Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 104 of 210
Found at i:30298603 original size:20 final size:20
Alignment explanation
Indices: 30298578--30298620 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
30298568 TGGTTCAAAG
30298578 GGTAAGAAAATGAATGGAAT
1 GGTAAGAAAATGAATGGAAT
* *
30298598 GGTAAGTAAATTAATGGAAT
1 GGTAAGAAAATGAATGGAAT
30298618 GGT
1 GGT
30298621 TCATGATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (20 bp):
GGTAAGAAAATGAATGGAAT
Found at i:30300007 original size:18 final size:18
Alignment explanation
Indices: 30299969--30300004 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30299959 TTAATTTGGT
30299969 TAAAACGGGTTTTAAAAA
1 TAAAACGGGTTTTAAAAA
*
30299987 TAAAATCGGGTTTGAAAA
1 TAAAA-CGGGTTTTAAAA
30300005 TAATTGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (18 bp):
TAAAACGGGTTTTAAAAA
Found at i:30300865 original size:22 final size:22
Alignment explanation
Indices: 30300837--30300879 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
30300827 TTTATTGTTC
30300837 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
30300859 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
30300880 TGGGAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:30301426 original size:28 final size:28
Alignment explanation
Indices: 30301382--30301451 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
30301372 GTTATGCATA
30301382 TTATAT-ATATATATGCATGACTTTATC
1 TTATATAATATATATGCATGACTTTATC
* * *
30301409 TTATATAATAAATATGCATGGCTTTATT
1 TTATATAATATATATGCATGACTTTATC
*
30301437 TTACATAATATATAT
1 TTATATAATATATAT
30301452 TAACGAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 6 0.16
28 31 0.84
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (28 bp):
TTATATAATATATATGCATGACTTTATC
Found at i:30308987 original size:14 final size:14
Alignment explanation
Indices: 30308964--30308994 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
30308954 AATGAGGAGG
30308964 AGCTCATCTGTTAC
1 AGCTCATCTGTTAC
*
30308978 AGCTCCTCTGTTAC
1 AGCTCATCTGTTAC
30308992 AGC
1 AGC
30308995 CCGTTTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.32
Consensus pattern (14 bp):
AGCTCATCTGTTAC
Found at i:30310837 original size:30 final size:30
Alignment explanation
Indices: 30310803--30310885 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
30310793 GTATATGTTT
* *
30310803 TATACATTTCCGAATTGATTTGTATGT-AGA
1 TATACATTACCGAATTGATTTGTATATGA-A
* *
30310833 TATACATTACCGAGTTTGATTCGTATATGAA
1 TATACATTACCGA-ATTGATTTGTATATGAA
* * *
30310864 TATATATTGCCAAATTGATTTG
1 TATACATTACCGAATTGATTTG
30310886 AGCATTGGAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
30 19 0.45
31 22 0.52
32 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (30 bp):
TATACATTACCGAATTGATTTGTATATGAA
Found at i:30311091 original size:43 final size:44
Alignment explanation
Indices: 30311008--30311107 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 44
30310998 GGTGAGGTTT
* * **
30311008 CGTGTAAGACCATAGCTGGGCTATTGGTATTGATTTGAGATTT-
1 CGTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATTTC
*
30311051 TGTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATTTC
1 CGTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATTTC
*
30311095 CATGTAAGACCAT
1 CGTGTAAGACCAT
30311108 GTCTAGGACA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 38 0.78
44 11 0.22
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (44 bp):
CGTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATTTC
Found at i:30312578 original size:4 final size:4
Alignment explanation
Indices: 30312571--30312602 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
30312561 TATATATATA
30312571 TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
30312603 AATTACATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:30313422 original size:25 final size:25
Alignment explanation
Indices: 30313392--30313475 Score: 96
Period size: 25 Copynumber: 3.4 Consensus size: 25
30313382 CAGCTCTTAT
*
30313392 GAGCTTACCGTTACTCAACTCGGAG
1 GAGCTTACCGTTATTCAACTCGGAG
* **
30313417 GAGCTTACCGTTATTCATCTTAGAG
1 GAGCTTACCGTTATTCAACTCGGAG
** * *
30313442 GAGCTTATAGTTATTCAGCTCGAAG
1 GAGCTTACCGTTATTCAACTCGGAG
30313467 GAGCTTACC
1 GAGCTTACC
30313476 ATCTACAGCT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAACTCGGAG
Found at i:30326678 original size:21 final size:21
Alignment explanation
Indices: 30326649--30326689 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30326639 TGTTCGAGCA
30326649 AATACAAAATACAATCAGACG
1 AATACAAAATACAATCAGACG
* * *
30326670 AATATAAAATTCAATTAGAC
1 AATACAAAATACAATCAGAC
30326690 AAAACTAACC
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:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (21 bp):
AATACAAAATACAATCAGACG
Found at i:30327634 original size:72 final size:72
Alignment explanation
Indices: 30327517--30327667 Score: 293
Period size: 72 Copynumber: 2.1 Consensus size: 72
30327507 TCGGTGACCA
30327517 TATGTTTTTTTGCACAAGGTAAGGAAATGTGTTCCAATAAATTGAAGTTAGAATTATATGTCTAA
1 TATGTTTTTTTGCACAAGGTAAGGAAATGTGTTCCAATAAATTGAAGTTAGAATTATATGTCTAA
30327582 ATTATTC
66 ATTATTC
30327589 TATGTTTTTTTGCACAAGGTAAGGAAATGTGTTCCAATAAATTGAAGTTAGAATTATATGTCTAA
1 TATGTTTTTTTGCACAAGGTAAGGAAATGTGTTCCAATAAATTGAAGTTAGAATTATATGTCTAA
30327654 ATTATTC
66 ATTATTC
*
30327661 AATGTTT
1 TATGTTT
30327668 ATTTAGGGCT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 78 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (72 bp):
TATGTTTTTTTGCACAAGGTAAGGAAATGTGTTCCAATAAATTGAAGTTAGAATTATATGTCTAA
ATTATTC
Found at i:30333997 original size:21 final size:22
Alignment explanation
Indices: 30333973--30334015 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
30333963 ATGTGAGAGG
*
30333973 AGGCACACGCCTGTGT-AGCTA
1 AGGCACACGCCCGTGTGAGCTA
*
30333994 AGGCACATGCCCGTGTGAGCTA
1 AGGCACACGCCCGTGTGAGCTA
30334016 GGGACATGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (22 bp):
