Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 186 of 211
Found at i:57572301 original size:24 final size:24
Alignment explanation
Indices: 57572247--57572301 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
57572237 CATATTTTTG
* *
57572247 AAATTATTGTGCATTATTATTCTA
1 AAATTATTATGCATTATTACTCTA
*
57572271 AAATTATTATGTATTATTACT-TA
1 AAATTATTATGCATTATTACTCTA
57572294 AAAGTTAT
1 AAA-TTAT
57572302 ACTATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (24 bp):
AAATTATTATGCATTATTACTCTA
Found at i:57574111 original size:21 final size:20
Alignment explanation
Indices: 57574085--57574132 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
57574075 AAGATAATAA
*
57574085 TTAACTATTAACTAACTATGT
1 TTAACTACTAACTAACTAT-T
*
57574106 TTAACTACTAACTAACTCTT
1 TTAACTACTAACTAACTATT
57574126 TTAACTA
1 TTAACTA
57574133 ACTTTATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.42
Consensus pattern (20 bp):
TTAACTACTAACTAACTATT
Found at i:57577784 original size:7 final size:7
Alignment explanation
Indices: 57577772--57577811 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
57577762 GTTCAAAAAT
57577772 TTTATTA
1 TTTATTA
57577779 TTTATTA
1 TTTATTA
57577786 TTTATTA
1 TTTATTA
57577793 TTTATTA
1 TTTATTA
57577800 TTTATTA
1 TTTATTA
57577807 TTTAT
1 TTTAT
57577812 GAGTTAAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:57579233 original size:105 final size:101
Alignment explanation
Indices: 57579050--57579243 Score: 273
Period size: 105 Copynumber: 1.9 Consensus size: 101
57579040 AATTGATGGA
* *
57579050 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGCTTGGCTATGACATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATATAAATGTAAGACCATAGCTTGGCTATGACATTTTAA
57579115 TGAAAAGAACATAACTGGGTTATGGCACCTTGAACG
66 TGAAAAGAACATAACTGGGTTATGGCACCTTGAACG
* *
57579151 TAAGACCATGGTTGGACCATGGCAGTATATATACATGTGTAAGACCATAG-TTGGGCTATGGCAT
1 TAAGACCATGGTTGGACCATGGCA--ATATATA-A-ATGTAAGACCATAGCTT-GGCTATGACAT
* * *
57579215 TTTGATGATAAGACCATAACTGGGTTATG
61 TTTAATGAAAAGAACATAACTGGGTTATG
57579244 ACACTAAAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
101 24 0.30
103 5 0.06
104 3 0.04
105 49 0.60
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATATAAATGTAAGACCATAGCTTGGCTATGACATTTTAA
TGAAAAGAACATAACTGGGTTATGGCACCTTGAACG
Found at i:57579259 original size:105 final size:101
Alignment explanation
Indices: 57579050--57579266 Score: 267
Period size: 105 Copynumber: 2.1 Consensus size: 101
57579040 AATTGATGGA
* *
57579050 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGCTTGGCTATGACATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATATAAATGTAAGACCATAGCTTGGCTATGACATTTTAA
* **
57579115 TGAAAAGAACATAACTGGGTTATGGCACCTTGAACG
66 TGAAAAGAACATAACTGGGTTATGACACCTAAAACG
* *
57579151 TAAGACCATGGTTGGACCATGGCAGTATATATACATGTGTAAGACCATAG-TTGGGCTATGGCAT
1 TAAGACCATGGTTGGACCATGGCA--ATATATA-A-ATGTAAGACCATAGCTT-GGCTATGACAT
* * * *
57579215 TTTGATGATAAGACCATAACTGGGTTATGACA-CTAAAAATG
61 TTTAATGAAAAGAACATAACTGGGTTATGACACCT-AAAACG
57579256 TAAGACCATGG
1 TAAGACCATGG
57579267 AAGGGCCATG
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
101 24 0.24
103 5 0.05
104 5 0.05
105 65 0.66
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATATAAATGTAAGACCATAGCTTGGCTATGACATTTTAA
TGAAAAGAACATAACTGGGTTATGACACCTAAAACG
Found at i:57581560 original size:21 final size:20
Alignment explanation
Indices: 57581534--57581580 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
57581524 ATATAATAAC
* *
57581534 TAACTATTAACTAACTGTGTT
1 TAACTACTAACTAACTCT-TT
57581555 TAACTACTAACTAACTCTTT
1 TAACTACTAACTAACTCTTT
57581575 TAACTA
1 TAACTA
57581581 ACTTTATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (20 bp):
TAACTACTAACTAACTCTTT
Found at i:57584925 original size:12 final size:12
Alignment explanation
Indices: 57584908--57584951 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
57584898 AAAGATATAT
57584908 AATATATTCCTA
1 AATATATTCCTA
**
57584920 AATATATTTTTA
1 AATATATTCCTA
*
57584932 AATATATGCCTAA
1 AATATATTCCT-A
57584945 AATATAT
1 AATATAT
57584952 ACAATATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (12 bp):
AATATATTCCTA
Found at i:57585205 original size:19 final size:18
Alignment explanation
Indices: 57585169--57585218 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
57585159 TAAAATTGGG
*
57585169 TGCAATTTTATTTTTTTA
1 TGCAATTTTATTTGTTTA
*
57585187 TGTAATTTATATTTGTTTA
1 TGCAATTT-TATTTGTTTA
57585206 TGCAATTTTATTT
1 TGCAATTTTATTT
57585219 CTCTGTCCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (18 bp):
TGCAATTTTATTTGTTTA
Found at i:57585448 original size:23 final size:23
Alignment explanation
Indices: 57585420--57585481 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
57585410 CTTCAGAAAC
57585420 AATAAAATTATAAATTAATAC-AT
1 AATAAAATTATAAATTAAT-CTAT
* **
57585443 AATAAACTTATATTTTAATCTAT
1 AATAAAATTATAAATTAATCTAT
57585466 AA-AAAATTAT-AATTAA
1 AATAAAATTATAAATTAA
57585482 AATCTTACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 4 0.12
22 8 0.25
23 20 0.62
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAAAATTATAAATTAATCTAT
Found at i:57588579 original size:15 final size:13
Alignment explanation
Indices: 57588555--57588588 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
57588545 AAAAATTATG
*
57588555 TAAAAATATATTTA
1 TAAAAAT-TATATA
57588569 TAAAAATTATATA
1 TAAAAATTATATA
57588582 TAAAAAT
1 TAAAAAT
57588589 ATTAATCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAAATTATATA
Found at i:57595927 original size:60 final size:60
Alignment explanation
Indices: 57595861--57595973 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
57595851 TTTTTTAAAA
* * * **
57595861 TTTTAGAGTTA-AGACTAAATTGACAAATTTTATAAATGTTGAGGGCCAAATTTAATGAAT
1 TTTTAGAATTAGA-ACTAAAATGAAAAATTTTATAAACATTGAGGGCCAAATTTAATGAAT
* *
57595921 TTTTAGAATTAGAACTAAAATGAAAAATTTTGTAAACATTGAGGGCTAAATTT
1 TTTTAGAATTAGAACTAAAATGAAAAATTTTATAAACATTGAGGGCCAAATTT
57595974 GTTAAATTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 44 0.98
61 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (60 bp):
TTTTAGAATTAGAACTAAAATGAAAAATTTTATAAACATTGAGGGCCAAATTTAATGAAT
Found at i:57595982 original size:60 final size:60
Alignment explanation
Indices: 57595850--57595984 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
57595840 AAATGAATTG
* * * * * **
57595850 ATTTTTTAAAATTTTAGAGTTAAGACTAAATTGACAAATTTTATAAATGTTGAGGGCCAA
1 ATTTATTAAATTTTTAGAATTAAGACTAAAATGAAAAATTTTATAAACATTGAGGGCCAA
* * * *
57595910 ATTTAATGAATTTTTAGAATT-AGAACTAAAATGAAAAATTTTGTAAACATTGAGGGCTAA
1 ATTTATTAAATTTTTAGAATTAAG-ACTAAAATGAAAAATTTTATAAACATTGAGGGCCAA
*
57595970 ATTTGTTAAATTTTT
1 ATTTATTAAATTTTT
57595985 TTATATTTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
59 2 0.03
60 58 0.97
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (60 bp):
ATTTATTAAATTTTTAGAATTAAGACTAAAATGAAAAATTTTATAAACATTGAGGGCCAA
Found at i:57603806 original size:25 final size:25
Alignment explanation
Indices: 57603778--57603828 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
57603768 TATATTTAAA
*
57603778 TTATTAAAATATTAATAAAAATATT
1 TTATTAAAATAATAATAAAAATATT
* **
57603803 TTATTAAATTAATGCTAAAAATATT
1 TTATTAAAATAATAATAAAAATATT
57603828 T
1 T
57603829 ATAATTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TTATTAAAATAATAATAAAAATATT
Found at i:57606223 original size:18 final size:19
Alignment explanation
Indices: 57606200--57606259 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
57606190 CAGAGCCACA
* *
57606200 AGCTCACT-TGAAGCTGGG
1 AGCTCACTCTAAAGCTGCG
57606218 AGCTCA-TCTAAAGCTGCG
1 AGCTCACTCTAAAGCTGCG
*
57606236 AGCTCAC-CCAAAGAC-GCG
1 AGCTCACTCTAAAG-CTGCG
57606254 AGCTCA
1 AGCTCA
57606260 ACTCAAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (19 bp):
AGCTCACTCTAAAGCTGCG
Found at i:57609728 original size:19 final size:19
Alignment explanation
Indices: 57609700--57609737 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
57609690 TTTTAAGAGA
57609700 ATATTGTAATTATA-ATTT
1 ATATTGTAATTATATATTT
57609718 ATATATGTAATTATATATTT
1 ATAT-TGTAATTATATATTT
57609738 TAGTGAAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATATTGTAATTATATATTT
Found at i:57622854 original size:8 final size:8
Alignment explanation
Indices: 57622841--57622872 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
57622831 TTCCAAGTTT
57622841 TAATGTTG
1 TAATGTTG
57622849 TAATGTTG
1 TAATGTTG
57622857 TAATGTTG
1 TAATGTTG
57622865 TAATGTTG
1 TAATGTTG
57622873 CTATTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (8 bp):
TAATGTTG
Found at i:57624114 original size:14 final size:14
Alignment explanation
Indices: 57624095--57624128 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
57624085 AAATTACATG
57624095 TTAGAATAGTATCA
1 TTAGAATAGTATCA
57624109 TTAGAATAGTATCA
1 TTAGAATAGTATCA
57624123 TTAGAA
1 TTAGAA
57624129 AAGAATGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (14 bp):
TTAGAATAGTATCA
Found at i:57625395 original size:3 final size:3
Alignment explanation
Indices: 57625389--57625413 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
57625379 TAAATACGAA
57625389 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
57625414 TTAAGATGAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:57628897 original size:42 final size:42
Alignment explanation
Indices: 57628833--57628915 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
57628823 GCTATAGCTG
*
57628833 TTGCCATTATTTTATAGTTGACATTGCATAAGCTAATAGGCT
1 TTGCCATTATTTTATAGATGACATTGCATAAGCTAATAGGCT
* *
57628875 TTGCCGTTATTTTATAGATGACATTGCATAAGTTAATAGGC
1 TTGCCATTATTTTATAGATGACATTGCATAAGCTAATAGGC
57628916 CTAAAATGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (42 bp):
TTGCCATTATTTTATAGATGACATTGCATAAGCTAATAGGCT
Found at i:57652037 original size:22 final size:20
Alignment explanation
Indices: 57652012--57652057 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
57652002 CGTTTTCAAT
57652012 AAAAAAATTATAAAAATAATTC
1 AAAAAAATTATAAAAAT--TTC
* *
57652034 AAAATATTTATAAAAATTTC
