Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 178 of 214
Found at i:52305525 original size:117 final size:119
Alignment explanation
Indices: 52305356--52305635 Score: 464
Period size: 117 Copynumber: 2.4 Consensus size: 119
52305346 TAACATAATT
*
52305356 ATTATTAAATATATTTTAATT-AAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTAT
1 ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATATTCTTAT
52305420 ATGAATTT-C-ATATAATAATAATATATGATACTATAAAATATAATTT-AACAT-A-
66 ATGAATTTACTA-AT-ATAATAATATATGATACTATAAAATATAATTTGAA-ATAAC
52305472 ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATATTCTTAT
1 ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATATTCTTAT
*
52305537 ATGAATTTACTAATATCATAATATATGATACTATAAAATATAATTTGAAATAATC
66 ATGAATTTACTAATATAATAATATATGATACTATAAAATATAATTTGAAATAA-C
52305592 ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
52305636 TAAAATAATT
Statistics
Matches: 155, Mismatches: 2, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
116 21 0.14
117 83 0.54
118 6 0.04
119 1 0.01
120 44 0.28
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (119 bp):
ATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATATTCTTAT
ATGAATTTACTAATATAATAATATATGATACTATAAAATATAATTTGAAATAAC
Found at i:52305573 original size:61 final size:59
Alignment explanation
Indices: 52305391--52305575 Score: 172
Period size: 61 Copynumber: 3.1 Consensus size: 59
52305381 ATATAATTTA
52305391 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTC-ATATAATAATAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTCTA-AT-AT-ATAATATATGATACT
* * * * *
52305452 ATAAAA-T-ATAATTTAA-C-ATAATTATTAAAT-ATATTT-TAAT-TAAAATATATGAT-TT
1 ATAAAATTCTTAA--TAATCAAT-ATTCTTATATGA-ATTTCTAATATATAATATATGATACT
52305507 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAATATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTT-CTAATAT-ATAATATATGATACT
52305569 ATAAAAT
1 ATAAAAT
52305576 ATAATTTGAA
Statistics
Matches: 98, Mismatches: 10, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
55 1 0.01
56 20 0.20
57 15 0.15
58 6 0.06
59 12 0.12
60 16 0.16
61 27 0.28
62 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (59 bp):
ATAAAATTCTTAATAATCAATATTCTTATATGAATTTCTAATATATAATATATGATACT
Found at i:52305621 original size:18 final size:17
Alignment explanation
Indices: 52305598--52305634 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
52305588 AATCATTATT
52305598 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
52305614 AAATATATGATTTAATA
1 AAATATATGATTTAATA
52305631 AAAT
1 AAAT
52305635 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:52305649 original size:51 final size:52
Alignment explanation
Indices: 52305350--52305649 Score: 169
Period size: 61 Copynumber: 5.2 Consensus size: 52
52305340 ATATTTTAAC
* *
52305350 ATAATTATTATTAAATATATTTTAATT-AAATATATAATTTAATAAAATTCTTA
1 ATAATAATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAA-T-TTA
** * *
52305403 ATAATCAA-TATTCTTATATGAATTTCATATAATAATAATATATGATACTATAAAATATAATTTA
1 ATAAT-AATTATT-AAATAT--ATTT--TA-ATTAA-AATATATGAT--T-T--AATAAAATTTA
*
52305467 A-CATAATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
1 ATAATAATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAA-T-TTA
** * *
52305520 ATAATCAA-TATTCTTATATGAATTTACTAATATCATAATATATGATACTATAAAATATAATTTG
1 ATAAT-AATTATT-AAATAT--ATTT--TAAT-T-AAAATATATGAT--T-T--AATAAAATTT-
52305584 AA
52 -A
*
52305586 ATAATCATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTA
1 ATAATAATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTA
52305638 A-AATAATTATTA
1 ATAATAATTATTA
52305650 CTAATAAATT
Statistics
Matches: 191, Mismatches: 22, Indels: 70
0.67 0.08 0.25
Matches are distributed among these distances:
51 16 0.08
52 3 0.02
53 14 0.07
54 21 0.11
55 6 0.03
56 15 0.08
57 9 0.05
58 4 0.02
59 17 0.09
60 7 0.04
61 24 0.13
62 6 0.03
63 12 0.06
64 8 0.04
65 7 0.04
66 22 0.12
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (52 bp):
ATAATAATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTA
Found at i:52305703 original size:101 final size:97
Alignment explanation
Indices: 52305574--52305857 Score: 285
Period size: 91 Copynumber: 3.0 Consensus size: 97
52305564 ATACTATAAA
* * *
52305574 ATATAATTTGAAATAATCATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTT-A
1 ATATAATTTAAAATAAT-AATATTAAATATAATTTAA-TAAAATATAT-ATTT-ATAAAATTTCA
52305638 AAATAATTATT-ACTAATAAATTTTCTTATATGAATTT
62 AAA-AATTATTGA-TAATAAATTTTCTTATATGAATTT
* *
52305675 GTATAATTTAAAATAATAATAATTAAATATAATTTAAT--AATA-ATA--TAT--AATTTCATAA
1 ATATAATTTAAAATAATAAT-ATTAAATATAATTTAATAAAATATATATTTATAAAATTTCAAAA
*
52305733 AATTCTTGATAATAAATTTTCTTATATGAATTT
65 AATTATTGATAATAAATTTTCTTATATGAATTT
* *
52305766 ATATAATTTAAAATAATTAATATTAAATATAATTTAAT--AAT-GATA--TAT--AATTTCATAA
1 ATATAATTTAAAATAA-TAATATTAAATATAATTTAATAAAATATATATTTATAAAATTTCAAAA
* * *
52305824 AATTCTTAATAATAAATATTCTTATATGAATTT
65 AATTATTGATAATAAATTTTCTTATATGAATTT
52305857 A
1 A
52305858 CTAAAATCAT
Statistics
Matches: 169, Mismatches: 9, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
91 118 0.70
92 8 0.05
93 2 0.01
94 1 0.01
96 1 0.01
97 2 0.01
98 4 0.02
100 3 0.02
101 30 0.18
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (97 bp):
ATATAATTTAAAATAATAATATTAAATATAATTTAATAAAATATATATTTATAAAATTTCAAAAA
ATTATTGATAATAAATTTTCTTATATGAATTT
Found at i:52305714 original size:18 final size:18
Alignment explanation
Indices: 52305691--52305732 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
52305681 TTTAAAATAA
52305691 TAATAATTAA-ATATAATT
1 TAATAA-TAATATATAATT
52305709 TAATAATAATATATAATT
1 TAATAATAATATATAATT
*
52305727 TCATAA
1 TAATAA
52305733 AATTCTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATAATATATAATT
Found at i:52305726 original size:44 final size:43
Alignment explanation
Indices: 52305676--52305818 Score: 123
Period size: 44 Copynumber: 3.2 Consensus size: 43
52305666 TATGAATTTG
52305676 TATAATTTAAAATAATAATAATTAAATATAATTTAATAATAATA
1 TATAATTTAAAATAATAATAATTAAATATAATTTAATAAT-ATA
** * * *
52305720 TATAATTTCATAAAATTCTTGATAA-TAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAA-TAATAATAATTAAATATAAT-TTA-AT-AATATA
52305767 TATAATTTAAAATAATTAAT-ATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAA-TAATAATTAAATATAATTTAATAAT-ATA
52305811 TATAATTT
1 TATAATTT
52305819 CATAAAATTC
Statistics
Matches: 77, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
43 5 0.06
44 30 0.39
45 7 0.09
46 7 0.09
47 19 0.25
48 9 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (43 bp):
TATAATTTAAAATAATAATAATTAAATATAATTTAATAATATA
Found at i:52305750 original size:91 final size:91
Alignment explanation
Indices: 52305642--52305857 Score: 362
Period size: 91 Copynumber: 2.4 Consensus size: 91
52305632 AATTTAAAAT
* * *
52305642 AATTATTACTAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAA-TAATAATTAAATATA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAAT-ATTAAATATA
52305706 ATTTAATAATAATATATAATTTCATAA
65 ATTTAATAATAATATATAATTTCATAA
*
52305733 AATTCTTGATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
*
52305798 TTTAATAATGATATATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
*
52305824 AATTCTTAATAATAAATATTCTTATATGAATTTA
1 AATTCTTAATAATAAATTTTCTTATATGAATTTA
52305858 CTAAAATCAT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
91 113 0.97
92 4 0.03
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA
TTTAATAATAATATATAATTTCATAA
Found at i:52305840 original size:47 final size:46
Alignment explanation
Indices: 52305691--52305842 Score: 161
Period size: 47 Copynumber: 3.3 Consensus size: 46
52305681 TTTAAAATAA
52305691 TAATAATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCT
1 TAATAA-TAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCT
* * * **
52305739 TGATAATAAAT-T-TTCTTATATGAATTTATATAA-TT--TAAAATAAT
1 TAATAATAAATATAAT-TTA-AT-AATATATATAATTTCATAAAATTCT
*
52305783 TAATATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCT
1 TAATAATAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCT
52305830 TAATAATAAATAT
1 TAATAATAAATAT
52305843 TCTTATATGA
Statistics
Matches: 83, Mismatches: 12, Indels: 19
0.73 0.11 0.17
Matches are distributed among these distances:
43 3 0.04
44 25 0.30
45 7 0.08
46 7 0.08
47 33 0.40
48 8 0.10
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (46 bp):
TAATAATAAATATAATTTAATAATATATATAATTTCATAAAATTCT
Found at i:52309789 original size:23 final size:23
Alignment explanation
Indices: 52309729--52309803 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
52309719 TCTACTCACT
52309729 AACAAATCAAGAACAATTTCCAG
1 AACAAATCAAGAACAATTTCCAG
*
52309752 CAGAC-TATCAA-AACAATTTCCAG
1 -A-ACAAATCAAGAACAATTTCCAG
*
52309775 AACAAATCAAGAACAATAT-CAG
1 AACAAATCAAGAACAATTTCCAG
52309797 AACAAAT
1 AACAAAT
52309804 GCAACAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
21 2 0.04
22 16 0.36
23 19 0.42
24 6 0.13
25 2 0.04
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.17
Consensus pattern (23 bp):
AACAAATCAAGAACAATTTCCAG
Found at i:52309944 original size:19 final size:18
Alignment explanation
Indices: 52309902--52309946 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
52309892 GTAAACTCTT
52309902 TCAAAAAACAGCAGACTA
1 TCAAAAAACAGCAGACTA
*
52309920 TCAAAAAATAGCAGACTA
1 TCAAAAAACAGCAGACTA
52309938 TCAAAAAAC
1 TCAAAAAAC
52309947 TGTCTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.58, C:0.20, G:0.09, T:0.13
Consensus pattern (18 bp):
TCAAAAAACAGCAGACTA
Found at i:52314332 original size:18 final size:19
Alignment explanation
Indices: 52314293--52314343 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
52314283 AAAATTACAA
*
52314293 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
*
52314312 AAAATTCATAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
52314330 AAAACTTTCAAAAT
1 AAAA--TTCAAAAT
52314344 TCATATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.33
19 11 0.41
20 7 0.26
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:52318680 original size:3 final size:3
Alignment explanation
Indices: 52318672--52318711 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
52318662 GAGGTGGGTT
52318672 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52318712 AAATTCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:52326784 original size:2 final size:2
Alignment explanation
Indices: 52326777--52326803 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52326767 TTCGATGTTT
52326777 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
52326804 TTTTAAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52337075 original size:18 final size:18
Alignment explanation
Indices: 52337054--52337096 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
52337044 TTTTTAACTA
52337054 ATAATTACAAATTAAATT
1 ATAATTACAAATTAAATT
52337072 ATAATTACAAATTAAATT
1 ATAATTACAAATTAAATT
52337090 ATAATTA
1 ATAATTA
52337097 TTTTTAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATTACAAATTAAATT
Found at i:52346127 original size:5 final size:5
Alignment explanation
Indices: 52346113--52346143 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
52346103 ATTTTTTGAT
*
52346113 GATGG AATGG GATGG GATGG GATGG GATGG G
1 GATGG GATGG GATGG GATGG GATGG GATGG G