AGGCACACGCCCGTGTGAGCTA
Found at i:30338854 original size:19 final size:18
Alignment explanation
Indices: 30338822--30338858 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
30338812 TTTTCTTATT
*
30338822 TTTAAAAATTAAAATAAA
1 TTTAAAAATAAAAATAAA
30338840 TTTAATAAATAAAAATAAA
1 TTTAA-AAATAAAAATAAA
30338859 AAATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TTTAAAAATAAAAATAAA
Found at i:30338854 original size:26 final size:26
Alignment explanation
Indices: 30338824--30338882 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
30338814 TTCTTATTTT
* *
30338824 TAAAAAT-TAAAATAAATTTAATAAA
1 TAAAAATAAAAAATAAATTTAAAAAA
* *
30338849 TAAAAATAAAAAATTATTTTAAAAAA
1 TAAAAATAAAAAATAAATTTAAAAAA
30338875 TAAAAATA
1 TAAAAATA
30338883 TTTCATACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAAAATAAAAAATAAATTTAAAAAA
Found at i:30342313 original size:20 final size:20
Alignment explanation
Indices: 30342288--30342334 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
30342278 AGTGCTTAGG
30342288 TCGTGTGGGGG-CTTACACGC
1 TCGTGTGGGGGTC-TACACGC
*
30342308 TCGTGTGGTGGTCTACACGC
1 TCGTGTGGGGGTCTACACGC
*
30342328 CCGTGTG
1 TCGTGTG
30342335 CAAGCTACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.09, C:0.26, G:0.38, T:0.28
Consensus pattern (20 bp):
TCGTGTGGGGGTCTACACGC
Found at i:30347453 original size:44 final size:44
Alignment explanation
Indices: 30347387--30347470 Score: 98
Period size: 44 Copynumber: 1.9 Consensus size: 44
30347377 AGGAATTAGT
* * * *
30347387 ACTTCGATCTACTTCACCGCAACGTC-GGAGAGATAGGATTATCA
1 ACTTCAATCTACTCCACCGCAACCTCAGG-GAGATAAGATTATCA
* *
30347431 ACTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATT
1 ACTTCAATCTACTCCACCGCAACCTCAGGGAGATAAGATT
30347471 TACTTCTTCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
44 31 0.94
45 2 0.06
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (44 bp):
ACTTCAATCTACTCCACCGCAACCTCAGGGAGATAAGATTATCA
Found at i:30347486 original size:44 final size:44
Alignment explanation
Indices: 30347438--30347557 Score: 138
Period size: 44 Copynumber: 2.7 Consensus size: 44
30347428 TCAACTTCAA
*
30347438 TCTGCTCCACTGCAACCTCAGGGAGATAAGA-TT-TACTTCTTCGG
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACTTGT-CTTC-TCAG
* * *
30347482 TCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTGTTTTCTCAG
1 TCTGCTCCACTGCAACCTCAGGGA-GATAAGACTTGTCTTCTCAG
* *
30347526 TCAGCTCCGCTGCAACCTCAGGGAGATAAGAC
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGAC
30347558 CTAATGCGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 3 0.05
44 52 0.81
45 8 0.12
46 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (44 bp):
TCTGCTCCACTGCAACCTCAGGGAGATAAGACTTGTCTTCTCAG
Found at i:30347667 original size:43 final size:45
Alignment explanation
Indices: 30347614--30347709 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 45
30347604 ACTTTAATCC
* * *
30347614 GCTCCACTGTAA-CTTCAGGGAGATAGGA-TAG-TGTCTTCGATCT
1 GCTCCGCTGTAATC-TCAGGGAGATAAGATTAGCCGTCTTCGATCT
* *
30347657 GCTCCGCTGTAATCTCAGGGAGATAAGATTCGCCGTCTTCGGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAAGATTAGCCGTCTTCGATCT
30347702 GCTCCGCT
1 GCTCCGCT
30347710 ACTGCTTAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
43 24 0.53
44 3 0.07
45 18 0.40
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (45 bp):
GCTCCGCTGTAATCTCAGGGAGATAAGATTAGCCGTCTTCGATCT
Found at i:30350141 original size:7 final size:6
Alignment explanation
Indices: 30350113--30350182 Score: 53
Period size: 6 Copynumber: 12.7 Consensus size: 6
30350103 AGATTTCTCT
* * *
30350113 TTTTCA TTTTGA TCTTGA TTTTGA TTTT-- TTTT-A -TTT-- TTTTCA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
* *
30350155 TTTTTA TTTTGA CTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
30350183 TCTTTTTCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
4 10 0.19
6 43 0.81
ACGTcount: A:0.14, C:0.06, G:0.09, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:30350201 original size:42 final size:42
Alignment explanation
Indices: 30350107--30350201 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
30350097 TCATCTAGAT
* *
30350107 TTCTCTTTTTCATTTTGATCTTGATTTTGATTTTTTTTATTT
1 TTCTCTTTTTTATTTTGATCTTGATTTTGATTTTTTTTATTC
* *
30350149 TTTTCATTTTTATTTTGA-CTTTGATTTTGATTTTTCTTT-TTC
1 TTCTCTTTTTTATTTTGATC-TTGATTTTGATTTTT-TTTATTC
30350191 TTCTCTTTTTT
1 TTCTCTTTTTT
30350202 GATCTGAGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 41 0.91
43 3 0.07
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.73
Consensus pattern (42 bp):
TTCTCTTTTTTATTTTGATCTTGATTTTGATTTTTTTTATTC
Found at i:30357975 original size:27 final size:27
Alignment explanation
Indices: 30357945--30358036 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
30357935 ATTAGAATAC
* *
30357945 GCCACAAAGGTGATCCATTCAGAGTAT
1 GCCACAAAGGCGATCCATTCAAAGTAT
* * *
30357972 GCCACATAGGCAATCCATTCAAAGTAC
1 GCCACAAAGGCGATCCATTCAAAGTAT
* *
30357999 ACCATAAAGGCGATCCATTCAAAGTAT
1 GCCACAAAGGCGATCCATTCAAAGTAT
30358026 GCCACAAAGGC
1 GCCACAAAGGC
30358037 TAACAGGATG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (27 bp):
GCCACAAAGGCGATCCATTCAAAGTAT
Found at i:30365746 original size:23 final size:23
Alignment explanation
Indices: 30365716--30365767 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
30365706 GGAGATTTTA
30365716 GCATATTCCCTGAAGCGAATATT
1 GCATATTCCCTGAAGCGAATATT
30365739 GCATATTCCCTGAAGCGAATATT
1 GCATATTCCCTGAAGCGAATATT
30365762 GCATAT
1 GCATAT
30365768 AATTGTTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (23 bp):
GCATATTCCCTGAAGCGAATATT
Found at i:30371904 original size:61 final size:61
Alignment explanation
Indices: 30371760--30371896 Score: 229
Period size: 61 Copynumber: 2.2 Consensus size: 61
30371750 GAAGTTTGAA
* *
30371760 GATCAAATTGATAGAATTTGTAAATATGAAGGGTTAAATTTATTGAATTATTTAGAATTAG