1 AAAAAAATTATAAAAATTTC
57652054 AAAA
1 AAAA
57652058 TTTCATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAAATTATAAAAATTTC
Found at i:57652054 original size:20 final size:21
Alignment explanation
Indices: 57652019--57652058 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
57652009 AATAAAAAAA
57652019 TTATAAAAATAATTCAAAATAT
1 TTATAAAAAT-ATTCAAAATAT
57652041 TTATAAAAAT-TTCAAAAT
1 TTATAAAAATATTCAAAAT
57652059 TTCATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
TTATAAAAATATTCAAAATAT
Found at i:57654437 original size:20 final size:20
Alignment explanation
Indices: 57654392--57654439 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
57654382 CACTCGAAGC
*
57654392 AAAAGATTAAGCAAAGGGAT
1 AAAAGATTAAGCAAAGAGAT
* *
57654412 ACAAGATTAATCAAA-AGATT
1 AAAAGATTAAGCAAAGAGA-T
57654432 AAAAGATT
1 AAAAGATT
57654440 CCACAAAGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAAGATTAAGCAAAGAGAT
Found at i:57661509 original size:16 final size:16
Alignment explanation
Indices: 57661488--57661519 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57661478 GCACCTTCAA
*
57661488 ACCAAAAGCTTAGTGG
1 ACCAAAAGCTCAGTGG
57661504 ACCAAAAGCTCAGTGG
1 ACCAAAAGCTCAGTGG
57661520 GGAAACAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.16
Consensus pattern (16 bp):
ACCAAAAGCTCAGTGG
Found at i:57676013 original size:55 final size:55
Alignment explanation
Indices: 57675877--57676013 Score: 152
Period size: 56 Copynumber: 2.5 Consensus size: 55
57675867 GATCTAACAT
* * *
57675877 TATGTAAAATTATTAAGCCAAAACAATTTTCTTAATGGTTAGAAAATTTTATCAAA
1 TATGTAAAATTATTAAGCCAAAA-AATTGTCTTAATGGTTAGAAAAGTGTATCAAA
* * * **
57675933 TAATCTCAAATTATTAAGTCC-AAAAATTGTGTTAATGGTTATTAAAGTGT-TCAAAA
1 T-ATGTAAAATTATTAAG-CCAAAAAATTGTCTTAATGGTTAGAAAAGTGTATC-AAA
57675989 TATGTAAAATTATTAAGCCAAAAAA
1 TATGTAAAATTATTAAGCCAAAAAA
57676014 ATTTAGGTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
54 2 0.03
55 21 0.31
56 25 0.37
57 17 0.25
58 2 0.03
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (55 bp):
TATGTAAAATTATTAAGCCAAAAAATTGTCTTAATGGTTAGAAAAGTGTATCAAA
Found at i:57676064 original size:28 final size:28
Alignment explanation
Indices: 57676013--57676504 Score: 597
Period size: 28 Copynumber: 17.4 Consensus size: 28
57676003 AAGCCAAAAA
* *
57676013 AATTTAGGTTAGTTTTGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
57676041 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
* * *
57676070 AACTTAGG-T---TTAAGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
57676094 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
57676122 AATTTAGGTTAGGGTTAGTTTAGGGTTTTTAGTT
1 AATTTAGGTTA--G--A--TTAGGGTTTTTAATT
*
57676156 AATTTAGGTTAGATTAGGGTTTTAAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
57676184 AATTTAGGTTAGATTAGGGTTTTAAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
57676212 AATTTAGGTTAGATTAGGGTTTTAAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* *
57676240 AATTTAGGTCAGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
57676268 AATTTAGGTTAGGTTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* * *
57676296 AATTTAGGTTAGGGTTACGGTTTTAAATT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
* * *
57676325 AATTTAGGTTAGATTAGGCTTTTAAATC
1 AATTTAGGTTAGATTAGGGTTTTTAATT
57676353 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
57676381 AATTTAGGTTAGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
57676409 AATTTAGGTTAGGGTTAGATTAGGGTTTTTAGTT
1 AA--T---TTA-GGTTAGATTAGGGTTTTTAATT
*
57676443 AATTTA-G---G-TTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
57676466 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
57676494 AATTTAGGTTA
1 AATTTAGGTTA
57676505 CACTACACCA
Statistics
Matches: 414, Mismatches: 27, Indels: 46
0.85 0.06 0.09
Matches are distributed among these distances:
23 21 0.05
24 22 0.05
25 1 0.00
27 2 0.00
28 258 0.62
29 52 0.13
30 3 0.01
32 3 0.01
33 3 0.01
34 49 0.12
ACGTcount: A:0.27, C:0.01, G:0.23, T:0.49
Consensus pattern (28 bp):
AATTTAGGTTAGATTAGGGTTTTTAATT
Found at i:57676078 original size:24 final size:24
Alignment explanation
Indices: 57676049--57676137 Score: 108
Period size: 24 Copynumber: 3.6 Consensus size: 24
57676039 TTAATTTAGG
*
57676049 TTAGGTTTAGGGTTTTTAATTAAC
1 TTAGGTTTAGGGTTTTTAATTAAT
* *
57676073 TTAGGTTTAAGGTTTTTAGTTAAT
1 TTAGGTTTAGGGTTTTTAATTAAT
57676097 TTAGGTTAGATTAGGGTTTTTAATTAAT
1 TTAGG-T---TTAGGGTTTTTAATTAAT
57676125 TTAGG-TTAGGGTT
1 TTAGGTTTAGGGTT
57676138 AGTTTAGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
23 8 0.14
24 26 0.46
25 1 0.02
28 21 0.38
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.51
Consensus pattern (24 bp):
TTAGGTTTAGGGTTTTTAATTAAT
Found at i:57676161 original size:18 final size:18
Alignment explanation
Indices: 57676107--57676163 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
57676097 TTAGGTTAGA
*
57676107 TTAGGGTTTTTAATTAAT
1 TTAGGGTTTTTAGTTAAT
*** *
57676125 TTA-GG-TTAGGGTTAGT
1 TTAGGGTTTTTAGTTAAT
57676141 TTAGGGTTTTTAGTTAAT
1 TTAGGGTTTTTAGTTAAT
57676159 TTAGG
1 TTAGG
57676164 TTAGATTAGG
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
16 9 0.32
17 4 0.14
18 15 0.54
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (18 bp):
TTAGGGTTTTTAGTTAAT
Found at i:57676348 original size:113 final size:112
Alignment explanation
Indices: 57676013--57676504 Score: 597
Period size: 113 Copynumber: 4.3 Consensus size: 112
57676003 AAGCCAAAAA
* * * *
57676013 AATTTAGGTTAGTTTTGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAATTAACTTAGG
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAATTAATTTAGG
* * * *
57676078 -T---TTAAGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
65 TTAGGTTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATT
* *
57676122 AATTTAGGTTAGGGTTAGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTAAATTAAT
1 AATTTAGGTTA--G--A--TTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAAT
*
57676187 TTAGGTTAGATTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATT
60 TTAGGTTAGGTTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATT
* * *
57676240 AATTTAGGTCAGATTAGGGTTTTTAGTTAATTTAGGTTAGGTTAGGGTTTTTAATTAATTTAGGT
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGT
* * *
57676305 TAGGGTTACGGTTTTAAATTAATTTAGGTTAGATTAGGCTTTTAAATC
66 TA-GGTTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATT
*
57676353 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGT
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGT
* * * *
57676418 TAGGGTTAGATTAGGGTTTTTAGTTAATTTA-G---G-TTAGGGTTTTTAGTT
66 TA--G---G-TTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATT
57676466 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTA
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTA
57676505 CACTACACCA
Statistics
Matches: 339, Mismatches: 28, Indels: 28
0.86 0.07 0.07
Matches are distributed among these distances:
109 11 0.03
111 1 0.00
112 52 0.15
113 154 0.45
114 26 0.08
115 25 0.07
116 1 0.00
117 2 0.01
118 67 0.20
ACGTcount: A:0.27, C:0.01, G:0.23, T:0.49
Consensus pattern (112 bp):
AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGT
TAGGTTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATT
Found at i:57676362 original size:141 final size:143
Alignment explanation
Indices: 57676013--57676504 Score: 648
Period size: 141 Copynumber: 3.5 Consensus size: 143
57676003 AAGCCAAAAA
* * * * * *
57676013 AATTTAGGTTAGTTTTGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAATTAACTTAGG
1 AATTTAGGTTAGGTTAGGGTTTTAAATTAATTTAGGTTA-GATTAGGGTTTTAAATTAATTTAGG
* * *
57676078 -T---TTAAGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGGTTA
65 TTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTA-GG-T-
*
57676139 GTTTAGGGTTTTTAGTT
127 GATTAGGGTTTTTAGTT
*
57676156 AATTTAGGTTAGATTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATTAATTTAGGT
1 AATTTAGGTTAGGTTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATTAATTTAGGT
* *
57676221 TAGATTAGGGTTTTAAATTAATTTAGGTCAGATTAGGGTTTTTAGTTAATTTAGGTTA-G-G-TT
66 TAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGTGATT
*
57676283 AGGGTTTTTAATT
131 AGGGTTTTTAGTT
* * *
57676296 AATTTAGGTTAGGGTTACGGTTTTAAATTAATTTAGGTTAGATTAGGCTTTTAAATCAATTTAGG
1 AATTTAGGTTA-GGTTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATTAATTTAGG
57676361 TTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTA
65 TTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTA-GG-T-
57676426 GATTAGGGTTTTTAGTT
127 GATTAGGGTTTTTAGTT
* * *
57676443 AA--T---TTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGT
1 AATTTAGGTTAGGTTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATTAATTTAGGT
57676503 TA
66 TA
57676505 CACTACACCA
Statistics
Matches: 313, Mismatches: 25, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
140 25 0.08
141 157 0.50
142 25 0.08
143 38 0.12
144 1 0.00
145 1 0.00
146 50 0.16
147 16 0.05
ACGTcount: A:0.27, C:0.01, G:0.23, T:0.49
Consensus pattern (143 bp):
AATTTAGGTTAGGTTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTAAATTAATTTAGGT
TAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGTGATT
AGGGTTTTTAGTT
Found at i:57676452 original size:17 final size:17
Alignment explanation
Indices: 57676398--57676452 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
57676388 GTTAGATTAG
57676398 GGTTTTTAGTTAATTTA
1 GGTTTTTAGTTAATTTA
***
57676415 GG-TTAGGGTTAGA-TTA
1 GGTTTTTAGTTA-ATTTA
57676431 GGGTTTTTAGTTAATTTA
1 -GGTTTTTAGTTAATTTA
57676449 GGTT
1 GGTT
57676453 AGGGTTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
16 9 0.32
17 10 0.36
18 9 0.32
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (17 bp):
GGTTTTTAGTTAATTTA
Found at i:57676454 original size:23 final size:23
Alignment explanation
Indices: 57676423--57676504 Score: 101
Period size: 23 Copynumber: 3.3 Consensus size: 23
57676413 TAGGTTAGGG
*
57676423 TTAGATTAGGGTTTTTAGTTAAT
1 TTAGGTTAGGGTTTTTAGTTAAT
57676446 TTAGGTTAGGGTTTTTAGTTAAT
1 TTAGGTTAGGGTTTTTAGTTAAT
*
