Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 159 of 187
Found at i:47041210 original size:3 final size:3
Alignment explanation
Indices: 47041202--47041234 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
47041192 TTGAAGGGAG
47041202 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
47041235 ATGGATTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:47053015 original size:15 final size:15
Alignment explanation
Indices: 47052967--47053018 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
47052957 TAACTCAGAT
47052967 ATTTA-TAATATTTATA
1 ATTTATTAAT-TTTA-A
*
47052983 ATTAATTTAATTTT-A
1 ATTTA-TTAATTTTAA
47052998 ATTTATTAATTTTAA
1 ATTTATTAATTTTAA
47053013 ATTTAT
1 ATTTAT
47053019 ATTATCCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 8 0.26
15 12 0.39
16 4 0.13
17 3 0.10
18 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTAATTTTAA
Found at i:47053812 original size:56 final size:62
Alignment explanation
Indices: 47053737--47053853 Score: 156
Period size: 56 Copynumber: 1.9 Consensus size: 62
47053727 TGACAAGTTC
47053737 ATGTACCAAATTAGAAAAAA-A-AA-TT-AAGTACCAAATT-A-AAAAAAAATGTCAAACCT
1 ATGTACCAAATTAGAAAAAAGATAAGTTCAAGTACCAAATTGACAAAAAAAATGTCAAACCT
*
47053793 ATGTACCAAATTAGGAAAAAGTATTAAGTTCAAGTACCAAATTGGACAAAAAAAATGTCAA
1 ATGTACCAAATTAGAAAAAAG-A-TAAGTTCAAGTACCAAATT-GACAAAAAAAATGTCAA
47053854 GTTTAAGTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
56 19 0.37
58 1 0.02
60 2 0.04
61 2 0.04
62 12 0.24
64 1 0.02
65 14 0.27
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.22
Consensus pattern (62 bp):
ATGTACCAAATTAGAAAAAAGATAAGTTCAAGTACCAAATTGACAAAAAAAATGTCAAACCT
Found at i:47054465 original size:16 final size:18
Alignment explanation
Indices: 47054428--47054466 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
47054418 AATTAATTGA
47054428 AAAATGTAATAAAATATT
1 AAAATGTAATAAAATATT
*
47054446 AAAAT-TAATAAGAT-TT
1 AAAATGTAATAAAATATT
47054462 AAAAT
1 AAAAT
47054467 AAAAATTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 8 0.40
18 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
AAAATGTAATAAAATATT
Found at i:47054978 original size:24 final size:25
Alignment explanation
Indices: 47054946--47055007 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 25
47054936 GGGTTTTATT
* *
47054946 AATAATATAAATATA-CA-ATTAATA
1 AATATTATAAAT-TACCATATTAAAA
47054970 AATATTATAAATTACGCATATTAAAA
1 AATATTATAAATTAC-CATATTAAAA
47054996 AATATGTATAAA
1 AATAT-TATAAA
47055008 AAATAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 2 0.06
24 11 0.34
25 2 0.06
26 11 0.34
27 6 0.19
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (25 bp):
AATATTATAAATTACCATATTAAAA
Found at i:47060636 original size:29 final size:30
Alignment explanation
Indices: 47060559--47060637 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
47060549 TCAAAATTCA
* *
47060559 AAAAGTATAAGGACTAAAATTGACTAATTT
1 AAAAGTATAAGGACTAAATTTGACTAATAT
* * *
47060589 AAATTGTACATA-GACTAAATTTGATTAA-AT
1 AAA-AGTATA-AGGACTAAATTTGACTAATAT
47060619 AAAAGTATAAGGACTAAAT
1 AAAAGTATAAGGACTAAAT
47060638 CTATAACTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
28 1 0.03
29 12 0.31
30 7 0.18
31 18 0.46
32 1 0.03
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (30 bp):
AAAAGTATAAGGACTAAATTTGACTAATAT
Found at i:47065247 original size:23 final size:23
Alignment explanation
Indices: 47065217--47065262 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
47065207 GTGTTTCATG
47065217 TCTGCTGCCTGATTAAGTTACAT
1 TCTGCTGCCTGATTAAGTTACAT
47065240 TCTGCTGCCTGATTAAGTTACAT
1 TCTGCTGCCTGATTAAGTTACAT
47065263 ACTAGCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (23 bp):
TCTGCTGCCTGATTAAGTTACAT
Found at i:47065622 original size:45 final size:46
Alignment explanation
Indices: 47065572--47065662 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
47065562 TTCTTCACAG
**
47065572 AATTAAA-TTCCTACTATAAAATTTTTGAAAAATACAACCACTATA
1 AATTAAATTTCCTACTATAAAATTTTCAAAAAATACAACCACTATA
* * *
47065617 AATTAAATTTCCTACTTTGAAATTTTCAAAAAATACAATCACTATA
1 AATTAAATTTCCTACTATAAAATTTTCAAAAAATACAACCACTATA
47065663 GACATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 7 0.17
46 33 0.82
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.35
Consensus pattern (46 bp):
AATTAAATTTCCTACTATAAAATTTTCAAAAAATACAACCACTATA
Found at i:47071298 original size:92 final size:90
Alignment explanation
Indices: 47071141--47071349 Score: 262
Period size: 92 Copynumber: 2.3 Consensus size: 90
47071131 TTGATTTTAG
* *
47071141 TAAATTCATATAAAAACATTTTATTATTAAGAATTTTATAAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAAAA-A-TTTATTATCAAGAATTTTATAAAATTATATATAACTATTAAATTAT
* *
47071206 ATTTAAT-ATTAATTATTTTAAATTGTA
64 ATGTAATAATT-ATTATTTTAAATTATA
* *
47071233 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAA-AAAATTTATTATCAAGAATTTTATAAAATTAT-ATA-TAACTATTAAATTA
47071297 TATGTAATAATTATTATTTTAAATTATA
63 TATGTAATAATTATTATTTTAAATTATA
*
47071325 CAAATTCATA-AAATATAATTTATTA
1 TAAATTCATATAAA-A-AATTTATTA
47071350 GTTATAATTA
Statistics
Matches: 104, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
90 2 0.02
91 30 0.29
92 66 0.63
93 6 0.06
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAAATTCATATAAAAAATTTATTATCAAGAATTTTATAAAATTATATATAACTATTAAATTATAT
GTAATAATTATTATTTTAAATTATA
Found at i:47071312 original size:24 final size:25
Alignment explanation
Indices: 47071277--47071324 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
47071267 TTATGAAATT
47071277 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
47071301 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
47071325 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:47071644 original size:15 final size:16
Alignment explanation
Indices: 47071616--47071659 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
47071606 AGAATTTTAT
*
47071616 TAATATATTTTAATTA
1 TAATATATTTTAATAA
47071632 TAATATA-TTTAATAA
1 TAATATATTTTAATAA
47071647 TAAT-TATGTTTAA
1 TAATATAT-TTTAA
47071660 ATATGATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TAATATATTTTAATAA
Found at i:47071880 original size:156 final size:156
Alignment explanation
Indices: 47071618--47071908 Score: 510
Period size: 156 Copynumber: 1.9 Consensus size: 156
47071608 AATTTTATTA
* ** *
47071618 ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTATTTATTATT
1 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAAAAATTTATTACT
* * *
47071683 GATATTAATAATCTTATTAAAATTTAAATAACAATATCAATAATAATTTACCAAAACAAATTTCT
66 GATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAACAAATTTAT
47071748 GCTAATTATAAGAATATTATTAAATT
131 GCTAATTATAAGAATATTATTAAATT
47071774 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAAAAATTTATTACT
1 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAAAAATTTATTACT
*
47071839 GATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAACAAATTTAT
66 GATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAACAAATTTAT
47071904 GCTAA
131 GCTAA
47071909 GGGTATTCTA
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
156 127 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (156 bp):
ATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAAAAATTTATTACT
GATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAACAAATTTAT
GCTAATTATAAGAATATTATTAAATT
Found at i:47072039 original size:45 final size:40
Alignment explanation
Indices: 47071941--47072047 Score: 108
Period size: 45 Copynumber: 2.6 Consensus size: 40
47071931 TTTTCCATTA
47071941 TGCTATTACACCTCTATTCC-ATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCAATTCAACCAAACACAAGAT
* * ***
47071980 TACTATTACGCCTCTATTCCATTACCTTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA--A--TTCAACCAAACACAAGA-T
*
47072025 TGCTATTACACCTCTAATCCAAT
1 TGCTATTACACCTCTATTCCAAT
47072048 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
39 18 0.33
41 1 0.02
42 1 0.02
43 1 0.02
44 14 0.26
45 19 0.35
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.33
Consensus pattern (40 bp):
TGCTATTACACCTCTATTCCAATTCAACCAAACACAAGAT
Found at i:47072052 original size:16 final size:16
Alignment explanation
Indices: 47072031--47072066 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
47072021 GATTTGCTAT
47072031 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
47072047 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
47072063 TACA
1 TACA
47072067 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:47075313 original size:20 final size:19
Alignment explanation
Indices: 47075272--47075314 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
47075262 GTTTACTCCA
* **
47075272 AAATCTCGATGTAAATCTT
1 AAATCTCGATCTAAATAAT
47075291 AAATCTCGATCTGAAATAAT
1 AAATCTCGATCT-AAATAAT
47075311 AAAT
1 AAAT
47075315 GTTGGAACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (19 bp):
AAATCTCGATCTAAATAAT
Found at i:47080689 original size:15 final size:13
Alignment explanation
Indices: 47080653--47080741 Score: 108