1 GATCAAATTGATAGAATTTGTAAATATGAAAGGTTAAATTTATTGAATTATTTAGAACTAG
* **
30371821 GATCAAATTGGTAGAATTTGTAAATATGAAAGGTTACGTTTATTGAATTATTTAGAACTAG
1 GATCAAATTGATAGAATTTGTAAATATGAAAGGTTAAATTTATTGAATTATTTAGAACTAG
30371882 GATCAAATTGATAGA
1 GATCAAATTGATAGA
30371897 TCATGTAAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 70 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (61 bp):
GATCAAATTGATAGAATTTGTAAATATGAAAGGTTAAATTTATTGAATTATTTAGAACTAG
Found at i:30372853 original size:17 final size:18
Alignment explanation
Indices: 30372827--30372860 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
30372817 AAATTTATAA
30372827 AAAAATTAAAAAAATATG
1 AAAAATTAAAAAAATATG
30372845 AAAAA-TAAAAAAATAT
1 AAAAATTAAAAAAATAT
30372861 AGGAAGGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAAATTAAAAAAATATG
Found at i:30372856 original size:28 final size:28
Alignment explanation
Indices: 30372803--30372857 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
30372793 ACTTAAAATC
* * *
30372803 ATTAAAATAATAGAAAATTTATAAAAAA
1 ATTAAAAAAATAGAAAATATAAAAAAAA
30372831 ATTAAAAAAATATGAAAA-ATAAAAAAA
1 ATTAAAAAAATA-GAAAATATAAAAAAA
30372858 TATAGGAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (28 bp):
ATTAAAAAAATAGAAAATATAAAAAAAA
Found at i:30373204 original size:20 final size:18
Alignment explanation
Indices: 30373179--30373234 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
30373169 GTTTCATAAT
30373179 TTTTTTTCATATATTTTTA
1 TTTTTTT-ATATATTTTTA
* *
30373198 ATTTTTTAAATAATTTTTA
1 TTTTTTTATAT-ATTTTTA
30373217 TGTTTTTTATAATATTTT
1 T-TTTTTTAT-ATATTTT
30373235 GTGAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.10
19 13 0.43
20 12 0.40
21 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTTTATATATTTTTA
Found at i:30373374 original size:17 final size:18
Alignment explanation
Indices: 30373354--30373410 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
30373344 ATTCTTTTCA
30373354 TTTTTAT-TTTTATATA-
1 TTTTTATCTTTTATATAT
30373370 TTTTTATCTTTTATA-AT
1 TTTTTATCTTTTATATAT
* * *
30373387 TTTCTATGTTTTTTATAAT
1 TTTTTATCTTTTATAT-AT
30373406 TTTTT
1 TTTTT
30373411 TGCACATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 8 0.24
17 19 0.58
19 6 0.18
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTTATCTTTTATATAT
Found at i:30374142 original size:3 final size:3
Alignment explanation
Indices: 30374136--30374173 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
30374126 CATTTTATTA
30374136 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
30374174 CCAATCATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:30375038 original size:37 final size:36
Alignment explanation
Indices: 30374996--30375065 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 36
30374986 GTTACTAGTT
30374996 TACTGAATGCATGCTAAGCATACCACTGATATTGTTA
1 TACTGAATGCATGCTAAGCATACCACTG-TATTGTTA
* *
30375033 TACTGAATGCATGTTAAGCATGCCACTGTATTG
1 TACTGAATGCATGCTAAGCATACCACTGTATTG
30375066 AAAGTGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 5 0.16
37 26 0.84
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (36 bp):
TACTGAATGCATGCTAAGCATACCACTGTATTGTTA
Found at i:30376258 original size:3 final size:3
Alignment explanation
Indices: 30376252--30376311 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
30376242 TTTTTGGACC
30376252 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30376300 ATT ATT ATT ATT
1 ATT ATT ATT ATT
30376312 TGCCATCATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:30384623 original size:18 final size:18
Alignment explanation
Indices: 30384580--30384623 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
30384570 ACCCAATCTA
* *
30384580 AACCCAAGTATTCAACCC
1 AACCCAATTATCCAACCC
30384598 AACCCAATTATCCAACCC
1 AACCCAATTATCCAACCC
30384616 AACCCAAT
1 AACCCAAT
30384624 CATAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.41, G:0.02, T:0.16
Consensus pattern (18 bp):
AACCCAATTATCCAACCC
Found at i:30384765 original size:27 final size:27
Alignment explanation
Indices: 30384730--30384823 Score: 154
Period size: 27 Copynumber: 3.5 Consensus size: 27
30384720 GTAGTGATTC
*
30384730 AATTTGGTTAATTCGGTTAATTCGGGT
1 AATTTGGTTAATTCGGTTAATTCGGTT
*
30384757 AATTCGGTTAATTCAGG-TAATTCGGTT
1 AATTTGGTTAATTC-GGTTAATTCGGTT
30384784 AATTTGGTTAATTCGGTTAATTCGGTT
1 AATTTGGTTAATTCGGTTAATTCGGTT
30384811 AATTTGGTTAATT
1 AATTTGGTTAATT
30384824 TTTAACCAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
26 2 0.03
27 58 0.94
28 2 0.03
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (27 bp):
AATTTGGTTAATTCGGTTAATTCGGTT
Found at i:30384824 original size:9 final size:9
Alignment explanation
Indices: 30384730--30384823 Score: 136
Period size: 9 Copynumber: 10.4 Consensus size: 9
30384720 GTAGTGATTC
*
30384730 AATTTGGTT
1 AATTCGGTT
30384739 AATTCGGTT
1 AATTCGGTT
*
30384748 AATTCGGGT
1 AATTCGGTT
30384757 AATTCGGTT
1 AATTCGGTT
30384766 AATTCAGG-T
1 AATTC-GGTT
30384775 AATTCGGTT
1 AATTCGGTT
*
30384784 AATTTGGTT
1 AATTCGGTT
30384793 AATTCGGTT
1 AATTCGGTT
30384802 AATTCGGTT
1 AATTCGGTT
*
30384811 AATTTGGTT
1 AATTCGGTT
30384820 AATT
1 AATT
30384824 TTTAACCAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
8 2 0.03
9 73 0.95
10 2 0.03
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (9 bp):
AATTCGGTT
Found at i:30389872 original size:15 final size:15
Alignment explanation
Indices: 30389837--30389878 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
30389827 TTAAGAATTT
*
30389837 TATTAAATTAT-ATA
1 TATTTAATTATAATA
30389851 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
30389865 TATTTAATAATAAT
1 TATTTAATTATAAT
30389879 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:30390123 original size:16 final size:16
Alignment explanation
Indices: 30390102--30390137 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
30390092 GATTTGCTAT
30390102 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