52346144 CTGTGGGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.58, T:0.19
Consensus pattern (5 bp):
GATGG
Found at i:52346545 original size:30 final size:30
Alignment explanation
Indices: 52346511--52346573 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
52346501 ACTTAACAAG
*
52346511 CAAATGCCTCTAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
52346541 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
52346571 CAA
1 CAA
52346574 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:52348926 original size:23 final size:24
Alignment explanation
Indices: 52348900--52348944 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
52348890 AAAAAAAATA
52348900 TTATTTAATAT-AAAATAATTTTC
1 TTATTTAATATGAAAATAATTTTC
* *
52348923 TTATTTATTATGAATATAATTT
1 TTATTTAATATGAAAATAATTT
52348945 AAAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
TTATTTAATATGAAAATAATTTTC
Found at i:52353350 original size:17 final size:17
Alignment explanation
Indices: 52353328--52353361 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52353318 AGGCCGTGCA
52353328 TTGTAATTGGGCTCGGG
1 TTGTAATTGGGCTCGGG
*
52353345 TTGTAATTGGGTTCGGG
1 TTGTAATTGGGCTCGGG
52353362 GTATTGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.41, T:0.38
Consensus pattern (17 bp):
TTGTAATTGGGCTCGGG
Found at i:52356253 original size:19 final size:19
Alignment explanation
Indices: 52356210--52356253 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
52356200 GGGACTAAAT
*
52356210 TGAAAAGTTGTAAAATTTA
1 TGAAAAATTGTAAAATTTA
* *
52356229 TGGAAAAATTTTAAATTTTA
1 T-GAAAAATTGTAAAATTTA
52356249 TGAAA
1 TGAAA
52356254 TACATGGGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.39
Consensus pattern (19 bp):
TGAAAAATTGTAAAATTTA
Found at i:52356944 original size:25 final size:26
Alignment explanation
Indices: 52356890--52356945 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
52356880 CCGATATATG
*
52356890 GCTCTTCGTGAGCTTCCCGATTAAAA
1 GCTCTTCGTGACCTTCCCGATTAAAA
* * *
52356916 GCTCTTTGTGACCTTCTCG-TTAATA
1 GCTCTTCGTGACCTTCCCGATTAAAA
52356941 GCTCT
1 GCTCT
52356946 CCGGAGCTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (26 bp):
GCTCTTCGTGACCTTCCCGATTAAAA
Found at i:52358236 original size:18 final size:16
Alignment explanation
Indices: 52358210--52358251 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
52358200 AAATTTTATT
*
52358210 ATATTATTTTTAATATAA
1 ATATAATTTTTAA-AT-A
52358228 ATATAA-TTTTAAATA
1 ATATAATTTTTAAATA
52358243 ATATAATTT
1 ATATAATTT
52358252 GTGTAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
17 6 0.27
18 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATTTTTAAATA
Found at i:52358247 original size:15 final size:17
Alignment explanation
Indices: 52358217--52358251 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
52358207 ATTATATTAT
52358217 TTTTAATATAAATATAA
1 TTTTAATATAAATATAA
52358234 TTTTAA-AT-AATATAA
1 TTTTAATATAAATATAA
52358249 TTT
1 TTT
52358252 GTGTAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 2 0.11
17 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTAATATAAATATAA
Found at i:52363717 original size:13 final size:13
Alignment explanation
Indices: 52363699--52363736 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
52363689 CAAAAACAAC
52363699 AAAAGAAGGGAAA
1 AAAAGAAGGGAAA
**
52363712 AAAAGAACAGAAA
1 AAAAGAAGGGAAA
52363725 AAAAG-AGGGAAA
1 AAAAGAAGGGAAA
52363737 TTAATTAGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAAGAAGGGAAA
Found at i:52367005 original size:29 final size:30
Alignment explanation
Indices: 52366960--52367024 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
52366950 ATCGATTGAG
* **
52366960 TTATTTTTGTATATAATTTTTA-TTTTAAA
1 TTATTTTCGTATATAATTAATATTTTTAAA
*
52366989 TTATTTTCGTA-ATTAATTAATATTTTTAAG
1 TTATTTTCGTATA-TAATTAATATTTTTAAA
52367019 TTATTT
1 TTATTT
52367025 ATAAGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 17 0.57
30 12 0.40
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (30 bp):
TTATTTTCGTATATAATTAATATTTTTAAA
Found at i:52369700 original size:51 final size:50
Alignment explanation
Indices: 52369570--52369710 Score: 176
Period size: 51 Copynumber: 2.8 Consensus size: 50
52369560 AAAGTGATGG
* * *
52369570 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGA
* * * * *
52369620 TCGCATATGTAGTACTATGTGCAGGCTACTATGTGTACCGG-ATAGTTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAT-G-ATAGA
*
52369671 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
52369711 AACATCATTG
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
49 2 0.03
50 37 0.48
51 38 0.49
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGA
Found at i:52369823 original size:23 final size:22
Alignment explanation
Indices: 52369790--52369843 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
52369780 TTAATCGGGA
52369790 AATTG-AT-TAAGTGT-AATTG
1 AATTGAATATAAGTGTGAATTG
52369809 AATAATGAATATAAGTGTGGAATTG
1 AAT--TGAATATAAGTGT-GAATTG
52369834 AATTGAATAT
1 AATTGAATAT
52369844 CGACTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.10
21 2 0.07
22 2 0.07
23 14 0.48
25 8 0.28
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (22 bp):
AATTGAATATAAGTGTGAATTG
Found at i:52370318 original size:16 final size:16
Alignment explanation
Indices: 52370275--52370310 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52370265 TAATTAAGAA
*
52370275 ATTATTATTATATTAC
1 ATTATTATAATATTAC
*
52370291 ATTATTATAATATTAT
1 ATTATTATAATATTAC
52370307 ATTA
1 ATTA
52370311 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTATAATATTAC
Found at i:52370350 original size:16 final size:18
Alignment explanation
Indices: 52370314--52370350 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
52370304 TATATTAATT
52370314 AAATAATAAACAAACGTA
1 AAATAATAAACAAACGTA
*
52370332 AAATAA-AAATAAA-GTA
1 AAATAATAAACAAACGTA
52370348 AAA
1 AAA
52370351 GAAAGAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 6 0.33
18 6 0.33
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (18 bp):
AAATAATAAACAAACGTA
Found at i:52370417 original size:15 final size:17
Alignment explanation
Indices: 52370389--52370425 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
52370379 ATAGCATTCG
*
52370389 AAAACAAAACAGAGA-A
1 AAAAGAAAACAGAGAGA
52370405 AAAAGAAAA-AGAGAGA
1 AAAAGAAAACAGAGAGA
52370421 AAAAG
1 AAAAG
52370426 GGAAAATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.76, C:0.05, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAGAAAACAGAGAGA
Found at i:52379060 original size:35 final size:33
Alignment explanation
Indices: 52379001--52379094 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 33
52378991 TGAATTGACG
* *
52379001 GATAAGACCATGGTTGGACCATGGCAATGTTTAAAT
1 GATAAGACCATAGTTGG-CTATGGCAAT-TTT-AAT
52379037 G-TAAGACCATAGTTAGGCTATGGC-ATTTTAAT
1 GATAAGACCATAGTT-GGCTATGGCAATTTTAAT
* * *
52379069 GAAAAGACCATAATTGGGTTATGGCA
1 GATAAGACCATAGTT-GGCTATGGCA
52379095 CCTTGAACAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
32 4 0.08
33 22 0.45
34 2 0.04
35 18 0.37
36 3 0.06
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (33 bp):
GATAAGACCATAGTTGGCTATGGCAATTTTAAT
Found at i:52379213 original size:33 final size:32
Alignment explanation
Indices: 52379141--52379217 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
52379131 TAGATACATG
** * * **
52379141 TGTAAGACCATAGTTGGGTTATGGCATTCTGA
1 TGTAAGACCATAACTGGGTTATGACATACAAA
52379173 TGATAAGACCATAACTGGGTTATGACACTACAAA
1 TG-TAAGACCATAACTGGGTTATGACA-TACAAA
52379207 TGTAAGACCAT
1 TGTAAGACCAT
52379218 GGCAGGGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGTTATGACATACAAA
Found at i:52393076 original size:24 final size:25
Alignment explanation
Indices: 52393032--52393080 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
52393022 TTCGTTTATC
*
52393032 TTTTTCTCAGATTTTTAAATCTAAAA
1 TTTTTCTCAAATTTTTAAATC-AAAA
52393058 TTTTT-TCAAATTTTT-AATCAAAA
1 TTTTTCTCAAATTTTTAAATCAAAA
52393081 GCTTCTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 4 0.18
25 9 0.41
26 5 0.23
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTTTCTCAAATTTTTAAATCAAAA
Found at i:52398834 original size:36 final size:36
Alignment explanation
Indices: 52398793--52399019 Score: 274
Period size: 36 Copynumber: 6.0 Consensus size: 36
52398783 GGTAGCTTTA
52398793 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
52398829 GCTACACTTATCTGATCAAGTGACAAAGTGATGAGTGATAGTTTT
1 GCTACACTTATCTGATCAAGTGA-AAA-AG-TGA-T-A-AG---T
* *
52398874 AGCTACACTTATCTGATAAAGTGAAAAACTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
52398911 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* **
52398947 GTTTTACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
52398983 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
52399019 G
1 G
52399020 GTAGCTTAAC
Statistics
Matches: 169, Mismatches: 12, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
36 124 0.73
37 4 0.02
38 1 0.01
39 3 0.02
40 3 0.02
41 2 0.01
42 3 0.02
43 3 0.02
45 4 0.02
46 22 0.13
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:52398896 original size:82 final size:81
Alignment explanation
Indices: 52398757--52399062 Score: 409
Period size: 82 Copynumber: 3.9 Consensus size: 81
52398747 TTTGAGTACT
*
52398757 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
52398822 GATAAGTGCTACACTTA
65 GATAAGTGCTATACTTA
* * * *
52398839 TCTGATCAAGTGACAAAGTGATGAGTGATAGTTTTAGCTACACTTATCTGATAAAGTGAAAAACT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
52398904 GATAAGTGTTATACTTA
65 GATAAGTGCTATACTTA
*
52398921 TCTGATCAAGTGAAAAAGTGATAA---GT-GTTT---T--ACTTATCTGATCAAGTGAAAAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
52398977 ATAAGTGCTATACTTA
66 ATAAGTGCTATACTTA
* * * *
52398993 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAACTACACTTATCTGATC-AGGGACAAA-TG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
52399056 ATAAGTG
66 ATAAGTG
52399063 ATCATACGTA
Statistics
Matches: 197, Mismatches: 18, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
72 61 0.31
74 1 0.01
75 2 0.01
76 3 0.02
77 3 0.02
78 1 0.01
79 11 0.06
80 7 0.04
81 12 0.06
82 96 0.49
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (81 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
ATAAGTGCTATACTTA
Found at i:52402874 original size:15 final size:16
Alignment explanation
Indices: 52402854--52402887 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
52402844 ACTAAAGTTC
52402854 AACTTTAAATTTAT-A
1 AACTTTAAATTTATCA
52402869 AACTTTAAATTTATCA
1 AACTTTAAATTTATCA
52402885 AAC
1 AAC
52402888 GCTTCATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
AACTTTAAATTTATCA
Found at i:52416531 original size:70 final size:70
Alignment explanation
Indices: 52416444--52416720 Score: 324
Period size: 70 Copynumber: 3.8 Consensus size: 70
52416434 TGTTCATGTT
* *
52416444 ATTTTGATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCT
1 ATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCT
52416509 GTCCA
66 GTCCA
* * * *
52416514 ATTTTGATGTAAAAATGTTGTTCAATTTGGTATATATATGCTGCCCAATTTGTTGCATATATGCT
1 ATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCT
52416579 GTCCA
66 GTCCA
* *
52416584 ATTTTTGGTGTAAATGTAAAAATGCTGCTCAATTTTGTTGTATATATGCTGCCCAAATTGTTGTA
1 A--TTT--TG---ATGTAAAAATGCTGCTCAA-TTTGGTATATATATGCTGCCCAAATTGTTGTA
