Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 158 of 345
Found at i:53819852 original size:16 final size:15
Alignment explanation
Indices: 53819833--53819862 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
53819823 TTCATTTCAT
53819833 TTGCATTTACGTTAAC
1 TTGCATTTA-GTTAAC
53819849 TTGCATTTAGTTAA
1 TTGCATTTAGTTAA
53819863 TTAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TTGCATTTAGTTAAC
Found at i:53821232 original size:21 final size:19
Alignment explanation
Indices: 53821205--53821255 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
53821195 TGGTTTAGTA
53821205 ATTTAATTTGTTTAATTACT
1 ATTTAATTTGTTTAA-TACT
*
53821225 ATTTTAATTTGGATTAATACT
1 A-TTTAATTT-GTTTAATACT
53821246 A-TTAATTTGT
1 ATTTAATTTGT
53821256 GAATCGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 1 0.04
19 7 0.26
20 1 0.04
21 13 0.48
22 5 0.19
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (19 bp):
ATTTAATTTGTTTAATACT
Found at i:53821692 original size:21 final size:21
Alignment explanation
Indices: 53821658--53821699 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53821648 ATCAATCACC
* * *
53821658 AATCCCATTTCATTTTATTTA
1 AATCCAATTCCATTTCATTTA
53821679 AATCCAATTCCATTTCATTTA
1 AATCCAATTCCATTTCATTTA
53821700 CTAGCCATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (21 bp):
AATCCAATTCCATTTCATTTA
Found at i:53827130 original size:56 final size:56
Alignment explanation
Indices: 53827043--53827151 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
53827033 TCTTACATGT
* *
53827043 AATCACATATCGATGCCAATGTACTAGACGTGGTCTTACTCGCACACATATATCAG
1 AATCACATATCGATGCCAACGTACTAAACGTGGTCTTACTCGCACACATATATCAG
* *
53827099 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACATATATAT
1 AATCACATATCGATGCCAACGTACTAAACGTGGTCTTACTCGCACACATATAT
53827152 ATCGACGCCA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (56 bp):
AATCACATATCGATGCCAACGTACTAAACGTGGTCTTACTCGCACACATATATCAG
Found at i:53837431 original size:85 final size:84
Alignment explanation
Indices: 53837312--53837467 Score: 231
Period size: 85 Copynumber: 1.8 Consensus size: 84
53837302 AAGATACCAA
* ** *
53837312 TGCCATATCTCAGATATGGTCTTACATGGGATCACATATCGATGCCGATAGCCCAGCTATGGTCT
1 TGCCATATCTCAGACATGGTCTTACATGAAATCACATATCGATGCC-ATAGCCCAGATATGGTCT
53837377 TACACGATGTCTCATACTAG
65 TACACGATGTCTCATACTAG
* * * *
53837397 TGCCATGTCTCAGACATGGTCTTATATGAAATCACATATTGATGCCATATCCCAGATATGGTCTT
1 TGCCATATCTCAGACATGGTCTTACATGAAATCACATATCGATGCCATAGCCCAGATATGGTCTT
53837462 ACACGA
66 ACACGA
53837468 AATCACAGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 23 0.37
85 40 0.63
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (84 bp):
TGCCATATCTCAGACATGGTCTTACATGAAATCACATATCGATGCCATAGCCCAGATATGGTCTT
ACACGATGTCTCATACTAG
Found at i:53839574 original size:20 final size:20
Alignment explanation
Indices: 53839549--53839600 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
53839539 AAGACTATGA
* *
53839549 ACCATTCTATTTACTTTCTT
1 ACCATTCCATTTACTTACTT
53839569 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
* *
53839589 TCCATTTCATTT
1 ACCATTCCATTT
53839601 TGTTAGCGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:53847581 original size:23 final size:22
Alignment explanation
Indices: 53847538--53847582 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
53847528 GTTAAATTGA
**
53847538 ATTGTATGTATATGATTGTATT
1 ATTGTATGTATATGAAAGTATT
53847560 ATTGTCATGTATATGAAAGTATT
1 ATTGT-ATGTATATGAAAGTATT
53847583 CACATATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (22 bp):
ATTGTATGTATATGAAAGTATT
Found at i:53847853 original size:26 final size:27
Alignment explanation
Indices: 53847824--53847896 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 27
53847814 CCCGTTATAT
53847824 GGCTCTTCGTGAGCTTCCCGATTAA-A
1 GGCTCTTCGTGAGCTTCCCGATTAATA
* * **
53847850 GGCTTTTTGTGAGCTTCTTGATTAATA
1 GGCTCTTCGTGAGCTTCCCGATTAATA
*
53847877 -GATCTTCG-GAGCTTCCCGAT
1 GGCTCTTCGTGAGCTTCCCGAT
53847897 ATGGCTCGCT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
25 10 0.27
26 26 0.70
27 1 0.03
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (27 bp):
GGCTCTTCGTGAGCTTCCCGATTAATA
Found at i:53848060 original size:25 final size:25
Alignment explanation
Indices: 53847995--53848068 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 25
53847985 CTTTTTGATT
** *
53847995 ATGGCTCTTATGAGCTTCCCGTTAT
1 ATGGCTCACATGAGCTTCCCGTTAG
* * ** *
53848020 ATAGCCCGGATAAGCTTCCCGTTAG
1 ATGGCTCACATGAGCTTCCCGTTAG
*
53848045 ATGGCTCACATGAGCTTCCTGTTA
1 ATGGCTCACATGAGCTTCCCGTTA
53848069 TATAGCTCGA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (25 bp):
ATGGCTCACATGAGCTTCCCGTTAG
Found at i:53848076 original size:25 final size:25
Alignment explanation
Indices: 53848004--53848076 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
53847994 TATGGCTCTT
* **
53848004 ATGAGCTTCCCGTTATATAGCCCGG
1 ATGAGCTTCCCGTTATATAGCTCAC
* * *
53848029 ATAAGCTTCCCGTTAGATGGCTCAC
1 ATGAGCTTCCCGTTATATAGCTCAC
*
53848054 ATGAGCTTCCTGTTATATAGCTC
1 ATGAGCTTCCCGTTATATAGCTC
53848077 GAGGGAGGGT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATAGCTCAC
Found at i:53849236 original size:27 final size:27
Alignment explanation
Indices: 53849198--53849253 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
53849188 CAATCATCCT
53849198 CTACACTCTACTCCATCCAGCCCCACA
1 CTACACTCTACTCCATCCAGCCCCACA
53849225 CTACACTCTACTCCATCCAGCCCCACA
1 CTACACTCTACTCCATCCAGCCCCACA
53849252 CT
1 CT
53849254 CTATGTGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.52, G:0.04, T:0.20
Consensus pattern (27 bp):
CTACACTCTACTCCATCCAGCCCCACA
Found at i:53853022 original size:24 final size:24
Alignment explanation
Indices: 53852990--53853037 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
53852980 TTAGATCAAG
*
53852990 AACAAAGAAAATCAGACTTAGATC
1 AACAAAGAAAATCAAACTTAGATC
53853014 AACAAAGAAAATCAAACTTAGATC
1 AACAAAGAAAATCAAACTTAGATC
53853038 GGAGGAAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (24 bp):
AACAAAGAAAATCAAACTTAGATC
Found at i:53853368 original size:42 final size:42
Alignment explanation
Indices: 53853308--53853495 Score: 170
Period size: 42 Copynumber: 4.4 Consensus size: 42
53853298 GATTTACATA
53853308 TAAGACCATGTCTGGGACATCAGCATCGTATCTGATTTCGTG
1 TAAGACCATGTCTGGGACATCAGCATCGTATCTGATTTCGTG
* * * * *
53853350 TAAGACCGTGTCTAGGACAT-AGGCCTCG-AT-TGAGATTTATGTA
1 TAAGACCATGTCTGGGACATCA-GCATCGTATCT--GATTT-CGTG
* *
53853393 TAAGACCATGTCTGGGACATCGGTATCGTATCTGATTTCGTG
1 TAAGACCATGTCTGGGACATCAGCATCGTATCTGATTTCGTG
* * * *
53853435 TAAGACCCTGTCTGGGACA-GAGGCATCGATAT-TGAATTACATG
1 TAAGACCATGTCTGGGACATCA-GCATCG-TATCTG-ATTTCGTG
*
53853478 TAAGACCACGTCTGGGAC
1 TAAGACCATGTCTGGGAC
53853496 GTCGGCATTG
Statistics
Matches: 116, Mismatches: 20, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 55 0.47
43 54 0.47
44 2 0.02
45 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACATCAGCATCGTATCTGATTTCGTG
Found at i:53853406 original size:85 final size:85
Alignment explanation
Indices: 53853263--53853495 Score: 326
Period size: 85 Copynumber: 2.7 Consensus size: 85
53853253 TGAGACATCA
*
53853263 TGTAAGACCGTGTCTGGGACACATGCCTCGATTGAGATTTACATATAAGACCATGTCTGGGACAT
1 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAGATTTACATATAAGACCATGTCTGGGACAT
53853328 CAGCATCGTATCTGATTTCG
66 CAGCATCGTATCTGATTTCG
* * **
53853348 TGTAAGACCGTGTCTAGGACATAGGCCTCGATTGAGATTTATGTATAAGACCATGTCTGGGACAT
1 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAGATTTACATATAAGACCATGTCTGGGACAT
* *
53853413 CGGTATCGTATCTGATTTCG
66 CAGCATCGTATCTGATTTCG
* * * * *
53853433 TGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGA-A-TTACATGTAAGACCACGTCTGGGAC
1 TGTAAGACCGTGTCTGGGACACAGGCCTCG--ATTGAGATTTACATATAAGACCATGTCTGGGAC
53853496 GTCGGCATTG
Statistics
Matches: 131, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
85 125 0.95
86 1 0.01
87 5 0.04
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (85 bp):
TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAGATTTACATATAAGACCATGTCTGGGACAT
CAGCATCGTATCTGATTTCG
Found at i:53853412 original size:43 final size:42
Alignment explanation
Indices: 53853265--53853412 Score: 158
Period size: 43 Copynumber: 3.5 Consensus size: 42
53853255 AGACATCATG
* * *
53853265 TAAGACCGTGTCTGGGACACATGCCTCGATTGAGATTTACATA
1 TAAGACCATGTCTGGGACATA-GCCTCGATTGAGATTTACGTA
* *
53853308 TAAGACCATGTCTGGGACATCAGCATCGTATCT--GATTT-CGTG
1 TAAGACCATGTCTGGGACAT-AGCCTCG-AT-TGAGATTTACGTA
* * *
53853350 TAAGACCGTGTCTAGGACATAGGCCTCGATTGAGATTTATGTA
1 TAAGACCATGTCTGGGACATA-GCCTCGATTGAGATTTACGTA
53853393 TAAGACCATGTCTGGGACAT
1 TAAGACCATGTCTGGGACAT
53853413 CGGTATCGTA
Statistics
Matches: 86, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 30 0.35
43 48 0.56
44 3 0.03
45 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACATAGCCTCGATTGAGATTTACGTA
Found at i:53853430 original size:43 final size:42
Alignment explanation
Indices: 53853306--53853503 Score: 177
Period size: 43 Copynumber: 4.7 Consensus size: 42
53853296 GAGATTTACA
*
53853306 TATAAGACCATGTCTGGGACATCAGCATCGTATCTGATTTCG
1 TATAAGACCATGTCTGGGACATCGGCATCGTATCTGATTTCG
* * * * * *
53853348 TGTAAGACCGTGTCTAGGACATAGGCCTCG-AT-TGAGATTTATG
1 TATAAGACCATGTCTGGGACATCGGCATCGTATCT--GATTT-CG
*
53853391 TATAAGACCATGTCTGGGACATCGGTATCGTATCTGATTTCG
1 TATAAGACCATGTCTGGGACATCGGCATCGTATCTGATTTCG
* * ** * *
53853433 TGTAAGACCCTGTCTGGGACAGAGGCATCGATAT-TGAATTACA
1 TATAAGACCATGTCTGGGACATCGGCATCG-TATCTG-ATTTCG
* * *
53853476 TGTAAGACCACGTCTGGGACGTCGGCAT
1 TATAAGACCATGTCTGGGACATCGGCAT
53853504 TGTACTTGTT
Statistics
Matches: 123, Mismatches: 26, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 57 0.46
43 60 0.49
44 2 0.02
