Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 176 of 410
Found at i:54069981 original size:21 final size:21
Alignment explanation
Indices: 54069924--54069991 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
54069914 TACTTGCCTC
* *
54069924 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
54069945 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
54069966 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
54069986 CTCTTT
1 -TCTTT
54069992 ACAAGAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:54072031 original size:46 final size:46
Alignment explanation
Indices: 54071981--54072153 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
54071971 TGGTTGAGCA
54071981 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
54072027 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54072072 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54072120 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54072154 GGGCGGGTTA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
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:54072137 original size:93 final size:93
Alignment explanation
Indices: 54071978--54072148 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54071968 GGATGGTTGA
* *
54071978 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54072043 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
54072071 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54072136 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54072149 ACTTAGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:54079592 original size:46 final size:46
Alignment explanation
Indices: 54079542--54079714 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
54079532 TGGTTGAGCA
54079542 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
54079588 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54079633 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54079681 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54079715 GGGCGGGTTA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
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:54079698 original size:93 final size:93
Alignment explanation
Indices: 54079539--54079709 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54079529 GGATGGTTGA
* *
54079539 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54079604 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
54079632 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54079697 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
54079710 ACTTAGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:54081266 original size:18 final size:18
Alignment explanation
Indices: 54081232--54081270 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54081222 CATTAAACAC
*
54081232 TTTTTTTTCAGATTTTTT
1 TTTTTTTTCAGAATTTTT
54081250 TTTTCTTTTC-GAATTTTT
1 TTTT-TTTTCAGAATTTTT
54081268 TTT
1 TTT
54081271 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.10, C:0.08, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTTTTTCAGAATTTTT
Found at i:54081269 original size:11 final size:11
Alignment explanation
Indices: 54081255--54081292 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
54081245 TTTTTTTTTC
54081255 TTTTCGAATTT
1 TTTTCGAATTT
*
54081266 TTTTTGAATTTT
1 TTTTCGAA-TTT
54081278 TTTTCGAATTT
1 TTTTCGAATTT
54081289 TTTT
1 TTTT
54081293 GACTTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.16, C:0.05, G:0.08, T:0.71
Consensus pattern (11 bp):
TTTTCGAATTT
Found at i:54081270 original size:12 final size:12
Alignment explanation
Indices: 54081250--54081292 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
54081240 CAGATTTTTT
54081250 TTTTCTTTTCGAA
1 TTTT-TTTTCGAA
54081263 TTTTTTTT-GAA
1 TTTTTTTTCGAA
54081274 TTTTTTTTCGAA
1 TTTTTTTTCGAA
54081286 TTTTTTT
1 TTTTTTT
54081293 GACTTGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.38
12 14 0.48
13 4 0.14
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:54083040 original size:30 final size:30
Alignment explanation
Indices: 54082954--54083051 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
54082944 TTAAACTAAA
* *
54082954 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
54082984 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
54083014 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
54083044 ATGAGCTA
1 ATGAGCTA
54083052 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:54088508 original size:30 final size:30
Alignment explanation
Indices: 54088423--54088519 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
54088413 TAAACTAAAA
* *
54088423 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
54088453 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
54088483 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
54088512 ATGAGCTA
1 -TGAGCTA
54088520 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:54091563 original size:11 final size:11
Alignment explanation
Indices: 54091547--54091584 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
54091537 ATAAAGCACA
*
54091547 TTTTTTTCAAT
1 TTTTTTTGAAT
54091558 TTTTTTTGAAT
1 TTTTTTTGAAT
54091569 TTTTTTTGAAT
1 TTTTTTTGAAT
54091580 TTTTT
1 TTTTT
54091585 ATATACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:54091594 original size:22 final size:22
Alignment explanation
Indices: 54091547--54091597 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
54091537 ATAAAGCACA
* *
54091547 TTTTTTTCAATTTTTTTTGAAT
1 TTTTTTTCAATTTTTTATGAAC
*
54091569 TTTTTTTGAATTTTTTAT-ATAC
1 TTTTTTTCAATTTTTTATGA-AC
54091591 TTTTTTT
1 TTTTTTT
54091598 AACTACTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTTTTTCAATTTTTTATGAAC
Found at i:54091967 original size:14 final size:14
Alignment explanation
Indices: 54091948--54092006 Score: 82
Period size: 14 Copynumber: 4.2 Consensus size: 14
54091938 TGGTAGGAGC
**
54091948 GGTATGAACAAAAT
1 GGTATGAATGAAAT
54091962 GGTATGAATGAAAT
1 GGTATGAATGAAAT
*
54091976 GGTATGAATGAAAG
1 GGTATGAATGAAAT
*
54091990 GGTATGAATGAATT
1 GGTATGAATGAAAT
54092004 GGT
1 GGT
54092007 CGGTTTAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.41, C:0.02, G:0.31, T:0.27
Consensus pattern (14 bp):
GGTATGAATGAAAT
Found at i:54092895 original size:17 final size:17
Alignment explanation
Indices: 54092873--54092916 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
54092863 GTACCTTGCC
54092873 ATTCATGCATTTAACCG
1 ATTCATGCATTTAACCG
54092890 ATTCATGCATTTAACCG
1 ATTCATGCATTTAACCG
54092907 ATTCATGCAT
1 ATTCATGCAT
54092917 CTTGAGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (17 bp):
ATTCATGCATTTAACCG
Found at i:54099964 original size:20 final size:20
Alignment explanation
Indices: 54099941--54099996 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
54099931 TAGATGTGAA
54099941 CTTGTTGAGCTGGAACTGAG
1 CTTGTTGAGCTGGAACTGAG
* **
54099961 CTTGCTGAGCTGGTTCTGAG
1 CTTGTTGAGCTGGAACTGAG
* *
54099981 CTGGTCGAGCTAGGAA
1 CTTGTTGAGCT-GGAA
54099997 TAAGTTACGA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.29
Consensus pattern (20 bp):
CTTGTTGAGCTGGAACTGAG
Found at i:54101157 original size:12 final size:12
Alignment explanation
Indices: 54101142--54101179 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
54101132 TTTTTTTTTC
54101142 TTTTCGAAATTT
1 TTTTCGAAATTT
*
54101154 TTTT-GAATTTT
1 TTTTCGAAATTT
54101165 TTTTCG-AATTT
1 TTTTCGAAATTT
54101176 TTTT
1 TTTT
54101180 TGACTTGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTCGAAATTT
