Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 80 of 91
Found at i:29745288 original size:20 final size:20
Alignment explanation
Indices: 29745263--29745301 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
29745253 ACCAAGAAAC
29745263 TAATGAAGTGGTTTAAAATA
1 TAATGAAGTGGTTTAAAATA
29745283 TAATGAAGTGGTTTAAAAT
1 TAATGAAGTGGTTTAAAAT
29745302 GAACAACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (20 bp):
TAATGAAGTGGTTTAAAATA
Found at i:29753702 original size:36 final size:36
Alignment explanation
Indices: 29753650--29753720 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
29753640 AAAAACCAAT
29753650 CAAATTTGGGTCAAGAAATGCTGTATAAACATGAAG
1 CAAATTTGGGTCAAGAAATGCTGTATAAACATGAAG
* *
29753686 CAAATTTTGGTTAAGAAATGCTGTATAAACATGAA
1 CAAATTTGGGTCAAGAAATGCTGTATAAACATGAA
29753721 TTGCTGCCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (36 bp):
CAAATTTGGGTCAAGAAATGCTGTATAAACATGAAG
Found at i:29755175 original size:20 final size:20
Alignment explanation
Indices: 29755150--29755190 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
29755140 GTTTATCTCC
29755150 TTTTTCAGATTTACATCCGT
1 TTTTTCAGATTTACATCCGT
29755170 TTTTTCAGATTTACATCCGT
1 TTTTTCAGATTTACATCCGT
29755190 T
1 T
29755191 AAACGGATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTTTCAGATTTACATCCGT
Found at i:29762110 original size:22 final size:21
Alignment explanation
Indices: 29762069--29762113 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
29762059 GACAAATATA
*
29762069 TATTTTATTATAATATATAAT
1 TATTTTATTAAAATATATAAT
29762090 TATTTT-TTAAAATAT-TAAT
1 TATTTTATTAAAATATATAAT
*
29762109 AATTT
1 TATTT
29762114 AAAATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 8 0.36
21 6 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTTTATTAAAATATATAAT
Found at i:29762119 original size:29 final size:28
Alignment explanation
Indices: 29762074--29762136 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
29762064 ATATATATTT
* **
29762074 TATT-ATAATATATAATTATTTTTTAAAA
1 TATTAATAATATAAAATTAAATTTT-AAA
*
29762102 TATTAATAATTTAAAATTAAATTTTAAA
1 TATTAATAATATAAAATTAAATTTTAAA
29762130 TATTAAT
1 TATTAAT
29762137 TTTTATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 14 0.47
29 16 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TATTAATAATATAAAATTAAATTTTAAA
Found at i:29762134 original size:14 final size:14
Alignment explanation
Indices: 29762094--29762141 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
29762084 TATAATTATT
29762094 TTTTAAAATATTAATA
1 TTTT-AAATATTAA-A
*
29762110 ATTTAAA-ATTAAA
1 TTTTAAATATTAAA
*
29762123 TTTTAAATATTAAT
1 TTTTAAATATTAAA
29762137 TTTTA
1 TTTTA
29762142 TAATTTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 7 0.25
14 15 0.54
15 3 0.11
16 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTAAATATTAAA
Found at i:29762145 original size:34 final size:32
Alignment explanation
Indices: 29762107--29762194 Score: 104
Period size: 34 Copynumber: 2.7 Consensus size: 32
29762097 TAAAATATTA
29762107 ATAATTTAAAATTAAATTTTAAATATTAATTTTT
1 ATAATTTAAAATTAAATTTTAAAT-TTAA-TTTT
* *
29762141 ATAATTTACAATTAAATTTTTAATTTAATTTT
1 ATAATTTAAAATTAAATTTTAAATTTAATTTT
* * *
29762173 AAAATATAAAATATTAATTTTA
1 ATAATTTAAAAT-TAAATTTTA
29762195 GTTTTTTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
32 13 0.28
33 11 0.24
34 22 0.48
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
ATAATTTAAAATTAAATTTTAAATTTAATTTT
Found at i:29762148 original size:21 final size:19
Alignment explanation
Indices: 29762124--29762168 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
29762114 AAAATTAAAT
*
29762124 TTTAAATATTAATTTTTATAA
1 TTTAAA-ATTAAATTTT-TAA
*
29762145 TTTACAATTAAATTTTTAA
1 TTTAAAATTAAATTTTTAA
29762164 TTTAA
1 TTTAA
29762169 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 7 0.33
20 9 0.43
21 5 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAAAATTAAATTTTTAA
Found at i:29763047 original size:28 final size:28
Alignment explanation
Indices: 29763007--29763072 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 28
29762997 CGTCATGATT
*
29763007 AAAAAAT-GTTGTTACACGTCATATTGGA
1 AAAAAATACTTGTTACACGTCATATT-GA
*
29763035 AAAAAATACTGTTGTTACACGTCATGTTGA
1 AAAAAATAC--TTGTTACACGTCATATTGA
29763065 AAAAAATA
1 AAAAAATA
29763073 TTATTATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 7 0.21
30 10 0.30
31 16 0.48
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (28 bp):
AAAAAATACTTGTTACACGTCATATTGA
Found at i:29763051 original size:31 final size:30
Alignment explanation
Indices: 29763013--29763098 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
29763003 GATTAAAAAA
29763013 TGTTGTTACACGTCATATTGGAAAAAAATAC
1 TGTTGTTACACGTCATATT-GAAAAAAATAC
* *
29763044 TGTTGTTACACGTCATGTTGAAAAAAATAT
1 TGTTGTTACACGTCATATTGAAAAAAATAC
* * * *
29763074 TATTATTACACGCCATATTCAAAAA
1 TGTTGTTACACGTCATATTGAAAAA
29763099 CATTTTGTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 30 0.62
31 18 0.38
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (30 bp):
TGTTGTTACACGTCATATTGAAAAAAATAC
Found at i:29786245 original size:27 final size:26
Alignment explanation
Indices: 29786209--29786293 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 26
29786199 TTTAATAATT
29786209 TTATAA-TTAATTA-AAATATTAATAA
1 TTATAATTTAATTACAAATATT-ATAA
* *
29786234 TTAATAATTTAAATATC-AATATTTTAA
1 TT-ATAATTTAATTA-CAAATATTATAA
* *
29786261 -TATAATTTAATTACTAATATTTTAA
1 TTATAATTTAATTACAAATATTATAA
29786286 TTAATAAT
1 TT-ATAAT
29786294 ATTTTATTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
24 1 0.02
25 23 0.46
26 6 0.12
27 14 0.28
28 6 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TTATAATTTAATTACAAATATTATAA
Found at i:29786279 original size:25 final size:25
Alignment explanation
Indices: 29786237--29786290 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
29786227 TTAATAATTA
29786237 ATAATTTAAATATCAATATTTTAAT
1 ATAATTTAAATATCAATATTTTAAT
*
29786262 ATAATTTAATTA-CTAATATTTTAAT
1 ATAATTTAAATATC-AATATTTTAAT
29786287 -TAAT
1 ATAAT
29786291 AATATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
ATAATTTAAATATCAATATTTTAAT
Found at i:29786282 original size:14 final size:14
Alignment explanation
Indices: 29786265--29786307 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
29786255 TTTTAATATA
*
29786265 ATTTAATTACTAAT
1 ATTTAATTAATAAT
29786279 ATTTTAATTAATAAT
1 A-TTTAATTAATAAT
* *
29786294 ATTTTATTTATAAT
1 ATTTAATTAATAAT
29786308 TTAATATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTAATTAATAAT
Found at i:29786285 original size:40 final size:41
Alignment explanation
Indices: 29786235--29786312 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
29786225 TATTAATAAT
29786235 TAATAATTTAAAT-ATCAATATTTTA-ATATAATTTAATTAC
1 TAATAATTTAAATAAT-AATATTTTATATATAATTTAATTAC
* * *
29786275 TAATATTTTAATTAATAATATTTTATTTATAATTTAAT
1 TAATAATTTAAATAATAATATTTTATATATAATTTAAT
29786313 ATTATTATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 20 0.61
41 13 0.39
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (41 bp):
TAATAATTTAAATAATAATATTTTATATATAATTTAATTAC
Found at i:29786286 original size:15 final size:15
Alignment explanation
Indices: 29786200--29786299 Score: 63
Period size: 15 Copynumber: 6.9 Consensus size: 15
29786190 TTTTAAATAT
29786200 TTAATAAT-TTTATAA
1 TTAATAATATTT-TAA
* *
29786215 TTAATTAAAATATTAA
1 TTAA-TAATATTTTAA
*
29786231 -TAATTAATAATTTAA
1 TTAA-TAATATTTTAA
*
29786246 AT-ATCAATATTTTAA
1 TTAAT-AATATTTTAA
29786261 -T-AT-A-A-TTTAA
1 TTAATAATATTTTAA
*
29786271 TTACTAATATTTTAA
1 TTAATAATATTTTAA
29786286 TTAATAATATTTTA
1 TTAATAATATTTTA
29786300 TTTATAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
10 5 0.07
11 2 0.03
12 2 0.03
13 1 0.01
14 5 0.07
15 44 0.65
16 7 0.10
17 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATAATATTTTAA
Found at i:29786399 original size:31 final size:31
Alignment explanation
Indices: 29786358--29786417 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
29786348 TTATATTCAT
* *
29786358 TAAAATTTTAATAGATTAATAAT-TTAATAAA
1 TAAAACTTTAACAGATTAA-AATATTAATAAA
*
29786389 TAAAACTTTAACAGTTTAAAATATTAATA
1 TAAAACTTTAACAGATTAAAATATTAATA
29786418 TTTAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (31 bp):
TAAAACTTTAACAGATTAAAATATTAATAAA
Found at i:29789076 original size:19 final size:19
Alignment explanation
Indices: 29789054--29789099 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 19
29789044 GTGCTAATGT
29789054 TAGTAATGTCTATTTTTGC
1 TAGTAATGTCTATTTTTGC
*
29789073 TAGT-ATG--TATTTTTGT
1 TAGTAATGTCTATTTTTGC
*
29789089 TAGTAACGTCT
1 TAGTAATGTCT
29789100 TGTGTCATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
16 12 0.55
17 2 0.09
18 3 0.14
19 5 0.23
ACGTcount: A:0.22, C:0.09, G:0.17, T:0.52
Consensus pattern (19 bp):
TAGTAATGTCTATTTTTGC
Found at i:29794306 original size:25 final size:27
Alignment explanation
