Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 146 of 427
Found at i:39898093 original size:40 final size:40
Alignment explanation
Indices: 39898049--39898273 Score: 360
Period size: 40 Copynumber: 5.6 Consensus size: 40
39898039 CCAACCTAAT
* * * *
39898049 TGCCTTCGGAATTTAGCTCGGATATAACAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
* * * *
39898089 TGCCTTCGGGACTTATCCCGGAAATAACAACCAGAACAAA
1 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
*
39898129 TGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
*
39898169 TGCCTTCGAGACTTAACCCGGATATAACAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
39898209 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
39898249 TGCCTTCGGGACTTAACCCGGATAT
1 TGCCTTCGGGACTTAACCCGGATAT
39898274 GATCCTCAAT
Statistics
Matches: 171, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 171 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATATAACAACCAGCACGAA
Found at i:39900257 original size:2 final size:2
Alignment explanation
Indices: 39900250--39900276 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39900240 ATGTTAACTT
39900250 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
39900277 AAGAAAGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39912753 original size:40 final size:39
Alignment explanation
Indices: 39912708--39912837 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
39912698 CGGAATATAA
39912708 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
39912748 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
39912788 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
39912828 CCGGATATAA
1 CCGGATATAA
39912838 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:39912852 original size:40 final size:40
Alignment explanation
Indices: 39912724--39912874 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 40
39912714 ATAACCATGT
* * *
39912724 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
39912764 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
39912804 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* * *
39912844 GCATAATTGTCTTCGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
39912875 CATTCAATTT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 14 0.16
40 74 0.82
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:39912858 original size:80 final size:79
Alignment explanation
Indices: 39912724--39912872 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 79
39912714 ATAACCATGT
* *
39912724 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGAT-TTAGCC
39912789 CGGATGTAGCCACTA
65 CGGATGTAGCCACTA
* * * * *
39912804 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGATTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGATTTAGC
39912867 CCGGAT
64 CCGGAT
39912873 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
79 14 0.23
80 46 0.77
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGATTTAGCCC
GGATGTAGCCACTA
Found at i:39919877 original size:40 final size:39
Alignment explanation
Indices: 39919832--39919961 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
39919822 CGGAATATAA
39919832 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
39919872 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
39919912 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
39919952 CCGGATATAA
1 CCGGATATAA
39919962 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:39919976 original size:40 final size:40
Alignment explanation
Indices: 39919848--39919999 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
39919838 ATAACCATGT
* * *
39919848 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
39919888 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
39919928 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
39919968 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
39920000 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:39919982 original size:80 final size:80
Alignment explanation
Indices: 39919848--39919997 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
39919838 ATAACCATGT
*
39919848 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
39919912 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
39919928 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
39919991 CCCGGAT
64 CCCGGAT
39919998 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:39934993 original size:37 final size:38
Alignment explanation
Indices: 39934952--39935026 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
39934942 ATTGAGTATG
*
39934952 AGAATGAT-AAAGATGGTACAGGTATGTACGTGACATA
1 AGAATGATAAAAGATGGTACAGGTACGTACGTGACATA
39934989 AGAATGATAAAAGATGGTACAGGTACGTACGTGACATA
1 AGAATGATAAAAGATGGTACAGGTACGTACGTGACATA
39935027 TATAAGCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 8 0.22
38 28 0.78
ACGTcount: A:0.41, C:0.09, G:0.27, T:0.23
Consensus pattern (38 bp):
AGAATGATAAAAGATGGTACAGGTACGTACGTGACATA
Found at i:39943375 original size:40 final size:40
Alignment explanation
Indices: 39943309--39943451 Score: 121
Period size: 40 Copynumber: 3.6 Consensus size: 40
39943299 AAATTGAATG
* ** *
39943309 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGAAACT
* * ***
39943348 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCAAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGAAACT
* * ** *
39943388 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-ATGCAAGAAACT
*
39943428 CTAT-CGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
39943452 TTTGTGCACA
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
39 35 0.41
40 51 0.59
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGAAACT
Found at i:39943446 original size:39 final size:39
Alignment explanation
Indices: 39943347--39943459 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 39
39943337 TGCTGGAAAT
* **
39943347 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCAAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCAAGTCAC
* *
39943387 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCAAGTCAC
*
39943427 TCTAT-CGGGCTAAGACCCGAAGGCATTTGTGCA
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCA
39943460 CATGGTTATA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
39 27 0.42
40 37 0.58
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCAAGTCAC
Found at i:39945348 original size:27 final size:27
Alignment explanation
Indices: 39945318--39945499 Score: 78
Period size: 27 Copynumber: 6.8 Consensus size: 27
39945308 CAAATTGTAA
*
39945318 AATTACCAAAGTACCCTCGATTTATAG
1 AATTACCAAAGTACCCTCGATTTACAG
*****
39945345 AATTACTGTTTTACCCTCGATTTACAG
1 AATTACCAAAGTACCCTCGATTTACAG
**** * *
39945372 AATTACCGTTTTA-CCTTGATTTATAG
1 AATTACCAAAGTACCCTCGATTTACAG
***** *
39945398 AATTACTGTTTTACCCTTGATTTACAG
1 AATTACCAAAGTACCCTCGATTTACAG
***** * *
39945425 AATTACTGTTTTACCCTTGATTTACAA
1 AATTACCAAAGTACCCTCGATTTACAG
* * * * *
39945452 AATTACTAAAATACCCTTGGTTTACAA
1 AATTACCAAAGTACCCTCGATTTACAG
*
39945479 AATTACCAAAATACCCTCGAT
1 AATTACCAAAGTACCCTCGAT
39945500 CAGTAAAATT
Statistics
Matches: 134, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 23 0.17
27 111 0.83
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.38
Consensus pattern (27 bp):
AATTACCAAAGTACCCTCGATTTACAG
Found at i:39945406 original size:53 final size:54
Alignment explanation
Indices: 39945329--39945458 Score: 208
Period size: 53 Copynumber: 2.4 Consensus size: 54
39945319 ATTACCAAAG
*
39945329 TACCCTCGATTTATAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTT
1 TACCCTTGATTTATAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTT
* *
39945383 TA-CCTTGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTT
1 TACCCTTGATTTATAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTT
* *
39945436 TACCCTTGATTTACAAAATTACT
1 TACCCTTGATTTATAGAATTACT
39945459 AAAATACCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
53 50 0.71
54 20 0.29
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (54 bp):
TACCCTTGATTTATAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTT
Found at i:39945467 original size:54 final size:53
Alignment explanation
Indices: 39945356--39945485 Score: 161
Period size: 54 Copynumber: 2.4 Consensus size: 53
39945346 ATTACTGTTT
* * * ****
39945356 TACCCTCGATTTACAGAATTACCGTTTTACCTTGATTTATAGAATTACTGTTT
1 TACCCTTGATTTACAGAATTACCGTTTTACCTTGATTTACAAAATTACTAAAA
*
39945409 TACCCTTGATTTACAGAATTACTGTTTTACCCTTGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAGAATTACCGTTTTA-CCTTGATTTACAAAATTACTAAAA
* *
39945463 TACCCTTGGTTTACAAAATTACC
1 TACCCTTGATTTACAGAATTACC
39945486 AAAATACCCT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
53 27 0.42
54 38 0.58
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (53 bp):
TACCCTTGATTTACAGAATTACCGTTTTACCTTGATTTACAAAATTACTAAAA
Found at i:39945494 original size:54 final size:54
Alignment explanation
Indices: 39945436--39945607 Score: 145
Period size: 54 Copynumber: 3.1 Consensus size: 54
39945426 ATTACTGTTT
39945436 TACCCTTGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
* * * * * **
39945490 TACCCTCGA-TCAGTAAAATTACCAAAATACCCCTAATTTACAAAATTA-CAGAAA
1 TACCCTTGATTTA-CAAAATTACTAAAATACCCTTGGTTTACAAAATTACCA-AAA
* ** * **
39945544 TACCCTTGACTTT-CTAAAAATTA-TGGAAATACTATTGGTTTGCAAAATTACTGAAA
1 TACCCTTGA-TTTAC--AAAATTACT-AAAATACCCTTGGTTTACAAAATTACCAAAA
39945600 TACCCTTG
1 TACCCTTG
39945608 GTTTGTAGAT
Statistics
Matches: 90, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
53 4 0.04
54 49 0.54
56 37 0.41
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
TACCCTTGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
Found at i:39945534 original size:27 final size:27
Alignment explanation
Indices: 39945436--39945548 Score: 115
Period size: 27 Copynumber: 4.2 Consensus size: 27
39945426 ATTACTGTTT
* *
39945436 TACCCTTGATTTACAAAATTACTAAAA
1 TACCCCTGATTTACAAAATTACCAAAA
* *
39945463 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCCTGATTTACAAAATTACCAAAA
* *
39945490 TA-CCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCCT-GATTTA-CAAAATTACCAAAA
*
39945517 TACCCCTAATTTACAAAATTA-CAGAAA
