Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 45 of 255
Found at i:12150063 original size:120 final size:119
Alignment explanation
Indices: 12149871--12150093 Score: 383
Period size: 120 Copynumber: 1.9 Consensus size: 119
12149861 CCTCGTTCAA
* **
12149871 ATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATTT
1 ATGCCTTCGGGACATAACCCGGATTTAACAACTCACACAATGCCTTCGGGACATAACCCGGATTT
12149936 AACAACTCGCACAAATGCCTTCGGAACTTAATCCGGATTTAACAACTCGCACGT
66 AACAACTCGCACAAATGCCTTCGGAACTTAATCCGGATTTAACAACTCGCACGT
* * *
12149990 ATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATT
1 ATGCCTTCGGGACATAACCCGGATTTAACAACTCACAC-AATGCCTTCGGGACATAACCCGGATT
12150055 TAACAACTCGCACAAATGCCTTCGGAACTTAATCCGGAT
65 TAACAACTCGCACAAATGCCTTCGGAACTTAATCCGGAT
12150094 ATATTCACTT
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 33 0.34
120 64 0.66
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (119 bp):
ATGCCTTCGGGACATAACCCGGATTTAACAACTCACACAATGCCTTCGGGACATAACCCGGATTT
AACAACTCGCACAAATGCCTTCGGAACTTAATCCGGATTTAACAACTCGCACGT
Found at i:12150116 original size:120 final size:118
Alignment explanation
Indices: 12149868--12150132 Score: 379
Period size: 120 Copynumber: 2.2 Consensus size: 118
12149858 GCTCCTCGTT
* **
12149868 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACATAACCCGGA
* *
12149933 TTTAACAACTCGCACAAATGCCTTCGGAACTTAATCCGGATTTAACAACTCGCA
65 TTTAACAACTCGCACAAATGCCTTCGGAACTTAATCCGGATATAACAACTAGCA
* * * * *
12149987 CGTATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAACAACTCACAC-AATGCCTTCGGGACATAACCCGG
*
12150052 ATTTAACAACTCGCACAAATGCCTTCGGAACTTAATCCGGATATATTC-ACTTAGCA
64 ATTTAACAACTCGCACAAATGCCTTCGGAACTTAATCCGGATATA-ACAAC-TAGCA
12150108 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
12150133 CAGCATTCAA
Statistics
Matches: 128, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
119 32 0.25
120 90 0.70
121 6 0.05
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACATAACCCGGAT
TTAACAACTCGCACAAATGCCTTCGGAACTTAATCCGGATATAACAACTAGCA
Found at i:12150141 original size:41 final size:41
Alignment explanation
Indices: 12150064--12150141 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 41
12150054 TTAACAACTC
* * *
12150064 GCACAAATGCCTTCGGAACTTAATCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGAACTTAACCCGGACACATTCACTTA
* *
12150105 GCACAAA-GCCTTCGGGACTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTCGGAACTTAACCCGGACA-CATTCA
12150142 ATTAATCATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 19 0.61
41 12 0.39
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (41 bp):
GCACAAATGCCTTCGGAACTTAACCCGGACACATTCACTTA
Found at i:12157662 original size:79 final size:79
Alignment explanation
Indices: 12157533--12157795 Score: 336
Period size: 79 Copynumber: 3.3 Consensus size: 79
12157523 GCTCCTCGTT
* * ** * *
12157533 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAATGCCTTCGGGACTTAACCCGGA
12157598 TTTAACAACTCGCA
66 TTTAACAACTCGCA
*
12157612 CAAATGCCTTC-GGACTTAACCCGGATTTAACAACTCGCACGTATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
12157676 ATTTAACAACTCGCA
65 ATTTAACAACTCGCA
* * *
12157691 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCG-ACAAATGCCTTCGGAACTTAATCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
* * *
12157755 ATATATTC-ACTTAGCA
65 ATTTA-ACAAC-TCGCA
*
12157771 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
12157796 CAGCATTCAA
Statistics
Matches: 163, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
78 24 0.15
79 105 0.64
80 34 0.21
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAACAACTCGCA
Found at i:12157678 original size:40 final size:40
Alignment explanation
Indices: 12157533--12157795 Score: 338
Period size: 39 Copynumber: 6.7 Consensus size: 40
12157523 GCTCCTCGTT
* * ** *
12157533 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
12157573 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
12157612 CAAATGCCTTC-GGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
**
12157651 CGTATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
12157691 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCG-A
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* * * * *
12157730 CAAATGCCTTCGGAACTTAATCCGGATATATTC-ACTTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCA
*
12157771 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
12157796 CAGCATTCAA
Statistics
Matches: 201, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
39 100 0.50
40 96 0.48
41 5 0.02
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
Found at i:12170477 original size:27 final size:27
Alignment explanation
Indices: 12170447--12170624 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
12170437 ATATTGAGTC
* *
12170447 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
12170474 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
12170501 CGCACACTTAGTGCTACATAATCAACCT
1 CGCACACTTAGTGCTACATAATCAA-CT
** ** *
12170529 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
12170556 CGCACACTTAGTGC-ATCCTATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
12170583 CGCACACTTAGTGCAACATAGTTAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
12170610 CGCATACTTAGTGCT
1 CGCACACTTAGTGCT
12170625 GTACAATTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:12170559 original size:55 final size:54
Alignment explanation
Indices: 12170447--12170624 Score: 187
Period size: 54 Copynumber: 3.3 Consensus size: 54
12170437 ATATTGAGTC
* * * *
12170447 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
* ** *
12170501 CGCACACTTAGTGCTACATAATCAACCTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAA-CTCGCACACTTAGTGCCACATAATCAAAT
* * ** * * *
12170556 CGCACACTTAGTGC-ATCCTATTCATTTCGCACACTTAGTGCAACATAGTTAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
*
12170610 CGCATACTTAGTGCT
1 CGCACACTTAGTGCT
12170625 GTACAATTTA
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
54 60 0.58
55 43 0.42
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
Found at i:12188975 original size:27 final size:27
Alignment explanation
Indices: 12188945--12189122 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
12188935 ATATTGAGTC
* *
12188945 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
12188972 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
12188999 CGCACACTTAGTGCTACATAATCAACCT
1 CGCACACTTAGTGCTACATAATCAA-CT
** ** *
12189027 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
12189054 CGCACACTTAGTGC-ATCCTATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
12189081 CGCACACTTAGTGCAACATAGTTAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
12189108 CGCATACTTAGTGCT
1 CGCACACTTAGTGCT
12189123 GTACAATTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:12189057 original size:55 final size:54
Alignment explanation
Indices: 12188945--12189122 Score: 187
Period size: 54 Copynumber: 3.3 Consensus size: 54
12188935 ATATTGAGTC
* * * *
12188945 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
* ** *
12188999 CGCACACTTAGTGCTACATAATCAACCTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAA-CTCGCACACTTAGTGCCACATAATCAAAT
* * ** * * *
12189054 CGCACACTTAGTGC-ATCCTATTCATTTCGCACACTTAGTGCAACATAGTTAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
*
12189108 CGCATACTTAGTGCT
1 CGCACACTTAGTGCT
12189123 GTACAATTTA
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
54 60 0.58
55 43 0.42
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
Found at i:12195947 original size:26 final size:27
Alignment explanation
Indices: 12195918--12196040 Score: 106
Period size: 27 Copynumber: 4.6 Consensus size: 27
12195908 TTAGTTTACT
*
12195918 AAATTACTAAAATACCCCCAG-TTGTA
1 AAATTACCAAAATACCCCCAGTTTGTA
* * *
12195944 AAATTACCAAAGTACCCCCGGTTTATA
1 AAATTACCAAAATACCCCCAGTTTGTA
* * *
12195971 AAATTACCCAAATATCCTC-GATTTGTA
1 AAATTACCAAAATACCCCCAG-TTTGTA
* * **
12195998 AAATTACCGAAATACTCTTAGTTTGTA
1 AAATTACCAAAATACCCCCAGTTTGTA
**
12196025 AAATTACTGAAATACC
1 AAATTACCAAAATACC
12196041 TTTGACTTGT
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
26 19 0.24
27 59 0.75
28 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCCAGTTTGTA
Found at i:12196050 original size:27 final size:27
Alignment explanation
Indices: 12195993--12196057 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
12195983 TATCCTCGAT
*
12195993 TTGTAAAATTACCGAAATACTCTTAGT
1 TTGTAAAATTACCGAAATACTCTTAGC
* *
12196020 TTGTAAAATTACTGAAATAC-CTTTGAC
1 TTGTAAAATTACCGAAATACTCTTAG-C
12196047 TTGTAAAATTA
1 TTGTAAAATTA
12196058 TCAAAGTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 4 0.12
27 30 0.88
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Consensus pattern (27 bp):
TTGTAAAATTACCGAAATACTCTTAGC
Found at i:12196094 original size:27 final size:27
Alignment explanation
Indices: 12196064--12196446 Score: 462
Period size: 27 Copynumber: 14.2 Consensus size: 27
12196054 ATTATCAAAG
* * *
12196064 TACCCTCGAATTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
12196091 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* * *
12196118 TACCCTCAATTTACAAAATTACAATTT
1 TACCCTCGATTTACAGAATTACTATTT
*
12196145 TACGCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* **
12196172 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTATTT
*
12196199 TACCCTCGATTGACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
12196226 TACCCTCGATTTACAGAATTATTATTC
1 TACCCTCGATTTACAGAATTACTATTT
* * * *
12196253 TACCCTCAATTTGCAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
