Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 125 of 193
Found at i:39517149 original size:35 final size:36
Alignment explanation
Indices: 39517110--39517178 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
39517100 TTTCAACTAA
**
39517110 AATAAAA-ATCATAAATTTTAGTTAAAAAT-TATTTC
1 AATAAAACAT-ATAAATTTTACATAAAAATCTATTTC
*
39517145 AATAAAACATTTAAATTTTACATAAAAATCTATT
1 AATAAAACATATAAATTTTACATAAAAATCTATT
39517179 ATTTATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 23 0.79
36 6 0.21
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (36 bp):
AATAAAACATATAAATTTTACATAAAAATCTATTTC
Found at i:39519278 original size:19 final size:22
Alignment explanation
Indices: 39519237--39519278 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
39519227 AAAAATTAAA
39519237 ATAAATAATATAATATATTATTT
1 ATAAATAATATAATATA-TATTT
39519260 ATAAATAA-ATAA-ATA-ATTT
1 ATAAATAATATAATATATATTT
39519279 CAATACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.21
21 3 0.16
22 4 0.21
23 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAAATAATATAATATATATTT
Found at i:39520511 original size:3 final size:3
Alignment explanation
Indices: 39520503--39520530 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39520493 AGCCATTTTC
39520503 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
39520531 AATGAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39521318 original size:31 final size:32
Alignment explanation
Indices: 39521283--39521344 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
39521273 TTTTACCCTC
*
39521283 AATTATTTGAAAGTTTTT-ATTTAACTCATTT
1 AATTATTTAAAAGTTTTTCATTTAACTCATTT
39521314 AATTATTTAAAAGTTTTTCATTTAACTCATT
1 AATTATTTAAAAGTTTTTCATTTAACTCATT
39521345 GAGTTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 17 0.59
32 12 0.41
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (32 bp):
AATTATTTAAAAGTTTTTCATTTAACTCATTT
Found at i:39523130 original size:42 final size:41
Alignment explanation
Indices: 39523077--39523196 Score: 117
Period size: 37 Copynumber: 3.0 Consensus size: 41
39523067 CTTTGTTTTA
39523077 GTTTGATTTTACTTTATAGTTGATCTAATATGTATATACTT
1 GTTTGATTTTACTTTATAGTTGATCTAATATGTATATACTT
* * * * **
39523118 TTTTGTTTTTTACTCTT-CA-TTCATCATGCTATGTAT-TA---
1 GTTTG-ATTTTACT-TTATAGTTGATC-TAATATGTATATACTT
39523156 GTTTGATTTTACTTTATAGTTGATCTAATATGTATATACTT
1 GTTTGATTTTACTTTATAGTTGATCTAATATGTATATACTT
39523197 ATGTGTATTT
Statistics
Matches: 58, Mismatches: 12, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
36 2 0.03
37 16 0.28
38 11 0.19
41 11 0.19
42 16 0.28
43 2 0.03
ACGTcount: A:0.24, C:0.10, G:0.11, T:0.55
Consensus pattern (41 bp):
GTTTGATTTTACTTTATAGTTGATCTAATATGTATATACTT
Found at i:39523135 original size:79 final size:80
Alignment explanation
Indices: 39523038--39523196 Score: 266
Period size: 79 Copynumber: 2.0 Consensus size: 80
39523028 TTGTTTGGAC
* ** * *
39523038 TTTTGTTTTTTTATTCTTCATTCATTGTGCTTTGTTTTAGTTTGATTTTACTTTATAGTTGATCT
1 TTTTGTTTTTTTACTCTTCATTCATCATGCTATGTATTAGTTTGATTTTACTTTATAGTTGATCT
39523103 AATATGTATATACTT
66 AATATGTATATACTT
39523118 TTTTG-TTTTTTACTCTTCATTCATCATGCTATGTATTAGTTTGATTTTACTTTATAGTTGATCT
1 TTTTGTTTTTTTACTCTTCATTCATCATGCTATGTATTAGTTTGATTTTACTTTATAGTTGATCT
39523182 AATATGTATATACTT
66 AATATGTATATACTT
39523197 ATGTGTATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 69 0.93
80 5 0.07
ACGTcount: A:0.21, C:0.10, G:0.11, T:0.58
Consensus pattern (80 bp):
TTTTGTTTTTTTACTCTTCATTCATCATGCTATGTATTAGTTTGATTTTACTTTATAGTTGATCT
AATATGTATATACTT
Found at i:39524511 original size:130 final size:130
Alignment explanation
Indices: 39524329--39524624 Score: 524
Period size: 130 Copynumber: 2.3 Consensus size: 130
39524319 TAATGATTGT
* *
39524329 CATTTGAGT-CAA-ACTAAAATTTCAAAATTAAAAAAATATATAGAGATGAAAAATGATTAAATT
1 CATTTGA-TACAAGACTCAAATTTCAAAATTAAAAAAAAATATAGAGATGAAAAATGATTAAATT
*
39524392 AGAGAATATAGATTAGATCAACAATTATGCATAGTACAAGATTAATAATAAAATTTAATCGGTTA
65 AGAGAATATAGACTAGATCAACAATTATGCATAGTACAAGATTAATAATAAAATTTAATCGGTTA
39524457 A
130 A
39524458 CATTTGATACAAGACTCAAATTTCAAAATTAAAAAAAAATATAGAGATGAAAAATGATTAAATTA
1 CATTTGATACAAGACTCAAATTTCAAAATTAAAAAAAAATATAGAGATGAAAAATGATTAAATTA
*
39524523 GAGAATATAGACTAGATCAATAATTATGCATAGTACAAGATTAATAATAAAATTTAATCGGTTAA
66 GAGAATATAGACTAGATCAACAATTATGCATAGTACAAGATTAATAATAAAATTTAATCGGTTAA
*
39524588 CATTTGATACAAGACTCAAATTTCATAATTAAAAAAA
1 CATTTGATACAAGACTCAAATTTCAAAATTAAAAAAA
39524625 TATAAATACT
Statistics
Matches: 160, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
128 1 0.01
129 10 0.06
130 149 0.93
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (130 bp):
CATTTGATACAAGACTCAAATTTCAAAATTAAAAAAAAATATAGAGATGAAAAATGATTAAATTA
GAGAATATAGACTAGATCAACAATTATGCATAGTACAAGATTAATAATAAAATTTAATCGGTTAA
Found at i:39525540 original size:208 final size:207
Alignment explanation
Indices: 39525173--39525590 Score: 827
Period size: 208 Copynumber: 2.0 Consensus size: 207
39525163 GCCCTTGCTA
39525173 ACTCTTCAGGTTTCCCTCTATTTGTATAGTCATGCCATTTTTTCATAATATAATTGGATGAAATT
1 ACTCTTCAGGTTTCCCTCTATTTGTATAGTCATGCCATTTTTTCATAATATAATTGGATGAAATT
39525238 TTTAATAAAAATGATTAATTTTTTTAATCTAACGTATAAAGATTAATTTATTTATATTTTAAATC
66 TTTAATAAAAATGATTAATTTTTTTAATCTAACGTATAAAGATTAATTTATTTATATTTTAAATC
39525303 AAGAAAACAAAATGTAATTTAACTCCTAGTATAAGAGCCAACATGTTAGTTTTACCATTTAAAAA
131 AAGAAAACAAAATGTAATTTAACTCCTAGTATAAGAGCCAACATGTTAGTTTTACCATTTAAAAA
39525368 CCCTACCAACTT
196 CCCTACCAACTT
39525380 ACTCTTCAGGTTTCCCTCTATTTGTATAGTCATGCCATTTTTTCATAATATAATTGGATGAAATT
1 ACTCTTCAGGTTTCCCTCTATTTGTATAGTCATGCCATTTTTTCATAATATAATTGGATGAAATT
39525445 TTTAATAAAAATGATATAATTTTTTTAATCTAACGTATAAAGATTAATTTATTTATATTTTAAAT
66 TTTAATAAAAATGAT-TAATTTTTTTAATCTAACGTATAAAGATTAATTTATTTATATTTTAAAT
39525510 CAAGAAAACAAAATGTAATTTAACTCCTAGTATAAGAGCCAACATGTTAGTTTTACCATTTAAAA
130 CAAGAAAACAAAATGTAATTTAACTCCTAGTATAAGAGCCAACATGTTAGTTTTACCATTTAAAA
39525575 ACCCTACCAACTT
195 ACCCTACCAACTT
39525588 ACT
1 ACT
39525591 TTATTCATGG
Statistics
Matches: 210, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
207 80 0.38
208 130 0.62
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (207 bp):
ACTCTTCAGGTTTCCCTCTATTTGTATAGTCATGCCATTTTTTCATAATATAATTGGATGAAATT
TTTAATAAAAATGATTAATTTTTTTAATCTAACGTATAAAGATTAATTTATTTATATTTTAAATC
AAGAAAACAAAATGTAATTTAACTCCTAGTATAAGAGCCAACATGTTAGTTTTACCATTTAAAAA
CCCTACCAACTT
Found at i:39531988 original size:10 final size:10
Alignment explanation
Indices: 39531973--39532021 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
39531963 TTTATTGTTG
39531973 TTATTTTAAT
1 TTATTTTAAT
*
39531983 TTATTTTAAAA
1 TTATTTT-AAT
39531994 TTATTTTAAT
1 TTATTTTAAT
39532004 TTATTTTTAA-
1 TTA-TTTTAAT
39532014 TTATTTTA
1 TTATTTTA
39532022 TAAAGTTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 5 0.14
10 15 0.43
11 15 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATTTTAAT
Found at i:39531997 original size:21 final size:20
Alignment explanation
Indices: 39531973--39532021 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
39531963 TTTATTGTTG
39531973 TTATTTTAATTTATTTTAAAA
1 TTATTTTAATTTATTTT-AAA
*
39531994 TTATTTTAATTTATTTTTAA
1 TTATTTTAATTTATTTTAAA
39532014 TTATTTTA
1 TTATTTTA
39532022 TAAAGTTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTAATTTATTTTAAA
Found at i:39532109 original size:27 final size:26
Alignment explanation
Indices: 39532070--39532123 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
39532060 TTATTATATA
*
39532070 TTTTTTTAATTTA-GTGTTTATGTAAG
1 TTTTTATAATTTATGTGTTTA-GTAAG
*
39532096 TTTTTATAATTTTATTTGTTTAGTAAG
1 TTTTTATAA-TTTATGTGTTTAGTAAG
39532123 T
1 T
39532124 AGATTAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.33
27 10 0.42
28 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (26 bp):
TTTTTATAATTTATGTGTTTAGTAAG
Found at i:39533119 original size:18 final size:17
Alignment explanation
Indices: 39533088--39533121 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39533078 GGACTAACAA
*
39533088 ATTAAAAAGAAAATTAT
1 ATTAAAAAAAAAATTAT
39533105 ATTAAAAAAACAAATTA
1 ATTAAAAAAA-AAATTA
39533122 AAAAGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
ATTAAAAAAAAAATTAT
Found at i:39564121 original size:53 final size:53
Alignment explanation
Indices: 39564041--39564234 Score: 289
Period size: 53 Copynumber: 3.6 Consensus size: 53
39564031 GTAAATGTAA
*
39564041 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTGCGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
* * * *
39564094 AAAGGTACGATGGCTCTGTGTCATCGTGTGTTATATGAATCCTATTATGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
* **
39564147 AAAGGTCCGATGACTTTGTGTCATTATGAGTTATATGAATCCCTATTACGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAAT-CCTATTACGGATT
* *
39564201 AAAGGTCCGAAGACTCCGTGTCATCGTGAGTTAT
1 AAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
39564235 CAAATGTGAG
Statistics
Matches: 123, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 82 0.67
54 41 0.33
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (53 bp):
AAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATTACGGATT
Found at i:39566830 original size:32 final size:32
Alignment explanation
Indices: 39566792--39566864 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
39566782 TTCTTTATTT
39566792 TCCATTCTCTTCTACTTCTCCTTTTGTTTTCC
1 TCCATTCTCTTCTACTTCTCCTTTTGTTTTCC
*
39566824 TCCATTCTCTTCTACTTCTCCTTTTGTTTTCT
1 TCCATTCTCTTCTACTTCTCCTTTTGTTTTCC
39566856 TCCATTCTC
1 TCCATTCTC
39566865 CATGTAACAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.07, C:0.34, G:0.03, T:0.56
Consensus pattern (32 bp):
TCCATTCTCTTCTACTTCTCCTTTTGTTTTCC
Found at i:39567116 original size:21 final size:21
Alignment explanation
Indices: 39567091--39567162 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
39567081 GGACAAGTAT
39567091 CGATACAAGAGACAATTCTAC
1 CGATACAAGAGACAATTCTAC
* *
39567112 TGATACAAGTGACAATTCTAC
1 CGATACAAGAGACAATTCTAC
**
39567133 CGATACAAGAGACTCTTCTAC
1 CGATACAAGAGACAATTCTAC
*
39567154 CGAAACAAG
1 CGATACAAG
39567163 TCATGCAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (21 bp):
CGATACAAGAGACAATTCTAC
Found at i:39570885 original size:8 final size:8
Alignment explanation
Indices: 39570863--39570895 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
39570853 TTTTCGAGTC
39570863 TTTCTTTT
1 TTTCTTTT
39570871 GTTTCTTTT
1 -TTTCTTTT
39570880 TTTC-TTT
1 TTTCTTTT
39570887 TTTCTTTT
1 TTTCTTTT
39570895 T
1 T
39570896 ACATACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
8 8 0.35
9 8 0.35
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (8 bp):
TTTCTTTT
Found at i:39574597 original size:52 final size:52