1 TACCCCTGATTTACAAAATTACCA-AAA
39945544 TACCC
1 TACCC
39945549 TTGACTTTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
26 7 0.10
27 59 0.82
28 6 0.08
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.27
Consensus pattern (27 bp):
TACCCCTGATTTACAAAATTACCAAAA
Found at i:39945599 original size:27 final size:27
Alignment explanation
Indices: 39945560--39945612 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39945550 TGACTTTCTA
*
39945560 AAAATTATGGAAATACTATTGGTTTGC
1 AAAATTATGGAAATACCATTGGTTTGC
*
39945587 AAAATTACT-GAAATACCCTTGGTTTG
1 AAAATTA-TGGAAATACCATTGGTTTG
39945613 TAGATTTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (27 bp):
AAAATTATGGAAATACCATTGGTTTGC
Found at i:39946378 original size:25 final size:25
Alignment explanation
Indices: 39946350--39946397 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39946340 TTATATTATG
* * *
39946350 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACCGTTATACCCCTAGGTA
39946375 AAAATGACCGTTATACCCCTAGG
1 AAAATGACCGTTATACCCCTAGG
39946398 ATTTACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (25 bp):
AAAATGACCGTTATACCCCTAGGTA
Found at i:39946607 original size:24 final size:25
Alignment explanation
Indices: 39946508--39946630 Score: 142
Period size: 26 Copynumber: 4.8 Consensus size: 25
39946498 GAGGAAGTGC
39946508 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCC-AGTTTATTG
*
39946534 AAAAAGGGCTTATGCCACAGTTTATTA
1 -AAAAGGGCTTATGCC-CAGTTTATTG
* *
39946561 AAAAAGGTTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATG-CCCAGTTTATTG
**
39946587 AAAAGGGCTT-TGCCCAGTTTACCG
1 AAAAGGGCTTATGCCCAGTTTATTG
39946611 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATG-CCCAGTT
39946631 ATTAAAGAGG
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
24 22 0.26
25 9 0.11
26 28 0.33
27 25 0.29
28 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (25 bp):
AAAAGGGCTTATGCCCAGTTTATTG
Found at i:39948428 original size:40 final size:39
Alignment explanation
Indices: 39948384--39948565 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
39948374 GTTCAAAACA
* * ** * *
39948384 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
39948424 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
39948464 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
39948503 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
39948542 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
39948566 CTCGAACATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:39948495 original size:39 final size:39
Alignment explanation
Indices: 39948414--39948566 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
39948404 TATGGTAACC
* *
39948414 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
39948454 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
39948493 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
39948532 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
39948567 TCGAACATTC
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:39956377 original size:40 final size:39
Alignment explanation
Indices: 39956333--39956514 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
39956323 GTTCAAAACA
* * ** * *
39956333 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
39956373 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
39956413 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
39956452 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
39956491 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
39956515 CTCGAACATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:39956444 original size:39 final size:39
Alignment explanation
Indices: 39956363--39956515 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
39956353 TATGGTAACC
* *
39956363 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
39956403 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
39956442 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
39956481 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
39956516 TCGAACATTC
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:39959948 original size:29 final size:29
Alignment explanation
Indices: 39959914--39960047 Score: 81
Period size: 29 Copynumber: 4.6 Consensus size: 29
39959904 TACTCGATTT
* * *
39959914 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
39959943 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
39959972 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
* * *** * *
39960001 TGCACACTCAGTGCCATATTTTTCCAGCA
1 CGCACACTTAGTGCCATACCATTCAAGCC
*
39960030 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
39960048 TATTTCCAGC
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
29 84 0.99
30 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:39960006 original size:58 final size:59
Alignment explanation
Indices: 39959913--39960103 Score: 201
Period size: 58 Copynumber: 3.3 Consensus size: 59
39959903 ATACTCGATT
** * ** *
39959913 TCGCACACTTAGTGCCATGCGATTT-AAGCCCGCACACACAGTGCCATACCCTTCGAGC-
1 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACACAGTGCCATACCCTTCCAGCA
* ***
39959971 TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATTTTTCCAGCA
1 TCGCACACTTAGTGCCATATATTTCCAGCATGCACACACAGTGCCATACCCTTCCAGCA
** * ***
39960030 T-GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGTCATATATTTCCAGCA
1 TCGCACACTTAGTGCCATATATTTCCAGCATGCACACACAGTGCCATACCCTTCCAGCA
39960088 T-GCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
39960104 ATGTCGTCAC
Statistics
Matches: 118, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
57 4 0.03
58 113 0.96
59 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.28
Consensus pattern (59 bp):
TCGCACACTTAGTGCCATATATTTCCAGCATGCACACACAGTGCCATACCCTTCCAGCA
Found at i:39960035 original size:87 final size:87
Alignment explanation
Indices: 39959944--39960103 Score: 232
Period size: 87 Copynumber: 1.8 Consensus size: 87
39959934 ATTTAAGCCC
* *
39959944 GCACACACAGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACAC
1 GCACACACAGTGCCATACACTTCCAGCAT-GCACACTTAGTGCCATATATTTCCAGCATGCACAC
39960008 TCAGTGCCATATTTTTCCAGCAT
65 TCAGTGCCATATTTTTCCAGCAT
** * * *
39960031 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGTCATATATTTCCAGCATGCACACT
1 GCACACACAGTGCCATACACTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCATGCACACT
*
39960096 TAGTGCCA
66 CAGTGCCA
39960104 ATGTCGTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
87 63 0.98
88 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (87 bp):
GCACACACAGTGCCATACACTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCATGCACACT
CAGTGCCATATTTTTCCAGCAT
Found at i:39960048 original size:29 final size:29
Alignment explanation
Indices: 39959973--39960103 Score: 235
Period size: 29 Copynumber: 4.5 Consensus size: 29
39959963 CTTCGAGCTC
39959973 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
* *
39960002 GCACACTCAGTGCCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
39960031 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
*
39960060 GCACACTTAGTGTCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
39960089 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
39960104 ATGTCGTCAC
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 96 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:39963359 original size:29 final size:29
Alignment explanation
Indices: 39963320--39963398 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
39963310 CTTAATAATC
*
39963320 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
39963350 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
39963379 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39963399 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:39964059 original size:2 final size:2
Alignment explanation
Indices: 39964041--39964082 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
39964031 TGATGGCCGA
* *
39964041 AT AT GT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39964083 CAACTATACT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39969695 original size:21 final size:21
Alignment explanation
Indices: 39969671--39969740 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
39969661 CACATCCATC
39969671 ATGAACTCAGACCACAACTCA
1 ATGAACTCAGACCACAACTCA
** *
39969692 ATGAGTTCAGATGCCACATATATC-
1 ATGAACTCAGA--CCACA-A-CTCA
*
39969716 ATGAACTCAGACCGCAACTCA
1 ATGAACTCAGACCACAACTCA
39969737 ATGA
1 ATGA
39969741 GTTCATATCT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
20 2 0.05
21 14 0.38
22 4 0.11
23 5 0.14
24 10 0.27
25 2 0.05
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (21 bp):
ATGAACTCAGACCACAACTCA
Found at i:39983157 original size:27 final size:27
Alignment explanation
Indices: 39983127--39983218 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
39983117 GGGTATCACG
* *
39983127 GTCATTTTACCCTACAAGGGCATTATA
1 GTCATTTTACCCTACAGGGGTATTATA
* *
39983154 GTCATTTTACCCTATAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTATA
* *
39983181 GTTATTTTACCCTACAGGGGTATTACA
1 GTCATTTTACCCTACAGGGGTATTATA
*
39983208 GTTATTTTACC
1 GTCATTTTACC
39983219 TATTTTGGGG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTATA
Found at i:39983170 original size:54 final size:54
Alignment explanation
Indices: 39983112--39983218 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 54
39983102 CATTTCTCCA
*
39983112 TATAGGGGTATCACGGTCATTTTACCCTACAAGGGCATTATAGTCATTTTACCC
1 TATAGGGGTATCACGGTCATTTTACCCTACAAGGGCATTACAGTCATTTTACCC
* * * * * *
39983166 TATAGGGGTATTATGGTTATTTTACCCTACAGGGGTATTACAGTTATTTTACC
1 TATAGGGGTATCACGGTCATTTTACCCTACAAGGGCATTACAGTCATTTTACC
39983219 TATTTTGGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (54 bp):
TATAGGGGTATCACGGTCATTTTACCCTACAAGGGCATTACAGTCATTTTACCC
Found at i:39991146 original size:42 final size:42
Alignment explanation
Indices: 39990993--39991157 Score: 183
Period size: 42 Copynumber: 3.9 Consensus size: 42
39990983 AATCATACTA
* **
39990993 ATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * * *
39991035 ATGCCAATAGCCCAGCTATGGTCTTACATG-ATTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