Indices: 29794272--29794323 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
29794262 TAAATAAACC
29794272 GGAAAAAAAGAAA-ACAAAA-AAAAAA
1 GGAAAAAAAGAAAGACAAAAGAAAAAA
*
29794297 GGAAAAAAAGAAAGAGAAAAGAAAAAA
1 GGAAAAAAAGAAAGACAAAAGAAAAAA
29794324 AATAAGCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 13 0.54
26 5 0.21
27 6 0.25
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (27 bp):
GGAAAAAAAGAAAGACAAAAGAAAAAA
Found at i:29794310 original size:13 final size:13
Alignment explanation
Indices: 29794272--29794316 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
29794262 TAAATAAACC
29794272 GGAAAAAAAGAAA
1 GGAAAAAAAGAAA
**
29794285 ACAAAAAAA-AAA
1 GGAAAAAAAGAAA
29794297 GGAAAAAAAGAAA
1 GGAAAAAAAGAAA
29794310 GAGAAAA
1 G-GAAAA
29794317 GAAAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 10 0.38
13 11 0.42
14 5 0.19
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (13 bp):
GGAAAAAAAGAAA
Found at i:29798404 original size:18 final size:18
Alignment explanation
Indices: 29798381--29798443 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 18
29798371 ATCATGACCA
29798381 TGATAGAGAGCGTGATCG
1 TGATAGAGAGCGTGATCG
* *
29798399 TGATAGGGAGCGTGAACG
1 TGATAGAGAGCGTGATCG
* * *
29798417 CGATAGGGACCGTGATCG
1 TGATAGAGAGCGTGATCG
*
29798435 TGATCGAGA
1 TGATAGAGA
29798444 TCGAGAACGG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.27, C:0.14, G:0.40, T:0.19
Consensus pattern (18 bp):
TGATAGAGAGCGTGATCG
Found at i:29798452 original size:36 final size:36
Alignment explanation
Indices: 29798382--29798452 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
29798372 TCATGACCAT
* * *
29798382 GATAGAGAGCGTGATCGTGATAGGGAGCGTGAACGC
1 GATAGAGACCGTGATCGTGATAGAGAGCGAGAACGC
* * *
29798418 GATAGGGACCGTGATCGTGATCGAGATCGAGAACG
1 GATAGAGACCGTGATCGTGATAGAGAGCGAGAACG
29798453 GGATCGTGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.39, T:0.17
Consensus pattern (36 bp):
GATAGAGACCGTGATCGTGATAGAGAGCGAGAACGC
Found at i:29798558 original size:18 final size:18
Alignment explanation
Indices: 29798535--29798569 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29798525 TGGCCGCAAT
29798535 CGTGATCATGACCGTGAC
1 CGTGATCATGACCGTGAC
*
29798553 CGTGATCATGATCGTGA
1 CGTGATCATGACCGTGA
29798570 GTGGGATCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (18 bp):
CGTGATCATGACCGTGAC
Found at i:29801349 original size:114 final size:113
Alignment explanation
Indices: 29801211--29801438 Score: 404
Period size: 114 Copynumber: 2.0 Consensus size: 113
29801201 GTGGGGTGGG
*
29801211 TGGGTGAGGGGAGTTACTTCATCTGGAATTTGGTGATCATGGTTACAAAAAGAAGGGGAGAGGAT
1 TGGGTGAGGGGAGTTACTTCATCTGGAATTTGGTGATCATGGTTACAAAAAGAAGGGGAGAGGAA
* *
29801276 TAGGGTTATGA-TTGTTAGGATTTCGGTAGAAATTTGATCTGGGGAATGC
66 TA-GGAT-TGACTTGTTAGGATTTCAGTAGAAATTTGATCTGGGGAATGC
29801325 TGGGTGAGGGGAGTTACTTCATCTGGAATTTGGTGATCATGGTTACAAAAAGAAGGGGAGAGGAA
1 TGGGTGAGGGGAGTTACTTCATCTGGAATTTGGTGATCATGGTTACAAAAAGAAGGGGAGAGGAA
29801390 TAGGATTGACTTGTTAGGATTTCAGTAGAAATTTGATCTGGGGAATGC
66 TAGGATTGACTTGTTAGGATTTCAGTAGAAATTTGATCTGGGGAATGC
29801438 T
1 T
29801439 TTCTTTCCTG
Statistics
Matches: 110, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
112 3 0.03
113 41 0.37
114 66 0.60
ACGTcount: A:0.28, C:0.07, G:0.34, T:0.30
Consensus pattern (113 bp):
TGGGTGAGGGGAGTTACTTCATCTGGAATTTGGTGATCATGGTTACAAAAAGAAGGGGAGAGGAA
TAGGATTGACTTGTTAGGATTTCAGTAGAAATTTGATCTGGGGAATGC
Found at i:29821033 original size:2 final size:2
Alignment explanation
Indices: 29821026--29821061 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
29821016 GCACATGAAG
* *
29821026 AT AT AT AT AG AT AT AT AT AG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29821062 TTGTCACAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29821039 original size:10 final size:10
Alignment explanation
Indices: 29821024--29821061 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
29821014 AAGCACATGA
29821024 AGATATATAT
1 AGATATATAT
29821034 AGATATATAT
1 AGATATATAT
29821044 AGATATATAT
1 AGATATATAT
*
29821054 ATATATAT
1 AGATATAT
29821062 TTGTCACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (10 bp):
AGATATATAT
Found at i:29822527 original size:37 final size:37
Alignment explanation
Indices: 29822477--29822552 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
29822467 ATAACATTTT
* * *
29822477 CAACTAATTGCTGACCATGCCTTTTCCTGAAAGTTAC
1 CAACTAATCGCTGACCATGCCTTGTCCTGAAAATTAC
*
29822514 CAACTTATCGCTGACCATGCCTTGTCCTGAAAATTAC
1 CAACTAATCGCTGACCATGCCTTGTCCTGAAAATTAC
29822551 CA
1 CA
29822553 TCCATTCTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (37 bp):
CAACTAATCGCTGACCATGCCTTGTCCTGAAAATTAC
Found at i:29844313 original size:3 final size:3
Alignment explanation
Indices: 29844307--29844331 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29844297 GTTTTTTTAT
29844307 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
29844332 AGATAGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29853271 original size:29 final size:31
Alignment explanation
Indices: 29853222--29853281 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
29853212 GTTGGCCTGA
29853222 AGATAACCCTGCAAATACCATATCCATCAAG
1 AGATAACCCTGCAAATACCATATCCATCAAG
29853253 AGATAACCCTG-AAA-ACCATATCCATCAAG
1 AGATAACCCTGCAAATACCATATCCATCAAG
29853282 CAAAGTAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 15 0.52
30 3 0.10
31 11 0.38
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.18
Consensus pattern (31 bp):
AGATAACCCTGCAAATACCATATCCATCAAG
Found at i:29858566 original size:11 final size:12
Alignment explanation
Indices: 29858546--29858593 Score: 55
Period size: 11 Copynumber: 4.1 Consensus size: 12
29858536 ATATATGAGC
*
29858546 AAATAGAATAA-
1 AAATAAAATAAT
29858557 AAATAAAATAAT
1 AAATAAAATAAT
*
29858569 TAAT-AAATAAT
1 AAATAAAATAAT
29858580 AAATAATAATAAT
1 AAATAA-AATAAT
29858593 A
1 A
29858594 TAAATTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 20 0.65
12 4 0.13
13 7 0.23
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:29870685 original size:22 final size:22
Alignment explanation
Indices: 29870660--29870701 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29870650 TTATATAAAA
*
29870660 TATTAATGAATATATGCTAGTT
1 TATTAATGAATATAGGCTAGTT
*
29870682 TATTTATGAATATAGGCTAG
1 TATTAATGAATATAGGCTAG
29870702 AATGAATGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.43
Consensus pattern (22 bp):
TATTAATGAATATAGGCTAGTT
Found at i:29873318 original size:2 final size:2
Alignment explanation
Indices: 29873311--29873337 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29873301 NNNNNNNNNN
29873311 TA 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 TA T
29873338 GAAATTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29880485 original size:93 final size:93
Alignment explanation
Indices: 29880316--29880502 Score: 311
Period size: 93 Copynumber: 2.0 Consensus size: 93
29880306 TACAAGAACG
*
29880316 CTGCAGAGGGCAAAAGTTAGATCACTGACATATTGGTGGAAGAACCGGGGTACTGTAATTTCCAC
1 CTGCAGAGGGAAAAAGTTAGATCACTGACATATTGGTGGAAGAACCGGGGTACTGTAATTTCCAC
*
29880381 TCGTTTATTACCTTCATTCTAATGTAGA
66 TCGTTTATTACCTTCATTATAATGTAGA
* * *
29880409 CTGCGGAGGGAAAAAGTTAGATCACTGACATATTGGTGGAAGAACCTGGGTATTGTAATTTCCAC
1 CTGCAGAGGGAAAAAGTTAGATCACTGACATATTGGTGGAAGAACCGGGGTACTGTAATTTCCAC
* *
29880474 TCGTTTGTTACCTTCATTATAGTGTAGA
66 TCGTTTATTACCTTCATTATAATGTAGA
29880502 C
1 C
29880503 ACTGAAGAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (93 bp):
CTGCAGAGGGAAAAAGTTAGATCACTGACATATTGGTGGAAGAACCGGGGTACTGTAATTTCCAC
TCGTTTATTACCTTCATTATAATGTAGA
Found at i:29902500 original size:16 final size:14
Alignment explanation
Indices: 29902479--29902541 Score: 67
Period size: 13 Copynumber: 4.5 Consensus size: 14
29902469 TAAAAGAATN
29902479 TTATTTTTAATTTAT
1 TTATTTTT-ATTTAT
29902494 ATTATTTTTATTTAT
1 -TTATTTTTATTTAT
*
29902509 TTATTTAT-TTTAT
1 TTATTTTTATTTAT
*
29902522 TTA-ATTTATTTAT
1 TTATTTTTATTTAT
*
29902535 GTATTTT
1 TTATTTT
29902542 AAATCTGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 2 0.05
13 15 0.38
14 9 0.22
15 6 0.15
16 8 0.20
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (14 bp):
TTATTTTTATTTAT
Found at i:29902509 original size:4 final size:4
Alignment explanation
Indices: 29902479--29902540 Score: 58
Period size: 4 Copynumber: 15.5 Consensus size: 4
29902469 TAAAAGAATN
*
29902479 TTAT TT-T TAAT TTAT ATTA- TT-T TTAT TTAT TTAT TTATT TTAT TTAAT
1 TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TT-AT
*
29902527 TTAT TTAT GTAT TT
1 TTAT TTAT TTAT TT
29902541 TAAATCTGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
3 6 0.12
4 31 0.65
5 11 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:29902518 original size:18 final size:19
Alignment explanation
Indices: 29902484--29902534 Score: 79
Period size: 18 Copynumber: 2.7 Consensus size: 19
29902474 GAATNTTATT
29902484 TTTAATTTATATTATTTTTA
1 TTTAATTTAT-TTATTTTTA
29902504 TTT-ATTTATTTA-TTTTA