Alignment explanation
Indices: 39574519--39574710 Score: 246
Period size: 52 Copynumber: 3.7 Consensus size: 52
39574509 ATAAACGAAG
* *
39574519 AGGTCTGATGACTTAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
39574571 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGA-TAAA
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
* * * ** *
39574622 GAGGTCCGATGACCAAGTGTCATCATGAGTATATGAATCCCTTGTGGATTATA
1 -AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
* *
39574675 AGGTCC-AGTGGCTATGTGTCA-CTGTGAGTATATGAA
1 AGGTCCGA-TGACTAAGTGTCATC-GTGAGTATATGAA
39574711 CGAAGTGAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
51 6 0.05
52 115 0.93
53 3 0.02
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (52 bp):
AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
Found at i:39575309 original size:21 final size:21
Alignment explanation
Indices: 39575285--39575362 Score: 111
Period size: 21 Copynumber: 3.6 Consensus size: 21
39575275 GACTTGAGTT
39575285 GTATCGGTAGTTGAATGGTAA
1 GTATCGGTAGTTGAATGGTAA
39575306 GTATCGGTAGTTGAATGGTAA
1 GTATCGGTAGTTGAATGGTAA
* *
39575327 GTATCGGTAGTTGTATGTATAGA
1 GTATCGGTAGTTGAATG-GTA-A
39575350 TGTATCGGTAGTT
1 -GTATCGGTAGTT
39575363 TGCATACTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
21 37 0.71
22 2 0.04
23 1 0.02
24 12 0.23
ACGTcount: A:0.26, C:0.05, G:0.32, T:0.37
Consensus pattern (21 bp):
GTATCGGTAGTTGAATGGTAA
Found at i:39576914 original size:19 final size:19
Alignment explanation
Indices: 39576890--39576981 Score: 114
Period size: 19 Copynumber: 4.9 Consensus size: 19
39576880 CAGTAATTTG
39576890 CTCTTACGAGCCAGTATCA
1 CTCTTACGAGCCAGTATCA
*
39576909 CTCTTACGAGCCAGTATCG
1 CTCTTACGAGCCAGTATCA
* ** *
39576928 CTCTCACGAGGTAGTAT-G
1 CTCTTACGAGCCAGTATCA
*
39576946 CTCTTACGAGCCAGTTTCA
1 CTCTTACGAGCCAGTATCA
*
39576965 CTCTTACAAGCCAGTAT
1 CTCTTACGAGCCAGTAT
39576982 GCTATAACGA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
18 14 0.23
19 47 0.77
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (19 bp):
CTCTTACGAGCCAGTATCA
Found at i:39576959 original size:37 final size:37
Alignment explanation
Indices: 39576898--39576998 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 37
39576888 TGCTCTTACG
* * *
39576898 AGCCAGTATCACTCTTACGAGCCAGTATCGCTCTCACG
1 AGCCAGTAT-GCTCTTACGAGCCAGTATCACTCTCACA
** * *
39576936 AGGTAGTATGCTCTTACGAGCCAGTTTCACTCTTACA
1 AGCCAGTATGCTCTTACGAGCCAGTATCACTCTCACA
* *
39576973 AGCCAGTATGCTATAACGAGCCAGTA
1 AGCCAGTATGCTCTTACGAGCCAGTA
39576999 CAGTGCTTTC
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
37 44 0.86
38 7 0.14
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (37 bp):
AGCCAGTATGCTCTTACGAGCCAGTATCACTCTCACA
Found at i:39582619 original size:21 final size:21
Alignment explanation
Indices: 39582593--39582647 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
39582583 TTTGTCTGAC
*
39582593 AATTCTTGCAACTGAGCCTTT
1 AATTCTTTCAACTGAGCCTTT
39582614 AATTCTTTCAACTGAGCCTTT
1 AATTCTTTCAACTGAGCCTTT
39582635 AATTCTTTCAACT
1 AATTCTTTCAACT
39582648 CGGTCGGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.42
Consensus pattern (21 bp):
AATTCTTTCAACTGAGCCTTT
Found at i:39584944 original size:21 final size:21
Alignment explanation
Indices: 39584896--39584935 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39584886 CAGTGCAAAC
*
39584896 TTCTACCGATACAAGTGACAA
1 TTCTACCGATACAAGAGACAA
39584917 TTCTACCGATACAAGAGAC
1 TTCTACCGATACAAGAGAC
39584936 TCTTTTACCT
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:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (21 bp):
TTCTACCGATACAAGAGACAA
Found at i:39590668 original size:20 final size:22
Alignment explanation
Indices: 39590643--39590682 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
39590633 AGCTTGACAC
39590643 ATTGAC-GAAAAT-AAAAAAAA
1 ATTGACTGAAAATGAAAAAAAA
39590663 ATTGACTGAAAATGAAAAAA
1 ATTGACTGAAAATGAAAAAA
39590683 TAAACTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 6 0.33
22 6 0.33
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.17
Consensus pattern (22 bp):
ATTGACTGAAAATGAAAAAAAA
Found at i:39590893 original size:20 final size:20
Alignment explanation
Indices: 39590868--39590913 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
39590858 TGAGAAAATT
39590868 AAATATCCTCAAATATTGAG
1 AAATATCCTCAAATATTGAG
39590888 AAATATCCTCAAATATTGAG
1 AAATATCCTCAAATATTGAG
39590908 AAATAT
1 AAATAT
39590914 GAAATGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (20 bp):
AAATATCCTCAAATATTGAG
Found at i:39591065 original size:14 final size:14
Alignment explanation
Indices: 39591046--39591072 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39591036 TTGGTTAGTT
39591046 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
39591060 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
39591073 AACATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:39595634 original size:109 final size:109
Alignment explanation
Indices: 39595443--39595661 Score: 420
Period size: 109 Copynumber: 2.0 Consensus size: 109
39595433 TATAATTCTA
* *
39595443 CCTGCCTTTTCTTTTGGACGATTTTACTGAAGTTATTTGTGAATGCTATAGATTTCTTGACCCTT
1 CCTGCCTTTTCTTTTGGAAGATTTTACTGAAGTTATTTGTGAATGCTATAGATTTCTTGACCATT
39595508 CAAAGTTTATATGATGCAACAAAGTAGTTACAGAGATAAAGTAG
66 CAAAGTTTATATGATGCAACAAAGTAGTTACAGAGATAAAGTAG
39595552 CCTGCCTTTTCTTTTGGAAGATTTTACTGAAGTTATTTGTGAATGCTATAGATTTCTTGACCATT
1 CCTGCCTTTTCTTTTGGAAGATTTTACTGAAGTTATTTGTGAATGCTATAGATTTCTTGACCATT
39595617 CAAAGTTTATATGATGCAACAAAGTAGTTACAGAGATAAAGTAG
66 CAAAGTTTATATGATGCAACAAAGTAGTTACAGAGATAAAGTAG
39595661 C
1 C
39595662 ATTAACAAAG
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (109 bp):
CCTGCCTTTTCTTTTGGAAGATTTTACTGAAGTTATTTGTGAATGCTATAGATTTCTTGACCATT
CAAAGTTTATATGATGCAACAAAGTAGTTACAGAGATAAAGTAG
Found at i:39607749 original size:29 final size:30
Alignment explanation
Indices: 39607631--39607889 Score: 237
Period size: 30 Copynumber: 8.7 Consensus size: 30
39607621 ATGGGGTTGA
* *
39607631 AAAATGAAATTTTAGAGAA-TTT-AGGGTT
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
* * * *** *
39607659 AAAATATGA-TTTTGGGAAAGTTCGGGGGCT
1 AAAATGTAATTTTTGAG-AAGTTTAAGGGTT
*
39607689 AAAATGTAATTTTT-ATGAAGTTTAAGAGTT
1 AAAATGTAATTTTTGA-GAAGTTTAAGGGTT
* *
39607719 AAAATGTAGTTTTTGTGAAGTTT-AGGGTT
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
*
39607748 AAAATGTAATTTTTGAGAAGTTTATAGGATT
1 AAAATGTAATTTTTGAGAAGTTTA-AGGGTT
* **
39607779 TAAATGTAATTTTTGAGAAGTTCGAGGGTT
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
* *
39607809 AAAATGTAATTTTT-ACAAAGTTTAAAGGTT
1 AAAATGTAATTTTTGA-GAAGTTTAAGGGTT
*
39607839 AAAATGTAATTTTT-ACAAAGTTTAAGGG-T
1 AAAATGTAATTTTTGA-GAAGTTTAAGGGTT
*
39607868 AAAATGTGATTTTTGAGAAGTT
1 AAAATGTAATTTTTGAGAAGTT
39607890 CGAGGACCTC
Statistics
Matches: 187, Mismatches: 34, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
27 5 0.03
28 8 0.04
29 48 0.26
30 95 0.51
31 31 0.17
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTTAAGGGTT
Found at i:39608335 original size:22 final size:22
Alignment explanation
Indices: 39608310--39608378 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
39608300 CTAGCTCCGC
*
39608310 TCATCGACCGGTCGTCCGTCAG
1 TCATCGACCGGTCGTCCGTCGG
*
39608332 TCATCGACCGGTCGTCCATCGG
1 TCATCGACCGGTCGTCCGTCGG
* *
39608354 TCACCGATCGGTCGTCCGTCGG
1 TCATCGACCGGTCGTCCGTCGG
39608376 TCA
1 TCA
39608379 CCTTCTACCG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.13, C:0.36, G:0.28, T:0.23
Consensus pattern (22 bp):
TCATCGACCGGTCGTCCGTCGG
Found at i:39612499 original size:59 final size:57
Alignment explanation
Indices: 39612435--39612759 Score: 316
Period size: 59 Copynumber: 5.5 Consensus size: 57
39612425 GAGAATTCAA
*
39612435 GGTTAAAATATAATTTTGGAAAAGTTTAGGAGTAAAAATGTAATTTTAGGAAAGTTTAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGG-GTAAAAATGTAATTTT-GGAAAGTTTAG
* * * *
39612494 GGTTAAAATGTAATTTTGGAAAAGTTTTAAGGTTAAAATATGATTTTGAGAAAGTTTAGG
1 GGTTAAAATGTAATTTTGGAAAAG-TTTAGGGTAAAAATGTAATTTTG-GAAAGTTTA-G
* * * * *
39612554 GGTTAAAATGTGATTTTAGG--TAGTTTGAGGGTAAAAATATGATTTTGAAAAGTTTAAG
1 GGTTAAAATGTAATTTT-GGAAAAGTTT-AGGGTAAAAATGTAATTTTGGAAAGTTT-AG
* * *
39612612 GGTCAAAATGTAATTTTGGAAAAG-TTAGTGTTCAAAATGTAATTTTGGAAAAGTTTAAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAG-GGTAAAAATGTAATTTTGG-AAAGTTT-AG
* * * ** *
39612671 GGTCAAAATGTAATTTTGG-AAAGTTAAGGGGTTAAAATGTAATTTTAAAAAAGTTTAA
1 GGTTAAAATGTAATTTTGGAAAAGTTTA-GGGTAAAAATGTAATTTT-GGAAAGTTTAG
* *
39612729 GGTTAAAATGTAATTTTAGAGAAGTTTAGGG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGGG
39612760 ATCATAATAT
Statistics
Matches: 224, Mismatches: 28, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
57 4 0.02
58 68 0.30
59 127 0.57
60 23 0.10
61 2 0.01
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.36
Consensus pattern (57 bp):
GGTTAAAATGTAATTTTGGAAAAGTTTAGGGTAAAAATGTAATTTTGGAAAGTTTAG
Found at i:39612517 original size:29 final size:29
Alignment explanation
Indices: 39612435--39612759 Score: 331
Period size: 29 Copynumber: 11.1 Consensus size: 29
39612425 GAGAATTCAA
*
39612435 GGTTAAAATATAATTTTGGAAAAGTTTAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAG
*
39612464 GAGTAAAAATGTAATTTTAGG-AAAGTTTAG
1 G-GTTAAAATGTAATTTT-GGAAAAGTTTAG
*
39612494 GGTTAAAATGTAATTTTGGAAAAGTTTTAA
1 GGTTAAAATGTAATTTTGGAAAAG-TTTAG
* *
39612524 GGTTAAAATATGATTTT-GAGAAAGTTTAGG
1 GGTTAAAATGTAATTTTGGA-AAAGTTTA-G
* *
39612554 GGTTAAAATGTGATTTTAGG--TAGTTTGAG
1 GGTTAAAATGTAATTTT-GGAAAAGTTT-AG
* * *
39612583 GGTAAAAATATGATTTT-GAAAAGTTTAAG
1 GGTTAAAATGTAATTTTGGAAAAGTTT-AG
*
39612612 GGTCAAAATGTAATTTTGGAAAAG-TTAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAG
*
39612640 TGTTCAAAATGTAATTTTGGAAAAGTTTAAG
1 GGTT-AAAATGTAATTTTGGAAAAGTTT-AG
* *
39612671 GGTCAAAATGTAATTTTGG-AAAGTTAAGG
1 GGTTAAAATGTAATTTTGGAAAAGTTTA-G
** *
39612700 GGTTAAAATGTAATTTTAAAAAAGTTTAA
1 GGTTAAAATGTAATTTTGGAAAAGTTTAG
* *
39612729 GGTTAAAATGTAATTTTAGAGAAGTTTAG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAG
39612758 GG
1 GG
39612760 ATCATAATAT
Statistics
Matches: 250, Mismatches: 29, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.00
28 7 0.03
29 141 0.56
30 94 0.38
31 6 0.02
32 1 0.00
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.36
Consensus pattern (29 bp):
GGTTAAAATGTAATTTTGGAAAAGTTTAG
Found at i:39614296 original size:14 final size:15
Alignment explanation
Indices: 39614269--39614301 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
39614259 TTGGGTTATT
39614269 TTGTAATCTTGGACA
1 TTGTAATCTTGGACA
*
39614284 TTGTAAT-TTGGACT
1 TTGTAATCTTGGACA
39614298 TTGT
1 TTGT