Found at i:54101172 original size:23 final size:24
Alignment explanation
Indices: 54101137--54101182 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
54101127 TCAGATTTTT
54101137 TTTTCTTTTCGAAATTTTTTTGAA
1 TTTTCTTTTCGAAATTTTTTTGAA
*
54101161 TTTT-TTTTCGAATTTTTTTTGA
1 TTTTCTTTTCGAAATTTTTTTGA
54101183 CTTGTATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.17, C:0.07, G:0.09, T:0.67
Consensus pattern (24 bp):
TTTTCTTTTCGAAATTTTTTTGAA
Found at i:54101180 original size:12 final size:12
Alignment explanation
Indices: 54101137--54101180 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
54101127 TCAGATTTTT
54101137 TTTTCTTTTCGAA
1 TTTT-TTTTCGAA
*
54101150 ATTTTTTT-GAA
1 TTTTTTTTCGAA
54101161 TTTTTTTTCGAA
1 TTTTTTTTCGAA
54101173 TTTTTTTT
1 TTTTTTTT
54101181 GACTTGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
12 15 0.54
13 3 0.11
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:54102160 original size:12 final size:12
Alignment explanation
Indices: 54102116--54102160 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
54102106 TCAGATTTTT
54102116 TTTTCTTTTCGAAA
1 TTTT-TTTTCG-AA
54102130 TTTTTTTT-GAA
1 TTTTTTTTCGAA
54102141 TTTTTTTTCGAA
1 TTTTTTTTCGAA
54102153 TTTTTTTT
1 TTTTTTTT
54102161 GACTTGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.33
12 12 0.40
13 4 0.13
14 4 0.13
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:54102702 original size:983 final size:979
Alignment explanation
Indices: 54100879--54103054 Score: 4255
Period size: 983 Copynumber: 2.2 Consensus size: 979
54100869 AGAACAAATG
* * * *
54100879 TTCATTAACAATTTTAGC-AAAAGTCCCTTACAATTGAAAGAAAACAAATACTTATAGGCACATA
1 TTCAATAAAAATTTTGGCAAAAAGTCTCTTACAATTGAAAGAAAACAAATACTTATAGGCACATA
54100943 GATGACCATTCAAATTCGGCATCTAGGTGTTCACACAATAATAAAAACGTTCACACTAATGTATT
66 GATGACCATTCAAATTCGGCATCTAGGTGTTCACACAATAATAAAAACGTTCACACTAATGTATT
54101008 AAAATAGTTCATAAATTCGGCAGATTCATGAACTAGTTGAATGGACACTTTCTTCCCCCTAAGTG
131 AAAATAGTTCATAAATTCGGCAGATTCATGAACTAGTTGAATGGACACTTTCTTCCCCCTAAGTG
54101073 TGTGCATGAATGCTTAATCACAATAATAATCGAATTGCATTAAACACTTTTTTTTCAGATTTTTT
196 TGTGCATGAATGCTTAATCACAATAATAATCGAATTGCATTAAACACTTTTTTTTCAGATTTTTT
54101138 TTTCTTTTCGAAATTTTTTTGAATTTTTTTTCGAATTTTTTTTGACTTGTATAACTTTTTTTGTA
261 TTTCTTTTCGAAATTTTTTTGAATTTTTTTTCGAATTTTTTTTGACTTGTATAACTTTTTTTGTA
54101203 CTATATTGACAAACTAAATACAATAAAACAATTTTTGTACACGATTTTTTTTTCTTCGGCTGCGT
326 CTATATTGACAAACTAAATACAATAAAACAATTTTTGTACACGATTTTTTTTTCTTCGGCTGCGT
54101268 AGATTTTTGTTTTTATAGCAACAGCAGCTAACTAATCAAAATGAGAAAACTTCGGTATACGAATT
391 AGATTTTTGTTTTTATAGCAACAGCAGCTAACTAATCAAAATGAGAAAACTTCGGTATACGAATT
54101333 TTTTTTCTATACTATTTTTTTCCCCGAATCCTACTTACTTGCGTTCACTTGGACTAGCCCAGGAT
456 TTTTTTCTATACTATTTTTTTCCCCGAATCCTACTTACTTGCGTTCACTTGGACTAGCCCAGGAT
54101398 TAATTTCATCGCACGGTCTTCTCGTTTTAGTAGCTCTGATACCAAATGATACGAATCGCCTCTGG
521 TAATTTCATCGCACGGTCTTCTCGTTTTAGTAGCTCTGATACCAAATGATACGAATCGCCTCTGG
54101463 GAGAGTCGAGTCGTATGCGAGTTTGCCCGATCGTCTGCGAGAAAGTATCGTCCGGTTTGTTCAAA
586 GAGAGTCGAGTCGTATGCGAGTTTGCCCGATCGTCTGCGAGAAAGTATCGTCCGGTTTGTTCAAA
54101528 AAGGATGTTTCTAAATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATAAAGGGTTTAAAATAT
651 AAGGATGTTTCTAAATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATAAAGGGTTTAAAATAT
54101593 GAATATTAAGGTTTGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGA
716 GAATATTAAGGTTTGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGA
54101658 ACCAATACTAGAGAGTATTGACCTAATCGTTTATAGACTTTCAAGGTGGAGGATGAAAATGATAA
781 ACCAATACTAGAGAGTATTGACCTAATCGTTTATAGACTTTCAAGGTGGAGGATGAAAATGATAA
54101723 ACCTTGACCCGCTACTTAGCAAAGTAGGAACCTCGGTATAAGGGTGAACGAAACAGGGTTGACGC
846 ACCTTGACCCGCTACTTAGCAAAGTAGGAACCTCGGTATAAGGGTGAACGAAACAGGGTTGACGC
54101788 CACTACTAGGTAGATAAGTCAACAAAGTCTCAAACAAAATTTAGAGAAGAAAATTCTCACAAGAT
911 CACTACTAGGTAGATAAGTCAACAAAGTCTCAAACAAAATTTAGAGAAGAAAATTCTCACAAGAT
54101853 TAAA
976 TAAA
54101857 TTCAATAAAAATTTTGGCAAAAAGTCTCTTACAATTGAAAGAAAACAAATACTTATAGGCACATA
1 TTCAATAAAAATTTTGGCAAAAAGTCTCTTACAATTGAAAGAAAACAAATACTTATAGGCACATA
54101922 GATGACCATTCAAATTCGGCATCTAGGTGTTCACACAATAATAAAAACGTTCACACTAATGTATT
66 GATGACCATTCAAATTCGGCATCTAGGTGTTCACACAATAATAAAAACGTTCACACTAATGTATT
54101987 AAAATAGTTCATAAATTCGGCAGATTCATGAACTAGTTGAATGGACACTTTCTTCCCCCTAAGTG
131 AAAATAGTTCATAAATTCGGCAGATTCATGAACTAGTTGAATGGACACTTTCTTCCCCCTAAGTG
54102052 TGTGCATGAATGCTTAATCACAATAATAATCGAATTGCATTAAACACTTTTTTTTCAGATTTTTT
196 TGTGCATGAATGCTTAATCACAATAATAATCGAATTGCATTAAACACTTTTTTTTCAGATTTTTT
54102117 TTTCTTTTCGAAATTTTTTTTGAATTTTTTTTCGAATTTTTTTTGACTTGTATAACTTTTTTTTG
261 TTTCTTTTCGAAA-TTTTTTTGAATTTTTTTTCGAATTTTTTTTGACTTGTATAAC-TTTTTTTG
54102182 TACTATATTGACAAACTAAATACAATAAAACAATTTTTGTACACGATTTTTTTTTCTTCGGCTGC
324 TACTATATTGACAAACTAAATACAATAAAACAATTTTTGTACACGATTTTTTTTTCTTCGGCTGC
54102247 GTAGATTTTTGTTTTTATAGCAACAGCAGCTAACTAATCAAAATGAGAAAACTTCGGTATACGAA
389 GTAGATTTTTGTTTTTATAGCAACAGCAGCTAACTAATCAAAATGAGAAAACTTCGGTATACGAA
54102312 TTTTTTTTTCTATACTATTTTTTTTCCCCGAATCCTACTTACTTGCGTTCACTTGGACTAGCCCA
454 -TTTTTTTTCTATACTA-TTTTTTTCCCCGAATCCTACTTACTTGCGTTCACTTGGACTAGCCCA
54102377 GGATTAATTTCATCGCACGGTCTTCTCGTTTTAGTAGCTCTGATACCAAATGATACGAATCGCCT
517 GGATTAATTTCATCGCACGGTCTTCTCGTTTTAGTAGCTCTGATACCAAATGATACGAATCGCCT
54102442 CTGGGAGAGTCGAGTCGTATGCGAGTTTGCCCGATCGTCTGCGAGAAAGTATCGTCCGGTTTGTT
582 CTGGGAGAGTCGAGTCGTATGCGAGTTTGCCCGATCGTCTGCGAGAAAGTATCGTCCGGTTTGTT
54102507 CAAAAAGGATGTTTCTAAATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATAAAGGGTTTAAA
647 CAAAAAGGATGTTTCTAAATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATAAAGGGTTTAAA
54102572 ATATGAATATTAAGGTTTGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGC
712 ATATGAATATTAAGGTTTGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGC
54102637 ACGAACCAATACTAGAGAGTATTGACCTAATCGTTTATAGACTTTCAAGGTGGAGGATGAAAATG
777 ACGAACCAATACTAGAGAGTATTGACCTAATCGTTTATAGACTTTCAAGGTGGAGGATGAAAATG
54102702 ATAAACCTTGACCCGCTACTTAGCAAAGTAGGAACCTCGGTATAAGGGTGAACGAAACAGGGTTG
842 ATAAACCTTGACCCGCTACTTAGCAAAGTAGGAACCTCGGTATAAGGGTGAACGAAACAGGGTTG
54102767 ACGCCACTACTAGGTAGATAAGTCAACAAAGTCTCAAACAAAATTTAGAGAAGAAAATTCTCACA
907 ACGCCACTACTAGGTAGATAAGTCAACAAAGTCTCAAACAAAATTTAGAGAAGAAAATTCTCACA
54102832 AGATTAAA
972 AGATTAAA
54102840 TTCAATAAAAATTTTGGCAAAAAGTCTCTTACAATTGAAAGAAAACAAATACTTATAGGCACATA
1 TTCAATAAAAATTTTGGCAAAAAGTCTCTTACAATTGAAAGAAAACAAATACTTATAGGCACATA
54102905 GATGACCATTCAAATTCGGCATCTAGGTGTTCACACAATAATAAAAACGTTCACACTAATGTATT
66 GATGACCATTCAAATTCGGCATCTAGGTGTTCACACAATAATAAAAACGTTCACACTAATGTATT
*
54102970 AAAATAGTTCATAAATTCGGCAAATTCATGAACTAGTTGAATGGACACTTTCTTCCCCCTAAGTG
131 AAAATAGTTCATAAATTCGGCAGATTCATGAACTAGTTGAATGGACACTTTCTTCCCCCTAAGTG
*
54103035 TGTGTATGAATGCTTAATCA
196 TGTGCATGAATGCTTAATCA
54103055 TAAAGAAAGG
Statistics
Matches: 1187, Mismatches: 6, Indels: 5
0.99 0.01 0.00
Matches are distributed among these distances:
978 15 0.01
979 253 0.21
980 42 0.04
981 138 0.12
982 16 0.01
983 723 0.61
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (979 bp):
TTCAATAAAAATTTTGGCAAAAAGTCTCTTACAATTGAAAGAAAACAAATACTTATAGGCACATA
GATGACCATTCAAATTCGGCATCTAGGTGTTCACACAATAATAAAAACGTTCACACTAATGTATT
AAAATAGTTCATAAATTCGGCAGATTCATGAACTAGTTGAATGGACACTTTCTTCCCCCTAAGTG
TGTGCATGAATGCTTAATCACAATAATAATCGAATTGCATTAAACACTTTTTTTTCAGATTTTTT
TTTCTTTTCGAAATTTTTTTGAATTTTTTTTCGAATTTTTTTTGACTTGTATAACTTTTTTTGTA
CTATATTGACAAACTAAATACAATAAAACAATTTTTGTACACGATTTTTTTTTCTTCGGCTGCGT
AGATTTTTGTTTTTATAGCAACAGCAGCTAACTAATCAAAATGAGAAAACTTCGGTATACGAATT