45 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (42 bp):
TATAAGACCATGTCTGGGACATCGGCATCGTATCTGATTTCG
Found at i:53856783 original size:19 final size:19
Alignment explanation
Indices: 53856759--53856805 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
53856749 ATAATAATTG
53856759 CCTTTGATTCATTCTAAAT
1 CCTTTGATTCATTCTAAAT
*
53856778 CCTTTGATTCGTTCTAAAT
1 CCTTTGATTCATTCTAAAT
53856797 CCTTTGATT
1 CCTTTGATT
53856806 GAAAATCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (19 bp):
CCTTTGATTCATTCTAAAT
Found at i:53857975 original size:22 final size:21
Alignment explanation
Indices: 53857945--53857987 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
53857935 CCTTTTTCAT
*
53857945 ATTCTAAGCTTAATATCTATCAA
1 ATTCTAAGCCTAAT-TC-ATCAA
53857968 ATTC-AAGCCTAATTCATCAA
1 ATTCTAAGCCTAATTCATCAA
53857988 TATCTCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 8 0.42
23 4 0.21
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.35
Consensus pattern (21 bp):
ATTCTAAGCCTAATTCATCAA
Found at i:53861109 original size:21 final size:21
Alignment explanation
Indices: 53861075--53861115 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
53861065 AATATAGTTT
*
53861075 TATTAATAT-TTTAATGAAAA
1 TATTAATATATTAAATGAAAA
53861095 TATTAGATATATTAAATGAAA
1 TATTA-ATATATTAAATGAAA
53861116 CGGTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
TATTAATATATTAAATGAAAA
Found at i:53861573 original size:13 final size:13
Alignment explanation
Indices: 53861555--53861581 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53861545 TCAATAATTG
53861555 CACACGGGCGTGT
1 CACACGGGCGTGT
53861568 CACACGGGCGTGT
1 CACACGGGCGTGT
53861581 C
1 C
53861582 CCTACCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:53878642 original size:137 final size:137
Alignment explanation
Indices: 53878396--53878672 Score: 509
Period size: 137 Copynumber: 2.0 Consensus size: 137
53878386 AGATTGTTAG
*
53878396 AAAATTTGGACATCAGATATATAATAAGTATAATTACATGTTATTATTTACTATCATGATAGGTT
1 AAAATTTGGACATCAGATATATAATAAGGATAATTACATGTTATTATTTACTATCATGATAGGTT
* *
53878461 AGCCTAAATTAAAAGTGGTCTAATATGGTTAGAATTTTATTGGGCTTTTAATTATTAAATAAAGT
66 AGCCCAAATTAAAAGTGGTCTAATATGGTTAGAATTTTATTGGGCTTTTAATTATTAAATAAAAT
53878526 ATGGGTC
131 ATGGGTC
*
53878533 AAAATTTGGACATCAGATATGTAATAAGGATAATTACATGTTATTATTTACTATCATGATAGGTT
1 AAAATTTGGACATCAGATATATAATAAGGATAATTACATGTTATTATTTACTATCATGATAGGTT
*
53878598 AGCCCAAATTAAAAGTGGTCTAATTTGGTTAGAATTTTATTGGGCTTTTAATTATTAAATAAAAT
66 AGCCCAAATTAAAAGTGGTCTAATATGGTTAGAATTTTATTGGGCTTTTAATTATTAAATAAAAT
53878663 ATGGGTC
131 ATGGGTC
53878670 AAA
1 AAA
53878673 TATGTGTAGA
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (137 bp):
AAAATTTGGACATCAGATATATAATAAGGATAATTACATGTTATTATTTACTATCATGATAGGTT
AGCCCAAATTAAAAGTGGTCTAATATGGTTAGAATTTTATTGGGCTTTTAATTATTAAATAAAAT
ATGGGTC
Found at i:53888479 original size:21 final size:19
Alignment explanation
Indices: 53888454--53888492 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
53888444 GTAAATCCTT
53888454 ATTCTACATTTATAGTATAAC
1 ATTCTACA-TTATA-TATAAC
*
53888475 ATTCTATATTATATATAA
1 ATTCTACATTATATATAA
53888493 AAGAAAGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTCTACATTATATATAAC
Found at i:53890887 original size:25 final size:25
Alignment explanation
Indices: 53890859--53890908 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
53890849 TTCAAGCGAG
*
53890859 CCATATCAGGAAGCTTAAAAAGAGC
1 CCATATCAGGAAGCTCAAAAAGAGC
* *
53890884 CCATATCAGGACGCTCATAAAGAGC
1 CCATATCAGGAAGCTCAAAAAGAGC
53890909 TGTGTTCGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (25 bp):
CCATATCAGGAAGCTCAAAAAGAGC
Found at i:53892860 original size:44 final size:43
Alignment explanation
Indices: 53892787--53892939 Score: 161
Period size: 42 Copynumber: 3.6 Consensus size: 43
53892777 CATAGGATTC
* *
53892787 CGATATGTGATTT-GTGTAAGACCACGTCTGGGATGTTGGCAT
1 CGATATGTGATTTCATGTAAGACCATGTCTGGGATGTTGGCAT
* ** *
53892829 CGATATGTGATTTACGTGTAAGACCATGTCTGGGACATCGGCAT
1 CGATATGTGATTT-CATGTAAGACCATGTCTGGGATGTTGGCAT
* *
53892873 CGCATA--TGAGTTCATGTAAGACCCTGTCTGGGATAG-TGGCAT
1 CG-ATATGTGATTTCATGTAAGACCATGTCTGGGAT-GTTGGCAT
* *
53892915 CAATATGTGATTACATGTAAGACCA
1 CGATATGTGATTTCATGTAAGACCA
53892940 CTTTGTACGA
Statistics
Matches: 91, Mismatches: 14, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
41 3 0.03
42 38 0.42
43 20 0.22
44 27 0.30
45 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
CGATATGTGATTTCATGTAAGACCATGTCTGGGATGTTGGCAT
Found at i:53899426 original size:43 final size:43
Alignment explanation
Indices: 53899267--53899427 Score: 150
Period size: 43 Copynumber: 3.8 Consensus size: 43
53899257 GATATGTGTA
* *
53899267 TTCATGTAAGACCACGTCTGGGACGTTGGCACTGATATGTGAT
1 TTCATGTAAGACCACGTCTGGGACGTTGGCATTGATATATGAT
* * * * * * * *
53899310 TACGTGTAAGACCATGTCTGGGACATCGACATCG-TATTTGA-
1 TTCATGTAAGACCACGTCTGGGACGTTGGCATTGATATATGAT
* *
53899351 TTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATTGAGATATGAT
1 TTCATGTAAGACCAC-GTCTGGGAC-GTTGGCATTGATATATGAT
* *
53899394 TTCATGTAAGACCACATCTAGGACGTTGGCATTG
1 TTCATGTAAGACCACGTCTGGGACGTTGGCATTG
53899428 TACGATATTG
Statistics
Matches: 92, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
41 26 0.28
42 12 0.13
43 53 0.58
44 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
TTCATGTAAGACCACGTCTGGGACGTTGGCATTGATATATGAT
Found at i:53908385 original size:27 final size:27
Alignment explanation
Indices: 53908354--53908528 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
53908344 TAAATTGTAC
53908354 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
53908381 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
53908407 ATGCACTAAGTGTGCGAATTGACCA-G-
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
53908433 CG-GCTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
53908460 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
53908487 AGCACTAAGTGTGCGAGTTGACTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
53908514 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53908529 GACTCAATAT
Statistics
Matches: 122, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
24 12 0.10
25 7 0.06
26 2 0.02
27 89 0.73
28 12 0.10
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:53908465 original size:79 final size:78
Alignment explanation
Indices: 53908358--53908508 Score: 223
Period size: 79 Copynumber: 1.9 Consensus size: 78
53908348 TTGTACAGCA
* *
53908358 CTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGC
1 CTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTGTGC
53908422 GAATTGACCAGCGG
65 GAATTGACCAGCGG
** *
53908436 CTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGC
1 CTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTGC
*
53908501 GAGTTGAC
65 GAATTGAC
53908509 TATATAGCAC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
78 12 0.18
79 52 0.80
80 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (78 bp):
CTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTGCG
AATTGACCAGCGG
Found at i:53912371 original size:22 final size:22
Alignment explanation
Indices: 53912343--53912387 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
53912333 GTTGCGGATT
53912343 CGAGATTCGGACGTACCCAAAA
1 CGAGATTCGGACGTACCCAAAA
53912365 CGAGATTCGGACGTACCCAAAA
1 CGAGATTCGGACGTACCCAAAA
53912387 C
1 C
53912388 TGCTTCAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.29, G:0.22, T:0.13
Consensus pattern (22 bp):
CGAGATTCGGACGTACCCAAAA
Found at i:53916656 original size:27 final size:27
Alignment explanation
Indices: 53916626--53916773 Score: 188
Period size: 27 Copynumber: 5.4 Consensus size: 27
53916616 ATTGTACAGG
*
53916626 ACTAAGTGTGCGATTTGACTATGTTGC
1 ACTAAGTGTGCGATTTGACTATGTAGC
* * **
53916653 ACTAAGTGTGCGAATTGACCATGCGGC
1 ACTAAGTGTGCGATTTGACTATGTAGC
53916680 ACTAAGTGTGCGAGTTTGACTATGTAGC
1 ACTAAGTGTGCGA-TTTGACTATGTAGC
* *
53916708 ACTAAGTGTGCGATTTGATTACGTAGC
1 ACTAAGTGTGCGATTTGACTATGTAGC
* * *
53916735 ACTAAGTGTGCGAGTTGATTATATAGC
1 ACTAAGTGTGCGATTTGACTATGTAGC
*
53916762 ACTGAGTGTGCG
1 ACTAAGTGTGCG
53916774 GACTCAATAT
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 83 0.78
28 23 0.22
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (27 bp):
ACTAAGTGTGCGATTTGACTATGTAGC
Found at i:53916710 original size:55 final size:55
Alignment explanation
Indices: 53916626--53916773 Score: 192
Period size: 55 Copynumber: 2.7 Consensus size: 55
53916616 ATTGTACAGG
* * *
53916626 ACTAAGTGTGCGA-TTTGACTATGTTGCACTAAGTGTGCGAATTGACCATGCGGC
1 ACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAATTGACCACGCAGC
* ** *
53916680 ACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGC
1 ACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAATTGACCACGCAGC
* * *
53916735 ACTAAGTGTGCGAG-TTGATTATATAGCACTGAGTGTGCG
1 ACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCG
53916774 GACTCAATAT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 35 0.42
55 48 0.58
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (55 bp):
ACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAATTGACCACGCAGC
Found at i:53921870 original size:17 final size:18
Alignment explanation
Indices: 53921850--53921883 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53921840 TACCAAAACA
*
53921850 TGAATTATG-GATTAATT
1 TGAATAATGTGATTAATT
53921867 TGAATAATGTGATTAAT
1 TGAATAATGTGATTAAT
53921884 AAAAAAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (18 bp):
TGAATAATGTGATTAATT
Found at i:53929321 original size:49 final size:49
Alignment explanation
Indices: 53929249--53929435 Score: 247
Period size: 49 Copynumber: 3.8 Consensus size: 49
53929239 TGAGGTCACG
*
53929249 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTTGCA
* *