39614302 GTTGAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.48
Consensus pattern (15 bp):
TTGTAATCTTGGACA
Found at i:39618297 original size:27 final size:26
Alignment explanation
Indices: 39618259--39618372 Score: 106
Period size: 27 Copynumber: 4.3 Consensus size: 26
39618249 CCCCGAAATA
39618259 TAGCTCATTCGAACCCAGAACAGAGTT
1 TAGCTCATTCGAACCCAGAA-AGAGTT
* * *
39618286 TAGCTCATTCGAGCCCAAAATAAAGTT
1 TAGCTCATTCGAACCCAGAA-AGAGTT
* * *
39618313 TAGCTCGTTCGAGCCCAGAAAGAGCT
1 TAGCTCATTCGAACCCAGAAAGAGTT
* *
39618339 TAACTTATTC-AAGCCTC-GAAAGAGTT
1 TAGCTCATTCGAA-CC-CAGAAAGAGTT
39618365 TAGCTCAT
1 TAGCTCAT
39618373 GTGAGCCCGA
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
25 1 0.01
26 27 0.39
27 42 0.60
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (26 bp):
TAGCTCATTCGAACCCAGAAAGAGTT
Found at i:39623800 original size:26 final size:26
Alignment explanation
Indices: 39623764--39623841 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
39623754 AACTCTTTTG
39623764 AGACAGAGTTTAGCTCATTCGAGCCC
1 AGACAGAGTTTAGCTCATTCGAGCCC
* *
39623790 AGACAGAGTTTCA-CTCATTTGAGCCT
1 AGACAGAGTTT-AGCTCATTCGAGCCC
* *
39623816 AGATAGAG-TAACGCTCATATCGAGCC
1 AGACAGAGTTTA-GCTCAT-TCGAGCC
39623842 AAAGTCTAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
24 1 0.02
25 1 0.02
26 34 0.79
27 7 0.16
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (26 bp):
AGACAGAGTTTAGCTCATTCGAGCCC
Found at i:39629869 original size:47 final size:47
Alignment explanation
Indices: 39629818--39629962 Score: 158
Period size: 47 Copynumber: 3.2 Consensus size: 47
39629808 CAAACCAATA
39629818 TATAAATATATAAACTCAAGTACCCAATCAAACTCAATCCTAAAAAT
1 TATAAATATATAAACTCAAGTACCCAATCAAACTCAATCCTAAAAAT
* * * * * * *
39629865 TATAAATAATATTAGC-CCACTACCC-A--AGACCCAATCC--AATAT
1 TATAAAT-ATATAAACTCAAGTACCCAATCAAACTCAATCCTAAAAAT
*
39629907 ATATATATATATAAACTCAAGTACCCAATCAAACTCAATCCTAAAAAT
1 -TATAAATATATAAACTCAAGTACCCAATCAAACTCAATCCTAAAAAT
39629955 TATAAATA
1 TATAAATA
39629963 ATTTAATAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
42 10 0.14
43 13 0.18
44 10 0.14
46 10 0.14
47 21 0.28
48 10 0.14
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.26
Consensus pattern (47 bp):
TATAAATATATAAACTCAAGTACCCAATCAAACTCAATCCTAAAAAT
Found at i:39629941 original size:90 final size:88
Alignment explanation
Indices: 39629782--39629968 Score: 322
Period size: 90 Copynumber: 2.1 Consensus size: 88
39629772 ATTATAATAT
*
39629782 ATAACATTAACCCACTACCCAAGACCCAAACCAATATATAAATATATAAACTCAAGTACCCAATC
1 ATAATATTAACCCACTACCCAAGACCCAAACCAATATATAAATATATAAACTCAAGTACCCAATC
39629847 AAACTCAATCCTAAAAATTATAA
66 AAACTCAATCCTAAAAATTATAA
* *
39629870 ATAATATTAGCCCACTACCCAAGACCCAATCCAATATATATATATATATAAACTCAAGTACCCAA
1 ATAATATTAACCCACTACCCAAGACCCAAACCAATATATA-A-ATATATAAACTCAAGTACCCAA
39629935 TCAAACTCAATCCTAAAAATTATAA
64 TCAAACTCAATCCTAAAAATTATAA
39629960 ATAAT-TTAA
1 ATAATATTAA
39629969 TAAATAAAAA
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
88 37 0.40
89 4 0.04
90 52 0.56
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.25
Consensus pattern (88 bp):
ATAATATTAACCCACTACCCAAGACCCAAACCAATATATAAATATATAAACTCAAGTACCCAATC
AAACTCAATCCTAAAAATTATAA
Found at i:39633043 original size:20 final size:20
Alignment explanation
Indices: 39633015--39633052 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39633005 ATCACCTAAT
39633015 TATTCGATTTTGATCATTAC
1 TATTCGATTTTGATCATTAC
*
39633035 TATTTGATTTTGATCATT
1 TATTCGATTTTGATCATT
39633053 TGGTCACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (20 bp):
TATTCGATTTTGATCATTAC
Found at i:39635540 original size:31 final size:31
Alignment explanation
Indices: 39635505--39635563 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
39635495 TACAAAATGA
*
39635505 TCATTGAACTATTC-AAGAGTTTTTATTTAAG
1 TCATTAAACTATTCGAA-AGTTTTTATTTAAG
39635536 TCATTAAACTATTCGAAAGTTTTTATTT
1 TCATTAAACTATTCGAAAGTTTTTATTT
39635564 GGCTAAGTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.47
Consensus pattern (31 bp):
TCATTAAACTATTCGAAAGTTTTTATTTAAG
Found at i:39641475 original size:21 final size:20
Alignment explanation
Indices: 39641425--39641475 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
39641415 TAATGATTAA
**
39641425 ATTAATTAAAAAATAATGGG
1 ATTAATTAAAAAATAAAAGG
*
39641445 ATTAATTTAAAACATAAAAGG
1 ATTAA-TTAAAAAATAAAAGG
39641466 ATTTAATTAA
1 A-TTAATTAA
39641476 TATTTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 17 0.65
22 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (20 bp):
ATTAATTAAAAAATAAAAGG
Found at i:39642703 original size:13 final size:13
Alignment explanation
Indices: 39642673--39642697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39642663 ATCATGCTTC
39642673 TTTGTTTTTTCCA
1 TTTGTTTTTTCCA
39642686 TTTGTTTTTTCC
1 TTTGTTTTTTCC
39642698 TCTTGTCGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.16, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTGTTTTTTCCA
Found at i:39642919 original size:19 final size:21
Alignment explanation
Indices: 39642891--39642938 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
39642881 GGGCCTTGTG
*
39642891 TGTAATTGAG-TTT-GGGTTA
1 TGTAAATGAGTTTTAGGGTTA
*
39642910 TGTAAATGAGTTTTAGGTTTA
1 TGTAAATGAGTTTTAGGGTTA
39642931 TGTAAATG
1 TGTAAATG
39642939 GACTTGGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 3 0.12
21 13 0.52
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (21 bp):
TGTAAATGAGTTTTAGGGTTA
Found at i:39644485 original size:5 final size:5
Alignment explanation
Indices: 39644475--39644499 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39644465 TATATGTGTC
39644475 ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT
39644500 TAACCTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:39647934 original size:12 final size:12
Alignment explanation
Indices: 39647917--39647963 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
39647907 AATTTAAATT
39647917 ATTAAATTTTGA
1 ATTAAATTTTGA
**
39647929 ATTAAATTTAAA
1 ATTAAATTTTGA
39647941 TTATTAAATTTTGA
1 --ATTAAATTTTGA
39647955 ATTAAATTT
1 ATTAAATTT
39647964 AAATTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 19 0.66
14 10 0.34
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (12 bp):
ATTAAATTTTGA
Found at i:39647937 original size:26 final size:26
Alignment explanation
Indices: 39647897--39647968 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
39647887 TTTTTAAATT
*
39647897 ATTTT-AAGTAAATTTAAATTATTAA
1 ATTTTGAATTAAATTTAAATTATTAA
39647922 ATTTTGAATTAAATTTAAATTATTAA
1 ATTTTGAATTAAATTTAAATTATTAA
39647948 ATTTTGAATTAAATTTAAATT
1 ATTTTGAATTAAATTTAAATT
39647969 TAAGTTAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 5 0.11
26 40 0.89
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
ATTTTGAATTAAATTTAAATTATTAA
Found at i:39648839 original size:31 final size:31
Alignment explanation
Indices: 39648756--39648850 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
39648746 TTAGTATTTG
*
39648756 AACTTGACACTTTTTCCTAATTTGGTATC-TA
1 AACTTGACACTTTTTCCTAATTTGATA-CATA
* *
39648787 AACTT-----TTTTTGACTCAATTTGATACATG
1 AACTTGACACTTTTT-CCT-AATTTGATACATA
39648815 AACTTGACACTTTTTCCTAATTTGATACATA
1 AACTTGACACTTTTTCCTAATTTGATACATA
39648846 AACTT
1 AACTT
39648851 TTTTGTACCG
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
26 5 0.10
27 3 0.06
28 14 0.27
31 22 0.43
32 2 0.04
33 5 0.10
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.44
Consensus pattern (31 bp):
AACTTGACACTTTTTCCTAATTTGATACATA
Found at i:39648898 original size:60 final size:58
Alignment explanation
Indices: 39648754--39648924 Score: 202
Period size: 59 Copynumber: 2.9 Consensus size: 58
39648744 ATTTAGTATT
39648754 TGAACTTGACACTTTTTCCTAATTTGGTATCTAAACTTTTTTTGACTCAATTTGATACA
1 TGAACTTGACACTTTTTCCTAATTTGGTA-CTAAACTTTTTTTGACTCAATTTGATACA
* * * *
39648813 TGAACTTGACACTTTTTCCTAATTTGATACATAAAC-TTTTTTGTAC-CGATTTGGTACC
1 TGAACTTGACACTTTTTCCTAATTTGGTAC-TAAACTTTTTTTG-ACTCAATTTGATACA
*** * *
39648871 TGAACTTGGTATTTTTTTTCCTAATTTGGTACTAAACTTTTTTAGATTCAATTT
1 TGAACTT-G-ACACTTTTTCCTAATTTGGTACTAAACTTTTTTTGACTCAATTT
39648925 AGTACCTAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
58 24 0.25
59 42 0.44
60 29 0.31
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (58 bp):
TGAACTTGACACTTTTTCCTAATTTGGTACTAAACTTTTTTTGACTCAATTTGATACA
Found at i:39649203 original size:89 final size:89
Alignment explanation
Indices: 39649047--39649237 Score: 213
Period size: 89 Copynumber: 2.1 Consensus size: 89
39649037 TTAAAAAAGA
* * ** *
39649047 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAAGTACCAAATTGAACCCCAAAAAGTTTAAGT
1 TTAGGTACCAAATGAGGAAAAAGAGTCAAATTCAAGTACCAAATTGAACCAAAAAAAATTTAAGT
*
39649112 ATCA-ACTTAAAAAAAGTGTCAAGT
66 ATCACA-TTAAAAAAAGTATCAAGT
* * * ** * *
39649136 TTAGGTACCAAATGAGTAAGAAGTGTCAAATTTGAGTACCAAATTGGACCAAAAAAAATTTAGGT
1 TTAGGTACCAAATGAGGAAAAAGAGTCAAATTCAAGTACCAAATTGAACCAAAAAAAATTTAAGT
**
39649201 ATCACATTAGGAAAAGTATCAAGT
66 ATCACATTAAAAAAAGTATCAAGT
* *
39649225 TCATGTACCAAAT
1 TTAGGTACCAAAT
39649238 ATTATATTAA
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
89 83 0.99
90 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.25
Consensus pattern (89 bp):
TTAGGTACCAAATGAGGAAAAAGAGTCAAATTCAAGTACCAAATTGAACCAAAAAAAATTTAAGT
ATCACATTAAAAAAAGTATCAAGT
Found at i:39653283 original size:2 final size:2
Alignment explanation
Indices: 39653276--39653344 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
39653266 GCAAAAGAAA
39653276 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39653318 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
39653345 AAGACCAAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39655301 original size:25 final size:24
Alignment explanation
Indices: 39655254--39655303 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
39655244 CTTTTAAAAA
39655254 TTTTAGTTTTTATTTTTTAGGGTT
1 TTTTAGTTTTTATTTTTTAGGGTT
*
39655278 TTTTA-TTTTTGAGTTTTTTGGGGTT
1 TTTTAGTTTTT-A-TTTTTTAGGGTT
39655303 T
1 T
39655304 AGTTTTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.22
24 6 0.26
25 12 0.52
ACGTcount: A:0.10, C:0.00, G:0.20, T:0.70
Consensus pattern (24 bp):
TTTTAGTTTTTATTTTTTAGGGTT
Found at i:39656911 original size:22 final size:23
Alignment explanation
Indices: 39656853--39656999 Score: 117
Period size: 23 Copynumber: 6.3 Consensus size: 23
39656843 ACAAAGTACT
*
39656853 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACGAAGTGCTAATCAGA
39656876 GAGCACACGAAGTGCTAATCAGA
1 GAGCACACGAAGTGCTAATCAGA
* *
39656899 GAGCA-TCGAAGTGCTAATTAGA
1 GAGCACACGAAGTGCTAATCAGA
* *
39656921 GAG-AGCATGAGACGTGATAAAT-AGA
1 GAGCA-CACGA-A-GTGCT-AATCAGA