Period size: 13 Copynumber: 6.8 Consensus size: 13
47080643 TGAGTTCGGT
47080653 TATATTGTTTTAA
1 TATATTGTTTTAA
47080666 TATACTT-TTTTAA
1 TATA-TTGTTTTAA
47080679 TATATTGTTTTAA
1 TATATTGTTTTAA
* *
47080692 TATATTGCTATAA
1 TATATTGTTTTAA
* *
47080705 TATACTGTTATAA
1 TATATTGTTTTAA
47080718 TTATATTGTTTTAA
1 -TATATTGTTTTAA
*
47080732 TATAATGTTT
1 TATATTGTTT
47080742 AAACTTTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
12 2 0.03
13 51 0.77
14 13 0.20
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (13 bp):
TATATTGTTTTAA
Found at i:47080801 original size:16 final size:16
Alignment explanation
Indices: 47080776--47080817 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
47080766 TTATAAATAT
* *
47080776 ACATTTAATTTGTAAC
1 ACATTAAATTTCTAAC
47080792 ACATTAAA-TTCTAAC
1 ACATTAAATTTCTAAC
47080807 ACATTAAATTT
1 ACATTAAATTT
47080818 TAGTTTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.40
Consensus pattern (16 bp):
ACATTAAATTTCTAAC
Found at i:47082981 original size:18 final size:18
Alignment explanation
Indices: 47082958--47082997 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
47082948 CAAAAAGGAC
*
47082958 GATGAGGGCGATGACGAT
1 GATGAGGACGATGACGAT
*
47082976 GATGAGGACGATGATGAT
1 GATGAGGACGATGACGAT
47082994 GATG
1 GATG
47082998 GTGTTTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.42, T:0.20
Consensus pattern (18 bp):
GATGAGGACGATGACGAT
Found at i:47083873 original size:25 final size:25
Alignment explanation
Indices: 47083839--47083886 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
47083829 TTAAGATTTG
47083839 ATTGTTTGTAATTAAATTCAAATTA
1 ATTGTTTGTAATTAAATTCAAATTA
47083864 ATTGTTTGTAATTAAATTCAAAT
1 ATTGTTTGTAATTAAATTCAAAT
47083887 AAGTAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (25 bp):
ATTGTTTGTAATTAAATTCAAATTA
Found at i:47083969 original size:16 final size:16
Alignment explanation
Indices: 47083950--47083983 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
47083940 ATATAAATTC
47083950 AATAACAATTAATTTT
1 AATAACAATTAATTTT
*
47083966 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
47083982 AA
1 AA
47083984 CTTTTAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTAATTTT
Found at i:47086312 original size:14 final size:16
Alignment explanation
Indices: 47086279--47086315 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
47086269 AATATTTATT
47086279 TAATATTTTACTTAAAG
1 TAATATTTTAC-TAAAG
47086296 TAATATTTTA-T-AAG
1 TAATATTTTACTAAAG
47086310 TAATAT
1 TAATAT
47086316 AATAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
17 10 0.50
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (16 bp):
TAATATTTTACTAAAG
Found at i:47091298 original size:2 final size:2
Alignment explanation
Indices: 47091291--47091330 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47091281 CCAAGTTGGC
47091291 AT AT AT AT AT 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
47091331 TCACATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47092216 original size:43 final size:42
Alignment explanation
Indices: 47092120--47092302 Score: 125
Period size: 43 Copynumber: 4.3 Consensus size: 42
47092110 CTAGCATCAC
** * * * * * *
47092120 AGTGCATCATCGGATAAACCGAAGGAAATATACTGGTACACA
1 AGTGCATCATCGGACGAACCAAAGCAAATGTAATGGCACAGA
* * * *
47092162 TAGTGCTTCATCGGAC-AAGTCAAAGCAATTGTATTGGCACACGA
1 -AGTGCATCATCGGACGAA-CCAAAGCAAATGTAATGGCACA-GA
* * * *
47092206 GGTGCATCATCTGACGAACCAAAGCAAATGTAATGGTACATA
1 AGTGCATCATCGGACGAACCAAAGCAAATGTAATGGCACAGA
* * * * * * *
47092248 AGTGCATCATCGAATGAACCGAAGCAAATATATTGACACATA
1 AGTGCATCATCGGACGAACCAAAGCAAATGTAATGGCACAGA
47092290 AGTGCATCATCGG
1 AGTGCATCATCGG
47092303 TTAAACCGAA
Statistics
Matches: 109, Mismatches: 28, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
42 48 0.44
43 58 0.53
44 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (42 bp):
AGTGCATCATCGGACGAACCAAAGCAAATGTAATGGCACAGA
Found at i:47092310 original size:42 final size:42
Alignment explanation
Indices: 47092120--47092357 Score: 165
Period size: 42 Copynumber: 5.6 Consensus size: 42
47092110 CTAGCATCAC
* *
47092120 AGTGCATCATCGGATAAACCGAAGGAAATATACTGGTACACAT-
1 AGTGCATCATCGGATAAACCGAAGCAAATATA-TTG-ACACATA
* * ** * * * * *
47092163 AGTGCTTCATCGGACAAGTCAAAGCAATTGTATTGGCACACGA
1 AGTGCATCATCGGATAAACCGAAGCAAATATATTGACACA-TA
* * ** * * * **
47092206 GGTGCATCATCTGACGAACCAAAGCAAATGTAATGGTACATA
1 AGTGCATCATCGGATAAACCGAAGCAAATATATTGACACATA
* *
47092248 AGTGCATCATCGAATGAACCGAAGCAAATATATTGACACATA
1 AGTGCATCATCGGATAAACCGAAGCAAATATATTGACACATA
* * *
47092290 AGTGCATCATCGGTTAAACCGAAGTAAATATACTGGTACACATA
1 AGTGCATCATCGGATAAACCGAAGCAAATATA-TTG-ACACATA
* *
47092334 AGTGCATTA-CCGACTAAACCGAAG
1 AGTGCATCATCGGA-TAAACCGAAG
47092358 TATAAACCCA
Statistics
Matches: 152, Mismatches: 38, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
41 4 0.03
42 64 0.42
43 59 0.39
44 25 0.16
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (42 bp):
AGTGCATCATCGGATAAACCGAAGCAAATATATTGACACATA
Found at i:47092354 original size:86 final size:87
Alignment explanation
Indices: 47092120--47092357 Score: 218
Period size: 86 Copynumber: 2.8 Consensus size: 87
47092110 CTAGCATCAC
* * **
47092120 AGTGCATCATCGGATAAACCGAAGGAAATATACTGGTACACAT-AGTGC-TTCATCGGAC-AAGT
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGTACACATAAGTGCATT-A-CCGACTAAAC
* * * *
47092182 CAAAGCAATTGTATTGGCACACGA
64 CGAAGCAAATATATTGACACACGA
* * ** * * * * * * *
47092206 GGTGCATCATCTGACGAACCAAAGCAAATGTAATGGT--ACATAAGTGCATCATCGAATGAACCG
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGTACACATAAGTGCATTACCGACTAAACCG
*
47092269 AAGCAAATATATTGACACA-TA
66 AAGCAAATATATTGACACACGA
* *
47092290 AGTGCATCATCGGTTAAACCGAAGTAAATATACTGGTACACATAAGTGCATTACCGACTAAACCG
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGTACACATAAGTGCATTACCGACTAAACCG
47092355 AAG
66 AAG
47092358 TATAAACCCA
Statistics
Matches: 114, Mismatches: 33, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
84 35 0.31
85 24 0.21
86 55 0.48
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (87 bp):
AGTGCATCATCGGATAAACCGAAGCAAATATACTGGTACACATAAGTGCATTACCGACTAAACCG
AAGCAAATATATTGACACACGA
Found at i:47093600 original size:2 final size:2
Alignment explanation
Indices: 47093588--47093618 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
47093578 GAATATGTGT
*
47093588 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47093619 CTTATAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:47095399 original size:17 final size:17
Alignment explanation
Indices: 47095377--47095409 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47095367 GCCTTTTCTA
47095377 ATTAAAAATTTATAATG
1 ATTAAAAATTTATAATG
*
47095394 ATTAAAATTTTATAAT
1 ATTAAAAATTTATAAT
47095410 TTAGTCCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTAAAAATTTATAATG
Found at i:47095621 original size:13 final size:14
Alignment explanation
Indices: 47095596--47095637 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
47095586 TTGTACTTTA
47095596 ATTTGATTAATTTT
1 ATTTGATTAATTTT
* *
47095610 TTTTGA-TAATTTA
1 ATTTGATTAATTTT
47095623 ATTTGATTAATTTT
1 ATTTGATTAATTTT
47095637 A
1 A
47095638 ATCCTTGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (14 bp):
ATTTGATTAATTTT
Found at i:47095622 original size:27 final size:26
Alignment explanation
Indices: 47095583--47095636 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
47095573 GTCGTTAAAA
*
47095583 TTTTTGTACTTTAATTTGATTAATTT
1 TTTTTGTAATTTAATTTGATTAATTT
47095609 TTTTTGATAATTTAATTTGATTAATTT
1 TTTTTG-TAATTTAATTTGATTAATTT
47095636 T
1 T
47095637 AATCCTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (26 bp):
TTTTTGTAATTTAATTTGATTAATTT
Found at i:47096668 original size:20 final size:21
Alignment explanation
Indices: 47096637--47096675 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
47096627 ATAATATCAA
47096637 ATAAATCTGAATTTTCATTGT
1 ATAAATCTGAATTTTCATTGT
47096658 ATAAA-CTGAATTTTCATT
1 ATAAATCTGAATTTTCATT
47096676 AATATCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (21 bp):
ATAAATCTGAATTTTCATTGT
Found at i:47102350 original size:3 final size:3
Alignment explanation
Indices: 47102342--47102369 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47102332 GCATATGAGA
47102342 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
47102370 CTTTGCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:47113956 original size:14 final size:12
Alignment explanation
Indices: 47113936--47113977 Score: 59
Period size: 11 Copynumber: 3.4 Consensus size: 12
47113926 TTACCCTTTG
47113936 TTTTTTGTTCTT
1 TTTTTTGTTCTT
47113948 TATTATTTGTTCTT
1 T-TT-TTTGTTCTT
47113962 TTTTTT-TTCTT
1 TTTTTTGTTCTT
47113973 TTTTT
1 TTTTT
47113978 GTGCTCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.36
12 4 0.14
13 4 0.14
14 10 0.36
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.83
Consensus pattern (12 bp):
TTTTTTGTTCTT
Found at i:47116485 original size:178 final size:179