30390118 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
30390134 TACA
1 TACA
30390138 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:30392827 original size:20 final size:19
Alignment explanation
Indices: 30392784--30392827 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
30392774 CTATTGTTTT
*
30392784 TTATTTTTTTATCTTATAG
1 TTATTTTTTTATCTTATAA
*
30392803 TTATTTTTTTATCTTTTAA
1 TTATTTTTTTATCTTATAA
30392822 TATATT
1 T-TATT
30392828 GCAGTTATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (19 bp):
TTATTTTTTTATCTTATAA
Found at i:30396093 original size:64 final size:63
Alignment explanation
Indices: 30395888--30396093 Score: 191
Period size: 62 Copynumber: 3.3 Consensus size: 63
30395878 GGATATAGAA
* * * *
30395888 GTGTGTCCAGGATGTGTAACTCACTGTTTGGATTTTAGAAG-CACACAGACTAGGGACACGGGC
1 GTGTGTCCAGGCTGTGTAACTCATTGTTTGGA-TTTATAAGTCACACAGGCTAGGGACACGGGC
* * * ** * * ***
30395951 GTGTGTCCAGGCCGTGTAAATCATTATTTGGATTT-TGGGTCACATAAGCTAGGGACACAACC
1 GTGTGTCCAGGCTGTGTAACTCATTGTTTGGATTTATAAGTCACACAGGCTAGGGACACGGGC
* * * * * *
30396013 ATGTGTCTAGGTTGTGTAACTCATTGTTAGGGATTTATAAGTCACACGGGCTAAGGACACGGGC
1 GTGTGTCCAGGCTGTGTAACTCATTGTT-TGGATTTATAAGTCACACAGGCTAGGGACACGGGC
*
30396077 GTGTGCCCAGGCTGTGT
1 GTGTGTCCAGGCTGTGT
30396094 GAGGGGTTGT
Statistics
Matches: 106, Mismatches: 34, Indels: 5
0.73 0.23 0.03
Matches are distributed among these distances:
61 1 0.01
62 41 0.39
63 33 0.31
64 31 0.29
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (63 bp):
GTGTGTCCAGGCTGTGTAACTCATTGTTTGGATTTATAAGTCACACAGGCTAGGGACACGGGC
Found at i:30412423 original size:15 final size:16
Alignment explanation
Indices: 30412403--30412435 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
30412393 GTAGTTAATT
30412403 AATTGAAAAAGAT-TA
1 AATTGAAAAAGATGTA
30412418 AATTGAAAAAGATGTA
1 AATTGAAAAAGATGTA
30412434 AA
1 AA
30412436 AGTTAACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (16 bp):
AATTGAAAAAGATGTA
Found at i:30413585 original size:8 final size:7
Alignment explanation
Indices: 30413557--30413591 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
30413547 CTTAATTGAG
30413557 GGGTTTA
1 GGGTTTA
30413564 GGGTTTA
1 GGGTTTA
30413571 GGGTTTA
1 GGGTTTA
30413578 GGGTTTTA
1 GGG-TTTA
30413586 GGGTTT
1 GGGTTT
30413592 GTTGCAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.11, C:0.00, G:0.43, T:0.46
Consensus pattern (7 bp):
GGGTTTA
Found at i:30422078 original size:25 final size:25
Alignment explanation
Indices: 30422050--30422101 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
30422040 TAGGTTTCAA
30422050 TTCCCATTC-ATTCCCATATCTTGTT
1 TTCCCATTCAATT-CCATATCTTGTT
30422075 TTCCCATTCAATTCCATATCTTGTT
1 TTCCCATTCAATTCCATATCTTGTT
30422100 TT
1 TT
30422102 GCCTGAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.17, C:0.29, G:0.04, T:0.50
Consensus pattern (25 bp):
TTCCCATTCAATTCCATATCTTGTT
Found at i:30427116 original size:21 final size:21
Alignment explanation
Indices: 30427091--30427161 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
30427081 ATTCTATGGC
30427091 ATCATGATGAAGATGAGTAAG
1 ATCATGATGAAGATGAGTAAG
* * **
30427112 ATCATGGCTGAAAGATG-CTATTT
1 ATCAT-GATG-AAGATGAGTA-AG
* *
30427135 ATCATGATAAATATGAGTAAG
1 ATCATGATGAAGATGAGTAAG
30427156 ATCATG
1 ATCATG
30427162 TCTGAAAGAC
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
21 16 0.44
22 9 0.25
23 11 0.31
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (21 bp):
ATCATGATGAAGATGAGTAAG
Found at i:30427123 original size:45 final size:45
Alignment explanation
Indices: 30427074--30427185 Score: 136
Period size: 44 Copynumber: 2.5 Consensus size: 45
30427064 AAAACCATAA
* *
30427074 CTGAAAGATTCTATGGCATCATGATGAAGATGAGTAAGATCATGG
1 CTGAAAGATTCTATGACATCATGATAAAGATGAGTAAGATCATGG
* ** * *
30427119 CTGAAAGATGCTAT-TTATCATGATAAATATGAGTAAGATCATGT
1 CTGAAAGATTCTATGACATCATGATAAAGATGAGTAAGATCATGG
* *
30427163 CTGAAAGACTCCATGACATCATG
1 CTGAAAGATTCTATGACATCATG
30427186 GTAACGGGAC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 36 0.65
45 19 0.35
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (45 bp):
CTGAAAGATTCTATGACATCATGATAAAGATGAGTAAGATCATGG
Found at i:30427128 original size:23 final size:23
Alignment explanation
Indices: 30427100--30427170 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
30427090 CATCATGATG
30427100 AAGATGAGTAAGATCATGGCTGA
1 AAGATGAGTAAGATCATGGCTGA
* ** *
30427123 AAGATG-CTATTTATCAT-GAT-A
1 AAGATGAGTA-AGATCATGGCTGA
* *
30427144 AATATGAGTAAGATCATGTCTGA
1 AAGATGAGTAAGATCATGGCTGA
30427167 AAGA
1 AAGA
30427171 CTCCATGACA
Statistics
Matches: 33, Mismatches: 11, Indels: 8
0.63 0.21 0.15
Matches are distributed among these distances:
21 11 0.33
22 7 0.21
23 15 0.45
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (23 bp):
AAGATGAGTAAGATCATGGCTGA
Found at i:30437399 original size:24 final size:23
Alignment explanation
Indices: 30437294--30437516 Score: 106
Period size: 24 Copynumber: 9.7 Consensus size: 23
30437284 ACAATATATA
*
30437294 ATAAATTTGAAATAATAATACAT-
1 ATAAATTTTAAATAAT-ATACATG
* * **
30437317 ATAAAATTTAAA-AATTTTGATG
1 ATAAATTTTAAATAATATACATG
*
30437339 AT-AATTCTAGAATAATCATACGA-G
1 ATAAATTTTA-AATAAT-ATAC-ATG
*** *
30437363 ATAAATCCAAAATAATAGTACATA
1 ATAAATTTTAAATAATA-TACATG
30437387 ATAAATTTTAAAT-AT-TA-ATG
1 ATAAATTTTAAATAATATACATG
30437407 ATAAATTTTAAATAAATATACATG
1 ATAAATTTTAAAT-AATATACATG
* *
30437431 ATAAATTTAAAATAATGTTAC--G
1 ATAAATTTTAAATAAT-ATACATG
* * *
30437453 ATGAATTTAAAATAATAATA-TTG
1 ATAAATTTTAAATAAT-ATACATG
** * *
30437476 ATAAATTACAAATAATAAAACGTG
1 ATAAATTTTAAATAAT-ATACATG
* *
30437500 ATAAATCTAAAATAATA
1 ATAAATTTTAAATAATA
30437517 ATATACAATA
Statistics
Matches: 154, Mismatches: 30, Indels: 32
0.71 0.14 0.15
Matches are distributed among these distances:
20 15 0.10
21 10 0.06
22 27 0.18
23 40 0.26
24 56 0.36
25 6 0.04
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (23 bp):