1 TTTAATTTATTTATTTTTA
29902521 TTTAATTTATTTAT
1 TTTAATTTATTTAT
29902535 GTATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.28
18 12 0.41
19 6 0.21
20 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTAATTTATTTATTTTTA
Found at i:29902520 original size:9 final size:9
Alignment explanation
Indices: 29902484--29902534 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
29902474 GAATNTTATT
*
29902484 TTTAATTTA
1 TTTATTTTA
29902493 TATTATTTTTA
1 T-TTA-TTTTA
29902504 TTTA-TTTA
1 TTTATTTTA
29902512 TTTATTTTA
1 TTTATTTTA
*
29902521 TTTAATTTA
1 TTTATTTTA
29902530 TTTAT
1 TTTAT
29902535 GTATTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 8 0.22
9 17 0.47
10 6 0.17
11 5 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTATTTTA
Found at i:29902531 original size:22 final size:23
Alignment explanation
Indices: 29902488--29902542 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
29902478 NTTATTTTTA
* *
29902488 ATTTATATTATTTTTATTTATTT
1 ATTTATTTTATTTTAATTTATTT
29902511 ATTTATTTTA-TTTAATTTATTT
1 ATTTATTTTATTTTAATTTATTT
*
29902533 ATGTATTTTA
1 ATTTATTTTA
29902543 AATCTGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
ATTTATTTTATTTTAATTTATTT
Found at i:29910143 original size:61 final size:61
Alignment explanation
Indices: 29910048--29910166 Score: 238
Period size: 61 Copynumber: 2.0 Consensus size: 61
29910038 GAACTTGCAC
29910048 GAGTAAGTGCAGTGAACTTCAAACAAATGAATCTCCTAATCTAGAATAGCGTATTAGGCAT
1 GAGTAAGTGCAGTGAACTTCAAACAAATGAATCTCCTAATCTAGAATAGCGTATTAGGCAT
29910109 GAGTAAGTGCAGTGAACTTCAAACAAATGAATCTCCTAATCTAGAATAGCGTATTAGG
1 GAGTAAGTGCAGTGAACTTCAAACAAATGAATCTCCTAATCTAGAATAGCGTATTAGG
29910167 AATTTAATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (61 bp):
GAGTAAGTGCAGTGAACTTCAAACAAATGAATCTCCTAATCTAGAATAGCGTATTAGGCAT
Found at i:29923381 original size:20 final size:20
Alignment explanation
Indices: 29923353--29923401 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
29923343 CTTCACTTTC
*
29923353 AATTTAAAAAAT-ATTTATTA
1 AATTAAAAAAATAATTTA-TA
*
29923373 AATTAAAAAATTAATTTATA
1 AATTAAAAAAATAATTTATA
29923393 AATTTAAAA
1 AA-TTAAAA
29923402 CTCATCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTAAAAAAATAATTTATA
Found at i:29923389 original size:21 final size:18
Alignment explanation
Indices: 29923356--29923401 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 18
29923346 CACTTTCAAT
29923356 TTAAAAAATATTTATTAAA
1 TTAAAAAATATTTA-TAAA
29923375 TTAAAAAATTAATTTATAAA
1 TTAAAAAA-T-ATTTATAAA
29923395 TTTAAAA
1 -TTAAAA
29923402 CTCATCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 11 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAAAAATATTTATAAA
Found at i:29923681 original size:18 final size:17
Alignment explanation
Indices: 29923652--29923699 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
29923642 ATAAAGATTT
29923652 ATTTAA-TTTTTTGAATA
1 ATTTAATTTTTTTGAA-A
*
29923669 ATTTAATTTTTTTTAAA
1 ATTTAATTTTTTTGAAA
29923686 ATATTATATTTTTT
1 AT-TTA-ATTTTTT
29923700 ATAATTCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 9 0.33
18 11 0.41
19 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTAATTTTTTTGAAA
Found at i:29928816 original size:15 final size:15
Alignment explanation
Indices: 29928796--29928838 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
29928786 GGGTGAAATT
29928796 ATAAAAAAATTTAAA
1 ATAAAAAAATTTAAA
*
29928811 ATAAAAATAAATTAAA
1 ATAAAAA-AATTTAAA
*
29928827 AAAATAAAAATT
1 ATAA-AAAAATT
29928839 ATCGGAGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 13 0.57
17 3 0.13
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAAAAAATTTAAA
Found at i:29940935 original size:230 final size:230
Alignment explanation
Indices: 29940493--29940957 Score: 740
Period size: 230 Copynumber: 2.0 Consensus size: 230
29940483 TAACTGTCCA
*
29940493 AAGCACACTGCTCTAGATGGCAGGATATATAGCGACAGAAACAGAGAATTCCCATTGAGAAAGGC
1 AAGCACACTGCTCTAGATGGCAGGATATATAGCGACAGAAACAGAGAAGTCCCATTGAGAAAGGC
*
29940558 CTTCTTAGATCCAATAAGAGAAGTTTAGGATATAATTCTAATCATGACCACTGCTCTGATAGCTA
66 CATCTTAGATCCAATAAGAGAAGTTTAGGATATAATTCTAATCATGACCACTGCTCTGATAGCTA
* *
29940623 CCAAAACTTCCTTATTTTTTCTGCTTGGGTAAAGCAACATATTTATGCATTCAGGCATTCTTGGA
131 CCAAAACTTCCTAATTTTTTCTGCTTGGGTAAAGCAACAGATTTATGCATTCAGGCATTCTTGGA
29940688 CAACATATAGAGTCCTATTAAAAACAGGCCATATC
196 CAACATATAGAGTCCTATTAAAAACAGGCCATATC
* * * * *
29940723 TAGCACATTGCTCTAGATGGTAGGGA-CTATAGTGACAGAAACAGCA-AAGTCCCACTT-AGAAA
1 AAGCACACTGCTCTAGATGGCA-GGATATATAGCGACAGAAACAG-AGAAGTCCCA-TTGAGAAA
*
29940785 GGCCATCTTAGATCCAATAAGAGAAGTTTAGGATATAATTCTAATCATGACCACTGTTCTGATAG
63 GGCCATCTTAGATCCAATAAGAGAAGTTTAGGATATAATTCTAATCATGACCACTGCTCTGATAG
* *
29940850 CTACCAAAATTTCCTAATTTTTTTCTGCTTGGGTAAAGCAACAGATTTATGCGTTCAGGCATTCT
128 CTACCAAAACTTCCTAA-TTTTTTCTGCTTGGGTAAAGCAACAGATTTATGCATTCAGGCATTCT
**
29940915 TGGACTGCATATAG-GTCCTATTAAAAACAGGCCATATC
192 TGGACAACATATAGAGTCCTATTAAAAACAGGCCATATC
29940953 AAGCA
1 AAGCA
29940958 TAAATCAATT
Statistics
Matches: 216, Mismatches: 15, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
230 153 0.71
231 63 0.29
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (230 bp):
AAGCACACTGCTCTAGATGGCAGGATATATAGCGACAGAAACAGAGAAGTCCCATTGAGAAAGGC
CATCTTAGATCCAATAAGAGAAGTTTAGGATATAATTCTAATCATGACCACTGCTCTGATAGCTA
CCAAAACTTCCTAATTTTTTCTGCTTGGGTAAAGCAACAGATTTATGCATTCAGGCATTCTTGGA
CAACATATAGAGTCCTATTAAAAACAGGCCATATC
Found at i:29944326 original size:23 final size:23
Alignment explanation
Indices: 29944296--29944341 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
29944286 TTGAAATGAA
29944296 CCTATGAGAAACAGTTAACAATC
1 CCTATGAGAAACAGTTAACAATC
29944319 CCTATGAGAAACAGTTAACAATC
1 CCTATGAGAAACAGTTAACAATC
29944342 ACAAAGTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (23 bp):
CCTATGAGAAACAGTTAACAATC
Found at i:29944804 original size:3 final size:3
Alignment explanation
Indices: 29944785--29944826 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
29944775 ATGAAATTTC
*
29944785 CTT C-T CTT -TT C-T CTT CTT CTT CTT CTT CTT CTT CTT GTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
29944827 TCTTTTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 6 0.18
3 28 0.82
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:29946860 original size:23 final size:23
Alignment explanation
Indices: 29946830--29946875 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
29946820 TAGGATCTAT
29946830 ATCTTTTTACATGATTTTTAAGG
1 ATCTTTTTACATGATTTTTAAGG
29946853 ATCTTTTTACATGATTTTTAAGG
1 ATCTTTTTACATGATTTTTAAGG
29946876 CTTATCCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.52
Consensus pattern (23 bp):
ATCTTTTTACATGATTTTTAAGG
Found at i:29951403 original size:116 final size:116
Alignment explanation
Indices: 29951199--29951433 Score: 470
Period size: 116 Copynumber: 2.0 Consensus size: 116
29951189 CTACGACCCT
29951199 CCAAGTAGCCTTTGAAGAACCGCCTTATATTTATTTCAACCTGTGGCATCCAGAACAGACAAACA
1 CCAAGTAGCCTTTGAAGAACCGCCTTATATTTATTTCAACCTGTGGCATCCAGAACAGACAAACA
29951264 CATAGTTCACATGCTAGGTTGTGCAAAATTACTTTTGGCATAAACCATAAG
66 CATAGTTCACATGCTAGGTTGTGCAAAATTACTTTTGGCATAAACCATAAG
29951315 CCAAGTAGCCTTTGAAGAACCGCCTTATATTTATTTCAACCTGTGGCATCCAGAACAGACAAACA
1 CCAAGTAGCCTTTGAAGAACCGCCTTATATTTATTTCAACCTGTGGCATCCAGAACAGACAAACA
29951380 CATAGTTCACATGCTAGGTTGTGCAAAATTACTTTTGGCATAAACCATAAG
66 CATAGTTCACATGCTAGGTTGTGCAAAATTACTTTTGGCATAAACCATAAG
29951431 CCA
1 CCA
29951434 GGTGTCACAC
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 119 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (116 bp):
CCAAGTAGCCTTTGAAGAACCGCCTTATATTTATTTCAACCTGTGGCATCCAGAACAGACAAACA
CATAGTTCACATGCTAGGTTGTGCAAAATTACTTTTGGCATAAACCATAAG
Found at i:29959201 original size:28 final size:28
Alignment explanation
Indices: 29959169--29959225 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
29959159 TACTTGGGAT
29959169 TAAAATTTTGTTCCAACTTAAAATTCTG
1 TAAAATTTTGTTCCAACTTAAAATTCTG
*
29959197 TAAAATTTTGTTCCAACTTGAAATTCTG
1 TAAAATTTTGTTCCAACTTAAAATTCTG
29959225 T
1 T
29959226 GATCTGACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (28 bp):
TAAAATTTTGTTCCAACTTAAAATTCTG
Found at i:29959266 original size:97 final size:97
Alignment explanation
Indices: 29959100--29959294 Score: 363
Period size: 97 Copynumber: 2.0 Consensus size: 97
29959090 AACTTGGGAT
*
29959100 TAAAATTTTGTTCCAACTTAAAATTCTGTGATCTGGCTTCTGCAAGCTACCTGTTTTTCTACTTG
1 TAAAATTTTGTTCCAACTTAAAATTCTGTGATCTGACTTCTGCAAGCTACCTGTTTTTCTACTTG
29959165 GGATTAAAATTTTGTTCCAACTTAAAATTCTG
66 GGATTAAAATTTTGTTCCAACTTAAAATTCTG
* *
29959197 TAAAATTTTGTTCCAACTTGAAATTCTGTGATCTGACTTCTGCAAGCTTCCTGTTTTTCTACTTG
1 TAAAATTTTGTTCCAACTTAAAATTCTGTGATCTGACTTCTGCAAGCTACCTGTTTTTCTACTTG
29959262 GGATTAAAATTTTGTTCCAACTTAAAATTCTG
66 GGATTAAAATTTTGTTCCAACTTAAAATTCTG
29959294 T
1 T
29959295 GATTTACAAT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (97 bp):
TAAAATTTTGTTCCAACTTAAAATTCTGTGATCTGACTTCTGCAAGCTACCTGTTTTTCTACTTG