53929298 TGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CATGAAAACT-GTAAT-CA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCA-GATAATTGGT--TGCA
* * *
53929347 CGTGTGTAGTACTAAGTGCAGGCTACTA-GTGTACCAGATTATTGGTCGCA
1 --TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTTGCA
53929397 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
53929436 GCTTCGGCTA
Statistics
Matches: 119, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
48 30 0.25
49 48 0.40
50 11 0.09
51 30 0.25
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTTGCA
Found at i:53929416 original size:99 final size:100
Alignment explanation
Indices: 53929244--53929429 Score: 347
Period size: 99 Copynumber: 1.9 Consensus size: 100
53929234 TATTGTGAGG
*
53929244 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTTGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCGCATGTGTAGTACT
53929309 AAGTGCAGGCTACTATGCGTACATGAAAACTGTAA
66 AAGTGCAGGCTACTATGCGTACATGAAAACTGTAA
*
53929344 TCACGTGTGTAGTACTAAGTGCAGGCTACTA-GTGTACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCGCATGTGTAGTACT
53929408 AAGTGCAGGCTACTATGCGTAC
66 AAGTGCAGGCTACTATGCGTAC
53929430 CAGATAGCTT
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
99 53 0.63
100 31 0.37
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACATGAAAACTGTAA
Found at i:53930261 original size:24 final size:24
Alignment explanation
Indices: 53930229--53930294 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
53930219 CTTAACCTGA
53930229 ACAATTATAGTGTTTTATAATTGT
1 ACAATTATAGTGTTTTATAATTGT
* ** *
53930253 ACAATTATAAT-AATAAGTAATTGT
1 ACAATTATAGTGTTTTA-TAATTGT
53930277 ACAATTATAGTGTTTTAT
1 ACAATTATAGTGTTTTAT
53930295 CTTGAAAAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
23 2 0.06
24 28 0.88
25 2 0.06
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (24 bp):
ACAATTATAGTGTTTTATAATTGT
Found at i:53933851 original size:27 final size:26
Alignment explanation
Indices: 53933781--53933855 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
53933771 CAACATGGCT
*
53933781 ACCAGAATAGATATTGTGACAGAGTC
1 ACCAGAATAGATATTGTGGCAGAGTC
53933807 ACCAGATATAGATATTGTGGCAGAG-C
1 ACCAGA-ATAGATATTGTGGCAGAGTC
*
53933833 GACCAGAACAGATATTTGTGGCA
1 -ACCAGAATAGATA-TTGTGGCA
53933856 TAGCCACCGG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 13 0.30
27 31 0.70
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (26 bp):
ACCAGAATAGATATTGTGGCAGAGTC
Found at i:53933868 original size:27 final size:26
Alignment explanation
Indices: 53933781--53933868 Score: 95
Period size: 27 Copynumber: 3.3 Consensus size: 26
53933771 CAACATGGCT
* * *
53933781 ACCAGAATAGATATTGTGACAGAGTC
1 ACCAGAACAGATATTGTGGCAGAGCC
* *
53933807 ACCAGATATAGATATTGTGGCAGAGCG
1 ACCAGA-ACAGATATTGTGGCAGAGCC
*
53933834 ACCAGAACAGATATTTGTGGCATAGCC
1 ACCAGAACAGATA-TTGTGGCAGAGCC
*
53933861 ACCGGAAC
1 ACCAGAAC
53933869 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 12 0.23
27 41 0.77
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (26 bp):
ACCAGAACAGATATTGTGGCAGAGCC
Found at i:53940903 original size:20 final size:21
Alignment explanation
Indices: 53940853--53940903 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
53940843 ACCCATCCCC
*
53940853 ATGCAATATGTCATGCATCGT
1 ATGCAATATATCATGCATCGT
*
53940874 A--CCATAATATCATGCAT-GT
1 ATGCAAT-ATATCATGCATCGT
53940893 ATGCAATATAT
1 ATGCAATATAT
53940904 AGAAATGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 7
0.71 0.09 0.21
Matches are distributed among these distances:
19 6 0.25
20 14 0.58
21 4 0.17
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (21 bp):
ATGCAATATATCATGCATCGT
Found at i:53952130 original size:38 final size:38
Alignment explanation
Indices: 53952079--53952161 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 38
53952069 AAGACAAGAG
*
53952079 TAAGTATACAATGATAATTATGAGAATGATTACATGAA
1 TAAGTATGCAATGATAATTATGAGAATGATTACATGAA
53952117 TAAGTATGCAATGATAATTATGAGAATGATTACATGAA
1 TAAGTATGCAATGATAATTATGAGAATGATTACATGAA
53952155 TAA-TATG
1 TAAGTATG
53952162 TAAACAACAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 4 0.09
38 40 0.91
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.33
Consensus pattern (38 bp):
TAAGTATGCAATGATAATTATGAGAATGATTACATGAA
Found at i:53953141 original size:30 final size:30
Alignment explanation
Indices: 53953107--53953167 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
53953097 CAAGAATAAC
53953107 TTAGTCATGGTTTTACTTAATCCAACATCT
1 TTAGTCATGGTTTTACTTAATCCAACATCT
53953137 TTAGTCATGGTTTTACTTAATCCAACATCT
1 TTAGTCATGGTTTTACTTAATCCAACATCT
53953167 T
1 T
53953168 ATCGAGGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (30 bp):
TTAGTCATGGTTTTACTTAATCCAACATCT
Found at i:53955004 original size:43 final size:42
Alignment explanation
Indices: 53954957--53955055 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 42
53954947 TCCCAGATGT
*
53954957 GGTCTTACATGTAATCAAATATCGATG-CCACTATCCCAGACAG
1 GGTCTTACACGTAATCAAATA-CGATGTCCA-TATCCCAGACAG
* * * *
53955000 GGTCTTACACGAAATCAAATACGATGTCGATGTCCCAGACAT
1 GGTCTTACACGTAATCAAATACGATGTCCATATCCCAGACAG
53955042 GGTCTTACACGTAA
1 GGTCTTACACGTAA
53955056 ATCATAAGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
42 28 0.57
43 21 0.43
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (42 bp):
GGTCTTACACGTAATCAAATACGATGTCCATATCCCAGACAG
Found at i:53955058 original size:43 final size:44
Alignment explanation
Indices: 53954938--53955059 Score: 137
Period size: 43 Copynumber: 2.8 Consensus size: 44
53954928 AGTTCATACA
** *
53954938 ATGCCAAC-GTCCCAGATGTGGTCTTACATGT-AATCAAATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGTAAATCAAATATCG
* *
53954981 ATGCCACTATCCCAGACAGGGTCTTACACG-AAATCAAATA-CG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAAATCAAATATCG
*
53955023 ATGTCGA-TGTCCCAGACATGGTCTTACACGTAAATCA
1 ATG-CCACTGTCCCAGACATGGTCTTACACGTAAATCA
53955060 TAAGTTGATG
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
42 28 0.42
43 39 0.58
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGTAAATCAAATATCG
Found at i:53957960 original size:25 final size:25
Alignment explanation
Indices: 53957932--53958010 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 25
53957922 CGAATGACCA
53957932 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
* * * *
53957957 ATGTG-TTAAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-TGAACAT-GCATAT
53957979 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
*
53958004 GTGTGAT
1 ATGTGAT
53958011 AAGGCCGAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 14
0.62 0.15 0.23
Matches are distributed among these distances:
22 6 0.16
23 10 0.26
24 10 0.26
25 12 0.32
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (25 bp):
ATGTGATGAATGTGAACATGCATAT
Found at i:53957980 original size:47 final size:47
Alignment explanation
Indices: 53957906--53958031 Score: 207
Period size: 47 Copynumber: 2.7 Consensus size: 47
53957896 TTTTATGTGT
* *
53957906 ATATATGAGATAAGGCCGAATGACCAATGTGATGAATGTGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
*
53957953 ATATATGTGTTAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* *
53958000 ATATGTGTGATAAGGCCGAATGGCTAATGTGA
1 ATATATGTGATAAGGCCGAATGGCCAATGTGA
53958032 AACATGTATG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
Found at i:53958070 original size:48 final size:48
Alignment explanation
Indices: 53957954--53958144 Score: 210
Period size: 48 Copynumber: 4.0 Consensus size: 48
53957944 TGAACATGCA
* * * * *
53957954 TATATGTGTTAAGGCCGAATGGCCAATGTGATGA-ATG--TGA-ACATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGA-AATATGTATGAGATATG
* * *
53957999 CATATGTGTGATAAGGCCGAATGGCTAATGTGAAACATGTATGAGATATG
1 TATATGTG-G-TAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
*
53958049 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* * * *
53958097 TATATGTGGTGAAGCCGAATGGCTAGTGTGAAATATGTAGGCGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
53958145 CGTATATCGT
Statistics
Matches: 128, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
45 7 0.05
46 1 0.01
47 24 0.19
48 81 0.63
49 4 0.03
50 11 0.09
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:53958336 original size:37 final size:37
Alignment explanation
Indices: 53958286--53958394 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
53958276 ATATATTCCA
*
53958286 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
53958323 GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
* *
53958360 GGTAAGACCCGATAACTTCGTGTGGAGATTTTGTC
1 GGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
53958395 TGAGCTAAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (37 bp):
GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
Found at i:53959581 original size:8 final size:8
Alignment explanation
Indices: 53959568--53959599 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
53959558 ATTAGCCCTC
53959568 ACATTTTG
1 ACATTTTG
53959576 ACATTTTTG
1 ACA-TTTTG
53959585 ACATTTTG
1 ACATTTTG
53959593 ACATTTT
1 ACATTTT
53959600 AGTCCCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (8 bp):
ACATTTTG
Found at i:53959585 original size:9 final size:9
Alignment explanation
Indices: 53959571--53959599 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
53959561 AGCCCTCACA
53959571 TTTTGACAT
1 TTTTGACAT
53959580 TTTTGACA-
1 TTTTGACAT
53959588 TTTTGACAT
1 TTTTGACAT
53959597 TTT
1 TTT
53959600 AGTCCCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (9 bp):
TTTTGACAT
Found at i:53963931 original size:24 final size:25
Alignment explanation
Indices: 53963896--53963954 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
53963886 TTAATCAGTA
*
53963896 TAAAATATTAA-TAATTCAAT-AAAT
