Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 5 of 15
Found at i:500752 original size:12 final size:12
Alignment explanation
Indices: 500710--500760 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
500700 TATTTGTGTC
500710 ATATTCATTTTTT
1 ATATT-ATTTTTT
*
500723 ATATTATGTTTT
1 ATATTATTTTTT
500735 A-ATTATTTTTT
1 ATATTATTTTTT
*
500746 ATGTTATATTTTT
1 ATATTAT-TTTTT
500759 AT
1 AT
500761 TTTTCGTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 10 0.30
12 11 0.33
13 12 0.36
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:500763 original size:18 final size:19
Alignment explanation
Indices: 500718--500763 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
500708 TCATATTCAT
* *
500718 TTTTTATATTATGTTTTAA
1 TTTTTATTTTATGTTATAA
*
500737 TTATT-TTTTATGTTAT-A
1 TTTTTATTTTATGTTATAA
500754 TTTTTATTTT
1 TTTTTATTTT
500764 TCGTATATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 5 0.23
18 13 0.59
19 4 0.18
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTTATTTTATGTTATAA
Found at i:501700 original size:16 final size:17
Alignment explanation
Indices: 501673--501713 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
501663 ATTTTTAAAT
501673 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
501688 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
501705 AAATTTTAT
1 AAATTTTAT
501714 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:502352 original size:2 final size:2
Alignment explanation
Indices: 502345--502385 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
502335 ATATTCAAGT
502345 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
502386 TAAGAAAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:502857 original size:95 final size:95
Alignment explanation
Indices: 502746--503126 Score: 672
Period size: 95 Copynumber: 4.0 Consensus size: 95
502736 GTAATTGTGA
* * * *
502746 TGCAATAGTAAAACTCGTTTTAAAAGAAGTTAATTAGAGATTCGTGTGATCATCACGTATAGAGA
1 TGCAATAATAAAACTCGTTTTAAAAGAAGTTGATTAAAGATTAGTGTGATCATCACGTATAGAGA
* *
502811 ATAAGTCTAAATATTTTTAATATAATTCAT
66 ATAAATCTAAATACTTTTAATATAATTCAT
502841 TGCAATAATAAAACTCGTTTTAAAAGAAGTTGATTAAAGATTAGTGTGATCATCACGTATAGAGA
1 TGCAATAATAAAACTCGTTTTAAAAGAAGTTGATTAAAGATTAGTGTGATCATCACGTATAGAGA
502906 ATAAATCTAAATACTTTTAATATAATTCAT
66 ATAAATCTAAATACTTTTAATATAATTCAT
502936 TGCAATAATAAAACTCGTTTTAAAAGAAGTTGATTAAAGATTAGTGTGATCATCACGTATAGAGA
1 TGCAATAATAAAACTCGTTTTAAAAGAAGTTGATTAAAGATTAGTGTGATCATCACGTATAGAGA
503001 ATAAATCTAAATACTTTTAATATAATTCAT
66 ATAAATCTAAATACTTTTAATATAATTCAT
* * * *
503031 TGTAATAATAAAACTCGTTTTAAAATAAGTTGATTAAAGACTAGTGTGATCATTACGTATAGAGA
1 TGCAATAATAAAACTCGTTTTAAAAGAAGTTGATTAAAGATTAGTGTGATCATCACGTATAGAGA
503096 ATAAATCTAAATACTTTTAATATAATTCAT
66 ATAAATCTAAATACTTTTAATATAATTCAT
503126 T
1 T
503127 ATTTATTATT
Statistics
Matches: 276, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 276 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (95 bp):
TGCAATAATAAAACTCGTTTTAAAAGAAGTTGATTAAAGATTAGTGTGATCATCACGTATAGAGA
ATAAATCTAAATACTTTTAATATAATTCAT
Found at i:503670 original size:22 final size:22
Alignment explanation
Indices: 503640--503682 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
503630 TCATGATTAA
*
503640 TTATGTTATAAAGATACAATTC
1 TTATATTATAAAGATACAATTC
*
503662 TTATATTATAAAGATATAATT
1 TTATATTATAAAGATACAATT
503683 TTTACATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (22 bp):
TTATATTATAAAGATACAATTC
Found at i:504325 original size:25 final size:25
Alignment explanation
Indices: 504278--504359 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
504268 CTTAAATTAT
*
504278 AATTTAATAAAAAAATTTTATTTTA
1 AATTTAATAAAAAAATTTAATTTTA
*
504303 AATTTAATTATAAAAA-TTAA-TTTA
1 AATTTAA-TAAAAAAATTTAATTTTA
*
504327 TTATTT-ATAAATAATAATTTAAATTTTTA
1 -AATTTAATAAA-AA-AATTT-AA-TTTTA
504356 AATT
1 AATT
504360 CGTTCAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
23 3 0.07
24 7 0.16
25 16 0.36
26 9 0.20
27 2 0.05
28 3 0.07
29 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTTAATAAAAAAATTTAATTTTA
Found at i:509047 original size:45 final size:45
Alignment explanation
Indices: 508982--509070 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
508972 TAATATCTTC
*
508982 TTGGATGTTCAAAACCAGAGGAAAAAATTTATTGTCAATTGAGTT
1 TTGGATGTTCAAAACCAGAGGAAAAAATTTATTCTCAATTGAGTT
**
509027 TTGGATGTTCAAAATGAGAGGAAAAAATTTATTCTCAATTGAGT
1 TTGGATGTTCAAAACCAGAGGAAAAAATTTATTCTCAATTGAGT
509071 AAATATGAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (45 bp):
TTGGATGTTCAAAACCAGAGGAAAAAATTTATTCTCAATTGAGTT
Found at i:509090 original size:7 final size:7
Alignment explanation
Indices: 509078--509130 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
509068 AGTAAATATG
509078 AAGGAAA
1 AAGGAAA
509085 AAGGAAA
1 AAGGAAA
*
509092 AAGAAAA
1 AAGGAAA
509099 AAGAGAAA
1 AAG-GAAA
*
509107 AAAGAAA
1 AAGGAAA
*
509114 GAAAGAAA
1 -AAGGAAA
*
509122 AAGCAAA
1 AAGGAAA
509129 AA
1 AA
509131 AGAGTAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
7 27 0.69
8 12 0.31
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (7 bp):
AAGGAAA
Found at i:509130 original size:8 final size:7
Alignment explanation
Indices: 509082--509133 Score: 52
Period size: 8 Copynumber: 7.0 Consensus size: 7
509072 AATATGAAGG
*
509082 AAAAAGG
1 AAAAAGA
509089 AAAAAGAA
1 AAAAAG-A
509097 AAAAGAGA
1 AAAA-AGA
509105 AAAAAGA
1 AAAAAGA
509112 AAGAAAG-
1 AA-AAAGA
509119 AAAAAGCA
1 AAAAAG-A
509127 AAAAAGA
1 AAAAAGA
509134 GTAAGAAAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
6 4 0.10
7 14 0.36
8 19 0.49
9 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:509131 original size:24 final size:23
Alignment explanation
Indices: 509082--509143 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
509072 AATATGAAGG
* *
509082 AAAAAGGAA-AAAGAAAAAAGAGA
1 AAAAAGAAAGAAAG-AAAAAGAAA
509105 AAAAAGAAAGAAAGAAAAAGCAAA
1 AAAAAGAAAGAAAGAAAAAG-AAA
* *
509129 AAAGAGTAAGAAAGA
1 AAAAAGAAAGAAAGA
509144 GTTCTTCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.02
Consensus pattern (23 bp):
AAAAAGAAAGAAAGAAAAAGAAA
Found at i:509939 original size:58 final size:58
Alignment explanation
Indices: 509846--509987 Score: 173
Period size: 58 Copynumber: 2.4 Consensus size: 58
509836 ACATCTAGGG
* * * *
509846 TTTTCTAGAAAATTTCAT-CATTTTAAGGTTATTTAGGTCATTTTAC-ATAATCTAAGA
1 TTTTTTAGAAATTTTCATGCATTTTAAGATTATTTAGGTCACTTT-CTATAATCTAAGA
* *
509903 TTTTTTAGAAATTTTCATGCATTTTAAGATTATTTAGGTTACTTTCTATAATCTAAGG
1 TTTTTTAGAAATTTTCATGCATTTTAAGATTATTTAGGTCACTTTCTATAATCTAAGA
*
509961 TTTTTTTGACAATATTT-ATGCATTTTA
1 TTTTTTAGA-AAT-TTTCATGCATTTTA
509988 GGACCATTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
57 17 0.23
58 41 0.55
59 13 0.18
60 3 0.04
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (58 bp):
TTTTTTAGAAATTTTCATGCATTTTAAGATTATTTAGGTCACTTTCTATAATCTAAGA
Found at i:510129 original size:131 final size:129
Alignment explanation
Indices: 509877--510119 Score: 287
Period size: 131 Copynumber: 1.9 Consensus size: 129
509867 TTTAAGGTTA
* * *
509877 TTTAGGTCATTTTACATAATCTAAGATTTTTTAGAAATTTTCATGCATTTTAAGATTATTTAGGT
1 TTTAGGTCATTTTACATAATCTAAGATTTTTTAGAAACTTTCATGCATTTTAAGACTATATAGGT
* *
509942 TACTTTCTATAATCTAAGGTTTTTTTGACAATATTTATGCATTTTAGGACCATTTAGGTGATTG
66 TACTTTCTATAATCTAAGGTTTTTTAGACAATATTTATACATTTTAGGACCATTTAGGTGATTG
* * ** * *
510006 TTTAGGTTATTTTACATAATTTAAGATTTTTTTTACTACTTTCTATGTATTTTACA-ACTATATA
1 TTTAGGTCATTTTACATAATCTAAGATTTTTTAGA-AACTTTC-ATGCATTTTA-AGACTATATA
* *
510070 GGTTATTTTACT-TAATCTAGGGTCTTTTTAG-CAAT-TTTCATACATTTTAG
63 GGTTACTTT-CTATAATCTAAGGT-TTTTTAGACAATATTT-ATACATTTTAG
510120 ATTTATTTAG
Statistics
Matches: 95, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
129 31 0.33
130 8 0.08
131 47 0.49
132 9 0.09
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (129 bp):
TTTAGGTCATTTTACATAATCTAAGATTTTTTAGAAACTTTCATGCATTTTAAGACTATATAGGT
TACTTTCTATAATCTAAGGTTTTTTAGACAATATTTATACATTTTAGGACCATTTAGGTGATTG
Found at i:510202 original size:58 final size:58
Alignment explanation
Indices: 510054--510277 Score: 202
Period size: 58 Copynumber: 3.8 Consensus size: 58
510044 CTTTCTATGT
* * * * * *
510054 ATTTTACAACTATATAGGTTATTTTACTTAATCTAGGGTCTTTTTAGC-AATTTTCATAC
1 ATTTTAGAACTATTTAAGTTATTTTACATAATCTAAGGTCATTTTAGCAAATTTT-AT-C
** * *
510113 ATTTTAGATTTATTT-AGATTATTTAACATAATCTAAGGTCATTTTAGCAAATTTTATT
1 ATTTTAGAACTATTTAAG-TTATTTTACATAATCTAAGGTCATTTTAGCAAATTTTATC
* * * * **
510171 ATTTTAGAATTATTTAAGTTATTTTATATAATTTAGGGTCATTTTAGCAAATTCCATC
1 ATTTTAGAACTATTTAAGTTATTTTACATAATCTAAGGTCATTTTAGCAAATTTTATC
* * * * *
510229 ATATTAGGACCATTTAAGTTATTTTACATAATAT-AGGATCACTTTAGCA
1 ATTTTAGAACTATTTAAGTTATTTTACATAATCTAAGG-TCATTTTAGCA
510278 TTTTTTGTGA
Statistics
Matches: 135, Mismatches: 26, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
57 2 0.01
58 86 0.64
59 41 0.30
60 6 0.04
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (58 bp):
ATTTTAGAACTATTTAAGTTATTTTACATAATCTAAGGTCATTTTAGCAAATTTTATC