* * *
12196280 TACCCTCGATTGACAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
12196307 TACCCTCGATTTATAGAATTATTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
12196334 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
12196361 TACCCTTGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
12196388 TACCCTCGATTTATAGAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-ATTT
* * * *
12196415 TACCCTCAATTTATAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACTATTT
12196442 TACCC
1 TACCC
12196447 CTACGGTGTT
Statistics
Matches: 305, Mismatches: 49, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
26 1 0.00
27 304 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTATTT
Found at i:12196801 original size:26 final size:27
Alignment explanation
Indices: 12196772--12196831 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
12196762 CCACATATAT
*
12196772 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
12196798 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
12196825 ATATCTG
1 ATATCTG
12196832 GTAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:12196985 original size:31 final size:31
Alignment explanation
Indices: 12196950--12197053 Score: 163
Period size: 31 Copynumber: 3.4 Consensus size: 31
12196940 TTGCATTCAC
* * *
12196950 ATTCTGATTTTGATTCTGTTACCTAATACTG
1 ATTCTGATTCTGATTCTGTCACCTAATTCTG
* *
12196981 ATTCTGATTCTAATTCTGTCACCTAATTTTG
1 ATTCTGATTCTGATTCTGTCACCTAATTCTG
12197012 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTCACCTAATTCTG
12197043 ATTCTGATTCT
1 ATTCTGATTCT
12197054 CATTTTGATT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTG
Found at i:12196989 original size:6 final size:6
Alignment explanation
Indices: 12196950--12197074 Score: 60
Period size: 6 Copynumber: 20.3 Consensus size: 6
12196940 TTGCATTCAC
* * * *
12196950 ATTCTG ATTTTG ATTCTG -TTACCTA ATACTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * * *
12196999 -TCACCTA ATTTTG ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
* *
12197049 ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG A-TTCTG AT
12197075 AATGTTTCTT
Statistics
Matches: 86, Mismatches: 22, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
5 5 0.06
6 71 0.83
7 7 0.08
8 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:12201156 original size:11 final size:11
Alignment explanation
Indices: 12201142--12201186 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
12201132 AGATAAATAT
12201142 TATTTTATTAA
1 TATTTTATTAA
*
12201153 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
12201166 TATTTTATTAT
1 TATTTTATTAA
12201177 TATTTTATTA
1 TATTTTATTA
12201187 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:12203101 original size:46 final size:46
Alignment explanation
Indices: 12203029--12203379 Score: 452
Period size: 46 Copynumber: 7.6 Consensus size: 46
12203019 GCTCTCTGAA
** *
12203029 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* ** * *
12203075 ATGAGATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
12203121 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATTGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
12203167 ATGAAAAGAATAAGACCATGGTTGAGAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *** *
12203213 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGTGTGGC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
12203259 ATGAAATGAATAAGACCGTGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
12203305 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
12203351 A-GAAAATGAGTAAGACCATAGTTGAAAGA
1 ATG-AAATGAATAAGACCATGGTTGAAAGA
12203380 CACTATGACA
Statistics
Matches: 269, Mismatches: 35, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.00
46 268 1.00
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:12203281 original size:138 final size:138
Alignment explanation
Indices: 12203039--12203394 Score: 514
Period size: 138 Copynumber: 2.6 Consensus size: 138
12203029 ATGAAATGTG
* * *
12203039 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAGATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAGTAAGACCATGGTTGAAAGA
* ** *
12203104 TACCATGACAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATTGCAACGTGACAT
66 TACCATGACAACATGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
12203169 GAAAAGAA
131 GAAAAGAA
* * *
12203177 TAAGACCATGGTTGAGAGATACCATGGCAACATGATGGGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAGTAAGACCATGGTTGAAAGA
* *** * *
12203242 TACCATGGCAGTGTGGCATGAAATGAATAAGACCGTGGTTGAAAGATACCATGGCAACGTGACAT
66 TACCATGACAACATGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
12203307 GAAAAGAA
131 GAAAAGAA
* * *
12203315 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAGTAAGACCATGGTTGAAAGA
* * *
12203380 CACTATGACATCATG
66 TACCATGACAACATG
12203395 TCAAAGATAA
Statistics
Matches: 190, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 190 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (138 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAGTAAGACCATGGTTGAAAGA
TACCATGACAACATGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
GAAAAGAA
Found at i:12206156 original size:42 final size:43
Alignment explanation
Indices: 12205979--12206169 Score: 258
Period size: 43 Copynumber: 4.5 Consensus size: 43
12205969 CGTTTATTTA
* * *
12205979 AAAAATGCCGCTAAAGGTCATGACCTTTAGTGGCGCTTTCCCA
1 AAAAATGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTCCCC
*
12206022 AAAAATGCCGCTAAAGGTCATGACTTTTAGCTGCGCTTTCCCC
1 AAAAATGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTCCCC
* *
12206065 AAAAACGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTACCCC
1 AAAAATGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTCCCC
* * * **
12206108 ACAAATGCCGCTAAAGGTCATG-GTTTTAGCGACGCTTTCCTT
1 AAAAATGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTCCCC
* *
12206150 AAAAATGCCACTAAAAGTCA
1 AAAAATGCCGCTAAAGGTCA
12206170 CCACTATCCC
Statistics
Matches: 131, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 32 0.24
43 99 0.76
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (43 bp):
AAAAATGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTCCCC
Found at i:12210902 original size:8 final size:8
Alignment explanation
Indices: 12210830--12210902 Score: 53
Period size: 7 Copynumber: 8.9 Consensus size: 8
12210820 ATATTAAATA
*
12210830 TTAAAGTT
1 TTAAATTT
*
12210838 TTAAGTTT
1 TTAAATTT
*
12210846 TT-TATTT
1 TTAAATTT
12210853 TT-AATTT
1 TTAAATTT
12210860 TTAAA-TT
1 TTAAATTT
12210867 TTAAATTTTT
1 TTAAA--TTT
12210877 TTGAAGATTT
1 TT-AA-ATTT
12210887 TTATAATTT
1 TTA-AATTT
12210896 TTAAATT
1 TTAAATT
12210903 ATCATATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
7 18 0.34
8 14 0.26
9 8 0.15
10 10 0.19
11 2 0.04
12 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (8 bp):
TTAAATTT
Found at i:12211663 original size:21 final size:21
Alignment explanation
Indices: 12211639--12211686 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
12211629 ACCTTAAAAA
*
12211639 CCTAAAACTT-AACCCATAACC
1 CCTAAAACTTAAACCC-CAACC
**
12211660 CCTAAGCCTTAAACCCCAACC
1 CCTAAAACTTAAACCCCAACC
12211681 CCTAAA
1 CCTAAA
12211687 CCATAATCCC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.40, C:0.42, G:0.02, T:0.17
Consensus pattern (21 bp):
CCTAAAACTTAAACCCCAACC
Found at i:12211708 original size:15 final size:14
Alignment explanation
Indices: 12211680--12211717 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
12211670 AAACCCCAAC
12211680 CCCTAAACCATAAT
1 CCCTAAACCATAAT
12211694 CCCTAAACTCATAAT
1 CCCTAAAC-CATAAT
*
12211709 CCGTAAACC
1 CCCTAAACC
12211718 TTAAAATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.39, C:0.37, G:0.03, T:0.21
Consensus pattern (14 bp):
CCCTAAACCATAAT
Found at i:12211763 original size:14 final size:14
Alignment explanation
Indices: 12211741--12211785 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
12211731 CCATACACTT
12211741 TAAACCCTAAACCA
1 TAAACCCTAAACCA
* *
12211755 TATACCCTAAACTA
1 TAAACCCTAAACCA
* *
12211769 TAAACTCTAAACTA
1 TAAACCCTAAACCA
12211783 TAA
1 TAA
12211786 TGATAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:12211891 original size:7 final size:7
Alignment explanation
Indices: 12211879--12211999 Score: 68
Period size: 7 Copynumber: 17.0 Consensus size: 7
12211869 ACTAATTAAT
12211879 CTAAACC
1 CTAAACC
12211886 CTAAACTC
1 CTAAAC-C
* *
12211894 TTAATCC
1 CTAAACC
12211901 CTAAACC
1 CTAAACC
12211908 CTAAACC
1 CTAAACC
* *
12211915 ATAAATC
1 CTAAACC
*
12211922 CTAAAAC
1 CTAAACC
*
12211929 ATAAACC
1 CTAAACC
12211936 CTAAACC
1 CTAAACC
* * *
12211943 TTGAACT
1 CTAAACC
12211950 C-ATAACC
1 CTA-AACC
*
12211957 CTTAACCC
1 C-TAAACC
12211965 CT-AACAC
1 CTAAAC-C
*
12211972 CTAAACA
1 CTAAACC
*
12211979 TTAAACC
1 CTAAACC
12211986 CT-AACC
1 CTAAACC
12211992 CTTAAACC
1 C-TAAACC
12212000 ACCTTTAAAC
Statistics
Matches: 83, Mismatches: 23, Indels: 15
0.69 0.19 0.12
Matches are distributed among these distances:
6 7 0.08
7 59 0.71
8 16 0.19
9 1 0.01
ACGTcount: A:0.42, C:0.36, G:0.01, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:12211921 original size:22 final size:20
Alignment explanation
Indices: 12211879--12211940 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
12211869 ACTAATTAAT
*
12211879 CTAAACCCTAAACTCTTAATCC
1 CTAAACCCTAAAC-CTAAAT-C
12211901 CTAAACCCTAAACCATAAATC
1 CTAAACCCTAAACC-TAAATC
* *
12211922 CTAAAACATAAACCCTAAA
1 CTAAACCCTAAA-CCTAAA
12211941 CCTTGAACTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (20 bp):
CTAAACCCTAAACCTAAATC