ATAAATTTTAAATAATATACATG
Found at i:30437443 original size:68 final size:69
Alignment explanation
Indices: 30437294--30437446 Score: 163
Period size: 69 Copynumber: 2.2 Consensus size: 69
30437284 ACAATATATA
* *
30437294 ATAAATTTGAAATAATAATACATATAAAATTTAAAAATTTTGATGATAATTCTAGAATAATCATA
1 ATAAATTTAAAATAATAATACATATAAAATTTAAAAATTATGATGATAATTCTAGAATAATCATA
30437359 CGAG
66 CGAG
** * * * *
30437363 ATAAATCCAAAATAATAGTACATAATAAATTTTAAATATTA--ATGATAAATTTTA-AATAAAT-
1 ATAAATTTAAAATAATAATACAT-ATAAAATTTAAAAATTATGATGAT-AATTCTAGAAT-AATC
30437424 ATAC-ATG
63 ATACGA-G
30437431 ATAAATTTAAAATAAT
1 ATAAATTTAAAATAAT
30437447 GTTACGATGA
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
67 1 0.01
68 27 0.39
69 28 0.40
70 14 0.20
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATATAAAATTTAAAAATTATGATGATAATTCTAGAATAATCATA
CGAG
Found at i:30441123 original size:35 final size:34
Alignment explanation
Indices: 30441066--30441139 Score: 80
Period size: 34 Copynumber: 2.1 Consensus size: 34
30441056 ATTTTTAAAA
30441066 TTAATATTAAAACATTAATTTAAAAAATTTTA-ATT
1 TTAATATTAAAACATTAATTT--AAAATTTTATATT
* * *
30441101 TTAATATT-AAAGATTATTTTTAACATTTTATATT
1 TTAATATTAAAACATTA-ATTTAAAATTTTATATT
30441135 TTAAT
1 TTAAT
30441140 TTTTTTCTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 8 0.24
34 15 0.44
35 11 0.32
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (34 bp):
TTAATATTAAAACATTAATTTAAAATTTTATATT
Found at i:30441193 original size:26 final size:24
Alignment explanation
Indices: 30441151--30441219 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 24
30441141 TTTTTCTGAT
* *
30441151 TTAAAACAAAATAAAATGTTATTAA
1 TTAAAACAAACTAAATTG-TATTAA
30441176 TTAAAAGCAAACTCAAATTGTATTAA
1 TTAAAA-CAAACT-AAATTGTATTAA
* *
30441202 ATATAATCAAACTAAATT
1 TTA-AAACAAACTAAATT
30441220 TAATGAATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 11 0.30
26 19 0.51
27 7 0.19
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (24 bp):
TTAAAACAAACTAAATTGTATTAA
Found at i:30442186 original size:16 final size:16
Alignment explanation
Indices: 30442156--30442190 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30442146 TGATTTTATC
30442156 TATTATTAATAATTAA
1 TATTATTAATAATTAA
30442172 TATTAATTAAT-ATTAA
1 TATT-ATTAATAATTAA
30442188 TAT
1 TAT
30442191 GTTAAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTATTAATAATTAA
Found at i:30445000 original size:21 final size:18
Alignment explanation
Indices: 30444945--30444988 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
30444935 TGGTCTCGGC
*
30444945 GGTTTAGGTGGGGCAGGA
1 GGTTTAGGTGGAGCAGGA
*
30444963 GGTTTAGGTGGACCAGGA
1 GGTTTAGGTGGAGCAGGA
30444981 GGTTTAGG
1 GGTTTAGG
30444989 CGGTGGAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.07, G:0.50, T:0.25
Consensus pattern (18 bp):
GGTTTAGGTGGAGCAGGA
Found at i:30447597 original size:33 final size:33
Alignment explanation
Indices: 30447558--30447631 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
30447548 TTTAATTTAT
30447558 ATTATTAAATATTTATATTTAGTCATATAAAAA
1 ATTATTAAATATTTATATTTAGTCATATAAAAA
* *
30447591 ATTATTAATTATTTATATTTAGTCATATAATAA
1 ATTATTAAATATTTATATTTAGTCATATAAAAA
*
30447624 ACTATTAA
1 ATTATTAA
30447632 TATAATTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (33 bp):
ATTATTAAATATTTATATTTAGTCATATAAAAA
Found at i:30447708 original size:15 final size:14
Alignment explanation
Indices: 30447683--30447722 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
30447673 TTTCAATTTT
30447683 ATTTT-AATAATAA
1 ATTTTAAATAATAA
30447696 ATTTTAAAATAAT-A
1 ATTTT-AAATAATAA
30447710 ATTTTAAATAATA
1 ATTTTAAATAATA
30447723 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 12 0.50
14 6 0.25
15 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:30447775 original size:15 final size:15
Alignment explanation
Indices: 30447749--30447811 Score: 65
Period size: 15 Copynumber: 4.0 Consensus size: 15
30447739 GAAAATATTC
30447749 AATAAT-AATATTTT
1 AATAATAAATATTTT
30447763 AATAATAAATATTTATT
1 AATAATAAATA-TT-TT
*
30447780 ACAGTAATAAATATATT
1 A-A-TAATAAATATTTT
*
30447797 AATAATAAATGTTTT
1 AATAATAAATATTTT
30447812 GTAGTATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
14 6 0.15
15 15 0.37
16 3 0.07
17 6 0.15
18 2 0.05
19 9 0.22
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (15 bp):
AATAATAAATATTTT
Found at i:30467579 original size:102 final size:92
Alignment explanation
Indices: 30467463--30467843 Score: 406
Period size: 102 Copynumber: 4.1 Consensus size: 92
30467453 TAATTAAACC
30467463 TTTTTTTTT-CACTCAATTGGGTACTTTAACTTTCATAATGTATAAAAAAACCCTCAAACTTTTT
1 TTTTTTTTTGCACTCAATTGGGTACTTTAACTTTCATAATGTATAAAAAAACCCTCAAACTTTTT
*
30467527 CCAAAAAAAAACCATTAAGCCTCTTTTCTTTTTTCTT
66 -CAAAAAAAAACAATTAAGCC-C---TC----TTC-T
*
30467564 TTTTTTTTTGCACTCAATTGGGTACTTTAACTTTCATAATGTATAAAAAATCCCTCAAACTTTTT
1 TTTTTTTTTGCACTCAATTGGGTACTTTAACTTTCATAATGTATAAAAAAACCCTCAAACTTTTT
* * *
30467629 CAAAAAAAATAAAAAAATTAAG-CATC-TAT
66 C---AAAAA-AAAACAATTAAGCCCTCTTCT
*
30467658 TTTTTTTTTGCACTCAATTGAGTACTTTAACTTTCATAATG-AT-AAAAAACCCTCAAACTTTTT
1 TTTTTTTTTGCACTCAATTGGGTACTTTAACTTTCATAATGTATAAAAAAACCCTCAAACTTTTT
** *
30467721 -AAAAAAAAGTAATTAAGCCC-CTGC-
66 CAAAAAAAAACAATTAAGCCCTCTTCT
* * *
30467745 TTTTTTTTTGTACTCAATTGGGTACTTTAGA-TTTCTTAATGTATAAAAAAAAACCTCAAACTTT
1 TTTTTTTTTGCACTCAATTGGGTACTTTA-ACTTTCATAATGTAT-AAAAAAACCCTCAAACTTT
* * *
30467809 TTC-AAAAAAAGCAATTAAG-CCTCTGCC
64 TTCAAAAAAAAACAATTAAGCCCTCTTCT
30467836 TTTTTTTT
1 TTTTTTTT
30467844 CTACTCAATT
Statistics
Matches: 249, Mismatches: 17, Indels: 38
0.82 0.06 0.12
Matches are distributed among these distances:
87 47 0.19
88 9 0.04
89 2 0.01
90 38 0.15
91 8 0.03
92 19 0.08
93 2 0.01
94 41 0.16
95 1 0.00
100 2 0.01
101 10 0.04
102 54 0.22
104 6 0.02
105 10 0.04
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (92 bp):