Found at i:515297 original size:21 final size:21
Alignment explanation
Indices: 515271--515311 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
515261 TTGTCTCCGC
515271 TCGACAGACCAAAAGAAACAT
1 TCGACAGACCAAAAGAAACAT
515292 TCGACAGACCAAAAGAAACA
1 TCGACAGACCAAAAGAAACA
515312 ATAATCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.24, G:0.15, T:0.07
Consensus pattern (21 bp):
TCGACAGACCAAAAGAAACAT
Found at i:517452 original size:47 final size:46
Alignment explanation
Indices: 517400--517493 Score: 111
Period size: 47 Copynumber: 2.0 Consensus size: 46
517390 TATTTTACTA
* *
517400 TTTAAAAT-ATTATTTTATATCAATATAAA-AATATTTTATAATTAAAT
1 TTTAAAATAAATATTTT-TATCAAT-TAAATAATAATTTA-AATTAAAT
* *
517447 TTTAAAATAAATATTTTTATTAATTAAATAATAATTTAAATTGAAT
1 TTTAAAATAAATATTTTTATCAATTAAATAATAATTTAAATTAAAT
517493 T
1 T
517494 AATTCAACTC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
46 12 0.29
47 22 0.54
48 7 0.17
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (46 bp):
TTTAAAATAAATATTTTTATCAATTAAATAATAATTTAAATTAAAT
Found at i:517712 original size:22 final size:24
Alignment explanation
Indices: 517673--517717 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
517663 CTTTTTCTTC
**
517673 GTTTATTTTTTCTATTGT-TTTTA
1 GTTTATTTTTAATATTGTATTTTA
517696 GTTTATTTTTAAT-TTGTATTTT
1 GTTTATTTTTAATATTGTATTTT
517718 TTATTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (24 bp):
GTTTATTTTTAATATTGTATTTTA
Found at i:518042 original size:53 final size:53
Alignment explanation
Indices: 517958--518065 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 53
517948 TTTTCTCCCA
* *
517958 CTGTTATTCTTTTTTCATCTAATTAAATTAAATATCAAAATACGTTCTTCAAT
1 CTGTTATTCTCTTTCCATCTAATTAAATTAAATATCAAAATACGTTCTTCAAT
* * * * *
518011 CTGTTATTCTCTTTCCATCTAGTTTAGTTAAATATCAAAATACGTTTTTGAAT
1 CTGTTATTCTCTTTCCATCTAATTAAATTAAATATCAAAATACGTTCTTCAAT
518064 CT
1 CT
518066 CAATTCTGAC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (53 bp):
CTGTTATTCTCTTTCCATCTAATTAAATTAAATATCAAAATACGTTCTTCAAT
Found at i:518150 original size:2 final size:2
Alignment explanation
Indices: 518143--518172 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
518133 TAGTTGAATG
518143 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
518173 TCCATGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:522628 original size:22 final size:23
Alignment explanation
Indices: 522591--522656 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 23
522581 ATTAATTTTG
*
522591 TTAATTTTTTA--AAATA-TAAA
1 TTAATTTTTTATTTAATATTAAA
*
522611 TTAATTTTTTATTTAATATTTAA
1 TTAATTTTTTATTTAATATTAAA
* *
522634 -TAATTTTATATTT-TTATTAAA
1 TTAATTTTTTATTTAATATTAAA
522655 TT
1 TT
522657 TTTATATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 11 0.30
21 6 0.16
22 17 0.46
23 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTAATTTTTTATTTAATATTAAA
Found at i:522636 original size:27 final size:28
Alignment explanation
Indices: 522606--522660 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
522596 TTTTTAAAAT
*
522606 ATAAATTAAT-TTTTTATTTAATATTTA
1 ATAAATTAATATTTTTATTAAATATTTA
* * *
522633 ATAATTTTATATTTTTATTAAATTTTTA
1 ATAAATTAATATTTTTATTAAATATTTA
522661 TATATAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATAAATTAATATTTTTATTAAATATTTA
Found at i:523268 original size:19 final size:19
Alignment explanation
Indices: 523246--523284 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
523236 CTTAATTTTT
*
523246 ATATTTGAT-TTTAATTTAA
1 ATATTT-ATATTTAAATTAA
523265 ATATTTATATTTAAATTAA
1 ATATTTATATTTAAATTAA
523284 A
1 A
523285 ATTGAGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATATTTATATTTAAATTAA
Found at i:523948 original size:23 final size:23
Alignment explanation
Indices: 523921--523976 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
523911 AAATGATCTA
523921 AACTCGAAATGA-TTCAGATAATT
1 AACTCGAAATGACTT-AGATAATT
*
523944 AACTCGAAGTGACTTAGATAATT
1 AACTCGAAATGACTTAGATAATT
523967 AACTCGAAAT
1 AACTCGAAAT
523977 AAACTAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (23 bp):
AACTCGAAATGACTTAGATAATT
Found at i:527296 original size:21 final size:21
Alignment explanation
Indices: 527270--527313 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
527260 TTACCCAAAA
527270 ATAGTTATGATCTCTACAAGC
1 ATAGTTATGATCTCTACAAGC
527291 ATAGTTATGATCTCTACAAGC
1 ATAGTTATGATCTCTACAAGC
527312 AT
1 AT
527314 CTTTTAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
ATAGTTATGATCTCTACAAGC
Found at i:528069 original size:35 final size:37
Alignment explanation
Indices: 528022--528091 Score: 101
Period size: 35 Copynumber: 1.9 Consensus size: 37
528012 ATTATAAAAT
528022 AATATTTAATATTAATT-TAA-TTTTTAAAAATTTAA
1 AATATTTAATATTAATTATAATTTTTTAAAAATTTAA
528057 AATA-TTACATATTAATTATAATTTTTTTAAAAATT
1 AATATTTA-ATATTAATTATAA-TTTTTTAAAAATT
528092 GATTACGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 3 0.10
35 13 0.42
36 3 0.10
38 12 0.39
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (37 bp):
AATATTTAATATTAATTATAATTTTTTAAAAATTTAA
Found at i:528226 original size:2 final size:2
Alignment explanation
Indices: 528219--528243 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
528209 TTTACCAAAT
528219 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
528244 CTATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:529321 original size:19 final size:18
Alignment explanation
Indices: 529290--529334 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
529280 AAAAATATTA
* *
529290 AAAAATTATTTTTATATT
1 AAAATTTATTTTTATAAT
*
529308 AATATTTATATTTTATAAT
1 AAAATTTAT-TTTTATAAT
529327 AAAATTTA
1 AAAATTTA
529335 AATAAAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAAATTTATTTTTATAAT
Found at i:530783 original size:64 final size:65
Alignment explanation
Indices: 530703--530834 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 65
530693 AATTAATTAT
*
530703 ATTAAGATAGGTTTAATTAT-AAGCTGTAATTTTATTTAAGTTTAAAGATAAAATAGTCTAAAAA
1 ATTAAGATAGGTTTAATT-TCAAGCTATAATTTTATTTAAGTTTAAAGATAAAATAGTCTAAAAA
530767 C
65 C
* *
530768 ATTAA-ATAGGTTTAATTTCAAGTTATAATTTTGTTTAAGTTTAAAGATAAAATAGTCTAAAAAC
1 ATTAAGATAGGTTTAATTTCAAGCTATAATTTTATTTAAGTTTAAAGATAAAATAGTCTAAAAAC
530832 ATT
1 ATT
530835 TAAAATGAGG
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
63 1 0.02
64 57 0.90
65 5 0.08
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (65 bp):
ATTAAGATAGGTTTAATTTCAAGCTATAATTTTATTTAAGTTTAAAGATAAAATAGTCTAAAAAC
Found at i:532509 original size:2 final size:2
Alignment explanation
Indices: 532502--532535 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
532492 AGCCTAATTC
*
532502 AT AT AT AT AT AT GT 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
532536 CCTTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:534334 original size:21 final size:21
Alignment explanation
Indices: 534310--534349 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
534300 AATTTATCCA
534310 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
534331 AATGTATCGATACATTTGT
1 AATGTATCGATACATTTGT
534350 GGATACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:534437 original size:19 final size:19
Alignment explanation
Indices: 534413--534480 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
534403 AATTCAACAA
534413 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
534432 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
534447 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
534464 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
534481 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:534452 original size:13 final size:13
Alignment explanation
Indices: 534434--534458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534424 ACATAAGTTT
534434 TGTATCGATACAA
1 TGTATCGATACAA
534447 TGTATCGATACA
1 TGTATCGATACA
534459 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:534456 original size:32 final size:32
Alignment explanation
Indices: 534415--534477 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
534405 TTCAACAATT
*
534415 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
534447 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
534478 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:534538 original size:13 final size:13
Alignment explanation
Indices: 534520--534545 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
534510 CATTTTTCTG
534520 TGTATCGATACAT
1 TGTATCGATACAT
534533 TGTATCGATACAT
1 TGTATCGATACAT
534546 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:534542 original size:33 final size:33
Alignment explanation
Indices: 534500--534566 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
534490 GCCAAGGAAA
***
534500 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
534533 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
534566 T
1 T
534567 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:537110 original size:31 final size:28