Alignment explanation
Indices: 47116185--47116515 Score: 556
Period size: 178 Copynumber: 1.9 Consensus size: 179
47116175 TTAAAATAAT
* * * *
47116185 ATTGTAAAAATAGGTAGTCATAAATCCTAAATATGAACCGTAAATTAGATATGTATTAAGAAAAC
1 ATTGTAAAAATAGGTAGTCATAAACCCCAAATATGAACCGTAAATTAAAGATGTATTAAGAAAAC
*
47116250 ACATAAACTTGAACTATTATTTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTAT
66 ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTAT
* *
47116315 TAGGAGGAACAGTTATGAACCCCTAAAAAGTTCAAGCCTTAAAAATGAC
131 TAGAAGGAACAGTTATAAACCCCTAAAAAGTTCAAGCCTTAAAAATGAC
* *
47116364 ATTGTAAAAATAGGTAGTCATGAACCCCAAATATGAACCGTAAATTAAAGATGTATT-AGTAAAC
1 ATTGTAAAAATAGGTAGTCATAAACCCCAAATATGAACCGTAAATTAAAGATGTATTAAGAAAAC
*
47116428 ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTGT
66 ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTAT
*
47116493 TAGAAGGGACAGTTATAAACCCC
131 TAGAAGGAACAGTTATAAACCCC
47116516 AAATTTGAAC
Statistics
Matches: 141, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
178 89 0.63
179 52 0.37
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (179 bp):
ATTGTAAAAATAGGTAGTCATAAACCCCAAATATGAACCGTAAATTAAAGATGTATTAAGAAAAC
ACATAAACTTGAACTATTAATTTTTGTTAATTTGTTGTATATAAATTGTTGAACGATGACATTAT
TAGAAGGAACAGTTATAAACCCCTAAAAAGTTCAAGCCTTAAAAATGAC
Found at i:47120464 original size:19 final size:20
Alignment explanation
Indices: 47120425--47120472 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
47120415 TTAAATTTTG
**
47120425 TTAATTTTAATAATGTTAAA
1 TTAATTTTTTTAATGTTAAA
*
47120445 TTTATTTTTTTAAT-TTAAA
1 TTAATTTTTTTAATGTTAAA
47120464 TTAATTTTT
1 TTAATTTTT
47120473 ATTGTGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTAATTTTTTTAATGTTAAA
Found at i:47130367 original size:15 final size:17
Alignment explanation
Indices: 47130336--47130368 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47130326 TTTCATCTTC
47130336 TTTTATTTATAAAATAT
1 TTTTATTTATAAAATAT
47130353 TTTTATTT-T-AAATAT
1 TTTTATTTATAAAATAT
47130368 T
1 T
47130369 ACTTACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATTTATAAAATAT
Found at i:47139710 original size:27 final size:27
Alignment explanation
Indices: 47139679--47139735 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
47139669 GCAATGTTGA
* * *
47139679 TTTTTGTATATTTACGTTGGATTTTTT
1 TTTTTGTAAATTCACGGTGGATTTTTT
*
47139706 TTTTTGTAAATTCATGGTGGATTTTTT
1 TTTTTGTAAATTCACGGTGGATTTTTT
47139733 TTT
1 TTT
47139736 AGATTTACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.65
Consensus pattern (27 bp):
TTTTTGTAAATTCACGGTGGATTTTTT
Found at i:47144537 original size:10 final size:11
Alignment explanation
Indices: 47144489--47144538 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
47144479 AATTGACCAA
47144489 AACAAAACAAG
1 AACAAAACAAG
*
47144500 AAC-TAACATAG
1 AACAAAACA-AG
47144511 ATA-AAAACAAG
1 A-ACAAAACAAG
47144522 AACAAAACAA-
1 AACAAAACAAG
47144532 AACAAAA
1 AACAAAA
47144539 AATCATTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
10 12 0.36
11 16 0.48
12 5 0.15
ACGTcount: A:0.72, C:0.16, G:0.06, T:0.06
Consensus pattern (11 bp):
AACAAAACAAG
Found at i:47146316 original size:2 final size:2
Alignment explanation
Indices: 47146311--47146348 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47146301 ACACACAGAG
47146311 AT AT AT AT 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
47146349 TTGTATGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47146788 original size:36 final size:36
Alignment explanation
Indices: 47146748--47146820 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
47146738 CATGGCCAAA
47146748 TGTGTTGGACCATATAAATACAATAAATACTAATTT
1 TGTGTTGGACCATATAAATACAATAAATACTAATTT
47146784 TGTGTTGGACCATATAAATACAATAAATACTAATTT
1 TGTGTTGGACCATATAAATACAATAAATACTAATTT
47146820 T
1 T
47146821 ACATCCTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (36 bp):
TGTGTTGGACCATATAAATACAATAAATACTAATTT
Found at i:47155101 original size:29 final size:29
Alignment explanation
Indices: 47155067--47155134 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 29
47155057 GGTTAATTGT
47155067 GTTGTGTGGGTCATACGGGCGTGTGT-AA
1 GTTGTGTGGGTCATACGGGCGTGTGTGAA
47155095 GGTTGTGTGGGTCATACGGGCGTGTGTGAA
1 -GTTGTGTGGGTCATACGGGCGTGTGTGAA
*
47155125 GTCGTGTGGG
1 GTTGTGTGGG
47155135 CCACCCGACT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.12, C:0.10, G:0.47, T:0.31
Consensus pattern (29 bp):
GTTGTGTGGGTCATACGGGCGTGTGTGAA
Found at i:47158675 original size:29 final size:28
Alignment explanation
Indices: 47158643--47158717 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
47158633 GTCATGTGGT
* * *
47158643 TCACACGACCATGTGGCTTACACGGTTTG
1 TCACA-GACCATGTGGCTCACACGGTCTA
* *
47158672 TCACATAGCCGTGTGGCTCACACGGTCTA
1 TCACAGA-CCATGTGGCTCACACGGTCTA
*
47158701 TCACATGATCATGTGGC
1 TCACA-GACCATGTGGC
47158718 GTCGACAGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
28 1 0.03
29 34 0.94
30 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (28 bp):
TCACAGACCATGTGGCTCACACGGTCTA
Found at i:47160825 original size:50 final size:50
Alignment explanation
Indices: 47160710--47160952 Score: 396
Period size: 50 Copynumber: 4.8 Consensus size: 50
47160700 GATCATAACA
* * *
47160710 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAC-CTCTCATCTCGG
* * * *
47160761 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
47160811 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
47160861 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
47160911 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
47160953 TTACCCAAAT
Statistics
Matches: 179, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
50 145 0.81
51 34 0.19
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:47161068 original size:13 final size:13
Alignment explanation
Indices: 47161047--47161077 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
47161037 GCTTGGATCA
*
47161047 TCATCAAATAAAT
1 TCATAAAATAAAT
47161060 TCATAAAATAAAT
1 TCATAAAATAAAT
47161073 TCATA
1 TCATA
47161078 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:47165214 original size:34 final size:34
Alignment explanation
Indices: 47165176--47165245 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
47165166 ATTGTTTACC
* *
47165176 ACTGTATTGTTTTGTTA-AAGACATATTAAATGCT
1 ACTGTATTGATCTGTTACAAG-CATATTAAATGCT
* *
47165210 ACTGTATTGATCTGTTACATGCATATTAATTGCT
1 ACTGTATTGATCTGTTACAAGCATATTAAATGCT
47165244 AC
1 AC
47165246 CATTTGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (34 bp):
ACTGTATTGATCTGTTACAAGCATATTAAATGCT
Found at i:47171337 original size:2 final size:2
Alignment explanation
Indices: 47171330--47171391 Score: 115
Period size: 2 Copynumber: 30.5 Consensus size: 2
47171320 TATAAGTTCT
47171330 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47171372 TA TA TA TA TA TA TCA TA TA T
1 TA TA TA TA TA TA T-A TA TA T
47171392 TTTAATCCCT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 57 0.97
3 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47176502 original size:17 final size:17
Alignment explanation
Indices: 47176461--47176516 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
47176451 AAAGCAATTA
47176461 AAATAAAA-AATTAAGAT
1 AAATAAAATAATTAA-AT
47176478 -AA-AAAATAATTAAAT
1 AAATAAAATAATTAAAT
* *
47176493 AAATAAAATATTTGAAT
1 AAATAAAATAATTAAAT
*
47176510 AATTAAA
1 AAATAAA
47176517 TAAGAGCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.18
16 10 0.30
17 17 0.52
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (17 bp):
AAATAAAATAATTAAAT
Found at i:47177352 original size:129 final size:129
Alignment explanation
Indices: 47177122--47177383 Score: 515
Period size: 129 Copynumber: 2.0 Consensus size: 129
47177112 CAATTAATTA
47177122 TAAGGGGGTAGTGCACGAGAAATCAAATCATATATAAAAAATCGAATCCCCCAACACCCCCATAA
1 TAAGGGGGTAGTGCACGAGAAATCAAATCATATATAAAAAATCGAATCCCCCAACACCCCCATAA
47177187 CATAAGGTGCTCGGAAATGATTGAAGTAGTTGAATAGGAGGATTGCTATGACTATAGCTCTTGG
66 CATAAGGTGCTCGGAAATGATTGAAGTAGTTGAATAGGAGGATTGCTATGACTATAGCTCTTGG
*
47177251 TAAGGGGGTAGTGCACGAGAAATCAAATCATATATAAAAAATCGAATCCCCCAGCACCCCCATAA
1 TAAGGGGGTAGTGCACGAGAAATCAAATCATATATAAAAAATCGAATCCCCCAACACCCCCATAA
47177316 CATAAGGTGCTCGGAAATGATTGAAGTAGTTGAATAGGAGGATTGCTATGACTATAGCTCTTGG
66 CATAAGGTGCTCGGAAATGATTGAAGTAGTTGAATAGGAGGATTGCTATGACTATAGCTCTTGG
47177380 TAAG
1 TAAG
47177384 TTTACCAAAG
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 132 1.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (129 bp):
TAAGGGGGTAGTGCACGAGAAATCAAATCATATATAAAAAATCGAATCCCCCAACACCCCCATAA
CATAAGGTGCTCGGAAATGATTGAAGTAGTTGAATAGGAGGATTGCTATGACTATAGCTCTTGG
Found at i:47181267 original size:24 final size:24
Alignment explanation
Indices: 47181240--47181289 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
47181230 TGACGTGATG
47181240 GGTGGAGATGTAGGTAGATTGCTA
1 GGTGGAGATGTAGGTAGATTGCTA
*
47181264 GGTGGAGGTGTAGGTAGATTGCTA
1 GGTGGAGATGTAGGTAGATTGCTA
47181288 GG
1 GG