GGATTAAAATTTTGTTCCAACTTAAAATTCTG
Found at i:29967851 original size:222 final size:222
Alignment explanation
Indices: 29967456--29968546 Score: 1344
Period size: 222 Copynumber: 5.0 Consensus size: 222
29967446 TTTATGATAA
29967456 AAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCA
1 AAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCA
29967521 CAACAAAATGATAAGTCAAAGCTCCAAACTTCAAATGTATGTTTCAGAAATGGCAGCATAATACT
66 CAACAAAATGATAAGTCAAAGCTCCAAACTTCAAATGTATGTTTCAGAAATGGCAGCATAATACT
* *
29967586 AAATTTTCTTTATCACAACAACATCAAACACATCAGTGGGGAATATGACACATCAATGGAAATTT
131 AAATTTTCTTTATCACAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATGGAAATTT
29967651 TCAAGAACCAAAACCAATTGTTAAACT
196 TCAAGAACCAAAACCAATTGTTAAACT
29967678 AAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCA
1 AAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCA
29967743 CAACAAAATGATAAGTCAAAGCTCCAAACTTCAAATGTATGTTTCAGAAATGGCAGCATAATACT
66 CAACAAAATGATAAGTCAAAGCTCCAAACTTCAAATGTATGTTTCAGAAATGGCAGCATAATACT
*
29967808 AAATTTTCTATATCACAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATGGAAATTT
131 AAATTTTCTTTATCACAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATGGAAATTT
29967873 TCAAGAACCAAAACCAATTGTTAAACT
196 TCAAGAACCAAAACCAATTGTTAAACT
*
29967900 AAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAACGTAACAAGTAGAATGCA
1 AAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCA
*
29967965 CAACAAAATGATAAGTTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATA
66 CAACAAAATGATAAGTCAAAGCTCCAAACTTCAAATG--TATGTTTCAGAAATGGCAGCATAATA
* ** ** * *** ****
29968030 ATAAATTTTCTTTAT-ATGAC-ACATCAATGGAAATTTTC-----A-A-GA-AC--CAAAACCAA
129 CTAAATTTTCTTTATCACAACAACATCAAACG-CATCAGCGGGGAATATGACACATCAATGGAAA
* * * *
29968083 TTGTC-A-AACTAAAAACTACTGGTGTT-AACT
193 TTTTCAAGAAC-CAAAACCAAT--TGTTAAACT
** **** * * * ** * * *
29968113 ----AC--CT--CATTAA-TTTGGCATCT--TTT-CCA-ATGTAACAA-GTAGA-ATGCACAA--
1 AAAAACTACTGGTGTTAACTACCTCAT-TAATTTGGCATCTTTTCCAATGTA-ACAAGTAGAATG
* * * * *
29968161 CAAAATGATAAGTCA-AAGCTCCAAA-CTTCAAA-TGT----T-TATGTTTCAGAAATGGCAGCA
64 CACAA-CA-AAATGATAAG-T-CAAAGCTCCAAACT-TCAAATGTATGTTTCAGAAATGGCAGCA
29968218 TAATACTAAATTTTCTTTATCACAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATG
124 TAATACTAAATTTTCTTTATCACAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATG
29968283 GAAATTTTCAAGAACCAAAACCAATTGTTAAACT
189 GAAATTTTCAAGAACCAAAACCAATTGTTAAACT
29968317 AAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCA
1 AAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCA
*
29968382 CAACAAAATGATAAGTTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATA
66 CAACAAAATGATAAGTCAAAGCTCCAAACTTCAAATG--TATGTTTCAGAAATGGCAGCATAATA
* * * *
29968447 CTAAATTTTCTTTATCACAACAACATTAAACACATCCAGTGGGGAATATGACACATCAACGGAAA
129 CTAAATTTTCTTTATCACAACAACATCAAACGCAT-CAGCGGGGAATATGACACATCAATGGAAA
29968512 TTTTCAAGAACCAAAACCAATTGTTAAACT
193 TTTTCAAGAACCAAAACCAATTGTTAAACT
29968542 AAAAA
1 AAAAA
29968547 TTAAATTGTT
Statistics
Matches: 729, Mismatches: 84, Indels: 109
0.79 0.09 0.12
Matches are distributed among these distances:
193 40 0.05
194 6 0.01
195 8 0.01
196 1 0.00
198 4 0.01
199 6 0.01
200 21 0.03
201 11 0.02
202 4 0.01
203 7 0.01
204 17 0.02
205 13 0.02
206 3 0.00
207 2 0.00
208 2 0.00
209 2 0.00
210 2 0.00
211 3 0.00
212 13 0.02
213 17 0.02
214 7 0.01
215 4 0.01
216 11 0.02
217 21 0.03
218 6 0.01
219 4 0.01
221 1 0.00
222 327 0.45
223 6 0.01
224 98 0.13
225 62 0.09
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.28
Consensus pattern (222 bp):
AAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCA
CAACAAAATGATAAGTCAAAGCTCCAAACTTCAAATGTATGTTTCAGAAATGGCAGCATAATACT
AAATTTTCTTTATCACAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATGGAAATTT
TCAAGAACCAAAACCAATTGTTAAACT
Found at i:29968181 original size:193 final size:193
Alignment explanation
Indices: 29967850--29968461 Score: 751
Period size: 193 Copynumber: 3.0 Consensus size: 193
29967840 TCAGCGGGGA
29967850 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAACTACTGGTGT
1 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAACTACTGGTGT
*
29967915 TAACTACCTCATTAATTTGGCATCTTTTCCAACGTAACAAGTAGAATGCACAACAAAATGATAAG
66 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
*
29967980 TTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATAATAAATTTTCTTT
131 TTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTTT
*
29968043 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTCAAACTAAAAACTACTGGTGT
1 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAACTACTGGTGT
29968108 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
66 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
*
29968173 TCAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTTT
131 TTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTTT
** ** * *** ****
29968236 ATCACAACAACATCAAACG-CATCAGCGGGGAATATGACACATCAATGGAAATT-TTCAAGAACC
1 AT-ATGAC-ACATCAATGGAAATTTTC-----A-A-GA-AC--CAAAACCAATTGTT--A-AA-C
* *
29968299 AAAACCAATTGTTAAACTAAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAA
50 TAAA--AA---CT--ACT----------GGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAA
29968364 TGTAACAAGTAGAATGCACAACAAAATGATAAGTTAAAGCTCCAAACTTCAAATGTTTATGTTTC
98 TGTAACAAGTAGAATGCACAACAAAATGATAAGTTAAAGCTCCAAACTTCAAATGTTTATGTTTC
29968429 AGAAATGGCAGCATAATACTAAATTTTCTTT
163 AGAAATGGCAGCATAATACTAAATTTTCTTT
29968460 AT
1 AT
29968462 CACAACAACA
Statistics
Matches: 366, Mismatches: 20, Indels: 35
0.87 0.05 0.08
Matches are distributed among these distances:
193 191 0.52
194 6 0.02
195 8 0.02
199 1 0.00
200 1 0.00
201 2 0.01
202 2 0.01
203 1 0.00
204 7 0.02
205 1 0.00
206 2 0.01
207 4 0.01
209 2 0.01
212 1 0.00
214 3 0.01
224 134 0.37
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (193 bp):
ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAACTACTGGTGT
TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
TTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTTT
Found at i:29968400 original size:417 final size:415
Alignment explanation
Indices: 29967628--29968461 Score: 1614
Period size: 417 Copynumber: 2.0 Consensus size: 415
29967618 TCAGTGGGGA
*
29967628 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAACTACTGGTGT
1 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTCAAACTAAAAACTACTGGTGT
29967693 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
66 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
29967758 TCAAAGCTCCAAACTTCAAATGTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTATATCA
131 TCAAAGCTCCAAACTTCAAATGTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTATATCA
29967823 CAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATGGAAATTTTCAAGAACCAAAACC
196 CAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATGGAAATTTTCAAGAACCAAAACC
29967888 AATTGTTAAACTAAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAACGTAAC
261 AATTGTTAAACTAAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAACGTAAC
29967953 AAGTAGAATGCACAACAAAATGATAAGTTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAAT
326 AAGTAGAATGCACAACAAAATGATAAGTTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAAT
29968018 GGCAGCATAATAATAAATTTTCTTT
391 GGCAGCATAATAATAAATTTTCTTT
29968043 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTCAAACTAAAAACTACTGGTGT
1 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTCAAACTAAAAACTACTGGTGT
29968108 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
66 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
*
29968173 TCAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTTTAT
131 TCAAAGCTCCAAACTTCAAATG--TATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTATAT
29968238 CACAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATGGAAATTTTCAAGAACCAAAA
194 CACAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATGGAAATTTTCAAGAACCAAAA
*
29968303 CCAATTGTTAAACTAAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAATGTA
259 CCAATTGTTAAACTAAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAACGTA
29968368 ACAAGTAGAATGCACAACAAAATGATAAGTTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAA
324 ACAAGTAGAATGCACAACAAAATGATAAGTTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAA
*
29968433 ATGGCAGCATAATACTAAATTTTCTTT
389 ATGGCAGCATAATAATAAATTTTCTTT
29968460 AT
1 AT
29968462 CACAACAACA
Statistics
Matches: 413, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
415 151 0.37
417 262 0.63
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (415 bp):
ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTCAAACTAAAAACTACTGGTGT
TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
TCAAAGCTCCAAACTTCAAATGTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTATATCA
CAACAACATCAAACGCATCAGCGGGGAATATGACACATCAATGGAAATTTTCAAGAACCAAAACC
AATTGTTAAACTAAAAACTACTGGTGTTAACTACCTCATTAATTTGGCATCTTTTCCAACGTAAC