Alignment explanation
Indices: 537027--537099 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
537017 TTTCACAATC
* * ***
537027 GGGGATACTCCAACACCGTTA-ATCATC
1 GGGGATACTCCAACCCCGTTATTTCCGA
537054 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCCGA
537082 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
537100 ACTTTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 20 0.50
28 20 0.50
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.21
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCGA
Found at i:537147 original size:52 final size:52
Alignment explanation
Indices: 537082--537256 Score: 226
Period size: 52 Copynumber: 3.3 Consensus size: 52
537072 TTATTTCCGA
* **
537082 GGGGATACTCCAACCCCGACTTTATTTCCAAAATACTGATTTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCCACAATC
* * * **
537134 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCC-ACAATC
* *
537187 GGGGATACTCCAACTCCGATTTTATTTTCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACCCCGATTTTA-TTTCCAAAATACCAATTTTTCCACAATC
*
537239 GAGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
537257 TTAATCATCG
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
52 60 0.58
53 27 0.26
54 17 0.16
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCCACAATC
Found at i:537280 original size:212 final size:211
Alignment explanation
Indices: 536909--537362 Score: 687
Period size: 212 Copynumber: 2.1 Consensus size: 211
536899 AGTTTCTCAA
* * * * *
536909 TTCTCCACAATTGGGGATATTTCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGG
1 TTCTCCACAATTGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
*
536974 GGATACTCCAACTCCGATTTTATTTCCAAAAAAAACACCAAATTTTCACAATCGGGGATACTCCA
66 GGATACTCCAACTCCGATTTTATTTCC--AAAAAACACCAAATTTTCACAATCGAGGATACTCCA
*
537039 ACACCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTT
129 ACACCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGACTT
*
537104 TATTTCCAAAATACTGAT
194 TATTCCCAAAATACTGAT
* * * *
537122 TTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTCCTTTAATC
1 TTCTCCACAATTGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA-TTTT-CTATAATC
* * *
537187 GGGGATACTCCAACTCCGATTTTATTTTC-AAAAATACCAATTTTTCACAATCGAGGATACTCCA
64 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCA
* * *
537251 ACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGACACTCCAACCCCGGCTT
129 ACACCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGACTT
537316 TATTCCCAAAATACTGAT
194 TATTCCCAAAATACTGAT
*
537334 TTCT-CATAATTGGGGATACTCCAACCCCG
1 TTCTCCACAATTGGGGATACTCCAACCCCG
537363 TTATTTTCGA
Statistics
Matches: 218, Mismatches: 21, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
211 23 0.11
212 113 0.52
213 43 0.20
214 4 0.02
215 35 0.16
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.30
Consensus pattern (211 bp):
TTCTCCACAATTGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAAC
ACCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGACTTTA
TTCCCAAAATACTGAT
Found at i:537306 original size:28 final size:27
Alignment explanation
Indices: 537245--537311 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
537235 AATCGAGGAT
* *
537245 ACTCCAACCCCGTTAATCATCGGGGAT
1 ACTCCAACCCCGTTAATCATAGGGGAC
*
537272 ACTCCAACCCCGTTATTTC-TGAGGGGAC
1 ACTCCAACCCCGTTA-ATCAT-AGGGGAC
537300 ACTCCAACCCCG
1 ACTCCAACCCCG
537312 GCTTTATTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (27 bp):
ACTCCAACCCCGTTAATCATAGGGGAC
Found at i:537447 original size:78 final size:79
Alignment explanation
Indices: 537265--537468 Score: 234
Period size: 78 Copynumber: 2.6 Consensus size: 79
537255 CGTTAATCAT
*
537265 CGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAATA
1 CGGGGATACTCCAACCCCGTTATTTTC-GAGGGGACACTCCAACCCCGACTTTATTCCCAAAATA
* *
537329 CTGATTTCTCATAAT
65 CTGATTTCTCACAAC
* * * * * * * *
537344 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTCTAATCAT-
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAA-AATA
*
537408 C-GATTTTTCACAAC
65 CTGATTTCTCACAAC
* * *
537422 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCG
537469 TTATTATCTC
Statistics
Matches: 105, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
78 51 0.49
79 48 0.46
80 6 0.06
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAAAATAC
TGATTTCTCACAAC
Found at i:538776 original size:99 final size:97
Alignment explanation
Indices: 538605--538793 Score: 227
Period size: 99 Copynumber: 1.9 Consensus size: 97
538595 TTTGTGTCTT
* * * * ** * ** *
538605 TGTCAGATCCACGAGGAAGCTATATGGGTATGAGTGTCACATGAATGTATCAAATGTGAGTGTTC
1 TGTCAGATCCACGAGGAAGCCATATAGGTATAAGTGTCAAACCAATGTACCAAATACGAGTATTC
538670 TTAATTTTTTAAAGTTTTGTTATATTTAAAAAAA
66 TTAATTTTTT-AA-TTTTGTTATATTTAAAAAAA
* *
538704 TGTCAGATCCACGAGTAGGCCATATAGGTATAAGTGTCAAACCAATGTACCAAATACGAGTATT-
1 TGTCAGATCCACGAGGAAGCCATATAGGTATAAGTGTCAAACCAATGTACCAAATACGAGTATTC
*
538768 TTCAATTTTTTAATTTTTTTATATTT
66 TT-AATTTTTTAATTTTGTTATATTT
538794 GAAAGATCTT
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
97 12 0.16
98 4 0.05
99 60 0.79
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (97 bp):
TGTCAGATCCACGAGGAAGCCATATAGGTATAAGTGTCAAACCAATGTACCAAATACGAGTATTC
TTAATTTTTTAATTTTGTTATATTTAAAAAAA
Found at i:539528 original size:20 final size:20
Alignment explanation
Indices: 539503--539614 Score: 81
Period size: 20 Copynumber: 6.3 Consensus size: 20
539493 ACCTAGATGT
*
539503 TCGATAAAAATTGTATTGTA
1 TCGATAAAAATTGCATTGTA
* *
539523 TCGAT--ATATTGTATTG-A
1 TCGATAAAAATTGCATTGTA
*
539540 T--A--AAAATTACATTGTA
1 TCGATAAAAATTGCATTGTA
*
539556 TTGATAAAAATTGCATTGTA
1 TCGATAAAAATTGCATTGTA
539576 TCGAT----A---CATTGTA
1 TCGATAAAAATTGCATTGTA
539589 TCGATAAAAATTGCATTGTA
1 TCGATAAAAATTGCATTGTA
539609 TCGATA
1 TCGATA
539615 CAACTTGCTT
Statistics
Matches: 73, Mismatches: 6, Indels: 26
0.70 0.06 0.25
Matches are distributed among these distances:
13 12 0.16
15 9 0.12
16 3 0.04
17 3 0.04
18 11 0.15
20 35 0.48
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (20 bp):
TCGATAAAAATTGCATTGTA
Found at i:539584 original size:33 final size:33
Alignment explanation
Indices: 539547--539616 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
539537 TGATAAAAAT
*
539547 TACATTGTATTGATAAAAATTGCATTGTATCGA
1 TACATTGTATCGATAAAAATTGCATTGTATCGA
539580 TACATTGTATCGATAAAAATTGCATTGTATCGA
1 TACATTGTATCGATAAAAATTGCATTGTATCGA
539613 TACA
1 TACA
539617 ACTTGCTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (33 bp):
TACATTGTATCGATAAAAATTGCATTGTATCGA
Found at i:539587 original size:13 final size:13
Alignment explanation
Indices: 539569--539594 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
539559 ATAAAAATTG
539569 CATTGTATCGATA
1 CATTGTATCGATA
539582 CATTGTATCGATA
1 CATTGTATCGATA
539595 AAAATTGCAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:539622 original size:20 final size:20
Alignment explanation
Indices: 539530--539614 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
539520 GTATCGATAT
* *
539530 ATTGTATTGATAAAAATTAC
1 ATTGTATCGATAAAAATTGC
*
539550 ATTGTATTGATAAAAATTGC
1 ATTGTATCGATAAAAATTGC
539570 ATTGTATCGAT----A---C
1 ATTGTATCGATAAAAATTGC
539583 ATTGTATCGATAAAAATTGC
1 ATTGTATCGATAAAAATTGC
539603 ATTGTATCGATA
1 ATTGTATCGATA
539615 CAACTTGCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
13 12 0.21
16 1 0.02
17 1 0.02
20 42 0.75
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (20 bp):
ATTGTATCGATAAAAATTGC
Found at i:539636 original size:53 final size:53
Alignment explanation
Indices: 539503--539614 Score: 179
Period size: 53 Copynumber: 2.1 Consensus size: 53
539493 ACCTAGATGT
* * *
539503 TCGATAAAAATTGTATTGTATCGATATATTGTATTGATAAAAATTACATTGTA
1 TCGATAAAAATTGCATTGTATCGATACATTGTATCGATAAAAATTACATTGTA
* *
539556 TTGATAAAAATTGCATTGTATCGATACATTGTATCGATAAAAATTGCATTGTA
1 TCGATAAAAATTGCATTGTATCGATACATTGTATCGATAAAAATTACATTGTA
539609 TCGATA
1 TCGATA
539615 CAACTTGCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (53 bp):
TCGATAAAAATTGCATTGTATCGATACATTGTATCGATAAAAATTACATTGTA
Found at i:539721 original size:21 final size:20
Alignment explanation
Indices: 539695--539748 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
539685 GTAACGATAC
*
539695 ATTGTATCAATACATGATTA-A
1 ATTGTATCAATACATCA--AGA
* *
539716 ATTGTATCGATATATCAAGA
1 ATTGTATCAATACATCAAGA
539736 ATTGTATCAATAC
1 ATTGTATCAATAC
539749 GTGTGGCCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.04
20 12 0.44
21 14 0.52
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (20 bp):
ATTGTATCAATACATCAAGA
Found at i:540236 original size:34 final size:34
Alignment explanation
Indices: 540178--540302 Score: 171
Period size: 34 Copynumber: 3.6 Consensus size: 34
540168 TGAGAGATTC
* *
540178 TATCTTAGCCTTTGAAAAAGATAGGGA-AAGGGTTT
1 TATCTTAGCCTGTG-AAAAGATAGGGAGAA-AGTTT
*
540213 TATCTTAGCCTGTGAAAAGATAGGGAGAAAGTTC
1 TATCTTAGCCTGTGAAAAGATAGGGAGAAAGTTT
* *
540247 TATCTTAGCTTGCGAAAAGATAGGGAGAAAGTTT