52416649 TATATGCTGTCCAA
58 TATATGCTGTCC-A
* * * * * *
52416663 ATTTTGGTGTGAAAATGCTG-TCTAGTTTGGTAT-TAAATGCTGTCCAAATTGATGTATA
1 ATTTTGATGTAAAAATGCTGCTC-AATTTGGTATATATATGCTGCCCAAATTGTTGTATA
52416721 AGGGCTGTCC
Statistics
Matches: 179, Mismatches: 18, Indels: 20
0.82 0.08 0.09
Matches are distributed among these distances:
70 89 0.50
71 8 0.04
72 16 0.09
74 2 0.01
75 2 0.01
77 20 0.11
78 40 0.22
79 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (70 bp):
ATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCT
GTCCA
Found at i:52416562 original size:23 final size:23
Alignment explanation
Indices: 52416466--52416720 Score: 131
Period size: 23 Copynumber: 10.6 Consensus size: 23
52416456 AAATGTTGCT
*
52416466 CAATTTGGTATATATATGCTG-C
1 CAATTTGGTGTATATATGCTGTC
* *
52416488 CTAAATTGTTGTATATATGCTGTC
1 C-AATTTGGTGTATATATGCTGTC
* * * * *
52416512 CAATTTTGATGTAAAAATGTTGTT
1 CAA-TTTGGTGTATATATGCTGTC
* *
52416536 CAATTTGGTATATATATGCTGCC
1 CAATTTGGTGTATATATGCTGTC
* *
52416559 CAATTTGTTGCATATATGCTGTC
1 CAATTTGGTGTATATATGCTGTC
*
52416582 CAATTTTTGGTGTAAATGTAAAAATGCTG-C
1 CAA--TTTGGTGT--A--T--ATATGCTGTC
* *
52416612 TCAATTTTGTTGTATATATGCTGCC
1 -CAA-TTTGGTGTATATATGCTGTC
* *
52416637 CAAATTGTTGTATATATGCTGTC
1 CAATTTGGTGTATATATGCTGTC
*
52416660 CAAATTTTGGTGTGA-AAATGCTGTC
1 C-AA-TTTGGTGT-ATATATGCTGTC
* * * *
52416685 TAGTTTGGTAT-TAAATGCTGTC
1 CAATTTGGTGTATATATGCTGTC
* *
52416707 CAAATTGATGTATA
1 CAATTTGGTGTATA
52416721 AGGGCTGTCC
Statistics
Matches: 177, Mismatches: 38, Indels: 35
0.71 0.15 0.14
Matches are distributed among these distances:
22 17 0.10
23 82 0.46
24 32 0.18
25 22 0.12
26 2 0.01
27 1 0.01
28 1 0.01
29 1 0.01
30 9 0.05
31 10 0.06
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (23 bp):
CAATTTGGTGTATATATGCTGTC
Found at i:52416728 original size:148 final size:147
Alignment explanation
Indices: 52416450--52416732 Score: 383
Period size: 148 Copynumber: 1.9 Consensus size: 147
52416440 TGTTATTTTG
* *
52416450 ATGTAAAAATGTTGCTCAATTTGGTATATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAA
1 ATGTAAAAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAA
* * * * *
52416515 TTTTGATGTAAAAATGTTGTTCAATTTGGTATATATATGCTGCCCAATTTGTTGCATATATGCTG
66 TTTTGATGTAAAAATGCTGTTCAATTTGGTATATAAATGCTGCCCAAATTGATGCATATAGGCTG
52416580 TCCAATTTTTGGTGTAA
131 TCCAATTTTTGGTGTAA
* *
52416597 ATGTAAAAATGCTGCTCAATTTTGTTGTATATATGCTGCCCAAATTGTTGTATATATGCTGTCCA
1 ATGTAAAAATGCTGCTCAA-TTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCTGTCC-
* * * * *
52416662 AATTTTGGTGTGAAAATGCTG-TCTAGTTTGGTAT-TAAATGCTGTCCAAATTGATGTATA-AGG
64 AATTTTGATGTAAAAATGCTGTTC-AATTTGGTATATAAATGCTGCCCAAATTGATGCATATA-G
52416724 GCTGTCCAA
127 GCTGTCCAA
52416733 ACAGGGTAGA
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
147 19 0.16
148 72 0.61
149 27 0.23
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (147 bp):
ATGTAAAAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAA
TTTTGATGTAAAAATGCTGTTCAATTTGGTATATAAATGCTGCCCAAATTGATGCATATAGGCTG
TCCAATTTTTGGTGTAA
Found at i:52417172 original size:30 final size:30
Alignment explanation
Indices: 52417138--52417233 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 30
52417128 ATTTTTTTTC
52417138 TTATATCAATATTCTTTTTAATTTTTAATT
1 TTATATCAATATTCTTTTTAATTTTTAATT
* *
52417168 TTATATCACATTTGATTTTTTTTAATTTTTAAATAA
1 TTATATCA-A--T-ATTCTTTTTAATTTTT-AAT-T
* *
52417204 TTGT-T-AATAATCTTTTATAATTTTTAATT
1 TTATATCAATATTCTTTT-TAATTTTTAATT
52417233 T
1 T
52417234 GTTTACCATT
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
29 1 0.02
30 17 0.32
31 10 0.19
33 2 0.04
34 16 0.30
35 4 0.08
36 3 0.06
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.61
Consensus pattern (30 bp):
TTATATCAATATTCTTTTTAATTTTTAATT
Found at i:52426076 original size:9 final size:10
Alignment explanation
Indices: 52426059--52426110 Score: 58
Period size: 9 Copynumber: 5.5 Consensus size: 10
52426049 TTTGGTTAAA
52426059 AATTACCCGG
1 AATTACCCGG
52426069 AA-TACCC-G
1 AATTACCCGG
*
52426077 AATTACCCGAA
1 AATTACCCG-G
52426088 AATTACCC-G
1 AATTACCCGG
52426097 AATTACCC-G
1 AATTACCCGG
52426106 AATTA
1 AATTA
52426111 AATCACTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
8 3 0.08
9 24 0.65
10 2 0.05
11 8 0.22
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (10 bp):
AATTACCCGG
Found at i:52426096 original size:20 final size:19
Alignment explanation
Indices: 52426059--52426107 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
52426049 TTTGGTTAAA
*
52426059 AATTACCCG-GAATACCCG
1 AATTACCCGAAAATACCCG
52426077 AATTACCCGAAAATTACCCG
1 AATTACCCGAAAA-TACCCG
52426097 AATTACCCGAA
1 AATTACCCGAA
52426108 TTAAATCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 9 0.32
19 2 0.07
20 17 0.61
ACGTcount: A:0.39, C:0.31, G:0.12, T:0.18
Consensus pattern (19 bp):
AATTACCCGAAAATACCCG
Found at i:52426139 original size:17 final size:17
Alignment explanation
Indices: 52426117--52426214 Score: 70
Period size: 17 Copynumber: 5.4 Consensus size: 17
52426107 ATTAAATCAC
52426117 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
** *
52426134 TACATAAATCTTTAAATCAC
1 TACAT-AAT-TAAAAAT-AT
52426154 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
52426171 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
52426191 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
52426208 TACATAA
1 TACATAA
52426215 GTCTTGAATT
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
17 21 0.35
18 12 0.20
19 13 0.22
20 14 0.23
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:52426154 original size:37 final size:37
Alignment explanation
Indices: 52426108--52426239 Score: 203
Period size: 37 Copynumber: 3.6 Consensus size: 37
52426098 ATTACCCGAA
*
52426108 TTAAATCACTACATAATTAAAAATATTACATAAATCT
1 TTAAATCACTACATAATTAAAAATATTACATAAGTCT
52426145 TTAAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTAAATCACTACATAATTAAAAATATTACATAAGTCT
* *
52426182 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTAAATCACTACATAATTAAAAATATTACATAAGTCT
* * *
52426219 TGAATTAAC-ACATAATTAAAA
1 TTAAATCACTACATAATTAAAA
52426240 TATAAGTCTT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
36 12 0.14
37 76 0.86
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (37 bp):
TTAAATCACTACATAATTAAAAATATTACATAAGTCT
Found at i:52426159 original size:20 final size:19
Alignment explanation
Indices: 52426108--52426197 Score: 62
Period size: 18 Copynumber: 4.8 Consensus size: 19
52426098 ATTACCCGAA
52426108 TTAAATCACTACAT-AATT
1 TTAAATCACTACATAAATT
** *
52426126 AAAAAT-ATTACATAAATCT
1 TTAAATCACTACATAAAT-T
52426145 TTAAATCACTACAT-AATT
1 TTAAATCACTACATAAATT
** * *
52426163 AAAAAT-ATTACATAAGTCT
1 TTAAATCACTACATAAAT-T
*
52426182 TTGAATCACTACATAA
1 TTAAATCACTACATAA
52426198 TTAAAAACAT
Statistics
Matches: 52, Mismatches: 14, Indels: 10
0.68 0.18 0.13
Matches are distributed among these distances:
17 12 0.23
18 14 0.27
19 12 0.23
20 14 0.27
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.34
Consensus pattern (19 bp):
TTAAATCACTACATAAATT
Found at i:52428558 original size:20 final size:20
Alignment explanation
Indices: 52428533--52428574 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
52428523 TTCTGCAAGA
52428533 AAAAAAGTATATAATAAATT
1 AAAAAAGTATATAATAAATT
52428553 AAAAAAGTATATAATAAATT
1 AAAAAAGTATATAATAAATT
52428573 AA
1 AA
52428575 TTAGCCTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAAAGTATATAATAAATT
Found at i:52429075 original size:23 final size:24
Alignment explanation
Indices: 52429049--52429104 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
52429039 TTGGTTTTTT
*
52429049 TATTTTTTATTT-AATT-TATTACA
1 TATTTTTTATTTAAATTAAATTA-A
52429072 TATTTTATT-TTTAAATTAAATTAA
1 TATTTT-TTATTTAAATTAAATTAA
52429096 TATTTTTTA
1 TATTTTTTA
52429105 CCTGCCCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 11 0.39
24 13 0.46
25 4 0.14
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTTTTTATTTAAATTAAATTAA
Found at i:52430123 original size:19 final size:19
Alignment explanation
Indices: 52430099--52430139 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
52430089 TAAGTGTGTG
52430099 AGTGAAAATTGAAAGTGAA
1 AGTGAAAATTGAAAGTGAA
52430118 AGTGAAAATTGAAAGTGAA
1 AGTGAAAATTGAAAGTGAA
52430137 AGT
1 AGT
52430140 AGGGAGGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (19 bp):
AGTGAAAATTGAAAGTGAA
Found at i:52431350 original size:50 final size:50
Alignment explanation
Indices: 52431296--52431511 Score: 188
Period size: 50 Copynumber: 4.3 Consensus size: 50
52431286 CATGTAACGG
* ** *
52431296 GAAGCTCATGTGAGCTGTATAACGGAAAGCTCTTGCGAGCTAATTATCGA
1 GAAGCTCATGAGAGCCATATAACGGAAAGCTCATGCGAGCTAATTATCGA
* * * *
52431346 GAAGCTTAT-ACGAGCCATA-AACGGAAAGCTCATGCGAGCAAAATATCGG
1 GAAGCTCATGA-GAGCCATATAACGGAAAGCTCATGCGAGCTAATTATCGA
* * * * * *
52431395 GAAGCTCGTGAGAGCCATATAACGGGAAGCTCAAGAGAG-TCATTAATTGA
1 GAAGCTCATGAGAGCCATATAACGGAAAGCTCATGCGAGCTAATT-ATCGA
* * * * * *
52431445 GAAGCTCATGAGAGCTAAATAACAGAAAGCTCATGAGAG-TCAAGTATCGG
1 GAAGCTCATGAGAGCCATATAACGGAAAGCTCATGCGAGCT-AATTATCGA
*
52431495 GAAGCTCGTGAGAGCCA
1 GAAGCTCATGAGAGCCA
52431512 AATATCAGCA
Statistics
Matches: 131, Mismatches: 30, Indels: 10
0.77 0.18 0.06
Matches are distributed among these distances:
49 43 0.33
50 86 0.66
51 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (50 bp):
GAAGCTCATGAGAGCCATATAACGGAAAGCTCATGCGAGCTAATTATCGA
Found at i:52431515 original size:50 final size:50
Alignment explanation
Indices: 52431369--52431533 Score: 165
Period size: 50 Copynumber: 3.3 Consensus size: 50
52431359 GCCATAAACG
* * *
52431369 GAAAGCTCATGCGAG-CAAAATATCGGGAAGCTCGTGAGAGCCATATAACG
1 GAAAGCTCATGAGAGTC-AAATATCGGGAAGCTCGTGAGAGCCAAATAACA
* * * * *
52431419 GGAAGCTCAAGAGAGTCATTAAT-T-GAGAAGCTCATGAGAGCTAAATAACA
1 GAAAGCTCATGAGAGTCA--AATATCGGGAAGCTCGTGAGAGCCAAATAACA
* *
52431469 GAAAGCTCATGAGAGTCAAGTATCGGGAAGCTCGTGAGAGCCAAATATCA
1 GAAAGCTCATGAGAGTCAAATATCGGGAAGCTCGTGAGAGCCAAATAACA
* * *
52431519 GCACGCTCATAAGAG
1 GAAAGCTCATGAGAG
52431534 CTGTTGTGTG
Statistics
Matches: 92, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
48 2 0.02
49 1 0.01
50 84 0.91
51 2 0.02
52 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (50 bp):
GAAAGCTCATGAGAGTCAAATATCGGGAAGCTCGTGAGAGCCAAATAACA
Found at i:52431517 original size:25 final size:25
Alignment explanation
Indices: 52431293--52431517 Score: 127
Period size: 25 Copynumber: 9.0 Consensus size: 25
52431283 AGCCATGTAA
* *** *
52431293 CGGGAAGCTCATGTGAGCTGTATAA
1 CGGGAAGCTCATGAGAGCCAAATAT
* * * * *
52431318 CGGAAAGCTCTTGCGAGCTAATTAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* *
52431343 CGAGAAGCTTAT-ACGAGCCATAA-A-
1 CGGGAAGCTCATGA-GAGCCA-AATAT
* * *
52431367 CGGAAAGCTCATGCGAGCAAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* * *
52431392 CGGGAAGCTCGTGAGAGCCATATAA
1 CGGGAAGCTCATGAGAGCCAAATAT
* *
52431417 CGGGAAGCTCAAGAGAGTCATTAAT-T
1 CGGGAAGCTCATGAGAGCCA--AATAT
* * *
52431443 -GAGAAGCTCATGAGAGCTAAATAA
1 CGGGAAGCTCATGAGAGCCAAATAT
* * * *
52431467 CAGAAAGCTCATGAGAGTCAAGTAT
1 CGGGAAGCTCATGAGAGCCAAATAT
*
52431492 CGGGAAGCTCGTGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
52431517 C
1 C
52431518 AGCACGCTCA
Statistics
Matches: 144, Mismatches: 47, Indels: 18
0.69 0.22 0.09
Matches are distributed among these distances:
23 5 0.03
24 15 0.10
25 121 0.84
26 1 0.01
27 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.20
Consensus pattern (25 bp):
CGGGAAGCTCATGAGAGCCAAATAT
Found at i:52431526 original size:25 final size:25
Alignment explanation
Indices: 52431369--52431534 Score: 102
Period size: 25 Copynumber: 6.6 Consensus size: 25
52431359 GCCATAAACG
* * *
52431369 GAAAGCTCATGCGAGCAAAATATCG
1 GAAAGCTCATGAGAGCCAAATATCA
* * * * *
52431394 GGAAGCTCGTGAGAGCCATATAACG
1 GAAAGCTCATGAGAGCCAAATATCA
* * * *
52431419 GGAAGCTCAAGAGAGTCATTAAT-TGA
1 GAAAGCTCATGAGAGCCA--AATATCA
* *
52431445 G-AAGCTCATGAGAGCTAAATAACA
1 GAAAGCTCATGAGAGCCAAATATCA
* * *
52431469 GAAAGCTCATGAGAGTCAAGTATCG
1 GAAAGCTCATGAGAGCCAAATATCA
* *
52431494 GGAAGCTCGTGAGAGCCAAATATCA
1 GAAAGCTCATGAGAGCCAAATATCA
* * *
52431519 GCACGCTCATAAGAGC
1 GAAAGCTCATGAGAGC
52431535 TGTTGTGTGT
Statistics
Matches: 105, Mismatches: 32, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
23 3 0.03
24 2 0.02
25 97 0.92
26 1 0.01
27 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (25 bp):
GAAAGCTCATGAGAGCCAAATATCA
Found at i:52438549 original size:92 final size:91
Alignment explanation
Indices: 52438392--52438600 Score: 260
Period size: 92 Copynumber: 2.3 Consensus size: 91
52438382 TTGATTTTAG
** *
52438392 TAAATTCATATAAGAACAATTTATTATTGAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
52438457 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
52438484 TAAATTCATATAAGAAAATTTATTATCAAGTATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
*
52438548 TATGTAATAATTATTATTTTAGATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
52438576 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
52438601 GTTATAATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.01
91 28 0.27
92 70 0.69
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:52438729 original size:66 final size:63
Alignment explanation
Indices: 52438654--52438864 Score: 192
Period size: 66 Copynumber: 3.4 Consensus size: 63
52438644 AAATATATTT
52438654 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
52438719 G
63 G
* * * * **
52438720 AATATTAATTATTAAGAATTTTA-TTAA--AT--TATA-TAT--TTTAATTAAAAT-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
*
52438774 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
52438838 AG
62 AG
*
52438840 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
52438865 AAATTATATA
Statistics
Matches: 113, Mismatches: 15, Indels: 35
0.69 0.09 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 12 0.11
57 1 0.01
58 3 0.03
59 6 0.05
61 6 0.05
62 3 0.03
63 1 0.01
64 12 0.11
65 9 0.08
66 32 0.28
67 5 0.04
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:52438762 original size:120 final size:120
Alignment explanation
Indices: 52438623--52438908 Score: 488
Period size: 120 Copynumber: 2.4 Consensus size: 120
52438613 TTAAATTATT
* * * *
52438623 TTAAATCATATATTATAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-TTTATAG
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTAT-ATTTTACAG
52438685 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
63 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
52438743 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
52438808 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
52438863 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
52438909 TAAATATGAT
Statistics
Matches: 159, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
119 6 0.04
120 151 0.95
121 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
Found at i:52438765 original size:18 final size:17
Alignment explanation
Indices: 52438737--52438771 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52438727 ATTATTAAGA
*
52438737 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
52438754 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
52438772 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:52438885 original size:18 final size:17
Alignment explanation
Indices: 52438857--52438891 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52438847 ATTATTAAGA
*
52438857 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
52438874 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
52438892 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:52439030 original size:156 final size:157
Alignment explanation
Indices: 52438845--52439160 Score: 571
Period size: 156 Copynumber: 2.0 Consensus size: 157
52438835 ATAAGAATAT
52438845 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* * *
52438910 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
52438975 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
52439002 TAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
52439066 AATTATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
52439131 TAATTATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
52439158 TAA
1 TAA
52439161 GGGTATTCTA
Statistics
Matches: 153, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
156 147 0.96
157 6 0.04
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:52439041 original size:18 final size:17
Alignment explanation
Indices: 52439013--52439047 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52439003 AATTATAAGA
*
52439013 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
52439030 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
52439048 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:52439047 original size:16 final size:16
Alignment explanation
Indices: 52439013--52439070 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
52439003 AATTATAAGA
52439013 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
52439030 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
52439046 A-TTTAA-TAATAAT-T
1 ATTTTAATTAA-AATAT
52439060 ATGTTTAATTA
1 AT-TTTAATTA
52439071 TGATTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.14
15 8 0.22
16 10 0.28
17 7 0.19
18 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:52445166 original size:20 final size:21
Alignment explanation
Indices: 52445141--52445186 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
52445131 AGAGTTCGAG
* *
52445141 GTTCAAGATTTGA-ATTTAAA
1 GTTCAAGATTCGAGATCTAAA
*
52445161 GTTCAAGGTTCGAGATCTAAA
1 GTTCAAGATTCGAGATCTAAA
52445182 GTTCA
1 GTTCA
52445187 GGGGTTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (21 bp):
GTTCAAGATTCGAGATCTAAA
Found at i:52446030 original size:21 final size:21
Alignment explanation
Indices: 52445987--52446032 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
52445977 GATGAAGGAT
* *
52445987 GAAAACATGAAGCAAAGCGAC
1 GAAAACACGAAGCAAAGCAAC
*
52446008 GAAAACACGAAGCAAAGTAAC
1 GAAAACACGAAGCAAAGCAAC
52446029 GAAA
1 GAAA
52446033 TCCCCCCCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.17, G:0.22, T:0.04
Consensus pattern (21 bp):
GAAAACACGAAGCAAAGCAAC
Found at i:52448964 original size:6 final size:6
Alignment explanation
Indices: 52448953--52448981 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52448943 TCATTATTGT
52448953 AAATAA AAATAA AAATAA AAATAA AAATA
1 AAATAA AAATAA AAATAA AAATAA AAATA
52448982 TATTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:52452690 original size:21 final size:21
Alignment explanation
Indices: 52452664--52452703 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52452654 TTTGGGTTGA
52452664 TCAGCTCTCAAGAGCTTCTGC
1 TCAGCTCTCAAGAGCTTCTGC
*
52452685 TCAGCTCTCACGAGCTTCT
1 TCAGCTCTCAAGAGCTTCT
52452704 ATTAGCGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.35, G:0.17, T:0.30
Consensus pattern (21 bp):
TCAGCTCTCAAGAGCTTCTGC
Found at i:52455639 original size:16 final size:17
Alignment explanation
Indices: 52455601--52455640 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
52455591 TTATTTATTA
52455601 TTTATTTTTATTGTGGT
1 TTTATTTTTATTGTGGT
52455618 TTTATTTTT-TTG-GGT
1 TTTATTTTTATTGTGGT
52455633 TTCTATTT
1 TT-TATTT
52455641 GGGCCCGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 8 0.36
17 9 0.41
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (17 bp):
TTTATTTTTATTGTGGT
Found at i:52455977 original size:45 final size:46
Alignment explanation
Indices: 52455905--52456527 Score: 306
Period size: 44 Copynumber: 13.8 Consensus size: 46
52455895 GGGTTTTAGT
* * * *
52455905 CTGCTCCACTGCAACATCAGGGAGATAATATTTGCTATA-TTCAGC
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATACTTCAAC
* ** * *
52455950 CTGCTCCGCTGTGACTTTAGGGCGATAAGACTTG-TA-ACTTCAAC
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATACTTCAAC
*
52455994 CTGCTCCACTGCAACTTTAGGGAGATAAGGTTTGCTATGA--T----
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTAT-ACTTCAAC
* * * * * *
52456035 CTGCTCTACTGCAACTTCAGAGAGATAAAATAT-CTAATTTATGGCTTCAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCT-A--TA---CTTCAAC
* * * * * **
52456086 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTAT-CTTCAGT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATACTTCAAC
* * * *
52456131 CTGCTCCCCTGCAACTTCAGGGAGATAAGAATTGTGACTTTAAGCTTTAATC
1 CTGCTCCACTGCAACTTTAGGGAGATAAG-ATT-TG-CTAT-A-CTTCAA-C
* * * * * * *
52456183 C-GTTCCACTGCAACCTCAGGGAAATAAGATTCGC-GT-CTTCAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATACTTCAAC
* * * * * * *
52456226 CTACTCCACTGCAGCTTCAGGGAGATAAGGTTT-ATA-ACTTTAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATACTTCAAC
* * * * *
52456270 CTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTAT-CTTCGAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATACTTCAAC
* * * *
52456315 TTACTCCACTGCAACTTTAGGGAGATAAGA--T-CCATAACTTCAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTAT-ACTTCAAC
* * * *
52456359 CTGTTCCACTGCAACTTTAGGGAAATAAGATTCGCTAT-CTTCAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATACTTCAAC
* * * * *
52456404 CTGCTCTACTGCAACTTCAGGGAGATAAGACTTACTAT-CTTCAGTC
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATACTTCA-AC
* * * * * ** * *
52456450 C-ACTCCACTGAAACTTTAGGTAGTTAAGACTTG-T-GGCTTTAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATACTTCAAC
* *
52456493 CTGCTCCACTGCAACTTCAAGGAGATAAGATTTGC
1 CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGC
52456528 AGTCTGTCCT
Statistics
Matches: 435, Mismatches: 105, Indels: 76
0.71 0.17 0.12
Matches are distributed among these distances:
40 2 0.00
41 28 0.06
42 4 0.01
43 5 0.01
44 160 0.37
45 160 0.37
46 4 0.01
47 7 0.02
48 4 0.01
49 2 0.00
50 3 0.01
51 53 0.12
52 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (46 bp):
CTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATACTTCAAC
Found at i:52456011 original size:44 final size:45
Alignment explanation
Indices: 52455905--52456527 Score: 210
Period size: 45 Copynumber: 13.8 Consensus size: 45
52455895 GGGTTTTAGT
* * * * *
52455905 CTGCTCCACTGCAACATCAGGGAGATAATATTTGCTATATTCAGC
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCTATATTCAAC
* ** *
52455950 CTGCTCCGCTGTGACTTTAGGGCGATAAGACTTG-TA-ACTTCAAC
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCTATA-TTCAAC
**
52455994 CTGCTCCACTGCAACTTTAGGGAGATAAGGTTTGCTATGA-T----
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCTAT-ATTCAAC
* * * * *
52456035 CTGCTCTACTGCAACTTCAGAGAGATAA-AATAT-CTAATTTATGGCTTCAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACT-TGCT-A--TA----TTCAAC
* * * * * **