Found at i:12212373 original size:40 final size:40
Alignment explanation
Indices: 12212317--12212585 Score: 211
Period size: 40 Copynumber: 6.7 Consensus size: 40
12212307 AAATTCTTTT
* * *
12212317 GCGGCGTTGTTCAAAAAACGCCGCTAAAGATTAAGCATTA
1 GCGGCGTTTTTTAAAAAACGCCGCTAAAGATTGAGCATTA
*
12212357 GCGGCGTTTTTTAAAAAAGCGCCGCTAAAGATCGAGCATTA
1 GCGGCGTTTTTTAAAAAA-CGCCGCTAAAGATTGAGCATTA
** * * *
12212398 GTAGCATTTTTTAAAAAGCGCCGCTAAAGATCGAGCATTA
1 GCGGCGTTTTTTAAAAAACGCCGCTAAAGATTGAGCATTA
* * * * *
12212438 GCGGCGTTTTTTAAAAGACGTCGCTAAAG-GTGTGCCTATA
1 GCGGCGTTTTTTAAAAAACGCCGCTAAAGATTGAGCAT-TA
* * * * *
12212478 GCAGCGTTTCTTAAAAAATGCCGCTAAAGGTTTA-CATATA
1 GCGGCGTTTTTTAAAAAACGCCGCTAAAGATTGAGCAT-TA
* ** * * ** *
12212518 GCGGTG-TTTTTAAAAAGTGCCGCTAATGCTTGTTCTTTA
1 GCGGCGTTTTTTAAAAAACGCCGCTAAAGATTGAGCATTA
* **
12212557 GCGGCGTTTTTCATTCAAACGCCGCTAAA
1 GCGGCGTTTTTTA-AAAAACGCCGCTAAA
12212586 TACCTGTTTT
Statistics
Matches: 180, Mismatches: 43, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
39 32 0.18
40 103 0.57
41 45 0.25
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (40 bp):
GCGGCGTTTTTTAAAAAACGCCGCTAAAGATTGAGCATTA
Found at i:12212520 original size:80 final size:81
Alignment explanation
Indices: 12212329--12212543 Score: 233
Period size: 80 Copynumber: 2.7 Consensus size: 81
12212319 GGCGTTGTTC
*
12212329 AAAAAACGCCGCTAAAGATTAAGCATTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGATCGAGC
1 AAAAAACGCCGCTAAAGATTAAGCATTAGCGGCGTTTTTTAAAAGAGCGCCGCTAAAGATCGAGC
* *
12212394 ATTAGTAGCATTTTTT
66 ATTAGCAGCATTTCTT
* ** * * *
12212410 AAAAAGCGCCGCTAAAGATCGAGCATTAGCGGCGTTTTTTAAAAGA-CGTCGCTAAAGGT-GTGC
1 AAAAAACGCCGCTAAAGATTAAGCATTAGCGGCGTTTTTTAAAAGAGCGCCGCTAAAGATCGAGC
* *
12212473 CTATAGCAGCGTTTCTT
66 AT-TAGCAGCATTTCTT
* * * * *
12212490 AAAAAATGCCGCTAAAGGTTTA-CATATAGCGGTG-TTTTTAAAA-AGTGCCGCTAA
1 AAAAAACGCCGCTAAAGATTAAGCAT-TAGCGGCGTTTTTTAAAAGAGCGCCGCTAA
12212544 TGCTTGTTCT
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
78 1 0.01
79 23 0.21
80 46 0.41
81 42 0.38
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (81 bp):
AAAAAACGCCGCTAAAGATTAAGCATTAGCGGCGTTTTTTAAAAGAGCGCCGCTAAAGATCGAGC
ATTAGCAGCATTTCTT
Found at i:12228892 original size:140 final size:139
Alignment explanation
Indices: 12228736--12228998 Score: 357
Period size: 140 Copynumber: 1.9 Consensus size: 139
12228726 GTCGAGGCCG
* * * * *
12228736 ATGCATGTCCCAGACATGTCTTACTCTGGCACTCATCTCTG-TGCCGATGCCCTGTCCCAGACAT
1 ATGCATGTCCCAGACATGTCTTACACTAGCACTCATCT-GGATGCCGATGCCATGTCCCAAACAT
** * **
12228800 GGTCTTACACTGGCTCTCATAATATGGCTGACGCATGTCCCTGACATGTCTTACACTGGCTCTCA
65 GGTCTTACACTGGCTCTCATAATATGGCCAAAGCATGTCCCAAACATGT-TTACACTGGCTCTCA
12228865 TAATATGGCTA
129 TAATATGGCTA
** * * *
12228876 ATGCATGTCCTTGACATGTCTTACACTAGCCCTCGTCTGGATGCTGATGCCATGTCCCAAACATG
1 ATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTGGATGCCGATGCCATGTCCCAAACATG
*
12228941 GTCTTACACTGGCTCTCATAATGTGGCCAAAGCATGTCCCAAACATGTTTACACTGGC
66 GTCTTACACTGGCTCTCATAATATGGCCAAAGCATGTCCCAAACATGTTTACACTGGC
12228999 GCACAAATCA
Statistics
Matches: 106, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
139 11 0.10
140 95 0.90
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29
Consensus pattern (139 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTGGATGCCGATGCCATGTCCCAAACATG
GTCTTACACTGGCTCTCATAATATGGCCAAAGCATGTCCCAAACATGTTTACACTGGCTCTCATA
ATATGGCTA
Found at i:12245011 original size:41 final size:41
Alignment explanation
Indices: 12244892--12245011 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 41
12244882 GTAAACTGCA
* * *
12244892 TCACACGACCATGTAGCT-GGCCATGTGGCAAACCATGTTGG
1 TCACACGATCATGT-GCTAGGCCATGTGGCAGACCGTGTTGG
* * *
12244933 TCACACAATCGTGTGGTAGGCCATGTGGCAGACCGTGTTGG
1 TCACACGATCATGTGCTAGGCCATGTGGCAGACCGTGTTGG
* *
12244974 TCACACGATCATGTGCTAGGCCATGTGGTAGATCGTGT
1 TCACACGATCATGTGCTAGGCCATGTGGCAGACCGTGT
12245012 AAGTTACACG
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
40 2 0.03
41 65 0.97
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.25
Consensus pattern (41 bp):
TCACACGATCATGTGCTAGGCCATGTGGCAGACCGTGTTGG
Found at i:12245039 original size:29 final size:29
Alignment explanation
Indices: 12244994--12245061 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
12244984 ATGTGCTAGG
* * *
12244994 CCATGTGGTAGATCGTGTAAGTTACACGA
1 CCATGTGGTAGACCGTGTAAGTCACACAA
* *
12245023 CCGTGTGGTAGACCGTGTAGGTCACACAA
1 CCATGTGGTAGACCGTGTAAGTCACACAA
12245052 CCATGTGGTA
1 CCATGTGGTA
12245062 AGCTGTGTCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (29 bp):
CCATGTGGTAGACCGTGTAAGTCACACAA
Found at i:12245069 original size:29 final size:28
Alignment explanation
Indices: 12244994--12245069 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
12244984 ATGTGCTAGG
* * *
12244994 CCATGTGGTAGATCGTGTAAGTTACACGA
1 CCATGTGGTAGCT-GTGTAAGTCACACAA
* * *
12245023 CCGTGTGGTAGACCGTGTAGGTCACACAA
1 CCATGTGGTAG-CTGTGTAAGTCACACAA
12245052 CCATGTGGTAAGCTGTGT
1 CCATGTGGT-AGCTGTGT
12245070 CGTAAACTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (28 bp):
CCATGTGGTAGCTGTGTAAGTCACACAA
Found at i:12251810 original size:27 final size:27
Alignment explanation
Indices: 12251772--12251876 Score: 126
Period size: 27 Copynumber: 3.9 Consensus size: 27
12251762 GCGAGGCTGC
*
12251772 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGACAG-AGCCACCAGATA
12251799 CAGATATTGTGACAGAGCCACCAGA-A
1 CAGATATTGTGACAGAGCCACCAGATA
*
12251825 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGACAGAGCCACCAGATA
* *
12251852 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGACAGAGCCACCAG
12251877 GACGCTTCCT
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 8 0.11
27 60 0.85
28 3 0.04
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGACAGAGCCACCAGATA
Found at i:12253501 original size:26 final size:26
Alignment explanation
Indices: 12253471--12253552 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
12253461 TGAAATGCCC
*
12253471 ATCATGGAACATTTAACTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12253497 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
12253523 ATCATGGAATATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
12253549 ATCA
1 ATCA
12253553 ATTTTTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12269479 original size:27 final size:27
Alignment explanation
Indices: 12269449--12269588 Score: 162
Period size: 27 Copynumber: 5.2 Consensus size: 27
12269439 GTGATGAAGT
12269449 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATATTGTGGCAGAGC
*
12269476 CACCAGA-ACAGATATATGTGGTAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
* *
12269503 CACCAGAT-CAGATAATCGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
* *
12269530 CACCA-AAACAGATATATGTGGAAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
*
12269557 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
12269584 CACCA
1 CACCA
12269589 AGACGCTTCC
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
26 11 0.12
27 79 0.83
28 5 0.05
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (27 bp):
CACCAGATACAGATATTGTGGCAGAGC
Found at i:12269509 original size:54 final size:54
Alignment explanation
Indices: 12269449--12269589 Score: 230
Period size: 54 Copynumber: 2.6 Consensus size: 54
12269439 GTGATGAAGT
* * *
12269449 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGTAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAAAACAGATATATGTGGAAGAGC
*
12269503 CACCAGATCAGATAATCGTGGCATAGCCACCAAAACAGATATATGTGGAAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAAAACAGATATATGTGGAAGAGC
12269557 CACCAGATCAGATAATTGTGGCATAGCCACCAA
1 CACCAGATCAGATAATTGTGGCATAGCCACCAA
12269590 GACGCTTCCT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 5 0.06
54 76 0.94
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAAAACAGATATATGTGGAAGAGC
Found at i:12271217 original size:26 final size:26
Alignment explanation
Indices: 12271187--12271306 Score: 222
Period size: 26 Copynumber: 4.6 Consensus size: 26
12271177 TGAAATGCCC
12271187 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12271213 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12271239 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
12271265 ATCATGGATCATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
12271291 ATCATGGAATATTTAC
1 ATCATGGAACATTTAC
12271307 ATATTGTCTA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 91 1.00
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12271436 original size:10 final size:10
Alignment explanation
Indices: 12271421--12271448 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
12271411 TAGCCTATAG
12271421 CATTTTCAAA
1 CATTTTCAAA
12271431 CATTTTCAAA
1 CATTTTCAAA
12271441 CATTTTCA
1 CATTTTCA
12271449 CATAGGTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (10 bp):
CATTTTCAAA
Found at i:12285012 original size:18 final size:18
Alignment explanation
Indices: 12284979--12285036 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
12284969 AGTAATAGTA
* *
12284979 GCAGTGACAGTAATCAGT
1 GCAGTAACAATAATCAGT
* * *
12284997 GCAGTAACCATGATCAAT
1 GCAGTAACAATAATCAGT
*
12285015 GCAGTAATAATAATCAGT
1 GCAGTAACAATAATCAGT
12285033 GCAG
1 GCAG
12285037 AATGCAAATA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (18 bp):
GCAGTAACAATAATCAGT
Found at i:12285469 original size:27 final size:27
Alignment explanation
Indices: 12285430--12285592 Score: 193
Period size: 27 Copynumber: 5.9 Consensus size: 27
12285420 TAGAGCAAAT
* *
12285430 CAGTCATTTTACCTTATAGGGGTATTA
1 CAGTCATTTTACCCTACAGGGGTATTA