47181290 ACACGGTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.04, G:0.46, T:0.28
Consensus pattern (24 bp):
GGTGGAGATGTAGGTAGATTGCTA
Found at i:47187047 original size:10 final size:11
Alignment explanation
Indices: 47187032--47187071 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
47187022 TTTATATTTT
47187032 TTTTA-TTTCA
1 TTTTATTTTCA
47187042 TTTTATTTTC-
1 TTTTATTTTCA
47187052 TTTTATTTTCA
1 TTTTATTTTCA
*
47187063 TTTTGTTTT
1 TTTTATTTT
47187072 ACCTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 15 0.56
11 12 0.44
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:47187049 original size:5 final size:5
Alignment explanation
Indices: 47187026--47187072 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
47187016 TTTTTGTTTA
* * *
47187026 TATTT T-TTT TATTT CATTT TATTT TCTTT TATTT TCATTT TGTTT TA
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT T-ATTT TATTT TA
47187073 CCTAAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 4 0.12
5 25 0.74
6 5 0.15
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:47187055 original size:21 final size:20
Alignment explanation
Indices: 47187026--47187071 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
47187016 TTTTTGTTTA
47187026 TATTTTTTTTA-TTTCATTT
1 TATTTTTTTTATTTTCATTT
47187045 TATTTTCTTTTATTTTCATTT
1 TATTTT-TTTTATTTTCATTT
*
47187066 TGTTTT
1 TATTTT
47187072 ACCTAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 5 0.21
21 13 0.54
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (20 bp):
TATTTTTTTTATTTTCATTT
Found at i:47187681 original size:15 final size:15
Alignment explanation
Indices: 47187663--47187691 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47187653 TATTTGACAT
47187663 TTTATTATTATATTA
1 TTTATTATTATATTA
47187678 TTTATTATTATATT
1 TTTATTATTATATT
47187692 TTCTATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTATTATATTA
Found at i:47187739 original size:24 final size:23
Alignment explanation
Indices: 47187687--47187739 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
47187677 ATTTATTATT
*
47187687 ATATTTTCTATACATATATTCGC
1 ATATTTTATATACATATATTCGC
*
47187710 ATATTTTATATATCATGTATAT-GC
1 ATATTTTATATA-CATATAT-TCGC
47187734 ATATTT
1 ATATTT
47187740 AACGTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
24 14 0.54
25 1 0.04
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (23 bp):
ATATTTTATATACATATATTCGC
Found at i:47192721 original size:7 final size:7
Alignment explanation
Indices: 47192692--47192737 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
47192682 TGAGTCGTAA
47192692 AAAAATG
1 AAAAATG
*
47192699 ATGAAAT-
1 A-AAAATG
47192706 AAAAATG
1 AAAAATG
*
47192713 AAAAGTG
1 AAAAATG
47192720 -AAAATG
1 AAAAATG
47192726 AAAAATG
1 AAAAATG
47192733 AAAAA
1 AAAAA
47192738 CGGAAAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
6 9 0.28
7 19 0.59
8 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:47192723 original size:13 final size:13
Alignment explanation
Indices: 47192702--47192736 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
47192692 AAAAATGATG
*
47192702 AAATAAAAATGAA
1 AAATGAAAATGAA
*
47192715 AAGTGAAAATGAA
1 AAATGAAAATGAA
47192728 AAATGAAAA
1 AAATGAAAA
47192737 ACGGAAAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAATGAAAATGAA
Found at i:47195286 original size:44 final size:43
Alignment explanation
Indices: 47194048--47195294 Score: 1284
Period size: 44 Copynumber: 28.3 Consensus size: 43
47194038 TGAAAAGCAG
*
47194048 CAGATCTTGTCTTCATGTATTGACATGAAGTATATCAGAGAAAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCA-AGAAAA
* *
47194092 CAGATCTTGTCTTCATGTATTGACATGGAGTAGATCAAGGATAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAA-GAAAA
* *
47194136 TAGATCTTGTCTTCATGTATTGACATGGAGTAGATCAGAGAAAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCA-AGAAAA
* * *
47194180 TAGATCTTGTCTTCATGTATTGACATGGAGTAGATCAAGGATAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAA-GAAAA
*
47194224 TAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAAAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCA-AGAAAA
* * * * * *
47194268 TAGATCTTATCTTTATGTATTGACATGGAGTGGATCAATGATAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAA-GAAAA
* * *
47194312 TAGATCTTGTCTTCATGTATTGACATGGAGTAGATCAAGGATAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAA-GAAAA
* * **
47194356 TAGATCTTGTCTTCATGTATTGACATGAAGTAGATTAGAGGTAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCA-AGAAAA
* *
47194400 -TGTATCTTGTATTCATGTATTGACATGAAGTAGATCAGAGAAAA
1 CAG-ATCTTGTCTTCATGTATTGACATGAAGTAGATCA-AGAAAA
* * *
47194444 CAGATTTTGTCTTCATGTATTGACATGACGTAGATCAAAAATAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAGAA-AA
** * *
47194488 TGGATCTTGTCTTCATGTATTGACATGACGTAGATCAAAAATAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAGAA-AA
** **
47194532 TGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGGTAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCA-AGAAAA
** *
47194576 TGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGGGAAAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCA-AGAAAA
* * *
47194620 CAAATCTTGTCTTCATGTATTGATATGAAGTAGATCGAAGATAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AAGAAAA
** *
47194664 TGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGAAAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AAGAAAA
* * * *
47194708 CGGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCCAAGAAAA
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGAT-CAAGAAAA
** * *
47194752 TGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCA-AGAAAA
* *
47194796 CAGATCTTGTCTTCATGTATT-AGCGTGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATC-AAGAAAA
* * *
47194840 CAGACCTTGTCTTCATGTATT-AGCGTGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATC-AAGAAAA
* *** *
47194884 CAAATCTTGTCTTCATGTATTGGTGTGAAGTAGATCAAAGAAAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AAGAAAA
* * *
47194928 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AAGAAAA
* * * *
47194972 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AAGAAAA
* * *
47195016 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AAGAAAA
* * * *
47195060 CAGATTTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AAGAAAA
* *
47195104 CAGATCTTGTCTTCATGTATT-AGCGTGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATC-AAGAAAA
* * * *
47195148 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AAGAAAA
* * ** * *
47195192 CAGATATTGTCTTCCCATACTGGTGGC--GAAATAGATCGAAGAAAA
1 CAGATCTTGTCTT--CAT-GTATTGACATGAAGTAGATC-AAGAAAA
* * * *
47195237 CAGATATTGTCTTCATGTACT-AGCATGAAGTAGATCAATGATAG
1 CAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCAA-GAAAA
*
47195281 CAGATATTGTCTTC
1 CAGATCTTGTCTTC
47195295 CCATATTGGT
Statistics
Matches: 1080, Mismatches: 98, Indels: 50
0.88 0.08 0.04
Matches are distributed among these distances:
42 3 0.00
43 15 0.01
44 1018 0.94
45 36 0.03
46 3 0.00
47 5 0.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (43 bp):
CAGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAGAAAA
Found at i:47196247 original size:12 final size:12
Alignment explanation
Indices: 47196226--47196262 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
47196216 TTTCTTTTTG
47196226 TTTATATTTCTT
1 TTTATATTTCTT
*
47196238 TTTTTATTTCTT
1 TTTATATTTCTT
47196250 TTTAT-TTTCTT
1 TTTATATTTCTT
47196261 TT
1 TT
47196263 ATTTTCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTATATTTCTT
Found at i:47196258 original size:11 final size:11
Alignment explanation
Indices: 47196226--47196278 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 11
47196216 TTTCTTTTTG
47196226 TTTATATTTCTT
1 TTTAT-TTTCTT
*
47196238 TTTTTATTTCTT
1 TTTAT-TTTCTT
47196250 TTTATTTTC-T
1 TTTATTTTCTT
*
47196260 TTTATTTTCAT
1 TTTATTTTCTT
*
47196271 TTTGTTTT
1 TTTATTTT
47196279 ACCTAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
10 10 0.27
11 12 0.32
12 15 0.41
ACGTcount: A:0.11, C:0.08, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTATTTTCTT
Found at i:47199683 original size:18 final size:19
Alignment explanation
Indices: 47199657--47199703 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
47199647 CAACCCATTT
*
47199657 TATTAATGT-TGCTTGGAA
1 TATTGATGTCTGCTTGGAA
*
47199675 TATTGATGTGCTTCTTGGAA
1 TATTGATGT-CTGCTTGGAA
47199695 TATTGATGT
1 TATTGATGT
47199704 GAAGCCTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
20 17 0.68
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.47
Consensus pattern (19 bp):
TATTGATGTCTGCTTGGAA
Found at i:47200974 original size:42 final size:40
Alignment explanation
Indices: 47200920--47201014 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 40
47200910 TTAAAAATAT
*
47200920 TTATATTAAAAAAACACTACCATAAATATAATAAATGA-TTTA
1 TTATATTAAAAAAACAC-A-AATAAATATAATAAAT-ATTTTA
47200962 TTATATT-AAAAAACACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAAACACAAATAAATATAATAAATATTTTA