1 TAAAAT-TTAATTAATTAAATAAAAT
53963920 TGAAAATTTAATTAATTAAATAAAAT
1 T-AAAATTTAATTAATTAAATAAAAT
53963946 TAAAATTTA
1 TAAAATTTA
53963955 GGAGAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 5 0.16
25 21 0.68
26 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
TAAAATTTAATTAATTAAATAAAAT
Found at i:53964650 original size:22 final size:19
Alignment explanation
Indices: 53964611--53964652 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
53964601 TGCAAAGTTG
53964611 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
53964630 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
53964652 A
1 A
53964653 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:53969014 original size:2 final size:2
Alignment explanation
Indices: 53969009--53969034 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53968999 TATATATATA
53969009 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
53969035 ATTATATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:53970099 original size:39 final size:39
Alignment explanation
Indices: 53970045--53970223 Score: 243
Period size: 39 Copynumber: 4.5 Consensus size: 39
53970035 TAATGGAGAA
* *
53970045 TTATATCCGGGCTAAGTCTCAAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
53970084 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
53970123 TTATATCCGGGCTAAGCCCCGAAGGTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
53970162 TTATATGCGGGCTAAAGTCCCGTAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
*
53970201 TTATATTCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
53970224 CATGCTTTGT
Statistics
Matches: 127, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 107 0.84
40 20 0.16
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:53976317 original size:46 final size:46
Alignment explanation
Indices: 53976267--53976439 Score: 176
Period size: 46 Copynumber: 3.7 Consensus size: 46
53976257 TGGTTGAGCA
53976267 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
53976313 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
53976358 CATCAGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
53976406 -CCTGAGCTCGTTGAGTTGAGTCCAAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
53976440 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 4 0.04
46 57 0.56
47 27 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53976401 original size:93 final size:93
Alignment explanation
Indices: 53976264--53976434 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
53976254 GGATGGTTGA
* *
53976264 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGAG
1 GCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAACTCGTTGAG
*
53976328 TTGAGTCCGAGTTCGTGAAATGTAACTAG
65 TTGAGTCCAAGTTCGTGAAATGTAACTAG
* *
53976357 GCATCAGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCTGAGCTCGTTGAGT
1 GCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAGT
53976422 TGAGTCCAAGTTC
66 TGAGTCCAAGTTC
53976435 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAGT
TGAGTCCAAGTTCGTGAAATGTAACTAG
Found at i:53977860 original size:2 final size:2
Alignment explanation
Indices: 53977855--53977898 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
53977845 TTTATATATA
*
53977855 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
53977897 TG
1 TG
53977899 ATTATATTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:53981193 original size:21 final size:22
Alignment explanation
Indices: 53981164--53981210 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
53981154 CAGAAGGAGT
*
53981164 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
53981186 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
53981207 GAGT
1 GAGT
53981211 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:53982606 original size:39 final size:39
Alignment explanation
Indices: 53982552--53982769 Score: 330
Period size: 39 Copynumber: 5.5 Consensus size: 39
53982542 TAATGGAGAA
*
53982552 TTATATCCGGGCTAAGTCTCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
53982591 TTATATCCGGGCTAAGTCCCGAAGGCATTCATGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
53982630 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
53982669 TTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
53982708 TTATATGCGGGCTAAAGTCCCGTAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
*
53982747 TTATATTCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
53982770 CATGCTTTGT
Statistics
Matches: 167, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
39 146 0.87
40 21 0.13
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:53992697 original size:20 final size:19
Alignment explanation
Indices: 53992661--53992711 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
53992651 AAGGTCTATT
*
53992661 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
53992680 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
53992700 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
53992712 GTTTCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:53995198 original size:13 final size:13
Alignment explanation
Indices: 53995175--53995206 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
53995165 TGTATCTAGG
53995175 CTTGATATGTGAAA
1 CTTG-TATGTGAAA
53995189 CTTGTATGTGAAA
1 CTTGTATGTGAAA
53995202 CTTGT
1 CTTGT
53995207 GAAACTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (13 bp):
CTTGTATGTGAAA
Found at i:54010029 original size:27 final size:27
Alignment explanation
Indices: 54009991--54010106 Score: 126
Period size: 27 Copynumber: 4.3 Consensus size: 27
54009981 CAAAACAATC
* * * *
54009991 ATTTTACCCTACAGGGGTATGTCGGTC
1 ATTTTACACTACAAGGGTATTTCGGTA
54010018 ATTTTACACTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
* * *
54010045 ATTTTACACCATAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATTTCGGTA
* * *
54010072 ATTTTACA-AATCAGGGGTGTTTCGGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
54010099 ATTTTACA
1 ATTTTACA
54010107 AATTGAGGGT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
26 1 0.01
27 75 0.99
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:54010444 original size:27 final size:27
Alignment explanation
Indices: 54010031--54010448 Score: 373
Period size: 27 Copynumber: 15.7 Consensus size: 27
54010021 TTACACTACA
* * *
54010031 AGGGTATTTCGGTAATTTTACACCA-TA
1 AGGGTATTTCAGTAATTTTACA-AATTG
*
54010058 AGGGTATTTC-GATAATTTTACAAA-TC
1 AGGGTATTTCAG-TAATTTTACAAATTG
* *
54010084 AGGGGTGTTTCGGTAATTTTACAAATTG
1 A-GGGTATTTCAGTAATTTTACAAATTG
* *
54010112 AGGGTATTT-TGACAATTTTACAAATTG
1 AGGGTATTTCAG-TAATTTTACAAATTG
* *
54010139 AAGGTATTTCAATAATTTTACAAATTG
1 AGGGTATTTCAGTAATTTTACAAATTG
* *
54010166 AGGGTGTTTC-GATAATTTTAAAAATCT-
1 AGGGTATTTCAG-TAATTTTACAAAT-TG
* *
54010193 AGGGTGTTTC-GATAATTTTACAAATCG
1 AGGGTATTTCAG-TAATTTTACAAATTG
* * * *
54010220 AGGGTGTTTC-GATAATTTCAAAAATCG
1 AGGGTATTTCAG-TAATTTTACAAATTG
*
54010247 -GGGTATTTC-GATAATTTTACAAATCG
1 AGGGTATTTCAG-TAATTTTACAAATTG
* *
54010273 AGGGTATTTTAGTAATTTCAC-AATTG
1 AGGGTATTTCAGTAATTTTACAAATTG
54010299 AGGGTA-TTCAGTAATTTTACAAATT-
1 AGGGTATTTCAGTAATTTTACAAATTG
*
54010324 AGGGGTATTTCAGTAATTTCAC-AATTG
1 A-GGGTATTTCAGTAATTTTACAAATTG
* *
54010351 AGGGTATTTC-GATAATTTTACGAATCG
1 AGGGTATTTCAG-TAATTTTACAAATTG
* **
54010378 AGGGTATTTCAGTAATTTCAC-AATCA
1 AGGGTATTTCAGTAATTTTACAAATTG
*
54010404 AGGGTATTTTAGTAATTTTACAAATTG
1 AGGGTATTTCAGTAATTTTACAAATTG
54010431 AGGGTATTTCAGTAATTT
1 AGGGTATTTCAGTAATTT
54010449 CTCTTTATTA
Statistics
Matches: 335, Mismatches: 37, Indels: 38
0.82 0.09 0.09
Matches are distributed among these distances:
25 14 0.04
26 91 0.27
27 224 0.67
28 6 0.02
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAATTG
Found at i:54013299 original size:27 final size:26
Alignment explanation
Indices: 54013265--54013345 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 26
54013255 AAGGGAAAAA
* **
54013265 TAGTCATTTTACCCTACCGGGGTATGT
1 TAGTCATTTTACACTACAAGGGTAT-T
54013292 TAGTCATTTTACACTACAAGGGTATT
1 TAGTCATTTTACACTACAAGGGTATT
*
54013318 TCAGTAATTTTACACTACAAGGGTATT
1 T-AGTCATTTTACACTACAAGGGTATT
54013345 T
1 T
54013346 CGATAATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 2 0.04
27 47 0.96
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (26 bp):
TAGTCATTTTACACTACAAGGGTATT
Found at i:54013346 original size:27 final size:27
Alignment explanation
Indices: 54013310--54013729 Score: 430
Period size: 27 Copynumber: 15.7 Consensus size: 27
54013300 TTACACTACA
* *
54013310 AGGGTATTTCAGTAATTTTAC-ACTACA
1 AGGGTATTTCAGTAATTTTACAAAT-CG
54013337 AGGGTATTTC-GATAATTTTACAAATCG
1 AGGGTATTTCAG-TAATTTTACAAATCG
*
54013364 AGGGTATTTCAATAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* ***
54013391 AGGGTATTTCGGTAATTTTTTTAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
54013418 AGGGTATTTC-GATAATTTTACAAATCG
1 AGGGTATTTCAG-TAATTTTACAAATCG
* *
54013445 AGGGTGTTTC-GATAATTTTACAAATCA
1 AGGGTATTTCAG-TAATTTTACAAATCG
* * *
54013472 AGGGTGTTTTC-GTAATTTCACAGATCG
1 AGGGT-ATTTCAGTAATTTTACAAATCG
**
54013499 AGGGTATTTC-GATAATTTTACAAATTA
1 AGGGTATTTCAG-TAATTTTACAAATCG
* * *
54013526 AGAGTATTTTAGTAA-TTT-CATAACCG
1 AGGGTATTTCAGTAATTTTACA-AATCG
* *
54013552 AGGGTATTTAAGTAACTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* *
54013579 AGGGTATTTCAGTAATTTAAC-AATTG
1 AGGGTATTTCAGTAATTTTACAAATCG
* **
54013605 AGGATATTTTGGTAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* *
54013632 AGGGTATTTTAGTAATTTCAC-AATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
*
54013658 AGGGTATTTC-GATAATTTTACAAATCA
1 AGGGTATTTCAG-TAATTTTACAAATCG
*
54013685 AGGGTATTTCAGTAATTTTACAAATCA
1 AGGGTATTTCAGTAATTTTACAAATCG
*
54013712 AGGATATTTCAGTAATTT
1 AGGGTATTTCAGTAATTT