TTTTTTCTATACTATTTTTTTCCCCGAATCCTACTTACTTGCGTTCACTTGGACTAGCCCAGGAT
TAATTTCATCGCACGGTCTTCTCGTTTTAGTAGCTCTGATACCAAATGATACGAATCGCCTCTGG
GAGAGTCGAGTCGTATGCGAGTTTGCCCGATCGTCTGCGAGAAAGTATCGTCCGGTTTGTTCAAA
AAGGATGTTTCTAAATAAATTATGCGGAAGCTATTCAAGGGGTTCAAATAAAGGGTTTAAAATAT
GAATATTAAGGTTTGGTTTAAAGTAAATGAAAGAATGGAAAGAAGGAACTCAAAAGCAAGCACGA
ACCAATACTAGAGAGTATTGACCTAATCGTTTATAGACTTTCAAGGTGGAGGATGAAAATGATAA
ACCTTGACCCGCTACTTAGCAAAGTAGGAACCTCGGTATAAGGGTGAACGAAACAGGGTTGACGC
CACTACTAGGTAGATAAGTCAACAAAGTCTCAAACAAAATTTAGAGAAGAAAATTCTCACAAGAT
TAAA
Found at i:54103872 original size:30 final size:30
Alignment explanation
Indices: 54103838--54103920 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
54103828 TAAACTAAAA
*
54103838 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * *
54103868 TGAGCTAAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCTAA-GCTTTAGCTCGTAAGCTAAAGT
*
54103898 TGAGCTAAGGTTTAGCTCGTAAG
1 TGAGCTAAGCTTTAGCTCGTAAG
54103921 TTGAAAGTGA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
29 1 0.02
30 39 0.93
31 2 0.05
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:54111138 original size:16 final size:16
Alignment explanation
Indices: 54111093--54111142 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
54111083 AATAAAATCA
**
54111093 AAAAAGAGTGTGAAAG
1 AAAAAGAGAATGAAAG
*
54111109 AAAAAAAGAAATGAAAG
1 AAAAAGAG-AATGAAAG
*
54111126 AAAAAGAGCATGAAAG
1 AAAAAGAGAATGAAAG
54111142 A
1 A
54111143 GAGCAAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.66, C:0.02, G:0.24, T:0.08
Consensus pattern (16 bp):
AAAAAGAGAATGAAAG
Found at i:54111779 original size:30 final size:30
Alignment explanation
Indices: 54111698--54111786 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
54111688 TCATTTTCAA
* *
54111698 CTCACGAGCTAAACCTTAGCTCAACTTCAG
1 CTCACGAGCTAAAGCTTAGCTCAACTTTAG
* * ** *
54111728 CTTAGGAG-TTTAGCCTCAGCTCAACTTTAG
1 CTCACGAGCTAAAG-CTTAGCTCAACTTTAG
54111758 CTCACGAGCTAAAGCTTAGCTC-ACTTTAG
1 CTCACGAGCTAAAGCTTAGCTCAACTTTAG
54111787 TTTAAACTCA
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
29 9 0.20
30 33 0.73
31 3 0.07
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (30 bp):
CTCACGAGCTAAAGCTTAGCTCAACTTTAG
Found at i:54119594 original size:11 final size:9
Alignment explanation
Indices: 54119578--54119619 Score: 52
Period size: 8 Copynumber: 4.7 Consensus size: 9
54119568 ATAAATCACT
54119578 TTTTTTTTCGA
1 TTTTTTTT--A
54119589 TTTTTTTTA
1 TTTTTTTTA
54119598 TTTTTTTT-
1 TTTTTTTTA
54119606 TTTTTTTT-
1 TTTTTTTTA
54119614 TTTTTT
1 TTTTTT
54119620 AACTTGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 14 0.45
9 9 0.29
11 8 0.26
ACGTcount: A:0.05, C:0.02, G:0.02, T:0.90
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:54119639 original size:1 final size:1
Alignment explanation
Indices: 54119589--54119619 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
54119579 TTTTTTTCGA
*
54119589 TTTTTTTTATTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54119620 AACTTGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:54126524 original size:12 final size:13
Alignment explanation
Indices: 54126491--54126523 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
54126481 TATACAAGTT
54126491 AAAAAAAATCCAA
1 AAAAAAAATCCAA
54126504 AAAAAAAATCCGAA
1 AAAAAAAATCC-AA
54126518 AAAAAA
1 AAAAAA
54126524 TTGAAGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.79, C:0.12, G:0.03, T:0.06
Consensus pattern (13 bp):
AAAAAAAATCCAA
Found at i:54130711 original size:30 final size:31
Alignment explanation
Indices: 54130677--54130773 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
54130667 AGCTCACTCC
*
54130677 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54130707 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
54130737 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54130767 TAGCTCA
1 TAGCTCA
54130774 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:54140007 original size:30 final size:30
Alignment explanation
Indices: 54139973--54140057 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
54139963 TAAACTAAAA
* * *
54139973 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCATGAGCTAAAGC
* * * * *
54140003 TGAGCTGAGATTAAACTCCTAAGCTAAAGC
1 TGAGCTAAGATTTAGCTCATGAGCTAAAGC
*
54140033 TGAGCTAAGGTTTAGCTCATGAGCT
1 TGAGCTAAGATTTAGCTCATGAGCT
54140058 GAATATGAGC
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCATGAGCTAAAGC
Found at i:54140939 original size:19 final size:19
Alignment explanation
Indices: 54140894--54140939 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
54140884 ATTAACACAC
*
54140894 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
54140913 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
54140931 AATTAATAA
1 AATTAATAA
54140940 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:54143966 original size:34 final size:31
Alignment explanation
Indices: 54143902--54143966 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 31
54143892 AATGTTGAAG
*
54143902 AGTCTTCCAATGTGAACAAGGTGAACCGAAT
1 AGTCTTCCAATGTGAACAAGGTGAAACGAAT
54143933 AGTCTTGCC-ATGTGAACATAGGTGTGAAACGAAT
1 AGTCTT-CCAATGTGAACA-A-G-GTGAAACGAAT
54143967 TAAGGAGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 15 0.52
32 3 0.10
33 1 0.03
34 10 0.34
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (31 bp):
AGTCTTCCAATGTGAACAAGGTGAAACGAAT
Found at i:54146405 original size:14 final size:14
Alignment explanation
Indices: 54146382--54146425 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54146372 GTAGAAAGAG
* *
54146382 GGGTACGAACGGAA
1 GGGTAGGAACGAAA
*
54146396 TGGTAGGAACGAAA
1 GGGTAGGAACGAAA
*
54146410 GGGTAGGAACAAAA
1 GGGTAGGAACGAAA
54146424 GG
1 GG
54146426 ATATGAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.41, C:0.09, G:0.41, T:0.09
Consensus pattern (14 bp):
GGGTAGGAACGAAA
Found at i:54151472 original size:10 final size:10
Alignment explanation
Indices: 54151459--54151493 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
54151449 AAGCTTGGTT
54151459 GAGCTCAAAC
1 GAGCTCAAAC
*
54151469 GAGCTGAAAC
1 GAGCTCAAAC
*
54151479 GAGCTCAAAT
1 GAGCTCAAAC
54151489 GAGCT
1 GAGCT
54151494 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:54151502 original size:20 final size:20
Alignment explanation
Indices: 54151456--54151503 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
54151446 AGTAAGCTTG
54151456 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
54151476 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
54151496 GTTGAGCT
1 GTTGAGCT
54151504 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:54153137 original size:11 final size:13
Alignment explanation
Indices: 54153112--54153143 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
54153102 ATAAATCACT
54153112 TTTTTTTTACGAA
1 TTTTTTTTACGAA
54153125 TTTTTTTT-C-AA
1 TTTTTTTTACGAA
54153136 TTTTTTTT
1 TTTTTTTT
54153144 TAACTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTTTTTACGAA
Found at i:54159631 original size:20 final size:19
Alignment explanation
Indices: 54159578--54159631 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
54159568 AGCTCCGTCC
54159578 AGCTCAACTCAGCTCATTTG
1 AGCTCAA-TCAGCTCATTTG
** *
54159598 AGCTCGTTCCAGCTCGTTTG
1 AGCTCAAT-CAGCTCATTTG
54159618 AGCTCAATCGAGCT
1 AGCTCAATC-AGCT
54159632 TACTTTCAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (19 bp):
AGCTCAATCAGCTCATTTG
