Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 140 of 208
Found at i:45629521 original size:43 final size:46
Alignment explanation
Indices: 45629405--45629524 Score: 128
Period size: 45 Copynumber: 2.7 Consensus size: 46
45629395 TTGGATTTAA
45629405 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCCACCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTCGCCACCTTCAG
** *
45629450 TCTGC-CTCACTGCAACTTCA-AAAGGATAAGACTT-GCTTA-CTT-AG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTCGC-CACCTTCAG
*
45629494 TC-GCTCCACTGCAACCTCAGGGAGATAAGAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAC
45629525 CTGATATCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
43 22 0.35
44 8 0.13
45 30 0.48
46 3 0.05
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (46 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTCGCCACCTTCAG
Found at i:45630107 original size:100 final size:100
Alignment explanation
Indices: 45629732--45630089 Score: 475
Period size: 100 Copynumber: 3.6 Consensus size: 100
45629722 CTAGGGAGAT
* * ** * * * * *
45629732 AAGATTCGCCGTCGTGGCTTCAATCTGCTCTGCTACAATGCCAGGGAAATGAGATTCGCCATTGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAAGGAAGTAAGATTCGCCATTGC
* *
45629797 GGCTTCGATCTTTTTAATTGCAATGTTGGGAAAAC
66 GGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
* * * *
45629832 AAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAGGAAGTAATATTCGCCGTTGC
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAAGGAAGTAAGATTCGCCATTGC
* *
45629897 GGCTTCAATATTTTTAATTGCAATTTTGGGGAAAC
66 GGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
* * * * *
45629932 AAGATTCGTCATCGTAGCTTCAATCTGTTCCATTACA-TCGCCAATGAAGTAAGATTTGCCATTG
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACT-GCCAAGGAAGTAAGATTCGCCATTG
45629996 CGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
65 CGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
* * *
45630032 GAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAGGGGAGTAAGATTCG
1 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAAGGAAGTAAGATTCG
45630090 TCGTCGTAGT
Statistics
Matches: 220, Mismatches: 36, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
100 219 1.00
101 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (100 bp):
AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAAGGAAGTAAGATTCGCCATTGC
GGCTTCAATCTTTTTAATTGCAATGTTGGGGAAAC
Found at i:45631787 original size:14 final size:15
Alignment explanation
Indices: 45631764--45631796 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
45631754 ATCGATGCTT
*
45631764 TTCCAGATAAGG-CC
1 TTCCACATAAGGTCC
45631778 TTCCACATAAGGTCC
1 TTCCACATAAGGTCC
45631793 TTCC
1 TTCC
45631797 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.27
Consensus pattern (15 bp):
TTCCACATAAGGTCC
Found at i:45634234 original size:40 final size:40
Alignment explanation
Indices: 45634151--45634373 Score: 213
Period size: 40 Copynumber: 5.6 Consensus size: 40
45634141 TTGAATGCTG
* * * * *
45634151 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGA-T-ACTAAA
* * *
45634191 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGATACTAAA
* **
45634231 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
**
45634271 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGA-ATTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGA-TACTAAA
* * *
45634311 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
* *
45634350 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
45634374 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
39 34 0.21
40 114 0.72
41 10 0.06
42 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
Found at i:45634288 original size:80 final size:79
Alignment explanation
Indices: 45634151--45634375 Score: 242
Period size: 80 Copynumber: 2.8 Consensus size: 79
45634141 TTGAATGCTG
* * * * * *
45634151 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAG-TGAATATATCCGGATTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTG-ATAAATCCGGGTTAAG-TCCCGAAGGCAT
45634214 TTGTGCGAGA-TACTAAA
63 TTGTGCGA-ATTACTAAA
* *
45634231 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTGATAAATCCGGGTTAAGTCCCGAAGGCATTT
**
45634296 GTGCGAATTGTTAAA
65 GTGCGAATTACTAAA
* * * *
45634311 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTT-ACTAAATCCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTGA-TAAATCCGGGTTAAGTCCCGAAGGCATTT
45634375 G
65 G
45634376 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
79 37 0.30
80 81 0.65
81 6 0.05
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTGATAAATCCGGGTTAAGTCCCGAAGGCATTTG
TGCGAATTACTAAA
Found at i:45634393 original size:79 final size:80
Alignment explanation
Indices: 45634226--45634408 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
45634216 GTGCGAGATA
** *
45634226 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGG
** **
45634291 CATTCGTGCGAATTG
66 CATTCGAACGAAGAG
* * * *
45634306 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGG
* *
45634370 CATTTGAACGAGGAG
66 CATTCGAACGAAGAG
* *
45634385 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
45634409 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGG
CATTCGAACGAAGAG
Found at i:45634393 original size:119 final size:120
Alignment explanation
Indices: 45634151--45634408 Score: 281
Period size: 119 Copynumber: 2.2 Consensus size: 120
45634141 TTGAATGCTG
* * * * *
45634151 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTTT
1 TCCGGGTTAAGTCCCGAAGGCTTCGTGCGAAGTGAATAAATCCGGATTAAGATCCGAAGGCCATT
* ** ** *
45634216 GTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
66 GTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTAAA
* * * *
45634271 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAATTG-TTAAATCCGGGTTATG-TCCCGAAGG-CA
1 TCCGGGTTAAGTCCCGAAGGC-TTCGTGCGAAGTGAATAAATCCGGATTAAGAT-CCGAAGGCCA
* * * * *
45634333 TTGTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATA
64 TTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTAAA
*
45634390 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
45634409 TACGTGATTT
Statistics
Matches: 115, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
118 15 0.13
119 51 0.44
120 39 0.34
121 10 0.09
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTCGTGCGAAGTGAATAAATCCGGATTAAGATCCGAAGGCCATT
GTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTAAA
Found at i:45647808 original size:20 final size:20
Alignment explanation
Indices: 45647785--45647829 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
45647775 ATTTATTTAT
45647785 TAAAATAATAAT-TCAATAAA
1 TAAAATAATAATCT-AATAAA
*
45647805 TAAAATAATAATCTTATAAA
1 TAAAATAATAATCTAATAAA
45647825 TAAAA
1 TAAAA
45647830 CTTTAAGCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAATAATAATCTAATAAA
Found at i:45658420 original size:37 final size:37
Alignment explanation
Indices: 45658370--45658448 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
45658360 TTATTACGAA
* * *
45658370 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
45658407 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
45658444 GTCTT
1 GTCTT
45658449 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:45658645 original size:47 final size:47
Alignment explanation
Indices: 45658567--45658875 Score: 438
Period size: 47 Copynumber: 6.7 Consensus size: 47
45658557 CCCTTCGGGA
* ** * * * *
45658567 CTTATCACATTTATACACTTTCACACCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45658614 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45658661 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45658708 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45658755 CTTATCACATATATACACTTTCACATTCATCACATCGGCC---A---
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45658796 --TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45658841 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
45658876 AGAATCCTAA
Statistics
Matches: 238, Mismatches: 15, Indels: 18
0.88 0.06 0.07
Matches are distributed among these distances:
39 38 0.16
42 1 0.00
44 1 0.00
46 1 0.00
47 197 0.83
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:45658807 original size:86 final size:86
Alignment explanation
Indices: 45658705--45658875 Score: 290
Period size: 86 Copynumber: 2.0 Consensus size: 86
45658695 TCGGCCATTA
* *
45658705 GGCCTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATA
1 GGCCATATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
*
45658770 CACT-TTCACATTCATCACATC
66 CA-TGTTCACATCCATCACATC
*
45658791 GGCCATATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATG
1 GGCCATATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
45658856 CATGTTCACATCCATCACAT
66 CATGTTCACATCCATCACAT
45658876 AGAATCCTAA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
85 1 0.01
86 79 0.99
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (86 bp):
GGCCATATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
CATGTTCACATCCATCACATC
Found at i:45658811 original size:39 final size:39
Alignment explanation
Indices: 45658752--45658835 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
45658742 TCGGCCATTA
*
45658752 GGCCTTATCACATATATACACTTTCACATTCATCACATC
1 GGCCATATCACATATATACACTTTCACATTCATCACATC
45658791 GGCCATATCACATATATACACTTTCACATTCATCACATC
1 GGCCATATCACATATATACACTTTCACATTCATCACATC
45658830 GGCCAT
1 GGCCAT
45658836 TAGGCCTTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (39 bp):
GGCCATATCACATATATACACTTTCACATTCATCACATC
Found at i:45662687 original size:40 final size:40
Alignment explanation
Indices: 45662630--45662809 Score: 186
Period size: 40 Copynumber: 4.5 Consensus size: 40
45662620 CCAGCATGAT
* * *
45662630 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
* *
45662670 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
* * * *
45662710 TGCTCTTCGGAACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGAACTTAGCCCGGATATA-TCACTAGCACGAA
* * *
45662751 TGC-CTTCGGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGAACTTAGCCCGGATAT-ATCAC-TAGCACGAA
* *
45662791 AGC-CTTCGGGACTTAGCCC