39991077 ATGCCATGTCCCAGACATGTTCTTACACGAAATCTCATAAT-G
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCAT-ATCG
*
39991119 ATGCCATATCCTAGATATGGTCTTACACGTAAA-CTCATA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAATCTCATA
39991158 ACCCTAATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
41 19 0.18
42 58 0.56
43 27 0.26
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:39995290 original size:35 final size:35
Alignment explanation
Indices: 39995250--39995415 Score: 179
Period size: 35 Copynumber: 4.7 Consensus size: 35
39995240 TAGGTATGTA
39995250 CATATGTGATGATATATTGAACTTGTATATTTGGC
1 CATATGTGATGATATATTGAACTTGTATATTTGGC
* * * * *
39995285 CATATGTAATGTTATATTAAACTTGAATATTTGAC
1 CATATGTGATGATATATTGAACTTGTATATTTGGC
* * * * * *
39995320 TACATGTGATGTTATATTGAGCTTGTATATTCGGT
1 CATATGTGATGATATATTGAACTTGTATATTTGGC
** * *
39995355 CATAAATGATGATATATTGTACTTGTATATTGGGC
1 CATATGTGATGATATATTGAACTTGTATATTTGGC
*
39995390 CATATGTGATGATATAATGAATCTTG
1 CATATGTGATGATATATTGAA-CTTG
39995416 AGTATTCGGC
Statistics
Matches: 103, Mismatches: 27, Indels: 1
0.79 0.21 0.01
Matches are distributed among these distances:
35 99 0.96
36 4 0.04
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (35 bp):
CATATGTGATGATATATTGAACTTGTATATTTGGC
Found at i:39997550 original size:24 final size:24
Alignment explanation
Indices: 39997514--39997584 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
39997504 CTGTCAGGAG
*
39997514 AGGATTTAAGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
*
39997538 AGGATTTAGGAGTTGATGAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
39997562 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
39997585 GGAAATCTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.35, C:0.01, G:0.38, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:39998075 original size:27 final size:27
Alignment explanation
Indices: 39998035--39998146 Score: 120
Period size: 27 Copynumber: 4.1 Consensus size: 27
39998025 AGGAAGCGTC
*
39998035 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
39998062 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* *
39998089 CTGGTGGCTCTGCCACGATTATCTATAT
1 CTGGTGGCTCTGCCACAATTATCT-GAT
* * * *
39998117 CTAGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
39998143 CTGG
1 CTGG
39998147 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 7 0.10
27 47 0.66
28 17 0.24
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:39998141 original size:54 final size:54
Alignment explanation
Indices: 39998035--39998146 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
39998025 AGGAAGCGTC
* * *
39998035 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTGTT
* * * *
39998089 CTGGTGGCTCTGCCACGATTATCTATATCTAGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCT-GATCTAGTGACTCTGCCACATATATCTGTT
39998143 CTGG
1 CTGG
39998147 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.66
55 17 0.34
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTGTT
Found at i:40014684 original size:43 final size:43
Alignment explanation
Indices: 40014637--40014814 Score: 225
Period size: 43 Copynumber: 4.2 Consensus size: 43
40014627 GTTCTTTAAC
** * *
40014637 GGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGTTTTATAGA
1 GGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTTCTATAGA
** *
40014680 GGCGTTTGTGGGAAAAGTGCCGCTAAAGGGCATGTTCTATAGC
1 GGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTTCTATAGA
* * * *
40014723 GGTGTTTGTGGG-AAAGTGCTGCTAAAGCTCATGTCCTATAGT
1 GGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTTCTATAGA
*
40014765 GGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTCCTATAGCA
1 GGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTTCTATAG-A
40014809 -GCGTTT
1 GGCGTTT
40014815 TTCCACATAA
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
42 36 0.30
43 83 0.70
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTTCTATAGA
Found at i:40014771 original size:85 final size:86
Alignment explanation
Indices: 40014625--40014814 Score: 247
Period size: 85 Copynumber: 2.2 Consensus size: 86
40014615 TTTAAAGGTT
* * * **
40014625 ATGTTCTTTAACGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGTTTTATAGAGGCGTTTGTG
1 ATGTTCTATAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGCTCATGTCCTATAGAGGCGTTTGTG
*
40014690 GGAAAAGTGCCGCTAAAGGGC
66 GGAAAAGTGCCGCTAAAGCGC
* ** * *
40014711 ATGTTCTATAGCGGTGTTTGTGGG-AAAGTGCTGCTAAAGCTCATGTCCTATAGTGGCGTTTGTG
1 ATGTTCTATAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGCTCATGTCCTATAGAGGCGTTTGTG
*
40014775 GGAAAAGTGCCGCTAAAGCTC
66 GGAAAAGTGCCGCTAAAGCGC
* *
40014796 ATGTCCTATAGCAGCGTTT
1 ATGTTCTATAGCGGCGTTT
40014815 TTCCACATAA
Statistics
Matches: 89, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 68 0.76
86 21 0.24
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (86 bp):
ATGTTCTATAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGCTCATGTCCTATAGAGGCGTTTGTG
GGAAAAGTGCCGCTAAAGCGC
Found at i:40015045 original size:85 final size:85
Alignment explanation
Indices: 40014894--40015088 Score: 284
Period size: 85 Copynumber: 2.3 Consensus size: 85
40014884 CGCCGCAAAT
* * **
40014894 TGCCGCTAAAGGTCATGTTCTATAGCGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGTTTTAT
1 TGCCGCTAAAGGTCATGTTCTATAGCGCGTTTGTGGGAAAAGCGCCGCTAAAGCTCATGTCCTAT
40014959 AGAGGCGTTTGTGGGAAAAG
66 AGAGGCGTTTGTGGGAAAAG
* * *
40014979 TGTCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGG-AAAGTGCTGCTAAAGCTCATGTCCTA
1 TGCCGCTAAAGGTCATGTTCTATAGC-GCGTTTGTGGGAAAAGCGCCGCTAAAGCTCATGTCCTA
*
40015043 TAGTGGCGTTTGTGGGAAAAG
65 TAGAGGCGTTTGTGGGAAAAG
* *
40015064 TGCCGCTAAAGCTCATGTCCTATAG
1 TGCCGCTAAAGGTCATGTTCTATAG
40015089 TAGCGTTTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 88 0.90
86 10 0.10
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (85 bp):
TGCCGCTAAAGGTCATGTTCTATAGCGCGTTTGTGGGAAAAGCGCCGCTAAAGCTCATGTCCTAT
AGAGGCGTTTGTGGGAAAAG
Found at i:40015089 original size:43 final size:43
Alignment explanation
Indices: 40014894--40015096 Score: 275
Period size: 43 Copynumber: 4.8 Consensus size: 43
40014884 CGCCGCAAAT
* *
40014894 TGCCGCTAAAGGTCATGTTCTATAG-CGCGTTTTTGGGAAAAG
1 TGCCGCTAAAGGTCATGTTCTATAGTGGCGTTTGTGGGAAAAG
* * *
40014936 CGCCGCTAAAGGTCATGTTTTATAGAGGCGTTTGTGGGAAAAG
1 TGCCGCTAAAGGTCATGTTCTATAGTGGCGTTTGTGGGAAAAG
* *
40014979 TGTCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGG-AAAG
1 TGCCGCTAAAGGTCATGTTCTATAGTGGCGTTTGTGGGAAAAG
* * *
40015021 TGCTGCTAAAGCTCATGTCCTATAGTGGCGTTTGTGGGAAAAG
1 TGCCGCTAAAGGTCATGTTCTATAGTGGCGTTTGTGGGAAAAG
* * *
40015064 TGCCGCTAAAGCTCATGTCCTATAGTAGCGTTT
1 TGCCGCTAAAGGTCATGTTCTATAGTGGCGTTT
40015097 TTCCACATAA
Statistics
Matches: 144, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
42 60 0.42
43 84 0.58
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.31
Consensus pattern (43 bp):
TGCCGCTAAAGGTCATGTTCTATAGTGGCGTTTGTGGGAAAAG
Found at i:40015149 original size:282 final size:283
Alignment explanation
Indices: 40014617--40015175 Score: 1012
Period size: 282 Copynumber: 2.0 Consensus size: 283
40014607 ATAATTTTTT
* *
40014617 TAAAGGTTATGTTCTTTAACGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGTTTTATAGAGG
1 TAAAGGTCATGTTCTATAACGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGTTTTATAGAGG
*
40014682 CGTTTGTGGGAAAAGTGCCGCTAAAGGGCATGTTCTATAGCGGTGTTTGTGGGAAAGTGCTGCTA
66 CGTTTGTGGGAAAAGTGCCGCTAAAGGGCATGTTCTATAGCGGCGTTTGTGGGAAAGTGCTGCTA
40014747 AAGCTCATGTCCTATAGTGGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTCCTATAGCAGCG
131 AAGCTCATGTCCTATAGTGGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTCCTATAGCAGCG
*
40014812 TTTTTCCACATAAACGCCATAAATTTTAGCGGCGTTAACTATAGCTGTTTTTTTTTGCAGCACTT
196 TTTTTCCACATAAACGCCACAAATTTTAGCGGCGTTAACTATAGCTGTTTTTTTTTGCAGCACTT
40014877 ATCAAAACGCCGCAAATTGCCGC
261 ATCAAAACGCCGCAAATTGCCGC
* * *
40014900 TAAAGGTCATGTTCTATAGC-GCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGTTTTATAGAGG
1 TAAAGGTCATGTTCTATAACGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGTTTTATAGAGG
* *
40014964 CGTTTGTGGGAAAAGTGTCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAGTGCTGCTA
66 CGTTTGTGGGAAAAGTGCCGCTAAAGGGCATGTTCTATAGCGGCGTTTGTGGGAAAGTGCTGCTA
*
40015029 AAGCTCATGTCCTATAGTGGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTCCTATAGTAGCG
131 AAGCTCATGTCCTATAGTGGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTCCTATAGCAGCG
40015094 TTTTTCCACATAAACGCCACAAATTTTAGCGGCGTTAACTATAGCTGTTTTTTTTTGCAGCACTT
196 TTTTTCCACATAAACGCCACAAATTTTAGCGGCGTTAACTATAGCTGTTTTTTTTTGCAGCACTT
*
40015159 ATCAAAATGCCGCAAAT
261 ATCAAAACGCCGCAAAT
40015176 AGTTTTAGTA
Statistics
Matches: 265, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
282 248 0.94
283 17 0.06
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (283 bp):
TAAAGGTCATGTTCTATAACGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCATGTTTTATAGAGG
CGTTTGTGGGAAAAGTGCCGCTAAAGGGCATGTTCTATAGCGGCGTTTGTGGGAAAGTGCTGCTA
AAGCTCATGTCCTATAGTGGCGTTTGTGGGAAAAGTGCCGCTAAAGCTCATGTCCTATAGCAGCG
TTTTTCCACATAAACGCCACAAATTTTAGCGGCGTTAACTATAGCTGTTTTTTTTTGCAGCACTT
ATCAAAACGCCGCAAATTGCCGC
Found at i:40018282 original size:21 final size:22
Alignment explanation
Indices: 40018243--40018283 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
40018233 ATTTATCTTA
*
40018243 AACTTAAAATTTTACAAATATT
1 AACTTAAAATTTGACAAATATT
*
40018265 AACTT-AAATTTGATAAATA
1 AACTTAAAATTTGACAAATA
40018284 AAATTGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (22 bp):
AACTTAAAATTTGACAAATATT
Found at i:40024154 original size:42 final size:42
Alignment explanation
Indices: 40024038--40024158 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
40024028 TAAGATTCCG
* *
40024038 TATAAGACCATATCTGGGATATGGCA-TCA-GTGTGTGATTTCA
1 TATAAGACCATATCTGGGATATGGCATTGATATG-GT-ATTTCA
* * * * *
40024080 TATAAGACCATGTCAGGGACATGAG-GTCGATATGGTATTTCA
1 TATAAGACCATATCTGGGATATG-GCATTGATATGGTATTTCA
40024122 TATAAGACCATATCTGGGATATGGCATTGATATGGTA
1 TATAAGACCATATCTGGGATATGGCATTGATATGGTA
40024159 CTAAGAGTAT
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
41 1 0.02
42 56 0.89