54013730 CTCTTTATTA
Statistics
Matches: 333, Mismatches: 46, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
25 3 0.01
26 68 0.20
27 251 0.75
28 11 0.03
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAATCG
Found at i:54014083 original size:28 final size:28
Alignment explanation
Indices: 54014046--54014109 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
54014036 TGGCCCCTTT
*
54014046 AGGCCCAATC-TCGTTCACATGGCCCATC
1 AGGCCCAATCAT-ATTCACATGGCCCATC
** *
54014074 AGGCCCAATCATATTCGTATGGCCTATC
1 AGGCCCAATCATATTCACATGGCCCATC
54014102 AGGCCCAA
1 AGGCCCAA
54014110 CTACTTCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (28 bp):
AGGCCCAATCATATTCACATGGCCCATC
Found at i:54030828 original size:50 final size:50
Alignment explanation
Indices: 54030709--54030935 Score: 269
Period size: 49 Copynumber: 4.5 Consensus size: 50
54030699 ACTGTGAGAA
* * * * **
54030709 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACGGGTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TAG-TTAGGT
* * *
54030761 CACGTGTGTAGTACTAAGAGCAGGCTACTACGTGTACCAGATAGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGGT
* * * *
54030811 CGCATGTGTAGTACTAAGTGCAGGC-ACTACGTGTTTCAAATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGGT
* * * *
54030860 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCGGATTGTT-GGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGGT
54030909 CACATGTGTAGTACTAAGTGCAGGCTA
1 CACATGTGTAGTACTAAGTGCAGGCTA
54030936 ATATGCGTAC
Statistics
Matches: 150, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
49 72 0.48
50 43 0.29
51 1 0.01
52 34 0.23
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGGT
Found at i:54030885 original size:99 final size:101
Alignment explanation
Indices: 54030709--54030935 Score: 327
Period size: 99 Copynumber: 2.3 Consensus size: 101
54030699 ACTGTGAGAA
* *
54030709 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACGGGTTTAGGTCACGTGTGTAGTA
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTTTAAGACGGGTTTAGGTCACGTGTGTAGTA
*
54030774 CTAAGAGCAGGCTACTACGTGTACCAGATAGTTAGGT
66 CTAAGAGCAGGCTACTACATGTACCAGATAGTT-GGT
* *
54030811 CGCATGTGTAGTACTAAGTGCAGGC-ACTACGTGTTTCAA-A-TGG-TTAGGTCACGTGTGTAGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTTT-AAGACGGGTTTAGGTCACGTGTGTAGT
* * * *
54030872 ACTAAGTGCAGGCTACTACATGTATCGGATTGTTGGT
65 ACTAAGAGCAGGCTACTACATGTACCAGATAGTTGGT
54030909 CACATGTGTAGTACTAAGTGCAGGCTA
1 CACATGTGTAGTACTAAGTGCAGGCTA
54030936 ATATGCGTAC
Statistics
Matches: 113, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
98 27 0.24
99 48 0.42
100 2 0.02
101 11 0.10
102 25 0.22
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (101 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTTTAAGACGGGTTTAGGTCACGTGTGTAGTA
CTAAGAGCAGGCTACTACATGTACCAGATAGTTGGT
Found at i:54037763 original size:101 final size:101
Alignment explanation
Indices: 54037603--54037784 Score: 265
Period size: 101 Copynumber: 1.8 Consensus size: 101
54037593 TGGTTTTAGG
* * * *
54037603 TCACGTGTGTAGTACTAAGAGTAGGCTATTACGTGTACCAAATAGTGAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTAAGAGTAGGCTACTACATGTACCAAATAGTGAGGTCACATGTGTAGTAC
54037668 TAAGTGCAGGCTACTATGCGTACCTGACAACTTCAA
66 TAAGTGCAGGCTACTATGCGTACCTGACAACTTCAA
* * * * * *
54037704 TCACATGTGTAGTACTAAGTGTAGGCTACTACATGTATCAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACATGTGTAGTACTAAGAGTAGGCTACTACATGTACCAAATAGTGAGGTCACATGTGTAGTAC
*
54037769 TAAGTGTAGGCTACTA
66 TAAGTGCAGGCTACTA
54037785 CGTGTATTGG
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 70 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTAAGAGTAGGCTACTACATGTACCAAATAGTGAGGTCACATGTGTAGTAC
TAAGTGCAGGCTACTATGCGTACCTGACAACTTCAA
Found at i:54037831 original size:49 final size:50
Alignment explanation
Indices: 54037552--54037833 Score: 212
Period size: 50 Copynumber: 5.6 Consensus size: 50
54037542 ATTGTAAGAA
* * * *
54037552 CACATGTGTAGTACTATGTGCAAGCTACT--ATGTATTTAAGATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGTAGGCTACTACATGTA--TCAGATGG--TTAGGT
* * * * * * * *
54037604 CACGTGTGTAGTACTAAGAGTAGGCTATTACGTGTACCAAATAGTGAGGT
1 CACATGTGTAGTACTAAGTGTAGGCTACTACATGTATCAGATGGTTAGGT
* * *** * * *** *
54037654 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGACAACTTCA-AT
1 CACATGTGTAGTACTAAGTGTAGGCTACTACATGTATCAGA-TGGTT-AGGT
54037705 CACATGTGTAGTACTAAGTGTAGGCTACTACATGTATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGTAGGCTACTACATGTATCAGATGGTTAGGT
* * ** *
54037755 CACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATTGGATTGTT-GGT
1 CACATGTGTAGTACTAAGTGTAGGCTACTACATGTATCAGATGGTTAGGT
* *
54037804 CGCATGTGTAGTACTAAGTGCAGGCTACTA
1 CACATGTGTAGTACTAAGTGTAGGCTACTA
54037834 TGCGTACCAG
Statistics
Matches: 181, Mismatches: 44, Indels: 13
0.76 0.18 0.05
Matches are distributed among these distances:
49 31 0.17
50 81 0.45
51 37 0.20
52 28 0.15
54 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGTAGGCTACTACATGTATCAGATGGTTAGGT
Found at i:54037840 original size:150 final size:151
Alignment explanation
Indices: 54037552--54037841 Score: 415
Period size: 151 Copynumber: 1.9 Consensus size: 151
54037542 ATTGTAAGAA
*
54037552 CACATGTGTAGTACTATGTGCAAGCTACTATGTATTTAAGATGGTTTTAGGTCACGTGTGTAGTA
1 CACATGTGTAGTACTAAGTGCAAGCTACTATGTA-TTAAGATGG-TTTAGGTCACGTGTGTAGTA
*
54037617 CTAAGAGTAGGCTATTACGTGTACCAAATAGTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTAC
64 CTAAGAGTAGGCTACTACGTGTACCAAATAGTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTAC
54037682 TATGCGTACCTGACAACTTCAAT
129 TATGCGTACCTGACAACTTCAAT
* * *
54037705 CACATGTGTAGTACTAAGTGTAGGCTACTACATGTA-TCAGATGG-TTAGGTCACGTGTGTAGTA
1 CACATGTGTAGTACTAAGTGCAAGCTACT--ATGTATTAAGATGGTTTAGGTCACGTGTGTAGTA
* **** * *
54037768 CTAAGTGTAGGCTACTACGTGTATTGGATTGT-TGGTCGCATGTGTAGTACTAAGTGCAGGCTAC
64 CTAAGAGTAGGCTACTACGTGTACCAAATAGTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTAC
54037832 TATGCGTACC
129 TATGCGTACC
54037842 AGATAGCTTC
Statistics
Matches: 123, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
150 41 0.33
151 44 0.36
153 33 0.27
155 5 0.04
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (151 bp):
CACATGTGTAGTACTAAGTGCAAGCTACTATGTATTAAGATGGTTTAGGTCACGTGTGTAGTACT
AAGAGTAGGCTACTACGTGTACCAAATAGTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
TGCGTACCTGACAACTTCAAT
Found at i:54037876 original size:150 final size:151
Alignment explanation
Indices: 54037598--54037877 Score: 382
Period size: 150 Copynumber: 1.9 Consensus size: 151
54037588 TAAGATGGTT
*
54037598 TTAGGTCACGTGTGTAGTACTAAGAGTAGGCTATTACGTGTACCAAATAGTGAGGTCGCATGTGT
1 TTAGGTCACGTGTGTAGTACTAAGAGTAGGCTACTACGTGTACCAAATAGTGAGGTCGCATGTGT
* * * *
54037663 AGTACTAAGTGCAGGCTACTATGCGTACCTGACAACTTCAATCACATGTGTAGTACTAAGTGTAG
66 AGTACTAAGTGCAGGCTACTATGCGTACCAGACAACTTCAATCACAAGGGTAGTAATAAGTGTAG
54037728 GCTACTACATGTATCAGATGG
131 GCTACTACATGTATCAGATGG
* **** * *
54037749 TTAGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATTGGATTGT-TGGTCGCATGTGT
1 TTAGGTCACGTGTGTAGTACTAAGAGTAGGCTACTACGTGTACCAAATAGTGAGGTCGCATGTGT
* * ** * * *
54037813 AGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTCGGTTACAAGGGTGGTAATATGTGTAG
66 AGTACTAAGTGCAGGCTACTATGCGTACCAGACAACTTCAATCACAAGGGTAGTAATAAGTGTAG
54037878 ACAACCGTGT
Statistics
Matches: 110, Mismatches: 19, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
150 66 0.60
151 44 0.40
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (151 bp):
TTAGGTCACGTGTGTAGTACTAAGAGTAGGCTACTACGTGTACCAAATAGTGAGGTCGCATGTGT
AGTACTAAGTGCAGGCTACTATGCGTACCAGACAACTTCAATCACAAGGGTAGTAATAAGTGTAG
GCTACTACATGTATCAGATGG
Found at i:54039851 original size:17 final size:18
Alignment explanation
Indices: 54039829--54039863 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54039819 CATTACGGGC
54039829 TGTGTGGG-CCACATGGG
1 TGTGTGGGCCCACATGGG
54039846 TGTGTGGGCCCACATGGG
1 TGTGTGGGCCCACATGGG
54039864 CTCGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.20, G:0.46, T:0.23
Consensus pattern (18 bp):
TGTGTGGGCCCACATGGG
Found at i:54043526 original size:43 final size:42
Alignment explanation
Indices: 54043491--54043581 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
54043481 TCTTACTTGT
* *
54043491 AATCAAATATCGATGCCACTGTCCCAGACAGGGTCTTACACGA
1 AATCAAATA-CGAAGCCAATGTCCCAGACAGGGTCTTACACGA
* *
54043534 AATCAAATACGAAGCCAATGTCCTAGACATGGTCTTACACGTA
1 AATCAAATACGAAGCCAATGTCCCAGACAGGGTCTTACACG-A
54043577 AATCA
1 AATCA
54043582 TAAGTCGATG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 28 0.65
43 15 0.35
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.22
Consensus pattern (42 bp):
AATCAAATACGAAGCCAATGTCCCAGACAGGGTCTTACACGA
Found at i:54043569 original size:42 final size:43
Alignment explanation
Indices: 54043470--54043619 Score: 142
Period size: 43 Copynumber: 3.5 Consensus size: 43
54043460 ATGCCAACAA
* ** * * *
54043470 CCCAGACGTGGTCTTACTTGTAATCAAATATCGATGCCACTGT
1 CCCAGACATGGTCTTACACGAAATCAAATATCGAAGCCAATGT
*
54043513 CCCAGACAGGGTCTTACACGAAATCAAATA-CGAAGCCAATGT
1 CCCAGACATGGTCTTACACGAAATCAAATATCGAAGCCAATGT
* * * **
54043555 CCTAGACATGGTCTTACACGTAAATCATAA-GTCGATGCCAACAT
1 CCCAGACATGGTCTTACACG-AAATCA-AATATCGAAGCCAATGT
**
54043599 CCCAGATGTGGTCTTACACGA
1 CCCAGACATGGTCTTACACGA
54043620 TAGCACATAT
Statistics
Matches: 88, Mismatches: 16, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 28 0.32
43 32 0.36
44 28 0.32
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (43 bp):
CCCAGACATGGTCTTACACGAAATCAAATATCGAAGCCAATGT
Found at i:54045443 original size:58 final size:58
Alignment explanation
Indices: 54045381--54045496 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
54045371 GAATTTGGAC
*