1 TGCTCTTCGGAACTTAGCCC
45662810 AGACATCATT
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
40 99 0.85
41 17 0.15
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAA
Found at i:45663160 original size:29 final size:29
Alignment explanation
Indices: 45663126--45663198 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
45663116 AATCAACCAT
* *
45663126 GCACACTTAGTGCCATGTACTTT-AAACTC
1 GCACACTTAGTGCCATGCA-TTTCAAACCC
*
45663155 GCACACTTAGTGCCATGCATTTCAAGCCC
1 GCACACTTAGTGCCATGCATTTCAAACCC
45663184 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
45663199 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATGCATTTCAAACCC
Found at i:45663241 original size:43 final size:43
Alignment explanation
Indices: 45663180--45663282 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
45663170 TGCATTTCAA
45663180 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
45663223 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
45663266 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
45663283 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:45665189 original size:37 final size:37
Alignment explanation
Indices: 45665139--45665217 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
45665129 TTATTACGAA
* * *
45665139 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* *
45665176 GTCTTACCTGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
45665213 GTCTT
1 GTCTT
45665218 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:45665414 original size:47 final size:47
Alignment explanation
Indices: 45665336--45665644 Score: 438
Period size: 47 Copynumber: 6.7 Consensus size: 47
45665326 CCCTTCGGGA
* ** * * * *
45665336 CTTATCACATTTATACACTTTCACACCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45665383 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45665430 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45665477 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45665524 CTTATCACATATATACACTTTCACATTCATCACATCGGCC---A---
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45665565 --TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45665610 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
45665645 AGAATCCTAA
Statistics
Matches: 238, Mismatches: 15, Indels: 18
0.88 0.06 0.07
Matches are distributed among these distances:
39 38 0.16
42 1 0.00
44 1 0.00
46 1 0.00
47 197 0.83
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:45665576 original size:86 final size:86
Alignment explanation
Indices: 45665474--45665644 Score: 290
Period size: 86 Copynumber: 2.0 Consensus size: 86
45665464 TCGGCCATTA
* *
45665474 GGCCTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATA
1 GGCCATATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
*
45665539 CACT-TTCACATTCATCACATC
66 CA-TGTTCACATCCATCACATC
*
45665560 GGCCATATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATG
1 GGCCATATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
45665625 CATGTTCACATCCATCACAT
66 CATGTTCACATCCATCACAT
45665645 AGAATCCTAA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
85 1 0.01
86 79 0.99
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (86 bp):
GGCCATATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
CATGTTCACATCCATCACATC
Found at i:45665580 original size:39 final size:39
Alignment explanation
Indices: 45665521--45665604 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
45665511 TCGGCCATTA
*
45665521 GGCCTTATCACATATATACACTTTCACATTCATCACATC
1 GGCCATATCACATATATACACTTTCACATTCATCACATC
45665560 GGCCATATCACATATATACACTTTCACATTCATCACATC
1 GGCCATATCACATATATACACTTTCACATTCATCACATC
45665599 GGCCAT
1 GGCCAT
45665605 TAGGCCTTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (39 bp):
GGCCATATCACATATATACACTTTCACATTCATCACATC
Found at i:45668117 original size:24 final size:24
Alignment explanation
Indices: 45668090--45668141 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
45668080 TTAGTAAGTC
*
45668090 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
45668114 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
45668138 AAAT
1 AAAT
45668142 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:45670086 original size:24 final size:24
Alignment explanation
Indices: 45670059--45670110 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
45670049 TTAGTAAGTC
*
45670059 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
45670083 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
45670107 AAAT
1 AAAT
45670111 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:45673994 original size:21 final size:21
Alignment explanation
Indices: 45673955--45673995 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
45673945 CTATTAAAGC
**
45673955 CTCGAGACAAGTGGTCTTTGT
1 CTCGAGACAAGTGACCTTTGT
*
45673976 CTCGAGACAGGTGACCTTTG
1 CTCGAGACAAGTGACCTTTG
45673996 AAGCTAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (21 bp):
CTCGAGACAAGTGACCTTTGT
Found at i:45699850 original size:16 final size:17
Alignment explanation
Indices: 45699823--45699857 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
45699813 AAGCCAGCAA
45699823 AAGAAGAAAAAATTGAG
1 AAGAAGAAAAAATTGAG
45699840 AAGAA-AAAAAATTGAG
1 AAGAAGAAAAAATTGAG
45699856 AA
1 AA
45699858 AATAAGCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (17 bp):
AAGAAGAAAAAATTGAG
Found at i:45715780 original size:359 final size:359
Alignment explanation
Indices: 45715121--45715841 Score: 1406
Period size: 359 Copynumber: 2.0 Consensus size: 359
45715111 GCAAAGACCT
45715121 AACCAATCTCAGGGGTTTAATCAGCAAGCTCTAAAACCACCTCAAGCTAAGGCATCAAACAGTTT
1 AACCAATCTCAGGGGTTTAATCAGCAAGCTCTAAAACCACCTCAAGCTAAGGCATCAAACAGTTT
45715186 GGAGAACTTGTTGAAAGCGTACATGGAAAAGAATGACGTTTTGATCCAAAGCCAAGCAGCAACAC
66 GGAGAACTTGTTGAAAGCGTACATGGAAAAGAATGACGTTTTGATCCAAAGCCAAGCAGCAACAC
45715251 TGAAAAATTTGGAAAACCAAATGGGTCAGTTGGCTACGGAGCTTCGTAATAGGCTGCAAGGAACC
131 TGAAAAATTTGGAAAACCAAATGGGTCAGTTGGCTACGGAGCTTCGTAATAGGCTGCAAGGAACC
45715316 TTGCCGAGCGATACTGAGAGTCTAAGAAATTTGGGTAAAGAACATATCAAGGCAGTGGCATTGCG
196 TTGCCGAGCGATACTGAGAGTCTAAGAAATTTGGGTAAAGAACATATCAAGGCAGTGGCATTGCG
45715381 AAGTGGTAAAATTCTAGAACCCCGATTGATTAATGTCAAAGATAATCCCATTGAGAAGAATCAAT
261 AAGTGGTAAAATTCTAGAACCCCGATTGATTAATGTCAAAGATAATCCCATTGAGAAGAATCAAT
* *
45715446 CAGCTGTTGAAGTTCTTACACCAAAAGAATCAGA
326 CAACTGTTGAAGTTCTTACACCAAAAGAATCAAA
45715480 AACCAATCTCAGGGGTTTAATCAGCAAGCTCTAAAACCACCTCAAGCTAAGGCATCAAACAGTTT
1 AACCAATCTCAGGGGTTTAATCAGCAAGCTCTAAAACCACCTCAAGCTAAGGCATCAAACAGTTT
45715545 GGAGAACTTGTTGAAAGCGTACATGGAAAAGAATGACGTTTTGATCCAAAGCCAAGCAGCAACAC
66 GGAGAACTTGTTGAAAGCGTACATGGAAAAGAATGACGTTTTGATCCAAAGCCAAGCAGCAACAC
45715610 TGAAAAATTTGGAAAACCAAATGGGTCAGTTGGCTACGGAGCTTCGTAATAGGCTGCAAGGAACC
131 TGAAAAATTTGGAAAACCAAATGGGTCAGTTGGCTACGGAGCTTCGTAATAGGCTGCAAGGAACC
*
45715675 TTGCCGAGCGATACTGGGAGTCTAAGAAATTTGGGTAAAGAACATATCAAGGCAGTGGCATTGCG
196 TTGCCGAGCGATACTGAGAGTCTAAGAAATTTGGGTAAAGAACATATCAAGGCAGTGGCATTGCG
*
45715740 AAGTGGTAAAATTCTAGAACCCCGATTGATTGATGTCAAAGATAATCCCATTGAGAAGAATCAAT
261 AAGTGGTAAAATTCTAGAACCCCGATTGATTAATGTCAAAGATAATCCCATTGAGAAGAATCAAT
45715805 CAACTGTTGAAGTTCTTACACCAAAAGAATCAAA
326 CAACTGTTGAAGTTCTTACACCAAAAGAATCAAA
45715839 AAC
1 AAC
45715842 TGCAAAGTCT
Statistics
Matches: 358, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
359 358 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (359 bp):
AACCAATCTCAGGGGTTTAATCAGCAAGCTCTAAAACCACCTCAAGCTAAGGCATCAAACAGTTT
GGAGAACTTGTTGAAAGCGTACATGGAAAAGAATGACGTTTTGATCCAAAGCCAAGCAGCAACAC
TGAAAAATTTGGAAAACCAAATGGGTCAGTTGGCTACGGAGCTTCGTAATAGGCTGCAAGGAACC
TTGCCGAGCGATACTGAGAGTCTAAGAAATTTGGGTAAAGAACATATCAAGGCAGTGGCATTGCG
AAGTGGTAAAATTCTAGAACCCCGATTGATTAATGTCAAAGATAATCCCATTGAGAAGAATCAAT
CAACTGTTGAAGTTCTTACACCAAAAGAATCAAA
Found at i:45729595 original size:18 final size:18
Alignment explanation
Indices: 45729560--45729597 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
45729550 TCGTGTGTCT
*
45729560 CCTTTCACATGGTCTGAG
1 CCTTTCACACGGTCTGAG
45729578 CCTTGTCACACGGT-TGAG
1 CCTT-TCACACGGTCTGAG
45729596 CC
1 CC
45729598 ACACGAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.16, C:0.32, G:0.24, T:0.29
Consensus pattern (18 bp):
CCTTTCACACGGTCTGAG
Found at i:45730372 original size:65 final size:64
Alignment explanation
Indices: 45730175--45730457 Score: 284
Period size: 65 Copynumber: 4.4 Consensus size: 64
45730165 ATTTGAAGAA
* * * * * *
45730175 AACTTAGATAGCCCACTTCTTTAAAGCGGTTGTATCTCTTTAAGGTAATGCATTTCTTGAAAGTG
1 AACTTAGATAACACACTTCTTTAAAGTGGTT-TACCTTTTTAAGGTAATACATTTCTTGAAAGTG
* *** * * *
45730240 AAATTAGATATA-ACACCAGTTTAAAGTGGTTTTACC--TTTAAAGTAATGCACTTCTTGAAAGT
1 AACTTAGATA-ACACACTTCTTTAAAGTGG-TTTACCTTTTTAAGGTAATACATTTCTTGAAAGT
45730302 G
64 G
*
45730303 AACTTAGATAACACACTTCTTTAAAGTGGCTTTACCTTTTTAAGGTAATACATATCTTGAAAGTG
1 AACTTAGATAACACACTTCTTTAAAGTGG-TTTACCTTTTTAAGGTAATACATTTCTTGAAAGTG
** ** ** **
45730368 AACTTAGATATTACACTTCTTTAAAGTGGAACTACCTTTTTAAGGTAATATGTTTCTTGAAAGCA
1 AACTTAGATAACACACTTCTTTAAAGTGG-TTTACCTTTTTAAGGTAATACATTTCTTGAAAGTG
**
45730433 AACTTAGATATTACACTTCTTTAAA
1 AACTTAGATAACACACTTCTTTAAA
45730458 AGAGTTAAAG
Statistics
Matches: 184, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
62 1 0.01
63 54 0.29
65 127 0.69
66 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (64 bp):
AACTTAGATAACACACTTCTTTAAAGTGGTTTACCTTTTTAAGGTAATACATTTCTTGAAAGTG
Found at i:45730404 original size:128 final size:129
Alignment explanation
Indices: 45730174--45730457 Score: 320
Period size: 128 Copynumber: 2.2 Consensus size: 129
45730164 TATTTGAAGA
* * * * *
45730174 AAACTTAGATAGCCCACTTCTTTAAAGCGGTTGTATCTCTTTAAGGTAATGCATTTCTTGAAAGT
1 AAACTTAGATAACACACTTCTTTAAAGCGGTTGTACCTCTTTAAGGTAATACATATCTTGAAAGT
* *** * *
45730239 GAAATTAGATATAACACCAGTTTAAAGTGGTTTTACC-TTTAAAGTAATGCACTTCTTGAAAGT
66 GAAATTAGATATAACACCACTTTAAAGTGGAACTACCTTTTAAAGTAATACACTTCTTGAAAGC
* * *
45730302 GAACTTAGATAACACACTTCTTTAAAGTGGCTT-TACCTTTTTAAGGTAATACATATCTTGAAAG
1 AAACTTAGATAACACACTTCTTTAAAGCGG-TTGTACCTCTTTAAGGTAATACATATCTTGAAAG
* * ** * ***