43 4 0.06
44 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (42 bp):
TATAAGACCATATCTGGGATATGGCATTGATATGGTATTTCA
Found at i:40037985 original size:40 final size:40
Alignment explanation
Indices: 40037940--40038107 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
40037930 CGGAATATAA
40037940 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40037980 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
40038020 CCGGATGTAGCCACTAGCGCAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40038060 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
40038100 CCGGATAT
1 CCGGATAT
40038108 CATTCAATTT
Statistics
Matches: 101, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
39 1 0.01
40 99 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40045191 original size:40 final size:40
Alignment explanation
Indices: 40045146--40045313 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
40045136 CGGAATATAA
40045146 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40045186 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
40045226 CCGGATGTAGCCACTAGCGCAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40045266 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
40045306 CCGGATAT
1 CCGGATAT
40045314 CATTCAATTT
Statistics
Matches: 101, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
39 1 0.01
40 99 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40046851 original size:14 final size:14
Alignment explanation
Indices: 40046832--40046862 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40046822 CAAAAATTAC
40046832 TTAGATTTTCCAAA
1 TTAGATTTTCCAAA
40046846 TTAGATTTTCCAAA
1 TTAGATTTTCCAAA
40046860 TTA
1 TTA
40046863 ATTCTACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (14 bp):
TTAGATTTTCCAAA
Found at i:40049541 original size:46 final size:48
Alignment explanation
Indices: 40049431--40049701 Score: 179
Period size: 46 Copynumber: 5.7 Consensus size: 48
40049421 TCATTGGTGT
* * * * * *
40049431 GAGCCAGTGTAAGACCAAGTCTGGGACATGGCACCGACAT-TGAGACG-A
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCAGAGATGTA
* *
40049479 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCA-AGATGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAGAGATGTA
40049526 -AGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CT-ACGAGATGT-
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCA-GAGATGTA
** * * * *
40049571 --GTTAGTGTAAGACCATGTCTGGGACATGGCCTC-GACACAGATATGTGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCAGAGATGT-A
* * * *
40049619 GAGCTAGAGTAAGACCATGTCTGGGACGTGACATCGGCCTC-GATAATG-A
1 GAGCCAGTGTAAGA-CATGTCTGGGACATG-CATCGGCCTCAGA-GATGTA
* * *
40049668 TAGCCAGTGTAAAACATGTCTAGGACATGGCATC
1 GAGCCAGTGTAAGACATGTCTGGGACAT-GCATC
40049702 AAAAACTTAC
Statistics
Matches: 179, Mismatches: 28, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
44 11 0.06
45 17 0.09
46 60 0.34
47 15 0.08
48 28 0.16
49 13 0.07
50 29 0.16
51 6 0.03
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (48 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAGAGATGTA
Found at i:40059107 original size:40 final size:40
Alignment explanation
Indices: 40059052--40059215 Score: 188
Period size: 40 Copynumber: 4.1 Consensus size: 40
40059042 TGAATGATAC
* * *
40059052 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
*
40059092 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * * * *
40059132 CCGGGTTAAGACCCGAAGGCAATTGTGCAAGTTACTAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
40059172 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
40059212 CCGG
1 CCGG
40059216 TTAAATCCCG
Statistics
Matches: 105, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.03
40 97 0.92
41 5 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:40059185 original size:80 final size:80
Alignment explanation
Indices: 40059052--40059229 Score: 209
Period size: 80 Copynumber: 2.2 Consensus size: 80
40059042 TGAATGATAC
* * * * * *
40059052 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGC-ATTC
1 CCGGGTTAAGACCCGAAGGCAATTATGCAAGTGACTAAATCCGGGCTAAGACCCGAAGGCAATT-
*
40059116 GTGCGAGTTGTTATAT
65 GTGCGAGTGGTTATAT
* * *
40059132 CCGGGTTAAGACCCGAAGGCAATTGTGCAAGTTACTAAATCCGGGTTAAGACCCGAAGGCAATTG
1 CCGGGTTAAGACCCGAAGGCAATTATGCAAGTGACTAAATCCGGGCTAAGACCCGAAGGCAATTG
**
40059197 TGCTTGTGGTTATAT
66 TGCGAGTGGTTATAT
40059212 CC-GGTTAA-ATCCCGAAGG
1 CCGGGTTAAGA-CCCGAAGG
40059230 TACGTGACTC
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
79 14 0.17
80 66 0.79
81 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGTTAAGACCCGAAGGCAATTATGCAAGTGACTAAATCCGGGCTAAGACCCGAAGGCAATTG
TGCGAGTGGTTATAT
Found at i:40067218 original size:40 final size:40
Alignment explanation
Indices: 40067163--40067326 Score: 188
Period size: 40 Copynumber: 4.1 Consensus size: 40
40067153 TGAATGATAC
* * *
40067163 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
*
40067203 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * * * *
40067243 CCGGGTTAAGACCCGAAGGCAATTGTGCAAGTTACTAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
40067283 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
40067323 CCGG
1 CCGG
40067327 TTAAATCCCG
Statistics
Matches: 105, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.03
40 97 0.92
41 5 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:40067296 original size:80 final size:80
Alignment explanation
Indices: 40067163--40067340 Score: 209
Period size: 80 Copynumber: 2.2 Consensus size: 80
40067153 TGAATGATAC
* * * * * *
40067163 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGC-ATTC
1 CCGGGTTAAGACCCGAAGGCAATTATGCAAGTGACTAAATCCGGGCTAAGACCCGAAGGCAATT-
*
40067227 GTGCGAGTTGTTATAT
65 GTGCGAGTGGTTATAT
* * *
40067243 CCGGGTTAAGACCCGAAGGCAATTGTGCAAGTTACTAAATCCGGGTTAAGACCCGAAGGCAATTG
1 CCGGGTTAAGACCCGAAGGCAATTATGCAAGTGACTAAATCCGGGCTAAGACCCGAAGGCAATTG
**
40067308 TGCTTGTGGTTATAT
66 TGCGAGTGGTTATAT
40067323 CC-GGTTAA-ATCCCGAAGG
1 CCGGGTTAAGA-CCCGAAGG
40067341 TACGTGACTC
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
79 14 0.17
80 66 0.79
81 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGTTAAGACCCGAAGGCAATTATGCAAGTGACTAAATCCGGGCTAAGACCCGAAGGCAATTG
TGCGAGTGGTTATAT
Found at i:40077726 original size:15 final size:15
Alignment explanation
Indices: 40077705--40077745 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
40077695 AATACAGAGG
40077705 AATCCAAGATAAAGA
1 AATCCAAGATAAAGA
* * *
40077720 TATCCAAGGTACAGA
1 AATCCAAGATAAAGA
40077735 AATCCAAGATA
1 AATCCAAGATA
40077746 CCATGTCATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (15 bp):
AATCCAAGATAAAGA
Found at i:40082656 original size:56 final size:56
Alignment explanation
Indices: 40082589--40082700 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
40082579 GATAAGGTGT
*
40082589 TTTTGAAAGTGTCTCCAAGGAAAAAGGTTTTGAGATTTGGTGGGAAAGGCAAATTA
1 TTTTGAAAGTGTCTCCAAGGAAAAAGGTTTTGAGATTTGGTAGGAAAGGCAAATTA
* *
40082645 TTTTGAAAGTGTCTCCATGGAAAAAGGTTTTGAGATTTGGTAGGAAAGGGAAATTA
1 TTTTGAAAGTGTCTCCAAGGAAAAAGGTTTTGAGATTTGGTAGGAAAGGCAAATTA
40082701 AGTCTATACT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (56 bp):
TTTTGAAAGTGTCTCCAAGGAAAAAGGTTTTGAGATTTGGTAGGAAAGGCAAATTA
Found at i:40085245 original size:40 final size:40
Alignment explanation
Indices: 40085189--40085283 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
40085179 TATGTGCATA
* * *
40085189 GCATTCGTGCGAGTTATTATAATCGGGTTAAGTCCTGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
40085229 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
40085269 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
40085284 GTTACATCTG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:40089738 original size:13 final size:13
Alignment explanation
Indices: 40089720--40089753 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
40089710 CGAACGTGTG
40089720 TGACCACATGGCC
1 TGACCACATGGCC
*
40089733 TGACCATATGGCC
1 TGACCACATGGCC
40089746 TGACCACA
1 TGACCACA
40089754 CGGACGTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.35, G:0.21, T:0.18
Consensus pattern (13 bp):
TGACCACATGGCC
Found at i:40092134 original size:40 final size:39
Alignment explanation
Indices: 40092089--40092218 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
40092079 CGGAATATAA
40092089 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
40092129 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40092169 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
40092209 CCGGATATAA
1 CCGGATATAA
40092219 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:40092233 original size:40 final size:40
Alignment explanation
Indices: 40092105--40092255 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 40
40092095 ATAACCATGT
* * *
40092105 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
40092145 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
40092185 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* * *
40092225 GCATAATTGTCTTCGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
40092256 CATTCAATTT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 14 0.16
40 74 0.82
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:40092239 original size:80 final size:79
Alignment explanation
Indices: 40092105--40092253 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 79
40092095 ATAACCATGT
* *
40092105 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGAT-TTAGCC
40092170 CGGATGTAGCCACTA
65 CGGATGTAGCCACTA
* * * * *
40092185 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGATTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGATTTAGC
40092248 CCGGAT
64 CCGGAT
40092254 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
79 14 0.23
80 46 0.77
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGATTTAGCCC
GGATGTAGCCACTA
Found at i:40095648 original size:45 final size:47
Alignment explanation
Indices: 40095536--40095656 Score: 138
Period size: 50 Copynumber: 2.6 Consensus size: 47
40095526 TGTCTTCGAC
** * *
40095536 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