TTTTTTTTTGCACTCAATTGGGTACTTTAACTTTCATAATGTATAAAAAAACCCTCAAACTTTTT
CAAAAAAAAACAATTAAGCCCTCTTCT
Found at i:30467816 original size:90 final size:89
Alignment explanation
Indices: 30467564--30467866 Score: 364
Period size: 90 Copynumber: 3.4 Consensus size: 89
30467554 CTTTTTTCTT
*
30467564 TTTTTTTTTGCACTCAATTGGGTACTTTAACTTTCATAATGTATAAAAAATCCCTCAAACTTTTT
1 TTTTTTTTTGCACTCAATTGGGTACTTTAACTTTCATAATGTATAAAAAAACCCTCAAACTTTTT
* * **
30467629 CAAAAAAAATAAAAAAATTAAGCATCTAT
66 CAAAAAAAGT-----AATTAAGCCTCTGC
*
30467658 TTTTTTTTTGCACTCAATTGAGTACTTTAACTTTCATAATG-AT-AAAAAACCCTCAAACTTTTT
1 TTTTTTTTTGCACTCAATTGGGTACTTTAACTTTCATAATGTATAAAAAAACCCTCAAACTTTTT
* *
30467721 AAAAAAAAGTAATTAAGCCCCTGC
66 CAAAAAAAGTAATTAAGCCTCTGC
* * *
30467745 TTTTTTTTTGTACTCAATTGGGTACTTTAGA-TTTCTTAATGTATAAAAAAAAACCTCAAACTTT
1 TTTTTTTTTGCACTCAATTGGGTACTTTA-ACTTTCATAATGTAT-AAAAAAACCCTCAAACTTT
*
30467809 TTCAAAAAAAGCAATTAAGCCTCTGC
64 TTCAAAAAAAGTAATTAAGCCTCTGC
* *
30467835 CTTTTTTTT-CTACTCAATTAGGTA-TTTGAACT
1 TTTTTTTTTGC-ACTCAATTGGGTACTTT-AACT
30467867 GCCAAAATGC
Statistics
Matches: 184, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
87 46 0.25
88 3 0.02
89 4 0.02
90 62 0.34
92 27 0.15
93 2 0.01
94 40 0.22
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (89 bp):
TTTTTTTTTGCACTCAATTGGGTACTTTAACTTTCATAATGTATAAAAAAACCCTCAAACTTTTT
CAAAAAAAGTAATTAAGCCTCTGC
Found at i:30467882 original size:90 final size:90
Alignment explanation
Indices: 30467701--30467886 Score: 223
Period size: 90 Copynumber: 2.1 Consensus size: 90
30467691 TCATAATGAT
* * * * *
30467701 AAAAAACCCTCAAACTTTTTAAAAAAAAGTAATTAAGCCCCTGCTTTTTTTTTGTACTCAATTGG
1 AAAAAAACCTCAAACTTTTTAAAAAAAAGCAATTAAGCCCCTGCCTTTTTTTTCTACTCAATTAG
** ** *
30467766 GTACTTTAGATTTCTTAATGTATAA
66 GTACTTTAGATGCCAAAATGCATAA
* *
30467791 AAAAAAACCTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCTGCCTTTTTTTTCTACTCAATTAG
1 AAAAAAACCTCAAACTTTTTAAAAAAAAGCAATTAAGCCCCTGCCTTTTTTTTCTACTCAATTAG
*
30467856 GTA-TTT-GAACTGCCAAAATGCGTAA
66 GTACTTTAG-A-TGCCAAAATGCATAA
30467881 AAAAAA
1 AAAAAA
30467887 GGTCATTTGA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
88 1 0.01
89 4 0.05
90 76 0.94
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (90 bp):
AAAAAAACCTCAAACTTTTTAAAAAAAAGCAATTAAGCCCCTGCCTTTTTTTTCTACTCAATTAG
GTACTTTAGATGCCAAAATGCATAA
Found at i:30468102 original size:18 final size:18
Alignment explanation
Indices: 30468063--30468166 Score: 65
Period size: 17 Copynumber: 5.8 Consensus size: 18
30468053 AAAGCATACT
*
30468063 TAAAATTTATAAAAA-AG
1 TAAAAATTATAAAAATAG
* *
30468080 AAAAAATTATAAAAATCG
1 TAAAAATTATAAAAATAG
30468098 TAAAAA-TATAAAATATA-
1 TAAAAATTATAAAA-ATAG
** *
30468115 TAGTAA-TATAAAAA-AA
1 TAAAAATTATAAAAATAG
* *
30468131 TATAAAATTTTATAAAATCG
1 TA-AAAATTATA-AAAATAG
30468151 TAAGAAATTATAAAAA
1 TAA-AAATTATAAAAA
30468167 AGTGTAAAGA
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
15 1 0.02
16 3 0.05
17 33 0.50
18 11 0.17
19 9 0.14
20 9 0.14
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
TAAAAATTATAAAAATAG
Found at i:30468405 original size:9 final size:9
Alignment explanation
Indices: 30468393--30468553 Score: 64
Period size: 9 Copynumber: 17.4 Consensus size: 9
30468383 TTTTTATGCA
30468393 TTTTATAATTT
1 TTTTATAA--T
*
30468404 TTTTATGAT
1 TTTTATAAT
30468413 TTTTATAAT
1 TTTTATAAT
* *
30468422 ATTCTACAAT
1 -TTTTATAAT
*
30468432 TTCT-T--T
1 TTTTATAAT
30468438 T-TTATATAT
1 TTTTATA-AT
*
30468447 TTTTATGAT
1 TTTTATAAT
*
30468456 TTTTATATT
1 TTTTATAAT
*
30468465 TTTTCTAAT
1 TTTTATAAT
*
30468474 TTTAATAAAT
1 TTTTAT-AAT
* *
30468484 TTTAAATATT
1 TTT-TATAAT
*
30468494 TTTTATTAAAA
1 TTTTA-T-AAT
*
30468505 TTTAATAATT
1 TTTTATAA-T
*
30468515 TTTTATAAA
1 TTTTATAAT
*
30468524 TTTTATTGAT
1 TTTTA-TAAT
30468534 TTTTAT--T
1 TTTTATAAT
30468541 TTTTATAAT
1 TTTTATAAT
30468550 TTTT
1 TTTT
30468554 TGTCACATGT
Statistics
Matches: 113, Mismatches: 23, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
5 1 0.01
6 3 0.03
7 7 0.06
9 49 0.43
10 38 0.34
11 15 0.13
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:30468406 original size:20 final size:20
Alignment explanation
Indices: 30468381--30468421 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
30468371 AAATGACCTT
30468381 TTTTTTTATGCA-TTTTATAA
1 TTTTTTTATG-ATTTTTATAA
30468401 TTTTTTTATGATTTTTATAA
1 TTTTTTTATGATTTTTATAA
30468421 T
1 T
30468422 ATTCTACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTTTATGATTTTTATAA
Found at i:30468476 original size:17 final size:19
Alignment explanation
Indices: 30468437--30468477 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
30468427 ACAATTTCTT
*
30468437 TTTTATATATTTTTATGAT
1 TTTTATATATTTTTATGAA
*
30468456 TTTTATAT-TTTTTCT-AA
1 TTTTATATATTTTTATGAA
30468473 TTTTA
1 TTTTA
30468478 ATAAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 6 0.30
18 6 0.30
19 8 0.40
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTATATATTTTTATGAA
Found at i:30468496 original size:20 final size:22
Alignment explanation
Indices: 30468473--30468528 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
30468463 TTTTTTCTAA
30468473 TTTTAATAAATTTTAAAT-ATT
1 TTTTAATAAATTTTAAATAATT
* *
30468494 TTTTATTAAAATTT-AATAATT
1 TTTTAATAAATTTTAAATAATT
30468515 TTTT-ATAAATTTTA
1 TTTTAATAAATTTTA
30468529 TTGATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAATAAATTTTAAATAATT
Found at i:30468503 original size:21 final size:21
Alignment explanation
Indices: 30468473--30468528 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
30468463 TTTTTTCTAA
*
30468473 TTTTAATAAATTTTAAAT-AT
1 TTTTTATAAATTTTAAATAAT
*
30468493 TTTTTATTAAAATTT-AATAAT
1 TTTTTA-TAAATTTTAAATAAT
30468514 TTTTTATAAATTTTA
1 TTTTTATAAATTTTA
30468529 TTGATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTATAAATTTTAAATAAT
Found at i:30468651 original size:20 final size:20
Alignment explanation
Indices: 30468615--30468652 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30468605 ATTAGAGAAA