52456086 CTGTTCCACTACAACTTCAGGGAAATAAGA-TTCGCTATCTTCAGT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTT-GCTATATTCAAC
* * * * *
52456131 CTGCTCCCCTGCAACTTCAGGGAGATAAGAATTGTGACTTTAAGCTTTAATC
1 CTGCTCCACTGCAACTTTAGGGAGATAAG-ACT-TG-CTAT-A--TTCAA-C
* * * * * * *
52456183 C-GTTCCACTGCAACCTCAGGGAAATAAGA-TTCGC-GTCTTCAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTT-GCTATATTCAAC
* * * * * *
52456226 CTACTCCACTGCAGCTTCAGGGAGATAAG-GTT--TATAACTTTAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCTAT-A-TTCAAC
* * * * * * *
52456270 CTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCGAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCTATATTCAAC
* * * *
52456315 TTACTCCACTGCAACTTTAGGGAGATAAGA--T-CCATAACTTCAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCTAT-A-TTCAAC
* * * *
52456359 CTGTTCCACTGCAACTTTAGGGAAATAAGA-TTCGCTATCTTCAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTT-GCTATATTCAAC
* * * * *
52456404 CTGCTCTACTGCAACTTCAGGGAGATAAGACTTACTATCTTCAGTC
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCTATATTCA-AC
* * * * *** * *
52456450 C-ACTCCACTGAAACTTTAGGTAGTTAAGACTTG-TGGCTTTAAT
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCTATATTCAAC
* * *
52456493 CTGCTCCACTGCAACTTCAAGGAGATAAGATTTGC
1 CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGC
52456528 AGTCTGTCCT
Statistics
Matches: 432, Mismatches: 100, Indels: 92
0.69 0.16 0.15
Matches are distributed among these distances:
40 3 0.01
41 27 0.06
42 5 0.01
43 5 0.01
44 154 0.36
45 157 0.36
46 4 0.01
47 11 0.03
48 6 0.01
49 3 0.01
50 2 0.00
51 51 0.12
52 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTTAGGGAGATAAGACTTGCTATATTCAAC
Found at i:52456339 original size:89 final size:89
Alignment explanation
Indices: 52456175--52456433 Score: 340
Period size: 89 Copynumber: 2.9 Consensus size: 89
52456165 TGACTTTAAG
* * *
52456175 CTTTAATCCGTTCCACTGCAACCTCAGGGAAATAAGATTCGC-GTCTTCAATCTACTCCACTGCA
1 CTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAATCTACTCCACTGCA
* * **
52456239 GCTTCAGGGAGATAAGGTTTATAA
66 ACTTCAGGGAGATAAGATCCATAA
* * * * * * *
52456263 CTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCGATTTACTCCACTGCA
1 CTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAATCTACTCCACTGCA
*
52456328 ACTTTAGGGAGATAAGATCCATAA
66 ACTTCAGGGAGATAAGATCCATAA
* * * *
52456352 CTTCAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTCGCTATCTTCAATCTGCTCTACTGCA
1 CTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAATCTACTCCACTGCA
52456417 ACTTCAGGGAGATAAGA
66 ACTTCAGGGAGATAAGA
52456434 CTTACTATCT
Statistics
Matches: 143, Mismatches: 27, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
88 35 0.24
89 108 0.76
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (89 bp):
CTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAATCTACTCCACTGCA
ACTTCAGGGAGATAAGATCCATAA
Found at i:52458083 original size:50 final size:50
Alignment explanation
Indices: 52457990--52458187 Score: 164
Period size: 50 Copynumber: 3.8 Consensus size: 50
52457980 TTTCATGTAC
* * * * **
52457990 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGACATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATTGG
* * * * *
52458040 TGCCCATGTCATGTCCCAGACATGATCTTAC-GGGGTACCTCTCATCTCGG
1 TGCCAATGACATGTCCCAGACATGGTCTTACAGGGG-ACCTCTCATATTGG
* * * *
52458090 TGCCAACGACATGTCCCAAACATGGTTTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGACATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT-AT-T---GG
* * *
52458145 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGACATGTCCCAGACATGGTCTTACAGGGGACCTCT
52458188 TTACCCAAAT
Statistics
Matches: 116, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
49 3 0.03
50 70 0.60
51 4 0.03
55 2 0.02
56 37 0.32
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGACATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATTGG
Found at i:52460983 original size:46 final size:46
Alignment explanation
Indices: 52460916--52461100 Score: 289
Period size: 46 Copynumber: 4.0 Consensus size: 46
52460906 ACATTGCTAT
* *
52460916 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* * * *
52460962 AACTCAATATGGTTTTCTTCACTGAAACATCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
*
52461008 AACTCAGTATGGTTTTCTTCACCGAAACACTATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* *
52461054 AACTCGGTATGGTTTCCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
52461100 A
1 A
52461101 CTTTTCCATG
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 126 1.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:52462375 original size:16 final size:17
Alignment explanation
Indices: 52462329--52462376 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
52462319 AAATTCTTTT
52462329 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
52462346 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
52462363 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
52462377 TTCTAGATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:52470431 original size:46 final size:46
Alignment explanation
Indices: 52470368--52470507 Score: 244
Period size: 46 Copynumber: 3.0 Consensus size: 46
52470358 CCATGGCAAA
52470368 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
52470414 TTGTAAAAAGTAAGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
52470460 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
52470506 TT
1 TT
52470508 ATAGCATTGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:52480503 original size:27 final size:26
Alignment explanation
Indices: 52480473--52480526 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
52480463 GAATGTTTTG
52480473 ATTTTGGTT-ATAATGGCATGTATATGT
1 ATTTTGGTTAATAATGGC-T-TATATGT
* *
52480500 ATTTTGTTTAATGATGGCTTATATGT
1 ATTTTGGTTAATAATGGCTTATATGT
52480526 A
1 A
52480527 GTGTGTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.33
27 9 0.38
28 7 0.29
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (26 bp):
ATTTTGGTTAATAATGGCTTATATGT
Found at i:52499602 original size:15 final size:15
Alignment explanation
Indices: 52499582--52499614 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
52499572 AGAATTTAAT
52499582 TTTAAAGATTT-AGGA
1 TTTAAAG-TTTAAGGA
52499597 TTTAAAGTTTAAGGA
1 TTTAAAGTTTAAGGA
52499612 TTT
1 TTT
52499615 TGTTGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (15 bp):
TTTAAAGTTTAAGGA
Found at i:52502890 original size:20 final size:20
Alignment explanation
Indices: 52502865--52502912 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
52502855 TTTTAAAAAC
*
52502865 AATTTTTTTTAGTTTAATGT
1 AATTTTTTTTAATTTAATGT
52502885 AATTTTTTTTAATTTAATGT
1 AATTTTTTTTAATTTAATGT
*
52502905 GATTTTTT
1 AATTTTTT
52502913 AATTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (20 bp):
AATTTTTTTTAATTTAATGT
Found at i:52507136 original size:44 final size:43
Alignment explanation
Indices: 52507000--52507181 Score: 204
Period size: 43 Copynumber: 4.2 Consensus size: 43
52506990 CCACATAAAT
* * * *
52507000 GCCGCTAAAGAACATGACGTTTAACAGCGCTTTTATAACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
* * * *
52507043 GTCGCTAAAGATCATGACCTTTAGCGGCACTTTTATCACAATC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
* * *
52507086 GTCGCTAAAGAACATGACATTTAGCGGTGCTTTTTATCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGC-TTTTATCACAAAC
* * *
52507130 GCCGCTAAATAACATGACCTTTAGCGACG-TTTTATTTACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA-TCACAAAC
*
52507173 GCTGCTAAA
1 GCCGCTAAA
52507182 AGTACCGTTC
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 5 0.04
43 76 0.65
44 36 0.31
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
Found at i:52513266 original size:47 final size:47
Alignment explanation
Indices: 52513215--52513562 Score: 261
Period size: 47 Copynumber: 7.0 Consensus size: 47
52513205 TATAAGTTGT
* *
52513215 TAAGTTATGTATGTATGTGAGTTATGTAAGTTAAGATATGATATATA
1 TAAGTTATGTATGTATGTAAGTTATGTAAGTTATGATATGATATATA
*
52513262 TAAGTTAT-TATGTTATGTAAGTTATGTGAGTTATGATATGATATATA
1 TAAGTTATGTATG-TATGTAAGTTATGTAAGTTATGATATGATATATA
52513309 TAAGTTATTAAGTTATGTATGTATGTGAGTTATGTAAGTTATGATATGATATATA
1 TAAGTTA-T--G-TATGTATGTA----AGTTATGTAAGTTATGATATGATATATA
*
52513364 T---TTATGTAT-TATGTAAGTTATGTAAGTTATG---TGAGT-TATG
1 TAAGTTATGTATGTATGTAAGTTATGTAAGTTATGATATGA-TATATA
* *
52513404 TAAGTTATGGTATGATATATATAAGTTAT-TAAGTTATG-TATGTATGTGAGTTATG
1 TAAGTTAT-GTATG---TATGTAAGTTATGTAAGTTATGATATG-A--T-A--TATA
* *
52513459 TAAGTTATGATATGGTATATATTTATGTATTATGTAAGTTATGGTATGATATATA
1 TAAGTTATG-TAT-GTATGTA---A-G--TTATGTAAGTTATGATATGATATATA
* *
52513514 TAAGTTAT-TAAGTTATGTAAGTTATGTGAGTTATGATATGATATATA
1 TAAGTTATGTATG-TATGTAAGTTATGTAAGTTATGATATGATATATA
52513561 TA
1 TA
52513563 TATATAAGTT
Statistics
Matches: 252, Mismatches: 11, Indels: 76
0.74 0.03 0.22
Matches are distributed among these distances:
40 7 0.03
41 1 0.00
43 20 0.08
44 4 0.02
46 4 0.02
47 87 0.35
48 15 0.06
49 4 0.02
50 2 0.01
51 9 0.04
52 8 0.03
53 13 0.05
54 1 0.00
55 54 0.21
56 2 0.01
57 2 0.01
58 1 0.00
59 4 0.02
60 10 0.04
61 4 0.02
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (47 bp):
TAAGTTATGTATGTATGTAAGTTATGTAAGTTATGATATGATATATA
Found at i:52513394 original size:218 final size:216
Alignment explanation
Indices: 52513016--52513636 Score: 835
Period size: 218 Copynumber: 2.9 Consensus size: 216
52513006 AGTATAAATA
*
52513016 AGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTGAGTTATGTGAGTTATGATAT
1 AGTTATGTAAGTTATGATATGATATATATTTATGT-AGTTATGTAAGTTATGTGAGTTATGATAT
*
52513081 GATATATAT---TTATGT-A-TTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATAGA
65 GATATATATAAGTTAT-TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATA
* * *
52513141 TTTATGTATTATGTAAGTTAAGTTATGTGAGTTATGTAAGTTATGTGAGTTATGATATGATATAT
129 TTTATGTATTA--T--G-TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATAT
*
52513206 ATAAGTTGTTAAGTTATGTATGTATGTG
189 ATAAGTTATTAAGTTATGTATGTATGTG
*
52513234 AGTTATGTAAGTTAAGATATGATATATATAAGTTAT-TATGTTATGTAAGTTATGTGAGTTATGA
1 AGTTATGTAAGTTATGATATGATATATAT---TTATGTA-GTTATGTAAGTTATGTGAGTTATGA
*
52513298 TATGATATATATAAGTTATTAAGTTATGTATG-TATGTGAGTTATGTAAGTTATGATATGATATA
62 TATGATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATA
*
52513362 TATTTATGTATTATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGGTATGATATATATA
127 TATTTATGTATTATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATA
52513427 AGTTATTAAGTTATGTATGTATGTG
192 AGTTATTAAGTTATGTATGTATGTG
*
52513452 AGTTATGTAAGTTATGATATGGTATATATTTATGTA-TTATGTAAGTTA--T--G----G-TATG
1 AGTTATGTAAGTTATGATATGATATATATTTATGTAGTTATGTAAGTTATGTGAGTTATGATATG
*
52513507 ATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATG--A--TATGATAT-ATATATATA
66 ATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATT
* * *
52513567 TAAG--TTAT-TAAGTTACGTAAG-TATGTGAGTTATGTAAGTTATGATCTGATATATATAAGTT
131 TATGTATTATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTT
52513628 ATTAAGTTA
196 ATTAAGTTA
52513637 AGATCCAAAG
Statistics
Matches: 375, Mismatches: 17, Indels: 43
0.86 0.04 0.10
Matches are distributed among these distances:
197 47 0.13
198 12 0.03
199 4 0.01
201 11 0.03
202 8 0.02
204 1 0.00
205 31 0.08
206 14 0.04
210 1 0.00
212 1 0.00
214 12 0.03
215 4 0.01
216 2 0.01
218 125 0.33
219 2 0.01