40095586 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATAT-TCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
40095631 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
40095657 CTGTCCTGTC
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
45 29 0.46
46 4 0.06
50 30 0.48
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:40102939 original size:39 final size:40
Alignment explanation
Indices: 40102802--40102939 Score: 217
Period size: 40 Copynumber: 3.5 Consensus size: 40
40102792 CGGATGATAA
40102802 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40102842 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
40102882 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
40102922 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40102940 TACTTGGTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 17 0.18
40 75 0.82
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40105647 original size:38 final size:38
Alignment explanation
Indices: 40105545--40105649 Score: 115
Period size: 38 Copynumber: 2.8 Consensus size: 38
40105535 AATCCGAGTT
* * * *
40105545 TAAAGACCCGCTGACTATATGTAGAGATTATGTCCGGG
1 TAAAGACCCGATGGCTATATATAGAGATTATGTCCGGA
* *
40105583 TAAAGACCCGATGGCTATGTACAGAGATTATGTCCGGA
1 TAAAGACCCGATGGCTATATATAGAGATTATGTCCGGA
*
40105621 TTAAGACCC-ACTGGCT-TCATATAGAGATT
1 TAAAGACCCGA-TGGCTAT-ATATAGAGATT
40105650 TCATCCGAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 2 0.04
38 54 0.96
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (38 bp):
TAAAGACCCGATGGCTATATATAGAGATTATGTCCGGA
Found at i:40105736 original size:40 final size:40
Alignment explanation
Indices: 40105677--40105990 Score: 560
Period size: 40 Copynumber: 7.9 Consensus size: 40
40105667 CTCGACGATG
* *
40105677 ATCCGGGCTAAGTCTCGAAGGGCATTCGTGCCGGTGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
40105717 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
*
40105757 AT-CGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
40105796 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
40105836 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
40105876 ATCC-GGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
* *
40105915 ATCCGGGCTAAATCCCGAAGGGTATTCGTGCCGATGTTAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
*
40105955 ATCCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTG
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTG
40105991 ATGTGTATTC
Statistics
Matches: 263, Mismatches: 9, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
39 77 0.29
40 186 0.71
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
Found at i:40105811 original size:79 final size:80
Alignment explanation
Indices: 40105677--40105990 Score: 560
Period size: 79 Copynumber: 4.0 Consensus size: 80
40105667 CTCGACGATG
* *
40105677 ATCCGGGCTAAGTCTCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
40105742 TCGTGCCGGTGTTAT
66 TCGTGCCGGTGTTAT
*
40105757 AT-CGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
40105821 TCGTGCCGGTGTTAT
66 TCGTGCCGGTGTTAT
40105836 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCC-GGCTAAATCCCGAAGGGCAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
40105900 TCGTGCCGGTGTTAT
66 TCGTGCCGGTGTTAT
* * *
40105915 ATCCGGGCTAAATCCCGAAGGGTATTCGTGCCGATGTTATATCCGGGCTAAGTCCCGAAGGGCAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
40105980 TCGTGCCGGTG
66 TCGTGCCGGTG
40105991 ATGTGTATTC
Statistics
Matches: 227, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
79 155 0.68
80 72 0.32
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
TCGTGCCGGTGTTAT
Found at i:40105891 original size:119 final size:119
Alignment explanation
Indices: 40105677--40105990 Score: 565
Period size: 119 Copynumber: 2.6 Consensus size: 119
40105667 CTCGACGATG
* *
40105677 ATCCGGGCTAAGTCTCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
* *
40105742 TCGTGCCGGTGTTATATCGGGCTAAGTCCCGAAGGGCATTCGTGCCGGTGTTAT
66 TCGTGCCGGTGTTATATCCGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
40105796 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
40105861 TCGTGCCGGTGTTATATCCGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
66 TCGTGCCGGTGTTATATCCGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
* * *
40105915 ATCCGGGCTAAATCCCGAAGGGTATTCGTGCCGATGTTATATCCGGGCTAAGTCCCGAAGGGCAT
1 ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
40105980 TCGTGCCGGTG
66 TCGTGCCGGTG
40105991 ATGTGTATTC
Statistics
Matches: 188, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
119 188 1.00
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (119 bp):
ATCCGGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTATATCCGGGCTAAATCCCGAAGGGCAT
TCGTGCCGGTGTTATATCCGGCTAAATCCCGAAGGGCATTCGTGCCGGTGTTAT
Found at i:40110444 original size:47 final size:47
Alignment explanation
Indices: 40110393--40110497 Score: 192
Period size: 47 Copynumber: 2.2 Consensus size: 47
40110383 TAGTATTAAT
*
40110393 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
40110440 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
*
40110487 AATGTGATAAG
1 TATGTGATAAG
40110498 TCCCGAAGGG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
Found at i:40112697 original size:15 final size:15
Alignment explanation
Indices: 40112679--40112708 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40112669 CTTTCAGATG
*
40112679 CATCACTACTAGACA
1 CATCACTACCAGACA
40112694 CATCACTACCAGACA
1 CATCACTACCAGACA
40112709 TGTTTTCTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.37, G:0.07, T:0.17
Consensus pattern (15 bp):
CATCACTACCAGACA
Found at i:40113102 original size:48 final size:48
Alignment explanation
Indices: 40113034--40113157 Score: 212
Period size: 48 Copynumber: 2.6 Consensus size: 48
40113024 TGGATACAAT
* * * *
40113034 CAATCGCAGATATACACAATAAACATCAGTTTGATAATGGCATCCATA
1 CAATGGCAGATACAAACAATAAACATCAATTTGATAATGGCATCCATA
40113082 CAATGGCAGATACAAACAATAAACATCAATTTGATAATGGCATCCATA
1 CAATGGCAGATACAAACAATAAACATCAATTTGATAATGGCATCCATA
40113130 CAATGGCAGATACAAACAATAAACATCA
1 CAATGGCAGATACAAACAATAAACATCA
40113158 CGCACATGGC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (48 bp):
CAATGGCAGATACAAACAATAAACATCAATTTGATAATGGCATCCATA
Found at i:40113236 original size:6 final size:6
Alignment explanation
Indices: 40113209--40113362 Score: 62
Period size: 6 Copynumber: 24.7 Consensus size: 6
40113199 AAATAACCCT
* * * * * * *
40113209 AAATCA AAGTCC AAATCG AAATCA AAATCT AAATCTA AAGT-T AAATCG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC-A AAATCA AAATCA
* * ** **
40113257 AGATCG AAATTG AAATCA AAATCA AAATCA AAATCA GTGAGTGTTTCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA ---A--AAT-CA
* * *
40113305 AAAT-A GAAATCA AAATCG AAAT-A GAAATCA AAATCA AAATCA GAATCG
1 AAATCA -AAATCA AAATCA AAATCA -AAATCA AAATCA AAATCA AAATCA
40113353 AAATCA AAAT
1 AAATCA AAAT
40113363 TGAAATAGAA
Statistics
Matches: 110, Mismatches: 26, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
5 4 0.04
6 95 0.86
7 6 0.05
9 2 0.02
11 1 0.01
12 2 0.02
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (6 bp):
AAATCA
Found at i:40113367 original size:12 final size:12
Alignment explanation
Indices: 40113311--40113368 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
40113301 TTCAAAATAG
* *
40113311 AAATCAAAATCG
1 AAATCGAAATCA
*
40113323 AAATAGAAATCA
1 AAATCGAAATCA
*
40113335 AAATCAAAATCA
1 AAATCGAAATCA
*
40113347 GAATCGAAATCA
1 AAATCGAAATCA
*
40113359 AAATTGAAAT
1 AAATCGAAAT
40113369 AGAAATAACC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (12 bp):
AAATCGAAATCA
Found at i:40113931 original size:31 final size:30
Alignment explanation
Indices: 40113896--40113963 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
40113886 GCTGTTAACC
* * *
40113896 AGTGACTATTTTGTCACTTTTTCATAATGTT-
1 AGTGACTATTTTCTAAC-TTTTCA-AAAGTTG
*
40113927 AGTGACTGTTTTCTAACTTTTCAAAAGTTG
1 AGTGACTATTTTCTAACTTTTCAAAAGTTG
40113957 AGTGACT
1 AGTGACT
40113964 GAAATAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.16
30 13 0.41
31 14 0.44
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (30 bp):
AGTGACTATTTTCTAACTTTTCAAAAGTTG
Found at i:40113961 original size:30 final size:31
Alignment explanation
Indices: 40113896--40113964 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
40113886 GCTGTTAACC
* * * *
40113896 AGTGACTATTTTGTCACTTTTTCATAATGTT
1 AGTGACTGTTTTCTAACTTTTTCATAAAGTT
40113927 AGTGACTGTTTTCTAAC-TTTTCA-AAAGTT
1 AGTGACTGTTTTCTAACTTTTTCATAAAGTT
40113956 GAGTGACTG
1 -AGTGACTG
40113965 AAATAAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 14 0.42
31 14 0.42
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (31 bp):
AGTGACTGTTTTCTAACTTTTTCATAAAGTT
Found at i:40115323 original size:2 final size:2
Alignment explanation
Indices: 40115316--40115346 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40115306 ATAACCAAAT
40115316 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
40115347 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40119672 original size:38 final size:38
Alignment explanation
Indices: 40119589--40119778 Score: 211
Period size: 38 Copynumber: 4.9 Consensus size: 38
40119579 GAATCTAGTC
* * * *
40119589 ACCAGCACAAAACCTGCGGGACTTTAAGCTCAGATATAAT
1 ACCAGCACTAAGCCTGCGGGA-TTTAA-CCCGGATATAAT
*
40119629 ACCAGCACTAGGCCTGCGGGATTTAACCCGGATATAAT
1 ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAAT
* *
40119667 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
1 ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAAT
* * * *
40119705 ACTAGCACAAAGCCTGCAGTATTTAACCCGGATATAAT
1 ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAAT
* *
40119743 TCCAGCA-TATAGCCTGCGGGTCTTTAAGCCCGGATA
1 ACCAGCACTA-AGCCTGCGGG-ATTTAA-CCCGGATA
40119779 CACATCAAAT
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
37 1 0.01
38 91 0.71
39 10 0.08
40 26 0.20
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (38 bp):
ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAAT
Found at i:40122600 original size:31 final size:31
Alignment explanation
Indices: 40122558--40122671 Score: 147
Period size: 31 Copynumber: 3.5 Consensus size: 31