*
47201001 TTTTATTAAAAAAA
1 TTATATTAAAAAAA
47201015 TTTAAATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
38 1 0.02
39 25 0.51
40 7 0.14
41 9 0.18
42 7 0.14
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (40 bp):
TTATATTAAAAAAACACAAATAAATATAATAAATATTTTA
Found at i:47201479 original size:21 final size:20
Alignment explanation
Indices: 47201441--47201479 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
47201431 AAATTTTTCG
* *
47201441 AATTAAGTCGAGTGAAATGA
1 AATTAAGTCGACTCAAATGA
47201461 AATTCAAGTCGACTCAAAT
1 AATT-AAGTCGACTCAAAT
47201480 CGAGTGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (20 bp):
AATTAAGTCGACTCAAATGA
Found at i:47201762 original size:17 final size:17
Alignment explanation
Indices: 47201735--47201772 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
47201725 CTTTACAACT
*
47201735 TTTTTTAAAAATTTATAA
1 TTTTTTAAAAATATA-AA
47201753 TTTTTT-AAAATATAAA
1 TTTTTTAAAAATATAAA
47201769 TTTT
1 TTTT
47201773 GAAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 7 0.37
18 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTTAAAAATATAAA
Found at i:47201815 original size:18 final size:18
Alignment explanation
Indices: 47201775--47201817 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
47201765 TAAATTTTGA
47201775 AAATTTTAAAAATATTTT
1 AAATTTTAAAAATATTTT
*
47201793 GAATTTTAAAAAT-TATTT
1 AAATTTTAAAAATAT-TTT
47201811 AAATTTT
1 AAATTTT
47201818 TTGATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AAATTTTAAAAATATTTT
Found at i:47201839 original size:11 final size:11
Alignment explanation
Indices: 47201816--47201849 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
47201806 TATTTAAATT
47201816 TTTTGATATTTA
1 TTTTGA-ATTTA
47201828 TTTTGAATTTA
1 TTTTGAATTTA
47201839 TTTTGTAATTT
1 TTTTG-AATTT
47201850 TTTACGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (11 bp):
TTTTGAATTTA
Found at i:47210229 original size:20 final size:21
Alignment explanation
Indices: 47210204--47210249 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
47210194 AAAAAGCAGC
47210204 CCACC-GGAGAAG-CCCATTGA
1 CCACCGGGA-AAGCCCCATTGA
*
47210224 CCACCGGGAAAGCCCCTTTGA
1 CCACCGGGAAAGCCCCATTGA
47210245 CCACC
1 CCACC
47210250 ACTTTAACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.26, C:0.41, G:0.22, T:0.11
Consensus pattern (21 bp):
CCACCGGGAAAGCCCCATTGA
Found at i:47217683 original size:17 final size:17
Alignment explanation
Indices: 47217661--47217694 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
47217651 CTCTGAATTG
*
47217661 GGGCAATGCAGAAGGAA
1 GGGCAATGCAAAAGGAA
47217678 GGGCAATGCAAAAGGAA
1 GGGCAATGCAAAAGGAA
47217695 CAATGACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.38, T:0.06
Consensus pattern (17 bp):
GGGCAATGCAAAAGGAA
Found at i:47217926 original size:6 final size:6
Alignment explanation
Indices: 47217915--47217959 Score: 81
Period size: 6 Copynumber: 7.3 Consensus size: 6
47217905 TTTTACATCG
47217915 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT AT
47217960 TCTTTTTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 32 0.84
7 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:47223131 original size:6 final size:6
Alignment explanation
Indices: 47223120--47223155 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
47223110 CGGTAACGGA
* *
47223120 TTGCTG TTGCTG TTGCTG TTGTTG TTGCTG CTGCTG
1 TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG
47223156 ATGGTGAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.17, G:0.33, T:0.50
Consensus pattern (6 bp):
TTGCTG
Found at i:47226491 original size:21 final size:20
Alignment explanation
Indices: 47226466--47226531 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
47226456 AGCAATTTAA
47226466 TTCTTTTATGTTCTTTTAACT
1 TTCTTTTAT-TTCTTTTAACT
* **
47226487 TTCTTTCTATTTTTTTTTTCT
1 TTCTTT-TATTTCTTTTAACT
*
47226508 TTTTTTTCATTCTCTTTTAACT
1 TTCTTTT-ATT-TCTTTTAACT
47226530 TT
1 TT
47226532 ATGTTCTTTC
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.03
21 22 0.63
22 12 0.34
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.73
Consensus pattern (20 bp):
TTCTTTTATTTCTTTTAACT
Found at i:47227808 original size:19 final size:20
Alignment explanation
Indices: 47227786--47227828 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
47227776 TAAATAAAAA
*
47227786 TTAATAAAAATATTAAAT-T
1 TTAATAAAAATATAAAATAT
47227805 TTAATAAAAATATAAAATAT
1 TTAATAAAAATATAAAATAT
47227825 TTAA
1 TTAA
47227829 AATTTACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAATAAAAATATAAAATAT
Found at i:47227828 original size:27 final size:29
Alignment explanation
Indices: 47227769--47227854 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 29
47227759 CATGTGACAA
47227769 AAAATTATAAATAAAAATTAATAAAAATATT
1 AAAATT-T-AATAAAAATTAATAAAAATATT
*
47227800 AAATTTTAATAAAAA-T-AT-AAAATATTT
1 AAAATTTAATAAAAATTAATAAAAATA-TT
* *
47227827 AAAATTTACTAAAAAATAGA-AAAAATAT
1 AAAATTTAATAAAAATTA-ATAAAAATAT
47227855 AAGAATCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
26 6 0.13
27 17 0.36
28 2 0.04
29 9 0.19
30 8 0.17
31 5 0.11
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (29 bp):
AAAATTTAATAAAAATTAATAAAAATATT
Found at i:47231154 original size:14 final size:14
Alignment explanation
Indices: 47231135--47231166 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
47231125 GGGTCTAGGA
47231135 ATAACAATGTGATT
1 ATAACAATGTGATT
47231149 ATAACAATGTGATT
1 ATAACAATGTGATT
47231163 ATAA
1 ATAA
47231167 GATATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (14 bp):
ATAACAATGTGATT
Found at i:47231252 original size:12 final size:12
Alignment explanation
Indices: 47231225--47231259 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
47231215 CACTTTTATA
*
47231225 TTTGAGAATATCT
1 TTTGAAAAT-TCT
47231238 TTTGAAAATTCT
1 TTTGAAAATTCT
47231250 TTTGAAAATT
1 TTTGAAAATT
47231260 ATTAACAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (12 bp):
TTTGAAAATTCT
Found at i:47233669 original size:8 final size:8
Alignment explanation
Indices: 47233656--47233680 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
47233646 AAGAAGGAAC
47233656 ACACATAG
1 ACACATAG
47233664 ACACATAG
1 ACACATAG
47233672 ACACATAG
1 ACACATAG
47233680 A
1 A
47233681 ATATATGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (8 bp):
ACACATAG
Found at i:47234751 original size:36 final size:36
Alignment explanation
Indices: 47234703--47234775 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
47234693 CACATAACTT
* *
47234703 AAAAAATGAACGATAGGTTGATATTTATGTTTGATA
1 AAAAAATAAACGATAGGTTGATATTTATGGTTGATA
47234739 AAAAAATAAACGATAGGTTGATATTTATGGTTGATA
1 AAAAAATAAACGATAGGTTGATATTTATGGTTGATA
47234775 A
1 A
47234776 TATCGATAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (36 bp):
AAAAAATAAACGATAGGTTGATATTTATGGTTGATA
Found at i:47234783 original size:30 final size:32
Alignment explanation
Indices: 47234706--47234791 Score: 95
Period size: 36 Copynumber: 2.6 Consensus size: 32
47234696 ATAACTTAAA
* *
47234706 AAATGAACGATAGGTTGATATTTATGTTTGAT
1 AAATAAACGATAGGTTGATATTTATGGTTGAT
47234738 AAAAAAATAAACGATAGGTTGATATTTATGGTTGAT
1 ----AAATAAACGATAGGTTGATATTTATGGTTGAT
*
47234774 -AAT-ATCGATAGGTTGATA
1 AAATAAACGATAGGTTGATA
47234792 AAATGAACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 14 0.30
31 3 0.06
36 30 0.64
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (32 bp):
AAATAAACGATAGGTTGATATTTATGGTTGAT
Found at i:47237651 original size:14 final size:15
Alignment explanation
Indices: 47237624--47237652 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
47237614 CGTGGCATCC
47237624 TTCTTATATCTTTTT
1 TTCTTATATCTTTTT
47237639 TTCTTAT-TCTTTTT
1 TTCTTATATCTTTTT
47237653 ATTTCCCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTATATCTTTTT
Found at i:47240837 original size:132 final size:137
Alignment explanation
Indices: 47240673--47240951 Score: 417
Period size: 144 Copynumber: 2.0 Consensus size: 137
47240663 CCTACGTTCC
47240673 ATTCAAACCGAAATCCAATTCAATATTATAATT-C-C-AA-CAAC-AATTCATTTCCAAAAATAG
1 ATTCAAACCGAAATCCAATTCAATATTATAATTCCACTAATCAACAAATTCATTTCCAAAAATAG
*
47240733 AATAAATAAATAATACCATTCATCAATTTATACAAAA-TATTAAATTTTAACCGTAAGAACTTAC
66 AATAAATAAATAATACCATTCATAAATTTATA-AAAATTATTAAATTTTAACCGTAAGAACTTAC
47240797 CTGGCTAA
130 CTGGCTAA
47240805 ATTCAAACCGAAATCCAATTCAATATTATAATTCCAACTATAATTCCAACAATAATTCATTTCCA
1 ATTCAAACCGAAATCCAATTCAATATTATAATTCC-AC--TAA-T-CAAC-A-AATTCATTTCCA
* *
47240870 ACAATAGAATAAATAAATAATACCATTCATAAATTTATAAAAATTATTAAATTTTAACTGTAAGA
59 AAAATAGAATAAATAAATAATACCATTCATAAATTTATAAAAATTATTAAATTTTAACCGTAAGA
47240935 ACTTACCTGGCTAA
124 ACTTACCTGGCTAA
47240949 ATT
1 ATT
47240952 GCAGAAATAT
Statistics
Matches: 131, Mismatches: 3, Indels: 14
0.89 0.02 0.09
Matches are distributed among these distances:
132 33 0.25
133 1 0.01
135 1 0.01
138 2 0.02
141 4 0.03
143 4 0.03
144 86 0.66
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (137 bp):