*
39656946 GAGCACAC-ACAGTGTTGAA-CAGA
1 GAGCACACGA-AGTGCT-AATCAGA
* *
39656969 GAGCACAC-ACGGTGCTAAACAGA
1 GAGCACACGA-AGTGCTAATCAGA
39656992 GAGCACAC
1 GAGCACAC
39657000 ACAGTGTTAA
Statistics
Matches: 104, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.01
22 20 0.19
23 64 0.62
24 3 0.03
25 12 0.12
26 4 0.04
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.14
Consensus pattern (23 bp):
GAGCACACGAAGTGCTAATCAGA
Found at i:39657010 original size:23 final size:23
Alignment explanation
Indices: 39656938--39657015 Score: 111
Period size: 23 Copynumber: 3.4 Consensus size: 23
39656928 TGAGACGTGA
*
39656938 TAAATAGAGAGCACACACAGTGT
1 TAAACAGAGAGCACACACAGTGT
* * *
39656961 TGAACAGAGAGCACACACGGTGC
1 TAAACAGAGAGCACACACAGTGT
39656984 TAAACAGAGAGCACACACAGTGT
1 TAAACAGAGAGCACACACAGTGT
*
39657007 TAAATAGAG
1 TAAACAGAG
39657016 CGCGCGCTAG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.14
Consensus pattern (23 bp):
TAAACAGAGAGCACACACAGTGT
Found at i:39660392 original size:83 final size:83
Alignment explanation
Indices: 39660292--39660455 Score: 202
Period size: 83 Copynumber: 2.0 Consensus size: 83
39660282 CATTGTTAGG
* * * *
39660292 GGGGCTAAAGTGAAATTTTACTATATATTAATTTATCATTTTTGTATTTATAAGAGGACTGAATT
1 GGGGCTAAAGTGAAATTTCACTATATATTAATTTATAATTTCTCTATTTATAAGAGGACTGAATT
39660357 AAAAATATTTCATTTTGA
66 AAAAATATTTCATTTTGA
* * * * * * *
39660375 GGGGTTAAAGTGCAATTTCATTGTATATTACTTTATAATTTCTCTATTTATAAGATGATTGAATT
1 GGGGCTAAAGTGAAATTTCACTATATATTAATTTATAATTTCTCTATTTATAAGAGGACTGAATT
* * *
39660440 GAAATTTTTTCATTTT
66 AAAAATATTTCATTTT
39660456 TTGGGAGGCC
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (83 bp):
GGGGCTAAAGTGAAATTTCACTATATATTAATTTATAATTTCTCTATTTATAAGAGGACTGAATT
AAAAATATTTCATTTTGA
Found at i:39661741 original size:29 final size:28
Alignment explanation
Indices: 39661709--39662105 Score: 177
Period size: 29 Copynumber: 13.7 Consensus size: 28
39661699 TGTTCAGGGA
39661709 TAAAATGGTAATTTTGGAAAGTTTGGGGT
1 TAAAAT-GTAATTTTGGAAAGTTTGGGGT
* * * * *
39661738 TAAAAATATAATTTTTAGATA-TTCGAGCG-
1 T-AAAATGTAA-TTTTGGAAAGTTTG-GGGT
**
39661767 TAAAATGTAATTTTTAAGAAGTTTGGGGT
1 TAAAATGTAATTTTGGA-AAGTTTGGGGT
* *
39661796 CAAAATGTGATTTTTGG-AAGTTTAGGGGT
1 TAAAATGT-AATTTTGGAAAGTTT-GGGGT
* **
39661825 AAAAATG-AGATTTTTTAAAGTTTGGGG-
1 TAAAATGTA-ATTTTGGAAAGTTTGGGGT
*
39661852 TAAAATTATAATTTTTGG-AAGTTTAGGGGT
1 TAAAA-TGTAA-TTTTGGAAAGTTT-GGGGT
* * *
39661882 AAAAATGTAATTTTTGAGAAGTTTGAGGT
1 TAAAATGTAATTTTGGA-AAGTTTGGGGT
* *
39661911 CAAAAATAAG-ATTTTTGG-AAGTTTAGGGGT
1 -TAAAAT--GTAATTTTGGAAAGTTT-GGGGT
* * * *
39661941 AAAAATGTAATTTTTGAGAAGTTTAGTGT
1 TAAAATGTAATTTTGGA-AAGTTTGGGGT
* *
39661970 CAAAATGTATTTTTGG-AAGTTTAGGGGT
1 TAAAATGTAATTTTGGAAAGTTT-GGGGT
* * ** *
39661998 AAAAAAGTAATTTTTTAGAAGTTTAGGGT
1 TAAAATGTAATTTTGGA-AAGTTTGGGGT
* * *
39662027 TAAAAATATGATTTTTGG-AAGTTTAAGGG-
1 T-AAAATGT-AATTTTGGAAAGTTT-GGGGT
* * *
39662056 TAAAATGTAATTTTTGAGAAGCTTAGGAGT
1 TAAAATGTAATTTTGGA-AAG-TTTGGGGT
39662086 TAAAATGTAATTTTTGGAAA
1 TAAAATGTAA-TTTTGGAAA
39662106 ATTCGAGAGT
Statistics
Matches: 275, Mismatches: 58, Indels: 69
0.68 0.14 0.17
Matches are distributed among these distances:
27 23 0.08
28 64 0.23
29 96 0.35
30 74 0.27
31 17 0.06
32 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.39
Consensus pattern (28 bp):
TAAAATGTAATTTTGGAAAGTTTGGGGT
Found at i:39661809 original size:57 final size:58
Alignment explanation
Indices: 39661710--39662104 Score: 423
Period size: 57 Copynumber: 6.8 Consensus size: 58
39661700 GTTCAGGGAT
* * * * *
39661710 AAAATGGTAATTTTGGA-AAGTTTGGGGTTAAAAATATAATTTTTAG-A-TATTCGAGCGT-
1 AAAAT-GTAATTTTTGAGAAGTTTGGGG-TCAAAATATAATTTTTGGAAGT-TTAG-GGGTA
* * *
39661768 AAAATGTAATTTTTAAGAAGTTTGGGGTCAAAATGTGATTTTTGGAAGTTTAGGGGTA
1 AAAATGTAATTTTTGAGAAGTTTGGGGTCAAAATATAATTTTTGGAAGTTTAGGGGTA
*
39661826 AAAATG-AGATTTTTTA-AAGTTTGGGGT-AAAATTATAATTTTTGGAAGTTTAGGGGTA
1 AAAATGTA-ATTTTTGAGAAGTTTGGGGTCAAAA-TATAATTTTTGGAAGTTTAGGGGTA
*
39661883 AAAATGTAATTTTTGAGAAGTTTGAGGTCAAAA-ATAAGATTTTTGGAAGTTTAGGGGTA
1 AAAATGTAATTTTTGAGAAGTTTGGGGTCAAAATAT-A-ATTTTTGGAAGTTTAGGGGTA
* * *
39661942 AAAATGTAATTTTTGAGAAGTTTAGTGTCAAAATGT-ATTTTTGGAAGTTTAGGGGTA
1 AAAATGTAATTTTTGAGAAGTTTGGGGTCAAAATATAATTTTTGGAAGTTTAGGGGTA
* * * * * *
39661999 AAAAAGTAATTTTTTAGAAGTTTAGGGTTAAAAATATGATTTTTGGAAGTTTAAGGGT-
1 AAAATGTAATTTTTGAGAAGTTT-GGGGTCAAAATATAATTTTTGGAAGTTTAGGGGTA
* * * *
39662057 AAAATGTAATTTTTGAGAAGCTTAGGAGTTAAAATGTAATTTTTGGAA
1 AAAATGTAATTTTTGAGAAG-TTTGGGGTCAAAATATAATTTTTGGAA
39662105 AATTCGAGAG
Statistics
Matches: 289, Mismatches: 33, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
56 4 0.01
57 118 0.41
58 89 0.31
59 77 0.27
60 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (58 bp):
AAAATGTAATTTTTGAGAAGTTTGGGGTCAAAATATAATTTTTGGAAGTTTAGGGGTA
Found at i:39661982 original size:116 final size:116
Alignment explanation
Indices: 39661768--39662104 Score: 452
Period size: 116 Copynumber: 2.9 Consensus size: 116
39661758 ATTCGAGCGT
* *
39661768 AAAATGTAATTTTTAAGAAGTTTGGGGTC-AAAATGTGATTTTTGGAAGTTTAGGGGTAAAAATG
1 AAAATGTAATTTTTAAGAAGTTTGAGGTCAAAAATATGATTTTTGGAAGTTTAGGGGTAAAAATG
* * * *
39661832 -AGATTTTTTA-AAGTTTGGGGTAAAATTATAATTTTTGGAAGTTTAGGGGTA
66 TA-ATTTTTGAGAAGTTTAGAGTAAAA-TGTAATTTTTGGAAGTTTAGGGGTA
* *
39661883 AAAATGTAATTTTTGAGAAGTTTGAGGTCAAAAATAAGATTTTTGGAAGTTTAGGGGTAAAAATG
1 AAAATGTAATTTTTAAGAAGTTTGAGGTCAAAAATATGATTTTTGGAAGTTTAGGGGTAAAAATG
*
39661948 TAATTTTTGAGAAGTTTAGTGTCAAAATGT-ATTTTTGGAAGTTTAGGGGTA
66 TAATTTTTGAGAAGTTTAGAGT-AAAATGTAATTTTTGGAAGTTTAGGGGTA
* * * *
39661999 AAAAAGTAATTTTTTAGAAGTTT-AGGGTTAAAAATATGATTTTTGGAAGTTTAAGGGT-AAAAT
1 AAAATGTAATTTTTAAGAAGTTTGA-GGTCAAAAATATGATTTTTGGAAGTTTAGGGGTAAAAAT
*
39662062 GTAATTTTTGAGAAGCTTAGGAGTTAAAATGTAATTTTTGGAA
65 GTAATTTTTGAGAAGTTTA-GAG-TAAAATGTAATTTTTGGAA
39662105 AATTCGAGAG
Statistics
Matches: 199, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
115 51 0.26
116 121 0.61
117 23 0.12
118 4 0.02
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (116 bp):
AAAATGTAATTTTTAAGAAGTTTGAGGTCAAAAATATGATTTTTGGAAGTTTAGGGGTAAAAATG
TAATTTTTGAGAAGTTTAGAGTAAAATGTAATTTTTGGAAGTTTAGGGGTA
Found at i:39662121 original size:30 final size:30
Alignment explanation
Indices: 39661860--39662121 Score: 100
Period size: 30 Copynumber: 9.0 Consensus size: 30
39661850 GGTAAAATTA
** * *
39661860 TAATTTTTG-GAAGTTTAGGGGTAAAAATG
1 TAATTTTTGAGAAAATTAGGAGTCAAAATG
* *
39661889 TAATTTTTGAG-AAGTT-TGAGGTCAAAAAT-
1 TAATTTTTGAGAAAATTAGGA-GTC-AAAATG
* ** * *
39661918 AAGATTTTTG-GAAGTTTAGGGGTAAAAATG
1 TA-ATTTTTGAGAAAATTAGGAGTCAAAATG
** *
39661948 TAATTTTTGAGAAGTTTA-GTGTCAAAATG
1 TAATTTTTGAGAAAATTAGGAGTCAAAATG
** * * *
39661977 T-ATTTTTG-GAAGTTTAGGGGTAAAAAAG
1 TAATTTTTGAGAAAATTAGGAGTCAAAATG
* ** * *
39662005 TAATTTTTTAGAAGTTTAGG-GTTAAAAATA
1 TAATTTTTGAGAAAATTAGGAG-TCAAAATG
* **
39662035 TGATTTTTG-GAAGTTTAAGG-GT-AAAATG
1 TAATTTTTGAGAAAATT-AGGAGTCAAAATG
** *
39662063 TAATTTTTGAGAAGCTTAGGAGTTAAAATG
1 TAATTTTTGAGAAAATTAGGAGTCAAAATG
*
39662093 TAATTTTTG-GAAAATTCGAGAGTCAAAAT
1 TAATTTTTGAGAAAATTAG-GAGTCAAAAT
39662122 ATGATTTCTG
Statistics
Matches: 187, Mismatches: 29, Indels: 33
0.75 0.12 0.13
Matches are distributed among these distances:
27 8 0.04
28 33 0.18
29 67 0.36
30 78 0.42
31 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
TAATTTTTGAGAAAATTAGGAGTCAAAATG
Found at i:39662331 original size:33 final size:33
Alignment explanation
Indices: 39662294--39662368 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
39662284 AAAATAATTA
*
39662294 AAAAATAGAAGGGACCATTTACATAAATAAACT
1 AAAAATAGAAGGGACCATTTACATAAATAAACC
*
39662327 AAAAATAGAAGGGACTATTTACATAAATAAACC
1 AAAAATAGAAGGGACCATTTACATAAATAAACC
39662360 AAAAATAGA
1 AAAAATAGA
39662369 GAGTTGAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.57, C:0.11, G:0.12, T:0.20
Consensus pattern (33 bp):
AAAAATAGAAGGGACCATTTACATAAATAAACC
Found at i:39663232 original size:6 final size:6
Alignment explanation
Indices: 39663203--39663264 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
39663193 CATTTTCCTT
* ** *
39663203 TTATTA TTTTTA TTATTA AAATTA TTATTA TTATAA TTA-TA TTTATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA -TTATTA
* *
39663251 TTAATA TTAATA TT
1 TTATTA TTATTA TT
39663265 CATTTAATAC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
5 1 0.02
6 42 0.93
7 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (6 bp):
TTATTA
Found at i:39663235 original size:9 final size:9
Alignment explanation
Indices: 39663203--39663264 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
39663193 CATTTTCCTT
*
39663203 TTATTATTT
1 TTATTATTA
39663212 TTATTATTA
1 TTATTATTA
**
39663221 AAATTATTA
1 TTATTATTA
*
39663230 TTATTATAA
1 TTATTATTA
39663239 TTA-TATTTA
1 TTATTA-TTA
*
39663248 TTATTAATA
1 TTATTATTA
*
39663257 TTAATATT
1 TTATTATT
39663265 CATTTAATAC
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
8 2 0.05
9 37 0.90
10 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTATTATTA
Found at i:39663248 original size:15 final size:15
Alignment explanation
Indices: 39663212--39663264 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
39663202 TTTATTATTT
*
39663212 TTATTATTAAAATTA
1 TTATTATTATAATTA
39663227 TTATTATTATAATTA
1 TTATTATTATAATTA
39663242 -TATTTATTATTAA-TA
1 TTA-TTATTA-TAATTA
*
39663257 TTAATATT
1 TTATTATT
39663265 CATTTAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 2 0.06
15 26 0.79
16 5 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTATTATAATTA
Found at i:39663248 original size:33 final size:33
Alignment explanation
Indices: 39663205--39663272 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
39663195 TTTTCCTTTT
* *
39663205 ATTATTTTTATTATTAAAATTATTATT-ATTATA
1 ATTATATTTATTATTAAAATTAATATTCATT-TA
*
39663238 ATTATATTTATTATTAATATTAATATTCATTTA
1 ATTATATTTATTATTAAAATTAATATTCATTTA
39663271 AT
1 AT
39663273 ACATTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (33 bp):
ATTATATTTATTATTAAAATTAATATTCATTTA
Found at i:39664219 original size:173 final size:173
Alignment explanation
Indices: 39663917--39664295 Score: 526
Period size: 173 Copynumber: 2.2 Consensus size: 173
39663907 GAAAGACAGA
* * * ** * *
39663917 TTTGGTTCACTTTTTTGTGTCTTGTCAGGAAGATGACCATTTTATTGCTTCGACATGCTTCTCCG
1 TTTGATTCGCTTTTTTGTATCTCATCAGGAAGATGACCACTTTATTGCTTCGACATGCTTCTCAG
* * * *
39663982 TATCTCATCGGGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTGATTTGGT
66 TACCTCATCAGGAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTAATTTGGT
* *
39664047 CTACTTCTCAGTATCTCATCAAGGAGACGACCACATCACTTAT
131 CTACTTCTCAGTATCTCATCAAGAAGACGACCACATCACTTAC
* *
39664090 TTTGATTCGCTTTTTTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCTGCTTCTCAG
1 TTTGATTCGCTTTTTTGTATCTCATCAGGAAGATGACCACTTTATTGCTTCGACATGCTTCTCAG
39664155 TACCTCATCAGGAAG-TCGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTAATTTGG
66 TACCTCATCAGGAAGCT-GAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTAATTTGG
* * * *
39664219 TCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCATTTGC
130 TCTACTTCTCAGTATCTCATCAAGAAGACGACCACATCACTTAC
** * * *
39664263 TTCAATTCGCTTCTCTGTATCTCATCGGGAAGA
1 TTTGATTCGCTTTTTTGTATCTCATCAGGAAGA
39664296 CGAATTTGGT
Statistics
Matches: 181, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
172 1 0.01
173 180 0.99
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.37
Consensus pattern (173 bp):
TTTGATTCGCTTTTTTGTATCTCATCAGGAAGATGACCACTTTATTGCTTCGACATGCTTCTCAG
TACCTCATCAGGAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTCATTAATTTGGT
CTACTTCTCAGTATCTCATCAAGAAGACGACCACATCACTTAC
Found at i:39664520 original size:124 final size:125
Alignment explanation
Indices: 39664358--39664628 Score: 395
Period size: 125 Copynumber: 2.2 Consensus size: 125
39664348 TTCGACCTGG
* * * *
39664358 TTCTCAGTATCTCAT-CAGGAAGCTGAGGTTTGAAGTTTCGCTCACATTGAGC-TTGGTTTCATT
1 TTCTCTGTATCTCATCCA-GAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGATTCATT
* * *
39664421 GAGTTGGTATACTTCTCTA-TATCTCATCAAGAAGATGGCCGCCTCACTTGTTTCAATTCGC
65 GAGTTGGTATACTTCTC-AGTATCTCATCAAGAAGATGACCGCATCACTTGCTTCAATTCGC
*
39664482 TTCTCTGTTTCTCATCCAGAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGATTCATTG
1 TTCTCTGTATCTCATCCAGAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGATTCATTG
* *
39664547 ATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGCTTCAATTCGC
66 AGTTGGTATACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGCTTCAATTCGC
* *
39664607 TTCTCTGTATCTTATCGAGAAG
1 TTCTCTGTATCTCATCCAGAAG
39664629 ATGAATTTGG
Statistics
Matches: 131, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
124 46 0.35
125 85 0.65
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (125 bp):
TTCTCTGTATCTCATCCAGAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGATTCATTG
AGTTGGTATACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGCTTCAATTCGC
Found at i:39664755 original size:334 final size:334
Alignment explanation
Indices: 39664146--39664831 Score: 1097
Period size: 334 Copynumber: 2.1 Consensus size: 334
39664136 GCTTCGACCT
* * *
39664146 GCTTCTCAGTACCTCAT-CAGGAAG-TCGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTTTC
1 GCTTCTCTGTATCTCATCCA-GAAGCT-GAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGATTC
*
39664209 ATTAATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCATTTGCTTCAATTCGCT
64 ATTAATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGCTTCAATTCGCT
* *
39664274 TCTCTGTATCTCATCGGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCA
129 TCTCTGTATCTCATCGAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * * * * *
39664339 TTTTATTGCTTCGACCTGGTTCTCAGTATCTCATCAGGAAGCTGAGGTTTGAAGTTTCGCTCACA
194 TTTTATTGCTTCAACATGCTTATCAGTATCTCATCAAGAAGCTGAGGTTCGAAGTTTCGCTCAAA
*
39664404 TTGAGCTTGGTTTCATTGAGTTGGTATACTTCTCTATATCTCATCAAGAAGATGGCCGCCTCACT
259 TTGAGCTTGGTTTCATTGAGTTGGTATACTTCTCTATATCTCATCAAGAAGATGACCGCCTCACT
*
39664469 TGTTTCAATTC
324 TATTTCAATTC
*
39664480 GCTTCTCTGTTTCTCATCCAGAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGATTCAT
1 GCTTCTCTGTATCTCATCCAGAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGATTCAT
*
39664545 TGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGCTTCAATTCGCTTC
66 TAATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGCTTCAATTCGCTTC
* * * *
39664610 TCTGTATCTTATCGAGAAGATGAATTTGGTCCACTTTTCAGTATCTCATCAGGAAGCTAACTATT
131 TCTGTATCTCATCGAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
*
39664675 TTATTGCTTCAACATGCTTATCAGTATCTCATCAAGAAGCTGAGGTTCGAAGTTTTGCTCAAATT
196 TTATTGCTTCAACATGCTTATCAGTATCTCATCAAGAAGCTGAGGTTCGAAGTTTCGCTCAAATT
* * *
39664740 GAGCTTGGTTTCATTGAGTTGGTATACTTCTCTGTATCTTATCAATAAGATGACCGCCTCACTTA
261 GAGCTTGGTTTCATTGAGTTGGTATACTTCTCTATATCTCATCAAGAAGATGACCGCCTCACTTA
*
39664805 TTTTAATTC
326 TTTCAATTC
*
39664814 GCTTCTTTGTATCTCATC
1 GCTTCTCTGTATCTCATC
39664832 GGGAAGACGG
Statistics
Matches: 322, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
334 319 0.99
335 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (334 bp):
GCTTCTCTGTATCTCATCCAGAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGATTCAT
TAATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGCTTCAATTCGCTTC
TCTGTATCTCATCGAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
TTATTGCTTCAACATGCTTATCAGTATCTCATCAAGAAGCTGAGGTTCGAAGTTTCGCTCAAATT
GAGCTTGGTTTCATTGAGTTGGTATACTTCTCTATATCTCATCAAGAAGATGACCGCCTCACTTA
TTTCAATTC
Found at i:39664852 original size:209 final size:209
Alignment explanation
Indices: 39664491--39665008 Score: 705
Period size: 209 Copynumber: 2.5 Consensus size: 209
39664481 CTTCTCTGTT
* * * * *
39664491 TCTCATCCAGAAGCTGAGGTTCGAAGTTTCGCTCACATCGAGCTTTGGATTCATTGATTTGGTCT
1 TCTCATCAAGAAGCTGAGGTTCGAAGTTTCGCTCACATTGAGC-TTGGTTTCATTGAGTTGGTAT
* * * *
39664556 ACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGCTTCAATTCGCTTCTCTGTATCTTA
65 ACTTCTCAGTATCTCATCAATAAGATGACCGCCTCACTTACTTCAATTCGCTTCTCTGTATCTCA
* * * *
39664621 TCGAGAAGATGAATTTGGTCCACTTTTCAGTATCTCATCAGGAAGCTAACTATTTTATTGCTTCA
130 TCGAGAAGAGGAATTTGGTCCACTTCTCAGTATCTCATCAGAAAGCTAACCATTTTATTGCTTCA
*
39664686 ACATGCTTATCAGTA
195 ACATACTTATCAGTA
* *
39664701 TCTCATCAAGAAGCTGAGGTTCGAAGTTTTGCTCAAATTGAGCTTGGTTTCATTGAGTTGGTATA
1 TCTCATCAAGAAGCTGAGGTTCGAAGTTTCGCTCACATTGAGCTTGGTTTCATTGAGTTGGTATA
* * * * *
39664766 CTTCTCTGTATCTTATCAATAAGATGACCGCCTCACTTATTTTAATTCGCTTCTTTGTATCTCAT
66 CTTCTCAGTATCTCATCAATAAGATGACCGCCTCACTTACTTCAATTCGCTTCTCTGTATCTCAT
* * * *
39664831 CGGGAAGACGGAA-TTGGTCCACTTCTCTGTATCTCGTCAGAAAGCTAACCATTTTATTGCTTCG
131 CGAGAAGA-GGAATTTGGTCCACTTCTCAGTATCTCATCAGAAAGCTAACCATTTTATTGCTTCA
* *
39664895 ACCTACTTCTCAGTA
195 ACATACTTATCAGTA
* * * * * *
39664910 TCTCATCAGGAAGCTTAGGTTCGAAGTTTCGTTCACATTGAGTTTTGTTTTATTGAGTTGGTATA
1 TCTCATCAAGAAGCTGAGGTTCGAAGTTTCGCTCACATTGAGCTTGGTTTCATTGAGTTGGTATA
*
39664975 CTTCTCAGTATCTCATCAGTAAGATGACCGCCTC
66 CTTCTCAGTATCTCATCAATAAGATGACCGCCTC
39665009 GTTTGTTTTG
Statistics
Matches: 269, Mismatches: 38, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
209 227 0.84
210 42 0.16
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (209 bp):
TCTCATCAAGAAGCTGAGGTTCGAAGTTTCGCTCACATTGAGCTTGGTTTCATTGAGTTGGTATA
CTTCTCAGTATCTCATCAATAAGATGACCGCCTCACTTACTTCAATTCGCTTCTCTGTATCTCAT
CGAGAAGAGGAATTTGGTCCACTTCTCAGTATCTCATCAGAAAGCTAACCATTTTATTGCTTCAA
CATACTTATCAGTA
Found at i:39665706 original size:50 final size:50
Alignment explanation
Indices: 39665485--39665857 Score: 292
Period size: 50 Copynumber: 7.7 Consensus size: 50
39665475 CTTCTTATCG
* * *
39665485 CATCTTCTTAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTTA
1 CATCTTTTTAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTA
* * *
39665535 CATCTTTTTAGGTACCGGGTTCACCGTTGCGACCTCAACCTTTCCCTTTA
1 CATCTTTTTAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTA
*** * * * *
39665585 CATCTTTTTAAGGTATCAAATTTGCCATTGCGGCCTCAATCC-TCCCCTGT-
1 CATCTTTTT-AGGTATCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCCCTTTA
* * * * * *
39665635 CATCTCTTTATGT-TACTGGGTTTGCCGTTGCGACCTCAACCTTTCCCATAA
1 CATCTTTTTAGGTAT-C-GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTA
*
39665686 CATCTTTTTAGGTATCGGGTTCGCCGTTGTGGCCTCAACCTTTCCC-TT-
1 CATCTTTTTAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTA
* *
39665734 CA-C-----A--TCT-GGGTTCGCCGTTGCGGTCTCAACCTTTCCCTTTA
1 CATCTTTTTAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTA
* ** * * * *
39665775 AATCTTCAT-GGTATCGGGTTCGCCATTGCGGCCTTAACTTTTCCCTTCA
1 CATCTTTTTAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTA
* * * * *
39665824 -ATCTTTTAAGGTACCGGATTTGCCGTCGCGGCCT
1 CATCTTTTTAGGTATCGGGTTCGCCGTTGCGGCCT
39665858 TAATCCTTCC
Statistics
Matches: 255, Mismatches: 49, Indels: 39
0.74 0.14 0.11
Matches are distributed among these distances:
39 28 0.11
40 4 0.02
41 1 0.00
42 2 0.01
47 1 0.00
48 10 0.04
49 56 0.22
50 111 0.44
51 39 0.15
52 3 0.01
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.36
Consensus pattern (50 bp):
CATCTTTTTAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTA
Found at i:39665740 original size:101 final size:99
Alignment explanation
Indices: 39665485--39665740 Score: 300
Period size: 101 Copynumber: 2.5 Consensus size: 99
39665475 CTTCTTATCG
* * *
39665485 CATCTTCTTAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTTACATCTTTTTAGGTAC
1 CATCTTTTTAGGTATCGGGTTCGCCGTTGTGGCCTCAACCTTTCCC-TTACATCTCTTTAGGTAC
* *
39665550 CGGGTTCACCGTTGCGACCTCAACCTTTCCCTTTA
65 CGGGTTCACCGTTGCGACCTCAACCTTTCCCATAA
*** * * * * *
39665585 CATCTTTTTAAGGTATCAAATTTGCCATTGCGGCCTCAATCC-TCCCCTGT-CATCTCTTTATGT
1 CATCTTTTT-AGGTATCGGGTTCGCCGTTGTGGCCTCAA-CCTTTCCCT-TACATCTCTTTA-GG
* **
39665648 TACTGGGTTTGCCGTTGCGACCTCAACCTTTCCCATAA
62 TACCGGGTTCACCGTTGCGACCTCAACCTTTCCCATAA
39665686 CATCTTTTTAGGTATCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCACATCT
1 CATCTTTTTAGGTATCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTT-ACATCT
39665741 GGGTTCGCCG
Statistics
Matches: 126, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
99 3 0.02
100 46 0.37
101 75 0.60
102 2 0.02
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.37
Consensus pattern (99 bp):
CATCTTTTTAGGTATCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTACATCTCTTTAGGTACC
GGGTTCACCGTTGCGACCTCAACCTTTCCCATAA
Found at i:39666824 original size:16 final size:15
Alignment explanation
Indices: 39666793--39666836 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 15
39666783 TTTTTCCTCT
39666793 TTTTTC-TTCTTTT-
1 TTTTTCTTTCTTTTA
*
39666806 TTCTTC-TT-TTTTA
1 TTTTTCTTTCTTTTA
39666819 TTTTTCTTTCTTTTA
1 TTTTTCTTTCTTTTA
39666834 TTT
1 TTT
39666837 ATTTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 4 0.15
13 12 0.46
14 2 0.08
15 8 0.31
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTCTTTTA
Found at i:39666832 original size:10 final size:10
Alignment explanation
Indices: 39666783--39666830 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
39666773 CTCCTTTTTC
*
39666783 TTTTTCCTCT
1 TTTTTCTTCT
39666793 TTTTTCTTCT
1 TTTTTCTTCT
39666803 TTTTTCTTCT
1 TTTTTCTTCT
*
39666813 TTTTTATT-T
1 TTTTTCTTCT
39666822 TTCTTTCTT
1 TT-TTTCTT
39666831 TTATTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
9 3 0.09
10 31 0.91
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:39666839 original size:19 final size:18