1 TATCTTAGCCTGTGAAAAGATAGGGAGAAAGTTT
*
540281 TATCTTAGCTTGTGAAAAGATA
1 TATCTTAGCCTGTGAAAAGATA
540303 AGGTTGTAAG
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
34 67 0.82
35 15 0.18
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (34 bp):
TATCTTAGCCTGTGAAAAGATAGGGAGAAAGTTT
Found at i:540285 original size:68 final size:69
Alignment explanation
Indices: 540175--540302 Score: 190
Period size: 68 Copynumber: 1.9 Consensus size: 69
540165 GATTGAGAGA
*
540175 TTCTATCTTAGCCTTTGAAAAAGATAGGGAAAGGGTTTTATCTTAGCCTGTGAAAAGATAGGGAG
1 TTCTATCTTAGCCTTTGAAAAAGATAGGGAAAGAGTTTTATCTTAGCCTGTGAAAAGATAGGGAG
540240 AAAG
66 AAAG
* *
540244 TTCTATCTTAG-C-TTGCGAAAAGATAGGGAGAA-AGTTTTATCTTAGCTTGTGAAAAGATA
1 TTCTATCTTAGCCTTTG-AAAAAGATAGGGA-AAGAGTTTTATCTTAGCCTGTGAAAAGATA
540303 AGGTTGTAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
67 3 0.06
68 38 0.70
69 13 0.24
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (69 bp):
TTCTATCTTAGCCTTTGAAAAAGATAGGGAAAGAGTTTTATCTTAGCCTGTGAAAAGATAGGGAG
AAAG
Found at i:543087 original size:48 final size:49
Alignment explanation
Indices: 542996--543103 Score: 139
Period size: 48 Copynumber: 2.2 Consensus size: 49
542986 TTTGCTCAAA
* *
542996 GTATCAATACTTCTAGATTTCTCTAGTATGTATCGATACAAAGCAAAAT
1 GTATCGATACATCTAGATTTCTCTAGTATGTATCGATACAAAGCAAAAT
* * **
543045 GTATCGATACATCTAGGTTT-TCTAG-ATTGTATCGATATAAAGCAACTT
1 GTATCGATACATCTAGATTTCTCTAGTA-TGTATCGATACAAAGCAAAAT
543093 GTATCGATACA
1 GTATCGATACA
543104 ATGTATCGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
47 1 0.02
48 34 0.65
49 17 0.33
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (49 bp):
GTATCGATACATCTAGATTTCTCTAGTATGTATCGATACAAAGCAAAAT
Found at i:543110 original size:13 final size:13
Alignment explanation
Indices: 543092--543117 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
543082 TAAAGCAACT
543092 TGTATCGATACAA
1 TGTATCGATACAA
543105 TGTATCGATACAA
1 TGTATCGATACAA
543118 CTTTGAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:544431 original size:20 final size:20
Alignment explanation
Indices: 544406--544455 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
544396 ACACCCTAGA
544406 TGTATCGATAAAAATTGCAT
1 TGTATCGATAAAAATTGCAT
* * *
544426 TGTATCGATACAACTTGCGT
1 TGTATCGATAAAAATTGCAT
*
544446 TGTATTGATA
1 TGTATCGATA
544456 TACTATGGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (20 bp):
TGTATCGATAAAAATTGCAT
Found at i:544521 original size:13 final size:13
Alignment explanation
Indices: 544503--544530 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
544493 CTACCCTTCA
544503 ATTGTATCGATAC
1 ATTGTATCGATAC
544516 ATTGTATCGATAC
1 ATTGTATCGATAC
544529 AT
1 AT
544531 GATTAAATTG
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:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:544542 original size:21 final size:20
Alignment explanation
Indices: 544516--544571 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
544506 GTATCGATAC
*
544516 ATTGTATCGATACATGATTA-A
1 ATTGTATCGATACATCA--AGA
* *
544537 ATTGTATCAATATATCAAGA
1 ATTGTATCGATACATCAAGA
544557 ATTGTATCGATACAT
1 ATTGTATCGATACAT
544572 ATGGCCTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 14 0.48
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (20 bp):
ATTGTATCGATACATCAAGA
Found at i:545037 original size:35 final size:35
Alignment explanation
Indices: 544990--545083 Score: 136
Period size: 34 Copynumber: 2.7 Consensus size: 35
544980 AAAGTGATTG
* *
544990 AGAGGTTCTATCTTAGCTTATGAAAAAGATAGGAA
1 AGAGGTTCTATCTTAGCCTATGAAAAAGACAGGAA
* *
545025 AGAGGTTTTATCTTAGCCTATG-AAAAGACAGGGA
1 AGAGGTTCTATCTTAGCCTATGAAAAAGACAGGAA
*
545059 AGATGTTCTATCTTAGCCTATGAAA
1 AGAGGTTCTATCTTAGCCTATGAAA
545084 GATAGGTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 30 0.58
35 22 0.42
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (35 bp):
AGAGGTTCTATCTTAGCCTATGAAAAAGACAGGAA
Found at i:550011 original size:59 final size:58
Alignment explanation
Indices: 549947--550064 Score: 146
Period size: 58 Copynumber: 2.0 Consensus size: 58
549937 ATTCATGGCT
* * *
549947 AGCGATACCGGGCTTGAAAAAAAAAGATTTGACAAGTGCTAATGTGTTGATTTAAGGCC
1 AGCGATACCGGGCTTG-AAAAAAAAGATCTAACAAATGCTAATGTGTTGATTTAAGGCC
** * ** *
550006 AGCGATATTGGGCTTGAGAACGAAGGTCTAACAAATGCTAATGTGTTGATTTAAGGCC
1 AGCGATACCGGGCTTGAAAAAAAAGATCTAACAAATGCTAATGTGTTGATTTAAGGCC
550064 A
1 A
550065 ACAACATTAG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
58 36 0.72
59 14 0.28
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (58 bp):
AGCGATACCGGGCTTGAAAAAAAAGATCTAACAAATGCTAATGTGTTGATTTAAGGCC
Found at i:550165 original size:32 final size:31
Alignment explanation
Indices: 550129--550371 Score: 141
Period size: 32 Copynumber: 7.4 Consensus size: 31
550119 TTGCCACCAA
550129 CTTGTGTGGGCTTTGAGAAAGATTACCATCAG
1 CTTGTGTGGGCTTTGAGAAAG-TTACCATCAG
* *
550161 CTTGTGTGGGCTTTGGAAAAAGGTTACCA-CTAA
1 CTTGTGTGGGCTTT-GAGAAA-GTTACCATC-AG
* *
550194 CTTATGTGGGCTTTGAGGAAAGTTGCCATCAG
1 CTTGTGTGGGCTTTGA-GAAAGTTACCATCAG
* * * *
550226 CTTGTGTTGGCTTTGAGAAAAAAAGTTGCCACCAA
1 CTTGTGTGGGCTTTGAG----AAAGTTACCATCAG
* * *
550261 CTTGTGTGGGCTTTTAGGAAAGTTGCCA-CCG
1 CTTGTGTGGGCTTTGA-GAAAGTTACCATCAG
* * * * * *
550292 ACTTGTGTAGGTTTTGGAAAAAAGGTTGCCACCAA
1 -CTTGTGTGGGCTTT-G-AGAAA-GTTACCATCAG
* * *
550327 CTTGTGTGGGCTTTGAGGAAGGTTGCCA-CTAA
1 CTTGTGTGGGCTTTGA-GAAAGTTACCATC-AG
550359 CTTGTGTGGGCTT
1 CTTGTGTGGGCTT
550372 AAAAAGATGA
Statistics
Matches: 170, Mismatches: 24, Indels: 34
0.75 0.11 0.15
Matches are distributed among these distances:
31 3 0.02
32 83 0.49
33 35 0.21
34 21 0.12
35 27 0.16
36 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (31 bp):
CTTGTGTGGGCTTTGAGAAAGTTACCATCAG
Found at i:550184 original size:65 final size:65
Alignment explanation
Indices: 550115--550371 Score: 338
Period size: 66 Copynumber: 3.9 Consensus size: 65
550105 AGCTTTTGCG
*
550115 AAGGTTGCCACCAACTTGTGTGGGCTTTGA-GAAAGATTACCATCAGCTTGTGTGGGCTTTGG-A
1 AAGGTTGCCACCAACTTGTGTGGGCTTTGAGGAAAG-TTGCCA-CAGCTTGTGTGGGCTTTGGAA
550178 AA
64 AA
* * * *
550180 AAGGTTACCACTAACTTATGTGGGCTTTGAGGAAAGTTGCCATCAGCTTGTGTTGGCTTTGAGAA
1 AAGGTTGCCACCAACTTGTGTGGGCTTTGAGGAAAGTTGCCA-CAGCTTGTGTGGGCTTTG-GAA
550245 AA
64 AA
* * * * *
550247 AAAGTTGCCACCAACTTGTGTGGGCTTTTAGGAAAGTTGCCACCGACTTGTGTAGGTTTTGGAAA
1 AAGGTTGCCACCAACTTGTGTGGGCTTTGAGGAAAGTTGCCACAG-CTTGTGTGGGCTTTGGAAA
550312 A
65 A
* *
550313 AAGGTTGCCACCAACTTGTGTGGGCTTTGAGGAAGGTTGCCACTAACTTGTGTGGGCTT
1 AAGGTTGCCACCAACTTGTGTGGGCTTTGAGGAAAGTTGCCAC-AGCTTGTGTGGGCTT
550372 AAAAAGATGA
Statistics
Matches: 167, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
65 50 0.30
66 64 0.38
67 53 0.32
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (65 bp):
AAGGTTGCCACCAACTTGTGTGGGCTTTGAGGAAAGTTGCCACAGCTTGTGTGGGCTTTGGAAAA
Found at i:551876 original size:9 final size:9
Alignment explanation
Indices: 551861--551896 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
551851 TCATCTGAAC
551861 ATTTTTTTA
1 ATTTTTTTA
*
551870 TTTTTTTTTA
1 -ATTTTTTTA
551880 ATTTTTTTA
1 ATTTTTTTA
551889 ATTTTTTT
1 ATTTTTTT
551897 GTTTTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:556542 original size:28 final size:28
Alignment explanation
Indices: 556509--556577 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
556499 AAAATCGGGA
*
556509 TTGGAGCATTCCCTCGAAAATAATGGGG
1 TTGGAGCATCCCCTCGAAAATAATGGGG
*
556537 TTGGAGTATCCCCTCGAAAATAATGGGG
1 TTGGAGCATCCCCTCGAAAATAATGGGG
*
556565 TTGGAGTATCCCC
1 TTGGAGCATCCCC
556578 GGTTGTGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (28 bp):
TTGGAGCATCCCCTCGAAAATAATGGGG
Found at i:556571 original size:107 final size:107
Alignment explanation
Indices: 556448--556656 Score: 366
Period size: 107 Copynumber: 2.0 Consensus size: 107
556438 TTTTGGAGAT
*
556448 AATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGATTTGGAAATAAAATCGGGATTGG
1 AATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATAATTTGGAAATAAAATCGGGATTGG
*
556513 AGCATTCCCTC-GAAAATAATGGGGTTGGAGTATCCCCTCGAA
66 AGCATTCCCTCAG-AAATAACGGGGTTGGAGTATCCCCTCGAA
* *
556555 AATAATGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATAATTTGGAAATAAAATTGGGATTGG
1 AATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATAATTTGGAAATAAAATCGGGATTGG
556620 AGCATTCCCTCAGAAATAACGGGGTTGGAGTATCCCC
66 AGCATTCCCTCAGAAATAACGGGGTTGGAGTATCCCC
556657 GACTATAAAA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
107 96 0.99
108 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (107 bp):
AATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATAATTTGGAAATAAAATCGGGATTGG
AGCATTCCCTCAGAAATAACGGGGTTGGAGTATCCCCTCGAA
Found at i:556716 original size:80 final size:79
Alignment explanation
Indices: 556533--556787 Score: 303
Period size: 79 Copynumber: 3.2 Consensus size: 79
556523 CGAAAATAAT
* * **
556533 GGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATAAT
1 GGGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTT
*