* *
12285457 TAGTCATTTTACCCTACAGGAGTATTA
1 CAGTCATTTTACCCTACAGGGGTATTA
*
12285484 GAGTCATTTTACCCTACATACAGGGGTATTA
1 CAGTCATTTTA-CC--C-TACAGGGGTATTA
12285515 CAGTCATTTTACCCTACAGGGGTATTA
1 CAGTCATTTTACCCTACAGGGGTATTA
*
12285542 CAGTCATTTTACCCTA-TGAGGGTATTA
1 CAGTCATTTTACCCTACAG-GGGTATTA
* * *
12285569 TAGTCATTTTGCCCTATAGGGGTA
1 CAGTCATTTTACCCTACAGGGGTA
12285593 AAATCATCAT
Statistics
Matches: 119, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.01
27 89 0.75
28 4 0.03
30 3 0.03
31 22 0.18
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (27 bp):
CAGTCATTTTACCCTACAGGGGTATTA
Found at i:12285520 original size:58 final size:58
Alignment explanation
Indices: 12285447--12285557 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
12285437 TTTACCTTAT
* *
12285447 AGGGGTATTATAGTCATTTTACCCTACAGGAGTATTAGAGTCATTTTACCCTACATAC
1 AGGGGTATTACAGTCATTTTACCCTACAGGAGTATTACAGTCATTTTACCCTACATAC
*
12285505 AGGGGTATTACAGTCATTTTACCCTACAGGGGTATTACAGTCATTTTACCCTA
1 AGGGGTATTACAGTCATTTTACCCTACAGGAGTATTACAGTCATTTTACCCTA
12285558 TGAGGGTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (58 bp):
AGGGGTATTACAGTCATTTTACCCTACAGGAGTATTACAGTCATTTTACCCTACATAC
Found at i:12285625 original size:27 final size:27
Alignment explanation
Indices: 12285595--12285671 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
12285585 TAGGGGTAAA
12285595 ATCATCATTTTATCACATAAGGGCAAT
1 ATCATCATTTTATCACATAAGGGCAAT
**
12285622 ATCATCATTTTATCATTTAAGGGCAAT
1 ATCATCATTTTATCACATAAGGGCAAT
*
12285649 ATCGTCATTTTATCACATAAGGG
1 ATCATCATTTTATCACATAAGGG
12285672 TTCAGGTGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (27 bp):
ATCATCATTTTATCACATAAGGGCAAT
Found at i:12294840 original size:47 final size:47
Alignment explanation
Indices: 12294781--12294902 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
12294771 GCATTGGCAC
*
12294781 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTAG
12294828 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTAG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTAG
* *
12294875 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
12294903 CCAAGGCATG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTAG
Found at i:12294945 original size:54 final size:54
Alignment explanation
Indices: 12294881--12295149 Score: 290
Period size: 54 Copynumber: 4.8 Consensus size: 54
12294871 TTAGTAAGAT
*
12294881 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* *
12294935 AAGGAAATCATGTAAGGCCATGCCAAGGCATGGCACTGATAAGTTCTATAAGGC
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* *
12294989 AAGGAAATCATGGTCCCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGG-AA--A---T--CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTT-CTATAAGGC
** * *
12295052 AAAGG-ACCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* * * * * * *
12295105 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTT
12295150 TAAAAAGGAA
Statistics
Matches: 186, Mismatches: 18, Indels: 23
0.82 0.08 0.10
Matches are distributed among these distances:
52 4 0.02
53 40 0.22
54 56 0.30
55 37 0.20
57 1 0.01
60 1 0.01
62 34 0.18
63 9 0.05
64 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
Found at i:12295108 original size:116 final size:116
Alignment explanation
Indices: 12294889--12295109 Score: 338
Period size: 116 Copynumber: 1.9 Consensus size: 116
12294879 ATAAGGATAT
* * *
12294889 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGGCC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAAACCATGTAAGACC
12294954 ATGCCAAGGCATGGCACTGATAAGTTCTATAAGGCAAGGAAATCATGGTCC
66 ATGCCAAGGCATGGCACTGATAAGTTCTATAAGGCAAGGAAATCATGGTCC
* *
12295005 CATGTAAGACCATGCCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGG-ACCCATGTAAGA
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGGC-AAGGAAACCATGTAAGA
* * *
12295069 CCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGA
64 CCATGCCAAGGCATGGCACTGATAAGTTCTATAAGGCAAGGA
12295110 TACCACGTAA
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
116 47 0.49
117 44 0.46
118 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (116 bp):
CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAAACCATGTAAGACC
ATGCCAAGGCATGGCACTGATAAGTTCTATAAGGCAAGGAAATCATGGTCC
Found at i:12307339 original size:43 final size:42
Alignment explanation
Indices: 12307199--12307354 Score: 131
Period size: 42 Copynumber: 3.7 Consensus size: 42
12307189 TTTCATTATG
* * *
12307199 TGATT-CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ACTT
1 TGATTACGTGTAAGACCATGTCTGGGACATCGGCATCGTA-TT
* *
12307240 CT-ATTTTACGTGTACGACCATGTCTGGGACATCGGTATCGTATT
1 -TGA--TTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATT
* * *
12307284 TGATTTCGTGTAAGACCCTGTCTGGGACAGT-GGCATCGATGTT
1 TGATTACGTGTAAGACCATGTCTGGGACA-TCGGCATCG-TATT
* * *
12307327 TGATTACATGTAAGACCACGTTTGGGAC
1 TGATTACGTGTAAGACCATGTCTGGGAC
12307355 GTTGGCATTG
Statistics
Matches: 92, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 30 0.33
43 30 0.33
44 30 0.33
45 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (42 bp):
TGATTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATT
Found at i:12307361 original size:43 final size:42
Alignment explanation
Indices: 12307199--12307362 Score: 149
Period size: 43 Copynumber: 3.9 Consensus size: 42
12307189 TTTCATTATG
12307199 TGATT-CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTCT
1 TGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TT-T
* * * * * *
12307242 AT-TTTACGTGTACGACCATGTCTGGGACATCGGTATCG-TATT
1 -TGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TT
*
12307284 TGATTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATGTT
1 TGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT-TT
* *
12307327 TGATTACATGTAAGACCACGTTTGGGACGTTGGCAT
1 TGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
12307363 TGTATATGTT
Statistics
Matches: 95, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
41 1 0.01
42 30 0.32
43 35 0.37
44 29 0.31
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (42 bp):
TGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCGATTT
Found at i:12317915 original size:18 final size:18
Alignment explanation
Indices: 12317887--12317950 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
12317877 GAACAATTAT
* *
12317887 TTATTTAGTAATAGTCAG
1 TTATTCAGTAATAATCAG
* * *
12317905 TTATTCGGTAACAATCAA
1 TTATTCAGTAATAATCAG
*
12317923 TTATTCAATAATAATCAG
1 TTATTCAGTAATAATCAG
12317941 TTATTCAGTA
1 TTATTCAGTA
12317951 TCAATCAATT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (18 bp):
TTATTCAGTAATAATCAG
Found at i:12317918 original size:36 final size:36
Alignment explanation
Indices: 12317853--12317960 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
12317843 CAATCAGTAA
* * * * * *
12317853 TATTCATTAACAATCAGTCAATCAG-AACAATTATT
1 TATTCAATAATAATCAGTTATTCAGTAACAATCAAT
* * * *
12317888 TATTTAGTAATAGTCAGTTATTCGGTAACAATCAAT
1 TATTCAATAATAATCAGTTATTCAGTAACAATCAAT
*
12317924 TATTCAATAATAATCAGTTATTCAGTATCAATCAAT
1 TATTCAATAATAATCAGTTATTCAGTAACAATCAAT
12317960 T
1 T
12317961 GATTGGTTAT
Statistics
Matches: 58, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
35 18 0.31
36 40 0.69
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (36 bp):
TATTCAATAATAATCAGTTATTCAGTAACAATCAAT
Found at i:12318033 original size:19 final size:19
Alignment explanation
Indices: 12317905--12318034 Score: 63
Period size: 18 Copynumber: 6.7 Consensus size: 19
12317895 TAATAGTCAG
*
12317905 TTATTCGGTAACAATC-AA
1 TTATTCAGTAACAATCAAA
* * *
12317923 TTATTCAATAATAATC-AG
1 TTATTCAGTAACAATCAAA
*
12317941 TTATTCAGTATCAATCAATTGA
1 TTATTCAGTAACAATCAA---A
* *
12317963 TTGGTTATCCAGTAACAGTC-AA
1 ----TTATTCAGTAACAATCAAA
* *
12317985 TTATTCAGTAAAAATCAGA
1 TTATTCAGTAACAATCAAA
*
12318004 -TATAT-AGTAACAATTAAA
1 TTAT-TCAGTAACAATCAAA
12318022 TTATTCAGTAACA
1 TTATTCAGTAACA
12318035 GTCGATCTTT
Statistics
Matches: 82, Mismatches: 18, Indels: 23
0.67 0.15 0.19
Matches are distributed among these distances:
18 54 0.66
19 13 0.16
22 1 0.01
25 1 0.01
26 13 0.16
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (19 bp):
TTATTCAGTAACAATCAAA
Found at i:12318223 original size:47 final size:47
Alignment explanation
Indices: 12318165--12318268 Score: 156
Period size: 47 Copynumber: 2.2 Consensus size: 47
12318155 TAACAATAAT
*
12318165 AGTAGCAGTACGGTACACAGAGTACCTCATCGGAACAAATCC-AGAAC
1 AGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA-AAC
* * *
12318212 AGTAACAGTACGGTACATAGAGTACCTCATTGGAACAAATTCGAAAC
1 AGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAAAC
12318259 AGTAACAGTA
1 AGTAACAGTA
12318269 ACGGCAACAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 51 0.98
48 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.18
Consensus pattern (47 bp):
AGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAAAC
Found at i:12318470 original size:16 final size:16
Alignment explanation
Indices: 12318441--12318474 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12318431 TAATTCACTT
12318441 TTCAATTTTCAATTAA
1 TTCAATTTTCAATTAA
12318457 TTCATATTTT-AATTAA
1 TTCA-ATTTTCAATTAA
12318473 TT
1 TT
12318475 AACTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (16 bp):
TTCAATTTTCAATTAA
Found at i:12323106 original size:37 final size:37
Alignment explanation
Indices: 12323063--12323139 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
12323053 AATAGTCTTC
12323063 AAGATGCTTTGTCAGTTCGATTTGAAATGAAAATTTT
1 AAGATGCTTTGTCAGTTCGATTTGAAATGAAAATTTT
*
12323100 AAGATGCTTTGTCAGTTTGATTTGAAATGAAAATTTT