45730366 TGAACTTAGATATTACACTTCTTTAAAGTGGAACTACCTTTTTAAGGTAATATGTTTCTTGAAAG
65 TGAAATTAGATATAACACCACTTTAAAGTGGAACTACC-TTTTAAAGTAATACACTTCTTGAAAG
45730431 C
129 C
**
45730432 AAACTTAGATATTACACTTCTTTAAA
1 AAACTTAGATAACACACTTCTTTAAA
45730458 AGAGTTAAAG
Statistics
Matches: 128, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
128 83 0.65
129 2 0.02
130 43 0.34
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (129 bp):
AAACTTAGATAACACACTTCTTTAAAGCGGTTGTACCTCTTTAAGGTAATACATATCTTGAAAGT
GAAATTAGATATAACACCACTTTAAAGTGGAACTACCTTTTAAAGTAATACACTTCTTGAAAGC
Found at i:45734900 original size:44 final size:44
Alignment explanation
Indices: 45734802--45734889 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
45734792 TGTGTGTTTG
45734802 AATAGAAATGAATGGAATGAATAGGAAAAGTGAAATGGGAAACA
1 AATAGAAATGAATGGAATGAATAGGAAAAGTGAAATGGGAAACA
45734846 AATAGAAATGAATGGAATGAATAGGAAAAGTGAAATGGGAAACA
1 AATAGAAATGAATGGAATGAATAGGAAAAGTGAAATGGGAAACA
45734890 TTCATGAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.55, C:0.02, G:0.27, T:0.16
Consensus pattern (44 bp):
AATAGAAATGAATGGAATGAATAGGAAAAGTGAAATGGGAAACA
Found at i:45735197 original size:27 final size:26
Alignment explanation
Indices: 45735143--45735196 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
45735133 ATTTTCTCAG
* *
45735143 AATTTTATCAAGGGAAAAATTGTCAA
1 AATTTTACCAAGGGAAAAATCGTCAA
*
45735169 AATTTTACCAAGGGTAAAATCGTCAA
1 AATTTTACCAAGGGAAAAATCGTCAA
45735195 AA
1 AA
45735197 AAACTTTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (26 bp):
AATTTTACCAAGGGAAAAATCGTCAA
Found at i:45735660 original size:20 final size:21
Alignment explanation
Indices: 45735637--45735683 Score: 78
Period size: 20 Copynumber: 2.2 Consensus size: 21
45735627 ATAAGAAGTT
45735637 TTGTAATAAGAAA-ACATGTG
1 TTGTAATAAGAAACACATGTG
45735657 TTGTAATAAGAAATCACATGTG
1 TTGTAATAAGAAA-CACATGTG
45735679 TTGTA
1 TTGTA
45735684 TTGTTCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 13 0.52
22 12 0.48
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.34
Consensus pattern (21 bp):
TTGTAATAAGAAACACATGTG
Found at i:45738624 original size:101 final size:101
Alignment explanation
Indices: 45738516--45738742 Score: 268
Period size: 101 Copynumber: 2.2 Consensus size: 101
45738506 TGTGGCATGG
* *
45738516 ACTATGTGTAGGCCACTATGTGAAAGTGA-A-ATT-GATGGTCACATGTGTAGTACTATGTGCAG
1 ACTATGTGCAGGCTACTATGTGAAAG-GATAGATTCGA---TCACATGTGTAGTACTATGTGCAG
*
45738578 GCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
62 GCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
** * *
45738617 ACTATGTGCAGGCTACTATGCCT-ACCGGATAGCTTCGATCACGTGTGTAGTACTATGTGCAGGC
1 ACTATGTGCAGGCTACTATG--TGAAAGGATAGATTCGATCACATGTGTAGTACTATGTGCAGGC
* *
45738681 TACTACGTGTATCGGATAGTGATGGTCACATGTGTAGT
64 TACTACGTGTACCAGATAGTGATGGTCACATGTGTAGT
45738719 ACTATGTGCAGGCTACTATGTGAA
1 ACTATGTGCAGGCTACTATGTGAA
45738743 CCGATATCAT
Statistics
Matches: 108, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
100 1 0.01
101 60 0.56
102 38 0.35
103 7 0.06
104 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (101 bp):
ACTATGTGCAGGCTACTATGTGAAAGGATAGATTCGATCACATGTGTAGTACTATGTGCAGGCTA
CTACGTGTACCAGATAGTGATGGTCACATGTGTAGT
Found at i:45738684 original size:51 final size:50
Alignment explanation
Indices: 45738554--45738738 Score: 196
Period size: 51 Copynumber: 3.7 Consensus size: 50
45738544 AAATTGATGG
* ** * *
45738554 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCCTACCGGATAGT-AT-GA
*
45738604 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCCTACCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCCTACCGGATAG-TAT-GA
* * ** * *
45738655 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCCTACCGGATAGT-ATGA
45738706 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
45738739 TGAACCGATA
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
50 38 0.33
51 74 0.65
52 1 0.01
53 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCCTACCGGATAGTATGA
Found at i:45738740 original size:26 final size:26
Alignment explanation
Indices: 45738660--45738740 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
45738650 TTCGATCACG
45738660 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
45738686 CGTGTA-T-CGGATAGTG-ATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
45738711 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
45738737 TGTG
1 TGTG
45738741 AACCGATATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:45738983 original size:16 final size:16
Alignment explanation
Indices: 45738962--45738993 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45738952 TGATTGAAAG
*
45738962 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
45738978 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
45738994 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:45750141 original size:26 final size:26
Alignment explanation
Indices: 45750100--45750180 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
45750090 AGGGTGTAGT
* * *
45750100 AGGCTTTATGCCAGTGTATATCTAGC
1 AGGCTTTGTGCTAGTGTATATTTAGC
*
45750126 AGGCTTTGTGCTAGTGCATATTTAGC
1 AGGCTTTGTGCTAGTGTATATTTAGC
* *
45750152 AGGCTTTGTGTTGGTGTATAATTTAGC
1 AGGCTTTGTGCTAGTGTAT-ATTTAGC
45750179 AG
1 AG
45750181 CCATTAGTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 38 0.81
27 9 0.19
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (26 bp):
AGGCTTTGTGCTAGTGTATATTTAGC
Found at i:45757600 original size:26 final size:26
Alignment explanation
Indices: 45757571--45757647 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
45757561 GGCGTAATAG
*
45757571 GCTTTATGTTGGTGTATATTTAGCAA
1 GCTTTGTGTTGGTGTATATTTAGCAA
* *
45757597 GCTTTGT-TTCGGTGTATATTTAGTAG
1 GCTTTGTGTT-GGTGTATATTTAGCAA
***
45757623 GCTTTGTGCCAGTGTATATTTAGCA
1 GCTTTGTGTTGGTGTATATTTAGCA
45757648 GGCATTAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.05
26 40 0.95
ACGTcount: A:0.19, C:0.10, G:0.25, T:0.45
Consensus pattern (26 bp):
GCTTTGTGTTGGTGTATATTTAGCAA
Found at i:45757650 original size:26 final size:26
Alignment explanation
Indices: 45757582--45757650 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
45757572 CTTTATGTTG
* ** *
45757582 GTGTATATTTAGCAAGCTTTGTTTCG
1 GTGTATATTTAGCAGGCTTTGTGCCA
*
45757608 GTGTATATTTAGTAGGCTTTGTGCCA
1 GTGTATATTTAGCAGGCTTTGTGCCA
45757634 GTGTATATTTAGCAGGC
1 GTGTATATTTAGCAGGC
45757651 ATTAGTTGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (26 bp):
GTGTATATTTAGCAGGCTTTGTGCCA
Found at i:45758225 original size:11 final size:12
Alignment explanation
Indices: 45758224--45758306 Score: 60
Period size: 11 Copynumber: 7.5 Consensus size: 12
45758214 TTTTAAAAAA
45758224 TTAAAAAAAGTATT
1 TTAA-AAAA-TATT
45758238 TT-AAAAATATT
1 TTAAAAAATATT
45758249 TT-AAAAATATT
1 TTAAAAAATATT
45758260 TT---AAA-A-T
1 TTAAAAAATATT
45758267 TTAAAAAA-A-T
1 TTAAAAAATATT
*
45758277 TAAAAAAAGTATT
1 TTAAAAAA-TATT
45758290 TT-AAAAATATT
1 TTAAAAAATATT
45758301 TTAAAA
1 TTAAAA
45758307 TTTAAAAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
7 3 0.05
8 1 0.02
9 3 0.05
10 12 0.20
11 23 0.38
12 13 0.22
13 3 0.05
14 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:45758239 original size:22 final size:21
Alignment explanation
Indices: 45758209--45758276 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
45758199 TTTTTATTTT
45758209 AAAAT-TTTTAAAAAATTAAA
1 AAAATATTTTAAAAAATTAAA
**
45758229 AAAAGTATTTTAAAAATATTTTA
1 AAAA-TATTTTAAAAA-ATTAAA
*
45758252 AAAATATTTT-AAAATTTAAA
1 AAAATATTTTAAAAAATTAAA
45758272 AAAAT
1 AAAAT
45758277 TAAAAAAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 12 0.30
21 5 0.12
22 15 0.38
23 8 0.20
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (21 bp):
AAAATATTTTAAAAAATTAAA
Found at i:45758293 original size:52 final size:53
Alignment explanation
Indices: 45758203--45758306 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 53
45758193 GGCCCATTTT
*
45758203 TATTTTAAAATTTTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
1 TATTTTAAAATTTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
45758256 TATTTTAAAA-TTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TATTTTAAAATTTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
45758307 TTTAAAAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 40 0.80
53 10 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (53 bp):
TATTTTAAAATTTTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
Found at i:45758314 original size:40 final size:41
Alignment explanation
Indices: 45758240--45758386 Score: 230
Period size: 40 Copynumber: 3.7 Consensus size: 41
45758230 AAAGTATTTT
45758240 AAAAA-TATTTTAAAAATATTTTAAAATTTAAAAAAATTAA
1 AAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAA
45758280 AAAAAGTATTTTAAAAATATTTTAAAATTT-AAAAAATTAA
1 AAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAA
*
45758320 AAAAAGTATTTT-AAAATATTTTAAAATTTAAAAAAATT-T
1 AAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAA
* * *
45758359 TAAAAGTATGTAAAAAATATTTTAAAAT
1 AAAAAGTATTTTAAAAATATTTTAAAAT
45758387 AAAAAATATA
Statistics
Matches: 100, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
39 26 0.26
40 50 0.50
41 24 0.24
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (41 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAA
Found at i:45758335 original size:11 final size:10
Alignment explanation
Indices: 45758321--45758387 Score: 57
Period size: 10 Copynumber: 6.6 Consensus size: 10
45758311 AAAAATTAAA
45758321 AAAAGTATTTT
1 AAAA-TATTTT
45758332 AAAATATTTT
1 AAAATATTTT
*
45758342 -AAA-ATTTA
1 AAAATATTTT
*
45758350 AAAAAATTTT
1 AAAATATTTT
**
45758360 AAAAGTATGTAA
1 AAAA-TAT-TTT
45758372 AAAATATTTT
1 AAAATATTTT
45758382 AAAATA
1 AAAATA
45758388 AAAAATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
8 4 0.09
9 6 0.13
10 21 0.47
11 9 0.20
12 5 0.11
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (10 bp):
AAAATATTTT
Found at i:45775321 original size:35 final size:35
Alignment explanation
Indices: 45775290--45775541 Score: 326
Period size: 35 Copynumber: 7.2 Consensus size: 35
45775280 GACGTGTTTT
* *