54045381 ATGTCTTGTCAAATACCAATTTAATAAGAAAAAAATGTTGATTTTCCAGAAACAAAGT
1 ATGTCTTGTCAAATACCAATTTAATAAGAAAAAAATGTTGAGTTTCCAGAAACAAAGT
* *
54045439 ATGTCTTGTCAAATACCAATTTAATGAGAAAATAATGTTGAGTTTCCAGAAACAAAGT
1 ATGTCTTGTCAAATACCAATTTAATAAGAAAAAAATGTTGAGTTTCCAGAAACAAAGT
54045497 TTTATATTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (58 bp):
ATGTCTTGTCAAATACCAATTTAATAAGAAAAAAATGTTGAGTTTCCAGAAACAAAGT
Found at i:54046395 original size:36 final size:35
Alignment explanation
Indices: 54046337--54046440 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 35
54046327 TTTACATGCA
* **
54046337 AATCAAAATCAGTATAGCAGCATGCTTAACATGTG
1 AATCAAAATCAGAATAATAGCATGCTTAACATGTG
54046372 AATCAAAAATCAGAATAATAGCATGCTTAACATGTG
1 AATC-AAAATCAGAATAATAGCATGCTTAACATGTG
* *
54046408 AATCGAAATCAGAATAATAGCATGTTTAACATG
1 AATCAAAATCAGAATAATAGCATGCTTAACATG
54046441 CAAATCAGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 31 0.49
36 32 0.51
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.26
Consensus pattern (35 bp):
AATCAAAATCAGAATAATAGCATGCTTAACATGTG
Found at i:54046446 original size:29 final size:32
Alignment explanation
Indices: 54046355--54046452 Score: 94
Period size: 35 Copynumber: 2.9 Consensus size: 32
54046345 TCAGTATAGC
*
54046355 AGCATGCTTAACATGTGAATCAAAAATCAGAATAAT
1 AGCATGCTTAACA-GTG-A-C-GAAATCAGAATAAT
54046391 AGCATGCTTAACATGTGAATCGAAATCAGAATAAT
1 AGCATGCTTAACA-GTG-A-CGAAATCAGAATAAT
*
54046426 AGCATGTTTAACA-TG-C-AAATCAGAATA
1 AGCATGCTTAACAGTGACGAAATCAGAATA
54046453 TTCAAATCAG
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.18
30 1 0.02
33 2 0.03
35 25 0.42
36 21 0.35
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (32 bp):
AGCATGCTTAACAGTGACGAAATCAGAATAAT
Found at i:54047750 original size:18 final size:20
Alignment explanation
Indices: 54047714--54047750 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
54047704 TTAATACATC
54047714 TAAAATTATTTGTTCAATAA
1 TAAAATTATTTGTTCAATAA
54047734 TAAAA-TATTTG-TCAATA
1 TAAAATTATTTGTTCAATA
54047751 TTCGGACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 6 0.35
20 5 0.29
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (20 bp):
TAAAATTATTTGTTCAATAA
Found at i:54047872 original size:16 final size:16
Alignment explanation
Indices: 54047851--54047883 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54047841 TTGTAACGCC
54047851 CCAAAAATCCTGAAAT
1 CCAAAAATCCTGAAAT
54047867 CCAAAAATCCTGAAAT
1 CCAAAAATCCTGAAAT
54047883 C
1 C
54047884 TTGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (16 bp):
CCAAAAATCCTGAAAT
Found at i:54049124 original size:16 final size:16
Alignment explanation
Indices: 54049103--54049153 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
54049093 ATGAATCTGC
*
54049103 AAAAGCCGAAATGCCA
1 AAAAGCCGAAAAGCCA
*
54049119 AAAAGCCAAAAAGCCA
1 AAAAGCCGAAAAGCCA
*
54049135 AAATGCCGAAAAGCCA
1 AAAAGCCGAAAAGCCA
54049151 AAA
1 AAA
54049154 GTTGGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.24, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAGCCGAAAAGCCA
Found at i:54049128 original size:8 final size:8
Alignment explanation
Indices: 54049103--54049153 Score: 66
Period size: 8 Copynumber: 6.4 Consensus size: 8
54049093 ATGAATCTGC
*
54049103 AAAAGCCG
1 AAAAGCCA
*
54049111 AAATGCCA
1 AAAAGCCA
54049119 AAAAGCCA
1 AAAAGCCA
54049127 AAAAGCCA
1 AAAAGCCA
* *
54049135 AAATGCCG
1 AAAAGCCA
54049143 AAAAGCCA
1 AAAAGCCA
54049151 AAA
1 AAA
54049154 GTTGGGCTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.57, C:0.24, G:0.16, T:0.04
Consensus pattern (8 bp):
AAAAGCCA
Found at i:54049133 original size:24 final size:24
Alignment explanation
Indices: 54049103--54049153 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
54049093 ATGAATCTGC
*
54049103 AAAAGCCGAAATGCCAAAAAGCCA
1 AAAAGCCAAAATGCCAAAAAGCCA
*
54049127 AAAAGCCAAAATGCCGAAAAGCCA
1 AAAAGCCAAAATGCCAAAAAGCCA
54049151 AAA
1 AAA
54049154 GTTGGGCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.24, G:0.16, T:0.04
Consensus pattern (24 bp):
AAAAGCCAAAATGCCAAAAAGCCA
Found at i:54049284 original size:9 final size:9
Alignment explanation
Indices: 54049260--54049295 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
54049250 AGAATTGGCC
54049260 AAATGGGCT
1 AAATGGGCT
54049269 GAAATGGGCT
1 -AAATGGGCT
54049279 AAATGGGCT
1 AAATGGGCT
54049288 AAATGGGC
1 AAATGGGC
54049296 CTGATGGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.33, C:0.11, G:0.36, T:0.19
Consensus pattern (9 bp):
AAATGGGCT
Found at i:54049306 original size:18 final size:18
Alignment explanation
Indices: 54049260--54049295 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
54049250 AGAATTGGCC
54049260 AAATGGGCTGAAATGGGCT
1 AAATGGGCT-AAATGGGCT
54049279 AAATGGGCTAAATGGGC
1 AAATGGGCTAAATGGGC
54049296 CTGATGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.33, C:0.11, G:0.36, T:0.19
Consensus pattern (18 bp):
AAATGGGCTAAATGGGCT
Found at i:54049431 original size:29 final size:29
Alignment explanation
Indices: 54049378--54049492 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
54049368 CAATGACTAT
* * * *
54049378 AATATGATTTAGGCCAAATGGGCCATATG
1 AATATGAATTGGGCCTAGTGGGCCATATG
* *
54049407 AATGTGAATTGGGCCTAGTGGGCCATAAG
1 AATATGAATTGGGCCTAGTGGGCCATATG
* *
54049436 AATATGAACTGGGCC-AGATGGGCCATTTG
1 AATATGAATTGGGCCTAG-TGGGCCATATG
*
54049465 AATAAG-ATTGGGCCTAGTGGGCCATATG
1 AATATGAATTGGGCCTAGTGGGCCATATG
54049493 CATGTATGTA
Statistics
Matches: 71, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
28 19 0.27
29 52 0.73
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (29 bp):
AATATGAATTGGGCCTAGTGGGCCATATG
Found at i:54053579 original size:16 final size:16
Alignment explanation
Indices: 54053558--54053592 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54053548 ATGAATCTGC
*
54053558 AAAAGCAGAAATGCCA
1 AAAAGCAGAAAAGCCA
*
54053574 AAAAGCCGAAAAGCCA
1 AAAAGCAGAAAAGCCA
54053590 AAA
1 AAA
54053593 GTTGGGCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.20, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAGCAGAAAAGCCA
Found at i:54053915 original size:28 final size:29
Alignment explanation
Indices: 54053804--54053922 Score: 118
Period size: 29 Copynumber: 4.2 Consensus size: 29
54053794 GTGAGAATGA
* * * *
54053804 ATAT-AATATGATTTAGGCCCAATGGGCC
1 ATATGAATATGAATTGGGCCTAGTGGGCC
* *
54053832 ATATGAATGTGAATTGGGCCTAGTAGGCC
1 ATATGAATATGAATTGGGCCTAGTGGGCC
* *
54053861 ATAAGATTATGAATTGGGCC-AGATGGGCC
1 ATATGAATATGAATTGGGCCTAG-TGGGCC
* *
54053890 ATTTGAATAAG-ATTGGGCCTAGTGGGCC
1 ATATGAATATGAATTGGGCCTAGTGGGCC
54053918 ATATG
1 ATATG
54053923 CATGTACGTA
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
28 24 0.33
29 49 0.67
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (29 bp):
ATATGAATATGAATTGGGCCTAGTGGGCC
Found at i:54071847 original size:20 final size:20
Alignment explanation
Indices: 54071822--54071862 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
54071812 GGTCAATCAA
54071822 AGTCCATACTTGGTTTTCAT
1 AGTCCATACTTGGTTTTCAT
54071842 AGTCCATACTTGGTTTTCAT
1 AGTCCATACTTGGTTTTCAT
54071862 A
1 A
54071863 CATGGAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (20 bp):
AGTCCATACTTGGTTTTCAT
Found at i:54085395 original size:30 final size:30
Alignment explanation
Indices: 54085361--54085421 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54085351 TCCTTAACTC
54085361 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
54085391 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
54085421 A
1 A
54085422 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:54092233 original size:30 final size:30
Alignment explanation
Indices: 54092199--54092259 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54092189 TCCTTAACTC
54092199 AAACTTTAGAAAAATTACAATTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
* * * * *
54092229 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
54092259 A
1 A
54092260 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTAGAAAAATTACAATTTTGCCCCT
Found at i:54094972 original size:39 final size:40
Alignment explanation
Indices: 54094927--54095151 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
54094917 GCTCCTCGTT
* * * *
54094927 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
54094967 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
54095006 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
54095046 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
54095086 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
54095127 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
54095152 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:54095160 original size:41 final size:41
Alignment explanation
Indices: 54095083--54095160 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
54095073 CTTGTATCTC
* * *
54095083 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
54095124 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
54095161 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:54102498 original size:39 final size:40
Alignment explanation
Indices: 54102453--54102677 Score: 215
Period size: 40 Copynumber: 5.7 Consensus size: 40
54102443 GCTCCTCGTT
* * * * *
54102453 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
54102493 C-AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* *
54102532 CGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * * *
54102572 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCA
** * * * *
54102612 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
54102653 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
54102678 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
39 37 0.24