Found at i:54160260 original size:30 final size:31
Alignment explanation
Indices: 54160226--54160322 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
54160216 AGCTCACTCC
*
54160226 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54160256 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
54160286 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54160316 TAGCTCA
1 TAGCTCA
54160323 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:54161252 original size:22 final size:20
Alignment explanation
Indices: 54161220--54161268 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
54161210 ACTGAATTTA
54161220 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
54161243 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
54161263 TGAACA
1 TGAACA
54161269 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:54162868 original size:9 final size:10
Alignment explanation
Indices: 54162861--54162917 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
54162851 AAGAGAAAAC
54162861 AAAGAAAAGA
1 AAAGAAAAGA
54162871 AAAGAAAAAGA
1 AAAG-AAAAGA
*
54162882 AAA-AGAAGAA
1 AAAGAAAAG-A
54162892 AAAGAAAACGA
1 AAAGAAAA-GA
54162903 AATA-AAAAGA
1 AA-AGAAAAGA
54162913 AAAGA
1 AAAGA
54162918 GAGGCAAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 5 0.13
10 13 0.33
11 19 0.49
12 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:54162871 original size:5 final size:5
Alignment explanation
Indices: 54162861--54162917 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54162851 AAGAGAAAAC
*
54162861 AAAGA AAAGA AAAGAA AAAGA AAA-A GAAGAA AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAGA AAA-GA AA-AGA
54162908 AAAGA AAAGA
1 AAAGA AAAGA
54162918 GAGGCAAAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 26 0.59
6 13 0.30
7 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:54162993 original size:12 final size:12
Alignment explanation
Indices: 54162985--54163009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54162975 TTTGAAAAGC
54162985 AAAAAGAAAATG
1 AAAAAGAAAATG
54162997 AAAAAGAAAATG
1 AAAAAGAAAATG
54163009 A
1 A
54163010 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:54163006 original size:18 final size:18
Alignment explanation
Indices: 54162979--54163034 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
54162969 AAAGCCTTTG
*
54162979 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
54162998 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
54163016 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
54163033 AA
1 AA
54163035 TTTGAGAGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:54163048 original size:30 final size:30
Alignment explanation
Indices: 54162985--54163065 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
54162975 TTTGAAAAGC
**
54162985 AAAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGAG
* *
54163015 AAAAAGAGAATG-AAAAGAAATTTGAGAGAG
1 AAAAAGAAAATGAAAAAGAAA-ATGAGAGAG
* **
54163045 AAAAATAAGTTGAAAAAGAAA
1 AAAAAGAAAATGAAAAAGAAA
54163066 TTGAAAAAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.20
30 25 0.61
31 8 0.20
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.14
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAAGAAAATGAGAGAG
Found at i:54165238 original size:30 final size:30
Alignment explanation
Indices: 54165204--54165300 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
54165194 AGCTCACTCC
*
54165204 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
54165234 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
54165264 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
54165294 TAGCTCA
1 TAGCTCA
54165301 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:54168827 original size:42 final size:42
Alignment explanation
Indices: 54168765--54168861 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
54168755 AGATTATGAC
* * * *
54168765 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAATAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
54168807 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
54168849 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
54168862 AAAGAAAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 10 0.20
42 40 0.80
ACGTcount: A:0.57, C:0.04, G:0.24, T:0.15
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:54168888 original size:18 final size:18
Alignment explanation
Indices: 54168865--54168914 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
54168855 GAAAGAAAAA
*
54168865 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
54168883 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
54168901 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
54168915 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:54168891 original size:24 final size:24
Alignment explanation
Indices: 54168858--54168939 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
54168848 AAGAAATGAA
54168858 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
54168882 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
54168906 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
54168930 AGAAAAAGAA
1 AGAAAAAGAA
54168940 TGTGAACAAG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:54168968 original size:18 final size:19
Alignment explanation
Indices: 54168932--54168970 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
54168922 TTTGAGAGAG
*
54168932 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
54168951 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
54168969 AA
1 AA
54168971 TTAAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:54170583 original size:20 final size:20
Alignment explanation
Indices: 54170560--54170613 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
54170550 AGCTCCGTCC
54170560 AGCTCAACCCAGCTCATTTG
1 AGCTCAACCCAGCTCATTTG
*** *
54170580 AGCTCGTTCCAGCTCCTTTG
1 AGCTCAACCCAGCTCATTTG
*
54170600 AGCTCAACCGAGCT
1 AGCTCAACCCAGCT
54170614 TACTTTCAGC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.26
Consensus pattern (20 bp):
AGCTCAACCCAGCTCATTTG
Found at i:54178368 original size:34 final size:31
Alignment explanation
Indices: 54178304--54178368 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 31
54178294 AATGTTGAAG
*
54178304 AGTCTTCCAATGTGAACAAGGTGAACCGAAT
1 AGTCTTCCAATGTGAACAAGGTGAAACGAAT
54178335 AGTCTTGCC-ATGTGAACATAGGTGTGAAACGAAT
1 AGTCTT-CCAATGTGAACA-A-G-GTGAAACGAAT
54178369 TAAGGAGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 15 0.52
32 3 0.10
33 1 0.03
34 10 0.34
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (31 bp):
AGTCTTCCAATGTGAACAAGGTGAAACGAAT
Found at i:54182157 original size:14 final size:14
Alignment explanation
Indices: 54182110--54182157 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
54182100 GTACGAATGG
*
54182110 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
54182124 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
54182138 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
54182152 ATTGGT
1 AATGGT
54182158 CAGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:54187884 original size:30 final size:30
Alignment explanation
Indices: 54187814--54187895 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
54187804 TTTTGTTTCA
* *
54187814 ATTTCTTTTTCATCTTCTTTTTCACTCTCAG
1 ATTTCTTTTTCTTC-TCTTTTTCAATCTCAG
54187845 ATTTC-TTTTCGTTCTCTTTTTCAATCTCA-
1 ATTTCTTTTTC-TTCTCTTTTTCAATCTCAG
* *
54187874 TTTTCTTTTTCATTTTCTTTTT
1 ATTTCTTTTTC-TTCTCTTTTT