**
30468615 GTTAAAGTTAATTGTCAAGT
1 GTTAAAGTTAACGGTCAAGT
30468635 GTTAAAGTTAACGGTCAA
1 GTTAAAGTTAACGGTCAA
30468653 AGGGTCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (20 bp):
GTTAAAGTTAACGGTCAAGT
Found at i:30470684 original size:14 final size:14
Alignment explanation
Indices: 30470665--30470693 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30470655 ATGTAAACTC
30470665 AAACTAACTCAATA
1 AAACTAACTCAATA
30470679 AAACTAACTCAATA
1 AAACTAACTCAATA
30470693 A
1 A
30470694 GGGAGATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACTAACTCAATA
Found at i:30472366 original size:35 final size:35
Alignment explanation
Indices: 30472327--30472572 Score: 309
Period size: 35 Copynumber: 7.1 Consensus size: 35
30472317 ACAAAACAAT
*
30472327 TTTGGACAACATTATAACATGTAAAAGCAACCACA
1 TTTGGACAACATTATAACATGTAAAAACAACCACA
* *
30472362 TTTGGACACCATTATAACATG-CAAAACAACCACA
1 TTTGGACAACATTATAACATGTAAAAACAACCACA
*
30472396 TTTGGACAACATTATAACATGTAAAAACAGCCACA
1 TTTGGACAACATTATAACATGTAAAAACAACCACA
* * * * *
30472431 TTTGGATATCATTGTAATATG-CAAAACAACCACA
1 TTTGGACAACATTATAACATGTAAAAACAACCACA
30472465 TTTGGACAACATTATAACATGTAAAAACAACCACA
1 TTTGGACAACATTATAACATGTAAAAACAACCACA
* * * * * *
30472500 TTTGGACACCGTTGTAACATG-CATACCAACCACA
1 TTTGGACAACATTATAACATGTAAAAACAACCACA
* * *
30472534 TTTGTACACCATTATAACATGTAAAAACAGCCACA
1 TTTGGACAACATTATAACATGTAAAAACAACCACA
30472569 TTTG
1 TTTG
30472573 TATCAATAAT
Statistics
Matches: 178, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
34 87 0.49
35 91 0.51
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (35 bp):
TTTGGACAACATTATAACATGTAAAAACAACCACA
Found at i:30472415 original size:69 final size:69
Alignment explanation
Indices: 30472229--30472572 Score: 380
Period size: 69 Copynumber: 5.1 Consensus size: 69
30472219 CTGCAAACAT
* * * ** ** *
30472229 ATTTGGACATCC-TTATAACATGCGAAACAA-C-CATTAGAACAACATTGCAACATACCAAAAGC
1 ATTTGGACA-CCATTATAACATGCAAAACAACCACATTTGGACAACATTATAACAT-GTAAAAAC
*
30472291 AGCCGC
64 AGCCAC
* * * * * *
30472297 CTTTGGACAACATTA-AACATACAAAAC-A--A-TTTTGGACAACATTATAACATGTAAAAGCAA
1 ATTTGGACACCATTATAACATGCAAAACAACCACATTTGGACAACATTATAACATGTAAAAACAG
30472357 CCAC
66 CCAC
30472361 ATTTGGACACCATTATAACATGCAAAACAACCACATTTGGACAACATTATAACATGTAAAAACAG
1 ATTTGGACACCATTATAACATGCAAAACAACCACATTTGGACAACATTATAACATGTAAAAACAG
30472426 CCAC
66 CCAC
* * * * *
30472430 ATTTGGATATCATTGTAATATGCAAAACAACCACATTTGGACAACATTATAACATGTAAAAACAA
1 ATTTGGACACCATTATAACATGCAAAACAACCACATTTGGACAACATTATAACATGTAAAAACAG
30472495 CCAC
66 CCAC
* * * * * *
30472499 ATTTGGACACCGTTGTAACATGCATACCAACCACATTTGTACACCATTATAACATGTAAAAACAG
1 ATTTGGACACCATTATAACATGCAAAACAACCACATTTGGACAACATTATAACATGTAAAAACAG
30472564 CCAC
66 CCAC
30472568 ATTTG
1 ATTTG
30472573 TATCAATAAT
Statistics
Matches: 236, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
64 23 0.10
65 27 0.11
66 2 0.01
67 11 0.05
68 12 0.05
69 161 0.68
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.24
Consensus pattern (69 bp):
ATTTGGACACCATTATAACATGCAAAACAACCACATTTGGACAACATTATAACATGTAAAAACAG
CCAC
Found at i:30472945 original size:17 final size:17
Alignment explanation
Indices: 30472917--30472949 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30472907 TTCAGAACTG
30472917 CTCCTAGCTTCTATCGTT
1 CTCCTAGCTTCT-TCGTT
30472935 CTCCT-GCTTCTTCGT
1 CTCCTAGCTTCTTCGT
30472950 GCTACAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.06, C:0.36, G:0.12, T:0.45
Consensus pattern (17 bp):
CTCCTAGCTTCTTCGTT
Found at i:30473077 original size:15 final size:15
Alignment explanation
Indices: 30473057--30473087 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30473047 CATTTAATAT
*
30473057 TTCCATGTATTTACA
1 TTCCATGCATTTACA
30473072 TTCCATGCATTTACA
1 TTCCATGCATTTACA
30473087 T
1 T
30473088 ATTTTTTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (15 bp):
TTCCATGCATTTACA
Found at i:30474305 original size:43 final size:43
Alignment explanation
Indices: 30474202--30474634 Score: 388
Period size: 43 Copynumber: 10.1 Consensus size: 43
30474192 GCATCGTAAC
* * * *
30474202 GCATCATCGGATAAACCGAAATAACTATACT-TCAAACATAGT
1 GCATCATCGGATAAACCGAAGTAACTATACTGGCACACACAGT
* * * *
30474244 ACATCATCGAATATACCGAAGTAAGTATACTGGCACACACAGT
1 GCATCATCGGATAAACCGAAGTAACTATACTGGCACACACAGT
* *
30474287 GCATCATCGGATAAACCGAAGCAACTATATTGGCACACACAGT
1 GCATCATCGGATAAACCGAAGTAACTATACTGGCACACACAGT
** * * * * * *
30474330 TAATCATCAGATATACCGAATTAACCATACTGGCATACACAAT
1 GCATCATCGGATAAACCGAAGTAACTATACTGGCACACACAGT
* ** *
30474373 ACATCATCGGATAAACCGAAACAACTATACTGGCATACACAGT
1 GCATCATCGGATAAACCGAAGTAACTATACTGGCACACACAGT
* * *
30474416 GCATCATCGAATATACCAAAGTAACTATACTGGCACACACTA-T
1 GCATCATCGGATAAACCGAAGTAACTATACTGGCACACAC-AGT
* * ** * *
30474459 GCATCATCAGATAAATCGAAACAACTATATTGACACACACAGT
1 GCATCATCGGATAAACCGAAGTAACTATACTGGCACACACAGT
* * * * *
30474502 GCTTTATC--AAAAACTGAAGAAACTATACTGGCACACACAGT
1 GCATCATCGGATAAACCGAAGTAACTATACTGGCACACACAGT
** * * *
30474543 GCATCATCGGATAAATTGAGGCAACTATACTGACACACACAGT
1 GCATCATCGGATAAACCGAAGTAACTATACTGGCACACACAGT
* * * * * * * *
30474586 ACATTATCGGATATATCGAAGTAACTATACTAGAACACAAAAT
1 GCATCATCGGATAAACCGAAGTAACTATACTGGCACACACAGT
30474629 GCATCA
1 GCATCA
30474635 ACAAATAGAC
Statistics
Matches: 309, Mismatches: 77, Indels: 9
0.78 0.19 0.02
Matches are distributed among these distances:
41 32 0.10
42 27 0.09
43 249 0.81
44 1 0.00
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (43 bp):
GCATCATCGGATAAACCGAAGTAACTATACTGGCACACACAGT
Found at i:30474653 original size:86 final size:86
Alignment explanation
Indices: 30474202--30474659 Score: 451
Period size: 86 Copynumber: 5.4 Consensus size: 86
30474192 GCATCGTAAC
* ** * * *
30474202 GCATCATCGGATAAACCGAAATAACTATACT-TCAAACATAGTACATCATCGAATATACCGAAGT
1 GCATCATCGGATAAACTGAAGCAACTATACTGACACACACAGTACATCATCGAATATACCGAAGT
* *