40122548 CCTTTTCGTA
40122558 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCAT
1 TTTCATATTTCATAATACTGGGCCGAAG-C----C-T
40122595 GTTTCATATTTCATAATACTGGGCCGAAGCCT
1 -TTTCATATTTCATAATACTGGGCCGAAGCCT
*
40122627 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
40122658 TTTCATGTTTCATA
1 TTTCATATTTCATA
40122672 TTTCATAATA
Statistics
Matches: 74, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
31 43 0.58
32 1 0.01
33 1 0.01
37 1 0.01
38 28 0.38
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:40122600 original size:38 final size:38
Alignment explanation
Indices: 40122535--40122697 Score: 223
Period size: 38 Copynumber: 4.4 Consensus size: 38
40122525 TCAATCATGC
* * *
40122535 ACTGGGCCGTAGCCCTTTTCGTATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATGTTTCATATTTCATAAT
40122574 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
1 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
*
40122612 ACTGGGCCGAAG-C----C-T-TTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
40122643 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
1 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
*
40122681 ACTGGGCCAAAGCCTTT
1 ACTGGGCCGAAGCCTTT
40122698 ACTGTAAACG
Statistics
Matches: 111, Mismatches: 6, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
31 27 0.24
32 2 0.02
33 1 0.01
36 1 0.01
37 2 0.02
38 67 0.60
39 11 0.10
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (38 bp):
ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
Found at i:40122669 original size:69 final size:69
Alignment explanation
Indices: 40122558--40122697 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 69
40122548 CCTTTTCGTA
*
40122558 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAATACTGGGCCGAA
1 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAATACTGGGCCAAA
40122623 GCCT
66 GCCT
*
40122627 TTTCATATTTCATATTACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAATACTGGGCCAAA
1 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAATACTGGGCCAAA
40122692 GCCT
66 GCCT
40122696 TT
1 TT
40122698 ACTGTAAACG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (69 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAATACTGGGCCAAA
GCCT
Found at i:40122935 original size:24 final size:24
Alignment explanation
Indices: 40122889--40122983 Score: 124
Period size: 24 Copynumber: 4.0 Consensus size: 24
40122879 GTTTTATCAT
*
40122889 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
40122914 ATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGGGG-CATAAGCCCTTTTA
40122938 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
40122961 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40122984 TCACTTCCTC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
23 25 0.39
24 26 0.41
25 13 0.20
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:40122968 original size:47 final size:49
Alignment explanation
Indices: 40122889--40122982 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 49
40122879 GTTTTATCAT
*
40122889 ATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGGAGGCATAGCCTCTTTTAATAACTGGGG-CATAAGCCCTTTCA
40122938 ATAACTGG-GGCATAAGCC-CTTTT-ATAACTGGGGCATAAGCCCTTT
1 ATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCATAAGCCCTTT
40122983 TTCACTTCCT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
46 2 0.05
47 19 0.45
48 9 0.21
49 12 0.29
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (49 bp):
ATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:40123059 original size:20 final size:20
Alignment explanation
Indices: 40123034--40123093 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
40123024 TATGATTACC
40123034 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
40123054 TCATGTGCGTATCATACATT
1 TCATGTGCATATCATACATA
40123074 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
40123094 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:40123168 original size:25 final size:25
Alignment explanation
Indices: 40123136--40123183 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40123126 ATACATAAAC
* * *
40123136 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
40123161 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
40123184 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:40130879 original size:44 final size:42
Alignment explanation
Indices: 40130800--40130904 Score: 138
Period size: 44 Copynumber: 2.5 Consensus size: 42
40130790 TCCCAGATAG
* * * * *
40130800 GGTCTTACACGAACTCATATATGATGCTAATGTCCCAAACAT
1 GGTCTTACACGAAATCACAAATGATGCCAACGTCCCAAACAT
*
40130842 GGTCTTACACGTAAATCACAAATTGATGCCAACGTCCCAAACGT
1 GGTCTTACACG-AAATCACAAA-TGATGCCAACGTCCCAAACAT
40130886 GGTCTTACACGAAATCACA
1 GGTCTTACACGAAATCACA
40130905 TATCAAAATC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 11 0.20
43 15 0.27
44 29 0.53
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (42 bp):
GGTCTTACACGAAATCACAAATGATGCCAACGTCCCAAACAT
Found at i:40137238 original size:12 final size:12
Alignment explanation
Indices: 40137221--40137245 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40137211 AGAGAATGAT
40137221 TGCAAAATACAA
1 TGCAAAATACAA
40137233 TGCAAAATACAA
1 TGCAAAATACAA
40137245 T
1 T
40137246 TAACATGAGT
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:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (12 bp):
TGCAAAATACAA
Found at i:40141552 original size:2 final size:2
Alignment explanation
Indices: 40141545--40141583 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
40141535 TTTAAATACA
40141545 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
40141584 TTTATTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:40142568 original size:21 final size:20
Alignment explanation
Indices: 40142525--40142573 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
40142515 TGAAACAGGG
* *
40142525 AACACGCCCGTGTGGTGGGC
1 AACACGCCCGTATGGTAGGC
40142545 AACACGCCCGTATGGATAGGC
1 AACACGCCCGTATGG-TAGGC
40142566 AACACGCC
1 AACACGCC
40142574 TGTGTGGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.24, C:0.33, G:0.31, T:0.12
Consensus pattern (20 bp):
AACACGCCCGTATGGTAGGC
Found at i:40142581 original size:21 final size:21
Alignment explanation
Indices: 40142525--40142581 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
40142515 TGAAACAGGG
*
40142525 AACACGCCCGTGTGG-TGGGC
1 AACACGCCCGTGTGGATAGGC
*
40142545 AACACGCCCGTATGGATAGGC
1 AACACGCCCGTGTGGATAGGC
*
40142566 AACACGCCTGTGTGGA
1 AACACGCCCGTGTGGA
40142582 ACTTGAACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.23, C:0.28, G:0.33, T:0.16
Consensus pattern (21 bp):
AACACGCCCGTGTGGATAGGC
Found at i:40143891 original size:50 final size:49
Alignment explanation
Indices: 40143778--40143908 Score: 158
Period size: 50 Copynumber: 2.7 Consensus size: 49
40143768 CATCAAGTCA
*
40143778 ATGCCATGTCCCAAACATGGTCTTACACTAACTATCGAAATCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAACTATCGAAATCGAGGCCG
* * * * * *
40143827 ACGCCATGTCCCAGACATGGTCTTACATTAGCTTTC-ACATATTCG-TGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAACTATCGA-A-A-TCGAGGCCG
40143877 ATGCCATGTCCCAGACATGGTCTTACACTAAC
1 ATGCCATGTCCCAGACATGGTCTTACACTAAC
40143909 ACCTCTATAC
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 32 0.46
50 33 0.48
51 3 0.04
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAACTATCGAAATCGAGGCCG
Found at i:40144024 original size:46 final size:47
Alignment explanation
Indices: 40143932--40144095 Score: 146
Period size: 46 Copynumber: 3.6 Consensus size: 47
40143922 CCAATGCTAT
* *
40143932 TTCCTAGACATGGTCTTACACTGAC--ACATCTCGTAGCTGATACATG
1 TTCCTAGACATGGTCTTACACTGGCTTACATCTCG-AGCTGATGCATG
*
40143978 TTCC-AGACAT-GTCTTACACTGGCTTACATCTCGAGGCCGATGCATG
1 TTCCTAGACATGGTCTTACACTGGCTTACATCTCGA-GCTGATGCATG
* * * * * *
40144024 -TCCCAGATAT-GTCTTACACTAGCTCT-CGTCTCAATTCTGATGCCATG
1 TTCCTAGACATGGTCTTACACTGGCT-TACATCTCGA-GCTGATG-CATG
40144071 -TCCTAGACATGGTCTTACACTGGCT
1 TTCCTAGACATGGTCTTACACTGGCT
40144096 CTCATAATGT
Statistics
Matches: 98, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
44 12 0.12
45 10 0.10
46 50 0.51
47 13 0.13
48 13 0.13
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (47 bp):
TTCCTAGACATGGTCTTACACTGGCTTACATCTCGAGCTGATGCATG
Found at i:40145900 original size:91 final size:90
Alignment explanation
Indices: 40145725--40145902 Score: 232
Period size: 90 Copynumber: 2.0 Consensus size: 90
40145715 GGTGGTCTAT
* * * * * **
40145725 CCACATATTATCTGACAGCTTTTATCTGCAATTAAGTTGTGTATTCAAACCATCTGGTAGTGTAT
1 CCACATATTATATGAAAGCTTTTATCTGCAATTAAGTTGTATACTCAAACCATCTGGCAGCATAT
*
40145790 TAACTTGCAACTTTAGGTGGTTCGC
66 TAACCTGCAACTTTAGGTGGTTCGC
* * *
40145815 CCACCTATTATATGAAAGCTTTTATCTGTAATTATGTTGTATACTCACAACCATCTGGCAGCATA
1 CCACATATTATATGAAAGCTTTTATCTGCAATTAAGTTGTATACTCA-AACCATCTGGCAGCATA
40145880 TTAACCTGCAACATTT-GGTGGTT
65 TTAACCTGCAAC-TTTAGGTGGTT
40145903 TATCCACAAC
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
90 40 0.53
91 32 0.43
92 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (90 bp):
CCACATATTATATGAAAGCTTTTATCTGCAATTAAGTTGTATACTCAAACCATCTGGCAGCATAT
TAACCTGCAACTTTAGGTGGTTCGC
Found at i:40148160 original size:137 final size:139
Alignment explanation
Indices: 40148003--40148261 Score: 323
Period size: 137 Copynumber: 1.9 Consensus size: 139
40147993 ACTTTTTGTT
** *
40148003 TTTTTTTAACACATTAGCTTCTTT-GTTTAGATGGTTAAATGTTAGTGGTTTTGTCT-TTGAATC
1 TTTTTTTAACACATTAGCTTCTTTAG-TTAGATGGTTAAATAATAGTGATTTT-TCTCTTGAATC
* ** *
40148066 TCTAGTTTGATTC-TCTTT-TACTCACATTTG-TTTTTTTATTCCAT-TTGTTTCAAGCTTAATT
64 TCAAGTTTGATTCAT-TTTCTAAGCACATTTGCATTTTTTATTCCATGTT-TTTCAAGCTTAATT
40148127 TTTTTTATATAAC
127 TTTTTTATATAAC
** * * *
40148140 TTTTTTTAACATGTTAGCTTCTTTAGTTAGATGGTTAATTAATAGTGATTTTTTTCTTGAGTCTC
1 TTTTTTTAACACATTAGCTTCTTTAGTTAGATGGTTAAATAATAGTGATTTTTCTCTTGAATCTC
*
40148205 AAGTTTGATTCATTTTCTAAGCACATTTGCATTTTTTATTTCATGTTTTTCAAGCTT
66 AAGTTTGATTCATTTTCTAAGCACATTTGCATTTTTTATTCCATGTTTTTCAAGCTT
40148262 TTTTTAATTA
Statistics
Matches: 103, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
136 2 0.02
137 65 0.63
138 12 0.12