556598 TTGGAAATAAAATT
66 TTGGAAATAAAATC
* * * * * * * * *
556612 GGGATTGGAGCATTCCCTCAGAAATAACGGGGTTGGAGTATCCCCGACTATAAAAAAATTGATGT
1 GGGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGGAGTATCCCCGATTGT-GAAAAATCGATGT
* *
556677 TTTAGAAATAAAACC
65 TTTGGAAATAAAATC
* * * *
556692 GGGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGAAATATCCCCGATTGTGAAAAGTCGGTGTT
1 GGGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTT
556757 TTGGAAATAAAATC
66 TTGGAAATAAAATC
* *
556771 GGAGTTGGAATATCCCC
1 GGGGTTGGAGTATCCCC
556788 GATTGCGGAG
Statistics
Matches: 142, Mismatches: 33, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
79 79 0.56
80 63 0.44
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTT
TTGGAAATAAAATC
Found at i:556786 original size:51 final size:51
Alignment explanation
Indices: 556723--556838 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 51
556713 AAATAATGGG
* * *
556723 GTTGAAATATCCCCGATTG-TGAAAAGTCGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAATATCCCCGATTGCGGAAAA-TCGGTGTTTTAGAAATAAAATCGGA
* * *
556774 GTTGGAATATCCCCGATTGCGGAGAATTGGTGTTTTAGAAATAAAATCGGG
1 GTTGGAATATCCCCGATTGCGGAAAATCGGTGTTTTAGAAATAAAATCGGA
*
556825 GTTGGAGTATCCCC
1 GTTGGAATATCCCC
556839 TCGGAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 53 0.93
52 4 0.07
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (51 bp):
GTTGGAATATCCCCGATTGCGGAAAATCGGTGTTTTAGAAATAAAATCGGA
Found at i:556831 original size:130 final size:130
Alignment explanation
Indices: 556668--556917 Score: 383
Period size: 130 Copynumber: 1.9 Consensus size: 130
556658 ACTATAAAAA
*
556668 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGAAATAT
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGAAATAT
* * * * *
556733 CCCCGATTGTGAAAAGTCGGTGTTTTGGAAATAAAATCGGAGTTGGAATATCCCCGATTGCGGAG
66 CCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGGAGTTGGAATATCCCCGATTGCGGAG
* * * *
556798 AATTGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTAT
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGAAATAT
* * *
556863 CCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
66 CCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGGAGTTGGAATATCCCC
556918 TCGAAAATAA
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (130 bp):
AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGAAATAT
CCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGGAGTTGGAATATCCCCGATTGCGGAG
Found at i:556857 original size:79 final size:78
Alignment explanation
Indices: 556774--557071 Score: 390
Period size: 79 Copynumber: 3.8 Consensus size: 78
556764 TAAAATCGGA
* * * *
556774 GTTGGAATATCCCCGATTGCGGAGAATTGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTG-GAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
*
556839 TCGGAAATAACGGG
65 TCGAAAATAACGGG
* *
556853 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATT-GGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
556918 TCGAAAATAACGGG
65 TCGAAAATAACGGG
* * *
556932 ATTGGAGTATCCCCGA-T-GAAAAATTGATGTTTTAGAAATAAAA-CTGGGTTGGAGTGTCCCCT
1 GTTGGAGTATCCCCGATTGGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCT
556994 CGAAAATAACGGG
66 CGAAAATAACGGG
* * * * *
557007 GTTGGAGTATCCCTGATTGTG-AAAAGTCAGTGTTTTGGAAATAAAATCGGAGTTGGAGTA-CCC
1 GTTGGAGTATCCCCGATTG-GAAAAATTGA-TGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
557070 CT
64 CT
557072 GATTATGGAA
Statistics
Matches: 195, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
75 44 0.23
76 27 0.14
77 6 0.03
78 22 0.11
79 96 0.49
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (78 bp):
GTTGGAGTATCCCCGATTGGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCT
CGAAAATAACGGG
Found at i:557062 original size:51 final size:50
Alignment explanation
Indices: 557007--557169 Score: 175
Period size: 51 Copynumber: 3.2 Consensus size: 50
556997 AAATAACGGG
*
557007 GTTGGAGTATCCCTGATTGTGAAAAGTCAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCTGATTATGAAAA-TCAGTGTTTTGGAAATAAAATCGGA
* ** * *
557058 GTTGGAGTACCCCTGATTATGGAAAATGGGTGTTTTAGAAATAAAATCAGA
1 GTTGGAGTATCCCTGATTAT-GAAAATCAGTGTTTTGGAAATAAAATCGGA
* * * ** *
557109 GTTAGAGTATCCCCGATTAAGAAAATTTGATGTTTTGGAAATGAAATCGG-
1 GTTGGAGTATCCCTGATTATGAAAATCAG-TGTTTTGGAAATAAAATCGGA
557159 GATTGGAGTAT
1 G-TTGGAGTAT
557170 TCCCGAGATG
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
50 8 0.09
51 80 0.86
52 5 0.05
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.31
Consensus pattern (50 bp):
GTTGGAGTATCCCTGATTATGAAAATCAGTGTTTTGGAAATAAAATCGGA
Found at i:557098 original size:284 final size:287
Alignment explanation
Indices: 556533--557122 Score: 830
Period size: 284 Copynumber: 2.1 Consensus size: 287
556523 CGAAAATAAT
* * *
556533 GGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATAAT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATAAT
* ** * *
556598 TTGGAAATAAAATTGGGATTGGAGCATTCCCTCAGAAATAACGGGGTTGGAGTATCCCCGACTAT
66 TTAGAAATAAAACCGGGATTGGAGCATCCCCTCAGAAATAACGGGATTGGAGTATCCCCGA--AT
* *
556663 AAAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGA
129 AAAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGA
* *
556728 AATATCCCCGATTGTGAAAAGTCGGTGTTTTGGAAATAAAATCGGAGTTGGAATATCCCCGATTG
194 AATATCCCCGATTGTGAAAAGTCAGTGTTTTGGAAATAAAATCGGAGTTGGAATATCCCCGATTA
* *
556793 CGGAGAATTGGTGTTTTAGAAATAAAATC
259 CGGAAAATGGGTGTTTTAGAAATAAAATC
* * **
556822 GGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATAAT
* *
556887 TTAGAAATAAAACCGGGGTTGGAGTATCCCCTC-GAAAATAACGGGATTGGAGTATCCCCG-AT-
66 TTAGAAATAAAACCGGGATTGGAGCATCCCCTCAG-AAATAACGGGATTGGAGTATCCCCGAATA
* * * *
556949 GAAAAATTGATGTTTTAGAAATAAAA-CTGGGTTGGAGTGTCCCCTCGAAAATAACGGGGTTGGA
130 AAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGAA
* * *
557013 GTATCCCTGATTGTGAAAAGTCAGTGTTTTGGAAATAAAATCGGAGTTGGAGTA-CCCCTGATTA
195 ATATCCCCGATTGTGAAAAGTCAGTGTTTTGGAAATAAAATCGGAGTTGGAATATCCCC-GATTA
*
557077 TGGAAAATGGGTGTTTTAGAAATAAAATC
259 CGGAAAATGGGTGTTTTAGAAATAAAATC
* * *
557106 AGAGTTAGAGTATCCCC
1 GGGGTTGGAGTATCCCC
557123 GATTAAGAAA
Statistics
Matches: 268, Mismatches: 31, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
283 4 0.01
284 127 0.47
285 25 0.09
286 2 0.01
288 1 0.00
289 109 0.41
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (287 bp):
GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATAAT
TTAGAAATAAAACCGGGATTGGAGCATCCCCTCAGAAATAACGGGATTGGAGTATCCCCGAATAA
AAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGAAA
TATCCCCGATTGTGAAAAGTCAGTGTTTTGGAAATAAAATCGGAGTTGGAATATCCCCGATTACG
GAAAATGGGTGTTTTAGAAATAAAATC
Found at i:559519 original size:20 final size:20
Alignment explanation
Indices: 559472--559525 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
559462 AAAATGCCTG
*
559472 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
*
559492 AATTTATCGATACAATGCA-A
1 AATGTATCGATACAATG-AGA
559512 AATGTATCGATACA
1 AATGTATCGATACA
559526 TCTGGGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:559757 original size:21 final size:20
Alignment explanation
Indices: 559731--559769 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
559721 GTTGGGACCT
559731 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
*
559752 TGTATCGATATATTTAGA
1 TGTATCGATACATTTAGA
559770 CAAAAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:560429 original size:42 final size:41
Alignment explanation
Indices: 560339--560443 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
560329 GGGTGTCCCA
*
560339 CTTTTTGAGGACAAA-GGAAAAAAGAATGAAATAGGTCTTG
1 CTTTTTGAGGACAAAGGGAAAAAAGAAAGAAATAGGTCTTG
** * * *
560379 CTCCTTGAGGACAAAGGGAGAGAAGAAAAGGAA-AGTGTCTTG
1 CTTTTTGAGGACAAAGGGAAAAAAG-AAAGAAATAG-GTCTTG
*
560421 CTTTTTGAGGACAAAGTGAAAAA
1 CTTTTTGAGGACAAAGGGAAAAA
560444 GAGTACGTCC
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
40 13 0.25
41 9 0.18
42 29 0.57
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.22
Consensus pattern (41 bp):
CTTTTTGAGGACAAAGGGAAAAAAGAAAGAAATAGGTCTTG
Found at i:560814 original size:60 final size:60
Alignment explanation
Indices: 560585--560813 Score: 275
Period size: 61 Copynumber: 3.8 Consensus size: 60
560575 GTGTGTCATA
* * * *
560585 CTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCGTCTTG
1 CTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAGAAGGCGTCCTG
* * * * * * *
560646 CCCTTTGAGGACCGGAAGGTGCCACCAACTTATGTGGGCTTTGCAAAA-AGAAAGCATCCTA
1 CTCTTTGAGGA-CTGAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAAGAGAAGGCGTCCTG
560707 CTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGCGTCCTG
1 CTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAGAAGGCGTCCTG
* *
560768 CTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTT-AAAAG
1 CTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAG
560814 GCATCCCGCT
Statistics
Matches: 143, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
59 5 0.03
60 31 0.22
61 102 0.71
62 5 0.03