45775290 GGTTGGATTAGCTCTTACGAGCATTGGCGTGTTTC
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTGTTAC
*
45775325 GGTTGGATTAGCTCTTATGAGAATTGGCGTGTTAC
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTGTTAC
* * * *
45775360 GGTTGGATTAGCTCTTATGATCACTGGTGTGTTTC
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTGTTAC
**
45775395 GGTTGGATTAGCTCTTATGAGCATTTCCGTGTTAC
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTGTTAC
*
45775430 GGTTGGATTAGCTCTTATGAGCATTGGTGTGTTAC
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTGTTAC
* * *
45775465 GGTTGGATTAGCTCTTATGAGCACTAGCATGCTT-C
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTG-TTAC
* * ** *
45775500 AGTTGGATTAGCTCTTATGAACATCAGCGTGTTAT
1 GGTTGGATTAGCTCTTATGAGCATTGGCGTGTTAC
45775535 GGTTGGA
1 GGTTGGA
45775542 CTGACGATGT
Statistics
Matches: 187, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
34 2 0.01
35 183 0.98
36 2 0.01
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.38
Consensus pattern (35 bp):
GGTTGGATTAGCTCTTATGAGCATTGGCGTGTTAC
Found at i:45775465 original size:105 final size:105
Alignment explanation
Indices: 45775282--45775541 Score: 360
Period size: 105 Copynumber: 2.5 Consensus size: 105
45775272 CTCTGTCTGA
* * * *
45775282 CGTGTTTTGGTTGGATTAGCTCTTACGAGCATTGGCGTGTTTCGGTTGGATTAGCTCTTATGAGA
1 CGTGTTTCGGTTGGATTAGCTCTTATGAGCATTGCCGTGTTACGGTTGGATTAGCTCTTATGAGA
* *
45775347 ATTGGCGTGTTACGGTTGGATTAGCTCTTATGATCACTGG
66 ATTGGCGTGTTACGGTTGGATTAGCTCTTATGAGCACTAG
* * *
45775387 TGTGTTTCGGTTGGATTAGCTCTTATGAGCATTTCCGTGTTACGGTTGGATTAGCTCTTATGAGC
1 CGTGTTTCGGTTGGATTAGCTCTTATGAGCATTGCCGTGTTACGGTTGGATTAGCTCTTATGAGA
*
45775452 ATTGGTGTGTTACGGTTGGATTAGCTCTTATGAGCACTAG
66 ATTGGCGTGTTACGGTTGGATTAGCTCTTATGAGCACTAG
* * * * * *
45775492 CATGCTTCAGTTGGATTAGCTCTTATGAACATCAG-CGTGTTATGGTTGGA
1 CGTGTTTCGGTTGGATTAGCTCTTATGAGCAT-TGCCGTGTTACGGTTGGA
45775542 CTGACGATGT
Statistics
Matches: 136, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
105 136 1.00
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.39
Consensus pattern (105 bp):
CGTGTTTCGGTTGGATTAGCTCTTATGAGCATTGCCGTGTTACGGTTGGATTAGCTCTTATGAGA
ATTGGCGTGTTACGGTTGGATTAGCTCTTATGAGCACTAG
Found at i:45776397 original size:13 final size:13
Alignment explanation
Indices: 45776379--45776403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45776369 TGAATAATGC
45776379 TTTGATGATATAT
1 TTTGATGATATAT
45776392 TTTGATGATATA
1 TTTGATGATATA
45776404 AATGTGGTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TTTGATGATATAT
Found at i:45779256 original size:56 final size:51
Alignment explanation
Indices: 45779194--45779340 Score: 154
Period size: 50 Copynumber: 2.8 Consensus size: 51
45779184 AGATCCCATG
* * *
45779194 TAAGACCATGTCGGGGGCATGACATTGGCATTATCGAGACTATGAGAGGTCCCACA
1 TAAGACCATGTCTGGGACATGACATTGGCA--ACCGAG---ATGAGAGGTCCCACA
* * *
45779250 TAAGACCATGTCTGGGACATGGCGTTGGC-ACCGAGATGAGAGGTCCCCCA
1 TAAGACCATGTCTGGGACATGACATTGGCAACCGAGATGAGAGGTCCCACA
* * *
45779300 TAAGACCATGTCTAGGACATGACATGGGC-ACCGATATGAGA
1 TAAGACCATGTCTGGGACATGACATTGGCAACCGAGATGAGA
45779341 ACTCCCATGT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
50 50 0.62
53 5 0.06
56 25 0.31
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (51 bp):
TAAGACCATGTCTGGGACATGACATTGGCAACCGAGATGAGAGGTCCCACA
Found at i:45779290 original size:50 final size:50
Alignment explanation
Indices: 45779235--45779340 Score: 158
Period size: 50 Copynumber: 2.1 Consensus size: 50
45779225 TATCGAGACT
* * * *
45779235 ATGAGAGGTCCCACATAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCACATAAGACCATGTCTAGGACATGACATGGGCACCGAG
* *
45779285 ATGAGAGGTCCCCCATAAGACCATGTCTAGGACATGACATGGGCACCGAT
1 ATGAGAGGTCCCACATAAGACCATGTCTAGGACATGACATGGGCACCGAG
45779335 ATGAGA
1 ATGAGA
45779341 ACTCCCATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (50 bp):
ATGAGAGGTCCCACATAAGACCATGTCTAGGACATGACATGGGCACCGAG
Found at i:45779656 original size:20 final size:20
Alignment explanation
Indices: 45779631--45779669 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
45779621 TGAATTATTT
45779631 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
45779651 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
45779670 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:45788712 original size:17 final size:17
Alignment explanation
Indices: 45788684--45788727 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
45788674 AGAAAGAAAG
45788684 AAAGAAAGGACATATGTC
1 AAAG-AAGGACATATGTC
*
45788702 AAAGGAGGACATATGTC
1 AAAGAAGGACATATGTC
45788719 AAAGAAGGA
1 AAAGAAGGA
45788728 AGGCCTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.50, C:0.09, G:0.27, T:0.14
Consensus pattern (17 bp):
AAAGAAGGACATATGTC
Found at i:45791414 original size:6 final size:6
Alignment explanation
Indices: 45791403--45791438 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
45791393 ATAGCAAACC
**
45791403 AAAAAG AAAAAG AAAGCG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
45791439 CTTACCTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:45793539 original size:15 final size:16
Alignment explanation
Indices: 45793519--45793548 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
45793509 ACAAAACACA
45793519 TTCTTTT-CATTTTTT
1 TTCTTTTGCATTTTTT
45793534 TTCTTTTGCATTTTT
1 TTCTTTTGCATTTTT
45793549 ATCTGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.77
Consensus pattern (16 bp):
TTCTTTTGCATTTTTT
Found at i:45793631 original size:22 final size:22
Alignment explanation
Indices: 45793603--45793652 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
45793593 CACGGCTGTA
45793603 AATTTTGTGATGATGGAATAAC
1 AATTTTGTGATGATGGAATAAC
45793625 AATTTTGTGATGATGGAATAAC
1 AATTTTGTGATGATGGAATAAC
*
45793647 ATTTTT
1 AATTTT
45793653 TCCCCTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.42
Consensus pattern (22 bp):
AATTTTGTGATGATGGAATAAC
Found at i:45810683 original size:18 final size:18
Alignment explanation
Indices: 45810660--45810711 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
45810650 TTAATAAATA
*
45810660 AATTAATTTAATTTTCCC
1 AATTAATTTAATTTTCAC
* *
45810678 AATTAAATT-ATTTTCAT
1 AATTAATTTAATTTTCAC
45810695 AATTCAATTATAATTTT
1 AATT-AATT-TAATTTT
45810712 GTTAAAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 10 0.37
18 11 0.41
19 1 0.04
20 5 0.19
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTAATTTAATTTTCAC
Found at i:45811647 original size:18 final size:19
Alignment explanation
Indices: 45811610--45811647 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
45811600 ATAAATAAAA
45811610 TAGAAAAATAAATCAAAGAT
1 TAGAAAAATAAA-CAAAGAT
*
45811630 TAGAACAATAAA-AAAGAT
1 TAGAAAAATAAACAAAGAT
45811648 AGTAAAGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (19 bp):
TAGAAAAATAAACAAAGAT
Found at i:45811853 original size:27 final size:28
Alignment explanation
Indices: 45811823--45811882 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 28
45811813 TTGTTAAAAC
45811823 TCTTTTAAAAG-AAAACTC-AAGAGAAAT
1 TCTTTTAAAAGAAAAACTCAAAGAG-AAT
*
45811850 TC--TTGAAAGAAAAACTCAAAGAGAAT
1 TCTTTTAAAAGAAAAACTCAAAGAGAAT
45811876 T-TTTTAA
1 TCTTTTAA
45811883 TTCAAAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
25 6 0.22
26 11 0.41
27 10 0.37
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (28 bp):
TCTTTTAAAAGAAAAACTCAAAGAGAAT
Found at i:45815564 original size:72 final size:72
Alignment explanation
Indices: 45815464--45815622 Score: 257
Period size: 72 Copynumber: 2.2 Consensus size: 72
45815454 ACACGGTTGA
* * *
45815464 GACACACGCTCGTGTCTCAGGCCATGTAACTCTCTGACTTGGGTCACAGGCCCATGTGTGTTGCC
1 GACAAACGCCCGTGTCTCAGGCCATGTAACTCTCTGACTTGGGTCACACGCCCATGTGTGTTGCC
45815529 CGTGTGT
66 CGTGTGT
* *
45815536 GACAAACGCCCGTGTCTCAGGCCATGTAACTCTCTGACTTGGGTCACACGTCCATGTGTGTTTCC
1 GACAAACGCCCGTGTCTCAGGCCATGTAACTCTCTGACTTGGGTCACACGCCCATGTGTGTTGCC
45815601 CGTGTGT
66 CGTGTGT
45815608 GACACAA-GCCCGTGT
1 GACA-AACGCCCGTGT
45815623 GGCCAGGCCG
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
72 79 0.98
73 2 0.02
ACGTcount: A:0.17, C:0.30, G:0.26, T:0.27
Consensus pattern (72 bp):
GACAAACGCCCGTGTCTCAGGCCATGTAACTCTCTGACTTGGGTCACACGCCCATGTGTGTTGCC
CGTGTGT
Found at i:45825919 original size:38 final size:40
Alignment explanation
Indices: 45825801--45826022 Score: 248
Period size: 40 Copynumber: 5.7 Consensus size: 40
45825791 TTGAATGATG
*
45825801 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
45825839 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
45825880 TCCGGGCTAAG-CCCGAAGGCATTTGT-CGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
45825918 TCCGGGCTAAG-CCCGAAGACATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
45825957 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
45825996 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
45826023 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 13, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
38 37 0.23
39 53 0.33
40 58 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:45826045 original size:79 final size:78
Alignment explanation
Indices: 45825874--45826055 Score: 185
Period size: 79 Copynumber: 2.3 Consensus size: 78
45825864 TGTGCGAGAT
* * *
45825874 ACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTCGAGATACTAATTCCGGGCTAAGCCCGAAGAC
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTCGAGATACTAATACCGGGCTAAGCCCGAAGAC
** *
45825938 ATTTGTGCGAGTT
66 ATTTGAACGAGTG
*
45825951 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGA
1 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT-CGAGA-TACTAAT-ACCGGGCTAAG-CCCGA
*
45826014 AGGCATTTGAACGAG-G
62 AGACATTTGAACGAGTG
* * *
45826030 AGCTATATCC-GGTTAAATTCCGAAGG
1 A-CTAAATCCGGGTTAAGTCCCGAAGG
45826056 TACGTGATTT
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
77 15 0.17
78 18 0.20
79 31 0.35
80 24 0.27
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (78 bp):
ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTCGAGATACTAATACCGGGCTAAGCCCGAAGAC
ATTTGAACGAGTG
Found at i:45836487 original size:10 final size:10
Alignment explanation