Alignment explanation
Indices: 39666803--39666850 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
39666793 TTTTTCTTCT
39666803 TTTTTC-TTC-TTTTTTA
1 TTTTTCTTTCTTTTTTTA
39666819 TTTTTCTTTCTTTTATTTA
1 TTTTTCTTTCTTTT-TTTA
39666838 TTTATT-TTTCTTT
1 TTT-TTCTTTCTTT
39666851 ATCGAATCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.21
17 3 0.11
18 3 0.11
19 14 0.50
20 2 0.07
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTCTTTTTTTA
Found at i:39666851 original size:10 final size:9
Alignment explanation
Indices: 39666777--39666850 Score: 60
Period size: 10 Copynumber: 8.0 Consensus size: 9
39666767 CGACTTCTCC
39666777 TTTTTCTTT
1 TTTTTCTTT
**
39666786 TTCCTCTTT
1 TTTTTCTTT
39666795 TTTCTTCTTT
1 TTT-TTCTTT
39666805 TTTCTTCTTT
1 TTT-TTCTTT
*
39666815 TTTAT-TTT
1 TTTTTCTTT
*
39666823 TCTTTCTTT
1 TTTTTCTTT
* *
39666832 TATTTATTT
1 TTTTTCTTT
39666841 ATTTTTCTTT
1 -TTTTTCTTT
39666851 ATCGAATCCA
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
8 6 0.12
9 20 0.39
10 25 0.49
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:39671671 original size:30 final size:29
Alignment explanation
Indices: 39671540--39671839 Score: 179
Period size: 29 Copynumber: 10.2 Consensus size: 29
39671530 TTTTGGACAC
** *
39671540 TTTAGGGGCAAAATGGTAATTTTTGA-ATG
1 TTTAGGGTAAAAAT-GTAATTTTTGAGAAG
* *
39671569 TTTGGGGGT-AAAATGGTAATTTTGGA-AAG
1 TTT-AGGGTAAAAAT-GTAATTTTTGAGAAG
*
39671598 TTTAGGGTTAAAAATATAATTTTT-AGATA-
1 TTTAGGG-TAAAAATGTAATTTTTGAGA-AG
*
39671627 ATT-GGGTTAAAAATGTAATTTTTGAGAAG
1 TTTAGGG-TAAAAATGTAATTTTTGAGAAG
*
39671656 TTTAGGGTCAAAAATGTGATTTTTG-GAAG
1 TTTAGGGT-AAAAATGTAATTTTTGAGAAG
* * * **
39671685 TTTTGGGGTTATAATGGGATTTTTGAGAAG
1 -TTTAGGGTAAAAATGTAATTTTTGAGAAG
* * * *
39671715 TTCAGGGTCAAAATATGATTTTTG-GAAG
1 TTTAGGGTAAAAATGTAATTTTTGAGAAG
* *
39671743 ATTAAGGGTAAAAATATAATTTTTGAGAAG
1 -TTTAGGGTAAAAATGTAATTTTTGAGAAG
** * *
39671773 TTCGGGGGTTAAAATGTAATTTTTG-GAAAA
1 TT-TAGGGTAAAAATGTAATTTTTGAG-AAG
* *
39671803 TTTAAGGGTCAAAATATAATTTTT-AGACAG
1 TTT-AGGGTAAAAATGTAATTTTTGAGA-AG
*
39671833 TTAAGGG
1 TTTAGGG
39671840 ATCTTTTAGG
Statistics
Matches: 218, Mismatches: 35, Indels: 36
0.75 0.12 0.12
Matches are distributed among these distances:
28 28 0.13
29 105 0.48
30 85 0.39
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (29 bp):
TTTAGGGTAAAAATGTAATTTTTGAGAAG
Found at i:39671722 original size:59 final size:58
Alignment explanation
Indices: 39671634--39671839 Score: 200
Period size: 59 Copynumber: 3.5 Consensus size: 58
39671624 ATAATTGGGT
* * **
39671634 TAAAAAT-GTAATTTTTGAGAAGTTTAGGGTCAAAAATGTGATTTTTGGAAGTTTTGGGG
1 TAAAAATAG-AATTTTTGAGAAGTTCAGGGTC-AAAATGTGATTTTTGGAAGATTAAGGG
* * * * *
39671693 TTATAATGGGATTTTTGAGAAGTTCAGGGTCAAAATATGATTTTTGGAAGATTAAGGG
1 TAAAAATAGAATTTTTGAGAAGTTCAGGGTCAAAATGTGATTTTTGGAAGATTAAGGG
* * * * *
39671751 TAAAAATATAATTTTTGAGAAGTTCGGGGGTTAAAATGTAATTTTTGGAAAATTTAAGGG
1 TAAAAATAGAATTTTTGAGAAGTTC-AGGGTCAAAATGTGATTTTTGGAAGA-TTAAGGG
* * *
39671811 TCAAAATATAATTTTT-AGACAGTTAAGGG
1 TAAAAATAGAATTTTTGAGA-AGTTCAGGG
39671840 ATCTTTTAGG
Statistics
Matches: 122, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
58 43 0.35
59 52 0.43
60 27 0.22
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (58 bp):
TAAAAATAGAATTTTTGAGAAGTTCAGGGTCAAAATGTGATTTTTGGAAGATTAAGGG
Found at i:39671819 original size:60 final size:58
Alignment explanation
Indices: 39671585--39671839 Score: 203
Period size: 58 Copynumber: 4.4 Consensus size: 58
39671575 GGTAAAATGG
* * * * * *
39671585 TAATTTTGGA-AAGTTTAGGGTTAAAAATATAATTTTTAGATAATT--GGGTTAAAAATG
1 TAATTTTTGAGAAGTTCAGGG-TCAAAATATAATTTTTGGAAAATTAAGGG-TAAAAATA
* * * ** ** * * *
39671642 TAATTTTTGAGAAGTTTAGGGTCAAAAATGTGATTTTTGGAAGTTTTGGGGTTATAATG
1 TAATTTTTGAGAAGTTCAGGGTC-AAAATATAATTTTTGGAAAATTAAGGGTAAAAATA
** * *
39671701 GGATTTTTGAGAAGTTCAGGGTCAAAATATGATTTTTGGAAGATTAAGGGTAAAAATA
1 TAATTTTTGAGAAGTTCAGGGTCAAAATATAATTTTTGGAAAATTAAGGGTAAAAATA
* * * *
39671759 TAATTTTTGAGAAGTTCGGGGGTTAAAATGTAATTTTTGGAAAATTTAAGGGTCAAAATA
1 TAATTTTTGAGAAGTTC-AGGGTCAAAATATAATTTTTGGAAAA-TTAAGGGTAAAAATA
*
39671819 TAATTTTT-AGACAGTTAAGGG
1 TAATTTTTGAGA-AGTTCAGGG
39671840 ATCTTTTAGG
Statistics
Matches: 161, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
57 10 0.06
58 69 0.43
59 53 0.33
60 29 0.18
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (58 bp):
TAATTTTTGAGAAGTTCAGGGTCAAAATATAATTTTTGGAAAATTAAGGGTAAAAATA
Found at i:39672922 original size:18 final size:18
Alignment explanation
Indices: 39672895--39672946 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
39672885 TCCTTTTTTA
* *
39672895 TTATTTTTATTTTTAAAG
1 TTATTATTATTATTAAAG
* *
39672913 TTATTATTATTATTATAT
1 TTATTATTATTATTAAAG
*
39672931 TTATTATTAATATTAA
1 TTATTATTATTATTAA
39672947 TATTCATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATTATTATTATTAAAG
Found at i:39673615 original size:17 final size:17
Alignment explanation
Indices: 39673594--39673683 Score: 130
Period size: 17 Copynumber: 5.4 Consensus size: 17
39673584 ATTTTGGATT
*
39673594 TTTAAATTTAGAA-TAAT
1 TTTAAATTTA-AATTAAA
*
39673611 TTTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
*
39673628 TTTAAACTTAAATTAAA
1 TTTAAATTTAAATTAAA
39673645 TTTAAA-TTAAATTAAA
1 TTTAAATTTAAATTAAA
39673661 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATTAAA
39673678 TTTAAA
1 TTTAAA
39673684 AAAGTGGGTT
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
16 18 0.26
17 50 0.74
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:39673620 original size:6 final size:6
Alignment explanation
Indices: 39673594--39673683 Score: 95
Period size: 6 Copynumber: 16.0 Consensus size: 6
39673584 ATTTTGGATT
* * *
39673594 TTTAAA TTTAGAA --TAAT TTTAAA TTTAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
39673640 -TTAAA TTTAAA -TTAAA -TTAAA TTTAAA TTTAAA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
39673684 AAAGTGGGTT
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
4 1 0.01
5 26 0.36
6 43 0.60
7 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:39673627 original size:11 final size:12
Alignment explanation
Indices: 39673612--39673683 Score: 73
Period size: 11 Copynumber: 6.4 Consensus size: 12
39673602 TAGAATAATT
39673612 TTAAATTTAAA-
1 TTAAATTTAAAC
*
39673623 ATAAATTTAAAC
1 TTAAATTTAAAC
*
39673635 TTAAA-TTAAAT
1 TTAAATTTAAAC
39673646 TTAAA-TTAAA-
1 TTAAATTTAAAC
*
39673656 TTAAATTTAAAT
1 TTAAATTTAAAC
*
39673668 TTAAA-TTAAAT
1 TTAAATTTAAAC
39673679 TTAAA
1 TTAAA
39673684 AAAGTGGGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
10 5 0.09
11 41 0.75
12 9 0.16
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAAATTTAAAC
Found at i:39673628 original size:28 final size:27
Alignment explanation
Indices: 39673612--39673683 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 27
39673602 TAGAATAATT
39673612 TTAAATTTAAAATAAATTTAAACTTAAA
1 TTAAATTTAAAATAAATTTAAAC-TAAA
*
39673640 TTAAATTTAAATTAAA-TTAAA-T---
1 TTAAATTTAAAATAAATTTAAACTAAA
*
39673662 TTAAATTTAAATTAAATTTAAA
1 TTAAATTTAAAATAAATTTAAA
39673684 AAAGTGGGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 16 0.38
23 5 0.12
25 1 0.02
27 5 0.12
28 15 0.36
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
TTAAATTTAAAATAAATTTAAACTAAA
Found at i:39673737 original size:25 final size:25
Alignment explanation
Indices: 39673709--39673761 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
39673699 TAGGTCCGGT
39673709 CAAAATTGGACTCCAACAGTAAAAA
1 CAAAATTGGACTCCAACAGTAAAAA
39673734 CAAAATTGGACTCCAACAGTAAAAA
1 CAAAATTGGACTCCAACAGTAAAAA
39673759 CAA
1 CAA
39673762 TATATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.15
Consensus pattern (25 bp):
CAAAATTGGACTCCAACAGTAAAAA
Found at i:39677496 original size:31 final size:31
Alignment explanation
Indices: 39677460--39677535 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
39677450 TTTTTGGTCC
39677460 AATTTGGTA-CTCAAACTTGACACTTTTTCTT
1 AATTTGGTACCT-AAACTTGACACTTTTTCTT
* **
39677491 AATTTGGTACCTGAACTTGACTTTTTTTCTT
1 AATTTGGTACCTAAACTTGACACTTTTTCTT
39677522 AATTTGGTACCTAA
1 AATTTGGTACCTAA
39677536 TCTTTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTGACACTTTTTCTT
Found at i:39677809 original size:31 final size:31
Alignment explanation
Indices: 39677714--39677867 Score: 96
Period size: 31 Copynumber: 5.2 Consensus size: 31
39677704 AAAAAATCTT
*
39677714 AGGTACCAAATTAGGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAGTGTTAAGTTC
* * *
39677745 ATGTACTAAATTGGGTCCAAAAA-----AAGTAT-
1 AGGTACCAAATTAGG---AAAAAGTGTTAAGT-TC
*
39677774 AGGTACCGAATTAGGAAAAAGTGTTAAGTTC
1 AGGTACCAAATTAGGAAAAAGTGTTAAGTTC
* * **
39677805 AGGTACCAAAATGGGTAAAAAAAGTT---TT-
1 AGGTACCAAATTAGG-AAAAAGTGTTAAGTTC
*
39677833 A-GTACCAAATCAGGAAAAAGTGTTAAGTTC
1 AGGTACCAAATTAGGAAAAAGTGTTAAGTTC
39677863 AGGTA
1 AGGTA
39677868 TCGAATGTTA
Statistics
Matches: 90, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
26 13 0.14
27 10 0.11
28 1 0.01
29 19 0.21
30 3 0.03
31 31 0.34
32 8 0.09
34 5 0.06
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (31 bp):
AGGTACCAAATTAGGAAAAAGTGTTAAGTTC
Found at i:39677853 original size:58 final size:59
Alignment explanation
Indices: 39677701--39677867 Score: 221
Period size: 60 Copynumber: 2.8 Consensus size: 59
39677691 AATTGAATCT
* * * * * *
39677701 TAAAAAAAATCTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCATGTACTAAATTGGG
1 TAAAAAAAGTTTTAGGTACCAAATTAGGAAAAAGTGTTAAGTTCAGGTACCAAAATGGG
* *
39677760 TCCAAAAAAAG-TATAGGTACCGAATTAGGAAAAAGTGTTAAGTTCAGGTACCAAAATGGG
1 T--AAAAAAAGTTTTAGGTACCAAATTAGGAAAAAGTGTTAAGTTCAGGTACCAAAATGGG
*
39677820 TAAAAAAAGTTTTA-GTACCAAATCAGGAAAAAGTGTTAAGTTCAGGTA
1 TAAAAAAAGTTTTAGGTACCAAATTAGGAAAAAGTGTTAAGTTCAGGTA
39677868 TCGAATGTTA
Statistics
Matches: 94, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
58 40 0.43
59 4 0.04
60 43 0.46
61 7 0.07
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.25
Consensus pattern (59 bp):
TAAAAAAAGTTTTAGGTACCAAATTAGGAAAAAGTGTTAAGTTCAGGTACCAAAATGGG
Found at i:39684203 original size:31 final size:32
Alignment explanation
Indices: 39684166--39684283 Score: 109
Period size: 33 Copynumber: 3.8 Consensus size: 32
39684156 GGATCCCAAA
* * * *
39684166 AAGTTTAAGTATCAACTTA-AAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAAATATC
*
39684197 AAGTTTAGGTACCAAATTAGGAAAAAAAATATC
1 AAGTTTAAGTACCAAATTA-GAAAAAAAATATC
* * *
39684230 AAGTTTGAGTACCAAATTGGACCAAAAAA-A--
1 AAGTTTAAGTACCAAATTAGA-AAAAAAATATC
*
39684260 AAGTTTAGGTACCAAATTAGAAAA
1 AAGTTTAAGTACCAAATTAGAAAA
39684284 GAGTGTCAAG
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
29 2 0.03
30 18 0.25
31 16 0.23