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (60 bp):
CTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAGAAGGCGTCCTG
Found at i:560845 original size:122 final size:118
Alignment explanation
Indices: 560584--560833 Score: 337
Period size: 122 Copynumber: 2.1 Consensus size: 118
560574 AGTGTGTCAT
* *
560584 ACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCGTCTTGCCC
1 ACTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCGTCCTGCCC
*
560649 TTTGAGGACCGGAAGGTGCCACCAACTTATGTGGGCTTTGCAAAAAGAAAGCATCCT
66 TTTGAGGACCGGAAGGTGCCACCAACTTATGTGGGCTTT--AAAAAG--AGCATCCC
* * *
560706 ACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAGAAGGCGTCCTGCT
1 ACTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAGGCGTCCTGCC
* * *
560770 CTTTGAGGA-CTGAAGGTGCCACCAGCTTGTGTGGGCTTT-AAAAG-GCATCCC
65 CTTTGAGGACCGGAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAGCATCCC
*
560821 GCTCTTTGAGGAC
1 ACTCTTTGAGGAC
560834 AAAAAGGTGA
Statistics
Matches: 117, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
115 18 0.15
118 5 0.04
121 31 0.26
122 63 0.54
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (118 bp):
ACTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCGTCCTGCCC
TTTGAGGACCGGAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAGCATCCC
Found at i:561052 original size:61 final size:60
Alignment explanation
Indices: 560856--561088 Score: 317
Period size: 61 Copynumber: 3.9 Consensus size: 60
560846 GGAGAGAGCG
* * * *
560856 TCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGAGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCA
** *
560917 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCA
* * *
560976 TCATGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGTA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCA
* *
561037 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
561089 GCATCACTGA
Statistics
Matches: 155, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
59 25 0.16
60 56 0.36
61 74 0.48
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCA
Found at i:562078 original size:19 final size:18
Alignment explanation
Indices: 562069--562137 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 18
562059 TTTTTTTCTC
562069 TTTTTTCTTTGTTTTTTTG
1 TTTTTT-TTTGTTTTTTTG
562088 TTTTTTTTTGTTTTTTTG
1 TTTTTTTTTGTTTTTTTG
562106 TTTTTTTTTTGGTTGTTTTTTG
1 -TTTTTTTTT-G-T-TTTTTTG
*
562128 TTTATTTTTG
1 TTTTTTTTTG
562138 AAAAAAAGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
18 12 0.27
19 15 0.33
20 2 0.04
21 9 0.20
22 7 0.16
ACGTcount: A:0.01, C:0.01, G:0.13, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTGTTTTTTTG
Found at i:562083 original size:9 final size:8
Alignment explanation
Indices: 562071--562135 Score: 62
Period size: 8 Copynumber: 7.9 Consensus size: 8
562061 TTTTTCTCTT
562071 TTTTCTTTG
1 TTTT-TTTG
562080 TTTTTTTG
1 TTTTTTTG
562088 TTTTTTTTTG
1 --TTTTTTTG
562098 TTTTTTTG
1 TTTTTTTG
562106 TTTTTTT-
1 TTTTTTTG
**
562113 TTTGGTTG
1 TTTTTTTG
562121 -TTTTTTG
1 TTTTTTTG
562128 TTTATTTT
1 TTT-TTTT
562136 TGAAAAAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
7 10 0.21
8 21 0.45
9 8 0.17
10 8 0.17
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.85
Consensus pattern (8 bp):
TTTTTTTG
Found at i:562094 original size:22 final size:21
Alignment explanation
Indices: 562059--562136 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 21
562049 GCAGATTCTT
* * *
562059 TTTTTTTCTCTTTTTTCTTTG
1 TTTTTTTGTTTTTTTTTTTTG
562080 TTTTTTTG---TTTTTTTTTG
1 TTTTTTTGTTTTTTTTTTTTG
562098 TTTTTTTGTTTTTTTTTTGGTTG
1 TTTTTTTGTTTTTTTTTT--TTG
*
562121 -TTTTTTGTTTATTTTT
1 TTTTTTTGTTTTTTTTT
562137 GAAAAAAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 17 0.35
21 14 0.29
22 15 0.31
23 3 0.06
ACGTcount: A:0.01, C:0.04, G:0.10, T:0.85
Consensus pattern (21 bp):
TTTTTTTGTTTTTTTTTTTTG
Found at i:562094 original size:30 final size:30
Alignment explanation
Indices: 562057--562135 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
562047 AAGCAGATTC
*
562057 TTTTTTTTTCTCTTTTTTCTTTGTTTTTTT-G
1 TTTTTTTTTCT-TTTTTT-GTTGTTTTTTTGG
* *
562088 TTTTTTTTTGTTTTTTTGTTTTTTTTTTGG
1 TTTTTTTTTCTTTTTTTGTTGTTTTTTTGG
* *
562118 TTGTTTTTTGTTTATTTT
1 TTTTTTTTTCTTT-TTTT
562136 TGAAAAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 9 0.21
30 19 0.45
31 14 0.33
ACGTcount: A:0.01, C:0.04, G:0.10, T:0.85
Consensus pattern (30 bp):
TTTTTTTTTCTTTTTTTGTTGTTTTTTTGG
Found at i:562112 original size:11 final size:11
Alignment explanation
Indices: 562069--562136 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
562059 TTTTTTTCTC
*
562069 TTTTTTCTTTGT
1 TTTTTTGTTT-T
562081 TTTTTTG-TTT
1 TTTTTTGTTTT
562091 TTTTTTG---T
1 TTTTTTGTTTT
562099 TTTTTTGTTTT
1 TTTTTTGTTTT
* *
562110 TTTTTTGGTTG
1 TTTTTTGTTTT
562121 TTTTTTGTTTAT
1 TTTTTTGTTT-T
562133 TTTT
1 TTTT
562137 GAAAAAAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
8 8 0.17
10 8 0.17
11 21 0.45
12 10 0.21
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.85
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:562126 original size:1 final size:1
Alignment explanation
Indices: 562057--562115 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
562047 AAGCAGATTC
* * * * * * *
562057 TTTTTTTTTCTCTTTTTTCTTTGTTTTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
562116 GGTTGTTTTT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:566927 original size:28 final size:28
Alignment explanation
Indices: 566887--566958 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
566877 GGAATAAAGC
** *
566887 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
566915 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
566943 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
566959 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:567016 original size:52 final size:52
Alignment explanation
Indices: 566947--567283 Score: 167
Period size: 52 Copynumber: 6.4 Consensus size: 52
566937 AAATAACGAG
*
566947 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * * ** * *
566999 GTTGGAGTATCCCCGATTAAAGGAAAATCGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * * *
567052 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATCAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
** **** * * *
567103 GTTGGAGTATCCCC---TCAGAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
* *
567158 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATATAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
567212 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
*
567263 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
567284 GAGAATTGAT
Statistics
Matches: 211, Mismatches: 47, Indels: 54
0.68 0.15 0.17
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
51 37 0.18
52 77 0.36
53 33 0.16
54 28 0.13
55 18 0.09
56 2 0.01
57 2 0.01
58 6 0.03
59 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:567143 original size:28 final size:27
Alignment explanation
Indices: 567103--567171 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
567093 TCAAACCGGA
567103 GTTGGAGTATCCCCTCA-GAAATAACGGG
1 GTTGGAGTATCCCC-CATG-AATAACGGG
* *
567131 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCCATGAATAACGGG
567158 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
567172 GATTGTGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (27 bp):
GTTGGAGTATCCCCCATGAATAACGGG
Found at i:567249 original size:212 final size:212
Alignment explanation
Indices: 566886--567285 Score: 617
Period size: 212 Copynumber: 1.9 Consensus size: 212
566876 GGGAATAAAG
* * *
566886 CCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTG
1 CCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTG
* *
566951 GAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGAT
66 GAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGAT
* *
567016 TAAAGGAAAATCGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGAAAAATT
131 TAAAGGAAAATCAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGAAAAATT
567080 AGTGTTTTAGCGATCAAA
195 AGTGTTTTAGCGATCAAA
* *
567098 CCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTG
1 CCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTG
* *
567162 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATATAATCGGAGTTAGAGTATCCCCG
66 GAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCG
* * * *
567227 ATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
129 ATTAAAGGAAAATCAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
567286 GAATTGATAA
Statistics
Matches: 170, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 32 0.19
212 100 0.59
213 38 0.22
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
CCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTG
GAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGAT
TAAAGGAAAATCAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTA
GTGTTTTAGCGATCAAA
Found at i:567260 original size:51 final size:53