54187896 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.09
30 33 0.75
31 7 0.16
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.65
Consensus pattern (30 bp):
ATTTCTTTTTCTTCTCTTTTTCAATCTCAG
Found at i:54187895 original size:18 final size:18
Alignment explanation
Indices: 54187846--54187901 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
54187836 CACTCTCAGA
* *
54187846 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
54187863 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
54187881 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
54187900 TT
1 TT
54187902 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:54187902 original size:12 final size:12
Alignment explanation
Indices: 54187871--54187895 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54187861 TTTTTCAATC
54187871 TCATTTTCTTTT
1 TCATTTTCTTTT
54187883 TCATTTTCTTTT
1 TCATTTTCTTTT
54187895 T
1 T
54187896 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:54190674 original size:30 final size:30
Alignment explanation
Indices: 54190589--54190685 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
54190579 TAAACTAAAA
* * *
54190589 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
54190619 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
54190649 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
54190678 ATGAGCTA
1 -TGAGCTA
54190686 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:54195744 original size:13 final size:13
Alignment explanation
Indices: 54195726--54195761 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
54195716 ATAAATCACT
54195726 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
54195739 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
54195752 TTTTTTTTTC
1 TTTTTTTTTC
54195762 AAACTTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.11, C:0.08, G:0.06, T:0.75
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:54197339 original size:10 final size:10
Alignment explanation
Indices: 54197324--54197350 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54197314 TAAGTTGAAG
54197324 TTGAGCTGAT
1 TTGAGCTGAT
54197334 TTGAGCTGAT
1 TTGAGCTGAT
54197344 TTGAGCT
1 TTGAGCT
54197351 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:54198338 original size:12 final size:12
Alignment explanation
Indices: 54198319--54198352 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54198309 AAAAAGAAAA
*
54198319 GAGTGAAAAGGT
1 GAGTGAAAAAGT
*
54198331 GTGTGAAAAAGT
1 GAGTGAAAAAGT
54198343 GAGTGAAAAA
1 GAGTGAAAAA
54198353 AAACGAGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.18
Consensus pattern (12 bp):
GAGTGAAAAAGT
Found at i:54198870 original size:20 final size:21
Alignment explanation
Indices: 54198845--54198893 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
54198835 ATCAGCTCAC
*
54198845 TTGAGCTCG-TTTTACCTTGT
1 TTGAGCTCGAATTTACCTTGT
*
54198865 TTGAGCTCGAATTTAGCTTGT
1 TTGAGCTCGAATTTACCTTGT
*
54198886 TTCAGCTC
1 TTGAGCTC
54198894 ATTCCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (21 bp):
TTGAGCTCGAATTTACCTTGT
Found at i:54199136 original size:13 final size:13
Alignment explanation
Indices: 54199118--54199146 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54199108 AATAGTTGTG
54199118 TGTTATTTAATTA
1 TGTTATTTAATTA
54199131 TGTTATTTAATTA
1 TGTTATTTAATTA
54199144 TGT
1 TGT
54199147 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:54200506 original size:29 final size:29
Alignment explanation
Indices: 54200461--54200520 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
54200451 AAGGATTCAA
* *
54200461 AGATGGGTTTATAGATATGAAGTTTATGT
1 AGATGGATTTATAGATATAAAGTTTATGT
* *
54200490 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATAGATATAAAGTTTATGT
54200519 AG
1 AG
54200521 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATAGATATAAAGTTTATGT
Found at i:54201541 original size:14 final size:14
Alignment explanation
Indices: 54201499--54201543 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
54201489 TTAAAGAAGC
54201499 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
54201513 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
54201526 AACTCATTTAATTA
1 AACTCATTAAATTA
54201540 AACT
1 AACT
54201544 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:54207017 original size:12 final size:11
Alignment explanation
Indices: 54207000--54207034 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
54206990 ATTATACAAG
54207000 TCAAAAAAAAT
1 TCAAAAAAAAT
*
54207011 TGGAAAAAAAAT
1 T-CAAAAAAAAT
54207023 TCAAAAAAAAT
1 TCAAAAAAAAT
54207034 T
1 T
54207035 TCGAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.20
Consensus pattern (11 bp):
TCAAAAAAAAT
Found at i:54207041 original size:12 final size:12
Alignment explanation
Indices: 54207002--54207046 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
54206992 TATACAAGTC
*
54207002 AAAAAAAATTGG
1 AAAAAAAATTCG
54207014 AAAAAAAATTC-
1 AAAAAAAATTCG
54207025 AAAAAAAATTTCG
1 AAAAAAAA-TTCG
54207038 AAAAGAAAA
1 AAAA-AAAA
54207047 AAAAATCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 8 0.28
12 13 0.45
13 4 0.14
14 4 0.14
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:54207058 original size:18 final size:18
Alignment explanation
Indices: 54207025--54207063 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
54207015 AAAAAAATTC
*
54207025 AAAAAAAATTTCGAAAAGA
1 AAAAAAAATCTCGAAAA-A
54207044 AAAAAAAATCT-GAAAAA
1 AAAAAAAATCTCGAAAAA
54207061 AAA
1 AAA
54207064 GTGTTTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAAAAATCTCGAAAAA
Found at i:54207983 original size:9 final size:10
Alignment explanation
Indices: 54207976--54208032 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
54207966 AAGAGAAAAC
54207976 AAAGAAAAGA
1 AAAGAAAAGA
54207986 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
54207998 AAAGAAGAG-
1 AAAGAAAAGA
54208007 AAAGAAAATGA
1 AAAGAAAA-GA
54208018 AATA-AAAAGA
1 AA-AGAAAAGA
54208028 AAAGA
1 AAAGA
54208033 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 8 0.21
10 10 0.26
11 15 0.38
12 6 0.15
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:54207999 original size:21 final size:20
Alignment explanation
Indices: 54207965--54208032 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
54207955 ACATTCTTGT
54207965 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
54207986 AAAGAAAAAGCAAAAGAAGA
1 AAAGAAAAAGCAAAAAAAGA
* *
54208006 GAAAGAAAATGAAATAAAAAGA
1 -AAAGAAAAAGCAA-AAAAAGA
54208028 AAAGA
1 AAAGA
54208033 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 9 0.22
21 25 0.62
22 6 0.15
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:54208000 original size:6 final size:5
Alignment explanation
Indices: 54207976--54208032 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54207966 AAGAGAAAAC
*
54207976 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGAG- AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
54208023 AAAGA AAAGA
1 AAAGA AAAGA
54208033 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:54208002 original size:17 final size:16
Alignment explanation
Indices: 54207976--54208032 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
54207966 AAGAGAAAAC
54207976 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
*
54207992 AAAGCAAAAG--AAGAG
1 AAAG-AAAAGAAAAGAA
*
54208007 AAAGAAAATG-AAATAA
1 AAAGAAAA-GAAAAGAA
54208023 AAAGAAAAGA
1 AAAGAAAAGA
54208033 GAGGCAAGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 4 0.12