ATTCAAACCGAAATCCAATTCAATATTATAATTCCACTAATCAACAAATTCATTTCCAAAAATAG
AATAAATAAATAATACCATTCATAAATTTATAAAAATTATTAAATTTTAACCGTAAGAACTTACC
TGGCTAA
Found at i:47240848 original size:12 final size:12
Alignment explanation
Indices: 47240831--47240862 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
47240821 AATTCAATAT
47240831 TATAATTCCAAC
1 TATAATTCCAAC
47240843 TATAATTCCAAC
1 TATAATTCCAAC
*
47240855 AATAATTC
1 TATAATTC
47240863 ATTTCCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (12 bp):
TATAATTCCAAC
Found at i:47243515 original size:23 final size:23
Alignment explanation
Indices: 47243489--47243546 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
47243479 CTTAATAGTG
**
47243489 ATCATATAACCAGAATGACACAA
1 ATCATATAACCAGAACAACACAA
*
47243512 ATCACATAACCAGAACAACACAA
1 ATCATATAACCAGAACAACACAA
*
47243535 ATCGTATAACCA
1 ATCATATAACCA
47243547 AAAGAGAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.16
Consensus pattern (23 bp):
ATCATATAACCAGAACAACACAA
Found at i:47248273 original size:2 final size:2
Alignment explanation
Indices: 47248262--47248298 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
47248252 TGTAGCCAAA
47248262 AT AT -T AT 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
47248299 TTACCTCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:47249474 original size:2 final size:2
Alignment explanation
Indices: 47249467--47249497 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47249457 TTATTTGTAG
47249467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47249498 AATAAACAAC
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47256362 original size:2 final size:2
Alignment explanation
Indices: 47256355--47256391 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
47256345 TAGTTATCAC
47256355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47256392 CTACTATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47259082 original size:43 final size:43
Alignment explanation
Indices: 47259035--47259122 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
47259025 CTTCAACAAA
*
47259035 AAAATCCAACACATTCTTGTTAGATCATTGATAAAGGCTATGT
1 AAAATCCAACACATTCTTGTTAGATCATTGATAAAGACTATGT
47259078 AAAATCCAACACATTCTTGTTAGATCATTGATAAAGACTATGT
1 AAAATCCAACACATTCTTGTTAGATCATTGATAAAGACTATGT
47259121 AA
1 AA
47259123 TAGAGGTTAC
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:0.16, G:0.12, T:0.32
Consensus pattern (43 bp):
AAAATCCAACACATTCTTGTTAGATCATTGATAAAGACTATGT
Found at i:47263855 original size:2 final size:2
Alignment explanation
Indices: 47263848--47263885 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47263838 TGCAGTTATG
47263848 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47263886 AGTAAACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47266393 original size:15 final size:16
Alignment explanation
Indices: 47266368--47266411 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
47266358 AAAACTCTTT
47266368 AAAATTCAAAAATAAA
1 AAAATTCAAAAATAAA
* *
47266384 AAAATT-AAAATTTAA
1 AAAATTCAAAAATAAA
*
47266399 AAAATTCCAAAAT
1 AAAATTCAAAAAT
47266412 TTAATGTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATTCAAAAATAAA
Found at i:47266585 original size:21 final size:22
Alignment explanation
Indices: 47266559--47266599 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
47266549 CAAGTGGACA
*
47266559 GATTTTATAAT-TTTTATTTTT
1 GATTTTATAATAATTTATTTTT
*
47266580 GATTTTTTAATAATTTATTT
1 GATTTTATAATAATTTATTT
47266600 GCTTTGAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
GATTTTATAATAATTTATTTTT
Found at i:47269228 original size:51 final size:50
Alignment explanation
Indices: 47269109--47269450 Score: 343
Period size: 51 Copynumber: 6.7 Consensus size: 50
47269099 TTATCATTCA
*
47269109 ATACACGTAGTAGCCTCCACATAGTACTACACACGTGATCAAG-TTTTACG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGA-CAAGTTTTTACG
* * *
47269159 GTTCACGTAATAGCCTTCACATAGTACTACACACGTGATCAAGTTTTTACG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGA-CAAGTTTTTACG
* * **
47269210 GTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAACTTTT-CG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGA-C-AAGTTTTTACG
* * * * *
47269261 ATACACATAGTAGCCTTCACTTAGTACTACACATGTGACCA-TCATTTATCG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGACAAGT-TTTTA-CG
* * * *
47269312 ATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGA-C-AAGTTTTTACG
* * * * * *
47269363 GTACACATTGTAGCCTTCACTTAGTACTAGACATGTGACAA-TTATTTATCG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGACAAGTT-TTTA-CG
*
47269414 ATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTG
47269451 TTCATCGATA
Statistics
Matches: 239, Mismatches: 42, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
48 1 0.00
49 8 0.03
50 41 0.17
51 179 0.75
52 7 0.03
53 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (50 bp):
ATACACGTAGTAGCCTTCACATAGTACTACACACGTGACAAGTTTTTACG
Found at i:47269324 original size:102 final size:101
Alignment explanation
Indices: 47269112--47269450 Score: 432
Period size: 102 Copynumber: 3.3 Consensus size: 101
47269102 TCATTCAATA
* * * * * * *
47269112 CACGTAGTAGCCTCCACATAGTACTACACACGTGATC--AAGTTTTACGGTTCACGTAATAGCCT
1 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAACTTTT-CGGTACACATAGTAGCCT
* * * * *
47269175 TCACATAGTACTACACACGTGATCA-AGTTTTTACGGTT
65 TCACTTAGTACTACACATGTGACCATA-TTTAT-CGATT
* *
47269213 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAACTTTTCGATACACATAGTAGCCTT
1 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAACTTTTCGGTACACATAGTAGCCTT
47269278 CACTTAGTACTACACATGTGACCATCATTTATCGATT
66 CACTTAGTACTACACATGTGACCAT-ATTTATCGATT
* * *
47269315 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCCTT
1 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAACTTTTCGGTACACATAGTAGCCTT
* * *
47269380 CACTTAGTACTAGACATGTGACAATTATTTATCGATA
66 CACTTAGTACTACACATGTGACCA-TATTTATCGATT
47269417 CACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACACAGTACTACACACGTG
47269451 TTCATCGATA
Statistics
Matches: 213, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
101 35 0.16
102 166 0.78
103 11 0.05
104 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (101 bp):
CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAACTTTTCGGTACACATAGTAGCCTT
CACTTAGTACTACACATGTGACCATATTTATCGATT
Found at i:47269376 original size:153 final size:152
Alignment explanation
Indices: 47269109--47269450 Score: 429
Period size: 153 Copynumber: 2.2 Consensus size: 152
47269099 TTATCATTCA
* * ** *
47269109 ATACACGTAGTAGCCTCCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAATAGCC
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTACGATTCACGTAATAGCC
* * * * * *
47269174 TTCACATAGTACTACACACGTGATCAAGTTTTTACGGTTCACGTAGTAGCCTTCACATAGTACTA
66 TTCACACAGTACTACACACGTGACCAAGCTTCTACGGTACACATAGTAGCCTTCACATAGTACTA
47269239 CACACGTGACCAA-AACTTT-TCG
131 CACACGTGA-CAATAA-TTTATCG
* * * * *
47269261 ATACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGC
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA-CGATTCACGTAATAGC
* *
47269326 CTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTACACATTGTAGCCTTCACTTAGTAC
65 CTTCACACAGTACTACACACGTGACC-AAGCTTCTACGGTACACATAGTAGCCTTCACATAGTAC
* * *
47269390 TAGACATGTGACAATTATTTATCG
129 TACACACGTGACAATAATTTATCG
*
47269414 ATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTG
47269451 TTCATCGATA
Statistics
Matches: 161, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
152 46 0.29
153 109 0.68
154 6 0.04
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (152 bp):
ATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTACGATTCACGTAATAGCC
TTCACACAGTACTACACACGTGACCAAGCTTCTACGGTACACATAGTAGCCTTCACATAGTACTA
CACACGTGACAATAATTTATCG
Found at i:47272119 original size:45 final size:45
Alignment explanation
Indices: 47272025--47272204 Score: 231
Period size: 45 Copynumber: 4.0 Consensus size: 45
47272015 CAGATACACG
* * * * * *
47272025 GTGG-ATCAGCACATAGC-ACTACCCTTATAGTCAATGATACTCG
1 GTGGAATCAGCACACAGCAACCACCTTTATAATCAATGATACCCA
* *
47272068 GTGGAATCAGCACATAGCAACCACCTTCATAATCAAT-AGTACCCA
1 GTGGAATCAGCACACAGCAACCACCTTTATAATCAATGA-TACCCA
* *
47272113 GTGGAATCAGCACACAACAACCACCTTTATAATCAATGATACCTA
1 GTGGAATCAGCACACAGCAACCACCTTTATAATCAATGATACCCA
*
47272158 GTGGAATCAGCACACAGCAACCACCTTTATAATCAATGGTACCCA
1 GTGGAATCAGCACACAGCAACCACCTTTATAATCAATGATACCCA
47272203 GT
1 GT
47272205 ACACGTAGTA
Statistics
Matches: 120, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
43 4 0.03
44 14 0.12
45 101 0.84
46 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (45 bp):
GTGGAATCAGCACACAGCAACCACCTTTATAATCAATGATACCCA
Found at i:47277408 original size:7 final size:7
Alignment explanation
Indices: 47277396--47277435 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
47277386 AACGTTATGA
47277396 GTTTAGG
1 GTTTAGG
47277403 GTTTAGG
1 GTTTAGG
47277410 GTTTAGG
1 GTTTAGG