Indices: 45836472--45836505 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
45836462 CGAAAAAATA
45836472 TTTTTTTAAT
1 TTTTTTTAAT
**
45836482 TTTTTTTCTT
1 TTTTTTTAAT
45836492 TTTTTTTAAT
1 TTTTTTTAAT
45836502 TTTT
1 TTTT
45836506 CTATTTTTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:45842175 original size:18 final size:18
Alignment explanation
Indices: 45842149--45842193 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
45842139 AAAATGTTTT
45842149 TAAATTGAATAATGATTTG
1 TAAA-TGAATAATGATTTG
*
45842168 TAAATGAATAATGTTTTG
1 TAAATGAATAATGATTTG
*
45842186 AAAATGAA
1 TAAATGAA
45842194 CGACATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (18 bp):
TAAATGAATAATGATTTG
Found at i:45842207 original size:20 final size:18
Alignment explanation
Indices: 45842154--45842207 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
45842144 GTTTTTAAAT
* *
45842154 TGAATAATGATTTGTAAA
1 TGAAGAATGATTTGAAAA
* *
45842172 TGAATAATGTTTTGAAAA
1 TGAAGAATGATTTGAAAA
45842190 TGAACGACATGATTTGAA
1 TGAA-GA-ATGATTTGAA
45842208 GTTAACATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 20 0.67
19 1 0.03
20 9 0.30
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.35
Consensus pattern (18 bp):
TGAAGAATGATTTGAAAA
Found at i:45847739 original size:16 final size:17
Alignment explanation
Indices: 45847707--45847739 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
45847697 ATAAAAATAA
*
45847707 TTATGTGTTATAATTTT
1 TTATGTGTTAAAATTTT
45847724 TTATGT-TTAAAATTTT
1 TTATGTGTTAAAATTTT
45847740 GAATTAGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (17 bp):
TTATGTGTTAAAATTTT
Found at i:45849004 original size:18 final size:18
Alignment explanation
Indices: 45848974--45849022 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
45848964 AATTAAAAAA
45848974 ATTT-AAAATTGAATAACG
1 ATTTGAAAA-TGAATAACG
* *
45848992 ATTTGTAAATGAATAATG
1 ATTTGAAAATGAATAACG
*
45849010 TTTTGAAAATGAA
1 ATTTGAAAATGAA
45849023 CGACACGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (18 bp):
ATTTGAAAATGAATAACG
Found at i:45852024 original size:17 final size:17
Alignment explanation
Indices: 45851970--45852096 Score: 103
Period size: 17 Copynumber: 7.5 Consensus size: 17
45851960 TCTTTCTATG
* *
45851970 AACTTAACCAAATTTTG
1 AACTTAAGCAAATTTTA
* * *
45851987 AA-TTCAATCAAATCTTG
1 AACTT-AAGCAAATTTTA
*
45852004 AACTTAAGCATATTTTA
1 AACTTAAGCAAATTTTA
* *
45852021 AACTTAAGCAAATTCTG
1 AACTTAAGCAAATTTTA
* *
45852038 AACTTAAGTAAATTTTG
1 AACTTAAGCAAATTTTA
**
45852055 GGCTTAAGCAAATTTTA
1 AACTTAAGCAAATTTTA
* * *
45852072 ATCTTAAGAAAATTCTA
1 AACTTAAGCAAATTTTA
45852089 AACTTAAG
1 AACTTAAG
45852097 TAGATTTCGA
Statistics
Matches: 88, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
16 2 0.02
17 84 0.95
18 2 0.02
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.35
Consensus pattern (17 bp):
AACTTAAGCAAATTTTA
Found at i:45852033 original size:51 final size:51
Alignment explanation
Indices: 45851970--45852098 Score: 145
Period size: 51 Copynumber: 2.5 Consensus size: 51
45851960 TCTTTCTATG
* * *
45851970 AACTTAACCAAATTTTGAA-TTCAA-TCAAATCTTGAACTTAAGCATATTTTA
1 AACTTAAGCAAATTCTGAACTT-AAGT-AAATCTTGAACTTAAGCAAATTTTA
* **
45852021 AACTTAAGCAAATTCTGAACTTAAGTAAATTTTGGGCTTAAGCAAATTTTA
1 AACTTAAGCAAATTCTGAACTTAAGTAAATCTTGAACTTAAGCAAATTTTA
* * *
45852072 ATCTTAAGAAAATTCTAAACTTAAGTA
1 AACTTAAGCAAATTCTGAACTTAAGTA
45852099 GATTTCGAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 64 0.96
52 3 0.04
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (51 bp):
AACTTAAGCAAATTCTGAACTTAAGTAAATCTTGAACTTAAGCAAATTTTA
Found at i:45852821 original size:68 final size:68
Alignment explanation
Indices: 45852599--45852834 Score: 217
Period size: 68 Copynumber: 3.4 Consensus size: 68
45852589 CCTTTATAAC
* * * * * * *
45852599 ATCAGCTGGGAGTGTAGGTCCGCTAGCTGTGTTAGAGTTACGAGCTTAACTCTACGAGCTCTTAG
1 ATCAACTGGGAGCGTAGGTCCGCTAGCTATGTTAGAGTTGCGAGCTTAAATCTGCAAGCTCTTAG
45852664 AAT
66 AAT
* * * * * * * * *
45852667 ATCAACTAGGAGCATAGGCCCAG-TAGCTATTTTTAGAGGTTGTGATCATAAA-CCGTCAAAC-C
1 ATCAACTGGGAGCGTAGGTCC-GCTAGCTA-TGTTAGA-GTTGCGAGCTTAAATCTG-CAAGCTC
* *
45852729 TTTATAAC
62 -TTAGAAT
* * *
45852737 ATCAACTGAGAGCGTAGGTCTGCTAGCTATGTTGGAGTTGCGAGCTTAAATCTGCAAGCTCTTAG
1 ATCAACTGGGAGCGTAGGTCCGCTAGCTATGTTAGAGTTGCGAGCTTAAATCTGCAAGCTCTTAG
45852802 AAT
66 AAT
45852805 ATCAACTGGGAGCGTAGGTCCGCTAGCTAT
1 ATCAACTGGGAGCGTAGGTCCGCTAGCTAT
45852835 TTTTGGAGGT
Statistics
Matches: 126, Mismatches: 34, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
68 69 0.55
69 18 0.14
70 39 0.31
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (68 bp):
ATCAACTGGGAGCGTAGGTCCGCTAGCTATGTTAGAGTTGCGAGCTTAAATCTGCAAGCTCTTAG
AAT
Found at i:45852874 original size:276 final size:276
Alignment explanation
Indices: 45852374--45852878 Score: 642
Period size: 276 Copynumber: 1.8 Consensus size: 276
45852364 TATGTTGGAG
* * * *
45852374 CTACAAGCTCTTTAAATATCAGCTAGTAGTATAGGTCCGCTAGCTATTTTTGAAGGTTTCAATCA
1 CTACAAGCTCTTTAAATATCAACTAGGAGCATAGGCCCGCTAGCTATTTTTGAAGGTTTCAATCA
* * * * * * *
45852439 TAAACCGGCAAATCTTTATAACATCAGCTGGGAGCGTATGTCCGCTAGTTGTGCTGGAGCTGTGA
66 TAAACCGGCAAACCTTTATAACATCAACTGAGAGCGTAGGTCCGCTAGCTATGCTGGAGCTGCGA
* * * * * * *
45852504 GCTTAACTTCGCGAGCTCTTTGAATATCAACTGGGAGCATAGGTTCGTTAGTTGTTTTTGGAGGT
131 GCTTAAATTCGCAAGCTCTTAGAATATCAACTGGGAGCATAGGTCCGCTAGCTATTTTTGGAGGT
* *
45852569 TGCAATCATAAAACAATAAACCTTTATAACATCAGCTGGGAGTGTAGGTCCGCTAGCTGTGTTAG
196 TGCAATCATAAAACAACAAACCATTATAACATCAGCTGGGAGTGTAGGTCCGCTAGCTGTGTTAG
45852634 AGTTACGAGCTTAACT
261 AGTTACGAGCTTAACT
* *
45852650 CTACGAGCTC-TTAGAATATCAACTAGGAGCATAGGCCCAG-TAGCTATTTTT-AGAGGTTGT-G
1 CTACAAGCTCTTTA-AATATCAACTAGGAGCATAGGCCC-GCTAGCTATTTTTGA-AGGTT-TCA
* * * *
45852711 ATCATAAACCGTCAAACCTTTATAACATCAACTGAGAGCGTAGGTCTGCTAGCTATGTTGGAGTT
62 ATCATAAACCGGCAAACCTTTATAACATCAACTGAGAGCGTAGGTCCGCTAGCTATGCTGGAGCT
*
45852776 GCGAGCTTAAA-TCTGCAAGCTCTTAGAATATCAACTGGGAGCGTAGGTCCGCTAGCTATTTTTG
127 GCGAGCTTAAATTC-GCAAGCTCTTAGAATATCAACTGGGAGCATAGGTCCGCTAGCTATTTTTG
** * **
45852840 GAGGTTGTGATCATAAACCGGCAAACCATTATAACATCA
191 GAGGTTGCAATCATAAAACAACAAACCATTATAACATCA
45852879 AGTACAAACA
Statistics
Matches: 192, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
275 6 0.03
276 184 0.96
277 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (276 bp):
CTACAAGCTCTTTAAATATCAACTAGGAGCATAGGCCCGCTAGCTATTTTTGAAGGTTTCAATCA
TAAACCGGCAAACCTTTATAACATCAACTGAGAGCGTAGGTCCGCTAGCTATGCTGGAGCTGCGA
GCTTAAATTCGCAAGCTCTTAGAATATCAACTGGGAGCATAGGTCCGCTAGCTATTTTTGGAGGT
TGCAATCATAAAACAACAAACCATTATAACATCAGCTGGGAGTGTAGGTCCGCTAGCTGTGTTAG
AGTTACGAGCTTAACT
Found at i:45852879 original size:138 final size:138
Alignment explanation
Indices: 45852404--45852879 Score: 580
Period size: 138 Copynumber: 3.4 Consensus size: 138
45852394 AGCTAGTAGT
* * *
45852404 ATAGGTCCGCTAGCTATTTTTGAAGGTT-TCAATCATAAACCGGCAAATCTTTATAACATCAGCT
1 ATAGGTCCGCTAGCTATTTTTGGAGGTTGT-AATCATAAACCGGCAAACCTTTATAACATCAACT
* * * * * *
45852468 GGGAGCGTATGTCCGCTAGTTGTGCTGGAGCTGTGAGCTTAACT-TCGCGAGCTCTTTGAATATC
65 GGGAGCGTAGGTCCGCTAGCTGTGTTGGAGTTGCGAGCTTAACTCT-GCGAGCTCTTAGAATATC
45852532 AACTGGGAGC
129 AACTGGGAGC
* * * * * * *** *
45852542 ATAGGTTCGTTAGTTGTTTTTGGAGGTTGCAATCATAAAACAATAAACCTTTATAACATCAGCTG
1 ATAGGTCCGCTAGCTATTTTTGGAGGTTGTAATCATAAACCGGCAAACCTTTATAACATCAACTG
* * * *
45852607 GGAGTGTAGGTCCGCTAGCTGTGTTAGAGTTACGAGCTTAACTCTACGAGCTCTTAGAATATCAA
66 GGAGCGTAGGTCCGCTAGCTGTGTTGGAGTTGCGAGCTTAACTCTGCGAGCTCTTAGAATATCAA
*
45852672 CTAGGAGC
131 CTGGGAGC
* * * *
45852680 ATAGGCCCAG-TAGCTATTTTTAGAGGTTGTGATCATAAACCGTCAAACCTTTATAACATCAACT
1 ATAGGTCC-GCTAGCTATTTTTGGAGGTTGTAATCATAAACCGGCAAACCTTTATAACATCAACT
* * * * *
45852744 GAGAGCGTAGGTCTGCTAGCTATGTTGGAGTTGCGAGCTTAAATCTGCAAGCTCTTAGAATATCA
65 GGGAGCGTAGGTCCGCTAGCTGTGTTGGAGTTGCGAGCTTAACTCTGCGAGCTCTTAGAATATCA
45852809 ACTGGGAGC
130 ACTGGGAGC
* * *
45852818 GTAGGTCCGCTAGCTATTTTTGGAGGTTGTGATCATAAACCGGCAAACCATTATAACATCAA
1 ATAGGTCCGCTAGCTATTTTTGGAGGTTGTAATCATAAACCGGCAAACCTTTATAACATCAA
45852880 GTACAAACAT
Statistics
Matches: 285, Mismatches: 49, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
137 1 0.00
138 282 0.99
139 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (138 bp):
ATAGGTCCGCTAGCTATTTTTGGAGGTTGTAATCATAAACCGGCAAACCTTTATAACATCAACTG
GGAGCGTAGGTCCGCTAGCTGTGTTGGAGTTGCGAGCTTAACTCTGCGAGCTCTTAGAATATCAA
CTGGGAGC
Found at i:45854190 original size:51 final size:51
Alignment explanation
Indices: 45854068--45854252 Score: 160
Period size: 51 Copynumber: 3.6 Consensus size: 51
45854058 AAAGTGATGG
* *** * * *
45854068 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGAT-ATG-
1 TCACATGTGTAGTACTATGTGCAGGCTACTATACGTACCGGATA-ATGACGA
** * * *
45854118 TCGTATGTGTAGTACTATGTGCAAGCTACTATACGTACCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATACGTACCGGATA-ATGACGA
* *** * *
45854169 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAATGACGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATACGTACCGGATAATGACGA
*
45854220 TCACATGTGTAGTACTATGTGTAGGCTACTATA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATA
45854253 TGAACCGGTA
Statistics
Matches: 106, Mismatches: 27, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
50 39 0.37
51 67 0.63
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATACGTACCGGATAATGACGA
Found at i:45854337 original size:46 final size:43
Alignment explanation
Indices: 45854256--45854359 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 43
45854246 TACTATATGA
*
45854256 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
*
45854299 ACCGGATATCATTAATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
45854345 ACCGTGTATCTATTA
1 ACCG-GTATC-ATTA
45854360 TTATTCCGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
43 5 0.09
44 12 0.23
45 2 0.04
46 27 0.51
47 7 0.13
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:45854523 original size:37 final size:38
Alignment explanation
Indices: 45854455--45854527 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
45854445 ATGTGTGGAA
* *
45854455 TTGAATTGAATATTGACTTGAAAATGGAAAAGTGAATT
1 TTGAATTAAATATTGACTTGAAAATGAAAAAGTGAATT