1 AAGATGCTTTGTCAGTTCGATTTGAAATGAAAATTTT
12323137 AAG
1 AAG
12323140 TTAAGCTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (37 bp):
AAGATGCTTTGTCAGTTCGATTTGAAATGAAAATTTT
Found at i:12325923 original size:21 final size:21
Alignment explanation
Indices: 12325885--12325924 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12325875 TATATTTTAA
* **
12325885 AATTTTAAAATTTTTAATTTT
1 AATTTAAAAATTAATAATTTT
12325906 AATTTAAAAATTAATAATT
1 AATTTAAAAATTAATAATT
12325925 ACTGTTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTAAAAATTAATAATTTT
Found at i:12330746 original size:49 final size:52
Alignment explanation
Indices: 12330688--12330831 Score: 132
Period size: 58 Copynumber: 2.6 Consensus size: 52
12330678 CAATAATCCT
* *
12330688 ATAATAATAAAAAATATGTTGA-AT-AATAATAATACTTATA-TCTTTAATA
1 ATAATAATAAAAAATATGTTAACATAAATAATAATACTTATACTATTTAATA
*
12330737 ATAATAATAATAATAATATTTAATAATCATACAATAATAATACTTATACTATTTAATA
1 ATAATAATAA-AA-AATATGT--TAA-CATA-AATAATAATACTTATACTATTTAATA
12330795 ATAATACAATAAAAAAATATGTTTAACAATTAAATAA
1 ATAAT--AAT-AAAAAATATG-TTAAC-A-TAAATAA
12330832 GATAAAAAAG
Statistics
Matches: 76, Mismatches: 4, Indels: 21
0.75 0.04 0.21
Matches are distributed among these distances:
49 10 0.13
50 2 0.03
51 6 0.08
53 2 0.03
55 2 0.03
57 17 0.22
58 22 0.29
59 7 0.09
60 6 0.08
61 2 0.03
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (52 bp):
ATAATAATAAAAAATATGTTAACATAAATAATAATACTTATACTATTTAATA
Found at i:12330773 original size:33 final size:33
Alignment explanation
Indices: 12330736--12330806 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
12330726 TATCTTTAAT
*
12330736 AATAATAATAATAATAATATTTAATAATCATAC
1 AATAATAATAATAATAATATTTAATAATAATAC
* * *
12330769 AATAATAATACTTATACTATTTAATAATAATAC
1 AATAATAATAATAATAATATTTAATAATAATAC
12330802 AATAA
1 AATAA
12330807 AAAAATATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (33 bp):
AATAATAATAATAATAATATTTAATAATAATAC
Found at i:12330798 original size:3 final size:3
Alignment explanation
Indices: 12330732--12330778 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
12330722 CTTATATCTT
* * *
12330732 TAA TAA TAA TAA TAA TAA TAA TATT TAA TAA TCA T-A CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
12330777 TA
1 TA
12330779 CTTATACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.92
4 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12341063 original size:9 final size:9
Alignment explanation
Indices: 12341049--12341082 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
12341039 TCAGAGCTCA
12341049 GGCGGCGAC
1 GGCGGCGAC
12341058 GGCGGCGAC
1 GGCGGCGAC
12341067 GGCGGCGAC
1 GGCGGCGAC
12341076 GGCGGCG
1 GGCGGCG
12341083 GCAGGTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.09, C:0.32, G:0.59, T:0.00
Consensus pattern (9 bp):
GGCGGCGAC
Found at i:12343049 original size:23 final size:23
Alignment explanation
Indices: 12343019--12343068 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
12343009 CAAAACTACA
12343019 TTGTGCAAGTAGTCATAAAGTGC
1 TTGTGCAAGTAGTCATAAAGTGC
12343042 TTGTGCAAGTAGTCATAAAGTGC
1 TTGTGCAAGTAGTCATAAAGTGC
12343065 TTGT
1 TTGT
12343069 AAGCTAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (23 bp):
TTGTGCAAGTAGTCATAAAGTGC
Found at i:12348952 original size:17 final size:19
Alignment explanation
Indices: 12348915--12348952 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
12348905 TACTTTTCTC
12348915 AAGGTATCGATATATTTCCT
1 AAGGTATCGA-ATATTTCCT
12348935 AAGGTATCG-ATA-TTCCT
1 AAGGTATCGAATATTTCCT
12348952 A
1 A
12348953 CACCAACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
20 9 0.50
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
AAGGTATCGAATATTTCCT
Found at i:12352636 original size:20 final size:20
Alignment explanation
Indices: 12352607--12352646 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12352597 ATTGTACAGG
*
12352607 ATTTGTACTTCGATGCCTCT
1 ATTTGCACTTCGATGCCTCT
* *
12352627 ATTTGCACTTTGGTGCCTCT
1 ATTTGCACTTCGATGCCTCT
12352647 GTATACACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.45
Consensus pattern (20 bp):
ATTTGCACTTCGATGCCTCT
Found at i:12355560 original size:21 final size:21
Alignment explanation
Indices: 12355536--12355581 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
12355526 CAGAAGCTCG
* *
12355536 TAAGAGCTGAATGAAAACCCA
1 TAAGAGCTGAACGAAAACCAA
* *
12355557 TAAGAGTTGAACGGAAACCAA
1 TAAGAGCTGAACGAAAACCAA
12355578 TAAG
1 TAAG
12355582 GTTAAACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (21 bp):
TAAGAGCTGAACGAAAACCAA
Found at i:12363905 original size:26 final size:26
Alignment explanation
Indices: 12363875--12363924 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
12363865 GCAATTTAAC
12363875 CATTTTTATTCAATTTCAAGTTTAGT
1 CATTTTTATTCAATTTCAAGTTTAGT
12363901 CATTTTTATTCAATTTCAAGTTTA
1 CATTTTTATTCAATTTCAAGTTTA
12363925 ACCGAATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (26 bp):
CATTTTTATTCAATTTCAAGTTTAGT
Found at i:12365148 original size:24 final size:24
Alignment explanation
Indices: 12365094--12365150 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 24
12365084 AATGTACGTG
12365094 AAAATATTAATTTATTAATATTTAA
1 AAAATA-TAATTTATTAATATTTAA
12365119 ATAAATATAATTTATT-ATATTTATA
1 A-AAATATAATTTATTAATATTTA-A
12365144 AAAATAT
1 AAAATAT
12365151 TGGTATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 13 0.43
25 12 0.40
26 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAATATAATTTATTAATATTTAA
Found at i:12365847 original size:17 final size:18
Alignment explanation
Indices: 12365810--12365848 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12365800 TTTAAAAAAA
* *
12365810 ATTAAAAAAATTACATAT
1 ATTAAAAAAATCAAATAT
12365828 ATTAAAAAAATCAAAT-T
1 ATTAAAAAAATCAAATAT
12365845 ATTA
1 ATTA
12365849 CTCAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTAAAAAAATCAAATAT
Found at i:12366866 original size:15 final size:15
Alignment explanation
Indices: 12366823--12366868 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
12366813 TCGGGTTACA
12366823 TTTTAGTCACTTATG
1 TTTTAGTCACTTATG
**
12366838 -TTT-GAAATCTTATG
1 TTTTAGTCA-CTTATG
12366852 TTTTAGTCACTTATG
1 TTTTAGTCACTTATG
12366867 TT
1 TT
12366869 ATTGTGTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (15 bp):
TTTTAGTCACTTATG
Found at i:12367273 original size:18 final size:19
Alignment explanation
Indices: 12367236--12367275 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
12367226 TAGTTTTTTC
12367236 TTTTTCTTTAAAGAAGGTT
1 TTTTTCTTTAAAGAAGGTT
*
12367255 TTTTTTTTTAAAGAA-GTT
1 TTTTTCTTTAAAGAAGGTT
12367273 TTT
1 TTT
12367276 AAAGAAGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.60
Consensus pattern (19 bp):
TTTTTCTTTAAAGAAGGTT
Found at i:12367276 original size:12 final size:12
Alignment explanation
Indices: 12367259--12367284 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12367249 AAGGTTTTTT
12367259 TTTTTAAAGAAG
1 TTTTTAAAGAAG
12367271 TTTTTAAAGAAG
1 TTTTTAAAGAAG
12367283 TT
1 TT
12367285 CAACTTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTTTAAAGAAG
Found at i:12369991 original size:65 final size:65
Alignment explanation
Indices: 12369916--12370058 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 65
12369906 TGAATGTAAT
* ** * * *
12369916 TGAAATATATTTGCATGTTTATATAATTTATTAAGAAATTAAAAATTAGACAATAAATATATATG
1 TGAAAAATATTTAAATGTGTATATAATTTATCAAGAAACTAAAAATTAGACAATAAATATATATG
**
12369981 TGAAAAATATTTAAATGTGTATATAATTTATCAAGAAACTAAAAATTAGATTATAAATATATA--
1 TGAAAAATATTTAAATGTGTATATAATTTATCAAGAAACTAAAAATTAGACAATAAATATATATG
*
12370044 TGAGAAATATTTAAA
1 TGAAAAATATTTAAA
12370059 AACATTGATA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 14 0.20
65 55 0.80
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (65 bp):
TGAAAAATATTTAAATGTGTATATAATTTATCAAGAAACTAAAAATTAGACAATAAATATATATG
Found at i:12372072 original size:20 final size:20
Alignment explanation
Indices: 12372014--12372079 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 20
12372004 ATTACAATTT
12372014 TATTTTAATAATAGATTTTAA
1 TATTTTAATAATA-ATTTTAA
*
12372035 CA--TTAATAATAATTTTAA
1 TATTTTAATAATAATTTTAA
12372053 -ATTTTAAGTAAT-ATTCTTAA
1 TATTTTAA-TAATAATT-TTAA
12372073 TATTTTA
1 TATTTTA
12372080 TTGAAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 1 0.03
18 7 0.18
19 16 0.41
20 8 0.21
21 7 0.18
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (20 bp):
TATTTTAATAATAATTTTAA
Found at i:12372125 original size:19 final size:20
Alignment explanation
Indices: 12372097--12372135 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12372087 AATTATATTA
*
12372097 ATATTTCAA-TAATAAATAT
1 ATATTACAATTAATAAATAT
*
12372116 ATATTACAATTTATAAATAT
1 ATATTACAATTAATAAATAT
12372136 TTAGTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTACAATTAATAAATAT
Found at i:12377867 original size:6 final size:6
Alignment explanation
Indices: 12377848--12377885 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
12377838 GATTGGTAGG
*
12377848 AGTTAC AGTGAC AGTTAC AGTTAC AGTTAC AGTTAC AG
1 AGTTAC AGTTAC AGTTAC AGTTAC AGTTAC AGTTAC AG
12377886 CATTCTATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (6 bp):
AGTTAC
Found at i:12377971 original size:25 final size:25
Alignment explanation
Indices: 12377943--12377994 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
12377933 AAATAATAAT
*
12377943 ATTCTCAATTAGATGATATAAATGA
1 ATTCTCAATAAGATGATATAAATGA
* *
12377968 A-T-TCAGTAAGGTGATATAAATGA
1 ATTCTCAATAAGATGATATAAATGA
12377991 ATTC
1 ATTC
12377995 CTAGGAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
