAGA
12483031 AAAAAAA
1 AAAAAAA
12483038 ATGATGAGAG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 14 0.35
9 26 0.65
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:12482992 original size:17 final size:16
Alignment explanation
Indices: 12482972--12483037 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 16
12482962 ATAATATAAG
*
12482972 AAAAAACAAAAAAAGA
1 AAAAAAAAAAAAAAGA
12482988 AAAAAAAAGAAAAAAGA
1 AAAAAAAA-AAAAAAGA
* *
12483005 AAATGAAGAAAAAATAGA
1 AAA--AAAAAAAAAAAGA
12483023 AAAAAAGAAAAAAAA
1 AAAAAA-AAAAAAAA
12483038 ATGATGAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
16 9 0.22
17 18 0.44
18 10 0.24
19 4 0.10
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:12482997 original size:25 final size:24
Alignment explanation
Indices: 12482969--12483036 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 24
12482959 AAAATAATAT
*
12482969 AAGAAAAAACAAAAAAAGAAAAAAA
1 AAGAAAAAAGAAAAAAAG-AAAAAA
*
12482994 AAGAAAAAAGAAAATGAAGAAAAAA
1 AAGAAAAAAGAAAA-AAAGAAAAAA
*
12483019 TAGAAAAAAAGAAAAAAA
1 AAG-AAAAAAGAAAAAAA
12483037 AATGATGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 23 0.62
26 14 0.38
ACGTcount: A:0.84, C:0.01, G:0.12, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAGAAAAAAAGAAAAAA
Found at i:12485947 original size:20 final size:20
Alignment explanation
Indices: 12485922--12485976 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
12485912 ATCGATTCAA
*
12485922 GGGGTATTGATACCAAGAGG
1 GGGGTATCGATACCAAGAGG
* *
12485942 GGGGTATCGATAGCATGAGG
1 GGGGTATCGATACCAAGAGG
**
12485962 ATGGTATCGATACCA
1 GGGGTATCGATACCA
12485977 TTTGATCACA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.22
Consensus pattern (20 bp):
GGGGTATCGATACCAAGAGG
Found at i:12486481 original size:55 final size:55
Alignment explanation
Indices: 12486420--12486561 Score: 239
Period size: 55 Copynumber: 2.6 Consensus size: 55
12486410 AAAAAGTTGT
*
12486420 GAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTTTTTGTGCAAAACTGA
1 GAAATTCATACTAAGTGTATGAATTTTCGTATGGGCACTTTTTGTGCAAAACTGA
*
12486475 GAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTTTGTGCAAAACTGA
1 GAAATTCATACTAAGTGTATGAATTTTCGTATGGGCACTTTTTGTGCAAAACTGA
* * *
12486530 TAAACTCATACTACGTGTATGAATTTTCGTAT
1 GAAATTCATACTAAGTGTATGAATTTTCGTAT
12486562 AGACACTACG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 81 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.37
Consensus pattern (55 bp):
GAAATTCATACTAAGTGTATGAATTTTCGTATGGGCACTTTTTGTGCAAAACTGA
Done.