AAGTAGAATGCACAACAAAATGATAAGTTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAAT
GGCAGCATAATAATAAATTTTCTTT
Found at i:29968433 original size:224 final size:225
Alignment explanation
Indices: 29968043--29968546 Score: 947
Period size: 224 Copynumber: 2.2 Consensus size: 225
29968033 AATTTTCTTT
*
29968043 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTCAAACTAAAAACTACTGGTGT
1 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAACTACTGGTGT
29968108 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
66 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
29968173 TCAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTTTAT
131 TCAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTTTAT
*
29968238 CACAACAACATCAAACGCAT-CAGCGGGGA
196 CACAACAACATCAAACACATCCAGCGGGGA
29968267 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAACTACTGGTGT
1 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAACTACTGGTGT
29968332 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
66 TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
*
29968397 TTAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTTTAT
131 TCAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTTTAT
* *
29968462 CACAACAACATTAAACACATCCAGTGGGGA
196 CACAACAACATCAAACACATCCAGCGGGGA
*
29968492 ATATGACACATCAACGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAA
1 ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAA
29968547 TTAAATTGTT
Statistics
Matches: 273, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
224 211 0.77
225 62 0.23
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (225 bp):
ATATGACACATCAATGGAAATTTTCAAGAACCAAAACCAATTGTTAAACTAAAAACTACTGGTGT
TAACTACCTCATTAATTTGGCATCTTTTCCAATGTAACAAGTAGAATGCACAACAAAATGATAAG
TCAAAGCTCCAAACTTCAAATGTTTATGTTTCAGAAATGGCAGCATAATACTAAATTTTCTTTAT
CACAACAACATCAAACACATCCAGCGGGGA
Found at i:29988172 original size:22 final size:20
Alignment explanation
Indices: 29988133--29988238 Score: 56
Period size: 22 Copynumber: 5.0 Consensus size: 20
29988123 CGTCGGCAGG
29988133 GAGAAAGAAGAGAA-AGAGAAA
1 GAGAAA-AAGA-AAGAGAGAAA
**
29988154 GAGGAAAAAGAAAGGAGAGGCCGA
1 GA-GAAAAAGAAA-GAGA-G-AAA
* *
29988178 GGGAAATA-AAAGAGAAGAAA
1 GAGAAAAAGAAAGAG-AGAAA
*
29988198 GAGAAAAAAATAAGAAAGAGAAA
1 GAGAAAAAGA-AAG--AGAGAAA
29988221 -AGAAAAAGAAAGAGAGAA
1 GAGAAAAAGAAAGAGAGAA
29988239 TAAGAGGGGA
Statistics
Matches: 66, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
19 6 0.09
20 9 0.14
21 14 0.21
22 22 0.33
23 11 0.17
24 4 0.06
ACGTcount: A:0.65, C:0.02, G:0.31, T:0.02
Consensus pattern (20 bp):
GAGAAAAAGAAAGAGAGAAA
Found at i:29988212 original size:17 final size:17
Alignment explanation
Indices: 29988192--29988235 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
29988182 AATAAAAGAG
29988192 AAGAAAGAGAAAA-AAA
1 AAGAAAGAGAAAAGAAA
29988208 TAAGAAAGAGAAAAGAAA
1 -AAGAAAGAGAAAAGAAA
29988226 AAGAAAGAGA
1 AAGAAAGAGA
29988236 GAATAAGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 23 0.88
18 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (17 bp):
AAGAAAGAGAAAAGAAA
Found at i:29988345 original size:16 final size:16
Alignment explanation
Indices: 29988307--29988338 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
29988297 AAAGGAAAGG
29988307 AAAGAAATAAAGAAAA
1 AAAGAAATAAAGAAAA
29988323 AAAGAAA-AAAGAAAA
1 AAAGAAATAAAGAAAA
29988338 A
1 A
29988339 GGAGAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAGAAATAAAGAAAA
Found at i:29988722 original size:23 final size:21
Alignment explanation
Indices: 29988688--29988730 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
29988678 TAAAAAATAG
*
29988688 ATATAAACAAATATCTGAAAAAA
1 ATATAAAAAAATA-CT-AAAAAA
29988711 ATATAAAAAAATACTAAAAA
1 ATATAAAAAAATACTAAAAA
29988731 GATGATAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (21 bp):
ATATAAAAAAATACTAAAAAA
Found at i:29988761 original size:2 final size:2
Alignment explanation
Indices: 29988754--29988778 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29988744 GTAATAGTAA
29988754 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29988779 ATTGGGATCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29991041 original size:2 final size:2
Alignment explanation
Indices: 29991034--29991096 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
29991024 CAAATTTCTT
*
29991034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29991075 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
29991097 ATGGAATCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29993617 original size:17 final size:17
Alignment explanation
Indices: 29993595--29993636 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
29993585 AAAATTTGGA
*
29993595 TTATTTATTATTTAT-TT
1 TTATTT-TTATATATATT
29993612 TTATTTTTATATATATT
1 TTATTTTTATATATATT
29993629 TTATTTTT
1 TTATTTTT
29993637 TGGTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTTTATATATATT
Found at i:30009146 original size:3 final size:3
Alignment explanation
Indices: 30009138--30009172 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
30009128 CAATGCTGTT
30009138 GAA GAA GAA GAA GAA GAA GAA GAA -AA GAAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GA
30009173 CGAAAAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:30009171 original size:21 final size:21
Alignment explanation
Indices: 30009145--30009185 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30009135 GTTGAAGAAG
30009145 AAGAAGAAGAAGAA-GAAAAGA
1 AAGAAGAAGAA-AAGGAAAAGA
*
30009166 AAGAAGACGAAAAGGAAAAG
1 AAGAAGAAGAAAAGGAAAAG
30009186 CGTGGTCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (21 bp):
AAGAAGAAGAAAAGGAAAAGA
Found at i:30009177 original size:15 final size:14
Alignment explanation
Indices: 30009138--30009179 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
30009128 CAATGCTGTT
30009138 GAAGAAGAAGAAGAA
1 GAAGAAGAA-AAGAA
30009153 GAAGAAGAAAAGAAA
1 GAAGAAGAAAAG-AA
*
30009168 GAAGACGAAAAG
1 GAAGAAGAAAAG
30009180 GAAAAGCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 3 0.12
15 22 0.88
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAAAGAA
Found at i:30010408 original size:6 final size:6
Alignment explanation
Indices: 30010397--30010443 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
30010387 ATTTAAGTAA
* *
30010397 ATATTT ATATTT TTA-TT ATATTT A-ATTA AGTATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT A-TATTT ATATTT ATATTT
30010444 TGAGTTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 8 0.24
6 22 0.65
7 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:30010430 original size:29 final size:29
Alignment explanation
Indices: 30010387--30010467 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
30010377 GTTTAAAAAA
*
30010387 ATTTAAGTAAATATTTATATTTTTATTAT
1 ATTTAAGTAAATATTTATATTTATATTAT
* * *
30010416 ATTTAATTAAGTATTTATATTTATATTTT
1 ATTTAAGTAAATATTTATATTTATATTAT
* * *
30010445 GAGTTAAATAAATTTTTATATTT
1 -ATTTAAGTAAATATTTATATTT
30010468 CTTTATTTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 25 0.58
30 18 0.42
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (29 bp):
ATTTAAGTAAATATTTATATTTATATTAT
Found at i:30010631 original size:23 final size:26
Alignment explanation
Indices: 30010595--30010654 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
30010585 TGTGGTATGT
30010595 TGATATATCATAA-TTG-ATGATAATA
1 TGATATAT-ATAATTTGAATGATAATA
30010620 TGATATAT-TAATTTGACATGATAATA
1 TGATATATATAATTTGA-ATGATAATA
*
30010646 TAAT-TATAT
1 TGATATATAT
30010655 GGTATGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.10
24 3 0.10
25 11 0.37
26 13 0.43
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (26 bp):
TGATATATATAATTTGAATGATAATA
Found at i:30025379 original size:15 final size:13
Alignment explanation
Indices: 30025349--30025374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30025339 AAGATGAACG
30025349 ATATATTTTAAAA
1 ATATATTTTAAAA
30025362 ATATATTTTAAAA
1 ATATATTTTAAAA
30025375 GAATACTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATTTTAAAA
Found at i:30039012 original size:2 final size:2
Alignment explanation
Indices: 30039005--30039031 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30038995 GTGAATGCAA
30039005 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
30039032 AAAGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30044431 original size:83 final size:84
Alignment explanation
Indices: 30044277--30044442 Score: 262
Period size: 83 Copynumber: 2.0 Consensus size: 84
30044267 TCATGATCAT
* * *
30044277 CATCATTTATCTCTCTTTATTGTCCTTTTTCCAAAGATTATATCTCTTTGATTTTACACCTTGCA
1 CATCATTTATCTCTCTTTATTGTCCTTTTGCCAAAGATTATATCTATTTGATTTTACACCTGGCA
* *
30044342 ATTTCAAGCCATAACCTTC
66 AGTTCAAGCCAAAACCTTC
* *
30044361 CATCATTTATCTCTCTTTATTGTCC-TTTGCCAAAGATTATATCTATTTGATTTTATACCTGGCG
1 CATCATTTATCTCTCTTTATTGTCCTTTTGCCAAAGATTATATCTATTTGATTTTACACCTGGCA
30044425 AGTTCAAGCCAAAACCTT
66 AGTTCAAGCCAAAACCTT