57676469 TTAGGTTAGATTAGGGTTTTTAATTAAT
1 TTA-G---G-TTAGGGTTTTTAGTTAAT
57676497 TTAGGTTA
1 TTAGGTTA
57676505 CACTACACCA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
23 28 0.54
24 2 0.04
27 2 0.04
28 20 0.38
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (23 bp):
TTAGGTTAGGGTTTTTAGTTAAT
Found at i:57676944 original size:114 final size:114
Alignment explanation
Indices: 57676596--57677353 Score: 1074
Period size: 114 Copynumber: 6.7 Consensus size: 114
57676586 GACATTTGAC
*
57676596 AAACGCCGCTAAAGCATACCATTAGCGGCGCATTATACAAAGCGCCGC-AAAAATCTTAACCAAA
1 AAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAA
**
57676660 ACGCATCGTTCTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAAGGCA
66 ACGCATCGTTCTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAAGTAA
* * * *
57676709 ACACGCCACTAAAGCACACCATTAGCGGCGCATCATACAAAGCGCCGC-AAAAATCTTAACCGAA
1 AAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAA
* * * * * *
57676773 ACGCATCGTTTTAGGTTGAGGTATATTAGAATTAGTGGCGCTTATGGAT
66 ACGCATCGTTCTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAAGTAA
* * * *
57676822 AAATGCCGCTAAAGCACACCATTAGCGGCGCATTAGACAGAGCGCCGCAAAAAATCATAACCAAA
1 AAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAA
*
57676887 ACGCATCGTTCTGGGTTGAGGTATTTTAGAATTAGTGGCGTTTAAGTAA
66 ACGCATCGTTCTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAAGTAA
* * * *
57676936 AAACGCCGCTAAAGTAGACCATTAGCGGCGCATCATACAAAGCGCCACAAAAAATCTTAACCAAA
1 AAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAA
*
57677001 ACGCATCGTTCTGGGTTGATGTATTTTAGAATTAGTGGCGCTTAAGTAA
66 ACGCATCGTTCTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAAGTAA
* * * ** *
57677050 AAACGCCGCTAAAGCACACTATTAGCGTCGCATCATACAAAGCGATGCAAAAAATCTTAACTAAA
1 AAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAA
*
57677115 ACGCATCGTTCTGGGTTGATGTATTTTAGAATTAGTGGCGCTTAAGTAA
66 ACGCATCGTTCTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAAGTAA
* * * *
57677164 AAACGCCGCTAAAGAACACAATTAGCGGCGCATTATTCAAAGCGCCGCAAAAAAAACTTAACCAA
1 AAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGC-AAAAAATCTTAACCAA
* * *
57677229 AACGCGTCGTTTTTGGTTGAGGTATTTTAGAATTAGTGGCGC-TATAGT-A
65 AACGCATCGTTCTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTA-AGTAA
* * ** * *
57677278 AAATGCCGCTAAAGTACATAATTAGCGGCGCATTATACAAAGCGCCGCGAATAAATCTTAACTAA
1 AAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGC-AAAAAATCTTAACCAA
57677343 AACGCATCGTT
65 AACGCATCGTT
57677354 TTAAACCGAG
Statistics
Matches: 576, Mismatches: 66, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
113 144 0.25
114 377 0.65
115 55 0.10
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (114 bp):
AAACGCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAA
ACGCATCGTTCTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTAAGTAA
Found at i:57677697 original size:14 final size:15
Alignment explanation
Indices: 57677652--57677699 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
57677642 ATGGTTTATT
57677652 GTTTAAGGGTTT-TA
1 GTTTAAGGGTTTGTA
* * *
57677666 TTTTAAGGGTTAGGA
1 GTTTAAGGGTTTGTA
57677681 GTTT-AGGGTTTGTA
1 GTTTAAGGGTTTGTA
57677695 GTTTA
1 GTTTA
57677700 TGTCTTATGA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (15 bp):
GTTTAAGGGTTTGTA
Found at i:57677809 original size:21 final size:21
Alignment explanation
Indices: 57677766--57677829 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
57677756 TTTACGGGCC
*
57677766 ATGGTTTAAGGGTT-GGGGTTTA
1 ATGG-TTAAGGGTTAAGGG-TTA
* *
57677788 AT-GTATAAGTGTTACGGGTTA
1 ATGGT-TAAGGGTTAAGGGTTA
57677809 ATGGTTAAGGGTTAAGGGTTA
1 ATGGTTAAGGGTTAAGGGTTA
57677830 GGGGTTTAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.03
21 27 0.77
22 7 0.20
ACGTcount: A:0.25, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
ATGGTTAAGGGTTAAGGGTTA
Found at i:57677814 original size:7 final size:7
Alignment explanation
Indices: 57677793--57677835 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
57677783 GTTTAATGTA
*
57677793 TAAGTGT
1 TAAGGGT
*
57677800 TACGGGT
1 TAAGGGT
*
57677807 TAATGGT
1 TAAGGGT
57677814 TAAGGGT
1 TAAGGGT
57677821 TAAGGGT
1 TAAGGGT
*
57677828 TAGGGGT
1 TAAGGGT
57677835 T
1 T
57677836 TAGGATTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.23, C:0.02, G:0.40, T:0.35
Consensus pattern (7 bp):
TAAGGGT
Found at i:57678059 original size:21 final size:21
Alignment explanation
Indices: 57678035--57678078 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
57678025 AAGGGTACTT
* *
57678035 GGTTTA-ATGGTTTGAGTTTAA
1 GGTTTAGAT-GTTGGAGATTAA
57678056 GGTTTAGATGTTGGAGATTAA
1 GGTTTAGATGTTGGAGATTAA
57678077 GG
1 GG
57678079 GATAGAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (21 bp):
GGTTTAGATGTTGGAGATTAA
Found at i:57679080 original size:191 final size:191
Alignment explanation
Indices: 57678742--57679090 Score: 518
Period size: 191 Copynumber: 1.8 Consensus size: 191
57678732 GCAAATCCCT
* ** * * *
57678742 AGACCTTTCACCTTTTCAACGGCGATTTCCCCTCTTCTCGGTCGAATATCGGTTCTCGTCTGGGC
1 AGACCATTCACCCCTTCAACGACGATTTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGGC
* * * * * *
57678807 TGACTGGTAAAAAACTTTCGAAATCCCTAATTTCTCCGTTGACTCCGTATGTGGCTGTTCATTTT
66 TGACTGGTAAAAAACTTTCCAAATCCCTAATTTATCCGTTGAATACGTATATGGCTATTCATTTT
* *
57678872 TATGTTCGATTTTTTCTTTCTGTAATGCCCGCTTTGTTTTTCCTTTCTCTTTAAAATCCAG
131 TATGTTCGACTTTTTCTTTCTCTAATGCCCGCTTTGTTTTTCCTTTCTCTTTAAAATCCAG
* *
57678933 AGACCATTCACCCCTTCAACGACGATTTCCCCTCTTTTCGATCGAATATTGCTTCTCGTCTGGGC
1 AGACCATTCACCCCTTCAACGACGATTTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGGC
* *
57678998 TGACTGGTAAAAATCTTTCCAAATCCCTAATTTATTCGTTGAATACGTATATGGCTATTCATTTT
66 TGACTGGTAAAAAACTTTCCAAATCCCTAATTTATCCGTTGAATACGTATATGGCTATTCATTTT
* *
57679063 TCTGTTTGACTTTTTCTTTCTCTAATGC
131 TATGTTCGACTTTTTCTTTCTCTAATGC
57679091 TCGGACAAAT
Statistics
Matches: 138, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
191 138 1.00
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (191 bp):
AGACCATTCACCCCTTCAACGACGATTTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGGC
TGACTGGTAAAAAACTTTCCAAATCCCTAATTTATCCGTTGAATACGTATATGGCTATTCATTTT
TATGTTCGACTTTTTCTTTCTCTAATGCCCGCTTTGTTTTTCCTTTCTCTTTAAAATCCAG
Found at i:57680626 original size:17 final size:17
Alignment explanation
Indices: 57680604--57680636 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
57680594 TTAATATCTA
57680604 TATAAGTTTTATAAATT
1 TATAAGTTTTATAAATT
*
57680621 TATAAGTTTTCTAAAT
1 TATAAGTTTTATAAAT
57680637 AAGTTTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTATAAATT
Found at i:57680640 original size:13 final size:13
Alignment explanation
Indices: 57680622--57680649 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
57680612 TTATAAATTT
57680622 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
57680635 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
57680648 AT
1 AT
57680650 TTATTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
ATAAGTTTTCTAA
Found at i:57680768 original size:27 final size:27
Alignment explanation
Indices: 57680730--57681347 Score: 457
Period size: 27 Copynumber: 22.5 Consensus size: 27
57680720 ATTAAGTTAT
57680730 ATAACTTACATAAATTAAATAACTTAC
1 ATAACTTACATAAATTAAATAACTTAC
*
57680757 ATAACTTACATAAA-T---T--CTTGC
1 ATAACTTACATAAATTAAATAACTTAC
* * * *
57680778 ATAAATTAAATAATTTACATAACTTAC
1 ATAACTTACATAAATTAAATAACTTAC
* * *
57680805 ATAAATTAAATAACTTAAATAA-TTGAC
1 ATAACTTACATAAATTAAATAACTT-AC
* * * * * * *
57680832 ATAAATTCCGTGGACTTACATAACTTGC
1 ATAACTTACAT-AAATTAAATAACTTAC
*
57680860 ATAAACTTGCATAAATTAAATAACTTAC
1 AT-AACTTACATAAATTAAATAACTTAC
57680888 ATAA---AC------TAAATAACTTAC
1 ATAACTTACATAAATTAAATAACTTAC
* *
57680906 ATAATTTACATAAACTAAATAACTTAC
1 ATAACTTACATAAATTAAATAACTTAC
57680933 ATAACTTACATAAATTAAATAACTTAC
1 ATAACTTACATAAATTAAATAACTTAC
57680960 ATAACTTACATAAATTAAATAACTTAC
1 ATAACTTACATAAATTAAATAACTTAC
*
57680987 ATAACTTACATAAACTTGCATAAATTAAATTAC
1 ATAACTTACATAAA--T---TAAA-TAACTTAC
*
57681020 TTACATAACTTACATAAATTAAATAACTTAA
1 ----ATAACTTACATAAATTAAATAACTTAC
*** *
57681051 ATAA-TTGACATAAATTCCGTGGACTTAC
1 ATAACTT-ACATAAATTAAAT-AACTTAC
** * *
57681079 ATAACTTACATAAACTTGCATAAATTAA
1 ATAACTTACATAAA-TTAAATAACTTAC
*
57681107 ATAACTTACATAAACTAAATAACTTAC
1 ATAACTTACATAAATTAAATAACTTAC
*
57681134 ATATCTTACATAAATTAAATAACTTAC
1 ATAACTTACATAAATTAAATAACTTAC
*
57681161 ATAACTTACATAAACTTGCATAAATTAAATTAC
1 ATAACTTACATAAA--T---TAAA-TAACTTAC
*
57681194 TTACATAACTTACATAAATTAAATAACTTAA
1 ----ATAACTTACATAAATTAAATAACTTAC
*** *
57681225 ATAA-TTGACATAAATTCCGTGGACTTAC
1 ATAACTT-ACATAAATTAAAT-AACTTAC
** *
57681253 ATAACTTACATAAACTTGCATAAAC-TAA
1 ATAACTTACATAAA-TTAAAT-AACTTAC
*
57681281 ATAACTTACATAAACTAAATAACTTAC
1 ATAACTTACATAAATTAAATAACTTAC
57681308 ATATA-TTACATAAATTAAATAACTTAC
1 ATA-ACTTACATAAATTAAATAACTTAC
57681335 ATAACTTACATAA
1 ATAACTTACATAA
57681348 TACATAAAAA
Statistics
Matches: 479, Mismatches: 62, Indels: 100
0.75 0.10 0.16
Matches are distributed among these distances:
18 16 0.03
21 17 0.04
22 1 0.00
23 1 0.00
24 1 0.00
25 1 0.00
26 11 0.02
27 242 0.51
28 93 0.19
29 24 0.05
31 12 0.03
32 16 0.03
33 14 0.03
35 2 0.00
37 28 0.06
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (27 bp):
ATAACTTACATAAATTAAATAACTTAC
Found at i:57681008 original size:10 final size:10
Alignment explanation
Indices: 57680732--57681347 Score: 353
Period size: 9 Copynumber: 67.1 Consensus size: 10
57680722 TAAGTTATAT
57680732 AACTTACATA
1 AACTTACATA
*
57680742 AA-TTAAAT-
1 AACTTACATA
57680750 AACTTACAT-
1 AACTTACATA
57680759 AACTTACATA
1 AACTTACATA
*
57680769 AATTCTTGCATA
1 AA--CTTACATA
*
57680781 AA-TTAAAT-
1 AACTTACATA
*
57680789 AATTTACAT-
1 AACTTACATA
57680798 AACTTACATA
1 AACTTACATA
*
57680808 AA-TTAAAT-
1 AACTTACATA
*
57680816 AACTTAAAT-
1 AACTTACATA
57680825 AA-TTGACATA
1 AACTT-ACATA
* * *
57680835 AA-TTCCGTG
1 AACTTACATA
*
57680844 GACTTACAT-
1 AACTTACATA
*
57680853 AACTTGCATA
1 AACTTACATA
*
57680863 AACTTGCATA
1 AACTTACATA
*
57680873 AA-TTAAAT-
1 AACTTACATA