40 104 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:54102686 original size:41 final size:41
Alignment explanation
Indices: 54102609--54102686 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
54102599 CTTGTATCTC
* * *
54102609 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
54102650 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
54102687 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:54106395 original size:68 final size:64
Alignment explanation
Indices: 54106181--54106388 Score: 199
Period size: 67 Copynumber: 3.2 Consensus size: 64
54106171 ATATAGTTCG
* * * *
54106181 GCTCTCTTGTAC-ACATGGTGAACACTCAGTACCACCCATGTGACCTAGCCA-ATTTA-TCTCGT
1 GCTCTCTTGT-CTACATGGTGTACACT-AGTACCACCCATGCGACCTAGCTACATATATTCTCGT
54106243 A
64 A
* * * * *
54106244 GCTCTCTTCTCTACATGGTGTCCTTCACCTAGAACCACGCATGCGACCTAGCTACATATA-TCCC
1 GCTCTCTTGTCTACATGGTG---TACA-CTAGTACCACCCATGCGACCTAGCTACATATATTCTC
54106308 GTA
62 GTA
* *
54106311 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATCATAATGTCTT
1 GCTCTCTTGTCTACATGGTGTACAC-TAGTACCACCCATGCGACCTAGCTACAT-AT-AT-TCTC
54106376 GTA
62 GTA
54106379 GCTCTCTTGT
1 GCTCTCTTGT
54106389 ACACATGATG
Statistics
Matches: 118, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
62 1 0.01
63 18 0.15
64 28 0.24
65 2 0.02
66 23 0.19
67 31 0.26
68 15 0.13
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACTAGTACCACCCATGCGACCTAGCTACATATATTCTCGTA
Found at i:54111157 original size:46 final size:45
Alignment explanation
Indices: 54111090--54111264 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 45
54111080 TGTAACCCGC
54111090 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* * * *
54111136 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCG-CAT
*** * * *
54111184 --ATCTCTCGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
*
54111229 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
54111265 ATGCCCAAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
45 3 0.03
46 67 0.64
47 30 0.29
48 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCAT
Found at i:54111210 original size:93 final size:93
Alignment explanation
Indices: 54111098--54111269 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
54111088 GCCCATAAGT
* *
54111098 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
54111163 CGAGCTCGGATGCCTAGTTATATCTCTC
66 CGAGCTCGGATGCCTAGTTATATCTCTC
* * *
54111191 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
54111256 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
54111270 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTATATCTCTC
Found at i:54111284 original size:46 final size:45
Alignment explanation
Indices: 54111095--54111284 Score: 113
Period size: 46 Copynumber: 4.1 Consensus size: 45
54111085 CCCGCCCATA
* ** ** **
54111095 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAATATCC-T
* * *
54111140 AAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTATATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---ATATC-CT
* * * *
54111190 --CGAACTCGGACTCAACTCAACGAGTTTGGACATTCGC---ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAATATCC-T
54111233 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AATATCCT
54111280 AGTGA
1 AGTGA
54111285 CATGTCACTT
Statistics
Matches: 110, Mismatches: 19, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
42 1 0.01
43 4 0.04
44 4 0.04
46 63 0.57
47 26 0.24
48 4 0.04
49 3 0.03
50 4 0.04
51 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAATATCCT
Found at i:54113693 original size:29 final size:29
Alignment explanation
Indices: 54113656--54113738 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
54113646 GATAACAAGA
*
54113656 AAACC-GAATAAAGAAATCCAAGATAGAG
1 AAACCAGAATAAAGAAATCCAAGATAAAG
54113684 AAACCAGAATAAAGAAATCCAA-ATAAAG
1 AAACCAGAATAAAGAAATCCAAGATAAAG
* * *
54113712 AGATCCAGGATAAAGAAACCCAAGATA
1 A-AACCAGAATAAAGAAATCCAAGATA
54113739 CGATACTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.23
29 34 0.71
30 3 0.06
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.11
Consensus pattern (29 bp):
AAACCAGAATAAAGAAATCCAAGATAAAG
Found at i:54113717 original size:14 final size:14
Alignment explanation
Indices: 54113652--54113734 Score: 78
Period size: 14 Copynumber: 5.8 Consensus size: 14
54113642 CAAAGATAAC
* *
54113652 AAGAAAACCGAATA
1 AAGAAATCCAAATA
54113666 AAGAAATCCAAGATA
1 AAGAAATCCAA-ATA
*
54113681 GAGAAA-CCAGAATA
1 AAGAAATCCA-AATA
54113695 AAGAAATCCAAATA
1 AAGAAATCCAAATA
* *
54113709 AAGAGATCCAGGATA
1 AAGAAATCCA-AATA
*
54113724 AAGAAACCCAA
1 AAGAAATCCAA
54113735 GATACGATAC
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
14 33 0.59
15 23 0.41
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.10
Consensus pattern (14 bp):
AAGAAATCCAAATA
Found at i:54116755 original size:46 final size:46
Alignment explanation
Indices: 54116688--54116862 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
54116678 TGTAACCCGC
*
54116688 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
* *
54116734 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C-ATTTGCAT
* * * * * *
54116784 CTC-T---CGAACTCGGACTCAACTCAATGAGTTTGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
* *
54116827 CCGTAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
54116863 ATGCCCAAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 1 0.01
43 7 0.07
44 1 0.01
46 61 0.58
47 25 0.24
48 1 0.01
49 1 0.01
50 8 0.08
51 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
Found at i:54116809 original size:93 final size:93
Alignment explanation
Indices: 54116696--54116867 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
54116686 GCCCATAAGT
* *
54116696 GAACTCGGACTCAACTCAATGAGCTCGGGCATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54116761 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
54116789 GAACTCGGACTCAACTCAATGAGTTTGGACATTCGCATCCGTAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
54116854 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
54116868 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAATGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:54116882 original size:46 final size:44
Alignment explanation
Indices: 54116739--54116882 Score: 98
Period size: 46 Copynumber: 3.1 Consensus size: 44
54116729 TGCATCCATA
* *
54116739 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * * * *
54116788 --CGAACTCGGACTCAACTCAATGAGTTTGGACATTCGC--ATCCGT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
54116831 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
54116878 AGTGA
1 AGTGA
54116883 CATGTCACTT
Statistics
Matches: 73, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 4 0.05
46 31 0.42
47 26 0.36
48 4 0.05
49 3 0.04
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:54120684 original size:46 final size:46
Alignment explanation
Indices: 54120634--54120809 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
54120624 TGGTTGAGCA
*
54120634 TCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54120680 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
**
54120725 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54120773 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54120810 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 29 0.27
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54120790 original size:93 final size:93
Alignment explanation
Indices: 54120631--54120802 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
54120621 GGATGGTTGA
***
54120631 GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
54120696 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
54120724 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
54120789 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
54120803 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54127169 original size:28 final size:29
Alignment explanation
Indices: 54127129--54127196 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
54127119 TCGGCAGCAT
*
54127129 CTAGAACACATTA-AAAGCATGT-TTTAAG
1 CTAGGACACATTAGAAA-CATGTATTTAAG
* *
54127157 CTAGGACATATTAGTAACATGTATTTAAG
1 CTAGGACACATTAGAAACATGTATTTAAG
*
54127186 CTAAGACACAT
1 CTAGGACACAT
54127197 GCAAAACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 16 0.48
29 17 0.52
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (29 bp):
CTAGGACACATTAGAAACATGTATTTAAG
Found at i:54130488 original size:19 final size:21
Alignment explanation
Indices: 54130450--54130488 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54130440 TTCTCGTTTT
54130450 TCTTTTCTTTTGTACTCTCAC
1 TCTTTTCTTTTGTACTCTCAC
54130471 TCTTTTCTTTT-T-CTCTCA
1 TCTTTTCTTTTGTACTCTCA
54130489 TTTGTTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.08, C:0.28, G:0.03, T:0.62
Consensus pattern (21 bp):
TCTTTTCTTTTGTACTCTCAC
Found at i:54137135 original size:23 final size:23
Alignment explanation
Indices: 54137095--54137170 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 23
54137085 AAATAAAAGC
* * *
54137095 TTATAAATTATAAAAATATATTT
1 TTATAAATTTTTATAATATATTT
**
54137118 TTATAAATTTTTAT-A-ATATGC
1 TTATAAATTTTTATAATATATTT
*
54137139 TTATAATTTTTTATACTATATATTTT
1 TTATAAATTTTTATA--ATATA-TTT
54137165 TTATAA
1 TTATAA
54137171 GTTTATACGC
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
21 17 0.43
22 1 0.03
23 11 0.28
24 1 0.03
25 3 0.08
26 7 0.17
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (23 bp):
TTATAAATTTTTATAATATATTT
Found at i:54137165 original size:16 final size:15
Alignment explanation
Indices: 54137140--54137169 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54137130 ATAATATGCT
54137140 TATAATTTTTTATAC
1 TATAATTTTTTATAC
54137155 TATATATTTTTTATA
1 TATA-ATTTTTTATA