30044443 TTTTATCTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
83 50 0.67
84 25 0.33
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.43
Consensus pattern (84 bp):
CATCATTTATCTCTCTTTATTGTCCTTTTGCCAAAGATTATATCTATTTGATTTTACACCTGGCA
AGTTCAAGCCAAAACCTTC
Found at i:30050563 original size:24 final size:24
Alignment explanation
Indices: 30050531--30050581 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
30050521 AGCTACGATT
*
30050531 AGGGAAACCCCAACATCTTCGGTC
1 AGGGAAACCCCAACATCTTCAGTC
*
30050555 AGGGAAACCCCGACATCTTCAGTC
1 AGGGAAACCCCAACATCTTCAGTC
30050579 AGG
1 AGG
30050582 TAAATGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (24 bp):
AGGGAAACCCCAACATCTTCAGTC
Found at i:30054457 original size:18 final size:19
Alignment explanation
Indices: 30054417--30054458 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
30054407 TTTATGTGTC
*
30054417 AAATAGAGATATTTTTTCG
1 AAATAGAGATATTTTTTCA
*
30054436 AAATAGAGA-ATTTTTTTA
1 AAATAGAGATATTTTTTCA
30054454 AAATA
1 AAATA
30054459 TTAATGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.40
Consensus pattern (19 bp):
AAATAGAGATATTTTTTCA
Found at i:30064909 original size:3 final size:3
Alignment explanation
Indices: 30064903--30064932 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30064893 AATAAACATA
30064903 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30064933 TACTTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:30083878 original size:2 final size:2
Alignment explanation
Indices: 30083862--30083918 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
30083852 CACTGTTTTC
*
30083862 AT AT TT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30083903 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
30083919 TGTTACATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30093461 original size:3 final size:3
Alignment explanation
Indices: 30093453--30093492 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
30093443 ATCTGACCCC
30093453 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATTG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A-TG ATG ATG ATG
30093493 CAAGAGTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:30114991 original size:2 final size:2
Alignment explanation
Indices: 30114984--30115053 Score: 64
Period size: 2 Copynumber: 38.0 Consensus size: 2
30114974 ATAATAAAAT
*
30114984 TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TT TA -A T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
30115022 -A TA -A TA -A AA NTA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
30115054 ATTTTAAACT
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
1 7 0.12
2 49 0.86
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:30115036 original size:46 final size:45
Alignment explanation
Indices: 30114987--30115076 Score: 141
Period size: 44 Copynumber: 2.0 Consensus size: 45
30114977 ATAAAATTAT
30114987 ATATATATATATATATATATATTAA-TTT-AA-TTATAATAATAAA
1 ATATATATATATATATATATA-TAATTTTAAACTTATAATAATAAA
30115030 ANTATATATATATATATATATATAATTTTAAACTTATAATAATAAA
1 A-TATATATATATATATATATATAATTTTAAACTTATAATAATAAA
30115076 A
1 A
30115077 AAATTAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
43 4 0.09
44 23 0.53
45 2 0.05
46 14 0.33
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.44
Consensus pattern (45 bp):
ATATATATATATATATATATATAATTTTAAACTTATAATAATAAA
Found at i:30129004 original size:2 final size:2
Alignment explanation
Indices: 30128997--30129035 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
30128987 GCTTTATGAA
* *
30128997 CT CT CT CT GT CT CT CT CT CT TT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
30129036 GGGGAAGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
CT
Found at i:30135060 original size:20 final size:18
Alignment explanation
Indices: 30135029--30135070 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
30135019 AATAAAAATT
30135029 TATTTAAATTTTTTAAAA
1 TATTTAAATTTTTTAAAA
*
30135047 TATTTAAGAGTTTTTTTAAA
1 TATTTAA-A-TTTTTTAAAA
30135067 TATT
1 TATT
30135071 ATGTCATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TATTTAAATTTTTTAAAA
Found at i:30136034 original size:2 final size:2
Alignment explanation
Indices: 30136021--30136058 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
30136011 ACTGATGTTT
*
30136021 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30136059 AAATCAAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30166534 original size:18 final size:19
Alignment explanation
Indices: 30166491--30166535 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
30166481 ACATAAAAAT
30166491 ATTTTTTATTATTTATATG
1 ATTTTTTATTATTTATATG
*
30166510 ATATTTTATT-TTTAT-TAG
1 ATTTTTTATTATTTATAT-G
30166528 ATTTTTTA
1 ATTTTTTA
30166536 AATATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 13 0.57
19 9 0.39
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
ATTTTTTATTATTTATATG
Found at i:30167052 original size:115 final size:111
Alignment explanation
Indices: 30166852--30167125 Score: 306
Period size: 115 Copynumber: 2.4 Consensus size: 111
30166842 NNNNNNNNNN
* * *
30166852 AATAATAGATAAATTAAATATTAATATTTTTATTTAATTTAAATATTATTATGATTAATTTTATT
1 AATAATTGATAATTTAAATATTAATATTTTTATATAATTTAAATATTATTATGATTAATTTTATT
* ** *
30166917 TATTTATTTTATTTTTAAATATTAATAATTGGTAA-TTATTTAAAATATT
66 TATTTATTTTAGTTTTAAATAGGAATAATTGATAATTTATTT----TATT
* * * *
30166966 AATAATTGATGATTTAATTATTAATATTGTTTATATAATTCAAATGA-TATTATG-TTTATTTAT
1 AATAATTGATAATTTAAATATTAATATT-TTTATATAATTTAAAT-ATTATTATGATTAATTT-T
* *
30167029 TTTTAATTTATTTT-GTTTTAAATAGGAATAATTTATAATTTATTTTATT
63 ATTT-ATTTATTTTAGTTTTAAATAGGAATAATTGATAATTTATTTTATT
*
30167078 AATAATTTATAATTTAAATATTAATA-TTTTATTATAATTTAAATATTA
1 AATAATTGATAATTTAAATATTAATATTTTTA-TATAATTTAAATATTA
30167126 ATATTTTATT
Statistics
Matches: 136, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
110 5 0.04
111 14 0.10
112 27 0.20
114 30 0.22
115 44 0.32
116 16 0.12
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (111 bp):
AATAATTGATAATTTAAATATTAATATTTTTATATAATTTAAATATTATTATGATTAATTTTATT
TATTTATTTTAGTTTTAAATAGGAATAATTGATAATTTATTTTATT
Found at i:30167118 original size:25 final size:25
Alignment explanation
Indices: 30167084--30167136 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
30167074 TATTAATAAT
30167084 TTATAATTTAAATATTAATATTTTA
1 TTATAATTTAAATATTAATATTTTA
30167109 TTATAATTTAAATATTAATATTTTA
1 TTATAATTTAAATATTAATATTTTA
30167134 TTA
1 TTA
30167137 AAAGTTGGAA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTATAATTTAAATATTAATATTTTA
Found at i:30167927 original size:21 final size:20
Alignment explanation
Indices: 30167903--30167942 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
30167893 AAAAATTTGA
*
30167903 TTAATGATAATTAATTTATTG
1 TTAATGATAA-AAATTTATTG
*
30167924 TTAATTATAAAAATTTATT
1 TTAATGATAAAAATTTATT
30167943 TGACTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TTAATGATAAAAATTTATTG
Found at i:30176296 original size:2 final size:2
Alignment explanation
Indices: 30176289--30176314 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30176279 GAGATTGTGT
30176289 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
30176315 TAATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30177814 original size:23 final size:21
Alignment explanation
Indices: 30177772--30177814 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
30177762 GATTAAAATA
* *
30177772 TTAATAATTTTTTAATTTAANT
1 TTAATAATTTTTAAAGTTAA-T
30177794 TTAATTAATTTTTAAAGTTAA
1 TTAA-TAATTTTTAAAGTTAA
30177815 AATACTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTAATAATTTTTAAAGTTAAT
Found at i:30177940 original size:27 final size:27
Alignment explanation
Indices: 30177834--30177946 Score: 76
Period size: 27 Copynumber: 4.1 Consensus size: 27
30177824 TTATAACATA
*
30177834 ATTAAA-ATTTTAATTTAT-TTTTAAAT
1 ATTAAATATTTT-ATTTATAATTTAAAT
* **
30177860 ATT-AATAATTTA-GAATTAATTTAATAT
1 ATTAAATATTTTATTTA-TAATTTAA-AT
*
30177887 ATT-AATAGTTGATCATTTA-AATATTAAAT
1 ATTAAATA-TT--TTATTTATAAT-TTAAAT
30177916 ATTAAATATTTTATTTATAATTTAAAT
1 ATTAAATATTTTATTTATAATTTAAAT
30177943 ATTA
1 ATTA
30177947 TTATGATTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
24 1 0.01
25 4 0.06
26 12 0.18
27 25 0.37
28 4 0.06
29 10 0.15
30 10 0.15
31 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (27 bp):
ATTAAATATTTTATTTATAATTTAAAT
Found at i:30177959 original size:17 final size:18
Alignment explanation
Indices: 30177916--30177962 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
30177906 AATATTAAAT
*
30177916 ATTAAATATTTTATTTATA
1 ATTAAA-ATATTATTTATA
* *
30177935 ATTTAAATATTA-TTATG
1 ATTAAAATATTATTTATA
30177952 ATTAAAATATT
1 ATTAAAATATT
30177963 GATAATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 14 0.58
18 5 0.21
19 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTAAAATATTATTTATA
Found at i:30177996 original size:179 final size:175