57680881 AACTTACATA
1 AACTTACATA
*
57680891 AAC-TAAAT-
1 AACTTACATA
57680899 AACTTACAT-
1 AACTTACATA
*
57680908 AATTTACATA
1 AACTTACATA
*
57680918 AAC-TAAAT-
1 AACTTACATA
57680926 AACTTACAT-
1 AACTTACATA
57680935 AACTTACATA
1 AACTTACATA
*
57680945 AA-TTAAAT-
1 AACTTACATA
57680953 AACTTACAT-
1 AACTTACATA
57680962 AACTTACATA
1 AACTTACATA
*
57680972 AA-TTAAAT-
1 AACTTACATA
57680980 AACTTACAT-
1 AACTTACATA
57680989 AACTTACATA
1 AACTTACATA
*
57680999 AACTTGCATA
1 AACTTACATA
*
57681009 AA-TTAAAT-
1 AACTTACATA
*
57681017 TACTTACAT-
1 AACTTACATA
57681026 AACTTACATA
1 AACTTACATA
*
57681036 AA-TTAAAT-
1 AACTTACATA
*
57681044 AACTTAAAT-
1 AACTTACATA
57681053 AA-TTGACATA
1 AACTT-ACATA
* * *
57681063 AA-TTCCGTG
1 AACTTACATA
*
57681072 GACTTACAT-
1 AACTTACATA
57681081 AACTTACATA
1 AACTTACATA
*
57681091 AACTTGCATA
1 AACTTACATA
*
57681101 AA-TTAAAT-
1 AACTTACATA
57681109 AACTTACATA
1 AACTTACATA
*
57681119 AAC-TAAAT-
1 AACTTACATA
57681127 AACTTACAT-
1 AACTTACATA
*
57681136 ATCTTACATA
1 AACTTACATA
*
57681146 AA-TTAAAT-
1 AACTTACATA
57681154 AACTTACAT-
1 AACTTACATA
57681163 AACTTACATA
1 AACTTACATA
*
57681173 AACTTGCATA
1 AACTTACATA
*
57681183 AA-TTAAAT-
1 AACTTACATA
*
57681191 TACTTACAT-
1 AACTTACATA
57681200 AACTTACATA
1 AACTTACATA
*
57681210 AA-TTAAAT-
1 AACTTACATA
*
57681218 AACTTAAAT-
1 AACTTACATA
57681227 AA-TTGACATA
1 AACTT-ACATA
* * *
57681237 AA-TTCCGTG
1 AACTTACATA
*
57681246 GACTTACAT-
1 AACTTACATA
57681255 AACTTACATA
1 AACTTACATA
*
57681265 AACTTGCATA
1 AACTTACATA
*
57681275 AAC-TAAAT-
1 AACTTACATA
57681283 AACTTACATA
1 AACTTACATA
*
57681293 AAC-TAAAT-
1 AACTTACATA
57681301 AACTTACATA
1 AACTTACATA
*
57681311 TA-TTACATA
1 AACTTACATA
*
57681320 AA-TTAAAT-
1 AACTTACATA
57681328 AACTTACAT-
1 AACTTACATA
57681337 AACTTACATA
1 AACTTACATA
57681347 A
1 A
57681348 TACATAAAAA
Statistics
Matches: 479, Mismatches: 80, Indels: 94
0.73 0.12 0.14
Matches are distributed among these distances:
8 45 0.09
9 316 0.66
10 109 0.23
12 9 0.02
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (10 bp):
AACTTACATA
Found at i:57681145 original size:174 final size:174
Alignment explanation
Indices: 57680900--57681347 Score: 808
Period size: 174 Copynumber: 2.6 Consensus size: 174
57680890 AAACTAAATA
* ** * * * *
57680900 ACTTACATAATTTACATAAAC-TAAATAACTTACATAACTTACATAAATTAAATAACTTACATAA
1 ACTTACATAACTTACATAAACTTGCATAAATTAAATAACTTACATAAACTAAATAACTTACATAT
57680964 CTTACATAAATTAAATAACTTACATAACTTACATAAACTTGCATAAATTAAATTACTTACATAAC
66 CTTACATAAATTAAATAACTTACATAACTTACATAAACTTGCATAAATTAAATTACTTACATAAC
57681029 TTACATAAATTAAATAACTTAAATAATTGACATAAATTCCGTGG
131 TTACATAAATTAAATAACTTAAATAATTGACATAAATTCCGTGG
57681073 ACTTACATAACTTACATAAACTTGCATAAATTAAATAACTTACATAAACTAAATAACTTACATAT
1 ACTTACATAACTTACATAAACTTGCATAAATTAAATAACTTACATAAACTAAATAACTTACATAT
57681138 CTTACATAAATTAAATAACTTACATAACTTACATAAACTTGCATAAATTAAATTACTTACATAAC
66 CTTACATAAATTAAATAACTTACATAACTTACATAAACTTGCATAAATTAAATTACTTACATAAC
57681203 TTACATAAATTAAATAACTTAAATAATTGACATAAATTCCGTGG
131 TTACATAAATTAAATAACTTAAATAATTGACATAAATTCCGTGG
*
57681247 ACTTACATAACTTACATAAACTTGCATAAACTAAATAACTTACATAAACTAAATAACTTACATAT
1 ACTTACATAACTTACATAAACTTGCATAAATTAAATAACTTACATAAACTAAATAACTTACATAT
*
57681312 ATTACATAAATTAAATAACTTACATAACTTACATAA
66 CTTACATAAATTAAATAACTTACATAACTTACATAA
57681348 TACATAAAAA
Statistics
Matches: 265, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
173 20 0.08
174 245 0.92
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.33
Consensus pattern (174 bp):
ACTTACATAACTTACATAAACTTGCATAAATTAAATAACTTACATAAACTAAATAACTTACATAT
CTTACATAAATTAAATAACTTACATAACTTACATAAACTTGCATAAATTAAATTACTTACATAAC
TTACATAAATTAAATAACTTAAATAATTGACATAAATTCCGTGG
Found at i:57688522 original size:4 final size:4
Alignment explanation
Indices: 57688513--57688540 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
57688503 AAACCCCTAT
57688513 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
57688541 CTTCCTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:57688619 original size:16 final size:16
Alignment explanation
Indices: 57688600--57688632 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
57688590 TTCTATTCTG
*
57688600 TTTCTTTTCTTTCTTT
1 TTTCTATTCTTTCTTT
57688616 TTTCTATTCTTTCTTT
1 TTTCTATTCTTTCTTT
57688632 T
1 T
57688633 GTTTTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTATTCTTTCTTT
Found at i:57688654 original size:5 final size:5
Alignment explanation
Indices: 57688641--57688712 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
57688631 TTGTTTTATG
57688641 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
57688689 CATAA TCATTAT TATAA TATAA TA
1 TATAA T-A-TAA TATAA TATAA TA
57688713 ATATTTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 34 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:57688680 original size:8 final size:8
Alignment explanation
Indices: 57688653--57688716 Score: 51
Period size: 8 Copynumber: 7.9 Consensus size: 8
57688643 TATATATAAT
57688653 ATAATATA
1 ATAATATA
57688661 AT-ATATTA
1 ATAATA-TA
57688669 ATAATA-A
1 ATAATATA
57688676 TATAATATA
1 -ATAATATA
* *
57688685 AAAACATA
1 ATAATATA
* *
57688693 ATCATTATT
1 AT-AATATA
57688702 ATAATATA
1 ATAATATA
57688710 ATAATAT
1 ATAATAT
57688717 TTTTTTAACA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
7 4 0.09
8 30 0.70
9 9 0.21
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (8 bp):
ATAATATA
Found at i:57688694 original size:24 final size:25
Alignment explanation
Indices: 57688648--57688713 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
57688638 ATGTATATAT
* *
57688648 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
57688672 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
57688697 TTATTATAATATAATAA
1 ATAATATAATATAATAA
57688714 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 18 0.51
25 13 0.37
26 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:57689863 original size:21 final size:21
Alignment explanation
Indices: 57689837--57689886 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
57689827 CTACAACTTA
* *
57689837 AAGCAGAGGCGGCAGTGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* *
57689858 AAGCAGAAGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
57689879 AAGCAGAG
1 AAGCAGAG
57689887 CAGGCCAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:57690336 original size:42 final size:42
Alignment explanation
Indices: 57690261--57690535 Score: 381
Period size: 42 Copynumber: 6.5 Consensus size: 42
57690251 CACTATTTTT
*
57690261 CATGTTCTTTAGCGGCG-TTTTTTCTAAGCGCCGCTAAAGAA
1 CATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAA
* *
57690302 CATTGTCTTTAGTGGCGTTTTTTTCTAAGCGCCGCTAAAGAA
1 CATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAA
* * *
57690344 CATGGTCTTTAGAGGCGTTTTTTTTCTAAGCACCGCCAAAGAA
1 CATGGTCTTTAGCGGCG-TTTTTTTCTAAGCGCCGCTAAAGAA
* * *
57690387 CATTGTCTTTAGTGGCGTTTTTTTCTAAGCACCGCTAAAGAA
1 CATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAA
* * *
57690429 CATGGTCTTTAGAGGCGTTTTTTTTCTAAGTGCTGCTAAAGAA
1 CATGGTCTTTAGCGGCG-TTTTTTTCTAAGCGCCGCTAAAGAA
* * *
57690472 CATGTTCTTTAACGGCGTTTTTTTCTAAGCGCTGCTAAAGAA
1 CATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAA
*
57690514 CATGGTCTTTAACGGCGTTTTT
1 CATGGTCTTTAGCGGCGTTTTT
57690536 GTTTGTAAAC
Statistics
Matches: 211, Mismatches: 20, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
41 14 0.07
42 123 0.58
43 74 0.35
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (42 bp):
CATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAA
Found at i:57690386 original size:85 final size:85
Alignment explanation
Indices: 57690261--57690535 Score: 414
Period size: 85 Copynumber: 3.3 Consensus size: 85
57690251 CACTATTTTT
* *
57690261 CATGTTCTTTAGCGGCG--TTTTTTCTAAGCGCCGCTAAAGAACATTGTCTTTAGTGGCGTTTTT
1 CATGGTCTTTAGAGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATTGTCTTTAGTGGCGTTTTT
57690324 TTCTAAGCGCCGCTAAAGAA
66 TTCTAAGCGCCGCTAAAGAA
* *
57690344 CATGGTCTTTAGAGGCGTTTTTTTTCTAAGCACCGCCAAAGAACATTGTCTTTAGTGGCGTTTTT
1 CATGGTCTTTAGAGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATTGTCTTTAGTGGCGTTTTT
*
57690409 TTCTAAGCACCGCTAAAGAA
66 TTCTAAGCGCCGCTAAAGAA
* * **
57690429 CATGGTCTTTAGAGGCGTTTTTTTTCTAAGTGCTGCTAAAGAACA-TGTTCTTTAACGGCGTTTT
1 CATGGTCTTTAGAGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATTG-TCTTTAGTGGCGTTTT
*
57690493 TTTCTAAGCGCTGCTAAAGAA
65 TTTCTAAGCGCCGCTAAAGAA
57690514 CATGGTCTTTA-ACGGCGTTTTT
1 CATGGTCTTTAGA-GGCGTTTTT
57690536 GTTTGTAAAC
Statistics
Matches: 175, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
83 15 0.09
84 3 0.02
85 157 0.90
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (85 bp):
CATGGTCTTTAGAGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATTGTCTTTAGTGGCGTTTTT
TTCTAAGCGCCGCTAAAGAA
Found at i:57690715 original size:28 final size:28
Alignment explanation
Indices: 57690683--57690928 Score: 253
Period size: 28 Copynumber: 8.2 Consensus size: 28
57690673 TTGGTGTAGT
*
57690683 GTTAGATTAGGGTTTTTAATTAATTTAG
1 GTTAGATTAGGGTTTTTAGTTAATTTAG
57690711 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGG
1 GTTAGATTAGGGTTTTTAGTTAA--T---TTA-G
57690745 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGG
1 GTTAGATTAGGGTTTTTAGTTAA--T---TTA-G
57690779 GTTAGATTAGGGTTTTTAGTTAATTTAG
1 GTTAGATTAGGGTTTTTAGTTAATTTAG
*
57690807 GTTAGATTAGGGTTTTTAATTAATTTAG
1 GTTAGATTAGGGTTTTTAGTTAATTTAG
57690835 GTTAGATTAGGG-TTTTAGTTAATTTAG
1 GTTAGATTAGGGTTTTTAGTTAATTTAG
* *
57690862 GTTAGGGTTAGGTTATGGTTTTTAGTTAATTTAT
1 GTTA--G--A--TTAGGGTTTTTAGTTAATTTAG
* *
57690896 GTTAGATTA-GGTCTTTAAATTAATTTAG
1 GTTAGATTAGGGT-TTTTAGTTAATTTAG
57690924 GTTAG
1 GTTAG
57690929 TGTTAGGTTA
Statistics
Matches: 196, Mismatches: 8, Indels: 28
0.84 0.03 0.12
Matches are distributed among these distances:
27 21 0.11
28 82 0.42
29 4 0.02
30 2 0.01
31 1 0.01
32 2 0.01
33 8 0.04
34 76 0.39
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (28 bp):
GTTAGATTAGGGTTTTTAGTTAATTTAG