54137170 AGTTTATACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TATAATTTTTTATAC
Found at i:54137563 original size:35 final size:36
Alignment explanation
Indices: 54137524--54137593 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
54137514 GTTTTTAGGG
*
54137524 TTAGGGTTTTGGTAAAATAAGTTAAGG-TTTAGTAT
1 TTAGGGTTTTGGTAAAACAAGTTAAGGTTTTAGTAT
* * *
54137559 TTAGGTTTTTGTTAAAACAAGTTAGGGTTTTAGTA
1 TTAGGGTTTTGGTAAAACAAGTTAAGGTTTTAGTA
54137594 GTTTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 23 0.77
36 7 0.23
ACGTcount: A:0.30, C:0.01, G:0.24, T:0.44
Consensus pattern (36 bp):
TTAGGGTTTTGGTAAAACAAGTTAAGGTTTTAGTAT
Found at i:54137706 original size:24 final size:23
Alignment explanation
Indices: 54137640--54137706 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 23
54137630 AAAAATTATT
*
54137640 TAAATTAGGGTTAATGGTTTTTAAA
1 TAAATTAGGGTTAGT-G-TTTTAAA
* *
54137665 TAAATTA-AGTTAGGGTTTTAAA
1 TAAATTAGGGTTAGTGTTTTAAA
54137687 TAAATTAGGGCTTAGTGTTT
1 TAAATTAGGG-TTAGTGTTT
54137707 ATAGTTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 14 0.40
23 2 0.06
24 12 0.34
25 7 0.20
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.43
Consensus pattern (23 bp):
TAAATTAGGGTTAGTGTTTTAAA
Found at i:54137777 original size:22 final size:22
Alignment explanation
Indices: 54137740--54137792 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
54137730 ATTAGGGTTC
* * *
54137740 TAGGATTTTAAATAAATTAAGT
1 TAGGGTTTAAAATAAATTAAAT
*
54137762 TAGTGTTTAAAATAAATTAAAT
1 TAGGGTTTAAAATAAATTAAAT
54137784 TAGGGTTTA
1 TAGGGTTTA
54137793 TGGTTTATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.42
Consensus pattern (22 bp):
TAGGGTTTAAAATAAATTAAAT
Found at i:54137788 original size:52 final size:50
Alignment explanation
Indices: 54137727--54137997 Score: 173
Period size: 52 Copynumber: 5.3 Consensus size: 50
54137717 ATAGATTAAG
54137727 TAAATTAGGGTTCTAGGATTTTAAATAAATTAAGTTAGTGTTTAAAATAAAT
1 TAAATTAGGGTT-TAGG-TTTTAAATAAATTAAGTTAGTGTTTAAAATAAAT
* ** * * * *
54137779 TAAATTAGGGTTTATGG-TTT-ATTAAATTCGGGTTTATGTTTTTTAAATAGAG
1 TAAATTAGGGTTTA-GGTTTTAAATAAATT-AAG-TTA-GTGTTTAAAATAAAT
* *
54137831 TAAATTAGGG--T---TTTTAAA-AAAATAAGTTAGGGTTTAAAATAAAT
1 TAAATTAGGGTTTAGGTTTTAAATAAATTAAGTTAGTGTTTAAAATAAAT
* * * * ** *
54137875 TAAATTAGTGTTTGGGGTTTATTAAATTAGGATTTATATTTTTTCG-TTAAAATTAAT
1 TAAATTAGGGTTT-AGG-TT-TTAAA-TA--AATTA-AGTTAGT-GTTTAAAATAAAT
*
54137932 TAAATTAGGGTTCTATGGTTTTAAATAAATTAAGTTAGGGTTTAAAATAAAT
1 TAAATTAGGGTT-TA-GGTTTTAAATAAATTAAGTTAGTGTTTAAAATAAAT
*
54137984 GAAATTAGGGTTTA
1 TAAATTAGGGTTTA
54137998 TAATTTTTGG
Statistics
Matches: 163, Mismatches: 33, Indels: 47
0.67 0.14 0.19
Matches are distributed among these distances:
44 19 0.12
45 3 0.02
46 2 0.01
47 7 0.04
48 1 0.01
49 7 0.04
50 5 0.03
51 10 0.06
52 64 0.39
53 4 0.02
54 1 0.01
55 2 0.01
56 8 0.05
57 26 0.16
58 4 0.02
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (50 bp):
TAAATTAGGGTTTAGGTTTTAAATAAATTAAGTTAGTGTTTAAAATAAAT
Found at i:54137805 original size:87 final size:86
Alignment explanation
Indices: 54137640--54137798 Score: 214
Period size: 87 Copynumber: 1.8 Consensus size: 86
54137630 AAAAATTATT
* * ** *
54137640 TAAATTAGGGTTAATGGTTTTTAAATAAATTAAGTTAGGGTTTTAAATAAATTAGGGCTTAGTGT
1 TAAATTAGGGTTAATGGATTTTAAATAAATTAAGTTAGGGTTTAAAATAAATTA-GAATTAGGGT
54137705 TTATAGTTTTAAATAGATTAAG
65 TTATAGTTTTAAATAGATTAAG
* *
54137727 TAAATTAGGGTT-CTAGGATTTTAAATAAATTAAGTTAGTGTTTAAAATAAATTA-AATTAGGGT
1 TAAATTAGGGTTAAT-GGATTTTAAATAAATTAAGTTAGGGTTTAAAATAAATTAGAATTAGGGT
*
54137790 TTATGGTTT
65 TTATAGTTT
54137799 ATTAAATTCG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 14 0.22
86 1 0.02
87 48 0.76
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.43
Consensus pattern (86 bp):
TAAATTAGGGTTAATGGATTTTAAATAAATTAAGTTAGGGTTTAAAATAAATTAGAATTAGGGTT
TATAGTTTTAAATAGATTAAG
Found at i:54137824 original size:21 final size:22
Alignment explanation
Indices: 54137777--54137826 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
54137767 TTTAAAATAA
54137777 ATTAAATTAGGGTTTATGGTTT
1 ATTAAATTAGGGTTTATGGTTT
*
54137799 ATTAAATTCGGGTTTAT-GTTT
1 ATTAAATTAGGGTTTATGGTTT
*
54137820 TTTAAAT
1 ATTAAAT
54137827 AGAGTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.28, C:0.02, G:0.18, T:0.52
Consensus pattern (22 bp):
ATTAAATTAGGGTTTATGGTTT
Found at i:54137866 original size:96 final size:103
Alignment explanation
Indices: 54137721--54137998 Score: 302
Period size: 96 Copynumber: 2.7 Consensus size: 103
54137711 TTTTAAATAG
*
54137721 ATTAAGTAAATTAGGGTTCTAGGATTTTAAATAAATTAAGTTAGTGTTTAAAATAAATTAAATTA
1 ATTAAGTAAATTAGGG-T-T--G-TTTTAAATAAATTAAGTTAGGGTTTAAAATAAATTAAATTA
*
54137786 GGGTTTATGGTTTATTAAATTCGG-GTT-TATGTTTT-TT-AA
61 GGGTTTATGGTTTATTAAATTAGGAGTTATATGTTTTCTTAAA
* *
54137825 A-TAGAGTAAATTAGGG-T-TTTTAAA-AAAATAAGTTAGGGTTTAAAATAAATTAAATTAGTGT
1 ATTA-AGTAAATTAGGGTTGTTTTAAATAAATTAAGTTAGGGTTTAAAATAAATTAAATTAGGGT
** * *
54137886 TTGGGGTTTATTAAATTAGGATTTATATTTTTTCGTTAAA
65 TTATGGTTTATTAAATTAGGAGTTATATGTTTTC-TTAAA
* *
54137926 ATTAATTAAATTAGGGTTCTATGGTTTTAAATAAATTAAGTTAGGGTTTAAAATAAATGAAATTA
1 ATTAAGTAAATTAGGG---T-T-GTTTTAAATAAATTAAGTTAGGGTTTAAAATAAATTAAATTA
54137991 GGGTTTAT
61 GGGTTTAT
54137999 AATTTTTGGT
Statistics
Matches: 145, Mismatches: 14, Indels: 25
0.79 0.08 0.14
Matches are distributed among these distances:
96 51 0.35
97 9 0.06
98 7 0.05
100 2 0.01
101 15 0.10
102 2 0.01
103 2 0.01
104 13 0.09
106 1 0.01
108 7 0.05
109 36 0.25
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (103 bp):
ATTAAGTAAATTAGGGTTGTTTTAAATAAATTAAGTTAGGGTTTAAAATAAATTAAATTAGGGTT
TATGGTTTATTAAATTAGGAGTTATATGTTTTCTTAAA
Found at i:54137882 original size:22 final size:20
Alignment explanation
Indices: 54137831--54137887 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
54137821 TTAAATAGAG
54137831 TAAATTAGGGTTTTTAAAAAAA
1 TAAATTAGGG--TTTAAAAAAA
*
54137853 TAAGTTAGGGTTTAAAATAAA
1 TAAATTAGGGTTTAAAA-AAA
*
54137874 TTAAATTAGTGTTT
1 -TAAATTAGGGTTT
54137888 GGGGTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 7 0.23
21 3 0.10
22 20 0.67
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (20 bp):
TAAATTAGGGTTTAAAAAAA
Found at i:54137963 original size:30 final size:29
Alignment explanation
Indices: 54137924--54138155 Score: 100
Period size: 30 Copynumber: 7.7 Consensus size: 29
54137914 TTTTTCGTTA
*
54137924 AAATTAATTAAATTAGGGTTCTATGGTTTT
1 AAATAAATTAAATTAGGGTT-TATGGTTTT
*
54137954 AAATAAATTAAGTTAGGGTTTA-------
1 AAATAAATTAAATTAGGGTTTATGGTTTT
* **
54137976 AAATAAATGAAATTAGGGTTTATAATTTTTGGTTAA
1 AAATAAATTAAATTAGGG-TT-T-A----TGGTTTT
* *
54138012 AAATTAATTAAATTAGGGTTCTAAGGTTTT
1 AAATAAATTAAATTAGGGTT-TATGGTTTT
* ***
54138042 AAATAAATTAACTTAGGGTTTAAAATATTT
1 AAATAAATTAAATTAGGGTTTATGGT-TTT
** ** * *
54138072 GTATTTATCAAATTAGGGCTTATGGTTTTT
1 AAATAAATTAAATTAGGGTTTATGG-TTTT
* *
54138102 AAATAGATTAAGTAAATTAGGGTTCTAGGGTTTT
1 AAAT--A--AATTAAATTAGGGTT-TATGGTTTT
54138136 AAATAAATTAAATTAGGGTT
1 AAATAAATTAAATTAGGGTT
54138156 AGGGTTTAGG
Statistics
Matches: 148, Mismatches: 33, Indels: 42
0.66 0.15 0.19
Matches are distributed among these distances:
22 16 0.11
23 2 0.01
24 1 0.01
25 1 0.01
29 6 0.04
30 77 0.52
31 1 0.01
32 1 0.01
34 20 0.14
35 7 0.05
36 16 0.11
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (29 bp):
AAATAAATTAAATTAGGGTTTATGGTTTT
Found at i:54137979 original size:22 final size:22
Alignment explanation
Indices: 54137948--54137997 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
54137938 AGGGTTCTAT
* * *
54137948 GGTTTTAAATAAATTAAGTTAG
1 GGTTTAAAATAAATGAAATTAG
54137970 GGTTTAAAATAAATGAAATTAG
1 GGTTTAAAATAAATGAAATTAG
54137992 GGTTTA
1 GGTTTA
54137998 TAATTTTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (22 bp):
GGTTTAAAATAAATGAAATTAG
Found at i:54138031 original size:88 final size:87
Alignment explanation
Indices: 54137898--54138068 Score: 288
Period size: 88 Copynumber: 2.0 Consensus size: 87
54137888 GGGGTTTATT
* *
54137898 AAATTAGGATTTATATTTTTTCGTTAAAATTAATTAAATTAGGGTTCTATGGTTTTAAATAAATT
1 AAATTAGGATTTATAATTTTTCGTTAAAATTAATTAAATTAGGGTTCTAAGGTTTTAAATAAATT
*
54137963 AAGTTAGGGTTTAAAATAAATG
66 AACTTAGGGTTTAAAATAAATG
* *
54137985 AAATTAGGGTTTATAATTTTTGGTTAAAAATTAATTAAATTAGGGTTCTAAGGTTTTAAATAAAT
1 AAATTAGGATTTATAATTTTTCGTT-AAAATTAATTAAATTAGGGTTCTAAGGTTTTAAATAAAT
54138050 TAACTTAGGGTTTAAAATA
65 TAACTTAGGGTTTAAAATA
54138069 TTTGTATTTA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 22 0.28
88 56 0.72
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.43
Consensus pattern (87 bp):
AAATTAGGATTTATAATTTTTCGTTAAAATTAATTAAATTAGGGTTCTAAGGTTTTAAATAAATT
AACTTAGGGTTTAAAATAAATG
Found at i:54138120 original size:34 final size:34
Alignment explanation
Indices: 54138081--54138146 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
54138071 TGTATTTATC
* *
54138081 AAATTAGGGCTTAT-GGTTTTTAAATAGATTAAGT
1 AAATTAGGG-TTATAGGGTTTTAAATAAATTAAGT
*
54138115 AAATTAGGGTTCTAGGGTTTTAAATAAATTAA
1 AAATTAGGGTTATAGGGTTTTAAATAAATTAA
54138147 ATTAGGGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (34 bp):
AAATTAGGGTTATAGGGTTTTAAATAAATTAAGT
Found at i:54138179 original size:34 final size:36
Alignment explanation
Indices: 54138118--54138189 Score: 112
Period size: 34 Copynumber: 2.1 Consensus size: 36
54138108 ATTAAGTAAA
*
54138118 TTAGGGTTCTAGGGTTTTAAATAAATTAAATTAGGG
1 TTAGGGTTCTAGGGTTTAAAATAAATTAAATTAGGG
*
54138154 TTAGGGTT-TAGGG-TTAAAATTAATTAAATTAGGG
1 TTAGGGTTCTAGGGTTTAAAATAAATTAAATTAGGG
54138188 TT
1 TT
54138190 TAGTTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 21 0.62
35 5 0.15
36 8 0.24
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.40
Consensus pattern (36 bp):
TTAGGGTTCTAGGGTTTAAAATAAATTAAATTAGGG
Done.