Alignment explanation
Indices: 30177667--30178036 Score: 414
Period size: 179 Copynumber: 2.0 Consensus size: 175
30177657 ATTATTTTGT
30177667 TTTATTTTTTAAATATTAATAATTTGTAATTAATTTAAAATATTAATAATTGATCATTTAAATAT
1 TTTA-TTTTTAAATATTAATAATTTGTAATTAATTTAAAATATTAATAATTGATCATTTAAATAT
* * *
30177732 TGATATTTATTTATAATTTAAATTTATTATGATTAAAATATTAATAATTTTTTAATTTAANTTTA
65 TAATATTTATTTATAATTTAAATTTATTATGATTAAAATATTAATAATTGTTTAATTTAAATTT-
30177797 ATTAATTTTTAAAGTTAAAATACTA-TTTTATAACAT-AATTAAAATTTTAA
129 ATTAA--TTT--A-TTAAAATACTATTTTTATAACATAAATTAAAATTTTAA
* *
30177847 TTTATTTTTAAATATTAATAATTTAG-AATTAATTTAATATATTAATAGTTGATCATTTAAATAT
1 TTTATTTTTAAATATTAATAATTT-GTAATTAATTTAAAATATTAATAATTGATC------AT-T
*
30177911 TAAATATTAAATATTTTATTTATAATTTAAATATTATTATGATTAAAATATTGATAATTGTTTAA
58 TAAATATT-AATA-TTTATTTATAATTTAAAT-TTATTATGATTAAAATATTAATAATTGTTTAA
* * * *
30177976 -TT-AATTT-TGTAA-TT-TTAAAATATTATTTTTATAATATAAATTAAATTTTTAT
120 TTTAAATTTAT-TAATTTATTAAAATACTATTTTTATAACATAAATTAAAATTTTAA
30178028 TATTATTTT
1 T-TTATTTT
30178037 AATTTTTAAA
Statistics
Matches: 165, Mismatches: 10, Indels: 28
0.81 0.05 0.14
Matches are distributed among these distances:
179 56 0.34
180 15 0.09
181 13 0.08
182 7 0.04
183 2 0.01
185 3 0.02
186 12 0.07
187 7 0.04
188 20 0.12
189 30 0.18
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (175 bp):
TTTATTTTTAAATATTAATAATTTGTAATTAATTTAAAATATTAATAATTGATCATTTAAATATT
AATATTTATTTATAATTTAAATTTATTATGATTAAAATATTAATAATTGTTTAATTTAAATTTAT
TAATTTATTAAAATACTATTTTTATAACATAAATTAAAATTTTAA
Found at i:30189936 original size:13 final size:13
Alignment explanation
Indices: 30189918--30189942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30189908 GATTTAAGGG
30189918 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
30189931 AAAAAGAAAAAA
1 AAAAAGAAAAAA
30189943 CCCTAAAACC
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:30190977 original size:22 final size:22
Alignment explanation
Indices: 30190949--30190992 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
30190939 GATATGCCGG
30190949 AGAATATAGTGTAAGAAATCTT
1 AGAATATAGTGTAAGAAATCTT
30190971 AGAATATAGTGTAAGAAATCTT
1 AGAATATAGTGTAAGAAATCTT
30190993 TGGCATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (22 bp):
AGAATATAGTGTAAGAAATCTT
Found at i:30191430 original size:49 final size:49
Alignment explanation
Indices: 30191371--30191468 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
30191361 GAAATTAAAG
30191371 GTGAAATTGGTTGTACTTCTTTTAAGACCTCTAAGAAGAAAGAGAGGCA
1 GTGAAATTGGTTGTACTTCTTTTAAGACCTCTAAGAAGAAAGAGAGGCA
*
30191420 GTGAAATTGGTTGTACTTCTTTTAAGGCCTCTAAGAAGAAAGAGAGGCA
1 GTGAAATTGGTTGTACTTCTTTTAAGACCTCTAAGAAGAAAGAGAGGCA
30191469 TACTTTTAGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (49 bp):
GTGAAATTGGTTGTACTTCTTTTAAGACCTCTAAGAAGAAAGAGAGGCA
Found at i:30197915 original size:24 final size:24
Alignment explanation
Indices: 30197872--30197917 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
30197862 CCTTTTATGA
* * *
30197872 CAACAAAGTTCAGGATATAGAAAG
1 CAACAAAGTTAAGCAAATAGAAAG
30197896 CAACAAAGTTAAGCAAATAGAA
1 CAACAAAGTTAAGCAAATAGAA
30197918 GAACTTACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.13, G:0.17, T:0.15
Consensus pattern (24 bp):
CAACAAAGTTAAGCAAATAGAAAG
Found at i:30200933 original size:22 final size:21
Alignment explanation
Indices: 30200908--30200959 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
30200898 ATTGATACAT
*
30200908 AATAAAATTGATTATT-TATATA
1 AATAAAATAGATT-TTAT-TATA
30200930 AATATAAATAGATTTTATTATA
1 AATA-AAATAGATTTTATTATA
*
30200952 AATTAAAT
1 AATAAAAT
30200960 CGTATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.15
22 13 0.50
23 9 0.35
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
AATAAAATAGATTTTATTATA
Found at i:30205804 original size:100 final size:100
Alignment explanation
Indices: 30205631--30205831 Score: 384
Period size: 100 Copynumber: 2.0 Consensus size: 100
30205621 CTGTTTTTAA
* *
30205631 TTAATTAAAACTGCACATTCCACTGTAGTCTTCATGTGCTTGAATTCCCTGGTGCGATTATCAGT
1 TTAATTAAAACAGCACATTCCACTATAGTCTTCATGTGCTTGAATTCCCTGGTGCGATTATCAGT
30205696 AATCAAATCTATGGGACACCCTAATTTTTACACCT
66 AATCAAATCTATGGGACACCCTAATTTTTACACCT
30205731 TTAATTAAAACAGCACATTCCACTATAGTCTTCATGTGCTTGAATTCCCTGGTGCGATTATCAGT
1 TTAATTAAAACAGCACATTCCACTATAGTCTTCATGTGCTTGAATTCCCTGGTGCGATTATCAGT
30205796 AATCAAATCTATGGGACACCCTAATTTTTACACCT
66 AATCAAATCTATGGGACACCCTAATTTTTACACCT
30205831 T
1 T
30205832 CCAACAGAAG
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 99 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (100 bp):
TTAATTAAAACAGCACATTCCACTATAGTCTTCATGTGCTTGAATTCCCTGGTGCGATTATCAGT
AATCAAATCTATGGGACACCCTAATTTTTACACCT
Found at i:30206707 original size:3 final size:3
Alignment explanation
Indices: 30206693--30206726 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
30206683 GTCGAGGGAA
*
30206693 AAG AAA AAG AAG AAG AAG AAG -AG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
30206727 AACGAACGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:30206719 original size:14 final size:14
Alignment explanation
Indices: 30206700--30206726 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30206690 GAAAAGAAAA
30206700 AGAAGAAGAAGAAG
1 AGAAGAAGAAGAAG
30206714 AGAAGAAGAAGAA
1 AGAAGAAGAAGAA
30206727 AACGAACGAG
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAGAAG
Found at i:30207199 original size:9 final size:9
Alignment explanation
Indices: 30207180--30207244 Score: 86
Period size: 9 Copynumber: 7.7 Consensus size: 9
30207170 TCACTCTACC
30207180 TTCTT-ACT
1 TTCTTCACT
30207188 TTCTTCACT
1 TTCTTCACT
30207197 TTCTTCACT
1 TTCTTCACT
30207206 TTCTTCACT
1 TTCTTCACT
30207215 TTCTT--CT
1 TTCTTCACT
30207222 TTCTTGC-C-
1 TTCTT-CACT
30207230 TTCTTCACT
1 TTCTTCACT
30207239 TTCTTC
1 TTCTTC
30207245 CTTCTTGCCT
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
7 8 0.15
8 11 0.21
9 33 0.63
ACGTcount: A:0.08, C:0.32, G:0.02, T:0.58
Consensus pattern (9 bp):
TTCTTCACT
Found at i:30207256 original size:21 final size:23
Alignment explanation
Indices: 30207207--30207254 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
30207197 TTCTTCACTT
*
30207207 TCTTCACTTTCTTCTTTCTTGCC
1 TCTTCACTTTCTTCCTTCTTGCC
30207230 TTCTTCACTTTCTTCCTTCTTGCC
1 -TCTTCACTTTCTTCCTTCTTGCC
30207254 T
1 T
30207255 TCTCCTCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.04, C:0.35, G:0.04, T:0.56
Consensus pattern (23 bp):
TCTTCACTTTCTTCCTTCTTGCC
Found at i:30207268 original size:24 final size:24
Alignment explanation
Indices: 30207217--30207268 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
30207207 TCTTCACTTT
* * * *
30207217 CTTCTTTCTTGCCTTCTTCACTTT
1 CTTCCTTCTTGCCTTCTCCACCTC
*
30207241 CTTCCTTCTTGCCTTCTCCTCCTC
1 CTTCCTTCTTGCCTTCTCCACCTC
30207265 CTTC
1 CTTC
30207269 TCACCTTGCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.02, C:0.42, G:0.04, T:0.52
Consensus pattern (24 bp):
CTTCCTTCTTGCCTTCTCCACCTC
Found at i:30207287 original size:25 final size:25
Alignment explanation
Indices: 30207248--30207297 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
30207238 TTTCTTCCTT
*
30207248 CTTGCCTTCTCCTCCTCCTTCTCAC
1 CTTGCCTTATCCTCCTCCTTCTCAC
* *
30207273 CTTGCCTTATTCTCCTTCTTCTCAC
1 CTTGCCTTATCCTCCTCCTTCTCAC
30207298 TGTTCACAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.06, C:0.46, G:0.04, T:0.44
Consensus pattern (25 bp):
CTTGCCTTATCCTCCTCCTTCTCAC
Found at i:30207701 original size:20 final size:20
Alignment explanation
Indices: 30207655--30207707 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
30207645 ACGACCATTT
30207655 ATCTATCGATAGATAATATA
1 ATCTATCGATAGATAATATA
* * * *
30207675 ATTTATCAATAGATAATGTG
1 ATCTATCGATAGATAATATA
30207695 ATCTATCGATAGA
1 ATCTATCGATAGA
30207708 ATTTTTTATC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (20 bp):
ATCTATCGATAGATAATATA
Found at i:30208092 original size:15 final size:15
Alignment explanation
Indices: 30208072--30208109 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
30208062 AACGCTACAA
30208072 AATTATATTCTT-AGC
1 AATTATATT-TTCAGC
30208087 AATTATATTTTCAGC
1 AATTATATTTTCAGC
*
30208102 AATCATAT
1 AATTATAT
30208110 ATCACACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (15 bp):
AATTATATTTTCAGC
Found at i:30210052 original size:46 final size:46
Alignment explanation
Indices: 30209985--30210077 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
30209975 GGCTGAAGAA
* * * *
30209985 AAGAGTTACTGGCTAAAGTTAAATTTGTAAATTCCTTATGGAATCC
1 AAGAGTTACCGGCTAAAGTTAAATCTGTAAATTCCTCATAGAATCC
* *
30210031 AAGAGTTACCGGTTAAAGTTAAATCTGTAAATTGCTCATAGAATCC
1 AAGAGTTACCGGCTAAAGTTAAATCTGTAAATTCCTCATAGAATCC
30210077 A
1 A
30210078 TTCTTTATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (46 bp):
AAGAGTTACCGGCTAAAGTTAAATCTGTAAATTCCTCATAGAATCC
Found at i:30238237 original size:18 final size:18
Alignment explanation