Found at i:57690758 original size:17 final size:17
Alignment explanation
Indices: 57690738--57690792 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
57690728 AGTTAATTTA
57690738 GGTTAGGGTTAGATTAG
1 GGTTAGGGTTAGATTAG
***
57690755 GGTTTTTAGTTA-ATTTA-
1 GG-TTAGGGTTAGA-TTAG
57690772 GGTTAGGGTTAGATTAG
1 GGTTAGGGTTAGATTAG
57690789 GGTT
1 GGTT
57690793 TTTAGTTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
16 9 0.32
17 10 0.36
18 9 0.32
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.44
Consensus pattern (17 bp):
GGTTAGGGTTAGATTAG
Found at i:57690944 original size:62 final size:62
Alignment explanation
Indices: 57690683--57690958 Score: 334
Period size: 62 Copynumber: 4.5 Consensus size: 62
57690673 TTGGTGTAGT
57690683 GTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGG
1 GTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGG
*
57690745 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGATTAGGGTTTTTAGTTAA--T---TT
1 GTTAGATTAGGGTTTTTAATTAA--T---TTA-GGTTAGATTAGGGTTTTTAGTTAATTTAGGTT
57690805 A-G
60 AGG
57690807 GTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGG-TTTTAGTTAATTTAGGTTAGG
1 GTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGG
* * * * * * *
57690868 GTTAGGTTATGGTTTTTAGTTAATTTATGTTAGATTA-GGTCTTTAAATTAATTTAGGTTAGT
1 GTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGT-TTTTAGTTAATTTAGGTTAGG
* * *
57690930 GTTAGGTTAGGGTTTTCAATTAAATTAGG
1 GTTAGATTAGGGTTTTTAATTAATTTAGG
57690959 GTTTTTATTT
Statistics
Matches: 186, Mismatches: 14, Indels: 28
0.82 0.06 0.12
Matches are distributed among these distances:
55 10 0.05
56 13 0.07
57 4 0.02
60 6 0.03
61 34 0.18
62 87 0.47
63 3 0.02
64 1 0.01
66 1 0.01
67 3 0.02
68 24 0.13
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.48
Consensus pattern (62 bp):
GTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGG
Found at i:57690952 original size:34 final size:33
Alignment explanation
Indices: 57690683--57690945 Score: 264
Period size: 34 Copynumber: 8.5 Consensus size: 33
57690673 TTGGTGTAGT
*
57690683 GTTAGATTAGGGTTTTTAATTAA--T---TTAG
1 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
57690711 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGG
1 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTA-G
57690745 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGG
1 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTA-G
57690779 GTTAGATTAGGGTTTTTAGTTAA--T---TTAG
1 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
*
57690807 GTTAGATTAGGGTTTTTAATTAA--T---TTAG
1 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
57690835 GTTAGATTAGGG-TTTTAGTTAATTTAGGTTAGG
1 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTA-G
* *
57690868 GTTAGGTTATGGTTTTTAGTTAATTTA---T--
1 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
* *
57690896 GTTAGATTA-GGTCTTTAAATTAATTTAGGTTAG
1 GTTAGATTAGGGT-TTTTAGTTAATTTAGGTTAG
*
57690929 TGTTAGGTTAGGGTTTT
1 -GTTAGATTAGGGTTTT
57690946 CAATTAAATT
Statistics
Matches: 205, Mismatches: 9, Indels: 36
0.82 0.04 0.14
Matches are distributed among these distances:
27 12 0.06
28 82 0.40
29 4 0.02
30 1 0.00
31 2 0.01
32 4 0.02
33 14 0.07
34 83 0.40
35 3 0.01
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (33 bp):
GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
Found at i:57691037 original size:26 final size:25
Alignment explanation
Indices: 57691006--57691054 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
57690996 CTTAAAAAAT
57691006 TTCTATGCATATTACATCAAATAAAC
1 TTCTAT-CATATTACATCAAATAAAC
**
57691032 TTCTATTTTATTACATCAAATAA
1 TTCTATCATATTACATCAAATAA
57691055 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (25 bp):
TTCTATCATATTACATCAAATAAAC
Found at i:57691498 original size:18 final size:18
Alignment explanation
Indices: 57691475--57691520 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
57691465 TATTTGGAAA
* *
57691475 AGGATACATGTAAGGGTT
1 AGGATACATATAAGGGCT
57691493 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
57691511 AGGAAACATA
1 AGGATACATA
57691521 CCTGGCATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.41, C:0.09, G:0.28, T:0.22
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:57692175 original size:7 final size:7
Alignment explanation
Indices: 57692165--57692189 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
57692155 TTATATACAT
57692165 AATACTA
1 AATACTA
57692172 AATACTA
1 AATACTA
57692179 AATACTA
1 AATACTA
57692186 AATA
1 AATA
57692190 ACAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:57693301 original size:21 final size:19
Alignment explanation
Indices: 57693275--57693321 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
57693265 GATGAAAATA
57693275 TAAAAAAATTTAAAATTATTT
1 TAAAAAAA--TAAAATTATTT
*
57693296 TAAAAAAATATAATTATTT
1 TAAAAAAATAAAATTATTT
57693315 TAAAAAA
1 TAAAAAA
57693322 TGGATTTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 17 0.68
21 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAAATAAAATTATTT
Found at i:57693392 original size:22 final size:22
Alignment explanation
Indices: 57693367--57693417 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
57693357 AAATATGAGT
57693367 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
57693389 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
57693411 TTGAGAG
1 TTGAGAG
57693418 GATTAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:57700146 original size:18 final size:17
Alignment explanation
Indices: 57700119--57700152 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
57700109 AGATTTGTAA
*
57700119 AATAATATAAATATTTTT
1 AATAAAATAAA-ATTTTT
57700137 AATAAAATAAAATTTT
1 AATAAAATAAAATTTT
57700153 AAAAATATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAAAATAAAATTTTT
Found at i:57701120 original size:29 final size:29
Alignment explanation
Indices: 57701065--57701121 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
57701055 TTTAAAAAAA
* **
57701065 ATAAAAAAATTGTAAAATTTATAAAAATC
1 ATAAAAAAATTATAAAATGCATAAAAATC
*
57701094 ATAAACAAATTATAAAATGCATCAAAAA
1 ATAAAAAAATTATAAAATGCAT-AAAAA
57701122 GATCCTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (29 bp):
ATAAAAAAATTATAAAATGCATAAAAATC
Found at i:57701321 original size:10 final size:10
Alignment explanation
Indices: 57701299--57701361 Score: 62
Period size: 9 Copynumber: 6.5 Consensus size: 10
57701289 GATACGAAAA
57701299 TTTTTATAA-
1 TTTTTATAAT
57701308 TTTTTATAAT
1 TTTTTATAAT
57701318 TTTTTATAAT
1 TTTTTATAAT
*
57701328 TTTCTTACT-AC
1 TTT-TTA-TAAT
*
57701339 TTTATA-AAT
1 TTTTTATAAT
57701348 TTTTTA-AAT
1 TTTTTATAAT
57701357 TTTTT
1 TTTTT
57701362 TTCTATATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
9 23 0.50
10 15 0.33
11 7 0.15
12 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:57701395 original size:19 final size:19
Alignment explanation
Indices: 57701300--57701405 Score: 51
Period size: 19 Copynumber: 5.5 Consensus size: 19
57701290 ATACGAAAAT
*
57701300 TTTTATAATTTTT-ATAATT
1 TTTTATAATTTTTAAT-ATA
57701319 TTTTATAATTTTCT--TACTA
1 TTTTATAATTTT-TAATA-TA
* *
57701338 CTTTATAAATTTTTTAA-ATT
1 TTTTAT-AA-TTTTTAATATA
* * *
57701358 TTTTTTCTATATTTCAATATA
1 TTTTAT-AAT-TTTTAATATA
*
57701379 TTTTATAATTTTTAATAAA
1 TTTTATAATTTTTAATATA
57701398 TTTT-TAAT
1 TTTTATAAT
57701406 ATATATTTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 17
0.69 0.14 0.18
Matches are distributed among these distances:
18 5 0.08
19 32 0.48
20 17 0.26
21 12 0.18
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTAATATA
Found at i:57701415 original size:13 final size:12
Alignment explanation
Indices: 57701382--57701415 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
57701372 CAATATATTT
57701382 TATAATTTTTAA
1 TATAATTTTTAA
57701394 TA-AATTTTTAA
1 TATAATTTTTAA
57701405 TATATATTTTT
1 TATA-ATTTTT
57701416 TAAGTTGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 3 0.15
13 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATAATTTTTAA
Found at i:57706064 original size:16 final size:16
Alignment explanation
Indices: 57706027--57706066 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
57706017 TTAATAAAAT
* *
57706027 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
57706043 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
57706059 TAAAATTA
1 TAAAATTA
57706067 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:57706099 original size:59 final size:64
Alignment explanation
Indices: 57706033--57706255 Score: 268
Period size: 59 Copynumber: 3.5 Consensus size: 64
57706023 AAATTAAAAC
*
57706033 TAATTGTTATTAAAAT-T-A-A-TTG-TTAGTAAAATTATCAAATTATTAATTGTTAATTGTAT
1 TAATTGTTATTAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTGTTAATTGTAT
*
57706092 TAATTGTTGTATTAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG-T-ATT-AA
1 TAATTG-T-TATTAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTGTTAATTGTA
57706154 T
64 T
* *
57706155 T-GTTG-TAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTA
1 TAATTGTTATTAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTG--TTAATTGTA
57706218 T
64 T
**
57706219 TAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTG-T-TATTAAAATCTAACATTTGATTAGTAAA
57706256 ATAAACTTGA
Statistics
Matches: 141, Mismatches: 7, Indels: 23
0.82 0.04 0.13
Matches are distributed among these distances:
59 52 0.37
60 1 0.01
61 9 0.06
62 5 0.04
63 7 0.05
64 7 0.05
65 7 0.05
66 26 0.18
68 27 0.19
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.46
Consensus pattern (64 bp):
TAATTGTTATTAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATTGTTAATTGTAT
Found at i:57706210 original size:9 final size:9
Alignment explanation
Indices: 57706198--57706225 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
57706188 TTTATCAAAT
57706198 TATTAATTG
1 TATTAATTG
57706207 TATTAATTG
1 TATTAATTG
57706216 TATTAATTG
1 TATTAATTG
57706225 T
1 T
57706226 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:57706352 original size:18 final size:18
Alignment explanation