32 3 0.04
33 32 0.45
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (32 bp):
AAGTTTAAGTACCAAATTAGAAAAAAAATATC
Found at i:39684232 original size:33 final size:33
Alignment explanation
Indices: 39684184--39684283 Score: 113
Period size: 33 Copynumber: 3.1 Consensus size: 33
39684174 GTATCAACTT
*
39684184 AAAAAAAAGTGTCAAGTTTAGGTACCAAATTAGG
1 AAAAAAAA-TATCAAGTTTAGGTACCAAATTAGG
39684218 AAAAAAAATATCAAGTTT-GAGTACCAAATT-GG
1 AAAAAAAATATCAAGTTTAG-GTACCAAATTAGG
*
39684250 ACCAAAAAA-A--AAGTTTAGGTACCAAATTA-G
1 A-AAAAAAATATCAAGTTTAGGTACCAAATTAGG
39684280 AAAA
1 AAAA
39684284 GAGTGTCAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
29 2 0.03
30 18 0.31
31 1 0.02
32 5 0.08
33 25 0.42
34 8 0.14
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (33 bp):
AAAAAAAATATCAAGTTTAGGTACCAAATTAGG
Found at i:39691533 original size:15 final size:16
Alignment explanation
Indices: 39691507--39691537 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
39691497 AATTTTATTC
39691507 ATTTTGTATTTTTTAA
1 ATTTTGTATTTTTTAA
39691523 ATTTT-TATTTTTTAA
1 ATTTTGTATTTTTTAA
39691538 TTGAGTTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
ATTTTGTATTTTTTAA
Found at i:39702105 original size:10 final size:10
Alignment explanation
Indices: 39702092--39702168 Score: 59
Period size: 10 Copynumber: 7.5 Consensus size: 10
39702082 GTTTTGGCGC
*
39702092 GTTTTTTACT
1 GTTTTTTGCT
39702102 GTTTTGGTTGCT
1 GTTTT--TTGCT
39702114 GTTTTTTGCT
1 GTTTTTTGCT
*
39702124 ATTTTGATTGCT
1 GTTTT--TTGCT
*
39702136 GTTTTTTGTT
1 GTTTTTTGCT
39702146 G-TTTTTG-T
1 GTTTTTTGCT
* *
39702154 TTTTTTTACT
1 GTTTTTTGCT
39702164 GTTTT
1 GTTTT
39702169 GATGCTTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
8 1 0.02
9 11 0.20
10 24 0.44
12 18 0.33
ACGTcount: A:0.05, C:0.06, G:0.18, T:0.70
Consensus pattern (10 bp):
GTTTTTTGCT
Found at i:39702120 original size:22 final size:22
Alignment explanation
Indices: 39702092--39702192 Score: 81
Period size: 22 Copynumber: 4.9 Consensus size: 22
39702082 GTTTTGGCGC
39702092 GTTTTTTACTGTTTTGGTTGCT
1 GTTTTTTACTGTTTTGGTTGCT
* * *
39702114 GTTTTTTGCTATTTTGATTGCT
1 GTTTTTTACTGTTTTGGTTGCT
**
39702136 GTTTTTTGTTG-TTT--TTG-T
1 GTTTTTTACTGTTTTGGTTGCT
* *
39702154 TTTTTTTACTGTTTT-GATGC-
1 GTTTTTTACTGTTTTGGTTGCT
*
39702174 -TTTTTTACTATTTTGGTTG
1 GTTTTTTACTGTTTTGGTTG
39702193 TTATTTTCGT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
18 9 0.14
19 19 0.30
20 5 0.08
21 3 0.05
22 28 0.44
ACGTcount: A:0.07, C:0.07, G:0.19, T:0.67
Consensus pattern (22 bp):
GTTTTTTACTGTTTTGGTTGCT
Found at i:39702223 original size:12 final size:12
Alignment explanation
Indices: 39702191--39702229 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
39702181 CTATTTTGGT
*
39702191 TGTTATTTTCG-
1 TGTTATTTTTGC
*
39702202 TGTTGTTTTTGC
1 TGTTATTTTTGC
39702214 TGTTATTTTTGC
1 TGTTATTTTTGC
39702226 TGTT
1 TGTT
39702230 TTTAATGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.05, C:0.08, G:0.21, T:0.67
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:39702238 original size:21 final size:22
Alignment explanation
Indices: 39702191--39702238 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
39702181 CTATTTTGGT
* **
39702191 TGTTATTTTCGTGTTGTTTTTGC
1 TGTTATTTTC-TGCTGTTTTTAA
39702214 TGTTATTTT-TGCTGTTTTTAA
1 TGTTATTTTCTGCTGTTTTTAA
39702235 TGTT
1 TGTT
39702239 GTTTGATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 13 0.59
23 9 0.41
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.67
Consensus pattern (22 bp):
TGTTATTTTCTGCTGTTTTTAA
Found at i:39702254 original size:43 final size:44
Alignment explanation
Indices: 39702202--39702298 Score: 106
Period size: 43 Copynumber: 2.2 Consensus size: 44
39702192 GTTATTTTCG
* * * * * *
39702202 TGTTGTTTTTGCTGTTATTTTTGCTGTTTTTAATGTTGTTT-GA
1 TGTTATTTTTGCTGCTATTTTGGCTGTTATTTATGTTATTTGGA
* * *
39702245 TGTTATTTTTGCTGCTGTTTTGGTTGTTATTTTTGTTATTTGGA
1 TGTTATTTTTGCTGCTATTTTGGCTGTTATTTATGTTATTTGGA
39702289 TGTTATTTTT
1 TGTTATTTTT
39702299 TATGCGTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 32 0.73
44 12 0.27
ACGTcount: A:0.09, C:0.04, G:0.21, T:0.66
Consensus pattern (44 bp):
TGTTATTTTTGCTGCTATTTTGGCTGTTATTTATGTTATTTGGA
Found at i:39702271 original size:31 final size:30
Alignment explanation
Indices: 39702209--39702272 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
39702199 TCGTGTTGTT
* *
39702209 TTTGCTGTTATTTTTGCTGTTTTTAATGTTG
1 TTTGATGTTATTTTTGCTGTTTTT-AGGTTG
39702240 TTTGATGTTATTTTTGCTGCTGTTTT-GGTTG
1 TTTGATGTTATTTTTGCTG-T-TTTTAGGTTG
39702271 TT
1 TT
39702273 ATTTTTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 24 0.83
32 1 0.03
33 4 0.14
ACGTcount: A:0.08, C:0.06, G:0.22, T:0.64
Consensus pattern (30 bp):
TTTGATGTTATTTTTGCTGTTTTTAGGTTG
Found at i:39702440 original size:21 final size:21
Alignment explanation
Indices: 39702416--39702470 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
39702406 TATAAAAAAA
*
39702416 TTTAATGTATTTTAAATTTTT
1 TTTAATGTATTTTAAATGTTT
* *
39702437 TTTAATGTTTGTTTTAATGTTT
1 TTTAATGTAT-TTTAAATGTTT
*
39702459 TTAAATGTATTT
1 TTTAATGTATTT
39702471 GATATATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.65
Consensus pattern (21 bp):
TTTAATGTATTTTAAATGTTT
Found at i:39702453 original size:12 final size:11
Alignment explanation
Indices: 39702416--39702460 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
39702406 TATAAAAAAA
*
39702416 TTTAATGTATT
1 TTTAATGTTTT
*
39702427 TTAAAT-TTTT
1 TTTAATGTTTT
39702437 TTTAATGTTTGT
1 TTTAATGTTT-T
39702449 TTTAATGTTTT
1 TTTAATGTTTT
39702460 T
1 T
39702461 AAATGTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 8 0.28
11 10 0.34
12 11 0.38
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (11 bp):
TTTAATGTTTT
Found at i:39711928 original size:3 final size:3
Alignment explanation
Indices: 39711920--39711958 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
39711910 AGATTAAGTG
*
39711920 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39711959 GTAAGAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:39715346 original size:17 final size:18
Alignment explanation
Indices: 39715324--39715359 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39715314 TAAATGAGTT
39715324 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
39715341 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
39715359 A
1 A
39715360 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:39715676 original size:18 final size:18
Alignment explanation
Indices: 39715653--39715689 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39715643 TTTGTGATCA
39715653 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
39715671 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
39715689 A
1 A
39715690 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:39719012 original size:22 final size:22
Alignment explanation
Indices: 39718974--39719033 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
39718964 TCGACTTCGT
*
39718974 TATTTTCTATTT-CTTTTAACTC
1 TATTTTCT-TTTATTTTTAACTC
*
39718996 TATTTTCTTTTATTTTTAATTC
1 TATTTTCTTTTATTTTTAACTC
*
39719018 T-GTTTCTTTTATTTTT
1 TATTTTCTTTTATTTTT
39719034 CCTCAGATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.15, C:0.12, G:0.02, T:0.72
Consensus pattern (22 bp):
TATTTTCTTTTATTTTTAACTC
Found at i:39720403 original size:13 final size:13
Alignment explanation
Indices: 39720385--39720413 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39720375 AAATTAAAAT
39720385 AAAAAAAATTCTC
1 AAAAAAAATTCTC
39720398 AAAAAAAATTCTC
1 AAAAAAAATTCTC
39720411 AAA
1 AAA
39720414 TGAGAATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTCTC
Found at i:39720736 original size:30 final size:30
Alignment explanation
Indices: 39720700--39720761 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
39720690 TTTTTTTTAT
39720700 ATAAATTTAATGAT-TTTTTAATTTTAAAAA
1 ATAAATTTAAT-ATATTTTTAATTTTAAAAA
* *
39720730 ATAAATTTTATATATTTTTAATTTTTAAAA
1 ATAAATTTAATATATTTTTAATTTTAAAAA
39720760 AT
1 AT
39720762 TTTAAATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATAAATTTAATATATTTTTAATTTTAAAAA
Found at i:39727422 original size:5 final size:5
Alignment explanation
Indices: 39727412--39727444 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
39727402 AATAAGAGCT
39727412 TATCA TATCA TATCA TATCA TATCA TATCA TAT
1 TATCA TATCA TATCA TATCA TATCA TATCA TAT
39727445 GCCTGCTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (5 bp):
TATCA
Found at i:39731083 original size:165 final size:165
Alignment explanation
Indices: 39730895--39731218 Score: 621
Period size: 165 Copynumber: 2.0 Consensus size: 165
39730885 CCAAATCCTC
*
39730895 AGTGAATTCTTAGAAATTTGACGTGACAATAATAATCGGTGAATGCATTTCAAAGTGCATTATTT
1 AGTGAATTCTTAGAAATTTGACGTGACAATAATAATCGGTGAATGCATCTCAAAGTGCATTATTT
39730960 CTTGACAATTAGCAAAACTTCATAAATACCCTGTATTCATCAGAGAATTCGAAGGGTACCTTACA
66 CTTGACAATTAGCAAAACTTCATAAATACCCTGTATTCATCAGAGAATTCGAAGGGTACCTTACA
39731025 GTTAAGTTAGAACCGCTAAGAGAGAACTATCTCAA
131 GTTAAGTTAGAACCGCTAAGAGAGAACTATCTCAA
* *
39731060 AGTGAATTCTTAGAACTTTGACGTGACAATAATAATCGGTGAATGTATCTCAAAGTGCATTATTT
1 AGTGAATTCTTAGAAATTTGACGTGACAATAATAATCGGTGAATGCATCTCAAAGTGCATTATTT
39731125 CTTGACAATTAGCAAAACTTCATAAATACCCTGTATTCATCAGAGAATTCGAAGGGTACCTTACA
66 CTTGACAATTAGCAAAACTTCATAAATACCCTGTATTCATCAGAGAATTCGAAGGGTACCTTACA
39731190 GTTAAGTTAGAACCGCTAAGAGAGAACTA
131 GTTAAGTTAGAACCGCTAAGAGAGAACTA
39731219 AAAGCAAAAA
Statistics
Matches: 156, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 156 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (165 bp):
AGTGAATTCTTAGAAATTTGACGTGACAATAATAATCGGTGAATGCATCTCAAAGTGCATTATTT
CTTGACAATTAGCAAAACTTCATAAATACCCTGTATTCATCAGAGAATTCGAAGGGTACCTTACA
GTTAAGTTAGAACCGCTAAGAGAGAACTATCTCAA
Found at i:39744647 original size:25 final size:26
Alignment explanation
Indices: 39744609--39744665 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
39744599 AAAAGTTAGT
39744609 AAAAAAAATTAA-CCTAT-AAAATTA
1 AAAAAAAATTAACCCTATAAAAATTA
*
39744633 AAAAAAAATTAAACCCTTTAAAAATTA
1 AAAAAAAATT-AACCCTATAAAAATTA
39744660 AAAAAA
1 AAAAAA
39744666 TAAAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 10 0.34
25 2 0.07
26 4 0.14
27 13 0.45
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (26 bp):
AAAAAAAATTAACCCTATAAAAATTA
Found at i:39744666 original size:25 final size:23
Alignment explanation
Indices: 39744608--39744665 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 23
39744598 TAAAAGTTAG
39744608 TAAAAAAAATTAACCTATAAAAT
1 TAAAAAAAATTAACCTATAAAAT
*
39744631 TAAAAAAAAATTAAACCCTTTAAAAAT
1 T-AAAAAAAATT-AA-CCTAT-AAAAT
39744658 TAAAAAAA
1 TAAAAAAA