47277417 GTTTAGG
1 GTTTAGG
47277424 GTTTAGG
1 GTTTAGG
47277431 GTTTA
1 GTTTA
47277436 TGAGTTTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:47286038 original size:72 final size:72
Alignment explanation
Indices: 47285916--47286063 Score: 278
Period size: 72 Copynumber: 2.1 Consensus size: 72
47285906 AAAACAAAAG
*
47285916 AAATCACTTCAGTAACATTTAACTTGTTGAAACATGATCTAAGAGCAAGCACCATAAATATGAGA
1 AAATCACTTCAGTAACATTTAACTTGTTGAAACATGATCTAAGAGAAAGCACCATAAATATGAGA
47285981 AATATGA
66 AATATGA
*
47285988 AAATCACTTCAGTAACATTTAACTTGTTGAAACATGATCTAAGAGAAAGCACCATATATATGAGA
1 AAATCACTTCAGTAACATTTAACTTGTTGAAACATGATCTAAGAGAAAGCACCATAAATATGAGA
47286053 AATATGA
66 AATATGA
47286060 AAAT
1 AAAT
47286064 ATATAGCCTA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (72 bp):
AAATCACTTCAGTAACATTTAACTTGTTGAAACATGATCTAAGAGAAAGCACCATAAATATGAGA
AATATGA
Found at i:47288480 original size:7 final size:8
Alignment explanation
Indices: 47288464--47288489 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
47288454 ATTACCACTA
47288464 TTTTATTT
1 TTTTATTT
47288472 TTTTATTT
1 TTTTATTT
47288480 TTTTATTT
1 TTTTATTT
47288488 TT
1 TT
47288490 GTCTTTGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:47288850 original size:30 final size:28
Alignment explanation
Indices: 47288749--47288851 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 28
47288739 TAAAATCAAT
*
47288749 AAAAATTATTAAATTTTAATAAAAAATATA
1 AAAAATTATAAAATTTT-AT-AAAAATATA
* *
47288779 AGAAATATT-T-AATTTTTATTAAAAATTTA
1 A-AAA-ATTATAAAATTTTA-TAAAAATATA
* *
47288808 AAAGATTGTAAAATTTTATAAAAATCATA
1 AAAAATTATAAAATTTTATAAAAAT-ATA
47288837 AAAAATTTATAAAAT
1 AAAAA-TTATAAAAT
47288852 ATATTGAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
27 3 0.05
28 10 0.17
29 23 0.39
30 16 0.27
31 4 0.07
32 3 0.05
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAAATTATAAAATTTTATAAAAATATA
Found at i:47288947 original size:21 final size:21
Alignment explanation
Indices: 47288886--47288947 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
47288876 TTTTATAAAG
* *
47288886 TTGTAAAAAATATTA-AAAAAA
1 TTGTAAAAGA-ATTATAAAAAT
*
47288907 TTGT-AAAGAAATAT-AAAAT
1 TTGTAAAAGAATTATAAAAAT
47288926 TTGTAAAAGAATTATAAAAAT
1 TTGTAAAAGAATTATAAAAAT
47288947 T
1 T
47288948 ATCATATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.32
20 13 0.38
21 10 0.29
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (21 bp):
TTGTAAAAGAATTATAAAAAT
Found at i:47289014 original size:9 final size:9
Alignment explanation
Indices: 47288966--47289015 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
47288956 AAAATAAGTA
47288966 TTTTATAAT
1 TTTTATAAT
*
47288975 ATTTCTATGAT
1 -TTT-TATAAT
47288986 TTTTATAGAT
1 TTTTATA-AT
47288996 TTTTAT--T
1 TTTTATAAT
47289003 TTTTATAAT
1 TTTTATAAT
47289012 TTTT
1 TTTT
47289016 CGTCACATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
7 7 0.21
9 8 0.24
10 14 0.41
11 5 0.15
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (9 bp):
TTTTATAAT
Found at i:47289146 original size:10 final size:10
Alignment explanation
Indices: 47289133--47289269 Score: 57
Period size: 9 Copynumber: 14.5 Consensus size: 10
47289123 TTTTTGATGC
47289133 ATTTTATAAT
1 ATTTTATAAT
47289143 A-TTTATAA-
1 ATTTTATAAT
*
47289151 ATTTTTACAAT
1 A-TTTTATAAT
*
47289162 TTTTTAT-AT
1 ATTTTATAAT
*
47289171 -TTTTATACT
1 ATTTTATAAT
*
47289180 ATTTTTATATT
1 A-TTTTATAAT
* *
47289191 TTTTTCTAAT
1 ATTTTATAAT
*
47289201 -TTGTAGTAA-
1 ATTTTA-TAAT
47289210 ATTTTA-AAT
1 ATTTTATAAT
*
47289219 ATTTT-TTAT
1 ATTTTATAAT
47289228 ATTTTTATTAA-
1 A-TTTTA-TAAT
*
47289239 A-GTT-TAAT
1 ATTTTATAAT
47289247 ATTTTATAAT
1 ATTTTATAAT
47289257 -TTTTATAA-
1 ATTTTATAAT
47289265 ATTTT
1 ATTTT
47289270 TATTTTATAA
Statistics
Matches: 95, Mismatches: 15, Indels: 35
0.66 0.10 0.24
Matches are distributed among these distances:
7 3 0.03
8 10 0.11
9 37 0.39
10 34 0.36
11 9 0.09
12 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (10 bp):
ATTTTATAAT
Found at i:47289166 original size:29 final size:28
Alignment explanation
Indices: 47289134--47289271 Score: 122
Period size: 29 Copynumber: 4.9 Consensus size: 28
47289124 TTTTGATGCA
*
47289134 TTTTATAATATTTATAAATTTTTACAATT
1 TTTTATAATTTTTATAAATTTTTA-AATT
* *
47289163 TTTTAT-ATTTTTATACTATTTTTATATTT
1 TTTTATAATTTTTATA-AATTTTTA-AATT
* * *
47289192 TTTTCTAATTTGTAGTAAATTTTAAATATT
1 TTTTATAATTTTTA-TAAATTTTTAA-ATT
* *
47289222 TTTTAT-ATTTTTATTAAA-GTTT-AATA
1 TTTTATAATTTTTA-TAAATTTTTAAATT
47289248 TTTTATAATTTTTATAAATTTTTA
1 TTTTATAATTTTTATAAATTTTTA
47289272 TTTTATAAAT
Statistics
Matches: 86, Mismatches: 16, Indels: 15
0.74 0.14 0.13
Matches are distributed among these distances:
26 12 0.14
27 11 0.13
28 10 0.12
29 32 0.37
30 19 0.22
31 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTATAATTTTTATAAATTTTTAAATT
Found at i:47289182 original size:11 final size:10
Alignment explanation
Indices: 47289134--47289272 Score: 82
Period size: 10 Copynumber: 14.6 Consensus size: 10
47289124 TTTTGATGCA
47289134 TTTTATA-AT
1 TTTTATATAT
* *
47289143 ATTTATAAAT
1 TTTTATATAT
*
47289153 TTTTACA-AT
1 TTTTATATAT
47289162 TTTT-TATAT
1 TTTTATATAT
47289171 TTTTATACTAT
1 TTTTATA-TAT
*
47289182 TTTTATATTT
1 TTTTATATAT
*
47289192 TTTTCTA-AT
1 TTTTATATAT
* *
47289201 TTGTAGTA-AA
1 TTTTA-TATAT
*
47289211 TTTTAAATAT
1 TTTTATATAT
47289221 TTTT-TATAT
1 TTTTATATAT
*
47289230 TTTTAT-TAAA
1 TTTTATAT-AT
*
47289240 GTTTA-ATA-
1 TTTTATATAT
47289248 TTTTATA-AT
1 TTTTATATAT
*
47289257 TTTTATAAAT
1 TTTTATATAT
47289267 TTTTAT
1 TTTTAT
47289273 TTTATAAATT
Statistics
Matches: 101, Mismatches: 17, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
8 6 0.06
9 41 0.41
10 44 0.44
11 10 0.10
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTATATAT
Found at i:47289259 original size:26 final size:24
Alignment explanation
Indices: 47289222--47289285 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 24
47289212 TTTAAATATT
47289222 TTTTAT-ATTTTTATTAAAGTTTAATA
1 TTTTATAATTTTTA-TAAA-TTT-ATA
*
47289248 TTTTATAATTTTTATAAATTTTTA
1 TTTTATAATTTTTATAAATTTATA
47289272 TTTTATAAATTTTT
1 TTTTAT-AATTTTT
47289286 TTGTCACATG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 8 0.23
25 10 0.29
26 10 0.29
27 7 0.20
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTATAATTTTTATAAATTTATA
Found at i:47289270 original size:19 final size:19
Alignment explanation
Indices: 47289134--47289272 Score: 99
Period size: 19 Copynumber: 7.3 Consensus size: 19
47289124 TTTTGATGCA
* *
47289134 TTTTATAATATTTATAAAT
1 TTTTATAATTTTTATATAT
*
47289153 TTTTACAATTTTT-TATAT
1 TTTTATAATTTTTATATAT
*
47289171 TTTTATACTATTTTTATATTT
1 TTTTATA--ATTTTTATATAT
* * *
47289192 TTTTCTAATTTGTAGTA-AA
1 TTTTATAATTTTTA-TATAT
*
47289211 TTTTA-AATATTTTTTATAT
1 TTTTATAAT-TTTTATATAT
**
47289230 TTTTATTAAAGTTTA-ATA-
1 TTTTA-TAATTTTTATATAT
*
47289248 TTTTATAATTTTTATAAAT
1 TTTTATAATTTTTATATAT
47289267 TTTTAT
1 TTTTAT
47289273 TTTATAAATT
Statistics
Matches: 91, Mismatches: 19, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
17 7 0.08
18 22 0.24
19 39 0.43
20 11 0.12
21 12 0.13
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTATATAT
Found at i:47289278 original size:24 final size:27
Alignment explanation
Indices: 47289192--47289285 Score: 86
Period size: 28 Copynumber: 3.5 Consensus size: 27
47289182 TTTTATATTT
* * * *
47289192 TTTTCTAATTTGTAGTAAATTTTAAATA
1 TTTTATAATTTTTATTAAAGTTT-AATA
*
47289220 TTTTTTATATTTTTATTAAAGTTTAATA
1 TTTTATA-ATTTTTATTAAAGTTTAATA
*
47289248 TTTTATAATTTTTA-TAAA-TTT-TTA
1 TTTTATAATTTTTATTAAAGTTTAATA
47289272 TTTTATAAATTTTT
1 TTTTAT-AATTTTT
47289286 TTGTCACATG
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
24 8 0.14
25 10 0.17
26 4 0.07
27 7 0.12
28 16 0.28
29 13 0.22
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (27 bp):
TTTTATAATTTTTATTAAAGTTTAATA
Found at i:47289286 original size:16 final size:15
Alignment explanation
Indices: 47289257--47289285 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47289247 ATTTTATAAT
47289257 TTTTATAAATTTTTA
1 TTTTATAAATTTTTA
47289272 TTTTATAAATTTTT
1 TTTTATAAATTTTT
47289286 TTGTCACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATAAATTTTTA
Found at i:47298270 original size:16 final size:16
Alignment explanation
Indices: 47298237--47298269 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47298227 TGTTCTTTTA
47298237 TTGTTTTCATTTGCTT
1 TTGTTTTCATTTGCTT
*
47298253 TTGTTTTCCTTTG-TT
1 TTGTTTTCATTTGCTT
47298268 TT
1 TT
47298270 TTTGAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.03, C:0.12, G:0.12, T:0.73
Consensus pattern (16 bp):
TTGTTTTCATTTGCTT
Found at i:47300168 original size:25 final size:25
Alignment explanation
Indices: 47300108--47300198 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
47300098 TGAGCACTTA
*
47300108 AACAGGAAGCTC-TCCCTCGAGCCATAT
1 AACAGGAAGCTCAT--CT-GAGTCATAT
* * *
47300135 AACAAGAAGCTCATGTGAGTCATGT
1 AACAGGAAGCTCATCTGAGTCATAT
* * * *