220 37 0.10
221 5 0.01
222 1 0.00
223 49 0.13
224 8 0.02
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (216 bp):
AGTTATGTAAGTTATGATATGATATATATTTATGTAGTTATGTAAGTTATGTGAGTTATGATATG
ATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATT
TATGTATTATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTT
ATTAAGTTATGTATGTATGTG
Found at i:52513410 original size:116 final size:116
Alignment explanation
Indices: 52513045--52513501 Score: 619
Period size: 116 Copynumber: 4.0 Consensus size: 116
52513035 TGATATATAT
*
52513045 TTATGTAAGTTATGTGAGTTATGTGAGTTATGATATGATATATAT---TTATGT-A-TTATGTAA
1 TTATGTAAGTTATGTGAGTTATGTGAGTTATGATATGATATATATAAGTTAT-TAAGTTATGTAT
*
52513105 GTTATGTGAGTTATGTAAGTTATGATATGATATAGATTTATGTATTATGTAAGTTAAG
65 G-TATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATTA--T--G-TAAG
* * *
52513163 TTATGTGAGTTATGTAAGTTATGTGAGTTATGATATGATATATATAAGTTGTTAAGTTATGTATG
1 TTATGTAAGTTATGTGAGTTATGTGAGTTATGATATGATATATATAAGTTATTAAGTTATGTATG
* * *
52513228 TATGTGAGTTATGTAAGTTAAGATATGATATATA--TAAG--TTAT-TATG
66 TATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
52513274 TTATGTAAGTTATGTGAG---T-T-----ATGATATGATATATATAAGTTATTAAGTTATGTATG
1 TTATGTAAGTTATGTGAGTTATGTGAGTTATGATATGATATATATAAGTTATTAAGTTATGTATG
52513330 TATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
66 TATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
* *
52513381 TTATGTAAGTTATGTGAGTTATGTAAGTTATGGTATGATATATATAAGTTATTAAGTTATGTATG
1 TTATGTAAGTTATGTGAGTTATGTGAGTTATGATATGATATATATAAGTTATTAAGTTATGTATG
*
52513446 TATGTGAGTTATGTAAGTTATGATATGGTATATATTTATGTATTATGTAAG
66 TATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
52513497 TTATG
1 TTATG
52513502 GTATGATATA
Statistics
Matches: 304, Mismatches: 16, Indels: 40
0.84 0.04 0.11
Matches are distributed among these distances:
102 68 0.22
104 3 0.01
106 4 0.01
107 22 0.07
108 1 0.00
110 1 0.00
111 20 0.07
115 1 0.00
116 90 0.30
117 3 0.01
118 43 0.14
119 3 0.01
120 1 0.00
121 36 0.12
122 8 0.03
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (116 bp):
TTATGTAAGTTATGTGAGTTATGTGAGTTATGATATGATATATATAAGTTATTAAGTTATGTATG
TATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
Found at i:52513527 original size:8 final size:9
Alignment explanation
Indices: 52513014--52513746 Score: 335
Period size: 9 Copynumber: 81.3 Consensus size: 9
52513004 TAAGTATAAA
52513014 TAAGTTATG
1 TAAGTTATG
52513023 TAAGTTATG
1 TAAGTTATG
* * *
52513032 ATATGATATA
1 -TAAGTTATG
*
52513042 T-ATTTATG
1 TAAGTTATG
52513050 TAAGTTATG
1 TAAGTTATG
*
52513059 TGAGTTATG
1 TAAGTTATG
*
52513068 TGAGTTATG
1 TAAGTTATG
* * *
52513077 ATATGATATA
1 -TAAGTTATG
*
52513087 T-ATTTATG
1 TAAGTTATG
52513095 T-A-TTATG
1 TAAGTTATG
52513102 TAAGTTATG
1 TAAGTTATG
*
52513111 TGAGTTATG
1 TAAGTTATG
52513120 TAAGTTATG
1 TAAGTTATG
* *
52513129 -ATA-TGATA
1 TA-AGTTATG
*
52513137 TAGATTTATG
1 TA-AGTTATG
52513147 T-A-TTATG
1 TAAGTTATG
52513154 TAAG---T-
1 TAAGTTATG
52513159 TAAGTTATG
1 TAAGTTATG
*
52513168 TGAGTTATG
1 TAAGTTATG
52513177 TAAGTTATG
1 TAAGTTATG
*
52513186 TGAGTTATG
1 TAAGTTATG
* *
52513195 ATATGATATATA
1 -TAAG-T-TATG
*
52513207 TAAGTTGT-
1 TAAGTTATG
52513215 TAAGTTATG
1 TAAGTTATG
*
52513224 TATG-TATG
1 TAAGTTATG
*
52513232 TGAGTTATG
1 TAAGTTATG
*
52513241 TAAGTTAAG
1 TAAGTTATG
* *
52513250 ATATGATATATA
1 -TAAG-T-TATG
52513262 TAAGTTAT-
1 TAAGTTATG
*
52513270 TATGTTATG
1 TAAGTTATG
52513279 TAAGTTATG
1 TAAGTTATG
*
52513288 TGAGTTATG
1 TAAGTTATG
* *
52513297 ATATGATATATA
1 -TAAG-T-TATG
52513309 TAAGTTAT-
1 TAAGTTATG
52513317 TAAGTTATG
1 TAAGTTATG
*
52513326 TATG-TATG
1 TAAGTTATG
*
52513334 TGAGTTATG
1 TAAGTTATG
52513343 TAAGTTATG
1 TAAGTTATG
* * *
52513352 ATATGATATA
1 -TAAGTTATG
*
52513362 T-ATTTATG
1 TAAGTTATG
52513370 T-A-TTATG
1 TAAGTTATG
52513377 TAAGTTATG
1 TAAGTTATG
52513386 TAAGTTATG
1 TAAGTTATG
*
52513395 TGAGTTATG
1 TAAGTTATG
52513404 TAAGTTATGG
1 TAAGTTAT-G
* *
52513414 TATGATATATA
1 TAAG-T-TATG
52513425 TAAGTTAT-
1 TAAGTTATG
52513433 TAAGTTATG
1 TAAGTTATG
*
52513442 TATG-TATG
1 TAAGTTATG
*
52513450 TGAGTTATG
1 TAAGTTATG
52513459 TAAGTTATG
1 TAAGTTATG
* * *
52513468 ATATGGTATA
1 -TAAGTTATG
*
52513478 T-ATTTATG
1 TAAGTTATG
52513486 T-A-TTATG
1 TAAGTTATG
52513493 TAAGTTATGG
1 TAAGTTAT-G
* *
52513503 TATGATATATA
1 TAAG-T-TATG
52513514 TAAGTTAT-
1 TAAGTTATG
52513522 TAAGTTATG
1 TAAGTTATG
52513531 TAAGTTATG
1 TAAGTTATG
*
52513540 TGAGTTATG
1 TAAGTTATG
* * *
52513549 ATATGATATA
1 -TAAGTTATG
*
52513559 T-A-TATATA
1 TAAGT-TATG
52513567 TAAGTTAT-
1 TAAGTTATG
*
52513575 TAAGTTACG
1 TAAGTTATG
52513584 TAAG-TATG
1 TAAGTTATG
*
52513592 TGAGTTATG
1 TAAGTTATG
52513601 TAAGTTATG
1 TAAGTTATG
** *
52513610 ATCTGATATATA
1 -TAAG-T-TATG
52513622 TAAGTTAT-
1 TAAGTTATG
*
52513630 TAAGTTAAG
1 TAAGTTATG
* *
52513639 ATCCAAAGTTTTTT
1 -T---AAG-TTATG
* *
52513653 TAA-TTCTT
1 TAAGTTATG
52513661 TAAAGTTATG
1 T-AAGTTATG
*
52513671 TAAATTATG
1 TAAGTTATG
*
52513680 TAACTTATG
1 TAAGTTATG
*
52513689 ATATGGTTAT-
1 -TA-AGTTATG
52513699 TAAGTTATG
1 TAAGTTATG
52513708 TAAGTTATG
1 TAAGTTATG
*
52513717 TGAGTTATG
1 TAAGTTATG
* *
52513726 TAAATTATA
1 TAAGTTATG
52513735 TAAGTTATG
1 TAAGTTATG
52513744 TAA
1 TAA
52513747 AATTTGATAT
Statistics
Matches: 548, Mismatches: 113, Indels: 126
0.70 0.14 0.16
Matches are distributed among these distances:
5 4 0.01
6 1 0.00
7 24 0.04
8 120 0.22
9 284 0.52
10 65 0.12
11 27 0.05
12 17 0.03
13 4 0.01
14 2 0.00
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:52513574 original size:53 final size:53
Alignment explanation
Indices: 52513488--52513636 Score: 194
Period size: 53 Copynumber: 2.7 Consensus size: 53
52513478 TATTTATGTA
* *
52513488 TTATGTAAGTTATGGTATGATATATATAAGTTATTAAGTTATGTAAGTTATGTGAG
1 TTATG-AAG-TATGATATGATATATATAAGTTATTAAGTTACGTAAG-TATGTGAG
*
52513544 TTATG-A-TATGATATATATATATATAAGTTATTAAGTTACGTAAGTATGTGAG
1 TTATGAAGTATGATAT-GATATATATAAGTTATTAAGTTACGTAAGTATGTGAG
*
52513596 TTATGTAAGTTATGATCTGATATATATAAGTTATTAAGTTA
1 TTATG-AAG-TATGATATGATATATATAAGTTATTAAGTTA
52513637 AGATCCAAAG
Statistics
Matches: 83, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
52 20 0.24
53 27 0.33
54 2 0.02
55 22 0.27
56 12 0.14
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.44
Consensus pattern (53 bp):
TTATGAAGTATGATATGATATATATAAGTTATTAAGTTACGTAAGTATGTGAG
Found at i:52513724 original size:18 final size:18
Alignment explanation
Indices: 52513663--52513787 Score: 103
Period size: 18 Copynumber: 6.9 Consensus size: 18
52513653 TAATTCTTTA
52513663 AAGTTATGTAAATTATGT
1 AAGTTATGTAAATTATGT
* **
52513681 AACTTATGATATGGTTAT-T
1 AAGTTATG-TA-AATTATGT
*
52513700 AAGTTATGTAAGTTATGT
1 AAGTTATGTAAATTATGT
* *
52513718 GAGTTATGTAAATTATAT
1 AAGTTATGTAAATTATGT
52513736 AAGTTATGTAAAATT-TGAT
1 AAGTTATGT-AAATTATG-T
* * * *
52513755 ATGATATAT-ATTTATGT
1 AAGTTATGTAAATTATGT
52513772 AAGTTATGTAAATTAT
1 AAGTTATGTAAATTAT
52513788 ATATTAATTT
Statistics
Matches: 82, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
17 15 0.18
18 41 0.50
19 22 0.27
20 4 0.05
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.46
Consensus pattern (18 bp):
AAGTTATGTAAATTATGT
Found at i:52514027 original size:73 final size:74
Alignment explanation
Indices: 52513941--52514232 Score: 500
Period size: 73 Copynumber: 4.0 Consensus size: 74
52513931 GGAAGAAATT
52513941 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAA-TTAAAAAAATAAGACTTTGAGT
1 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATTTAAAAAAATAAGACTTTGAGT
*
52514005 TGGCATTAC
66 TGGCATCAC
*
52514014 AAAATATAATTAATTTGTCGATATTTATCAAAATAAGTAAAATTTAAAAAAA-AAGACTTTGAGT
1 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATTTAAAAAAATAAGACTTTGAGT
52514078 TGGCATCAC
66 TGGCATCAC
*
52514087 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATTTAAAAAAAAAAAAGACTTTGA
1 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATTT--AAAAAAATAAGACTTTGA
52514152 GTTGGCATCAC
64 GTTGGCATCAC
* *
52514163 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAA-TTAAAAAGATAAGACTTTCAGT
1 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATTTAAAAAAATAAGACTTTGAGT
52514227 TGGCAT
66 TGGCAT
52514233 TAGAAAATCA
Statistics
Matches: 209, Mismatches: 6, Indels: 8
0.94 0.03 0.04
Matches are distributed among these distances:
73 128 0.61
74 9 0.04
75 9 0.04
76 63 0.30
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (74 bp):
AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATTTAAAAAAATAAGACTTTGAGT
TGGCATCAC
Found at i:52514240 original size:149 final size:146
Alignment explanation
Indices: 52513941--52514232 Score: 496
Period size: 149 Copynumber: 2.0 Consensus size: 146
52513931 GGAAGAAATT
*
52513941 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATTAAAAAAATAAGACTTTGAGTT
1 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATTAAAAAAAAAAGACTTTGAGTT
*
52514006 GGCATTACAAAATATAATTAATTTGTCGATATTTATCAAAATAAGTAAAATTTAAAAAAAAAGAC
66 GGCATCACAAAATATAATTAATTTGTCGATATTTATCAAAATAAGTAAAATTTAAAAAAAAAGAC
*
52514071 TTTGAGTTGGCATCAC
131 TTTCAGTTGGCATCAC
52514087 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATTTAAAAAAAAAAAAGACTTTGA
1 AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAA-TT--AAAAAAAAAAGACTTTGA
* *
52514152 GTTGGCATCACAAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAA-TTAAAAAGATA
63 GTTGGCATCACAAAATATAATTAATTTGTCGATATTTATCAAAATAAGTAAAATTTAAAAA-AAA
52514216 AGACTTTCAGTTGGCAT
127 AGACTTTCAGTTGGCAT
52514233 TAGAAAATCA
Statistics
Matches: 137, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
146 42 0.31
147 2 0.01
148 7 0.05
149 86 0.63
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (146 bp):
AAAATATAATTAATTTGTCTATATTTATCAAAATAAGTAAAATTAAAAAAAAAAGACTTTGAGTT
GGCATCACAAAATATAATTAATTTGTCGATATTTATCAAAATAAGTAAAATTTAAAAAAAAAGAC
TTTCAGTTGGCATCAC
Found at i:52514451 original size:66 final size:66
Alignment explanation
Indices: 52514370--52514518 Score: 210
Period size: 66 Copynumber: 2.3 Consensus size: 66
52514360 TATAAAATCG
* * * *
52514370 ATAATTTATTAAATTAAGTAAAAAATT-GTTAATTTATTCACATAAAATCAAATAAACTAATCAA
1 ATAATTTATTCAATTAAAT-AAAAATTCGATAATTTATTCACATAAAACCAAATAAACTAATCAA
52514434 AC
65 AC
* * * *
52514436 ATAATTTAATCAATTAAATCAAAATTCGATAATTTATTCACATTAAACCGAATAAACTAATCAAA
1 ATAATTTATTCAATTAAATAAAAATTCGATAATTTATTCACATAAAACCAAATAAACTAATCAAA
52514501 C
66 C
52514502 ATAATTTATTCAATTAA
1 ATAATTTATTCAATTAA
52514519 TCAAATATAT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 6 0.08
66 67 0.92
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (66 bp):
ATAATTTATTCAATTAAATAAAAATTCGATAATTTATTCACATAAAACCAAATAAACTAATCAAA
C
Found at i:52516677 original size:24 final size:24
Alignment explanation
Indices: 52516630--52516677 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52516620 GAACAAAAGG
*
52516630 GAAAATGAGAAGGAAAAGTTGAGA
1 GAAAATGAGAAGGAAAAGTAGAGA
*
52516654 GAAAGTGAGAGAGGAAAAG-AGAGA
1 GAAAATGAGA-AGGAAAAGTAGAGA
52516678 ATGAGAGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.38, T:0.08
Consensus pattern (24 bp):
GAAAATGAGAAGGAAAAGTAGAGA
Found at i:52518618 original size:124 final size:125
Alignment explanation
Indices: 52518395--52518693 Score: 381
Period size: 124 Copynumber: 2.4 Consensus size: 125
52518385 TTTCTGTAGT
* * * *
52518395 GAAACGGCACCG-TTCTGAGAAATTTTAATACATAGTTGCAGCGTTTTTTGGTCCAAACGCCGAT