Indices: 57706329--57706365 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
57706319 AAACTGAAAA
57706329 TAAAAAACTAT-TATATTT
1 TAAAAAA-TATATATATTT
57706347 TAAAAAATATATATATTT
1 TAAAAAATATATATATTT
57706365 T
1 T
57706366 GTAACAGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAAAATATATATATTT
Found at i:57707751 original size:104 final size:104
Alignment explanation
Indices: 57707571--57707837 Score: 428
Period size: 104 Copynumber: 2.6 Consensus size: 104
57707561 TGTATATAAA
** * * * *
57707571 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
57707635 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
57707675 AGGGGTTGCTAAGTGTTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
57707740 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
57707779 AGGGGTTGCTAAGTGATGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
57707838 ATAACGGTTA
Statistics
Matches: 151, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
104 150 0.99
105 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGATGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:57714588 original size:20 final size:19
Alignment explanation
Indices: 57714563--57714615 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
57714553 ATCTAATTAC
*
57714563 AAATATTTAATTATTATTTT
1 AAATATTTAATTA-TAGTTT
*
57714583 AAATATTTAAATATAGTTT
1 AAATATTTAATTATAGTTT
*
57714602 ATATATTCTAATTA
1 AAATATT-TAATTA
57714616 AATTTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
AAATATTTAATTATAGTTT
Found at i:57719070 original size:50 final size:51
Alignment explanation
Indices: 57718989--57719102 Score: 169
Period size: 50 Copynumber: 2.3 Consensus size: 51
57718979 CTTACGTATG
* *
57718989 ATCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
57719039 ATCACTTGCCACTTGTCACTGATCA-ACTAAGTGTAGCTAAATCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGA-TAAGTGTAGCTAAAGCTACCACTT
57719090 ATCACTTGTCACT
1 ATCACTTGTCACT
57719103 GATCAGATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
49 1 0.02
50 33 0.58
51 23 0.40
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.32
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:57720801 original size:41 final size:41
Alignment explanation
Indices: 57720740--57720949 Score: 330
Period size: 41 Copynumber: 5.1 Consensus size: 41
57720730 ATTGGTGAAT
57720740 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
1 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
* * * *
57720781 TGAATCAGGCTACAAGCCTAGCAGGCTAAGTGCCGGTGATA
1 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
57720822 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
1 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
* * *
57720863 TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATA
1 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
* *
57720904 TTAATCAGGTTATAAACCTAGCAGGCTAAGTACCGGTGATC
1 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
*
57720945 CGAAT
1 TGAAT
57720950 ATGCTAAATT
Statistics
Matches: 151, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 151 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (41 bp):
TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
Found at i:57720870 original size:82 final size:82
Alignment explanation
Indices: 57720740--57720949 Score: 384
Period size: 82 Copynumber: 2.6 Consensus size: 82
57720730 ATTGGTGAAT
57720740 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTACAAGCCTAGCAG
1 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTACAAGCCTAGCAG
57720805 GCTAAGTGCCGGTGATA
66 GCTAAGTGCCGGTGATA
*
57720822 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
1 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTACAAGCCTAGCAG
57720887 GCTAAGTGCCGGTGATA
66 GCTAAGTGCCGGTGATA
* * *
57720904 TTAATCAGGTTATAAACCTAGCAGGCTAAGTACCGGTGATCCGAAT
1 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAAT
57720950 ATGCTAAATT
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 124 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (82 bp):
TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTACAAGCCTAGCAG
GCTAAGTGCCGGTGATA
Found at i:57725064 original size:46 final size:46
Alignment explanation
Indices: 57725014--57725105 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
57725004 AAATCTATTC
*
57725014 ATGTTATAAATGAGTTTATATGTTTTGTCAATGAATCTACTAACAT
1 ATGTTATAAATGAGTTTATATGATTTGTCAATGAATCTACTAACAT
57725060 ATGTTATAAATGAGTTTATATGATTTGTCAATGAATCTACTAACAT
1 ATGTTATAAATGAGTTTATATGATTTGTCAATGAATCTACTAACAT
57725106 GTAAGCTTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (46 bp):
ATGTTATAAATGAGTTTATATGATTTGTCAATGAATCTACTAACAT
Found at i:57731674 original size:2 final size:2
Alignment explanation
Indices: 57731667--57731691 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57731657 GGATTATTAT
57731667 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
57731692 TTGGTGGATT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:57738848 original size:25 final size:25
Alignment explanation
Indices: 57738815--57738865 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
57738805 TAAAATTTTA
57738815 ATAAATTTATAACTTATATTATTTG
1 ATAAATTTATAACTTATATTATTTG
*
57738840 ATAAATTTATAATTTATATTATTTG
1 ATAAATTTATAACTTATATTATTTG
57738865 A
1 A
57738866 ACTTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (25 bp):
ATAAATTTATAACTTATATTATTTG
Found at i:57746268 original size:31 final size:32
Alignment explanation
Indices: 57746202--57746268 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
57746192 CATTTTTGTC
* * *
57746202 AATTTGACCATCAACCTTTTAAAAATAGTTTA
1 AATTTGACCATCAACCTTTAAAAAAGAGTTCA
57746234 AATTTGACCATCAACCTTTAAAAAAGAG-TCA
1 AATTTGACCATCAACCTTTAAAAAAGAGTTCA
57746265 AATT
1 AATT
57746269 ATATATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.33
Consensus pattern (32 bp):
AATTTGACCATCAACCTTTAAAAAAGAGTTCA
Found at i:57747397 original size:31 final size:31
Alignment explanation
Indices: 57747342--57747414 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
57747332 GGCCTCCCCT
** *
57747342 TTTTGAAAATTTTTAATATTCCTTTGAAATC
1 TTTTGAAAATTTTTAATAGACCTTTAAAATC
* *
57747373 TTTTGAAACTTTTTATTAGACCTTTAAAA--
1 TTTTGAAAATTTTTAATAGACCTTTAAAATC
*
57747402 TTCTGAAAATTTT
1 TTTTGAAAATTTT
57747415 CATTATACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 11 0.31
31 24 0.69
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.51
Consensus pattern (31 bp):
TTTTGAAAATTTTTAATAGACCTTTAAAATC
Found at i:57748174 original size:21 final size:21
Alignment explanation
Indices: 57748148--57748187 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
57748138 AATATATATA
57748148 TAAATTTTCAAGTGATGACAT
1 TAAATTTTCAAGTGATGACAT
*
57748169 TAAATTTTTAAGTGATGAC
1 TAAATTTTCAAGTGATGAC
57748188 GTCGCACAAT
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:0.07, G:0.15, T:0.40
Consensus pattern (21 bp):
TAAATTTTCAAGTGATGACAT
Found at i:57750430 original size:20 final size:21
Alignment explanation
Indices: 57750401--57750439 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
57750391 CCAAAAATTT
57750401 ATTTTAAAAATTTAAAAAAGC
1 ATTTTAAAAATTTAAAAAAGC
57750422 ATTTT-AAAATTTAAAAAA
1 ATTTTAAAAATTTAAAAAA
57750440 TTTAAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (21 bp):
ATTTTAAAAATTTAAAAAAGC
Found at i:57750458 original size:11 final size:11
Alignment explanation
Indices: 57750431--57750510 Score: 64
Period size: 11 Copynumber: 7.6 Consensus size: 11
57750421 CATTTTAAAA
57750431 TTTAAAAA-A-
1 TTTAAAAATAT
57750440 TTTAAAAAGTAT
1 TTTAAAAA-TAT
57750452 TTTAAAAATAT
1 TTTAAAAATAT
57750463 TTT--AAA-A-
1 TTTAAAAATAT
* *
57750470 TTAAAAAATAA
1 TTTAAAAATAT
**
57750481 TAAAAAAAGTAT
1 TTTAAAAA-TAT
57750493 TTTAAAAATAT
1 TTTAAAAATAT
57750504 TTTAAAA
1 TTTAAAA
57750511 TTAAAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
7 2 0.03
8 1 0.02
9 14 0.24
10 1 0.02
11 24 0.41
12 16 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
TTTAAAAATAT
Found at i:57750460 original size:29 final size:29
Alignment explanation
Indices: 57750401--57750458 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
57750391 CCAAAAATTT
*
57750401 ATTTTAAAAATTTAAAAAAGCATTTTAAA
1 ATTTAAAAAATTTAAAAAAGCATTTTAAA
*
57750430 ATTTAAAAAATTT-AAAAAGTATTTTAAA
1 ATTTAAAAAATTTAAAAAAGCATTTTAAA
57750458 A
1 A
57750459 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (29 bp):
ATTTAAAAAATTTAAAAAAGCATTTTAAA
Found at i:57750473 original size:29 final size:30
Alignment explanation
Indices: 57750400--57750499 Score: 89
Period size: 29 Copynumber: 3.3 Consensus size: 30
57750390 ACCAAAAATT
*
57750400 TATTTTAAAAATTTAAAAAAGCATTTT-AAAA
1 TATTTT-AAAATTT-AAAAAGTATTTTAAAAA
**
57750431 T-TTAAAAAATTTAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAGTATTTTAAAAA
* * **
57750460 TATTTTAAAA-TTAAAAAATAATAAAAAAA
1 TATTTTAAAATTTAAAAAGTATTTTAAAAA
57750489 GTATTTTAAAA
1 -TATTTTAAAA
57750500 ATATTTTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 11 0.19
29 27 0.47
30 18 0.32
31 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (30 bp):
TATTTTAAAATTTAAAAAGTATTTTAAAAA
Found at i:57750477 original size:30 final size:30
Alignment explanation
Indices: 57750400--57750499 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 30
57750390 ACCAAAAATT
*
57750400 TATTTTAAAAATTTAAAAAAGCATTTT-AAAA
1 TATTTT-AAAA-TTAAAAAAGTATTTTAAAAA
** *
57750431 T-TTAAAAAATTTAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAGTATTTTAAAAA
* **
57750460 TATTTTAAAATTAAAAAA-TAATAAAAAAA
1 TATTTTAAAATTAAAAAAGTATTTTAAAAA
57750489 GTATTTTAAAA
1 -TATTTTAAAA
57750500 ATATTTTAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
28 13 0.23
29 17 0.30
30 25 0.45
31 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (30 bp):
TATTTTAAAATTAAAAAAGTATTTTAAAAA
Found at i:57750528 original size:41 final size:41
Alignment explanation
Indices: 57750422--57750528 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
57750412 TTAAAAAAGC
* *