15 10 0.29
16 15 0.44
17 5 0.15
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:54208112 original size:11 final size:12
Alignment explanation
Indices: 54208080--54208110 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54208070 TTGAGAGAAC
*
54208080 TTGAAAAATCCT
1 TTGAAAAAGCCT
54208092 TTGAAAAAGCCT
1 TTGAAAAAGCCT
54208104 TTGAAAA
1 TTGAAAA
54208111 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:54208121 original size:12 final size:12
Alignment explanation
Indices: 54208113--54208137 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54208103 TTTGAAAAGC
54208113 AAAAAGAAAATG
1 AAAAAGAAAATG
54208125 AAAAAGAAAATG
1 AAAAAGAAAATG
54208137 A
1 A
54208138 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:54208134 original size:18 final size:18
Alignment explanation
Indices: 54208107--54208162 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
54208097 AAAGCCTTTG
54208107 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
54208126 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
54208144 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
54208161 AA
1 AA
54208163 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:54208147 original size:30 final size:31
Alignment explanation
Indices: 54208113--54208194 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
54208103 TTTGAAAAGC
*
54208113 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
54208143 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
54208173 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
54208195 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:54209079 original size:19 final size:19
Alignment explanation
Indices: 54209055--54209094 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
54209045 AGCTCCCATG
54209055 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
54209074 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
54209093 TA
1 TA
54209095 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:54210373 original size:14 final size:14
Alignment explanation
Indices: 54210356--54210390 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
54210346 AATTTGTTCA
54210356 TACCATTTTCTTCC
1 TACCATTTTCTTCC
* *
54210370 TACCCTTTTGTTCC
1 TACCATTTTCTTCC
54210384 TACCATT
1 TACCATT
54210391 CCATTCGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.14, C:0.34, G:0.03, T:0.49
Consensus pattern (14 bp):
TACCATTTTCTTCC
Found at i:54212053 original size:29 final size:29
Alignment explanation
Indices: 54212012--54212106 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
54212002 AGCTCACTCC
*
54212012 TAGCTC-ACTTTCAACTACGAGCTAAACCT
1 TAGCTCAAC-TTCAGCTACGAGCTAAACCT
* * *
54212041 TAGCTCAACTTCAGCTTA-GAGTTTAGCCT
1 TAGCTCAACTTCAGC-TACGAGCTAAACCT
* * * *
54212070 CAGCTTAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCT-ACGAGCTAAACCT
54212100 TAGCTCA
1 TAGCTCA
54212107 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
28 1 0.02
29 32 0.65
30 16 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
TAGCTCAACTTCAGCTACGAGCTAAACCT
Found at i:54212084 original size:17 final size:18
Alignment explanation
Indices: 54212051--54212084 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54212041 TAGCTCAACT
*
54212051 TCAGCTTAGAGTTTAGCC
1 TCAGCTTAGACTTTAGCC
54212069 TCAGCTTA-ACTTTAGC
1 TCAGCTTAGACTTTAGC
54212085 TCACGAGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (18 bp):
TCAGCTTAGACTTTAGCC
Found at i:54213813 original size:26 final size:26
Alignment explanation
Indices: 54213763--54213812 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
54213753 ATTATACAAG
54213763 TCAAAAAAAAATTCGAAAAAGAAAAT
1 TCAAAAAAAAATTCGAAAAAGAAAAT
*
54213789 TCAAAAAAAATTTCG-AAAAGAAAA
1 TCAAAAAAAAATTCGAAAAAGAAAA
54213813 AAAAATCTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (26 bp):
TCAAAAAAAAATTCGAAAAAGAAAAT
Found at i:54213824 original size:18 final size:18
Alignment explanation
Indices: 54213791--54213829 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
54213781 AAGAAAATTC
*
54213791 AAAAAAAATTTCGAAAAGA
1 AAAAAAAATCTCGAAAA-A
54213810 AAAAAAAATCT-GAAAAA
1 AAAAAAAATCTCGAAAAA
54213827 AAA
1 AAA
54213830 GTGTTTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAAAAATCTCGAAAAA
Found at i:54214751 original size:9 final size:10
Alignment explanation
Indices: 54214744--54214800 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
54214734 AAGAGAAAAT
54214744 AAAGAAAAGA
1 AAAGAAAAGA
54214754 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
54214766 AAAGAAGA-A
1 AAAGAAAAGA
54214775 AAAGAAAATGA
1 AAAGAAAA-GA
54214786 AATA-AAAAGA
1 AA-AGAAAAGA
54214796 AAAGA
1 AAAGA
54214801 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:54214768 original size:6 final size:5
Alignment explanation
Indices: 54214744--54214800 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54214734 AAGAGAAAAT
*
54214744 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
54214791 AAAGA AAAGA
1 AAAGA AAAGA
54214801 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:54214775 original size:15 final size:14
Alignment explanation
Indices: 54214744--54214800 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
54214734 AAGAGAAAAT
54214744 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
54214760 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
54214775 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
54214791 AAAGAAAAGA
1 AAAGAAAAGA
54214801 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:54214880 original size:11 final size:12
Alignment explanation
Indices: 54214848--54214878 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54214838 TTGAGAGAAC
*
54214848 TTGAAAAATCCT
1 TTGAAAAAGCCT
54214860 TTGAAAAAGCCT
1 TTGAAAAAGCCT
54214872 TTGAAAA
1 TTGAAAA
54214879 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:54214889 original size:12 final size:12
Alignment explanation
Indices: 54214881--54214905 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54214871 TTTGAAAAGC
54214881 AAAAAGAAAATG
1 AAAAAGAAAATG
54214893 AAAAAGAAAATG
1 AAAAAGAAAATG
54214905 A
1 A
54214906 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:54214902 original size:18 final size:18
Alignment explanation
Indices: 54214875--54214930 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
54214865 AAAGCCTTTG
54214875 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
54214894 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
54214912 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
54214929 AA
1 AA
54214931 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:54214915 original size:30 final size:31
Alignment explanation
Indices: 54214881--54214962 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
54214871 TTTGAAAAGC
*
54214881 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
54214911 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
54214941 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
54214963 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:54216846 original size:30 final size:30
Alignment explanation
Indices: 54216760--54216857 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
54216750 TTAAACTAAA
* *
54216760 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
54216790 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
54216820 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
54216850 ATGAGCTA
1 ATGAGCTA