Alignment explanation
Indices: 567162--567280 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
567152 AACGGGGTTG
* * * *
567162 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATATAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
567216 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
567267 GAATATCCCCGATT
1 GAGTATCCCCGATT
567281 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:569667 original size:13 final size:13
Alignment explanation
Indices: 569649--569674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
569639 ACAAAGATCC
569649 ATGTATCGATACA
1 ATGTATCGATACA
569662 ATGTATCGATACA
1 ATGTATCGATACA
569675 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:569670 original size:33 final size:33
Alignment explanation
Indices: 569628--569694 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
569618 AAAATTTCCA
***
569628 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
569661 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
569694 A
1 A
569695 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:569738 original size:19 final size:18
Alignment explanation
Indices: 569714--569781 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
569704 CAGTAGCTAA
569714 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
569733 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
569748 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
569765 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
569782 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:569754 original size:13 final size:13
Alignment explanation
Indices: 569736--569760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
569726 ACAATACTTA
569736 TGTATCGATACAT
1 TGTATCGATACAT
569749 TGTATCGATACA
1 TGTATCGATACA
569761 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:569758 original size:32 final size:32
Alignment explanation
Indices: 569717--569779 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
569707 TAGCTAATTA
*
569717 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
569749 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
569780 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:569861 original size:20 final size:20
Alignment explanation
Indices: 569817--569892 Score: 107
Period size: 21 Copynumber: 3.7 Consensus size: 20
569807 GTTGGGACCC
***
569817 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTCACA-AA
569838 TGTATCGATACATTCACAAA
1 TGTATCGATACATTCACAAA
569858 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTC-ACAAA
569879 TGTATCGATACATT
1 TGTATCGATACATT
569893 TGGAATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 17 0.33
21 34 0.67
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTCACAAA
Found at i:580358 original size:52 final size:52
Alignment explanation
Indices: 580210--580338 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
580200 CGAAATATGA
* * *
580210 AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
580262 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
580314 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
580339 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:580365 original size:13 final size:13
Alignment explanation
Indices: 580347--580371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
580337 CAAAGATCAG
580347 TGTATCGATACAA
1 TGTATCGATACAA
580360 TGTATCGATACA
1 TGTATCGATACA
580372 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:580450 original size:19 final size:19
Alignment explanation
Indices: 580424--580506 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
580414 AGCAGTACAT
*
580424 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
*
580443 TATATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
580456 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
580475 TGTATCGATACAACACTAA
1 TGTATCGATACAACACTTA
580494 TGTATCGATACAA
1 TGTATCGATACAA
580507 GTCATTGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
13 8 0.15
14 1 0.02
16 5 0.09
18 1 0.02
19 39 0.72
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:580460 original size:32 final size:32
Alignment explanation
Indices: 580419--580486 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
580409 TTCGTAGCAG
580419 TACATTGTATCGATACAAAACTTATATATCGA
1 TACATTGTATCGATACAAAACTTATATATCGA
* *
580451 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATATATCGA
580483 TACA
1 TACA
580487 ACACTAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATATATCGA
Found at i:581022 original size:75 final size:76
Alignment explanation
Indices: 580932--581084 Score: 218
Period size: 75 Copynumber: 2.0 Consensus size: 76
580922 ATCCCCAATT
* * * * *
580932 ATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGAATTG
1 ATGAAAAATTAATGTTTTAAAAATAAAACCGGGGTTGAAGTATCCCCTCAAAAATAACGGAATTA
580997 GAGTATC-CCG
66 GAGTATCGCCG
* * **
581007 ATGAAAAATTAATGTTTTAAAAATAAAATCGGGGTTGAAGTGTCCCCTCAAAAATAACGGGGTTA
1 ATGAAAAATTAATGTTTTAAAAATAAAACCGGGGTTGAAGTATCCCCTCAAAAATAACGGAATTA
581072 GAGTATCGCCG
66 GAGTATCGCCG
581083 AT
1 AT
581085 TATGAAAAGT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
75 63 0.93
76 5 0.07
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (76 bp):
ATGAAAAATTAATGTTTTAAAAATAAAACCGGGGTTGAAGTATCCCCTCAAAAATAACGGAATTA
GAGTATCGCCG
Found at i:581127 original size:51 final size:50
Alignment explanation
Indices: 581072--581230 Score: 187
Period size: 51 Copynumber: 3.1 Consensus size: 50
581062 AACGGGGTTA
* *
581072 GAGTATCGCCGATTATGAAAAGTCAGTGTTTTGGAAATAAAATTGGAGTTG
1 GAGTATCCCCGATTATGAAAA-TCAGTGTTTTGGAAATAAAATCGGAGTTG
* * *
581123 GAGTACCCCCGATTATGGAAAATCGGTGTTTTAGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTAT-GAAAATCAGTGTTTTGGAAATAAAATCGGAGTTG
* * *
581174 GAGTATCCCCGATTAAGAAAAAT-TGATGTTTTGGAAATGAAATCGG-GATTG
1 GAGTATCCCCGATTATG-AAAATCAG-TGTTTTGGAAATAAAATCGGAG-TTG
581225 GAGTAT
1 GAGTAT
581231 TCTCGAGATG
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
50 3 0.03
51 86 0.91
52 5 0.05
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (50 bp):
GAGTATCCCCGATTATGAAAATCAGTGTTTTGGAAATAAAATCGGAGTTG
Found at i:583567 original size:20 final size:20
Alignment explanation
Indices: 583541--583596 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
583531 ATGTATCGAT
583541 ACAATGTATCGATACAATG-
1 ACAATGTATCGATACAATGC
583560 AGCAATGTATCGATACAATGC
1 A-CAATGTATCGATACAATGC
*
583581 AAAATGTATCGATACA
1 ACAATGTATCGATACA
583597 TCTGGGTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (20 bp):
ACAATGTATCGATACAATGC
Found at i:583578 original size:13 final size:13
Alignment explanation
Indices: 583530--583559 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
583520 AAAATGACTG
583530 AATGTATCGATAC
1 AATGTATCGATAC
583543 AATGTATCGATAC
1 AATGTATCGATAC
583556 AATG
1 AATG
583560 AGCAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:594450 original size:20 final size:22
Alignment explanation
Indices: 594425--594480 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
594415 AAAAACCCAG
594425 AATGTATCGATATAA-TG-AAA
1 AATGTATCGATATAATTGTAAA
*
594445 AATGTATCGATACAATTGTAAA
1 AATGTATCGATATAATTGTAAA
*
594467 CATGTATCGATATA
1 AATGTATCGATATA
594481 TTTTGTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 14 0.45
21 2 0.06
22 15 0.48
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (22 bp):
AATGTATCGATATAATTGTAAA
Found at i:594474 original size:22 final size:20
Alignment explanation
Indices: 594425--594478 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
594415 AAAAACCCAG
*
594425 AATGTATCGATATAATGAAA
1 AATGTATCGATACAATGAAA
594445 AATGTATCGATACAATTGTAAA
1 AATGTATCGATACAA-TG-AAA
*
594467 CATGTATCGATA
1 AATGTATCGATA
594479 TATTTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 14 0.47
21 2 0.07
22 14 0.47
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:594573 original size:21 final size:21
Alignment explanation
Indices: 594526--594576 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 21
594516 GCAGAGTAGT
594526 TTTGTATCGAGACATTTACTG
1 TTTGTATCGAGACATTTACTG
594547 -TTGTATCGAGACATTTACTG
1 TTTGTATCGAGACATTTACTG
594567 TTTGTATCGA
1 TTTGTATCGA
594577 TACAAATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.43
Consensus pattern (21 bp):
TTTGTATCGAGACATTTACTG
Found at i:598530 original size:2 final size:2
Alignment explanation
Indices: 598523--598585 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
598513 CTGCATCCTA
598523 AT AT AT AT AT 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
*
598565 AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
598586 ACCAAGACAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:609845 original size:29 final size:30
Alignment explanation
Indices: 609789--609865 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
609779 AAATTAAATT
* * * *
609789 AAATTATATTAAAAAAATTATTTTATTATTT
1 AAATAATATT-AAAATATTATTATATTATTA