139 22 0.21
140 2 0.02
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.54
Consensus pattern (139 bp):
TTTTTTTAACACATTAGCTTCTTTAGTTAGATGGTTAAATAATAGTGATTTTTCTCTTGAATCTC
AAGTTTGATTCATTTTCTAAGCACATTTGCATTTTTTATTCCATGTTTTTCAAGCTTAATTTTTT
TTATATAAC
Found at i:40148362 original size:25 final size:24
Alignment explanation
Indices: 40148328--40148389 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
40148318 CTTTTTAATT
* *
40148328 AATAACTATTTTATTTATAAAATCA
1 AATAAATATTTTAATTATAAAAT-A
* *
40148353 AATAATTATTGTTAATTATATAATA
1 AATAAATATT-TTAATTATAAAATA
*
40148378 AAAAAATATTTT
1 AATAAATATTTT
40148390 TGATAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 2 0.06
25 18 0.58
26 11 0.35
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (24 bp):
AATAAATATTTTAATTATAAAATA
Found at i:40148664 original size:16 final size:16
Alignment explanation
Indices: 40148624--40148665 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
40148614 ATATTTGGAA
*
40148624 ATAATTATAAGATTTT
1 ATAATTAAAAGATTTT
*
40148640 ATAAATAAAAGA-TTT
1 ATAATTAAAAGATTTT
40148655 ATTAATTAAAA
1 A-TAATTAAAA
40148666 ATATGAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
ATAATTAAAAGATTTT
Found at i:40150339 original size:35 final size:35
Alignment explanation
Indices: 40150300--40150370 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
40150290 TTTAGACTCT
*
40150300 TGCAAGTAAGTGATTTTGATGGTCTTCCTTGATGA
1 TGCAAGTAAGTGATTTTGACGGTCTTCCTTGATGA
* *
40150335 TGCAAGTAAGTGATTTTTACGGTCTTTCTTGATGA
1 TGCAAGTAAGTGATTTTGACGGTCTTCCTTGATGA
40150370 T
1 T
40150371 TTTTTGTACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (35 bp):
TGCAAGTAAGTGATTTTGACGGTCTTCCTTGATGA
Found at i:40151138 original size:48 final size:47
Alignment explanation
Indices: 40151056--40151242 Score: 196
Period size: 48 Copynumber: 3.9 Consensus size: 47
40151046 ATACTAGGGT
* * * * *
40151056 TATGTGAGCCAGTGTAAGACCATATTTTGAACATGGCATCGACATTTA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGAC-CTTA
* * *
40151104 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-AGCCTCA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGA-CCTTA
* * * *
40151151 TTATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCACCGATA
1 -TATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATC-G-ACC-TTA
*
40151202 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 TATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCG
40151243 TCATCTTACC
Statistics
Matches: 116, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
47 3 0.03
48 72 0.62
49 1 0.01
50 38 0.33
51 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (47 bp):
TATGAGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGACCTTA
Found at i:40151236 original size:98 final size:96
Alignment explanation
Indices: 40151055--40151241 Score: 293
Period size: 98 Copynumber: 1.9 Consensus size: 96
40151045 GATACTAGGG
* ** *
40151055 TTATGTGAGCCAGTGTAAGACCATATTTTGAACATGGCATCGACATTTATATGAGAGCTAGTGTA
1 TTATGTGAGCCAGTGTAAGACCATATTTGGAACATGGCATCGACAGATATATGAGAGCCAGTGTA
40151120 AGACCATGTCTGGGACATGGCATCAGCCTCA
66 AGACCATGTCTGGGACATGGCATCAGCCTCA
* * *
40151151 TTATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCACCGATATATGAGAGCCAGTG
1 TTATGTGAGCCAGTGTAAGACCATATTTGGAACATGGCATC-G-ACAGATATATGAGAGCCAGTG
40151216 TAAGACCATGTCTGGGACATGGCATC
64 TAAGACCATGTCTGGGACATGGCATC
40151242 GTCATCTTAC
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
96 38 0.46
97 1 0.01
98 43 0.52
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (96 bp):
TTATGTGAGCCAGTGTAAGACCATATTTGGAACATGGCATCGACAGATATATGAGAGCCAGTGTA
AGACCATGTCTGGGACATGGCATCAGCCTCA
Found at i:40151947 original size:6 final size:6
Alignment explanation
Indices: 40151936--40151961 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40151926 TGTGTTTATG
40151936 TGGTAT TGGTAT TGGTAT TGGTAT TG
1 TGGTAT TGGTAT TGGTAT TGGTAT TG
40151962 TTTGATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
TGGTAT
Found at i:40161708 original size:27 final size:27
Alignment explanation
Indices: 40161672--40161839 Score: 185
Period size: 27 Copynumber: 6.2 Consensus size: 27
40161662 GGCTTAAATG
*
40161672 ATGACTGAAATACCCCTACAGGGTAAA
1 ATGACTGAAATACCCCTATAGGGTAAA
* *
40161699 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACTGAAATACCCCTATAGGGTAAA
*
40161726 ATGA-TCGAAATACCCCTATAAGGTAAA
1 ATGACT-GAAATACCCCTATAGGGTAAA
* * * *
40161753 ATGACTGTAATGCCCCTGTATGGTAAA
1 ATGACTGAAATACCCCTATAGGGTAAA
* * *
40161780 ATAACTGTAATACCCTTATAGGGTAAA
1 ATGACTGAAATACCCCTATAGGGTAAA
* * * *
40161807 ATCACTGTAATACCCCTGTAAGGTAAA
1 ATGACTGAAATACCCCTATAGGGTAAA
40161834 ATGACT
1 ATGACT
40161840 AATTTTCCCT
Statistics
Matches: 119, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
27 118 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (27 bp):
ATGACTGAAATACCCCTATAGGGTAAA
Found at i:40164113 original size:13 final size:13
Alignment explanation
Indices: 40164095--40164121 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40164085 TATATCTGTA
40164095 TCTGTATCTATTT
1 TCTGTATCTATTT
40164108 TCTGTATCTATTT
1 TCTGTATCTATTT
40164121 T
1 T
40164122 GGGGTGGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (13 bp):
TCTGTATCTATTT
Found at i:40164337 original size:13 final size:12
Alignment explanation
Indices: 40164318--40164356 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
40164308 AGGATTTTGA
40164318 TTATCTGATCTG
1 TTATCTGATCTG
40164330 TATATCTGACTCTG
1 T-TATCTGA-TCTG
40164344 TTATCTGTATCTG
1 TTATCTG-ATCTG
40164357 AAGTGGGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 17 0.71
14 6 0.25
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (12 bp):
TTATCTGATCTG
Found at i:40183120 original size:26 final size:26
Alignment explanation
Indices: 40183084--40183133 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
40183074 ATTCTACACC
* * *
40183084 TAGGGGTATTTTGGTTATTTTTCCCT
1 TAGGGGCATTTCGGTAATTTTTCCCT
40183110 TAGGGGCATTTCGGTAATTTTTCC
1 TAGGGGCATTTCGGTAATTTTTCC
40183134 ATAATTACGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.48
Consensus pattern (26 bp):
TAGGGGCATTTCGGTAATTTTTCCCT
Found at i:40183477 original size:29 final size:29
Alignment explanation
Indices: 40183409--40183544 Score: 168
Period size: 29 Copynumber: 4.7 Consensus size: 29
40183399 CAATTTCACA
* *
40183409 CACCTGTATTTGGCCCATTAAGCCC-AAT
1 CACCTGTATATGGCCCATTAGGCCCAAAT
***
40183437 CGTAT-TCATATGGCCCATTAGGCCCAAAT
1 CACCTGT-ATATGGCCCATTAGGCCCAAAT
40183466 CACCTGTATATGGCCCATTAGGCCCAAAT
1 CACCTGTATATGGCCCATTAGGCCCAAAT
40183495 CACCTGTATATGGCCCATTAGGCCCAAAT
1 CACCTGTATATGGCCCATTAGGCCCAAAT
* * * *
40183524 CACATTTATATAGCCCGTTAG
1 CACCTGTATATGGCCCATTAG
40183545 ACCTAGTCAC
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
27 1 0.01
28 18 0.19
29 73 0.78
30 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
CACCTGTATATGGCCCATTAGGCCCAAAT
Found at i:40183526 original size:58 final size:57
Alignment explanation
Indices: 40183409--40183561 Score: 173
Period size: 58 Copynumber: 2.7 Consensus size: 57
40183399 CAATTTCACA
* * **
40183409 CACCTGTATTTGGCCCATTAAGCCCAATCGTATTCATATGGCCCATTAGGCCCAAAT
1 CACCTGTATATGGCCCATTAGGCCCAATCACATTCATATGGCCCATTAGGCCCAAAT
*
40183466 CACCTGTATATGGCCCATTAGGCCCAAATCACCTGT-ATATGGCCCATTAGGCCCAAAT
1 CACCTGTATATGGCCCATTAGGCCC-AATCACAT-TCATATGGCCCATTAGGCCCAAAT
* * * * * * *
40183524 CACATTTATATAGCCCGTTAGACCTAGTCACATTCATA
1 CACCTGTATATGGCCCATTAGGCCCAATCACATTCATA
40183562 ATCATGCTCA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
56 1 0.01
57 32 0.40
58 46 0.57
59 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.27
Consensus pattern (57 bp):
CACCTGTATATGGCCCATTAGGCCCAATCACATTCATATGGCCCATTAGGCCCAAAT
Found at i:40183643 original size:17 final size:18
Alignment explanation
Indices: 40183621--40183666 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
40183611 TGCCTATTAT
40183621 GGGCCCA-ATAGCCCATC
1 GGGCCCATATAGCCCATC
*
40183638 GGGCCCATTTAGCCCATTC
1 GGGCCCATATAGCCCA-TC
*
40183657 TGGCCCATAT
1 GGGCCCATAT
40183667 GGCCAAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 10 0.42
ACGTcount: A:0.20, C:0.37, G:0.22, T:0.22
Consensus pattern (18 bp):
GGGCCCATATAGCCCATC
Found at i:40184908 original size:16 final size:16
Alignment explanation
Indices: 40184887--40184936 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
40184877 AGAAAGTTCA
40184887 GGATTTCGGGATTTTT
1 GGATTTCGGGATTTTT
40184903 GGATTTCGGGATTTTT
1 GGATTTCGGGATTTTT
* *
40184919 GGGTTTCAGGATTTTT
1 GGATTTCGGGATTTTT
40184935 GG
1 GG
40184937 GGCGTTACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.12, C:0.06, G:0.34, T:0.48
Consensus pattern (16 bp):
GGATTTCGGGATTTTT
Found at i:40186895 original size:24 final size:24
Alignment explanation
Indices: 40186868--40186944 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
40186858 TTACCAATCA
40186868 ATCAATCAATGCAACAACATTAGT
1 ATCAATCAATGCAACAACATTAGT
40186892 ATC-AT-AGA-G-AGA-AAGTCGATCTAGT
1 ATCAATCA-ATGCA-ACAA--C-AT-TAGT
40186917 ATCAATCAATGCAACAACATTAGT
1 ATCAATCAATGCAACAACATTAGT
40186941 ATCA
1 ATCA
40186945 TAGAGAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 22
0.66 0.00 0.34
Matches are distributed among these distances:
21 3 0.07
22 3 0.07
23 4 0.10
24 13 0.31
25 9 0.21
26 4 0.10
27 3 0.07
28 3 0.07
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCAATCAATGCAACAACATTAGT
Found at i:40189965 original size:16 final size:16
Alignment explanation
Indices: 40189944--40189999 Score: 112
Period size: 16 Copynumber: 3.5 Consensus size: 16
40189934 CTAAAACAGG
40189944 GGTCACACGCTTGTGT
1 GGTCACACGCTTGTGT
40189960 GGTCACACGCTTGTGT
1 GGTCACACGCTTGTGT
40189976 GGTCACACGCTTGTGT
1 GGTCACACGCTTGTGT
40189992 GGTCACAC
1 GGTCACAC
40190000 ACACCTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (16 bp):
GGTCACACGCTTGTGT
Found at i:40191206 original size:17 final size:17
Alignment explanation
Indices: 40191181--40191221 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
40191171 AGGAAGAAAG
40191181 GAAACAGAGAATGAGAC
1 GAAACAGAGAATGAGAC
*
40191198 GAAAGAGAGAATGAGAC
1 GAAACAGAGAATGAGAC
40191215 GAAACAG