23 19 0.86
24 2 0.09
25 1 0.05
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (25 bp):
ATTCTCAATAAGATGATATAAATGA
Found at i:12379573 original size:39 final size:39
Alignment explanation
Indices: 12379398--12379576 Score: 173
Period size: 39 Copynumber: 4.6 Consensus size: 39
12379388 TTTTGCTATT
* * * *
12379398 TCAGGGCCAAAGAGGAAAAT-AGAAGTTTCCTATGATTTT
1 TCAGGGCCAAAGA-GAAAATCAGAAGATTCCTGTAATTTC
* * * * * *
12379437 TCAGGGGCAAAGCGAAAACCAGAAGATTCTTGTGATGTC
1 TCAGGGCCAAAGAGAAAATCAGAAGATTCCTGTAATTTC
* * * *
12379476 TCAGGGGCAAAGAGAAAAT-ATGGAGATTCCTCTAATTCC
1 TCAGGGCCAAAGAGAAAATCA-GAAGATTCCTGTAATTTC
* * *
12379515 TCAGGACCAAAGAGAAAATCTGAAGATTCCTGTAATTTA
1 TCAGGGCCAAAGAGAAAATCAGAAGATTCCTGTAATTTC
12379554 TCAGGGCCAAAGAGAAAATCAGA
1 TCAGGGCCAAAGAGAAAATCAGA
12379577 GGACTCTTCC
Statistics
Matches: 112, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
38 6 0.05
39 106 0.95
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (39 bp):
TCAGGGCCAAAGAGAAAATCAGAAGATTCCTGTAATTTC
Found at i:12382575 original size:68 final size:68
Alignment explanation
Indices: 12382458--12382596 Score: 260
Period size: 68 Copynumber: 2.0 Consensus size: 68
12382448 CAATTGAATG
12382458 TCACATTCTAATTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAACATATTGGTTAATATAAT
1 TCACATTCTAATTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAACATATTGGTTAATATAAT
12382523 TAT
66 TAT
* *
12382526 TCACGTTCTAATTATTTTCGTCTAAGTACACTTGTAATTTTTTCGAACATATTGGTTAATATAAT
1 TCACATTCTAATTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAACATATTGGTTAATATAAT
12382591 TAT
66 TAT
12382594 TCA
1 TCA
12382597 TGAATTATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.47
Consensus pattern (68 bp):
TCACATTCTAATTATTTTCGTCTAAGTACACTTGTAATTTTTTCAAACATATTGGTTAATATAAT
TAT
Found at i:12383640 original size:6 final size:6
Alignment explanation
Indices: 12383624--12383688 Score: 69
Period size: 6 Copynumber: 10.7 Consensus size: 6
12383614 GGTTTTCTCA
* * *
12383624 AAATGG GAATGG AAATGG AAATGG AAATGG AAATGA AAATGA AAAT-G
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
*
12383671 AACATGA AAATGAG AAAT
1 AA-ATGG AAATG-G AAAT
12383689 AATTCAGTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
5 2 0.04
6 42 0.84
7 6 0.12
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:12383647 original size:18 final size:18
Alignment explanation
Indices: 12383623--12383688 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
12383613 TGGTTTTCTC
*
12383623 AAAATGGGAATGGAAATG
1 AAAATGGAAATGGAAATG
*
12383641 GAAATGGAAATGGAAATG
1 AAAATGGAAATGGAAATG
*
12383659 AAAATGAAAAT-GAACATG
1 AAAATGGAAATGGAA-ATG
12383677 AAAATGAGAAAT
1 AAAATG-GAAAT
12383689 AATTCAGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
17 3 0.07
18 34 0.83
19 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.17
Consensus pattern (18 bp):
AAAATGGAAATGGAAATG
Found at i:12384706 original size:41 final size:41
Alignment explanation
Indices: 12384661--12384752 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
12384651 TTACCGAATC
* *
12384661 AATGAAAAGGTTGAAAACGATGTTATCCAAAAATGATATA-A
1 AATGAAAAGGTTGAAAACGATGCTATCCAAAAAGGATA-ACA
** *
12384702 AATGAAAATATTGAAAAGGATGCTATCCAAAAAGGATAACA
1 AATGAAAAGGTTGAAAACGATGCTATCCAAAAAGGATAACA
12384743 AATGAAAAGG
1 AATGAAAAGG
12384753 ATGTTGTAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.02
41 42 0.98
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.21
Consensus pattern (41 bp):
AATGAAAAGGTTGAAAACGATGCTATCCAAAAAGGATAACA
Found at i:12407894 original size:17 final size:18
Alignment explanation
Indices: 12407872--12407905 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12407862 CTGATTTGGG
*
12407872 TCGTGTG-GGCCACACGA
1 TCGTGTGAGCCCACACGA
12407889 TCGTGTGAGCCCACACG
1 TCGTGTGAGCCCACACG
12407906 GGTGAACAGC
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:0.18, C:0.32, G:0.32, T:0.18
Consensus pattern (18 bp):
TCGTGTGAGCCCACACGA
Found at i:12408003 original size:17 final size:18
Alignment explanation
Indices: 12407977--12408010 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12407967 CATATAGGGT
12407977 CGTGTAGG-CCACACGGG
1 CGTGTAGGCCCACACGGG
*
12407994 CGTGTGGGCCCACACGG
1 CGTGTAGGCCCACACGG
12408011 ACAAACAATG
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:0.15, C:0.32, G:0.41, T:0.12
Consensus pattern (18 bp):
CGTGTAGGCCCACACGGG
Found at i:12409313 original size:19 final size:19
Alignment explanation
Indices: 12409289--12409328 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
12409279 ATGCTATAGA
*
12409289 TAGTAAATACTGAGACTAT
1 TAGTAAACACTGAGACTAT
12409308 TAGTAAACACTGAGACTAT
1 TAGTAAACACTGAGACTAT
12409327 TA
1 TA
12409329 TAGATAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (19 bp):
TAGTAAACACTGAGACTAT
Found at i:12415589 original size:17 final size:18
Alignment explanation
Indices: 12415567--12415601 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12415557 TATAGGGTCA
12415567 TGTGGG-CCACACAGGCG
1 TGTGGGCCCACACAGGCG
*
12415584 TGTGGGCCCACACGGGCG
1 TGTGGGCCCACACAGGCG
12415602 AACAACATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.31, G:0.43, T:0.11
Consensus pattern (18 bp):
TGTGGGCCCACACAGGCG
Found at i:12420928 original size:39 final size:39
Alignment explanation
Indices: 12420885--12420980 Score: 99
Period size: 39 Copynumber: 2.5 Consensus size: 39
12420875 CCCCACATTT
*
12420885 TTTTTGGTATTTCCTCGT-AATTTTAGTATTTCTTCATAA
1 TTTTTGGTATTTCCTCATCAATTTTAGTATTTCTT-ATAA
* * *
12420924 TTTTT--TAATATTCCTCATCATTTTTGGTATTTCTTATAT
1 TTTTTGGT-AT-TTCCTCATCAATTTTAGTATTTCTTATAA
*
12420963 TTTTTGGTATTCCCTCAT
1 TTTTTGGTATTTCCTCAT
12420981 ATTAGTATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
37 1 0.02
38 2 0.04
39 27 0.57
40 16 0.34
41 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (39 bp):
TTTTTGGTATTTCCTCATCAATTTTAGTATTTCTTATAA
Found at i:12420928 original size:40 final size:39
Alignment explanation
Indices: 12420884--12420980 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
12420874 TCCCCACATT
*
12420884 TTTTTTGGTATTTCCTCGT-AATTTTAGTATTTCTTCATAA
1 TTTTTTGGTATTTCCTCATCAATTTTAGTATTTCTT-AT-A
** * *
12420924 TTTTTTAATA-TTCCTCATCATTTTTGGTATTTCTTATA
1 TTTTTTGGTATTTCCTCATCAATTTTAGTATTTCTTATA
*
12420962 TTTTTTGGTATTCCCTCAT
1 TTTTTTGGTATTTCCTCAT
12420981 ATTAGTATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
38 9 0.19
39 16 0.34
40 22 0.47
ACGTcount: A:0.19, C:0.14, G:0.08, T:0.59
Consensus pattern (39 bp):
TTTTTTGGTATTTCCTCATCAATTTTAGTATTTCTTATA
Found at i:12420954 original size:19 final size:19
Alignment explanation
Indices: 12420884--12420983 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
12420874 TCCCCACATT
*
12420884 TTTTTTGGTATTTCCTCGTA
1 TTTTTTGGTA-TTCCTCATA
* * *
12420904 -ATTTTAGTATTTCTTCATAA
1 TTTTTTGGTA-TTCCTCAT-A
**
12420924 TTTTTTAATATTCCTCATCA
1 TTTTTTGGTATTCCTCAT-A
* *
12420944 -TTTTTGGTATTTCTTATA
1 TTTTTTGGTATTCCTCATA
12420962 TTTTTTGGTATTCCCTCATA
1 TTTTTTGGTATT-CCTCATA
12420982 TT
1 TT
12420984 AGTATTTTGA
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
18 1 0.02
19 38 0.61
20 16 0.26
21 7 0.11
ACGTcount: A:0.19, C:0.14, G:0.08, T:0.59
Consensus pattern (19 bp):
TTTTTTGGTATTCCTCATA
Found at i:12436584 original size:21 final size:21
Alignment explanation
Indices: 12436554--12436642 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
12436544 CTCACAAAGA
* *
12436554 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
12436574 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
12436595 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
12436616 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
12436640 AAA
1 AAA
12436643 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:12436635 original size:24 final size:21
Alignment explanation
Indices: 12436554--12436622 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
12436544 CTCACAAAGA
* * *
12436554 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
12436574 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
12436595 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
12436616 AAAAAGA
1 AAAAAGA
12436623 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:12443530 original size:19 final size:19
Alignment explanation
Indices: 12443506--12443545 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12443496 TTGTTTTTTT
* *
12443506 ATTAGAATCGAAAAGTTTA
1 ATTAGAATAGAAAAGTGTA
12443525 ATTAGAATAGAAAAGTGTA
1 ATTAGAATAGAAAAGTGTA
12443544 AT
1 AT
12443546 AAAAGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (19 bp):
ATTAGAATAGAAAAGTGTA
Found at i:12445254 original size:20 final size:19
Alignment explanation
Indices: 12445200--12445257 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
12445190 ATAAAAAACA
* *
12445200 AAATAGAGTAGAAAAAAAT
1 AAATAAAGTAGAACAAAAT
* *
12445219 AAATCATA-TAGTACAAAAT
1 AAAT-AAAGTAGAACAAAAT
12445238 CAAATAAAGTAGAACAAAAT
1 -AAATAAAGTAGAACAAAAT
12445258 TGAATGGTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.19
Consensus pattern (19 bp):
AAATAAAGTAGAACAAAAT
Found at i:12445304 original size:15 final size:15
Alignment explanation
Indices: 12445284--12445318 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12445274 GAGCAAAATT
*
12445284 GAACAAAATAGAACA
1 GAACAAAACAGAACA
12445299 GAACAAAACAGAACA
1 GAACAAAACAGAACA
*
12445314 AAACA
1 GAACA
12445319 GAGTAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.17, G:0.11, T:0.03
Consensus pattern (15 bp):
GAACAAAACAGAACA
Found at i:12445308 original size:10 final size:10