Indices: 30238214--30238256 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
30238204 TAAAAAACGG
30238214 AGGATCAAAAACAAGACC
1 AGGATCAAAAACAAGACC
** * *
30238232 AGGATCGCAAACAATATC
1 AGGATCAAAAACAAGACC
30238250 AGGATCA
1 AGGATCA
30238257 TGGTTACCAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (18 bp):
AGGATCAAAAACAAGACC
Found at i:30254318 original size:28 final size:26
Alignment explanation
Indices: 30254282--30254335 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
30254272 GTTTATTTTT
*
30254282 TTAACTTTTTGATATATAAAATTTTTAA
1 TTAAATTTTT-ATA-ATAAAATTTTTAA
* *
30254310 TTAAATTTTTATAATTAAGTTTTTAA
1 TTAAATTTTTATAATAAAATTTTTAA
30254336 ATTTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 11 0.48
27 3 0.13
28 9 0.39
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (26 bp):
TTAAATTTTTATAATAAAATTTTTAA
Found at i:30254349 original size:14 final size:14
Alignment explanation
Indices: 30254298--30254338 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
30254288 TTTTGATATA
*
30254298 TAAAATTTT-TAAT
1 TAAATTTTTATAAT
30254311 TAAATTTTTATAAT
1 TAAATTTTTATAAT
*
30254325 TAAGTTTTTA-AAT
1 TAAATTTTTATAAT
30254338 T
1 T
30254339 TTTTTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TAAATTTTTATAAT
Found at i:30254995 original size:15 final size:14
Alignment explanation
Indices: 30254940--30255002 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
30254930 AAAAATAATT
30254940 TTATTA-ATTATTAA
1 TTATTATATTA-TAA
*
30254954 TTATT-TTTTATATA
1 TTATTATATTATA-A
*
30254968 TT-TT-TAATATAA
1 TTATTATATTATAA
30254980 TTAATTATATTATAA
1 TT-ATTATATTATAA
30254995 TTATTATA
1 TTATTATA
30255003 AAATTATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 3 0.08
13 9 0.22
14 19 0.47
15 9 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTATATTATAA
Found at i:30261221 original size:5 final size:5
Alignment explanation
Indices: 30261211--30261243 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
30261201 AGTGGTCCCC
*
30261211 TTTCT TTTCT TTTCT TTTCT TTTTT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
30261244 TGAGTTCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTCT
Found at i:30272233 original size:3 final size:3
Alignment explanation
Indices: 30272227--30272283 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
30272217 AGAATAGTGT
30272227 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
30272275 TTC TTC TTC
1 TTC TTC TTC
30272284 CTTGTCATGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:30272482 original size:8 final size:8
Alignment explanation
Indices: 30272415--30272463 Score: 66
Period size: 8 Copynumber: 6.2 Consensus size: 8
30272405 AAAATAAAAT
30272415 AATTTATAA
1 AATTT-TAA
30272424 AATTTT--
1 AATTTTAA
*
30272430 AATTTTNA
1 AATTTTAA
30272438 AATTTTAA
1 AATTTTAA
30272446 AATTTTAA
1 AATTTTAA
30272454 AATTTTAA
1 AATTTTAA
30272462 AA
1 AA
30272464 CAAAGATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
6 6 0.16
8 26 0.70
9 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
AATTTTAA
Found at i:30273272 original size:81 final size:81
Alignment explanation
Indices: 30273084--30273284 Score: 218
Period size: 81 Copynumber: 2.5 Consensus size: 81
30273074 TGGATTTCTT
* *
30273084 TTAAATTATTTATGTTATTAGTTAAGA--TTTTATTTTTCTAAGCATCCCTAACATATTTATATT
1 TTAAATTATTTATGTTATTAGTTAAAATTTTTTATTTTTCTAAGCATCCCTAACATATATATATT
30273147 ACGCATCCTTAACATA
66 ACGCATCCTTAACATA
* * * * * * *
30273163 TTAAATTATTTATATTATAAATTGAAATTTTCCTTTTTTTTTTAAG-ATCCGTAACATATAT-TA
1 TTAAATTATTTATGTTATTAGTTAAAATTTT--TTATTTTTCTAAGCATCCCTAACATATATATA
* * *
30273226 TTATGTAT-TTGTAACATA
64 TTACGCATCCT-TAACATA
30273244 TTAAATTATTTATGTTATTAGTTAAAA--TTTTATTTTTCTAA
1 TTAAATTATTTATGTTATTAGTTAAAATTTTTTATTTTTCTAA
30273285 ACAATAAAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
77 10 0.10
79 24 0.24
80 1 0.01
81 40 0.40
82 13 0.13
83 11 0.11
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (81 bp):
TTAAATTATTTATGTTATTAGTTAAAATTTTTTATTTTTCTAAGCATCCCTAACATATATATATT
ACGCATCCTTAACATA
Found at i:30279784 original size:69 final size:68
Alignment explanation
Indices: 30279668--30279800 Score: 221
Period size: 69 Copynumber: 1.9 Consensus size: 68
30279658 GAAAGCCAGA
* *
30279668 TATCAAGTTGGATTCAAGTCCGATACCCTACACTTTAAGCCCGATATCATATTGAGTTAAAGGTC
1 TATCAAGTTGGATTCAAGTCCGATACCCTACACTTTAAGCCCCATATCATAATGAGTTAAAGGTC
30279733 CGT
66 CGT
* *
30279736 TATCAAGTTGGATTCAAGTCCAGATACCCTACATTTTGAGCCCCATATCATAATGAGTTAAAGGT
1 TATCAAGTTGGATTCAAGTCC-GATACCCTACACTTTAAGCCCCATATCATAATGAGTTAAAGGT
30279801 TATCAAGTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
68 21 0.35
69 39 0.65
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (68 bp):
TATCAAGTTGGATTCAAGTCCGATACCCTACACTTTAAGCCCCATATCATAATGAGTTAAAGGTC
CGT
Found at i:30281607 original size:24 final size:26
Alignment explanation
Indices: 30281556--30281608 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
30281546 CTGTAATCTT
** *
30281556 GCTCTATCTGTTTTGACTTCCATCTA
1 GCTCTATCTGTTTTGACAACCATATA
30281582 GCTCT-TCTGTTTTGA-AACCATATA
1 GCTCTATCTGTTTTGACAACCATATA
30281606 GCT
1 GCT
30281609 ACTTGGCGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.38
25 10 0.42
26 5 0.21
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.43
Consensus pattern (26 bp):
GCTCTATCTGTTTTGACAACCATATA
Found at i:30298124 original size:21 final size:21
Alignment explanation
Indices: 30298100--30298153 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
30298090 CAGCATCATC
* *
30298100 ACCATCACCACTACCATCACA
1 ACCACCACCACGACCATCACA
30298121 ACCACCACCACGACCATCACA
1 ACCACCACCACGACCATCACA
30298142 ACCACCACCACG
1 ACCACCACCACG
30298154 TCTGGTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.37, C:0.52, G:0.04, T:0.07
Consensus pattern (21 bp):
ACCACCACCACGACCATCACA
Found at i:30327807 original size:19 final size:18
Alignment explanation
Indices: 30327767--30327814 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
30327757 TTATTTAATT
30327767 TAAAATTAAAATATATAA
1 TAAAATTAAAATATATAA
30327785 -AAAATTAGCAAATATA-AA
1 TAAAATTA--AAATATATAA
*
30327803 TAAAAATAAAAT
1 TAAAATTAAAAT
30327815 TTTATTGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.42
18 2 0.08
19 13 0.50
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
TAAAATTAAAATATATAA
Found at i:30335357 original size:21 final size:21
Alignment explanation
Indices: 30335314--30335357 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
30335304 CGAACAACTT
* * *
30335314 CTACAGCTGCTTGGGCTGTTG
1 CTACAGCTGCTTGAGCAGCTG
*
30335335 CTACTGCTGCTTGAGCAGCTG
1 CTACAGCTGCTTGAGCAGCTG
30335356 CT
1 CT
30335358 GTAGTGGCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.11, C:0.27, G:0.30, T:0.32
Consensus pattern (21 bp):
CTACAGCTGCTTGAGCAGCTG
Found at i:30335988 original size:48 final size:48
Alignment explanation
Indices: 30335917--30336014 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
30335907 TATCTATAAA
30335917 TGCAAAAGTCTCAGAGATATAAATGAAAGGAAAGGAACAAAATTATGT
1 TGCAAAAGTCTCAGAGATATAAATGAAAGGAAAGGAACAAAATTATGT
30335965 TGCAAAAGTCTCAGAGATATAAATGAAAGGAAAGGAACAAAATTATGT
1 TGCAAAAGTCTCAGAGATATAAATGAAAGGAAAGGAACAAAATTATGT
30336013 TG
1 TG
30336015 GCTGCAACTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.49, C:0.08, G:0.21, T:0.21
Consensus pattern (48 bp):
TGCAAAAGTCTCAGAGATATAAATGAAAGGAAAGGAACAAAATTATGT
Found at i:30341445 original size:65 final size:65
Alignment explanation
Indices: 30341341--30341469 Score: 258
Period size: 65 Copynumber: 2.0 Consensus size: 65
30341331 ATTGTCCTTT
30341341 GGGGGCTATACATATTAATGTCTTCTACCCTGAAATTCTACTTAAATAAAAGCCTATTATTCTAA
1 GGGGGCTATACATATTAATGTCTTCTACCCTGAAATTCTACTTAAATAAAAGCCTATTATTCTAA
30341406 GGGGGCTATACATATTAATGTCTTCTACCCTGAAATTCTACTTAAATAAAAGCCTATTATTCTA
1 GGGGGCTATACATATTAATGTCTTCTACCCTGAAATTCTACTTAAATAAAAGCCTATTATTCTA
30341470 TAAATTAACT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (65 bp):
GGGGGCTATACATATTAATGTCTTCTACCCTGAAATTCTACTTAAATAAAAGCCTATTATTCTAA
Found at i:30344021 original size:27 final size:27
Alignment explanation
Indices: 30343978--30344047 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
30343968 TTATGGTAGA
* * **
30343978 AGATGTTATACACCAAACTTCAATCGC
1 AGATGTTACACATCAAACTTCAATAAC
*
30344005 AGATGTTACACATCAAATTTCAATAAC
1 AGATGTTACACATCAAACTTCAATAAC
*
30344032 AGATGTTACACGTCAA
1 AGATGTTACACATCAA
30344048 GATCAAAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.27
Consensus pattern (27 bp):
AGATGTTACACATCAAACTTCAATAAC
Found at i:30359942 original size:17 final size:17
Alignment explanation
Indices: 30359920--30359954 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
30359910 TTGATTTAAG
30359920 CCCTAAAACATCTGCAT
1 CCCTAAAACATCTGCAT
30359937 CCCTAAAACATCTGCAT
1 CCCTAAAACATCTGCAT
30359954 C
1 C
30359955 ATGGTTAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.37, G:0.06, T:0.23
Consensus pattern (17 bp):
CCCTAAAACATCTGCAT
Done.