1 GAAACAG
40191222 GGGAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.10, G:0.32, T:0.05
Consensus pattern (17 bp):
GAAACAGAGAATGAGAC
Found at i:40193382 original size:46 final size:46
Alignment explanation
Indices: 40193330--40193559 Score: 370
Period size: 46 Copynumber: 5.0 Consensus size: 46
40193320 AGTGTGCTCT
40193330 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
40193376 CTGATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
40193422 CTGATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
40193468 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * **
40193514 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
40193560 ATGACAGAAA
Statistics
Matches: 177, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 177 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:40193565 original size:46 final size:46
Alignment explanation
Indices: 40193331--40193612 Score: 341
Period size: 46 Copynumber: 6.0 Consensus size: 46
40193321 GTGTGCTCTC
** *
40193331 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
** * *
40193377 TGATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
** * *
40193423 TGATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
*
40193469 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* *
40193515 TGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
40193561 TGACA-GAAAATGAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGATATG-AAATG-A--A-TAAGACCATGGTTGAAAGATACCATGGCAACA
40193611 TG
1 TG
40193613 TCAAAGATAA
Statistics
Matches: 218, Mismatches: 13, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
45 1 0.00
46 185 0.85
47 1 0.00
49 1 0.00
50 30 0.14
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:40195324 original size:43 final size:43
Alignment explanation
Indices: 40195263--40195350 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
40195253 TGAATAAAAC
*
40195263 ATGTTATATCATAACTCAATTTGGCCCGAAAACCAATTACACA
1 ATGTTATATCACAACTCAATTTGGCCCGAAAACCAATTACACA
40195306 ATGTTATATCACAACTCAATTTGGCCCGAAAACCAATTACACA
1 ATGTTATATCACAACTCAATTTGGCCCGAAAACCAATTACACA
40195349 AT
1 AT
40195351 CGCCAACTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (43 bp):
ATGTTATATCACAACTCAATTTGGCCCGAAAACCAATTACACA
Found at i:40195651 original size:42 final size:42
Alignment explanation
Indices: 40195540--40195690 Score: 207
Period size: 42 Copynumber: 3.6 Consensus size: 42
40195530 TACTGTACCA
* * **
40195540 ATGCCATATCCTAGATATGGTCTTACATGTTATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
40195582 ATGTCAATAACCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATG-CCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
*
40195625 ACGCCATATCCCAGATATGGTCTTACACGAAATCTCATA-CG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
40195666 ATGCCATATCCCA-ATATGGTCTTAC
1 ATGCCATATCCCAGATATGGTCTTAC
40195691 GCGTAGTCTT
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
40 12 0.12
41 14 0.15
42 36 0.38
43 34 0.35
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:40206120 original size:40 final size:40
Alignment explanation
Indices: 40206039--40206216 Score: 272
Period size: 40 Copynumber: 4.5 Consensus size: 40
40206029 AAACCAAGTA
* * * *
40206039 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCACACAAATG
40206078 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
*
40206118 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
40206158 CCTTCGGGACTTAGCCCGGATATAGTAACT-AGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCA-CACAAATG
40206198 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40206217 TTATCATCCG
Statistics
Matches: 130, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
39 14 0.11
40 116 0.89
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
Found at i:40214042 original size:40 final size:40
Alignment explanation
Indices: 40213972--40214145 Score: 291
Period size: 40 Copynumber: 4.4 Consensus size: 40
40213962 AAACCAAGTA
* * *
40213972 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
40214011 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40214051 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40214091 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40214131 CCTTC-GGACTTAGCC
1 CCTTCGGGACTTAGCC
40214146 GGTTATCATC
Statistics
Matches: 130, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
39 24 0.18
40 106 0.82
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40221960 original size:40 final size:40
Alignment explanation
Indices: 40221890--40222027 Score: 226
Period size: 40 Copynumber: 3.5 Consensus size: 40
40221880 AAACCAAGTA
* * *
40221890 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
40221929 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40221969 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40222009 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40222028 TTATCATCCG
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
39 14 0.15
40 80 0.85
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40224364 original size:44 final size:44
Alignment explanation
Indices: 40224301--40224473 Score: 206
Period size: 44 Copynumber: 3.8 Consensus size: 44
40224291 TGTAACCCGC
*
40224301 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGTTCGCAT
* *
40224345 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGTTCGC-A--T
* * * *
40224391 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GTTCGCAT
40224438 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
40224474 ATGCCAATCC
Statistics
Matches: 108, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 38 0.35
45 2 0.02
46 31 0.29
47 31 0.29
48 2 0.02
49 2 0.02
50 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGTTCGCAT
Found at i:40224466 original size:93 final size:91
Alignment explanation
Indices: 40224309--40224478 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 91
40224299 GCCCATAAGT
*
40224309 GAACTCGGACTCAACTCAACGAGCTCGGGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 GAACTCGGACTCAACTCAACGAGCTCGGGCTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
40224374 AGTTCGGATGCCTAGTTACATCTCAC
66 AGTTCGGATGCCTAGTTACATCTCAC
*
40224400 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG--GCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40224465 CGAGTTCGGATGCC
64 CGAGTTCGGATGCC
40224479 AATCCTAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 27 0.36
93 48 0.64
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGGCTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCAC
Found at i:40227578 original size:13 final size:13
Alignment explanation
Indices: 40227560--40227585 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40227550 TTAACATTCA
40227560 GGAAGATTCACTT
1 GGAAGATTCACTT
40227573 GGAAGATTCACTT
1 GGAAGATTCACTT
40227586 CTGTCCCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GGAAGATTCACTT
Found at i:40230760 original size:29 final size:29
Alignment explanation
Indices: 40230728--40230786 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
40230718 TTTGAGCTTT
40230728 GGGGAAAAAGTGTAAATATGCAAAAGTTA
1 GGGGAAAAAGTGTAAATATGCAAAAGTTA
* * * *
40230757 GGGGCAAAATTGTAATTTTGCAAAAGTTA
1 GGGGAAAAAGTGTAAATATGCAAAAGTTA
40230786 G
1 G
40230787 AGTTAAGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.27, T:0.25
Consensus pattern (29 bp):
GGGGAAAAAGTGTAAATATGCAAAAGTTA
Found at i:40232335 original size:27 final size:27
Alignment explanation
Indices: 40232305--40232587 Score: 165
Period size: 27 Copynumber: 10.4 Consensus size: 27
40232295 ATTACTAAAG
* * * * *
40232305 TACCCCCGATTTACAGAATTATCGTTC
1 TACCCTCGATTTATAGAATTACCATTT
40232332 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
40232359 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* * ***
40232386 TACCCTCGATTTATAAAATTACTAAAA
1 TACCCTCGATTTATAGAATTACCATTT
* * * * ***
40232413 TA-CCTCTGGTTTGTAAAATTACTAAAA
1 TACCCTC-GATTTATAGAATTACCATTT
* * * * * ***
40232440 TACCCCCTGATTTGTAAAATCACTAAAA
1 TACCCTC-GATTTATAGAATTACCATTT
* * ***
40232468 TACCCTTGACTTGTA-AAAATTACCAAAG
1 TACCCTCGA-TT-TATAGAATTACCATTT
**
40232496 TACCCTCGATTTATAGAATTATTATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
40232523 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTATAGAATTACCATTT
* * * **
40232550 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
40232577 TACCCTCGATT
1 TACCCTCGATT
40232588 GTGAAATTAC
Statistics
Matches: 217, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
26 6 0.03
27 163 0.75
28 47 0.22
29 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCATTT
Found at i:40232464 original size:28 final size:27
Alignment explanation
Indices: 40232388--40232753 Score: 163
Period size: 27 Copynumber: 13.4 Consensus size: 27
40232378 TACCATTTTA
*
40232388 CCCTCGATTTATAAAATTACTAAAATAC
1 CCCT-GATTTGTAAAATTACTAAAATAC
* *
40232416 CTCTGGTTTGTAAAATTACTAAAATACC
1 CCCTGATTTGTAAAATTACTAAAATA-C
*
40232444 CCCTGATTTGTAAAATCACTAAAATAC
1 CCCTGATTTGTAAAATTACTAAAATAC
* * * *
40232471 CCTTGACTTGTAAAAATTACCAAAGTA-
1 CCCTGATTTGT-AAAATTACTAAAATAC
* * * ***
40232498 CCCTCGATTTATAGAATTATTATTTTA-
1 CCCT-GATTTGTAAAATTACTAAAATAC
** * ***
40232525 CCCTCGATTTACAGAATTACTATTTTAC
1 CCCT-GATTTGTAAAATTACTAAAATAC
* ** ****
40232553 CCTTGATTTACAAAATTACTGTTTTA-
1 CCCTGATTTGTAAAATTACTAAAATAC
* *
40232579 CCCTCGA-TTGTGAAATTACTGAAATAC
1 CCCT-GATTTGTAAAATTACTAAAATAC
** * * *
40232606 CCCT-ATAGGGTAGAATTACCAAAACAC
1 CCCTGAT-TTGTAAAATTACTAAAATAC
*
40232633 CCCT-AGTTTGTAAAATTACCAAAATAC
1 CCCTGA-TTTGTAAAATTACTAAAATAC
* * * **
40232660 CACTGGTTTGTGAAATTACCGAAATA-
1 CCCTGATTTGTAAAATTACTAAAATAC
* *
40232686 CCCTCAATTTGTAAAATTACCAAAATAC
1 CCCT-GATTTGTAAAATTACTAAAATAC
* **
40232714 CCCTAATTTACAAAAATTAC-AGAAATAC
1 CCCTGATTT-GTAAAATTACTA-AAATAC
*
40232742 CCTTGATTTGTA
1 CCCTGATTTGTA
40232754 GATTTACCAA
Statistics
Matches: 266, Mismatches: 58, Indels: 29
0.75 0.16 0.08
Matches are distributed among these distances:
25 1 0.00
26 19 0.07
27 173 0.65
28 73 0.27
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.33
Consensus pattern (27 bp):
CCCTGATTTGTAAAATTACTAAAATAC
Done.