54216858 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:54217298 original size:15 final size:15
Alignment explanation
Indices: 54217278--54217309 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
54217268 TTGTGCGAAA
54217278 TTTCCATGTAGTGAT
1 TTTCCATGTAGTGAT
54217293 TTTCCATGTAGTGAT
1 TTTCCATGTAGTGAT
54217308 TT
1 TT
54217310 ACATTCCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (15 bp):
TTTCCATGTAGTGAT
Found at i:54220468 original size:12 final size:11
Alignment explanation
Indices: 54220451--54220495 Score: 72
Period size: 11 Copynumber: 3.9 Consensus size: 11
54220441 ATTATACAAG
54220451 TCAAAAAAAAT
1 TCAAAAAAAAT
54220462 TCGAAAAAAAAT
1 TC-AAAAAAAAT
54220474 TCAAAAAAAAT
1 TCAAAAAAAAT
54220485 TCAAAAGAAAA
1 TCAAAA-AAAA
54220496 AAAAATCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.53
12 15 0.47
ACGTcount: A:0.71, C:0.09, G:0.04, T:0.16
Consensus pattern (11 bp):
TCAAAAAAAAT
Found at i:54220478 original size:23 final size:24
Alignment explanation
Indices: 54220451--54220496 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
54220441 ATTATACAAG
*
54220451 TCAAAAAAAATTCGAAA-AAAAAT
1 TCAAAAAAAATTCAAAAGAAAAAT
54220474 TCAAAAAAAATTCAAAAGAAAAA
1 TCAAAAAAAATTCAAAAGAAAAA
54220497 AAAATCTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.72, C:0.09, G:0.04, T:0.15
Consensus pattern (24 bp):
TCAAAAAAAATTCAAAAGAAAAAT
Found at i:54221290 original size:10 final size:10
Alignment explanation
Indices: 54221275--54221301 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54221265 TACTCCTTCA
54221275 AGCTCAAATC
1 AGCTCAAATC
54221285 AGCTCAAATC
1 AGCTCAAATC
54221295 AGCTCAA
1 AGCTCAA
54221302 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:54229145 original size:27 final size:26
Alignment explanation
Indices: 54229114--54229169 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
54229104 ATGAGAGAGG
*
54229114 GAAAAGA-AAGTGAAAATGAAAAAGAAA
1 GAAAAGAGAA-TGAAAAAGAAAAA-AAA
*
54229141 GAAAAGAGAATGAAAAAGAAAGAAAA
1 GAAAAGAGAATGAAAAAGAAAAAAAA
54229167 GAA
1 GAA
54229170 CATGGGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 18 0.69
28 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.05
Consensus pattern (26 bp):
GAAAAGAGAATGAAAAAGAAAAAAAA
Found at i:54229154 original size:21 final size:21
Alignment explanation
Indices: 54229128--54229168 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
54229118 AGAAAGTGAA
54229128 AATGAAAAAGAAAGAAAAGAG
1 AATGAAAAAGAAAGAAAAGAG
54229149 AATGAAAAAGAAAGAAAAGA
1 AATGAAAAAGAAAGAAAAGA
54229169 ACATGGGAGA
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:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (21 bp):
AATGAAAAAGAAAGAAAAGAG
Found at i:54229160 original size:10 final size:10
Alignment explanation
Indices: 54229131--54229166 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
54229121 AAGTGAAAAT
54229131 GAAAAAGAAA
1 GAAAAAGAAA
*
54229141 GAAAAGAGAAT
1 GAAAA-AGAAA
54229152 GAAAAAGAAA
1 GAAAAAGAAA
54229162 GAAAA
1 GAAAA
54229167 GAACATGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:54230804 original size:5 final size:5
Alignment explanation
Indices: 54230794--54230849 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
54230784 AAGAGAAAAC
* * *
54230794 AAAGA AAAGA AAAGA AAAGA AAA-A GAAGAA AAAGA AAACA AAATAA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAG-A AAAGA AAAGA AAA-GA AAAGA
54230845 AAAGA
1 AAAGA
54230850 GAGGCAAGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
4 3 0.07
5 32 0.74
6 8 0.19
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:54230826 original size:25 final size:25
Alignment explanation
Indices: 54230798--54230845 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
54230788 GAAAACAAAG
*
54230798 AAAAGAAAAGAAAAGAAAAAGAAGA
1 AAAAGAAAACAAAAGAAAAAGAAGA
*
54230823 AAAAGAAAACAAAATAAAAAGAA
1 AAAAGAAAACAAAAGAAAAAGAA
54230846 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (25 bp):
AAAAGAAAACAAAAGAAAAAGAAGA
Found at i:54230926 original size:12 final size:12
Alignment explanation
Indices: 54230918--54230942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54230908 TTTGAAAAGC
54230918 AAAAAGAAAATG
1 AAAAAGAAAATG
54230930 AAAAAGAAAATG
1 AAAAAGAAAATG
54230942 A
1 A
54230943 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:54230939 original size:18 final size:18
Alignment explanation
Indices: 54230912--54230964 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
54230902 AAAGCCTTTG
54230912 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
54230931 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
54230949 AAAAGAGAACGAAAAT
1 AAAAGAAAAAGAAAAT
54230965 AAATCTGAGA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.68, C:0.04, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:54230952 original size:30 final size:30
Alignment explanation
Indices: 54230918--54230998 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
54230908 TTTGAAAAGC
*
54230918 AAAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAAGAAAATGAAAAAGAAAATGAGAGTG
* * **
54230948 AAAAAGAGAACGAAAATA-AATCTGAGAGTG
1 AAAAAGAAAATGAAAA-AGAAAATGAGAGTG
*
54230978 AAAAAGAAGATGAAAAAGAAA
1 AAAAAGAAAATGAAAAAGAAA
54230999 TTGAAACAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
29 1 0.03
30 38 0.95
31 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.21, T:0.11
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAAGAAAATGAGAGTG
Found at i:54239478 original size:16 final size:16
Alignment explanation
Indices: 54239457--54239495 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
54239447 CATAAATCAC
54239457 TTTTTTTTTTC-GAAT
1 TTTTTTTTTTCAGAAT
54239472 TTTTTTTTTTCAGAAT
1 TTTTTTTTTTCAGAAT
54239488 TTTTTTTT
1 TTTTTTTT
54239496 CAAACTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (16 bp):
TTTTTTTTTTCAGAAT
Found at i:54239497 original size:14 final size:15
Alignment explanation
Indices: 54239457--54239495 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
54239447 CATAAATCAC
54239457 TTTTTTTTTTC-GAA
1 TTTTTTTTTTCAGAA
54239471 TTTTTTTTTTTCAGAA
1 -TTTTTTTTTTCAGAA
54239487 TTTTTTTTT
1 TTTTTTTTT
54239496 CAAACTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (15 bp):
TTTTTTTTTTCAGAA
Found at i:54241124 original size:10 final size:10
Alignment explanation
Indices: 54241109--54241135 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54241099 TAAGTTGAAG
54241109 TTGAGCTGAT
1 TTGAGCTGAT
54241119 TTGAGCTGAT
1 TTGAGCTGAT
54241129 TTGAGCT
1 TTGAGCT
54241136 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:54242952 original size:12 final size:12
Alignment explanation
Indices: 54242933--54242964 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
54242923 AAAATAGATG
54242933 AATGAAAAAGAA
1 AATGAAAAAGAA
*
54242945 ATTGAAAAAGAA
1 AATGAAAAAGAA
54242957 AATGAAAA
1 AATGAAAA
54242965 TGTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (12 bp):
AATGAAAAAGAA
Found at i:54242957 original size:18 final size:21
Alignment explanation
Indices: 54242936--54242979 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
54242926 ATAGATGAAT
54242936 GAAAAAG-AAAT-TGAA-AAA
1 GAAAAAGAAAATGTGAAGAAA
*
54242954 GAAAATGAAAATGTGAAGAAA
1 GAAAAAGAAAATGTGAAGAAA
54242975 GAAAA
1 GAAAA
54242980 TGAGCTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 4 0.18
20 4 0.18
21 8 0.36
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.11
Consensus pattern (21 bp):
GAAAAAGAAAATGTGAAGAAA
Found at i:54242958 original size:17 final size:21