*
609820 TAATAATATTAAAATATT-TTATATTATTA
1 AAATAATATTAAAATATTATTATATTATTA
*
609849 AAATAATAATTTAAATA
1 AAATAAT-ATTAAAATA
609866 AAATCAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 15 0.39
30 15 0.39
31 8 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
AAATAATATTAAAATATTATTATATTATTA
Found at i:609849 original size:18 final size:19
Alignment explanation
Indices: 609815--609853 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
609805 ATTATTTTAT
609815 TATTTTAATAATATTAAAA
1 TATTTTAATAATATTAAAA
*
609834 TATTTT-ATATTATTAAAA
1 TATTTTAATAATATTAAAA
609852 TA
1 TA
609854 ATAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTAATAATATTAAAA
Found at i:610677 original size:16 final size:16
Alignment explanation
Indices: 610635--610682 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
610625 TTAAAAACTC
*
610635 AAGTTTGAAAAATTTT
1 AAGTTTGAAAAAATTT
** **
610651 AAAATAAAAAAAATTT
1 AAGTTTGAAAAAATTT
610667 AAGTTTGAAAAAATTT
1 AAGTTTGAAAAAATTT
610683 TAAACTTGAT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (16 bp):
AAGTTTGAAAAAATTT
Found at i:610691 original size:17 final size:16
Alignment explanation
Indices: 610642--610700 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
610632 CTCAAGTTTG
* *
610642 AAAAATTTTAAAATAA
1 AAAAATTTTAAATTGA
* *
610658 AAAAAATTTAAGTTTGA
1 AAAAATTTTAA-ATTGA
610675 AAAAATTTTAAACTTGA
1 AAAAATTTTAAA-TTGA
*
610692 TAAAATTTT
1 AAAAATTTT
610701 GTCGCGACGT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 10 0.29
17 24 0.71
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (16 bp):
AAAAATTTTAAATTGA
Found at i:612944 original size:18 final size:21
Alignment explanation
Indices: 612921--612967 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
612911 TAGTCACAAC
*
612921 AATGCATG-AACAT-GT-TAA
1 AATGCATGAAACATAGTAAAA
612939 AATGCATGAAACATAGTAAAA
1 AATGCATGAAACATAGTAAAA
612960 AATGCATG
1 AATGCATG
612968 GTCAAAGGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 5 0.20
20 2 0.08
21 10 0.40
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (21 bp):
AATGCATGAAACATAGTAAAA
Found at i:612996 original size:88 final size:89
Alignment explanation
Indices: 612841--613007 Score: 318
Period size: 88 Copynumber: 1.9 Consensus size: 89
612831 TAGATGTTAG
*
612841 ACATGTTAAAATGCATGAAACATAGTAAAAAAATGCATGGTCAAAGGCAACTAGGATGAACATGG
1 ACATGTTAAAATGCATGAAACATAGTAAAAAAATGCATGGTCAAAGGCAACTAGGATGAACACGG
612906 CATTTTAGTCACAACAATGCATGA
66 CATTTTAGTCACAACAATGCATGA
612930 ACATGTTAAAATGCATGAAACATAGT-AAAAAATGCATGGTCAAAGGCAACTAGGATGAACACGG
1 ACATGTTAAAATGCATGAAACATAGTAAAAAAATGCATGGTCAAAGGCAACTAGGATGAACACGG
612994 CATTTTAGTCACAA
66 CATTTTAGTCACAA
613008 AAGATGGCTT
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
88 51 0.66
89 26 0.34
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (89 bp):
ACATGTTAAAATGCATGAAACATAGTAAAAAAATGCATGGTCAAAGGCAACTAGGATGAACACGG
CATTTTAGTCACAACAATGCATGA
Found at i:613580 original size:29 final size:30
Alignment explanation
Indices: 613537--613597 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
613527 CCACCATCAA
613537 TTTGCAAAATAAGTTGCTGACATTATGAAG
1 TTTGCAAAATAAGTTGCTGACATTATGAAG
613567 TTTGC-AAATAAGTTGCTGACATTATGAAG
1 TTTGCAAAATAAGTTGCTGACATTATGAAG
613596 TT
1 TT
613598 GTTCAGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (30 bp):
TTTGCAAAATAAGTTGCTGACATTATGAAG
Found at i:613598 original size:17 final size:17
Alignment explanation
Indices: 613547--613598 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
613537 TTTGCAAAAT
613547 AAGTTGCTGACATTATG
1 AAGTTGCTGACATTATG
*
613564 AAGTT--TG-CA-AAT-
1 AAGTTGCTGACATTATG
613576 AAGTTGCTGACATTATG
1 AAGTTGCTGACATTATG
613593 AAGTTG
1 AAGTTG
613599 TTCAGTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
12 5 0.18
13 2 0.07
14 4 0.14
15 4 0.14
16 2 0.07
17 11 0.39
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.35
Consensus pattern (17 bp):
AAGTTGCTGACATTATG
Found at i:615032 original size:24 final size:25
Alignment explanation
Indices: 614992--615039 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
614982 AAATTAAGGT
614992 TACATATATATAATATAAATTATATA
1 TACATATATAT-ATATAAATTATATA
*
615018 TACATATATAT-TATAGATTATA
1 TACATATATATATATAAATTATA
615040 CTTATCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
26 11 0.52
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
TACATATATATATATAAATTATATA
Found at i:615157 original size:21 final size:21
Alignment explanation
Indices: 615118--615158 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
615108 TCTTGATAAT
*
615118 TTTTAAAATTATTTATTTATC
1 TTTTAAAATGATTTATTTATC
615139 TTTTATAAATGATTT-TTTAT
1 TTTTA-AAATGATTTATTTAT
615159 TAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTAAAATGATTTATTTATC
Found at i:615543 original size:38 final size:37
Alignment explanation
Indices: 615462--615571 Score: 112
Period size: 38 Copynumber: 2.9 Consensus size: 37
615452 AAATTGAATT
* *
615462 GGCTGACGGTTAAAAAATTCAATTTGAAATTAGCTACC
1 GGCTGAC-GTTAAAGAATTCAATTTGGAATTAGCTACC
* * **
615500 AGCTGACAGTTAAAGAATTCAATTTGGAATTGGCTGGC
1 GGCTGAC-GTTAAAGAATTCAATTTGGAATTAGCTACC
* * *
615538 GGCTGACGACTAGAGAATTTAATTTGGAATTAGC
1 GGCTGACG-TTAAAGAATTCAATTTGGAATTAGC
615572 CGTTGGTTAG
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 1 0.02
38 58 0.98
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (37 bp):
GGCTGACGTTAAAGAATTCAATTTGGAATTAGCTACC
Found at i:619282 original size:52 final size:52
Alignment explanation
Indices: 619204--619331 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
619194 CGAAATATGA
*
619204 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
619256 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
619308 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
619332 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:619358 original size:13 final size:13
Alignment explanation
Indices: 619340--619364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
619330 CAAAGATCAG
619340 TGTATCGATACAA
1 TGTATCGATACAA
619353 TGTATCGATACA
1 TGTATCGATACA
619365 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:619442 original size:33 final size:33
Alignment explanation
Indices: 619405--619471 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
619395 AGTAGCTTAA
619405 ATTGTA-CTGATACAAAAAAATATGTATCGATAC
1 ATTGTATC-GATACAAAAAAATATGTATCGATAC
* ***
619438 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
619471 A
1 A
619472 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:619445 original size:13 final size:13
Alignment explanation
Indices: 619427--619451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
619417 CAAAAAAATA
619427 TGTATCGATACAT
1 TGTATCGATACAT
619440 TGTATCGATACA
1 TGTATCGATACA
619452 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:623881 original size:38 final size:38
Alignment explanation
Indices: 623736--623882 Score: 154
Period size: 38 Copynumber: 3.9 Consensus size: 38
623726 GGCTGATGGT
* ** * **
623736 TAGAGAATTCAATTTGAAATTGGTTGGCGGTTGACGGT
1 TAGAGAATTCAATTTGAAATTGGCTGATGGCTGACGAC
* *
623774 TAGAGAATTCAATTT-AGAATTGGTTGATGACTGACGAC
1 TAGAGAATTCAATTTGA-AATTGGCTGATGGCTGACGAC
* *
623812 TAGAGAATTCAATTTGAAATTGACCGATGGCT-AGCGAC
1 TAGAGAATTCAATTTGAAATTGGCTGATGGCTGA-CGAC
* *
623850 TAGAGAATTCAATTTGAAATTAGCTGGTGGCTG
1 TAGAGAATTCAATTTGAAATTGGCTGATGGCTG
623883 GTGGTTAGGG
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
37 2 0.02
38 88 0.97
39 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (38 bp):
TAGAGAATTCAATTTGAAATTGGCTGATGGCTGACGAC
Found at i:623896 original size:38 final size:38
Alignment explanation
Indices: 623725--623897 Score: 152
Period size: 38 Copynumber: 4.6 Consensus size: 38
623715 CAAATTGAAT
* * *
623725 TGGCTGATGGTTAGAGAATTCAATTTGAAATTGGTTGG
1 TGGCTGACGGTTAGAGAATTCAATTTGAAATTGGCTGA
* * *
623763 CGGTTGACGGTTAGAGAATTCAATTT-AGAATTGGTTGA
1 TGGCTGACGGTTAGAGAATTCAATTTGA-AATTGGCTGA
* ** * *
623801 TGACTGACGACTAGAGAATTCAATTTGAAATTGACCGA
1 TGGCTGACGGTTAGAGAATTCAATTTGAAATTGGCTGA
** * *
623839 TGGCT-AGCGACTAGAGAATTCAATTTGAAATTAGCTGG
1 TGGCTGA-CGGTTAGAGAATTCAATTTGAAATTGGCTGA
** *
623877 TGGCTGGTGGTTAGGGAATTC
1 TGGCTGACGGTTAGAGAATTC
623898 CAACATGAAT
Statistics
Matches: 109, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
37 2 0.02
38 106 0.97
39 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (38 bp):
TGGCTGACGGTTAGAGAATTCAATTTGAAATTGGCTGA
Found at i:626542 original size:12 final size:11
Alignment explanation
Indices: 626525--626575 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
626515 TATATATATG
626525 AATAATAATAAT
1 AATAATAA-AAT
626537 AATAATAAATAT
1 AATAATAAA-AT
*
626549 ATTAA-AAAAT
1 AATAATAAAAT
626559 AATAGATAAAAAT
1 AATA-AT-AAAAT
626572 AATA
1 AATA
626576 TCGAACTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 5 0.15
11 5 0.15
12 14 0.42
13 9 0.27
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AATAATAAAAT
Done.