47300160 AACGGGAAGCTTATCTGGGTTATAT
1 AACAGGAAGCTCATCTGAGTCATAT
47300185 AACAGGAAGCTCAT
1 AACAGGAAGCTCAT
47300199 AAGAGCCATA
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
25 37 0.74
26 1 0.02
27 11 0.22
28 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (25 bp):
AACAGGAAGCTCATCTGAGTCATAT
Found at i:47300270 original size:25 final size:25
Alignment explanation
Indices: 47300240--47300380 Score: 78
Period size: 25 Copynumber: 5.6 Consensus size: 25
47300230 AATAACGGGT
47300240 AGCTCCGAAGAGCCATTAATCAAGA
1 AGCTCCGAAGAGCCATTAATCAAGA
* *
47300265 AGCTCCGAATAGTCA-TATATCGAA-A
1 AGCTCCGAAGAGCCATTA-ATC-AAGA
* * **
47300290 A-TTTC-AAGCGAGCCA-T-ATCGGGA
1 AGCTCCGAA--GAGCCATTAATCAAGA
* * *
47300313 AACTCTGGAGAGCCATTAATCAAGA
1 AGCTCCGAAGAGCCATTAATCAAGA
* * *
47300338 AGCTCACAAAGAGCCTTTAATCAGGA
1 AGCTC-CGAAGAGCCATTAATCAAGA
47300364 AGCTCACGAAGAGCCAT
1 AGCTC-CGAAGAGCCAT
47300381 ATATCAGGAT
Statistics
Matches: 84, Mismatches: 22, Indels: 19
0.67 0.18 0.15
Matches are distributed among these distances:
23 13 0.15
24 6 0.07
25 33 0.39
26 32 0.38
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATTAATCAAGA
Found at i:47300386 original size:26 final size:26
Alignment explanation
Indices: 47300321--47300395 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
47300311 GAAACTCTGG
*
47300321 AGAGCCATTAATCAAGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* *
47300347 AGAGCCTTTAATCAGGAAGCTCACGA
1 AGAGCCATTAATCAGGAAGCTCACAA
*
47300373 AGAGCCA-TATATCAGGATGCTCA
1 AGAGCCATTA-ATCAGGAAGCTCA
47300396 TAAGAGCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 2 0.05
26 41 0.95
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:47301776 original size:12 final size:12
Alignment explanation
Indices: 47301759--47301783 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47301749 GGTGTTCATT
47301759 CGGTTAACCGAC
1 CGGTTAACCGAC
47301771 CGGTTAACCGAC
1 CGGTTAACCGAC
47301783 C
1 C
47301784 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:47301957 original size:9 final size:9
Alignment explanation
Indices: 47301943--47302005 Score: 81
Period size: 9 Copynumber: 6.9 Consensus size: 9
47301933 TTTGGTTAAA
47301943 AATTACCCG
1 AATTACCCG
47301952 AATTACCCG
1 AATTACCCG
47301961 AATTACCCG
1 AATTACCCG
*
47301970 AATTAACCG
1 AATTACCCG
**
47301979 AATTACCTAA
1 AATTACC-CG
*
47301989 AAATACCCG
1 AATTACCCG
47301998 AATTACCC
1 AATTACCC
47302006 AAAAAATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
9 39 0.87
10 6 0.13
ACGTcount: A:0.40, C:0.30, G:0.08, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:47302168 original size:13 final size:13
Alignment explanation
Indices: 47302150--47302179 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
47302140 TTTTAGTTTT
47302150 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
47302163 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
47302176 ATTG
1 ATTG
47302180 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:47302922 original size:23 final size:23
Alignment explanation
Indices: 47302892--47302937 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
47302882 CCTGGAGGCT
47302892 CATCTACATAGTAAGGGGTGGCA
1 CATCTACATAGTAAGGGGTGGCA
47302915 CATCTACATAGTAAGGGGTGGCA
1 CATCTACATAGTAAGGGGTGGCA
47302938 ACCATAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (23 bp):
CATCTACATAGTAAGGGGTGGCA
Found at i:47308302 original size:15 final size:15
Alignment explanation
Indices: 47308282--47308317 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
47308272 ATATTTAAGA
47308282 AAAAATGGATGTTGT
1 AAAAATGGATGTTGT
*
47308297 AAAAATGGATGTTTT
1 AAAAATGGATGTTGT
47308312 AAAAAT
1 AAAAAT
47308318 ATTAGTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (15 bp):
AAAAATGGATGTTGT
Found at i:47311103 original size:10 final size:11
Alignment explanation
Indices: 47311082--47311114 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
47311072 AACCCGCCCG
47311082 TATTAATTTTTA
1 TATT-ATTTTTA
47311094 TATT-TTTTTA
1 TATTATTTTTA
47311104 TATTATTTTTA
1 TATTATTTTTA
47311115 AATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 6 0.30
12 4 0.20
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:47314764 original size:23 final size:23
Alignment explanation
Indices: 47314732--47314777 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
47314722 AAAGAAAAGG
*
47314732 AAAAATAAATTATACCTATATTT
1 AAAAAAAAATTATACCTATATTT
*
47314755 AAAAAAAAATTATACTTATATTT
1 AAAAAAAAATTATACCTATATTT
47314778 CTTTAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAAAAAAATTATACCTATATTT
Found at i:47314918 original size:87 final size:88
Alignment explanation
Indices: 47314820--47315022 Score: 247
Period size: 88 Copynumber: 2.3 Consensus size: 88
47314810 TTTAAAGGTA
* * *
47314820 CAAAAAGCTCTCAAATTTTTTCAAAAATAAATAAATAAACCCCTA-TTTTT-TT-TA-TCATTTT
1 CAAAAAGCTCTCAAAATTTTTCAAAAA-AAATAAATAAACCCCTACTTTTTCTTGCACTCA-ATT
47314881 GGGTACTTGAACTTTT-AAAATGTAT
64 GGGTACTTGAA-TTTTCAAAATGTAT
* * *
47314906 CAAAAAAGCTCTCAAAACTTTT-AAAAAAAATAATTAAGCCCCTACTTTTTCTTGCACTCAATTG
1 C-AAAAAGCTCTCAAAATTTTTCAAAAAAAATAAATAAACCCCTACTTTTTCTTGCACTCAATTG
47314970 GGTACTTGAATTTTCAAAATGTAT
65 GGTACTTGAATTTTCAAAATGTAT
* *
47314994 CAAAAAGACCCTCAAACTTTTTCAAAAAA
1 CAAAAAG-CTCTCAAAATTTTTCAAAAAA
47315023 TCAATTAGGC
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
85 15 0.15
86 11 0.11
87 30 0.30
88 35 0.35
89 9 0.09
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (88 bp):
CAAAAAGCTCTCAAAATTTTTCAAAAAAAATAAATAAACCCCTACTTTTTCTTGCACTCAATTGG
GTACTTGAATTTTCAAAATGTAT
Found at i:47314989 original size:88 final size:85
Alignment explanation
Indices: 47314820--47315042 Score: 238
Period size: 87 Copynumber: 2.6 Consensus size: 85
47314810 TTTAAAGGTA
** * * * *
47314820 CAAAAAGCTCTCAAATTTTTTCAAAAATAAATAAATAAACCCCTA-TTTTTTTTATCATTTTGGG
1 CAAAAAGCTCTCAAAACTTTT-AAAAA-AAATAATTAAGCCCCTACTTTTTTTCATCATATTGGG
47314884 TACTTGAACTTTTAAAATGTAT
64 TACTTGAACTTTTAAAATGTAT
47314906 CAAAAAAGCTCTCAAAACTTTTAAAAAAAATAATTAAGCCCCTACTTTTTCTTGCACTCA-ATTG
1 C-AAAAAGCTCTCAAAACTTTTAAAAAAAATAATTAAGCCCCTACTTTTT-TT-CA-TCATATTG
47314970 GGTACTTGAA-TTTTCAAAATGTAT
62 GGTACTTGAACTTTT-AAAATGTAT
* ** * *
47314994 CAAAAAGACCCTC-AAACTTTTTCAAAAAATCAATTAGGCCCCTGCTTTT
1 CAAAAAG-CTCTCAAAACTTTTAAAAAAAAT-AATTAAGCCCCTACTTTT
47315043 ATTAAAAAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
85 15 0.13
86 11 0.09
87 45 0.38
88 44 0.37
89 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (85 bp):
CAAAAAGCTCTCAAAACTTTTAAAAAAAATAATTAAGCCCCTACTTTTTTTCATCATATTGGGTA
CTTGAACTTTTAAAATGTAT
Found at i:47315181 original size:23 final size:22
Alignment explanation
Indices: 47315138--47315194 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
47315128 GAAAAATTAG
47315138 AAAAAA-ATAT-AAAAATAGTA
1 AAAAAATATATAAAAAATAGTA
*
47315158 AAAGAAATATATAAAAAATTGTA
1 AAA-AAATATATAAAAAATAGTA
47315181 AAAAAAT-TATAAAA
1 AAAAAATATATAAAA
47315195 TATATAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 3 0.09
21 10 0.30
22 8 0.24
23 12 0.36
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
AAAAAATATATAAAAAATAGTA
Found at i:47315191 original size:21 final size:21
Alignment explanation
Indices: 47315118--47315292 Score: 79
Period size: 19 Copynumber: 8.7 Consensus size: 21
47315108 TTCAAATATT
* *
47315118 AAAAATTTATGAAAAATTAG-A
1 AAAAAATTATAAAAAATT-GTA
*
47315139 AAAAAA-TAT-AAAAATAGTA
1 AAAAAATTATAAAAAATTGTA
47315158 AAAGAAATATATAAAAAATTGTA
1 AAA-AAAT-TATAAAAAATTGTA
*
47315181 AAAAAATTAT--AAAA-TATA
1 AAAAAATTATAAAAAATTGTA
* *
47315199 TAGAAA-TATAAAAAATT-T-
1 AAAAAATTATAAAAAATTGTA
* * * * *
47315217 ATAAAATTTTATAAAGTCGTA
1 AAAAAATTATAAAAAATTGTA
* *
47315238 AGAAAATTATACAAAA-TGTA
1 AAAAAATTATAAAAAATTGTA
* *
47315258 AAGAAA-TAT--AAATTTCGTA
1 AAAAAATTATAAAAAATT-GTA
47315277 AAAAAATTTATAAAAA
1 AAAAAA-TTATAAAAA
47315293 TTATATTACC
Statistics
Matches: 115, Mismatches: 22, Indels: 32
0.68 0.13 0.19
Matches are distributed among these distances:
17 6 0.05
18 12 0.10
19 37 0.32
20 15 0.13
21 23 0.20
22 7 0.06
23 15 0.13
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAAAATTATAAAAAATTGTA
Found at i:47315222 original size:10 final size:10
Alignment explanation
Indices: 47315117--47315231 Score: 58
Period size: 10 Copynumber: 11.4 Consensus size: 10
47315107 ATTCAAATAT
47315117 TAAAAATTTA
1 TAAAAATTTA
47315127 TGAAAAA-TTA
1 T-AAAAATTTA
* **
47315137 GAAAAAAATA
1 TAAAAATTTA
*
47315147 TAAAAATAGTA
1 TAAAAAT-TTA
* *
47315158 AAAGAAATATA
1 TAA-AAATTTA
47315169 TAAAAAATTGTA
1 T-AAAAATT-TA
*
47315181 -AAAAAATTA
1 TAAAAATTTA
*
47315190 T-AAAATATA
1 TAAAAATTTA
* *
47315199 TAGAAATATA
1 TAAAAATTTA
47315209 -AAAAATTTA
1 TAAAAATTTA
*
47315218 TAAAATTTTA
1 TAAAAATTTA
47315228 TAAA
1 TAAA
47315232 GTCGTAAGAA
Statistics
Matches: 80, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
9 21 0.26
10 36 0.45
11 15 0.19
12 8 0.10
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (10 bp):
TAAAAATTTA
Done.