Alignment explanation
Indices: 12445295--12445320 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12445285 AACAAAATAG
12445295 AACAGAACAA
1 AACAGAACAA
12445305 AACAGAACAA
1 AACAGAACAA
12445315 AACAGA
1 AACAGA
12445321 GTAGAATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.19, G:0.12, T:0.00
Consensus pattern (10 bp):
AACAGAACAA
Found at i:12447387 original size:26 final size:26
Alignment explanation
Indices: 12447357--12447433 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 26
12447347 TTGCCACATA
*
12447357 TACTGATATTGGCAGCTCTGCTGCGT
1 TACTGATACTGGCAGCTCTGCTGCGT
* * * *
12447383 TACTGTTACTGGCGGCTTTGCTGCGA
1 TACTGATACTGGCAGCTCTGCTGCGT
* * *
12447409 TA-TTATTACTGGCAGATTTGCTGCG
1 TACTGA-TACTGGCAGCTCTGCTGCG
12447434 ATATTAGTGT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 1 0.02
26 40 0.98
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36
Consensus pattern (26 bp):
TACTGATACTGGCAGCTCTGCTGCGT
Found at i:12447434 original size:26 final size:26
Alignment explanation
Indices: 12447388--12447439 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
12447378 TGCGTTACTG
* *
12447388 TTACTGGCGGCTTTGCTGCGATATTA
1 TTACTGGCAGATTTGCTGCGATATTA
12447414 TTACTGGCAGATTTGCTGCGATATTA
1 TTACTGGCAGATTTGCTGCGATATTA
12447440 GTGTGTTGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (26 bp):
TTACTGGCAGATTTGCTGCGATATTA
Found at i:12455064 original size:26 final size:25
Alignment explanation
Indices: 12455035--12455084 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
12455025 TGTGTTACTG
*
12455035 TTACTGGTAGCTTTGCTGCGATATTA
1 TTACTGGCAGCTTTGCTGCG-TATTA
12455061 TTACTGGCAGCTTTGCTGCGTATT
1 TTACTGGCAGCTTTGCTGCGTATT
12455085 GGCTGGGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (25 bp):
TTACTGGCAGCTTTGCTGCGTATTA
Found at i:12456596 original size:14 final size:14
Alignment explanation
Indices: 12456565--12456611 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
12456555 TTAAAATAAG
12456565 AAACGAAAATGATG-
1 AAAC-AAAATGATGA
**
12456579 AAACTGAATGATGA
1 AAACAAAATGATGA
12456593 AAACAAAATGATAGA
1 AAACAAAATGAT-GA
12456608 AAAC
1 AAAC
12456612 GTTGCAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 7 0.26
14 14 0.52
15 6 0.22
ACGTcount: A:0.60, C:0.09, G:0.17, T:0.15
Consensus pattern (14 bp):
AAACAAAATGATGA
Found at i:12458227 original size:13 final size:13
Alignment explanation
Indices: 12458209--12458234 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12458199 TAAGACAAAG
12458209 GGTTTTAGAAAAT
1 GGTTTTAGAAAAT
12458222 GGTTTTAGAAAAT
1 GGTTTTAGAAAAT
12458235 AAGGTATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
GGTTTTAGAAAAT
Found at i:12462724 original size:22 final size:22
Alignment explanation
Indices: 12462694--12462736 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12462684 ATCCATGTCA
* *
12462694 TATAGCATATTAGAGCATATCT
1 TATAACATATCAGAGCATATCT
12462716 TATAACATATCAGAGCATATC
1 TATAACATATCAGAGCATATC
12462737 CTACCCCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (22 bp):
TATAACATATCAGAGCATATCT
Found at i:12469306 original size:26 final size:26
Alignment explanation
Indices: 12469277--12469357 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 26
12469267 TCCCTTTGAA
* * *
12469277 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
12469303 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
* * *
12469331 CCATTCTCAATATTTCGTACACTAAGT
1 TCA-T-TCAATATCTCGCACACTAAGT
12469358 ACGATATTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 3 0.06
27 1 0.02
28 43 0.91
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:12469322 original size:28 final size:28
Alignment explanation
Indices: 12469291--12469357 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
12469281 TCGATATTTT
*
12469291 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
12469319 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
12469347 GTACACTAAGT
1 GCACACTAAGT
12469358 ACGATATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:12474362 original size:28 final size:28
Alignment explanation
Indices: 12474328--12474482 Score: 157
Period size: 28 Copynumber: 5.5 Consensus size: 28
12474318 AACTGATCTT
* *
12474328 GCACACACAGTGCTTGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
12474356 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
* *
12474385 GCACACACAGTGCTTGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
12474413 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
12474442 GCACACACAGTGCTCGATTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
*
12474470 ACACACACAGTGC
1 GCACACACAGTGC
12474483 CTATGTTCAC
Statistics
Matches: 98, Mismatches: 27, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
28 56 0.57
29 42 0.43
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.17
Consensus pattern (28 bp):
GCACACACAGTGCTCGATTACGGAACTC
Found at i:12474375 original size:57 final size:57
Alignment explanation
Indices: 12474314--12474484 Score: 297
Period size: 57 Copynumber: 3.0 Consensus size: 57
12474304 CTTAGTTCCC
* *
12474314 CAACAACTGATCTTGCACACACAGTGCTTGGTTACGGAACTCGCACACACAGTGCCT
1 CAACAACCGATCTCGCACACACAGTGCTTGGTTACGGAACTCGCACACACAGTGCCT
12474371 CAACAACCGATCTCGCACACACAGTGCTTGGTTACGGAACTCGCACACACAGTGCCT
1 CAACAACCGATCTCGCACACACAGTGCTTGGTTACGGAACTCGCACACACAGTGCCT
* * *
12474428 CAACAACCGATCTCGCACACACAGTGCTCGATTACGGAACTCACACACACAGTGCCT
1 CAACAACCGATCTCGCACACACAGTGCTTGGTTACGGAACTCGCACACACAGTGCCT
12474485 ATGTTCACTT
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 109 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (57 bp):
CAACAACCGATCTCGCACACACAGTGCTTGGTTACGGAACTCGCACACACAGTGCCT
Found at i:12474394 original size:29 final size:29
Alignment explanation
Indices: 12474353--12474454 Score: 134
Period size: 29 Copynumber: 3.6 Consensus size: 29
12474343 GGTTACGGAA
12474353 CTCGCACACACAGTGCCTCAACAACCGAT
1 CTCGCACACACAGTGCCTCAACAACCGAT
***** * *
12474382 CTCGCACACACAGTG-CTTGGTTACGGAA
1 CTCGCACACACAGTGCCTCAACAACCGAT
12474410 CTCGCACACACAGTGCCTCAACAACCGAT
1 CTCGCACACACAGTGCCTCAACAACCGAT
12474439 CTCGCACACACAGTGC
1 CTCGCACACACAGTGC
12474455 TCGATTACGG
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 21 0.36
29 37 0.64
ACGTcount: A:0.28, C:0.38, G:0.18, T:0.16
Consensus pattern (29 bp):
CTCGCACACACAGTGCCTCAACAACCGAT
Found at i:12476487 original size:26 final size:26
Alignment explanation
Indices: 12476458--12476538 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 26
12476448 TCCCTTTGAA
* * *
12476458 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
12476484 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
* * *
12476512 CCATTCTCAATATTTCGTACACTAAGT
1 TCA-T-TCAATATCTCGCACACTAAGT
12476539 ACCAATTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 3 0.06
27 1 0.02
28 43 0.91
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:12476503 original size:28 final size:28
Alignment explanation
Indices: 12476472--12476538 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
12476462 TCGATATTTT
*
12476472 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
12476500 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
12476528 GTACACTAAGT
1 GCACACTAAGT
12476539 ACCAATTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:12484630 original size:104 final size:105
Alignment explanation
Indices: 12484499--12484690 Score: 235
Period size: 105 Copynumber: 1.8 Consensus size: 105
12484489 CTAAGTCGTG
* ** * * *
12484499 TAACTCACTGTTTGTGATTTAGGACCACATAGCCAG-GGACAT-AGGCGTGTGCCTAGGCCGTGT
1 TAACTCACTGTTTATGATTTAAAACCACAAAGCCAGAGGACATGA-ACATGTGCCTAGGCCGTGT
*
12484562 GAGTCACACAGGAAAGGACATGGGAATTTGTTTAGGCCGTT
65 GAGCCACACAGGAAAGGACATGGGAATTTGTTTAGGCCGTT
* ** * *
12484603 TAACTCACTGTTTATGTTTTAAAACCACAAAGGTAGAGGACATGAACATGTGTCTAGGCCTTGTG
1 TAACTCACTGTTTATGATTTAAAACCACAAAGCCAGAGGACATGAACATGTGCCTAGGCCGTGTG
* *
12484668 AGCCACACGGGCAAGGACATGGG
66 AGCCACACAGGAAAGGACATGGG
12484691 CTTGTGTCTA
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
104 29 0.40
105 42 0.58
106 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (105 bp):
TAACTCACTGTTTATGATTTAAAACCACAAAGCCAGAGGACATGAACATGTGCCTAGGCCGTGTG
AGCCACACAGGAAAGGACATGGGAATTTGTTTAGGCCGTT
Found at i:12486169 original size:87 final size:87
Alignment explanation
Indices: 12486023--12486196 Score: 339
Period size: 87 Copynumber: 2.0 Consensus size: 87
12486013 TGTGTTGGTG
12486023 TAACTCATCCAAGTTCGGCTTAAACTTCTATGCCAGGTTTGGGGTGTTACACTATATTTTATTTC
1 TAACTCATCCAAGTTCGGCTTAAACTTCTATGCCAGGTTTGGGGTGTTACACTATATTTTATTTC
12486088 AACAAGGATTCAAGTCACTCAA
66 AACAAGGATTCAAGTCACTCAA
*
12486110 TAACTCATCCAAGTTCGGCTTAAACTTCTATGCCAGGTTTGGGGTGTTACACTATATTTTATTTT
1 TAACTCATCCAAGTTCGGCTTAAACTTCTATGCCAGGTTTGGGGTGTTACACTATATTTTATTTC
12486175 AACAAGGATTCAAGTCACTCAA
66 AACAAGGATTCAAGTCACTCAA
12486197 CTCTAACAAT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (87 bp):
TAACTCATCCAAGTTCGGCTTAAACTTCTATGCCAGGTTTGGGGTGTTACACTATATTTTATTTC
AACAAGGATTCAAGTCACTCAA
Found at i:12488054 original size:16 final size:16
Alignment explanation
Indices: 12488030--12488060 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12488020 TAAGTAAATA
*
12488030 AAATGAAATAAAGAAT
1 AAATAAAATAAAGAAT
12488046 AAATAAAATAAAGAA
1 AAATAAAATAAAGAA
12488061 ACAAAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (16 bp):
AAATAAAATAAAGAAT
Found at i:12490053 original size:20 final size:20
Alignment explanation
Indices: 12490028--12490080 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