57750422 ATTTTAAAATT-TAAAAAATT-TAAAAAGTATTTTAAAAAT
1 ATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAAT
57750461 ATTTTAAAATTAAAAAATAA-TAAAAAAAGTATTTTAAAAAT
1 ATTTTAAAATTAAAAAA-AATTAAAAAAAGTATTTTAAAAAT
57750502 ATTTTAAAATTAAAAAAAATTAAAAAA
1 ATTTTAAAATTAAAAAAAATTAAAAAA
57750529 TAAATATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
39 11 0.18
40 7 0.11
41 44 0.71
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (41 bp):
ATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAAT
Found at i:57751099 original size:16 final size:16
Alignment explanation
Indices: 57751078--57751109 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57751068 TACACGTGAA
57751078 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
*
57751094 AAATAATAAATTAAAT
1 AAATAATAAAATAAAT
57751110 TAAAAAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:57751400 original size:25 final size:26
Alignment explanation
Indices: 57751353--57751403 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
57751343 GACCCAACCC
* * *
57751353 ATTTTTAAAATAAACATTAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAATT
57751379 ATTTTAAAAATAAAAAATAAAAAAT
1 ATTTTAAAAATAAAAAATAAAAAAT
57751404 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
ATTTTAAAAATAAAAAATAAAAAATT
Found at i:57751413 original size:8 final size:7
Alignment explanation
Indices: 57751384--57751409 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
57751374 AAATTATTTT
57751384 AAAAATA
1 AAAAATA
57751391 AAAAATA
1 AAAAATA
57751398 AAAAATA
1 AAAAATA
57751405 AAAAA
1 AAAAA
57751410 ATAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:57756258 original size:21 final size:21
Alignment explanation
Indices: 57756202--57756259 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
57756192 CAAATAAATT
*
57756202 ACAAATTTTAAAAAAATTCAA
1 ACAAATTTTAAAAAAGTTCAA
* *
57756223 ACAAATTAT-AAAAAGTTCGTA
1 ACAAATTTTAAAAAAGTTC-AA
57756244 A-AAATTTTAAAAAAGT
1 ACAAATTTTAAAAAAGT
57756260 ATGTAGTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (21 bp):
ACAAATTTTAAAAAAGTTCAA
Found at i:57756498 original size:9 final size:9
Alignment explanation
Indices: 57756484--57756510 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
57756474 ATGCCTTTTA
57756484 CAATAAACT
1 CAATAAACT
57756493 CAATAAACT
1 CAATAAACT
57756502 CAATAAACT
1 CAATAAACT
57756511 AACTCATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (9 bp):
CAATAAACT
Found at i:57757504 original size:14 final size:15
Alignment explanation
Indices: 57757482--57757558 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
57757472 CAATCAAACA
57757482 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
57757496 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
57757511 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
57757531 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
57757545 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
57757559 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:57757523 original size:20 final size:20
Alignment explanation
Indices: 57757498--57757537 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
57757488 AATATTTTCC
*
57757498 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
57757518 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
57757538 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:57757543 original size:34 final size:35
Alignment explanation
Indices: 57757486--57757552 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
57757476 CAAACACCAG
*
57757486 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
57757521 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
57757553 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:57759532 original size:2 final size:2
Alignment explanation
Indices: 57759525--57759555 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57759515 TTGTTGGTGG
57759525 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
57759556 TACATGTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:57765147 original size:23 final size:22
Alignment explanation
Indices: 57765096--57765147 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
57765086 ATACTAATTA
* *
57765096 GAAGAAGATCTAAGGGTACACT
1 GAAGAAGATCTAAGAGAACACT
57765118 GAGAGAAGAT-TGAAGAGAACACT
1 GA-AGAAGATCT-AAGAGAACACT
57765141 CGAAGAA
1 -GAAGAA
57765148 CGCTGGCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.12
23 20 0.80
24 2 0.08
ACGTcount: A:0.46, C:0.12, G:0.29, T:0.13
Consensus pattern (22 bp):
GAAGAAGATCTAAGAGAACACT
Found at i:57788227 original size:393 final size:396
Alignment explanation
Indices: 57787484--57788272 Score: 1415
Period size: 393 Copynumber: 2.0 Consensus size: 396
57787474 TTAAAACTCC
*
57787484 ACTACCACTCTCCTCAAACAAATAAAACACTTTCACCAATCAAATACCCAGTTGCCCCCCATTTG
1 ACTACCACTCTCCTCAAACAAATAAAACACTTTCACCAATCAAATACCCAGTTACCCCCCATTTG
57787549 ACCGACCATAAACTAAAACCCCTTTTTCAAATCCTACCATTTTTTTCTTTTTACTAAGTTCCTCC
66 ACCGACCATAAACTAAAACCCCTTTTTCAAATCCTACCATTTTTTTCTTTTTACTAAGTTCCTCC
*
57787614 CTTTACCATCTTCAAAACCACCATCCACCACCTCTTTCTTTCTTTCAAACCAACCACCCCACCAT
131 CTTTACCATCTTCAAAACCACCACCCACCACCTC-TTCTTTCTTTCAAACCAACCACCCCACCAT
* * *
57787679 GGTCCGCACCAACGACTGCGCGGCACAAGAACCACCCTTAGTGGTAAACCGACGTCAACACCATT
195 GGTCCGCACCAACGACCGCGCAGCACAAGAACCACCCTCAGTGGTAAACCGACGTCAACACCATT
* * *
57787744 TCTCCGCTCCACCCTTTGGCACCATCGACTCCGATAAGTCTCTTCCATCTCCGATGCTGCAACCG
260 TCTCCGCTCCACCCTTTGGCACCATCGACTCCGATAAGTCTCCTCCATCTCCGATACTACAACCG
57787809 CGCCGTCCTAGAAGAAACTGTAGCCCAACTCCGATAGTTGTAGTCTACCCGCCCCATGAGCCACC
325 CGCCGTCCTAGAAGAAACTGTAGCCCAACTCCGATAGTTGTAGTCTACCCGCCCCATGAGCCACC
57787874 CAATTCT
390 CAATTCT
57787881 ACTACCACTCTCCTCAAACAAATAAAACACTTTCACCAATCAAATACCCAGTTACCCCCCATTTG
1 ACTACCACTCTCCTCAAACAAATAAAACACTTTCACCAATCAAATACCCAGTTACCCCCCATTTG
*
57787946 ACCTG-CCATAAACTAAAACCCTTTTTTCAAATCCTACCATTTTTTTCTTTTTACTAAGTTCCTC
66 ACC-GACCATAAACTAAAACCCCTTTTTCAAATCCTACCATTTTTTTCTTTTTACTAAGTTCCTC
57788010 CCTTTACCATCTTCAAAACCACCACCCACCA-C-C-TCTTTCTTTCAAACCAACCACCCCACCAT
130 CCTTTACCATCTTCAAAACCACCACCCACCACCTCTTCTTTCTTTCAAACCAACCACCCCACCAT
57788072 GGTCCGCACCAACGACCGCGCAGCACAAGAACCACCCTCAGTGGTAAACCGACGTCAACACCATT
195 GGTCCGCACCAACGACCGCGCAGCACAAGAACCACCCTCAGTGGTAAACCGACGTCAACACCATT
* *
57788137 TCTCCGCTCCACCCTTTGGCACCATCGACTCCGATAAGTCTCCTCTATCTCCGCTACTACAACCG
260 TCTCCGCTCCACCCTTTGGCACCATCGACTCCGATAAGTCTCCTCCATCTCCGATACTACAACCG
*
57788202 CGCTGTCCTAGAAGAAACTGTAGCCCAACTCCGATAGTTGTAGTCTACCCGCCCCATGAGCCACC
325 CGCCGTCCTAGAAGAAACTGTAGCCCAACTCCGATAGTTGTAGTCTACCCGCCCCATGAGCCACC
*
57788267 TAATTC
390 CAATTC
57788273 AGCTGACCAT
Statistics
Matches: 378, Mismatches: 13, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
393 220 0.58
395 1 0.00
396 1 0.00
397 155 0.41
398 1 0.00
ACGTcount: A:0.27, C:0.38, G:0.10, T:0.25
Consensus pattern (396 bp):
ACTACCACTCTCCTCAAACAAATAAAACACTTTCACCAATCAAATACCCAGTTACCCCCCATTTG
ACCGACCATAAACTAAAACCCCTTTTTCAAATCCTACCATTTTTTTCTTTTTACTAAGTTCCTCC
CTTTACCATCTTCAAAACCACCACCCACCACCTCTTCTTTCTTTCAAACCAACCACCCCACCATG
GTCCGCACCAACGACCGCGCAGCACAAGAACCACCCTCAGTGGTAAACCGACGTCAACACCATTT
CTCCGCTCCACCCTTTGGCACCATCGACTCCGATAAGTCTCCTCCATCTCCGATACTACAACCGC
GCCGTCCTAGAAGAAACTGTAGCCCAACTCCGATAGTTGTAGTCTACCCGCCCCATGAGCCACCC
AATTCT
Found at i:57791685 original size:25 final size:25
Alignment explanation
Indices: 57791656--57791729 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 25
57791646 TAAACTCTTT
*
57791656 CGAGCTAAATAACGGGAAGCTCATG
1 CGAGCTGAATAACGGGAAGCTCATG
* *
57791681 TGAGCTGAATAACAGGAAGCTCATG
1 CGAGCTGAATAACGGGAAGCTCATG
* *
57791706 CGAGCTGAGTATCGGGAAGCTCAT
1 CGAGCTGAATAACGGGAAGCTCAT
57791730 AAGAGCTGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.19
Consensus pattern (25 bp):
CGAGCTGAATAACGGGAAGCTCATG
Found at i:57792392 original size:25 final size:25
Alignment explanation
Indices: 57792352--57792426 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
57792342 AAAGAAATAG
* * *
57792352 AAAAAGAATGAGAGAAAGAAACGAA
1 AAAAAGAAAGAAAGAAAGAAAAGAA
* * *
57792377 ACAGAGAAGGAAAGAAAGAAAAGAA
1 AAAAAGAAAGAAAGAAAGAAAAGAA
57792402 AAAAAGAAAGAAAGAAGGAGAAAAG
1 AAAAAGAAAGAAAGAA--AGAAAAG
57792427 TTAAGGTTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 33 0.82
27 7 0.17
ACGTcount: A:0.69, C:0.03, G:0.27, T:0.01
Consensus pattern (25 bp):
AAAAAGAAAGAAAGAAAGAAAAGAA
Found at i:57792395 original size:4 final size:4
Alignment explanation
Indices: 57792354--57792417 Score: 56
Period size: 4 Copynumber: 15.5 Consensus size: 4
57792344 AGAAATAGAA
* * * * * *
57792354 AAAG AATG AGAG AAAG AAACG AAAC AGAG AAGG AAAG AAAG AAAAG AAAA
1 AAAG AAAG AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG -AAAG AAAG
57792404 AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AA
57792418 GGAGAAAAGT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
4 38 0.83
5 8 0.17
ACGTcount: A:0.70, C:0.03, G:0.25, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:57792401 original size:17 final size:16
Alignment explanation
Indices: 57792381--57792420 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
57792371 AACGAAACAG
57792381 AGAAGGAAAGAAAGAAA
1 AGAAGGAAAGAAAG-AA
**
57792398 AGAAAAAAAGAAAGAA
1 AGAAGGAAAGAAAGAA
57792414 AGAAGGA
1 AGAAGGA
57792421 GAAAAGTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
AGAAGGAAAGAAAGAA
Found at i:57792425 original size:21 final size:21
Alignment explanation
Indices: 57792335--57792417 Score: 71
Period size: 25 Copynumber: 3.7 Consensus size: 21
57792325 ATGATAAAGT
57792335 AAAAG-AA-AAAGAAATAGAAA
1 AAAAGAAAGAAAGAAA-AGAAA
* *
57792355 AAGAATGAGAGAAAGAAACGAAA
1 AA-AA-GAAAGAAAGAAAAGAAA
57792378 CAGAGAAGGAAAGAAAGAAAAGAAA
1 -A-A-AA-GAAAGAAAGAAAAGAAA
57792403 AAAAGAAAGAAAGAA
1 AAAAGAAAGAAAGAA
57792418 GGAGAAAAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 2 0.04
21 13 0.25
22 3 0.06
23 6 0.12
24 9 0.17
25 19 0.37
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.02
Consensus pattern (21 bp):
AAAAGAAAGAAAGAAAAGAAA