*
45854493 TTGAATTAAATAGTT-A-TTGAAAGTGAAAAAGTGAA
1 TTGAATTAAATA-TTGACTTGAAAATGAAAAAGTGAA
45854528 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 17 0.55
38 12 0.39
39 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.21, T:0.33
Consensus pattern (38 bp):
TTGAATTAAATATTGACTTGAAAATGAAAAAGTGAATT
Found at i:45859229 original size:18 final size:18
Alignment explanation
Indices: 45859203--45859241 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
45859193 TCAACACATT
*
45859203 TTACCTAATTCACATATA
1 TTACATAATTCACATATA
*
45859221 TTACATAATTCACATGTA
1 TTACATAATTCACATATA
45859239 TTA
1 TTA
45859242 TAAATGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (18 bp):
TTACATAATTCACATATA
Found at i:45859762 original size:35 final size:35
Alignment explanation
Indices: 45859694--45859813 Score: 159
Period size: 35 Copynumber: 3.4 Consensus size: 35
45859684 AACAATCCAA
** * *
45859694 CCAAAACACACCAGATGCTCACAAGAGCCAATCCAT
1 CCAAAACACACCA-ATGCTCGTAAGAGCTAATCCTT
** *
45859730 CTTAAACACACCAATGCTCGTAAAAGCTAATCCTT
1 CCAAAACACACCAATGCTCGTAAGAGCTAATCCTT
*
45859765 CCGAAACACACCAATGCTCGTAAGAGCTAATCCTT
1 CCAAAACACACCAATGCTCGTAAGAGCTAATCCTT
45859800 CCAAAACACACCAA
1 CCAAAACACACCAA
45859814 AACAGAGAGT
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 62 0.85
36 11 0.15
ACGTcount: A:0.40, C:0.33, G:0.10, T:0.17
Consensus pattern (35 bp):
CCAAAACACACCAATGCTCGTAAGAGCTAATCCTT
Found at i:45868072 original size:12 final size:12
Alignment explanation
Indices: 45868047--45868080 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
45868037 GAATTATTTC
45868047 TTAAATTT-TT-
1 TTAAATTTATTA
45868057 TTAAATTTATTA
1 TTAAATTTATTA
45868069 TTAAATTTATTA
1 TTAAATTTATTA
45868081 CAATCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAAATTTATTA
Found at i:45868574 original size:18 final size:18
Alignment explanation
Indices: 45868540--45868613 Score: 83
Period size: 15 Copynumber: 4.6 Consensus size: 18
45868530 CTTAGTGTCT
45868540 TATTTGT-TTAGATATTG
1 TATTTGTATTAGATATTG
*
45868557 TATTTGTATTATATATTG
1 TATTTGTATTAGATATTG
45868575 TA-TTGTATT-G-TATTG
1 TATTTGTATTAGATATTG
45868590 TA-TTGTATT-G-TATTG
1 TATTTGTATTAGATATTG
45868605 TA-TTGTATT
1 TATTTGTATT
45868614 GTATTTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
15 29 0.54
17 14 0.26
18 11 0.20
ACGTcount: A:0.23, C:0.00, G:0.16, T:0.61
Consensus pattern (18 bp):
TATTTGTATTAGATATTG
Found at i:45868578 original size:5 final size:5
Alignment explanation
Indices: 45868570--45868618 Score: 98
Period size: 5 Copynumber: 9.8 Consensus size: 5
45868560 TTGTATTATA
45868570 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATT
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATT
45868619 TTTTTGTTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.61
Consensus pattern (5 bp):
TATTG
Found at i:45868730 original size:31 final size:31
Alignment explanation
Indices: 45868685--45868772 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 31
45868675 TAGTATGTAC
* *
45868685 ATTAGTATGAATATTATGTATTTTATGATAT
1 ATTAGTGTGAATATTATGTATGTTATGATAT
*
45868716 ATTAGTGTGCATATTATGTATGTTATGATAT
1 ATTAGTGTGAATATTATGTATGTTATGATAT
*
45868747 TTTAGTGT-ATATATTATGTATGTTAT
1 ATTAGTGTGA-ATATTATGTATGTTAT
45868773 TTTTCAGACC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.52
Consensus pattern (31 bp):
ATTAGTGTGAATATTATGTATGTTATGATAT
Found at i:45868888 original size:15 final size:15
Alignment explanation
Indices: 45868868--45868897 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45868858 GTGCATATGC
45868868 ATTTGGGGGAAAGTT
1 ATTTGGGGGAAAGTT
*
45868883 ATTTGGGTGAAAGTT
1 ATTTGGGGGAAAGTT
45868898 TTGTCACAGA
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:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (15 bp):
ATTTGGGGGAAAGTT
Found at i:45870484 original size:25 final size:26
Alignment explanation
Indices: 45870456--45870517 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
45870446 ACGAATTTTC
*
45870456 TCAAAATTTTAT-TGGGGTAAAATAG
1 TCAAAATTTTATCGGGGGTAAAATAG
*
45870481 TCAAAATTTTATCGGGGGTAAAATTG
1 TCAAAATTTTATCGGGGGTAAAATAG
45870507 TCAAAATTTTA
1 TCAAAATTTTA
45870518 CTAGAGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 12 0.35
26 22 0.65
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (26 bp):
TCAAAATTTTATCGGGGGTAAAATAG
Found at i:45871329 original size:15 final size:15
Alignment explanation
Indices: 45871309--45871342 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
45871299 CACTAGGGAA
45871309 AGGGAAATAAATAGT
1 AGGGAAATAAATAGT
45871324 AGGGAAATAAATAGT
1 AGGGAAATAAATAGT
45871339 AGGG
1 AGGG
45871343 TACACATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (15 bp):
AGGGAAATAAATAGT
Found at i:45876419 original size:27 final size:26
Alignment explanation
Indices: 45876373--45876430 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
45876363 TTGACACACT
45876373 TTAAATATGTAGGAAATTAAACAAAC
1 TTAAATATGTAGGAAATTAAACAAAC
** * *
45876399 ATTAAATATGTCTGAATTTAAACATAC
1 -TTAAATATGTAGGAAATTAAACAAAC
45876426 TTAAA
1 TTAAA
45876431 ACATGTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (26 bp):
TTAAATATGTAGGAAATTAAACAAAC
Found at i:45876509 original size:38 final size:38
Alignment explanation
Indices: 45876459--45876545 Score: 129
Period size: 38 Copynumber: 2.3 Consensus size: 38
45876449 ATAAACTATG
* * *
45876459 ACATAATTAAAACCCTTATTAATGTTGTTCAGATTATA
1 ACATAATTAAAACCCATATTAATGATGTTCAAATTATA
* *
45876497 ACATAATTAAAACTCATATTAATGATGTTCAAATTATG
1 ACATAATTAAAACCCATATTAATGATGTTCAAATTATA
45876535 ACATAATTAAA
1 ACATAATTAAA
45876546 GACTCAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (38 bp):
ACATAATTAAAACCCATATTAATGATGTTCAAATTATA
Found at i:45880434 original size:19 final size:19
Alignment explanation
Indices: 45880402--45880547 Score: 63
Period size: 19 Copynumber: 7.8 Consensus size: 19
45880392 AAAATTAGAA
* *
45880402 AAAAAATTGT-AAAATTGT
1 AAAAAATTATAAAAATCGT
**
45880420 AAAATTTTATAAAAATCGT
1 AAAAAATTATAAAAATCGT
*
45880439 AAAAAATTAT-AAAAT-AT
1 AAAAAATTATAAAAATCGT
* **
45880456 ATAGAAA-TAT-AAAATTTT
1 A-AAAAATTATAAAAATCGT
* * * *
45880474 ATAAAATTTTATAAAGTCAT
1 AAAAAATTATA-AAAATCGT
45880494 AAGAAAATTATACAAAAT-GT
1 AA-AAAATTATA-AAAATCGT
** *
45880514 AAAGAAA-TATAAATTTCAT
1 AAA-AAATTATAAAAATCGT
45880533 AAAAAATTATAAAAA
1 AAAAAATTATAAAAA
45880548 ACTATTGTAA
Statistics
Matches: 93, Mismatches: 25, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
17 13 0.14
18 26 0.28
19 30 0.32
20 12 0.13
21 12 0.13
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAAAATTATAAAAATCGT
Found at i:45880481 original size:10 final size:10
Alignment explanation
Indices: 45880463--45880488 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
45880453 TATATAGAAA
45880463 TATAAAATTT
1 TATAAAATTT
45880473 TATAAAATTT
1 TATAAAATTT
45880483 TATAAA
1 TATAAA
45880489 GTCATAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TATAAAATTT
Found at i:45880501 original size:56 final size:55
Alignment explanation
Indices: 45880419--45880546 Score: 150
Period size: 56 Copynumber: 2.3 Consensus size: 55
45880409 TGTAAAATTG
* * *
45880419 TAAAATTTTATAAAAATCGTAAAAAATTAT-AAAATATATAGAAATATAAAATTTTA
1 TAAAATTTTAT-AAAATCATAAAAAATTATAAAAATATAAAGAAATAT-AAATTTCA
* *
45880475 TAAAATTTTATAAAGTCATAAGAAAATTATACAAAATGTAAAGAAATATAAATTTCA
1 TAAAATTTTATAAAATCATAA-AAAATTATA-AAAATATAAAGAAATATAAATTTCA
**
45880532 TAAAAAATTATAAAA
1 TAAAATTTTATAAAA
45880547 AACTATTGTA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
55 8 0.13
56 19 0.31
57 19 0.31
58 15 0.25
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (55 bp):
TAAAATTTTATAAAATCATAAAAAATTATAAAAATATAAAGAAATATAAATTTCA
Found at i:45880716 original size:19 final size:19
Alignment explanation
Indices: 45880694--45880743 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
45880684 AATTTTTATG
45880694 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTACA
* *** *
45880713 ATTTTTTTATTTTTTTACG
1 ATTTTTATAAAATTTTACA
45880732 ATTTTTATAAAA
1 ATTTTTATAAAA
45880744 AATTTAATTT
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTTATAAAATTTTACA
Found at i:45880809 original size:47 final size:45
Alignment explanation
Indices: 45880706--45880831 Score: 121
Period size: 47 Copynumber: 2.7 Consensus size: 45
45880696 TTTTATAAAA
* * *
45880706 TTTTACAATTTTTTTATTTTTTTACGATTTTTATAAAAAATTTAATTT
1 TTTTA-AA-TTTTATATTTTTTTA-TATTTTTATAAAAAATATAATTT
*
45880754 TTAATAAATTTTATATTTTTTTATATTTTTATTAAAATTAA-ATAATTT
1 TT-TTAAATTTTATATTTTTTTATATTTTTA-TAAAA--AATATAATTT
*
45880802 TTTTAAATTTTAT-TGTTTTTTTTATTTTTA
1 TTTTAAATTTTATAT-TTTTTTATATTTTTA
45880832 ATAAGAGCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
46 8 0.12
47 43 0.64
48 12 0.18
49 4 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (45 bp):
TTTTAAATTTTATATTTTTTTATATTTTTATAAAAAATATAATTT
Found at i:45883449 original size:15 final size:15
Alignment explanation
Indices: 45883429--45883458 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
45883419 TGTTTTTGGC
45883429 TTTTCAGAAGTGCTT
1 TTTTCAGAAGTGCTT
45883444 TTTTCAGAAGTGCTT
1 TTTTCAGAAGTGCTT
45883459 AAAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
TTTTCAGAAGTGCTT
Found at i:45893944 original size:16 final size:17
Alignment explanation
Indices: 45893901--45893945 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
45893891 TTTTAAATAG
45893901 AAGTTGTTCC-AAACAA
1 AAGTTGTTCCTAAACAA
*
45893917 AAGTTATT-CTAAAC-A
1 AAGTTGTTCCTAAACAA
*
45893932 TAGTTGTTCCTAAA
1 AAGTTGTTCCTAAA
45893946 ACACCATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (17 bp):
AAGTTGTTCCTAAACAA
Found at i:45898107 original size:36 final size:36
Alignment explanation
Indices: 45898032--45898107 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
45898022 AGCAAATAAT
* * * *
45898032 TATACTTATCAACCACATGTGCTGAATGCACATATA
1 TATACTTATCAACCACATATGCCGAATGCACACACA
*
45898068 TATACTTAT-AATTCACATATGCCGAATGCACACACA
1 TATACTTATCAA-CCACATATGCCGAATGCACACACA
45898104 TATA
1 TATA
45898108 TATATCCAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 2 0.06