1 GAAACGGCGCCGCTT-TTAGAAATTTAAATACATAGTTGCAGCGTTTTTTGCTCCAAACGCCGAT
* * *
52518459 ACTGATTACCATTTGCAACGTTTTCAGCAAAAATGCCACTAAAAAATTAAATTCCTATACC
65 ACTGAATACCATTTGCAACATTTTCAGCAAAAATGCCACTAAAAAATTAAATTCCTATACA
* * * *
52518520 GAAACGGCGCTGCTTTTAGAAATTTAAATACATAGTTGCGGCGTTTTTT-CTCCAAATGCCGCTA
1 GAAACGGCGCCGCTTTTAGAAATTTAAATACATAGTTGCAGCGTTTTTTGCTCCAAACGCCGATA
* ***
52518584 -TTACATACCATTTGTGGCATTTTCTAG-AAAAATGCCACTAAAAAATTAAATTCCTATACA
66 CTGA-ATACCATTTGCAACATTTTC-AGCAAAAATGCCACTAAAAAATTAAATTCCTATACA
* * *
52518644 GAAACGGCTCCGTTTTTAGAAATTTAAATACATAGTTGCAACGTTTTTTG
1 GAAACGGCGCCGCTTTTAGAAATTTAAATACATAGTTGCAGCGTTTTTTG
52518694 GACAAAACAC
Statistics
Matches: 150, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
123 2 0.01
124 103 0.69
125 43 0.29
126 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (125 bp):
GAAACGGCGCCGCTTTTAGAAATTTAAATACATAGTTGCAGCGTTTTTTGCTCCAAACGCCGATA
CTGAATACCATTTGCAACATTTTCAGCAAAAATGCCACTAAAAAATTAAATTCCTATACA
Found at i:52518748 original size:82 final size:85
Alignment explanation
Indices: 52518618--52518786 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 85
52518608 TAGAAAAATG
* *
52518618 CCACTAAAAAATTAAATTCCTATACAGAAACGGCTCCGTTTTTAGAAATTTAAATACATAGTTGC
1 CCACTAAAAAATTAAATTCCTATACAGAAACGGCTCCGTTTTAAGAAATTTAAATACATAATTGC
*
52518683 AACGTTTTTTGGACAAAACA
66 AACATTTTTTGGACAAAACA
** *
52518703 CCACTAAAAAATTAAATT-CT-TGTA-AAACGG-TGCCGTTTTAAGAAATTTTAATACATAATTG
1 CCACTAAAAAATTAAATTCCTATACAGAAACGGCT-CCGTTTTAAGAAATTTAAATACATAATTG
* * *
52518764 CGACATTTTTTGGTCCAAACA
65 CAACATTTTTTGGACAAAACA
52518785 CC
1 CC
52518787 GCTATATCTT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
81 1 0.01
82 51 0.69
83 2 0.03
84 2 0.03
85 18 0.24
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (85 bp):
CCACTAAAAAATTAAATTCCTATACAGAAACGGCTCCGTTTTAAGAAATTTAAATACATAATTGC
AACATTTTTTGGACAAAACA
Found at i:52518911 original size:14 final size:14
Alignment explanation
Indices: 52518894--52518997 Score: 97
Period size: 14 Copynumber: 7.5 Consensus size: 14
52518884 ACTAATTAAT
52518894 CTAAACCTTAAACC
1 CTAAACCTTAAACC
* *
52518908 CT-AA-CTCATATCC
1 CTAAACCTTA-AACC
* *
52518921 TTTAAACCATAAACC
1 CT-AAACCTTAAACC
52518936 CTAAACCTTAAACC
1 CTAAACCTTAAACC
*
52518950 C-CAACCTTAAACC
1 CTAAACCTTAAACC
*
52518963 CTAAACCCTAAACC
1 CTAAACCTTAAACC
* *
52518977 CTAAACCATAATCC
1 CTAAACCTTAAACC
52518991 CTAAACC
1 CTAAACC
52518998 CCTAACTTAT
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
12 3 0.04
13 18 0.25
14 43 0.60
15 6 0.08
16 2 0.03
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAAACCTTAAACC
Found at i:52518935 original size:7 final size:7
Alignment explanation
Indices: 52518923--52519099 Score: 92
Period size: 7 Copynumber: 25.3 Consensus size: 7
52518913 TCATATCCTT
*
52518923 TAAACCA
1 TAAACCC
52518930 TAAACCC
1 TAAACCC
*
52518937 TAAACCT
1 TAAACCC
52518944 TAAACCC
1 TAAACCC
* *
52518951 -CAACCT
1 TAAACCC
52518957 TAAACCC
1 TAAACCC
52518964 TAAACCC
1 TAAACCC
52518971 TAAACCC
1 TAAACCC
*
52518978 TAAACCA
1 TAAACCC
*
52518985 TAATCCC
1 TAAACCC
52518992 TAAACCCC
1 TAAA-CCC
*
52519000 T-AA-CT
1 TAAACCC
*
52519005 TATATCCC
1 TA-AACCC
*
52519013 TTAAACCT
1 -TAAACCC
* * *
52519021 TGAATCA
1 TAAACCC
* *
52519028 TAAAACA
1 TAAACCC
***
52519035 TAAATTA
1 TAAACCC
52519042 TAAACCC
1 TAAACCC
52519049 TAAACCCC
1 TAAA-CCC
52519057 TAAACCC
1 TAAACCC
*
52519064 TAACCCC
1 TAAACCC
*
52519071 T-AACCT
1 TAAACCC
*
52519077 TAAACCA
1 TAAACCC
*
52519084 TAAACCA
1 TAAACCC
*
52519091 TAATCCC
1 TAAACCC
52519098 TA
1 TA
52519100 TCCCCTATCC
Statistics
Matches: 130, Mismatches: 32, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
5 2 0.02
6 8 0.06
7 103 0.79
8 15 0.12
9 2 0.02
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:52518946 original size:21 final size:21
Alignment explanation
Indices: 52518894--52518998 Score: 99
Period size: 21 Copynumber: 5.0 Consensus size: 21
52518884 ACTAATTAAT
*
52518894 CTAAACCTTAAACCCT-AACT
1 CTAAACCTTAAACCCTAAACC
* *
52518914 C-ATATCCTTTAAACCATAAACC
1 CTA-AACC-TTAAACCCTAAACC
*
52518936 CTAAACCTTAAACCC-CAACC
1 CTAAACCTTAAACCCTAAACC
* *
52518956 TTAAACCCTAAACCCTAAACC
1 CTAAACCTTAAACCCTAAACC
* *
52518977 CTAAACCATAATCCCTAAACC
1 CTAAACCTTAAACCCTAAACC
52518998 C
1 C
52518999 CTAACTTATA
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
19 1 0.01
20 21 0.31
21 38 0.56
22 7 0.10
23 1 0.01
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (21 bp):
CTAAACCTTAAACCCTAAACC
Found at i:52518960 original size:20 final size:20
Alignment explanation
Indices: 52518932--52518983 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
52518922 TTAAACCATA
*
52518932 AACCCTAAACCTTAAACCCC
1 AACCCTAAACCCTAAACCCC
* *
52518952 AACCTTAAACCCTAAACCCTA
1 AACCCTAAACCCTAAACCC-C
52518973 AACCCTAAACC
1 AACCCTAAACC
52518984 ATAATCCCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (20 bp):
AACCCTAAACCCTAAACCCC
Found at i:52519130 original size:105 final size:106
Alignment explanation
Indices: 52518923--52519199 Score: 312
Period size: 105 Copynumber: 2.6 Consensus size: 106
52518913 TCATATCCTT
* ** * * * *
52518923 TAAACCATAAACCCTAAACCTTAAACCCC-AA-CCTTAAACCCTAAACCCTAAACCCTAAACCAT
1 TAAAACATAAACTATAAACCCTAAACCCCTAACCCTTAAACCC-CAACCTTAAACCATAAACCAT
** *
52518986 AATCCCTAAACCCCTAACTTATATCCCTTAAACCTTGAATCA
65 AATCCCTAAACCCCTAACCCATATCCCCTAAACCTTGAATCA
*
52519028 TAAAACATAAATTATAAACCCTAAACCCCTAAACCC-T-AACCCCTAACCTTAAACCATAAACCA
1 TAAAACATAAACTATAAACCCTAAACCCCT-AACCCTTAAACCCC-AACCTTAAACCATAAACCA
* * * * *
52519091 TAATCCCT-ATCCCCTATCCCCTGTCCCCTAAACCTTGAATTA
64 TAATCCCTAAACCCCTAACCCATATCCCCTAAACCTTGAATCA
* * *
52519133 TAAAACATAAACTATAAACCCTAAATCCCTAACCCTTAAACCCCAACCCTTAAACAATAAACAAT
1 TAAAACATAAACTATAAACCCTAAACCCCTAACCCTTAAACCCCAA-CCTTAAACCATAAACCAT
52519198 AA
65 AA
52519200 ATTATAATCC
Statistics
Matches: 145, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
104 5 0.03
105 81 0.56
106 54 0.37
107 3 0.02
108 2 0.01
ACGTcount: A:0.42, C:0.35, G:0.01, T:0.22
Consensus pattern (106 bp):
TAAAACATAAACTATAAACCCTAAACCCCTAACCCTTAAACCCCAACCTTAAACCATAAACCATA
ATCCCTAAACCCCTAACCCATATCCCCTAAACCTTGAATCA
Found at i:52519243 original size:15 final size:15
Alignment explanation
Indices: 52519203--52519243 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
52519193 ACAATAAATT
52519203 ATAATCCCT-AAACC
1 ATAATCCCTAAAACC
**
52519217 ATAATCTGTAAAACC
1 ATAATCCCTAAAACC
52519232 ATAATCCCTAAA
1 ATAATCCCTAAA
52519244 CTGCTAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.24
Consensus pattern (15 bp):
ATAATCCCTAAAACC
Found at i:52522278 original size:20 final size:21
Alignment explanation
Indices: 52522232--52522279 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
52522222 TATTTTTAGC
52522232 AATTTTTAGATATTGTTTTAT
1 AATTTTTAGATATTGTTTTAT
**
52522253 TGTTTTTAG-TATTGTTTGTA-
1 AATTTTTAGATATTGTTT-TAT
52522273 AATTTTT
1 AATTTTT
52522280 TTAAAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (21 bp):
AATTTTTAGATATTGTTTTAT
Found at i:52522930 original size:24 final size:23
Alignment explanation
Indices: 52522896--52522948 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
52522886 CGCACGTAAC
*
52522896 AAAAATTAAAA-AAATAACATTTTA
1 AAAAATGAAAACAAAT-A-ATTTTA
*
52522920 AAAAATGAAAACAAATATTTTTA
1 AAAAATGAAAACAAATAATTTTA
52522943 AAAAAT
1 AAAAAT
52522949 ATTTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
24 11 0.42
25 4 0.15
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAAATGAAAACAAATAATTTTA
Found at i:52555012 original size:27 final size:26
Alignment explanation
Indices: 52554971--52555023 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
52554961 AATGCGTTCA
*
52554971 TGCTTATATGTAGGTGCTGAAAGATTC
1 TGCTTATATGAAGGTGCTGAAA-ATTC
*
52554998 TGCTTATGTGAAGGTGCTGAAAATTC
1 TGCTTATATGAAGGTGCTGAAAATTC
52555024 CAAGAAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.36
Consensus pattern (26 bp):
TGCTTATATGAAGGTGCTGAAAATTC
Found at i:52563175 original size:16 final size:16
Alignment explanation
Indices: 52563154--52563223 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
52563144 TTTGGTTCGC
52563154 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
52563170 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
* *
52563186 TGTAATAGAATAGATG
1 TGTAATGGAATAGAGG
*
52563202 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
52563218 CGTAAT
1 TGTAAT
52563224 AGGTAATTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.39, C:0.03, G:0.33, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:52563292 original size:44 final size:46
Alignment explanation
Indices: 52563205--52563293 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 46
52563195 ATAGATGCGT
*
52563205 AATGGAATAGAGGCGTAATAGGTAATTCTTTTATTTCGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTATTTCGTTGAATGG
* * *
52563251 AATGGAATATAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTATTTCGTTGAATG
52563294 TAATAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 18 0.46
45 3 0.08
46 18 0.46
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTATTTCGTTGAATGG
Found at i:52563503 original size:15 final size:16
Alignment explanation
Indices: 52563483--52563512 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52563473 ATATATAATT
52563483 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
52563498 TAATAAATATTCTTA
1 TAATAAATATTCTTA
52563513 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:52563679 original size:38 final size:38
Alignment explanation
Indices: 52563637--52563799 Score: 91
Period size: 38 Copynumber: 4.2 Consensus size: 38
52563627 TTCTTTTATG
52563637 AATTTACTAAAATCATAATATATAATACTATAAAATAA
1 AATTTACTAAAATCATAATATATAATACTATAAAATAA
* *** * *
52563675 AATTTAATTAGTTTTTATTAA-ATATAAT-TTAATAAAAATATA
1 AATTT-ACTA-AAATCA-TAATATATAATACT-AT-AAAATA-A
* * * * * * *
52563717 TAATTTAATAAAATTCTTAATA-ATAAATATTCTTATAT-G
1 -AATTTACTAAAA-TCATAATATAT-AATACTATAAAATAA
*
52563756 AATTTACTAAAATCATAATATATAATACTATAAAATAT
1 AATTTACTAAAATCATAATATATAATACTATAAAATAA
52563794 AATTTA
1 AATTTA
52563800 ATTAGTTTTA
Statistics
Matches: 89, Mismatches: 23, Indels: 26
0.64 0.17 0.19
Matches are distributed among these distances:
37 16 0.18
38 24 0.27
39 4 0.04
40 11 0.12
41 17 0.19
42 10 0.11
43 7 0.08
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (38 bp):
AATTTACTAAAATCATAATATATAATACTATAAAATAA
Found at i:52563742 original size:15 final size:16
Alignment explanation
Indices: 52563722--52563751 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52563712 ATATATAATT
52563722 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
52563737 TAATAAATATTCTTA
1 TAATAAATATTCTTA
52563752 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:52563756 original size:119 final size:118
Alignment explanation
Indices: 52563450--52563878 Score: 759
Period size: 119 Copynumber: 3.6 Consensus size: 118
52563440 AACATAATTA
52563450 TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATA
1 TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATA
* * *
52563515 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAAGTA
66 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATT--TAATTAGTT
*
52563570 TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTTTA
1 TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATA
*
52563635 TGAATTTACTAAAATCATAATATATAATACTATAAAATAAAATTTAATTAGTTT
66 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAATTAG-TT
52563689 TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATA
1 TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATA
52563754 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAATTAGTT
66 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAATTAGTT
* * *
52563807 TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTTTTAGTAATAAATATTCATATA
1 TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATA
52563872 TGAATTT
66 TGAATTT
52563879 GTATAATTTA
Statistics
Matches: 298, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
118 76 0.26
119 115 0.39
120 107 0.36
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (118 bp):
TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATA
TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAATTAGTT
Found at i:52563884 original size:47 final size:46
Alignment explanation
Indices: 52563831--52564060 Score: 165
Period size: 47 Copynumber: 5.0 Consensus size: 46
52563821 TTAATAAAAA
* *
52563831 TATATAATTTAATAAAATTTTTAGTAATAAATATTCATATATGAATT
1 TATATAATTTAATAAAATTATTACTAATAAAT-TTCATATATGAATT
* * *
52563878 TGTATAATTTAA-AATAATTATTATTAAATATAATTTAATA-AT-AA--
1 TATATAATTTAATAA-AATTATTACT-AATA-AATTTCATATATGAATT
* * * *
52563922 TATATAATTTCATAAAATTCTTACTAATAAATTTTCTTATACGAATT
1 TATATAATTTAATAAAATTATTACTAATAAA-TTTCATATATGAATT
* * *
52563969 TGTATAATTTAA-AATAATTATTATTAAATATAATTTAATA-AT-AA--
1 TATATAATTTAATAA-AATTATTACT-AATA-AATTTCATATATGAATT
* * * *
52564013 TATATAATTTCATAAAATTCTTACTAACAAATTTTCTTATATGAATT
1 TATATAATTTAATAAAATTATTACTAATAAA-TTTCATATATGAATT
52564060 T
1 T
52564061 TCTAAAATCA
Statistics
Matches: 140, Mismatches: 25, Indels: 36
0.70 0.12 0.18
Matches are distributed among these distances:
42 4 0.03
43 17 0.12
44 39 0.28
45 8 0.06
46 8 0.06
47 41 0.29
48 18 0.13
49 5 0.04
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (46 bp):
TATATAATTTAATAAAATTATTACTAATAAATTTCATATATGAATT
Found at i:52563915 original size:91 final size:91
Alignment explanation
Indices: 52563791--52564060 Score: 436
Period size: 91 Copynumber: 3.0 Consensus size: 91
52563781 TACTATAAAA
* * * * *
52563791 TATAATTT-AATTAGTT-TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTTTTA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTA
* * *
52563854 GTAATAAATATTCATATATGAATTTG
66 CTAATAAATTTTCTTATATGAATTTG
52563880 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTA
*
52563945 CTAATAAATTTTCTTATACGAATTTG
66 CTAATAAATTTTCTTATATGAATTTG
52563971 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTA
1 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTA
*
52564036 CTAACAAATTTTCTTATATGAATTT
66 CTAATAAATTTTCTTATATGAATTT
52564061 TCTAAAATCA
Statistics
Matches: 168, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
89 8 0.05
90 6 0.04
91 154 0.92
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (91 bp):
TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTA
CTAATAAATTTTCTTATATGAATTTG
Found at i:52566644 original size:15 final size:15
Alignment explanation
Indices: 52566624--52566653 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52566614 GAATTGGGAT
52566624 TCACTGCATTTGAAG
1 TCACTGCATTTGAAG
52566639 TCACTGCATTTGAAG
1 TCACTGCATTTGAAG
52566654 ATAACTGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (15 bp):
TCACTGCATTTGAAG
Found at i:52567819 original size:21 final size:21
Alignment explanation
Indices: 52567775--52567835 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
52567765 ATGCCCGTGC
* ** *
52567775 GAAGGCCACTCACGCTTGTGT
1 GAAGGCCACACACGCCCGTAT
*
52567796 GAAGGCCACACGCGCCCGTAT
1 GAAGGCCACACACGCCCGTAT
*
52567817 GAAGGCCATACACGCCCGT
1 GAAGGCCACACACGCCCGT
52567836 GTGGAGGGGC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.34, G:0.28, T:0.15
Consensus pattern (21 bp):
GAAGGCCACACACGCCCGTAT
Found at i:52571374 original size:17 final size:16
Alignment explanation
Indices: 52571348--52571379 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
52571338 TTTTACTTCC
52571348 AAAAATAAAATAAATT
1 AAAAATAAAATAAATT
52571364 AAAAATCAAAATAAAT
1 AAAAAT-AAAATAAAT
52571380 AACTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATAAAATAAATT
Found at i:52577691 original size:21 final size:21
Alignment explanation
Indices: 52577665--52577769 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 21
52577655 CTAGGTTTTT
*
52577665 AGTTTAGCTCTTTTGAGCTTC
1 AGTTTAGCTCTTATGAGCTTC
* * * * * *
52577686 AGTTTAACCCTAATGGGTTTT
1 AGTTTAGCTCTTATGAGCTTC
*
52577707 AGTTTAGCTCTTCTGAGCTTC
1 AGTTTAGCTCTTATGAGCTTC
* * * *
52577728 AGATTCACCT-TTATGGGTTTC
1 AG-TTTAGCTCTTATGAGCTTC
* *
52577749 CGTTCAGCTCTTATGAGCTTC
1 AGTTTAGCTCTTATGAGCTTC
52577770 CGTTCAACCC
Statistics
Matches: 59, Mismatches: 23, Indels: 4
0.69 0.27 0.05
Matches are distributed among these distances:
20 6 0.10
21 48 0.81
22 5 0.08
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTTTAGCTCTTATGAGCTTC
Found at i:52577724 original size:42 final size:42
Alignment explanation
Indices: 52577633--52577789 Score: 179
Period size: 42 Copynumber: 3.7 Consensus size: 42
52577623 AGTCAACTCA
* * *
52577633 TATGAGTTTCAGTTTAACCCTTCTAGGTTTTTAGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTAT-GGGTTTTAGTTTAGCTCT
* *
52577676 TTTGAGCTTCAGTTTAACCCTAATGGGTTTTAGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTTAGTTTAGCTCT
* * * * ** *
52577718 TCTGAGCTTCAGATTCACCTTTATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTTAGTTTAGCTCT
* *
52577760 TATGAGCTTCCGTTCAACCCTTATGGGTTT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTT
52577790 CTTTTTAGCA
Statistics
Matches: 95, Mismatches: 19, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
42 75 0.79
43 20 0.21
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.44
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTTAGTTTAGCTCT
Found at i:52577770 original size:21 final size:21
Alignment explanation
Indices: 52577712--52577784 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
52577702 GTTTTAGTTT
* *
52577712 AGCTCTTCTGAGCTTCAGATTC
1 AGCTCTTATGAGCTTCCG-TTC
* * *
52577734 ACCT-TTATGGGTTTCCGTTC
1 AGCTCTTATGAGCTTCCGTTC
52577754 AGCTCTTATGAGCTTCCGTTC
1 AGCTCTTATGAGCTTCCGTTC
* *
52577775 AACCCTTATG
1 AGCTCTTATG
52577785 GGTTTCTTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
20 6 0.15
21 31 0.77
22 3 0.08
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.38
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCCGTTC
Found at i:52580018 original size:20 final size:21
Alignment explanation
Indices: 52579982--52580020 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
52579972 GTTGTATTAA
*
52579982 AAATAGATAAATGAATAAAGT
1 AAATAGATAAATAAATAAAGT
52580003 AAATAGA-AAATAAATAAA
1 AAATAGATAAATAAATAAA
52580021 TAGGGGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (21 bp):
AAATAGATAAATAAATAAAGT
Found at i:52588081 original size:6 final size:6
Alignment explanation
Indices: 52588072--52588105 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
52588062 AAAACGACCA
*
52588072 CCACGT CCACGT CCACGT CCACGC CCACGT CCAC
1 CCACGT CCACGT CCACGT CCACGT CCACGT CCAC
52588106 CTCGATGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.56, G:0.15, T:0.12
Consensus pattern (6 bp):
CCACGT
Found at i:52591986 original size:27 final size:27
Alignment explanation
Indices: 52591956--52592008 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
52591946 GCATAACAGA
*
52591956 TTTTTATTTGAATTTGTTTATTTTGTC
1 TTTTTATTTGAATTTGTTTACTTTGTC
52591983 TTTTTATTTGAATTTGTTTACTTTGT
1 TTTTTATTTGAATTTGTTTACTTTGT
52592009 GTTTGATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.04, G:0.11, T:0.70
Consensus pattern (27 bp):
TTTTTATTTGAATTTGTTTACTTTGTC
Found at i:52593627 original size:51 final size:51
Alignment explanation
Indices: 52593513--52593728 Score: 362
Period size: 51 Copynumber: 4.3 Consensus size: 51
52593503 CTTATGTATG
* * *
52593513 ATCACTTATCACTTGTCCCTGATCAGATAAGTGTAGC-AAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
*
52593563 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
*
52593614 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
52593665 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
52593716 ATCACTTGTCACT
1 ATCACTTGTCACT
52593729 GATCAGAAAT
Statistics
Matches: 155, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 34 0.22
51 121 0.78
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
Found at i:52594325 original size:43 final size:43
Alignment explanation
Indices: 52594250--52594341 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
52594240 TTTGGAAAAG
*
52594250 CGCCGCTAAAGACCATGACCTATAGCAACACTTCTCTAACAAA
1 CGCCGCTAAAGACCATGACCTATAGCAACACTTCTCCAACAAA
* * ** * *
52594293 CGCCGCTAAAGA-CATTGAGCTTTAGCGGCACTTTTCCCACAAA
1 CGCCGCTAAAGACCA-TGACCTATAGCAACACTTCTCCAACAAA
52594336 CGCCGC
1 CGCCGC
52594342 CATAGCTCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 2 0.05
43 39 0.95
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.20
Consensus pattern (43 bp):
CGCCGCTAAAGACCATGACCTATAGCAACACTTCTCCAACAAA
Found at i:52594355 original size:43 final size:43
Alignment explanation
Indices: 52594288--52594436 Score: 158
Period size: 43 Copynumber: 3.5 Consensus size: 43
52594278 CACTTCTCTA
* * * *
52594288 ACAAACGCCGCTAAAG-ACATTGAGCTTTAGCGGCACTTTTCCC
1 ACAAACGCCGCTATAGCTCA-TGAGCTTTAGCGACGCTTTTCCC
* * *
52594331 ACAAACGCCGCCATAGCTCATGAGCTTTAGCAACGCTTTTTCC
1 ACAAACGCCGCTATAGCTCATGAGCTTTAGCGACGCTTTTCCC
* * *
52594374 ACAAACGTCGCTATAGCTCTAT-ACCTTTAGCGACGCTTTTCTC
1 ACAAACGCCGCTATAGCTC-ATGAGCTTTAGCGACGCTTTTCCC
* *
52594417 ACAAATGCCGCTATAACTCA
1 ACAAACGCCGCTATAGCTCA
52594437 ATAGCGGCGC
Statistics
Matches: 88, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
42 1 0.01
43 83 0.94
44 4 0.05
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (43 bp):
ACAAACGCCGCTATAGCTCATGAGCTTTAGCGACGCTTTTCCC
Found at i:52599762 original size:19 final size:20
Alignment explanation
Indices: 52599734--52599776 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
52599724 AAATTATAAA
*
52599734 TTTTAGTTTTTTTATTTCAT
1 TTTTAGTTTTTGTATTTCAT
*
52599754 TTTTA-TTTTTGTATTTTAT
1 TTTTAGTTTTTGTATTTCAT
52599773 TTTT
1 TTTT
52599777 TTCTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTAGTTTTTGTATTTCAT
Found at i:52600158 original size:7 final size:7
Alignment explanation
Indices: 52600148--52600189 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
52600138 TAACTTCTAG
52600148 CCCCTAA
1 CCCCTAA
52600155 CCCCTAA
1 CCCCTAA
*
52600162 CTCCTAA
1 CCCCTAA
52600169 CCCCTAA
1 CCCCTAA
**
52600176 CTTCTAA
1 CCCCTAA
52600183 CCCCTAA
1 CCCCTAA
52600190 ACCATAATCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCCTAA
Found at i:52600167 original size:14 final size:14
Alignment explanation
Indices: 52600150--52600189 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
52600140 ACTTCTAGCC
52600150 CCTAACCCCTAACT
1 CCTAACCCCTAACT
52600164 CCTAACCCCTAACT
1 CCTAACCCCTAACT
*
52600178 TCTAACCCCTAA
1 CCTAACCCCTAA
52600190 ACCATAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.30, C:0.47, G:0.00, T:0.23
Consensus pattern (14 bp):
CCTAACCCCTAACT
Done.