Alignment explanation
Indices: 54242943--54242982 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54242933 AATGAAAAAG
54242943 AAAT-TGAA-AAAGAAAATGA
1 AAATGTGAAGAAAGAAAATGA
54242962 AAATGTGAAGAAAGAAAATGA
1 AAATGTGAAGAAAGAAAATGA
54242983 GCTTACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 11 0.58
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (21 bp):
AAATGTGAAGAAAGAAAATGA
Found at i:54243779 original size:17 final size:18
Alignment explanation
Indices: 54243746--54243784 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
54243736 AGCAGCCAAA
54243746 AATTAATGTGTCTAAATT
1 AATTAATGTGTCTAAATT
54243764 AATTAATGTG-CTAAATT
1 AATTAATGTGTCTAAATT
54243781 AATT
1 AATT
54243785 TGTGTGCAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (18 bp):
AATTAATGTGTCTAAATT
Found at i:54243790 original size:17 final size:17
Alignment explanation
Indices: 54243752--54243791 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
54243742 CAAAAATTAA
54243752 TGTGT-CTAAATTAATT
1 TGTGTGCTAAATTAATT
**
54243768 AATGTGCTAAATTAATT
1 TGTGTGCTAAATTAATT
54243785 TGTGTGC
1 TGTGTGC
54243792 AGGTGCAATG
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (17 bp):
TGTGTGCTAAATTAATT
Found at i:54246000 original size:12 final size:12
Alignment explanation
Indices: 54245983--54246018 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
54245973 AAATTCGAAG
54245983 TTGAAAAAAAAA
1 TTGAAAAAAAAA
54245995 TTGAAAAAAAAA
1 TTGAAAAAAAAA
*
54246007 TTCAAAAAAAAA
1 TTGAAAAAAAAA
54246019 GTTCTGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.17
Consensus pattern (12 bp):
TTGAAAAAAAAA
Found at i:54247230 original size:13 final size:13
Alignment explanation
Indices: 54247212--54247240 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54247202 CGGCTAACCT
54247212 ACATAATTAAATA
1 ACATAATTAAATA
54247225 ACATAATTAAATA
1 ACATAATTAAATA
54247238 ACA
1 ACA
54247241 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:54247508 original size:20 final size:20
Alignment explanation
Indices: 54247462--54247512 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
54247452 ATGAAAAAGG
*
54247462 AATGAGCT-GAACGAGCTAA
1 AATGAGCTCAAACGAGCTAA
*
54247481 ATTCGAGCTCAAACGAGCTAA
1 AAT-GAGCTCAAACGAGCTAA
54247502 AATGAGCTCAA
1 AATGAGCTCAA
54247513 GTGAGCTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 13 0.48
21 12 0.44
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AATGAGCTCAAACGAGCTAA
Found at i:54247519 original size:20 final size:21
Alignment explanation
Indices: 54247471--54247512 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
54247461 GAATGAGCTG
*
54247471 AACGAGCTAAATTCGAGCTCA
1 AACGAGCTAAAATCGAGCTCA
54247492 AACGAGCTAAAAT-GAGCTCA
1 AACGAGCTAAAATCGAGCTCA
54247512 A
1 A
54247513 GTGAGCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (21 bp):
AACGAGCTAAAATCGAGCTCA
Found at i:54250501 original size:16 final size:16
Alignment explanation
Indices: 54250476--54250509 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54250466 ATCCTAAAAA
* *
54250476 TTCTATTTCTGTTTTT
1 TTCTAATTCTATTTTT
54250492 TTCTAATTCTATTTTT
1 TTCTAATTCTATTTTT
54250508 TT
1 TT
54250510 AGGAGTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.74
Consensus pattern (16 bp):
TTCTAATTCTATTTTT
Found at i:54253585 original size:30 final size:31
Alignment explanation
Indices: 54253551--54253647 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 31
54253541 AGCTCACTCC
*
54253551 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
54253581 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
*
54253611 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
54253641 TAGCTCA
1 TAGCTCA
54253648 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 49 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:54256194 original size:9 final size:10
Alignment explanation
Indices: 54256187--54256243 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
54256177 AAGAGAAAAT
54256187 AAAGAAAAGA
1 AAAGAAAAGA
*
54256197 AAAGAAAAAGC
1 AAAG-AAAAGA
54256208 AAA-AAAAGAA
1 AAAGAAAAG-A
54256218 AAAGAAAATGA
1 AAAGAAAA-GA
54256229 AATA-AAAAGA
1 AA-AGAAAAGA
54256239 AAAGA
1 AAAGA
54256244 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 6 0.15
10 12 0.31
11 19 0.49
12 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:54256211 original size:6 final size:5
Alignment explanation
Indices: 54256187--54256243 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54256177 AAGAGAAAAT
*
54256187 AAAGA AAAGA AAAGAA AAAGC AAA-A AAAGAA AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAGA AAA-GA AA-AGA
54256234 AAAGA AAAGA
1 AAAGA AAAGA
54256244 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:54256216 original size:15 final size:14
Alignment explanation
Indices: 54256196--54256241 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
54256186 TAAAGAAAAG
54256196 AAAAGAAAAAGCAAA
1 AAAAGAAAAAG-AAA
54256211 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
*
54256225 ATGAAATAAAAAGAAA
1 A--AAAGAAAAAGAAA
54256241 A
1 A
54256242 GAGAGGCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 4 0.14
15 11 0.39
16 13 0.46
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAGAAAAAGAAA
Found at i:54256242 original size:21 final size:20
Alignment explanation
Indices: 54256176--54256243 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
54256166 ACATTCTTGT
* *
54256176 AAAGAGAAAATAAAGAAAAGA
1 AAAGA-AAAAGAAAAAAAAGA
*
54256197 AAAGAAAAAGCAAAAAAAGAA
1 AAAGAAAAAGAAAAAAAAG-A
*
54256218 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGAAA-AAAAAGA
54256239 AAAGA
1 AAAGA
54256244 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.28
21 23 0.57
22 6 0.15
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.04
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAAAGA
Found at i:54256316 original size:12 final size:12
Alignment explanation
Indices: 54256308--54256332 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54256298 TTTGAAAAGC
54256308 AAAAAGAAAATG
1 AAAAAGAAAATG
54256320 AAAAAGAAAATG
1 AAAAAGAAAATG
54256332 A
1 A
54256333 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:54256329 original size:18 final size:18
Alignment explanation
Indices: 54256302--54256344 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
54256292 AAAGCCTTTG
54256302 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
54256321 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
54256339 AAAAGA
1 AAAAGA
54256345 GATTGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:54256340 original size:12 final size:12
Alignment explanation
Indices: 54256325--54256358 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
54256315 AAATGAAAAA
*
54256325 GAAAATGAGATT
1 GAAAAAGAGATT
54256337 GAAAAAGAGATT
1 GAAAAAGAGATT
54256349 GAAAAAGAGA
1 GAAAAAGAGA
54256359 ACGAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (12 bp):
GAAAAAGAGATT
Found at i:54256395 original size:30 final size:31
Alignment explanation
Indices: 54256343--54256402 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
54256333 GATTGAAAAA
*
54256343 GAGATTGAAAAAGAGAACG-AAAAGAAATTT
1 GAGAGTGAAAAAGAGAACGAAAAAGAAATTT
*
54256373 GAGAGTGAAAAAGA-AGATGAAAAAGAAATT
1 GAGAGTGAAAAAGAGA-ACGAAAAAGAAATT
54256403 GAAACAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 15 0.58
31 10 0.38
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (31 bp):
GAGAGTGAAAAAGAGAACGAAAAAGAAATTT
Done.