39744666 TAAAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 1 0.03
24 10 0.33
25 2 0.07
26 11 0.37
27 6 0.20
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (23 bp):
TAAAAAAAATTAACCTATAAAAT
Found at i:39745456 original size:2 final size:2
Alignment explanation
Indices: 39745449--39745480 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39745439 CATGGTAAGA
39745449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39745481 GATAAATAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39746357 original size:43 final size:47
Alignment explanation
Indices: 39746288--39746382 Score: 135
Period size: 45 Copynumber: 2.1 Consensus size: 47
39746278 TGAAAAATCT
*
39746288 TTATAATCAATAATTAACTCAATCCT-AAAATAAAATCTCATC-AAA
1 TTATAATCAAAAATTAACTCAATCCTAAAAATAAAATCTCATCAAAA
*
39746333 TTATAAT-AAAAATTTACT-AATCCTAAAAAATAAAATCTCATCAAAA
1 TTATAATCAAAAATTAACTCAATCCT-AAAAATAAAATCTCATCAAAA
39746379 TTAT
1 TTAT
39746383 TTCAGTTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
43 6 0.13
44 9 0.20
45 23 0.51
46 7 0.16
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (47 bp):
TTATAATCAAAAATTAACTCAATCCTAAAAATAAAATCTCATCAAAA
Found at i:39748351 original size:2 final size:2
Alignment explanation
Indices: 39748344--39748368 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39748334 GATACAAGAG
39748344 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39748369 GTGTGTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39763967 original size:23 final size:24
Alignment explanation
Indices: 39763909--39763971 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
39763899 TCATTAACAT
*
39763909 TGTTCATGAATATGTTCAATTGTA
1 TGTTCATGAACATGTTCAATTGTA
*
39763933 TGTTCATAAACATGTTC-ATT-TA
1 TGTTCATGAACATGTTCAATTGTA
*
39763955 CTGTTCGTGAACATGTT
1 -TGTTCATGAACATGTT
39763972 TAAGTTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.06
23 17 0.50
24 15 0.44
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (24 bp):
TGTTCATGAACATGTTCAATTGTA
Found at i:39764053 original size:27 final size:27
Alignment explanation
Indices: 39763994--39764058 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
39763984 ATATGTTCGT
* * * *
39763994 AAATATTAAACAAATGAACATGAACAC
1 AAATTTTAAATAAACGAACATGAACAA
* *
39764021 ATATTTTAAATAAACGAACATGAGCAA
1 AAATTTTAAATAAACGAACATGAACAA
*
39764048 AAATTTGAAAT
1 AAATTTTAAAT
39764059 TCTTAACGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (27 bp):
AAATTTTAAATAAACGAACATGAACAA
Found at i:39770372 original size:6 final size:6
Alignment explanation
Indices: 39770357--39770396 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
39770347 TAGACTTGAA
* * *
39770357 AAAAAT AAAAAG AAAAAG AAAAAG AAAATG GAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
39770397 TTCCCCTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:39775203 original size:19 final size:20
Alignment explanation
Indices: 39775168--39775205 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
39775158 CAAAAATCTT
*
39775168 CAAAACTTTTTATTTTCTCC
1 CAAAACTTTTTACTTTCTCC
39775188 CAAAAC-TTTTACTTTCTC
1 CAAAACTTTTTACTTTCTC
39775206 ACACTTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (20 bp):
CAAAACTTTTTACTTTCTCC
Found at i:39775243 original size:5 final size:5
Alignment explanation
Indices: 39775230--39775264 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
39775220 AAACTTTTAC
*
39775230 TCCCT TCCCA TCCCA TCCCA TCCCA TCCCTA TCCC
1 TCCCA TCCCA TCCCA TCCCA TCCCA TCCC-A TCCC
39775265 CATCTACCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.14, C:0.60, G:0.00, T:0.26
Consensus pattern (5 bp):
TCCCA
Found at i:39778145 original size:21 final size:21
Alignment explanation
Indices: 39778112--39778277 Score: 109
Period size: 21 Copynumber: 7.9 Consensus size: 21
39778102 ACTGTACCCA
*
39778112 GGAGAAGTGGGGCTATATGCT
1 GGAGAAGTGGGGCTATATGAT
* * *
39778133 GGGGAAGTAGGGCTGTATGAT
1 GGAGAAGTGGGGCTATATGAT
* * *
39778154 GGAGATGTGGGGCTATAGGAG
1 GGAGAAGTGGGGCTATATGAT
* * * * *
39778175 GGTGAGGTGGGGCTGTAAGAA
1 GGAGAAGTGGGGCTATATGAT
* * * *
39778196 GGAGATGTTGGACTGTATGAT
1 GGAGAAGTGGGGCTATATGAT
* * * *
39778217 GGGGATGTTGGGCTGTATGAT
1 GGAGAAGTGGGGCTATATGAT
*
39778238 GGAGAAGTGGGGCTGTATGCA-
1 GGAGAAGTGGGGCTATATG-AT
* *
39778259 GGTGAAGTTGGGCTATATG
1 GGAGAAGTGGGGCTATATG
39778278 CCGGTGAAGT
Statistics
Matches: 115, Mismatches: 29, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
21 114 0.99
22 1 0.01
ACGTcount: A:0.22, C:0.06, G:0.46, T:0.25
Consensus pattern (21 bp):
GGAGAAGTGGGGCTATATGAT
Found at i:39778158 original size:42 final size:42
Alignment explanation
Indices: 39778112--39778277 Score: 156
Period size: 42 Copynumber: 4.0 Consensus size: 42
39778102 ACTGTACCCA
* *
39778112 GGAGAAGTGGGGCTATATGCTGGGGAAGTAGGGCTGTATGAT
1 GGAGAAGTGGGGCTATATGCAGGGGAAGTTGGGCTGTATGAT
* * * * * *
39778154 GGAGATGTGGGGCTATA-GGAGGGTGAGGTGGGGCTGTAAGAA
1 GGAGAAGTGGGGCTATATGCAGGG-GAAGTTGGGCTGTATGAT
* * * * *
39778196 GGAGATGTTGGACTGTATG-ATGGGGATGTTGGGCTGTATGAT
1 GGAGAAGTGGGGCTATATGCA-GGGGAAGTTGGGCTGTATGAT
* * *
39778238 GGAGAAGTGGGGCTGTATGCAGGTGAAGTTGGGCTATATG
1 GGAGAAGTGGGGCTATATGCAGGGGAAGTTGGGCTGTATG
39778278 CCGGTGAAGT
Statistics
Matches: 100, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 4 0.04
42 91 0.91
43 5 0.05
ACGTcount: A:0.22, C:0.06, G:0.46, T:0.25
Consensus pattern (42 bp):
GGAGAAGTGGGGCTATATGCAGGGGAAGTTGGGCTGTATGAT
Found at i:39778191 original size:84 final size:84
Alignment explanation
Indices: 39778091--39778251 Score: 205
Period size: 84 Copynumber: 1.9 Consensus size: 84
39778081 ACCGTAACTT
* * * *
39778091 GGTGAGGTCGGACTGTACCCAGGAGAAGTGGGGCTATATGCTGGGGAAGTAGGGCTGTATGATGG
1 GGTGAGGTCGGACTGTAACAAGGAGAAGTGGGACTATATGATGGGGAAGTAGGGCTGTATGATGG
*
39778156 AGATGTGGGGCTATAGGAG
66 AGAAGTGGGGCTATAGGAG
* * * * * * * *
39778175 GGTGAGGTGGGGCTGTAAGAAGGAGATGTTGGACTGTATGATGGGGATGTTGGGCTGTATGATGG
1 GGTGAGGTCGGACTGTAACAAGGAGAAGTGGGACTATATGATGGGGAAGTAGGGCTGTATGATGG
39778240 AGAAGTGGGGCT
66 AGAAGTGGGGCT
39778252 GTATGCAGGT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 64 1.00
ACGTcount: A:0.22, C:0.08, G:0.47, T:0.24
Consensus pattern (84 bp):
GGTGAGGTCGGACTGTAACAAGGAGAAGTGGGACTATATGATGGGGAAGTAGGGCTGTATGATGG
AGAAGTGGGGCTATAGGAG
Found at i:39778269 original size:63 final size:63
Alignment explanation
Indices: 39778112--39778269 Score: 172
Period size: 63 Copynumber: 2.5 Consensus size: 63
39778102 ACTGTACCCA
* * * * *
39778112 GGAGAAGTGGGGCTATATGCTGGGGAAGTAGGGCTGTATGATGGAGATGTGGGGCTATAGGAG
1 GGAGAAGTGGGGCTGTATGCAGGAGAAGTTGGACTGTATGATGGAGATGTGGGGCTATAGGAG
* * * * * * * * * *
39778175 GGTGAGGTGGGGCTGTAAGAAGGAGATGTTGGACTGTATGATGGGGATGTTGGGCTGTATGAT
1 GGAGAAGTGGGGCTGTATGCAGGAGAAGTTGGACTGTATGATGGAGATGTGGGGCTATAGGAG
*
39778238 GGAGAAGTGGGGCTGTATGCAGGTGAAGTTGG
1 GGAGAAGTGGGGCTGTATGCAGGAGAAGTTGG
39778270 GCTATATGCC
Statistics
Matches: 74, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
63 74 1.00
ACGTcount: A:0.22, C:0.06, G:0.47, T:0.25
Consensus pattern (63 bp):
GGAGAAGTGGGGCTGTATGCAGGAGAAGTTGGACTGTATGATGGAGATGTGGGGCTATAGGAG
Found at i:39778278 original size:21 final size:21
Alignment explanation
Indices: 39778223--39778311 Score: 92
Period size: 21 Copynumber: 4.2 Consensus size: 21
39778213 TGATGGGGAT
*
39778223 GTTGGGCTGTATG-ATGGAGAA
1 GTTGGGCTGTATGCA-GGTGAA
*
39778244 GTGGGGCTGTATGCAGGTGAA
1 GTTGGGCTGTATGCAGGTGAA
* *
39778265 GTTGGGCTATATGCCGGTGAA
1 GTTGGGCTGTATGCAGGTGAA
* *
39778286 GTAGGGCTGTA-GCTTGGTGAA
1 GTTGGGCTGTATGC-AGGTGAA
39778307 GTTGG
1 GTTGG
39778312 ACTATAGCTG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.04
21 54 0.95
22 1 0.02
ACGTcount: A:0.19, C:0.09, G:0.44, T:0.28
Consensus pattern (21 bp):
GTTGGGCTGTATGCAGGTGAA
Found at i:39778287 original size:42 final size:42
Alignment explanation
Indices: 39778223--39778317 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
39778213 TGATGGGGAT
* * *
39778223 GTTGGGCTGTATGATGGAGAAGTGGGGCTGTATGC-AGGTGAA
1 GTTGGGCTATATGACGGAGAAGTAGGGCTGTA-GCTAGGTGAA
* * *
39778265 GTTGGGCTATATGCCGGTGAAGTAGGGCTGTAGCTTGGTGAA
1 GTTGGGCTATATGACGGAGAAGTAGGGCTGTAGCTAGGTGAA
*
39778307 GTTGGACTATA
1 GTTGGGCTATA
39778318 GCTGGGAGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.04
42 43 0.96
ACGTcount: A:0.21, C:0.09, G:0.41, T:0.28
Consensus pattern (42 bp):
GTTGGGCTATATGACGGAGAAGTAGGGCTGTAGCTAGGTGAA
Found at i:39778347 original size:63 final size:63
Alignment explanation
Indices: 39778280--39778410 Score: 163
Period size: 63 Copynumber: 2.1 Consensus size: 63
39778270 GCTATATGCC
* * * * *
39778280 GGTGAAGTAGGGCTGTAGCTTGGTGAAGTTGGACTATAGCTGGGAGATGTGGGACTATAACTT
1 GGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTGGGACTATAACTT
* * * * * *
39778343 GGTGAAGTAGGACTGTAACTTGGAGACGTAGGGCTGTAGCTTGGAGAGGTGGGGCTATAGCTT
1 GGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTGGGACTATAACTT
39778406 GGTGA
1 GGTGA
39778411 GGTTGGAGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.27
Consensus pattern (63 bp):
GGTGAAGTAGGACTGTAACTTGGAGAAGTAGGACTATAGCTGGGAGAGGTGGGACTATAACTT
Found at i:39778407 original size:42 final size:42
Alignment explanation
Indices: 39778286--39778407 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
39778276 TGCCGGTGAA
* * *
39778286 GTAGGGCTGTAGCTTGGTGAAGTTGGACTATAGCTGGGAGAT
1 GTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCTTGGAGAC
* * * *
39778328 GT-GGGACTATAACTTGGTGAAGTAGGACTGTAACTTGGAGAC
1 GTAGGG-CTGTAGCTTGGTGAAGTAGGACTATAGCTTGGAGAC
* * * *
39778370 GTAGGGCTGTAGCTTGGAGAGGTGGGGCTATAGCTTGG
1 GTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCTTGG
39778408 TGAGGTTGGA
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
41 3 0.05
42 57 0.90
43 3 0.05
ACGTcount: A:0.22, C:0.11, G:0.40, T:0.27
Consensus pattern (42 bp):
GTAGGGCTGTAGCTTGGTGAAGTAGGACTATAGCTTGGAGAC
Found at i:39778413 original size:21 final size:21
Alignment explanation
Indices: 39778280--39778410 Score: 100
Period size: 21 Copynumber: 6.2 Consensus size: 21
39778270 GCTATATGCC
* *
39778280 GGTGAAGTAGGGCTGTAGCTT
1 GGTGAAGTAGGACTATAGCTT
* *
39778301 GGTGAAGTTGGACTATAGCTG
1 GGTGAAGTAGGACTATAGCTT
* * * *
39778322 GGAGATGTGGGACTATAACTT
1 GGTGAAGTAGGACTATAGCTT
* *
39778343 GGTGAAGTAGGACTGTAACTT
1 GGTGAAGTAGGACTATAGCTT
* * * *
39778364 GGAGACGTAGGGCTGTAGCTT
1 GGTGAAGTAGGACTATAGCTT
* * * *
39778385 GGAGAGGTGGGGCTATAGCTT
1 GGTGAAGTAGGACTATAGCTT
39778406 GGTGA
1 GGTGA
39778411 GGTTGGAGAA
Statistics
Matches: 89, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 89 1.00
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.27
Consensus pattern (21 bp):
GGTGAAGTAGGACTATAGCTT
Done.