12490018 ACCTATGGGT
*
12490028 AGGCCACACGGGCATGTTCC
1 AGGCCACACGGGCATGTCCC
12490048 AGGCCACACGGGCATGTCCC
1 AGGCCACACGGGCATGTCCC
12490068 AGGCCACACGGGC
1 AGGCCACACGGGC
12490081 GTGTGCCCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.38, G:0.32, T:0.09
Consensus pattern (20 bp):
AGGCCACACGGGCATGTCCC
Found at i:12491996 original size:48 final size:47
Alignment explanation
Indices: 12491924--12492045 Score: 129
Period size: 48 Copynumber: 2.6 Consensus size: 47
12491914 TCCAAATATT
* * * * * **
12491924 GATGCCATATCCCGGATATGGTCTTATACGAAGTCTC-ATATCAGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACAC-AAG-CACAATATCAACGCC
* *
12491972 TATGCCATGTCCCAGACATGGTCTTACACTAGCACATATATCAACGCC
1 GATGCCATGTCCCAGACATGGTCTTACACAAGCACA-ATATCAACGCC
12492020 GATGCCATGTCCCAGACATGGTCTTA
1 GATGCCATGTCCCAGACATGGTCTTA
12492046 AGTTGGCTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 2 0.03
47 2 0.03
48 58 0.94
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACAAGCACAATATCAACGCC
Found at i:12492101 original size:48 final size:48
Alignment explanation
Indices: 12491973--12492102 Score: 163
Period size: 48 Copynumber: 2.7 Consensus size: 48
12491963 ATCAGTGCCT
* * *
12491973 ATGCCATGTCCCAGACATGGTCTTACACTAGCACATATATCAACGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAACGCCG
* * **
12492021 ATGCCATGTCCCAGACATGGTCTTA-AGTTGGCTCACATATCAATGTTG
1 ATGCCATGTCCCAGACATGGTCTTACA-CTGGCTCACATATCAACGCCG
* *
12492069 ATTCCATGTCCTAGACATGGTCTTACACTGGCTC
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTC
12492103 TCATTAACCA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
47 1 0.01
48 68 0.97
49 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.28
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAACGCCG
Found at i:12499806 original size:16 final size:17
Alignment explanation
Indices: 12499775--12499807 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12499765 AATTTCTATC
12499775 CAATTTATACCCTAATT
1 CAATTTATACCCTAATT
*
12499792 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
12499808 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
CAATTTATACCCTAATT
Found at i:12528411 original size:28 final size:29
Alignment explanation
Indices: 12528346--12528410 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
12528336 TTATGGATTG
* *
12528346 ATGGATTTTGTTTGTTATGTTAATTTTTT
1 ATGGATTTTGTTTGTGATATTAATTTTTT
12528375 ATGGATTTTGTTTGTGATATT-A-TTTTT
1 ATGGATTTTGTTTGTGATATTAATTTTTT
*
12528402 ATTGATTTT
1 ATGGATTTT
12528411 TTAATGGAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 13 0.39
28 1 0.03
29 19 0.58
ACGTcount: A:0.18, C:0.00, G:0.17, T:0.65
Consensus pattern (29 bp):
ATGGATTTTGTTTGTGATATTAATTTTTT
Found at i:12542805 original size:43 final size:43
Alignment explanation
Indices: 12542744--12542900 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 43
12542734 TAAGTGTATT
* * *
12542744 CATGTAAGACCACATCTGGGACGTTGGCATTGATATGTGATTA
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
* * * *
12542787 CATGTAAGACCATGTCTGGGACATCGGCATCG-TATTTGATT-
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
* *
12542828 CATGTAAGACC-CTGTCTGGGACAG-TGGCATCAAGATATGATTA
1 CATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATATGATTA
*
12542871 CATGTAAGACCACGTCTGGAACGTTGGCAT
1 CATGTAAGACCACGTCTGGGACGTTGGCAT
12542901 TGTACGATAT
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
41 26 0.27
42 16 0.17
43 52 0.55
44 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
Found at i:12552116 original size:35 final size:35
Alignment explanation
Indices: 12552040--12552169 Score: 120
Period size: 37 Copynumber: 3.6 Consensus size: 35
12552030 CTAAAACTAT
* * *
12552040 ATACACATATATATA-AATTATATAAAATAAGACCC
1 ATACACATATTTATATTA-TATATAAAACAAGACCC
*
12552075 ATATACACATATTTATATTATATATAAAACAGGACCC
1 --ATACACATATTTATATTATATATAAAACAAGACCC
*
12552112 ATACACGAGTATTTATATTATATATATAACAAGA-CC
1 ATACAC-A-TATTTATATTATATATAAAACAAGACCC
**
12552148 ATGTATGCATATTTATATTATA
1 A--TACACATATTTATATTATA
12552170 CATATACATA
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
35 6 0.08
36 17 0.21
37 53 0.66
38 4 0.05
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (35 bp):
ATACACATATTTATATTATATATAAAACAAGACCC
Found at i:12556926 original size:25 final size:25
Alignment explanation
Indices: 12556898--12556950 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
12556888 TTCATTTTAT
*
12556898 ATTTATTTAT-TGCATACAAAAATAA
1 ATTTATTTATCT-AATACAAAAATAA
*
12556923 ATTTATTTATCTAATATAAAAATAA
1 ATTTATTTATCTAATACAAAAATAA
12556948 ATT
1 ATT
12556951 AATGTGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTTATTTATCTAATACAAAAATAA
Found at i:12562054 original size:5 final size:5
Alignment explanation
Indices: 12562044--12562079 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
12562034 CAATTTGAGA
12562044 AAAAT AAAAT AAAAT AAGAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT -A-AAAT AAAAT AAAAT AAAA
12562080 ACACACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 23 0.79
6 2 0.07
7 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:12562067 original size:17 final size:17
Alignment explanation
Indices: 12562045--12562077 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12562035 AATTTGAGAA
12562045 AAATAAAATAAAATAAG
1 AAATAAAATAAAATAAG
12562062 AAATAAAATAAAATAA
1 AAATAAAATAAAATAA
12562078 AAACACACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAAATAAAATAAG
Found at i:12577304 original size:19 final size:19
Alignment explanation
Indices: 12577280--12577339 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
12577270 GAATAAAAAA
12577280 TTGGTATTCCTCATAATTT
1 TTGGTATTCCTCATAATTT
* **
12577299 TTGGTATCCCCTCATGGTTT
1 TTGGTAT-TCCTCATAATTT
**
12577319 TTTATATTCTCTCATAATTT
1 TTGGTATTC-CTCATAATTT
12577339 T
1 T
12577340 GATGTTTCCT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.18, C:0.18, G:0.10, T:0.53
Consensus pattern (19 bp):
TTGGTATTCCTCATAATTT
Found at i:12577409 original size:39 final size:37
Alignment explanation
Indices: 12577283--12577410 Score: 98
Period size: 40 Copynumber: 3.3 Consensus size: 37
12577273 TAAAAAATTG
* **
12577283 GTATTC-CTCATAATTTTTGGTATCCCCTCATGGTTTTTT
1 GTATTCTCTCATAATTTTTTGTA---CCTCATATTTTTTT
* * *
12577322 ATATTCTCTCATAATTTTGATGTTTCCTCATATTTTTTT
1 GTATTCTCTCATAATTTT-TTG-TACCTCATATTTTTTT
*
12577361 -AATTCTCTCTCATAATTTTTTGTACCTTTCATATTTTTTT
1 GTA-T-TCTCTCATAATTTTTTGTACC--TCATATTTTTTT
12577401 GTATTCTCTC
1 GTATTCTCTC
12577411 GTGTTAGCGT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
38 4 0.06
39 26 0.37
40 38 0.54
41 2 0.03
42 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.07, T:0.56
Consensus pattern (37 bp):
GTATTCTCTCATAATTTTTTGTACCTCATATTTTTTT
Found at i:12584897 original size:284 final size:282
Alignment explanation
Indices: 12584382--12585016 Score: 599
Period size: 284 Copynumber: 2.2 Consensus size: 282
12584372 TAAAAATATT
*
12584382 AATATAAATATTATTAATATTATTTTCATTATTATAAAAGGGGTTAGTTTGGTCCCAACCCCCCA
1 AATATTAATATTATTAATATTATTTTCATTATTATAAAAGGGGTTAGTTTGGTCCCAACCCCCCA
* * * ** * *
12584447 CATATCCATTCATTGATTTGAAAGAGAAAAAAAAACAACTCAGTTGAAGGTCTCCCCCCTTTTGA
66 CAGATCCAATCATTGATTTGAAAGAGAAAAAAAAACAACCCAGCCGAAGGTCTACCCCCTTTGGA
* * * *
12584512 AAATCAATAAGAAACTGTATGTTGTATTTTTTTTAGTAGTATAATTAGTTTTATTTTTGTAGTCT
131 AAA-CAAAAAGAAACTGTATGTTGTATTTTTTTTAGTAGTATAATTAGTTATATTTTAGTAGTCC
* * *** * * *
12584577 AACCAGAGGTCCTACCATCGATGTGATTTATCAGTCATAGGTCCGG-GTTCTAATAATCGAATAT
195 AACCAGACGTCCTACCACCGATGTGACCCATCAGTCACAGGTCCGGATTTC-AATAACCGAATAT
* * *
12584641 TTCAATTTTTTTCCTTTTTTGTTTAA
259 TT-AAGTTTTTT-CTCTTTTATTTAA
* * *
12584667 AATATTAATATTATT-ATATTGTTTTTATTATTATAAAAGGGGGTTAGTTTGGTCCTAACCTCCC
1 AATATTAATATTATTAATATTATTTTCATTATTATAAAA-GGGGTTAGTTTGGTCCCAA-C-CCC
** * * *
12584731 CACACAGATTTAATCATTTATTTGAAAGA-AAAACAACAAACAACCCAGCCGAAGGTCTATCCTC
63 C-CACAGATCCAATCATTGATTTGAAAGAGAAAA-AA-AAACAACCCAGCCGAAGGTCTACCCCC
12584795 TTTCGGAAAA-AAGAAAG-AA-T-T-TGTTGTA-TTTTTTTAGTAGTATAATTAGTTATATTTTA
125 TTT-GGAAAACAA-AAAGAAACTGTATGTTGTATTTTTTTTAGTAGTATAATTAGTTATATTTTA
** *** * * * *
12584854 GTAGTCCGGCACAG-CG-CCATGTTACCGATGTGACCCCTCAGTCACGGGTCTGGATTTCAATAC
188 GTAGTCCAAC-CAGACGTCC-TACCACCGATGTGACCCATCAGTCACAGGTCCGGATTTCAATAA
*
12584917 CCGAATATTTTAGTTTTTTCTCTTTTATTTAA
251 CCGAATATTTAAGTTTTTTCTCTTTTATTTAA
* * * *
12584949 AATATTAATATTAATATTATTATATTACTTTCATGATTATAAAAGGGAGTTGGTTTTGTTCCCAA
1 AATATTAATA-T--TATTA--ATATTATTTTCATTATTATAAAAGGG-GTTAG-TTTGGTCCCAA
12585014 CCC
59 CCC
12585017 TCGTAGATTC
Statistics
Matches: 283, Mismatches: 48, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
282 21 0.07
283 10 0.04
284 94 0.33
285 49 0.17
286 2 0.01
287 14 0.05
288 52 0.18
289 36 0.13
290 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (282 bp):
AATATTAATATTATTAATATTATTTTCATTATTATAAAAGGGGTTAGTTTGGTCCCAACCCCCCA
CAGATCCAATCATTGATTTGAAAGAGAAAAAAAAACAACCCAGCCGAAGGTCTACCCCCTTTGGA
AAACAAAAAGAAACTGTATGTTGTATTTTTTTTAGTAGTATAATTAGTTATATTTTAGTAGTCCA
ACCAGACGTCCTACCACCGATGTGACCCATCAGTCACAGGTCCGGATTTCAATAACCGAATATTT
AAGTTTTTTCTCTTTTATTTAA
Found at i:12590499 original size:10 final size:10
Alignment explanation
Indices: 12590472--12590510 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
12590462 TTAAATTCTA
12590472 AAAGATAAAT
1 AAAGATAAAT
12590482 ACAA-ATAAAT
1 A-AAGATAAAT
*
12590492 AAAGATAACT
1 AAAGATAAAT
12590502 AAAGATAAA
1 AAAGATAAA
12590511 AGCTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.69, C:0.05, G:0.08, T:0.18
Consensus pattern (10 bp):
AAAGATAAAT
Done.