36 32 0.94
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.30
Consensus pattern (36 bp):
TATACTTATCAACCACATATGCCGAATGCACACACA
Found at i:45898335 original size:41 final size:40
Alignment explanation
Indices: 45898290--45898402 Score: 181
Period size: 41 Copynumber: 2.8 Consensus size: 40
45898280 ACAGATTTTC
45898290 CGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCA
1 CGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCA
* *
45898330 TCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCA
1 -CGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCA
*
45898371 CTGGCACTTAGCCTGCTAGGCTTTAAGCCTGA
1 C-GGCACTTAGCCTGCTAGGCTTAAAGCCTGA
45898403 ATTGATTCAC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.01
41 66 0.99
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.28
Consensus pattern (40 bp):
CGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCA
Found at i:45898412 original size:41 final size:40
Alignment explanation
Indices: 45898291--45898432 Score: 166
Period size: 41 Copynumber: 3.5 Consensus size: 40
45898281 CAGATTTTCC
*
45898291 GGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGA-TCA-T
1 GGCACTTAGCCTGCTAGGCTTTAAGCCTGATT--GATTCACT
*
45898331 CGGCACTTAGCCTGCTAGGC-TTATAGCCTGATTCAGTTCACT
1 -GGCACTTAGCCTGCTAGGCTTTA-AGCCTGATTGA-TTCACT
45898373 GGCACTTAGCCTGCTAGGCTTTAAGCCTGAATTGATTCACT
1 GGCACTTAGCCTGCTAGGCTTTAAGCCTG-ATTGATTCACT
*
45898414 GGCAATATA-CCTGCTAGGC
1 GGCACT-TAGCCTGCTAGGC
45898433 GCTGAGCCTG
Statistics
Matches: 90, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 77 0.86
42 10 0.11
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (40 bp):
GGCACTTAGCCTGCTAGGCTTTAAGCCTGATTGATTCACT
Found at i:45898441 original size:82 final size:81
Alignment explanation
Indices: 45898291--45898443 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 81
45898281 CAGATTTTCC
* * *
45898291 GGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCATCGGCACTTAGCCTGCTAGGCTTATA
1 GGCACTTAGCCTGCTAGGCTTAAAGCCTGATT-AGATCATCGGCAATTAGCCTGCTAGGCCTAGA
45898356 GCCTGATTCAGTTCACT
65 GCCTGATTCAGTTCACT
*
45898373 GGCACTTAGCCTGCTAGGCTTTAAGCCTGAATT-GATTCA-CTGGCAATATA-CCTGCTAGGCGC
1 GGCACTTAGCCTGCTAGGCTTAAAGCCTG-ATTAGA-TCATC-GGCAAT-TAGCCTGCTAGGC-C
45898435 T-GAGCCTGA
61 TAGAGCCTGA
45898444 ATACACAATT
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
81 3 0.05
82 53 0.85
83 6 0.10
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (81 bp):
GGCACTTAGCCTGCTAGGCTTAAAGCCTGATTAGATCATCGGCAATTAGCCTGCTAGGCCTAGAG
CCTGATTCAGTTCACT
Found at i:45904623 original size:101 final size:102
Alignment explanation
Indices: 45904508--45904692 Score: 313
Period size: 101 Copynumber: 1.8 Consensus size: 102
45904498 AAAGCGATGG
* *
45904508 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCG-CATGTGTAG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGCGAT-GGT-GACATATGTAG
45904570 TACTATGTGCAGGCTACTATGCGTACCAGATAGCTTTGA
64 TACTATGTGCAGGCTACTATGCGTACCAGATAGCTTTGA
45904609 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGCGATGGTGACATATGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGCGATGGTGACATATGTAGTA
45904674 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
45904693 TGAACCGGTA
Statistics
Matches: 79, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
101 43 0.54
102 33 0.42
103 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGCGATGGTGACATATGTAGTA
CTATGTGCAGGCTACTATGCGTACCAGATAGCTTTGA
Found at i:45904638 original size:51 final size:51
Alignment explanation
Indices: 45904505--45904690 Score: 243
Period size: 51 Copynumber: 3.7 Consensus size: 51
45904495 GTGAAAGCGA
*
45904505 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATG-AT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA-GCAT
* * * * *
45904555 AGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGCTT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGCAT
* *
45904606 TGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGCGA-
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGC-AT
* *
45904657 TGGTGACATATGTAGTACTATGTGCAGGCTACTA
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
45904691 TGTGAACCGG
Statistics
Matches: 116, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
50 41 0.35
51 75 0.65
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (51 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGCAT
Found at i:45904769 original size:46 final size:43
Alignment explanation
Indices: 45904696--45904794 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
45904686 TACTATGTGA
*
45904696 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* *
45904739 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
45904785 ACCGTGTATC
1 ACCG-GTATC
45904795 TGTTATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 11 0.23
45 2 0.04
46 27 0.56
47 3 0.06
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:45904939 original size:16 final size:16
Alignment explanation
Indices: 45904918--45904949 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45904908 TGATTGAAAG
*
45904918 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
45904934 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
45904950 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:45912009 original size:42 final size:42
Alignment explanation
Indices: 45911949--45912062 Score: 135
Period size: 42 Copynumber: 2.7 Consensus size: 42
45911939 TATGAGTTTT
* *
45911949 AGTTTAACCCTTCTGGGTTTCACTTCT-GCTCTTTTGAGCTTC
1 AGTTTAACCCTTATGGGTTTCACTT-TAGCTCTTCTGAGCTTC
* * *
45911991 TGTTTAACCCTAATGGGTTTCAGTTTAGCTCTTCTGAGCTTC
1 AGTTTAACCCTTATGGGTTTCACTTTAGCTCTTCTGAGCTTC
*
45912033 AGATTAA-CCTTATGGGTTTC-CGTTTAGCTC
1 AGTTTAACCCTTATGGGTTTCAC-TTTAGCTC
45912063 CTATCAGCTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 21 0.34
42 40 0.66
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (42 bp):
AGTTTAACCCTTATGGGTTTCACTTTAGCTCTTCTGAGCTTC
Found at i:45912072 original size:41 final size:39
Alignment explanation
Indices: 45911985--45912102 Score: 101
Period size: 41 Copynumber: 2.8 Consensus size: 39
45911975 TGCTCTTTTG
* * * * *
45911985 AGCTTCTGTTTAACCCTAATGGGTTTCAGTTTAGCTCTTCTG
1 AGCTTC-G-TTAA-CCTTATGGGTTTCCGTTTAGCTCCTATC
45912027 AGCTTCAGATTAACCTTATGGGTTTCCGTTTAGCTCCTATC
1 AGCTTC-G-TTAACCTTATGGGTTTCCGTTTAGCTCCTATC
* *
45912068 AGCTTTCGTTCAACCTTTACGAGTTTCCGTTTAGC
1 AGC-TTCGTT-AACC-TTATGGGTTTCCGTTTAGC
45912103 ACTTGGGTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 2 0.03
41 31 0.48
42 31 0.48
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (39 bp):
AGCTTCGTTAACCTTATGGGTTTCCGTTTAGCTCCTATC
Found at i:45912240 original size:21 final size:21
Alignment explanation
Indices: 45912186--45912240 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
45912176 CAGATTAACC
*
45912186 CTTATGGGTTTCCGTTCAGCT
1 CTTATGGGTTTCCGTTCAACT
* * *
45912207 CCTATGAGCTTCCGTTCAACT
1 CTTATGGGTTTCCGTTCAACT
45912228 CTTATGGGTTTCC
1 CTTATGGGTTTCC
45912241 ATTTAGCACT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.13, C:0.27, G:0.20, T:0.40
Consensus pattern (21 bp):
CTTATGGGTTTCCGTTCAACT
Found at i:45912240 original size:42 final size:41
Alignment explanation
Indices: 45912106--45912239 Score: 142
Period size: 42 Copynumber: 3.2 Consensus size: 41
45912096 GTTTAGCACT
* * * *
45912106 TGGGTTTTAGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTAA
1 TGGGTTTCAGTTCAGCTCTTATGAGCTTCAG-TTAACCCTTA
* * *
45912148 TAGGTTTCAGTTTAGCTCTTCTGAGCTTCAGATTAACCCTTA
1 TGGGTTTCAGTTCAGCTCTTATGAGCTTCAG-TTAACCCTTA
* * * *
45912190 TGGGTTTCCGTTCAGCTCCTATGAGCTTCCGTTCAACTCTTA
1 TGGGTTTCAGTTCAGCTCTTATGAGCTTCAGTT-AACCCTTA
45912232 TGGGTTTC
1 TGGGTTTC
45912240 CATTTAGCAC
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 2 0.03
42 75 0.97
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.42
Consensus pattern (41 bp):
TGGGTTTCAGTTCAGCTCTTATGAGCTTCAGTTAACCCTTA
Found at i:45914302 original size:27 final size:27
Alignment explanation
Indices: 45914272--45914449 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
45914262 ATATTGAGCC
* *
45914272 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
45914299 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
45914326 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
45914354 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
45914381 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
45914408 CGCACACTTAGTACAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
45914435 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
45914450 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 102 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:45914411 original size:82 final size:81
Alignment explanation
Indices: 45914293--45914448 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
45914283 TGCTATATAA
* * * *
45914293 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTACAACATAGTC-GAATCGCA
45914358 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
45914375 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTACAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTACAACATAGTCGAATCGCA
45914439 CACTTAGTGC
65 CACTTAGTGC
45914449 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTACAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:45927624 original size:27 final size:27
Alignment explanation
Indices: 45927594--45927771 Score: 164
Period size: 27 Copynumber: 6.6 Consensus size: 27
45927584 ATATTGAGCC
* *
45927594 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
45927621 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
45927648 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
* ** *
45927676 CGCACACTTAGTG-TCGCATGGTCAATT
1 CGCACACTTAGTGCT-ACATAATCAACT
* **
45927703 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
45927730 CGCACACTTAGTACAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
45927757 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
45927772 GTACAATTTA
Statistics
Matches: 126, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