Found at i:57793356 original size:37 final size:38
Alignment explanation
Indices: 57793264--57793365 Score: 107
Period size: 37 Copynumber: 2.6 Consensus size: 38
57793254 ACTTCGAGCT
* *
57793264 GATGAGACATTGGGTGTCAATTTATTACTTCGGATTAATTC
1 GATGAGACATTGGGTGTCAA--T-TTACTTCAGATTAATCC
* * * * *
57793305 GATGGGGCACTGGGTGCCAATTTACTTCAGTTTAA-CC
1 GATGAGACATTGGGTGTCAATTTACTTCAGATTAATCC
57793342 GATGAGACATTGGGTGTCAATTTA
1 GATGAGACATTGGGTGTCAATTTA
57793366 TTACTTCGAA
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
37 21 0.42
38 12 0.24
39 1 0.02
41 16 0.32
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (38 bp):
GATGAGACATTGGGTGTCAATTTACTTCAGATTAATCC
Found at i:57793384 original size:40 final size:40
Alignment explanation
Indices: 57793264--57793396 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 40
57793254 ACTTCGAGCT
* * *
57793264 GATGAGACATTGGGTGTCAATTTATTACTTCGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGAATT-ATCC
* * * * *
57793305 GATGGGGCACTGGGTGCCAA--T-TTACTTC-AGTTTAACC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGA-ATTATCC
*
57793342 GATGAGACATTGGGTGTCAATTTATTACTTCGAATTATCC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGAATTATCC
*
57793382 GATGAGGCACTGGGT
1 GATGAGACACTGGGT
57793397 TCCAAACTGG
Statistics
Matches: 71, Mismatches: 16, Indels: 11
0.72 0.16 0.11
Matches are distributed among these distances:
37 18 0.25
38 9 0.13
39 2 0.03
40 25 0.35
41 17 0.24
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAATTTATTACTTCGAATTATCC
Found at i:57795104 original size:4 final size:5
Alignment explanation
Indices: 57795076--57795101 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
57795066 TGATAATAGA
57795076 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
57795102 ATTATAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:57799882 original size:2 final size:2
Alignment explanation
Indices: 57799877--57799905 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57799867 TTCAGCCTTT
57799877 TA 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 TA T
57799906 GTATTTGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57805096 original size:24 final size:24
Alignment explanation
Indices: 57805069--57805153 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
57805059 TTTTAACAAT
57805069 AATATCAATTAGACCTAAAATTCA
1 AATATCAATTAGACCTAAAATTCA
* * * *
57805093 AATATACAAAAGGTTTAAACTTCATAATTAA
1 AATAT-C--AA---TTAGACCT-AAAATTCA
57805124 TAATATCAATTAGACCTAAAATTCA
1 -AATATCAATTAGACCTAAAATTCA
57805149 AATAT
1 AATAT
57805154 ACAAAAGGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 16
0.65 0.12 0.23
Matches are distributed among these distances:
24 10 0.22
25 7 0.16
26 6 0.13
27 2 0.04
29 2 0.04
30 6 0.13
31 7 0.16
32 5 0.11
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.32
Consensus pattern (24 bp):
AATATCAATTAGACCTAAAATTCA
Found at i:57805127 original size:56 final size:56
Alignment explanation
Indices: 57805066--57805177 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
57805056 CAATTTTAAC
57805066 AATAATATCAATTAGACCTAAAATTCAAATATACAAAAGGTTTAAACTTCATAATT
1 AATAATATCAATTAGACCTAAAATTCAAATATACAAAAGGTTTAAACTTCATAATT
57805122 AATAATATCAATTAGACCTAAAATTCAAATATACAAAAGGTTTAAACTTCATAATT
1 AATAATATCAATTAGACCTAAAATTCAAATATACAAAAGGTTTAAACTTCATAATT
57805178 TAACATAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.32
Consensus pattern (56 bp):
AATAATATCAATTAGACCTAAAATTCAAATATACAAAAGGTTTAAACTTCATAATT
Found at i:57806053 original size:18 final size:19
Alignment explanation
Indices: 57806030--57806066 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
57806020 TGACCAAATG
57806030 TAAAATAAATATTT-TTAT
1 TAAAATAAATATTTATTAT
*
57806048 TAAAATAGATATTTATTAT
1 TAAAATAAATATTTATTAT
57806067 AATCATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TAAAATAAATATTTATTAT
Found at i:57806172 original size:12 final size:12
Alignment explanation
Indices: 57806155--57806185 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57806145 GAAGCAGGGG
57806155 AGAAAAAGCGAA
1 AGAAAAAGCGAA
*
57806167 AGAAAAAGGGAA
1 AGAAAAAGCGAA
57806179 AGAAAAA
1 AGAAAAA
57806186 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGCGAA
Found at i:57807712 original size:80 final size:80
Alignment explanation
Indices: 57807579--57807742 Score: 292
Period size: 80 Copynumber: 2.0 Consensus size: 80
57807569 ACTCAGCGTA
* *
57807579 CGGTTGTTTCCGTGCGCAGGTCGATAGAAGTCAAAGGTTCCGATTCAGCATCCAGATCAATCCCG
1 CGGTTGTTTCCATGCACAGGTCGATAGAAGTCAAAGGTTCCGATTCAGCATCCAGATCAATCCCG
57807644 ACTTCAACATAACTT
66 ACTTCAACATAACTT
* *
57807659 CGGTTGTTTCCATGCACAGGTCGATAGAAGTCAAAGGTTTCGGTTCAGCATCCAGATCAATCCCG
1 CGGTTGTTTCCATGCACAGGTCGATAGAAGTCAAAGGTTCCGATTCAGCATCCAGATCAATCCCG
57807724 ACTTCAACATAACTT
66 ACTTCAACATAACTT
57807739 CGGT
1 CGGT
57807743 GATGTATTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (80 bp):
CGGTTGTTTCCATGCACAGGTCGATAGAAGTCAAAGGTTCCGATTCAGCATCCAGATCAATCCCG
ACTTCAACATAACTT
Found at i:57814716 original size:18 final size:17
Alignment explanation
Indices: 57814695--57814762 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
57814685 ATAAAGAGAT
57814695 ATATAGATATATAATAAG
1 ATATA-ATATATAATAAG
57814713 ATATAAATATATAATAAG
1 ATAT-AATATATAATAAG
57814731 ATGAT-ATATATAA-ATAG
1 AT-ATAATATATAATA-AG
*
57814748 TTATAATA-ATAATAA
1 ATATAATATATAATAA
57814763 TAATAATAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
16 8 0.18
17 15 0.34
18 18 0.41
19 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (17 bp):
ATATAATATATAATAAG
Found at i:57817994 original size:13 final size:13
Alignment explanation
Indices: 57817976--57818004 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
57817966 TTGATATATT
57817976 ATTATATTTCTAG
1 ATTATATTTCTAG
57817989 ATTATATTTCTAG
1 ATTATATTTCTAG
57818002 ATT
1 ATT
57818005 GATAGTCAGC
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:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTATATTTCTAG
Found at i:57826535 original size:15 final size:15
Alignment explanation
Indices: 57826515--57826544 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
57826505 CCTGCCCCCA
57826515 TATCCAACTCGAACC
1 TATCCAACTCGAACC
57826530 TATCCAACTCGAACC
1 TATCCAACTCGAACC
57826545 CAACATAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.07, T:0.20
Consensus pattern (15 bp):
TATCCAACTCGAACC
Found at i:57846986 original size:14 final size:16
Alignment explanation
Indices: 57846965--57847002 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
57846955 GAAAAGAGAG
* *
57846965 ATTTTTTTA-AATTTT
1 ATTTTTTAATAATTAT
57846980 ATTTTTTAATAATTAT
1 ATTTTTTAATAATTAT
57846996 ATTTTTT
1 ATTTTTT
57847003 TTTTTGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTAATAATTAT
Found at i:57849848 original size:31 final size:29
Alignment explanation
Indices: 57849784--57849850 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
57849774 TTAAAATTTA
* * *
57849784 ATGTATAGAATTACACAAAATCAAATTTC
1 ATGTATACAATTACACAAAAACAAACTTC
*
57849813 ATGTATACAATTACACATTAAAACATACTTC
1 ATGTATACAATTACACA--AAAACAAACTTC
57849844 ATGTATA
1 ATGTATA
57849851 GTTTTGATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.50
31 16 0.50
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (29 bp):
ATGTATACAATTACACAAAAACAAACTTC
Found at i:57850119 original size:21 final size:22
Alignment explanation
Indices: 57850095--57850138 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
57850085 TAAAAGGTTT
* *
57850095 TAAA-AAGTTGCCAAAATTATA
1 TAAAGAAGTTACCAAAATAATA
57850116 TAAAGAAGTTACCAAAATAATA
1 TAAAGAAGTTACCAAAATAATA
57850138 T
1 T
57850139 CGCAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (22 bp):
TAAAGAAGTTACCAAAATAATA
Found at i:57851979 original size:24 final size:24
Alignment explanation
Indices: 57851952--57852039 Score: 133
Period size: 24 Copynumber: 3.7 Consensus size: 24
57851942 TTTATAGAAG
* * *
57851952 ATTTAGCATTTATGAGTATAATAT
1 ATTTAACATTTATTAGCATAATAT
57851976 ATTTAACATTTATTAGCATAATAT
1 ATTTAACATTTATTAGCATAATAT
57852000 ATTTAACATTTATTAGCATAATAT
1 ATTTAACATTTATTAGCATAATAT
57852024 ATTTAAC-TTTGATTAG
1 ATTTAACATTT-ATTAG
57852040 AATTAGGTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 3 0.05
24 57 0.95
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.47
Consensus pattern (24 bp):
ATTTAACATTTATTAGCATAATAT
Found at i:57862090 original size:34 final size:34
Alignment explanation
Indices: 57862043--57862119 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
57862033 GGCCTCACGA
* * *
57862043 TACATCAATATTCAATTATAAAGTAACTCACCATT
1 TACA-CAACATTCAACTATAAAGTAACGCACCATT
* * *
57862078 TACACAACATTCAACTATAAATTGACGCATCATT
1 TACACAACATTCAACTATAAAGTAACGCACCATT
57862112 TACACAAC
1 TACACAAC
57862120 TCCCAACCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 32 0.89
35 4 0.11
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (34 bp):
TACACAACATTCAACTATAAAGTAACGCACCATT
Found at i:57866747 original size:22 final size:22
Alignment explanation
Indices: 57866722--57866763 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
57866712 AATCCAGTGA
57866722 ATCCACCTCCAGTCCTCCACCG
1 ATCCACCTCCAGTCCTCCACCG
* *
57866744 ATCCACCTCCGGTCGTCCAC
1 ATCCACCTCCAGTCCTCCAC
57866764 AGACCACGGC
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:0.17, C:0.52, G:0.12, T:0.19
Consensus pattern (22 bp):
ATCCACCTCCAGTCCTCCACCG
Found at i:57868603 original size:13 final size:13
Alignment explanation
Indices: 57868582--57868669 Score: 113
Period size: 13 Copynumber: 6.7 Consensus size: 13
57868572 ACTAGATTAT
57868582 TATACTGTTTTAA
1 TATACTGTTTTAA
* *
57868595 TATATTGTTTTAG
1 TATACTGTTTTAA
57868608 TATACTGTTATTAA
1 TATACTGTT-TTAA
*
57868622 TATATTGTTTTAA
1 TATACTGTTTTAA
*
57868635 TATAATGTTTTAA
1 TATACTGTTTTAA
* *
57868648 TAAATTGTTTTAA
1 TATACTGTTTTAA
57868661 TATACTGTT
1 TATACTGTT
57868670 ATAAAATTAG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
13 53 0.83
14 11 0.17
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (13 bp):
TATACTGTTTTAA
Done.