27 102 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:45927735 original size:82 final size:81
Alignment explanation
Indices: 45927615--45927769 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 81
45927605 TGCTATATAA
* * * *
45927615 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTACAACATAGTC-GAATCGCA
45927680 CACTTAGTGTCGCATGG
65 CACTTAGTGTCGCATGG
* * **
45927697 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTACAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTACAACATAGTCGAATCGCA
45927761 CACTTAGTG
65 CACTTAGTG
45927770 CTGTACAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
81 17 0.27
82 47 0.73
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTACAACATAGTCGAATCGCAC
ACTTAGTGTCGCATGG
Found at i:45930850 original size:25 final size:25
Alignment explanation
Indices: 45930820--45930929 Score: 89
Period size: 25 Copynumber: 4.4 Consensus size: 25
45930810 GTATGCTCTC
45930820 ACGAGCTGTGAATCGGGAAGCTCAT
1 ACGAGCTGTGAATCGGGAAGCTCAT
* ** ** *
45930845 ATGAGCTGCAAATTAGGAAGCTGAT
1 ACGAGCTGTGAATCGGGAAGCTCAT
* *
45930870 ACGAGCTGTTAATTGGGAAGCTCAT
1 ACGAGCTGTGAATCGGGAAGCTCAT
**
45930895 GTGAG-T-TGAATAACGGGAAGCTCAT
1 ACGAGCTGTGAAT--CGGGAAGCTCAT
*
45930920 GCGAGCTGTG
1 ACGAGCTGTG
45930930 GTGTGTCCGC
Statistics
Matches: 65, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
23 4 0.06
24 1 0.02
25 57 0.88
26 1 0.02
27 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (25 bp):
ACGAGCTGTGAATCGGGAAGCTCAT
Found at i:45930914 original size:50 final size:49
Alignment explanation
Indices: 45930820--45930929 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 49
45930810 GTATGCTCTC
* *
45930820 ACGAGCTGTGAATCGGGAAGCTCATATGAGCTGCAAATTAGGAAGCTGAT
1 ACGAGCTGTGAATCGGGAAGCTCATATGAGCTG-AAATAAGGAAGCTCAT
* * * *
45930870 ACGAGCTGTTAATTGGGAAGCTCATGTGAGTTG-AATAACGGGAAGCTCAT
1 ACGAGCTGTGAATCGGGAAGCTCATATGAGCTGAAATAA--GGAAGCTCAT
*
45930920 GCGAGCTGTG
1 ACGAGCTGTG
45930930 GTGTGTCCGC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 4 0.08
50 46 0.92
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (49 bp):
ACGAGCTGTGAATCGGGAAGCTCATATGAGCTGAAATAAGGAAGCTCAT
Found at i:45933656 original size:11 final size:11
Alignment explanation
Indices: 45933640--45933671 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
45933630 TAATCATGCA
*
45933640 AATAATTAAAT
1 AATAATAAAAT
45933651 AATAATAAAAT
1 AATAATAAAAT
45933662 AATAATAAAA
1 AATAATAAAA
45933672 AACTCGGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:45935689 original size:28 final size:28
Alignment explanation
Indices: 45935643--45935699 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
45935633 TATAGTTTTT
45935643 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
45935671 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
45935699 A
1 A
45935700 AACAAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:45936646 original size:43 final size:43
Alignment explanation
Indices: 45936596--45936711 Score: 157
Period size: 43 Copynumber: 2.7 Consensus size: 43
45936586 TATGTGTTTT
45936596 CATGTAAGACCACGTCTGGGA-AGTCGGCATCGATATCTGATTA
1 CATGTAAGACCACGTCTGGGACAGT-GGCATCGATATCTGATTA
* *
45936639 CGTGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGTGATTA
1 CATGTAAGACCAC-GTCTGGGACAGTGGCATCGATATCTGATTA
*
45936682 CATGTAAGACCACATCTGGGAC-GATGGCAT
1 CATGTAAGACCACGTCTGGGACAG-TGGCAT
45936712 TGTACGAGCT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
42 2 0.03
43 59 0.91
44 4 0.06
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGGGACAGTGGCATCGATATCTGATTA
Found at i:45937590 original size:23 final size:23
Alignment explanation
Indices: 45937563--45937733 Score: 171
Period size: 23 Copynumber: 7.3 Consensus size: 23
45937553 ATGAGTTGAA
45937563 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACATATATGCTGT
* * * * *
45937586 CCAATTTTGATGCTTAAATGCTGC
1 CCAA-TTTGTTACATATATGCTGT
45937610 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACATATATGCTGT
* * * * *
45937633 CCAATTTTGATGCTTAAATGCTGC
1 CCAA-TTTGTTACATATATGCTGT
45937657 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACATATATGCTGT
* *** * *
45937680 CCAATTTTGATGTTTAAATGCTGC
1 CCAA-TTTGTTACATATATGCTGT
45937704 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACATATATGCTGT
45937727 CCAATTT
1 CCAATTT
45937734 TGATGGTTAA
Statistics
Matches: 113, Mismatches: 32, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
23 60 0.53
24 53 0.47
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (23 bp):
CCAATTTGTTACATATATGCTGT
Found at i:45937606 original size:24 final size:24
Alignment explanation
Indices: 45937579--45937746 Score: 162
Period size: 24 Copynumber: 7.1 Consensus size: 24
45937569 TGTTACATAT
45937579 ATGCTGTCCAATTTTGATGCTTAA
1 ATGCTGTCCAATTTTGATGCTTAA
* * * * *
45937603 ATGCTGCCCAA-TTTGTTACATAT
1 ATGCTGTCCAATTTTGATGCTTAA
45937626 ATGCTGTCCAATTTTGATGCTTAA
1 ATGCTGTCCAATTTTGATGCTTAA
* * * * *
45937650 ATGCTGCCCAA-TTTGTTACATAT
1 ATGCTGTCCAATTTTGATGCTTAA
*
45937673 ATGCTGTCCAATTTTGATGTTTAA
1 ATGCTGTCCAATTTTGATGCTTAA
* * * * *
45937697 ATGCTGCCCAA-TTTGTTACATAT
1 ATGCTGTCCAATTTTGATGCTTAA
*
45937720 ATGCTGTCCAATTTTGATGGTTAA
1 ATGCTGTCCAATTTTGATGCTTAA
45937744 ATG
1 ATG
45937747 TGGCATATAT
Statistics
Matches: 108, Mismatches: 33, Indels: 6
0.73 0.22 0.04
Matches are distributed among these distances:
23 53 0.49
24 55 0.51
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (24 bp):
ATGCTGTCCAATTTTGATGCTTAA
Found at i:45937617 original size:47 final size:47
Alignment explanation
Indices: 45937563--45937746 Score: 350
Period size: 47 Copynumber: 3.9 Consensus size: 47
45937553 ATGAGTTGAA
45937563 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
45937610 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
*
45937657 CCAATTTGTTACATATATGCTGTCCAATTTTGATGTTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
*
45937704 CCAATTTGTTACATATATGCTGTCCAATTTTGATGGTTAAATG
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATG
45937747 TGGCATATAT
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 135 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (47 bp):
CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
Found at i:45937812 original size:23 final size:23
Alignment explanation
Indices: 45937786--45937837 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
45937776 AAATGTTGCT
*
45937786 CAAATTGTTGT-TTATATGCTGCC
1 CAAATTGATGTATT-TATGCTGCC
*
45937809 CAAATTGATGTATTTATGCTGTC
1 CAAATTGATGTATTTATGCTGCC
45937832 CAAATT
1 CAAATT
45937838 TTGGTGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (23 bp):
CAAATTGATGTATTTATGCTGCC
Found at i:45937855 original size:25 final size:25
Alignment explanation
Indices: 45937824--45937907 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 25
45937814 TGATGTATTT
*
45937824 ATGCTGTCCAAATTTTGGTGTGA-AA
1 ATGCTGTCCAAATTTTGGTAT-ATAA
*
45937849 ATGCTGT-CTAA-TTTGGTATATAA
1 ATGCTGTCCAAATTTTGGTATATAA
*
45937872 ATGCTGTCCAAATTGAT-GTATA-AA
1 ATGCTGTCCAAATT-TTGGTATATAA
45937896 A-GCTGTCCAAAT
1 ATGCTGTCCAAAT
45937908 AGGGTAGATT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
22 1 0.02
23 27 0.53
24 9 0.18
25 13 0.25
26 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (25 bp):
ATGCTGTCCAAATTTTGGTATATAA
Found at i:45937876 original size:71 final size:70
Alignment explanation
Indices: 45937751--45937907 Score: 185
Period size: 71 Copynumber: 2.2 Consensus size: 70
45937741 TAAATGTGGC
* * * *
45937751 ATATATGCTGTCC-AGTTTTGGTGTAAAATGTTGCTCAAATTGTTGTTTATATGCTGCCCAAATT
1 ATATATGCTGTCCAAATTTTGGTGTAAAATGCTGCTCAAATTGTGGTTTAAATGCTGCCCAAATT
45937815 GATGT
66 GATGT
* * *
45937820 ATTTATGCTGTCCAAATTTTGGTGTGAAAATGCTG-TCTAATT-TGGTATATAAATGCTGTCCAA
1 ATATATGCTGTCCAAATTTTGGTGT-AAAATGCTGCTCAAATTGTGGT-T-TAAATGCTGCCCAA
45937883 ATTGATGT
63 ATTGATGT
* *
45937891 ATAAAAGCTGTCCAAAT
1 ATATATGCTGTCCAAAT
45937908 AGGGTAGATT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
69 15 0.20
70 17 0.23
71 42 0.57
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (70 bp):
ATATATGCTGTCCAAATTTTGGTGTAAAATGCTGCTCAAATTGTGGTTTAAATGCTGCCCAAATT
GATGT
Found at i:45939502 original size:13 final size:15
Alignment explanation
Indices: 45939475--45939506 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
45939465 CAAACAAAAG
45939475 AAAATTAGAATTTAA
1 AAAATTAGAATTTAA
45939490 AAAATTA-AA-TTAA
1 AAAATTAGAATTTAA
45939503 AAAA
1 AAAA
45939507 ACTATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 2 0.12
15 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAATTAGAATTTAA
Found at i:45939507 original size:14 final size:15
Alignment explanation
Indices: 45939475--45939507 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
45939465 CAAACAAAAG
*
45939475 AAAATTAGAATTTAA
1 AAAATTAGAATTAAA
45939490 AAAATTA-AATTAAA
1 AAAATTAGAATTAAA
45939504 AAAA
1 AAAA
45939508 CTATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAAATTAGAATTAAA
Found at i:45943056 original size:8 final size:8
Alignment explanation
Indices: 45943039--45943083 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
45943029 TTGGTTAAAA
*
45943039 ATTAATCG
1 ATTAACCG
45943047 ATTAACCG
1 ATTAACCG
45943055 ATTTAACCG
1 A-TTAACCG
*
45943064 ATTAACTG
1 ATTAACCG
45943072 ATTTAACCG
1 A-TTAACCG
45943081 ATT
1 ATT
45943084 TAACTGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 17 0.53
9 15 0.47
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (8 bp):
ATTAACCG
Found at i:45943062 original size:9 final size:9
Alignment explanation
Indices: 45943048--45943120 Score: 94
Period size: 9 Copynumber: 8.2 Consensus size: 9
45943038 AATTAATCGA
45943048 TTAACCGAT
1 TTAACCGAT
45943057 TTAACCGA-
1 TTAACCGAT
*
45943065 TTAACTGAT
1 TTAACCGAT
45943074 TTAACCGAT
1 TTAACCGAT
*
45943083 TTAACTGAT
1 TTAACCGAT
**
45943092 TTAACTAAT
1 TTAACCGAT
*
45943101 TTAATCGAT
1 TTAACCGAT
45943110 TTAACCGAT
1 TTAACCGAT
45943119 TT
1 TT
45943121 TCTATATAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
8 7 0.13
9 48 0.87
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (9 bp):
TTAACCGAT
Done.