30474266 AAGTATACTGGCACACACAGT
66 AACTATACTGGCACACACAAT
* * *
30474287 GCATCATCGGATAAACCGAAGCAACTATATTGGCACACACAGTTA-ATCATC-AGATATACCGAA
1 GCATCATCGGATAAACTGAAGCAACTATACTGACACACACAG-TACATCATCGA-ATATACCGAA
* * *
30474350 TTAACCATACTGGCATACACAAT
64 GTAACTATACTGGCACACACAAT
* * * * * * *
30474373 ACATCATCGGATAAACCGAAACAACTATACTGGCATACACAGTGCATCATCGAATATACCAAAGT
1 GCATCATCGGATAAACTGAAGCAACTATACTGACACACACAGTACATCATCGAATATACCGAAGT
*
30474438 AACTATACTGGCACACACTAT
66 AACTATACTGGCACACACAAT
* * * * * * * *
30474459 GCATCATCAGATAAA-TCGAAACAACTATATTGACACACACAGTGCTTTATC-AA-AAACTGAAG
1 GCATCATCGGATAAACT-GAAGCAACTATACTGACACACACAGTACATCATCGAATATACCGAAG
* *
30474521 AAACTATACTGGCACACACAGT
65 TAACTATACTGGCACACACAAT
* * * * *
30474543 GCATCATCGGATAAATTGAGGCAACTATACTGACACACACAGTACATTATCGGATATATCGAAGT
1 GCATCATCGGATAAACTGAAGCAACTATACTGACACACACAGTACATCATCGAATATACCGAAGT
* * *
30474608 AACTATACTAGAACACAAAAT
66 AACTATACTGGCACACACAAT
* ** *
30474629 GCATCAACAAATAGACTGAAGCAACTATACT
1 GCATCATCGGATAAACTGAAGCAACTATACT
30474660 TCCACACCAA
Statistics
Matches: 308, Mismatches: 56, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
84 68 0.22
85 34 0.11
86 203 0.66
87 3 0.01
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (86 bp):
GCATCATCGGATAAACTGAAGCAACTATACTGACACACACAGTACATCATCGAATATACCGAAGT
AACTATACTGGCACACACAAT
Found at i:30480547 original size:13 final size:13
Alignment explanation
Indices: 30480529--30480605 Score: 118
Period size: 13 Copynumber: 5.9 Consensus size: 13
30480519 AGTTCTTCAT
*
30480529 TGCTTTTGAGAAA
1 TGCTTTTGAGAAG
30480542 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
30480555 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
30480568 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
30480581 TGATTTTGAGAAG
1 TGCTTTTGAGAAG
*
30480594 TACTTTTGAGAA
1 TGCTTTTGAGAA
30480606 ATTTGAGTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 58 1.00
ACGTcount: A:0.27, C:0.08, G:0.26, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:30482245 original size:14 final size:14
Alignment explanation
Indices: 30482226--30482256 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
30482216 TCGAAGAAGA
30482226 ATATGACATCAGGG
1 ATATGACATCAGGG
30482240 ATATGACATCAGGG
1 ATATGACATCAGGG
30482254 ATA
1 ATA
30482257 GAGAAGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (14 bp):
ATATGACATCAGGG
Found at i:30487677 original size:16 final size:16
Alignment explanation
Indices: 30487656--30487689 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
30487646 ATAGTTAAGC
30487656 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
30487672 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
30487688 TA
1 TA
30487690 CCCAAATTAT
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:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:30487721 original size:25 final size:25
Alignment explanation
Indices: 30487670--30487725 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
30487660 TAAGTTATGT
* *
30487670 ATTATGTAAGTTATTTATTACCCAA
1 ATTATGTAAGTTATGTATTACCAAA
* **
30487695 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATGTATTACCAAA
30487720 ATTATG
1 ATTATG
30487726 CTATGTAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATGTATTACCAAA
Found at i:30489728 original size:17 final size:17
Alignment explanation
Indices: 30489708--30489741 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30489698 TTAAAGTTCA
30489708 CAAGGAAGTAAAGGCTG
1 CAAGGAAGTAAAGGCTG
*
30489725 CAAGGAAGTAGAGGCTG
1 CAAGGAAGTAAAGGCTG
30489742 NNNNNNNNNN
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:0.38, C:0.12, G:0.38, T:0.12
Consensus pattern (17 bp):
CAAGGAAGTAAAGGCTG
Found at i:30493186 original size:41 final size:42
Alignment explanation
Indices: 30493100--30493205 Score: 169
Period size: 41 Copynumber: 2.5 Consensus size: 42
30493090 NNNNNNNNNN
* *
30493100 GCTTAGACAAAAGCGCCGCTAAAGACTCGGAGCATTAGCGAC
1 GCTTAGACAAAAACGCCGCTAAAGACTCCGAGCATTAGCGAC
* *
30493142 GCTTAGACAAAAACGCCGCTATAGAC-CCGAGCATTAGCGGC
1 GCTTAGACAAAAACGCCGCTAAAGACTCCGAGCATTAGCGAC
30493183 GCTTAGACAAAAACGCCGCTAAA
1 GCTTAGACAAAAACGCCGCTAAA
30493206 TGTTTAAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
41 35 0.59
42 24 0.41
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (42 bp):
GCTTAGACAAAAACGCCGCTAAAGACTCCGAGCATTAGCGAC
Found at i:30493523 original size:15 final size:15
Alignment explanation
Indices: 30493499--30493532 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30493489 AACAATTATG
* *
30493499 ATAATGCGAGTAAAA
1 ATAATACGAGCAAAA
30493514 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
30493529 ATAA
1 ATAA
30493533 CAAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.18
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:30495010 original size:17 final size:16
Alignment explanation
Indices: 30494976--30495016 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
30494966 TGAAAGAAAA
*
30494976 AAAAAAGAAAAAAGAG
1 AAAAAATAAAAAAGAG
*
30494992 AAAAAATAAATAAATAG
1 AAAAAATAAA-AAAGAG
30495009 AAAAAATA
1 AAAAAATA
30495017 TCAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAAAAGAG
Found at i:30495015 original size:9 final size:9
Alignment explanation
Indices: 30494974--30495016 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
30494964 TTTGAAAGAA
*
30494974 AAAAAAAAG
1 AAAAAATAG
*
30494983 AAAAAAGAG
1 AAAAAATAG
30494992 AAAAAATA-
1 AAAAAATAG
*
30495000 AATAAATAG
1 AAAAAATAG
30495009 AAAAAATA
1 AAAAAATA
30495017 TCAAAAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (9 bp):
AAAAAATAG
Found at i:30495837 original size:40 final size:40
Alignment explanation
Indices: 30495791--30495992 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 40
30495781 TTTTTTTCTG
*
30495791 TCTGCTCCACTACTGCTCAGGGA-AGTAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGA-TAAGACTTGATGCGA
* * ***
30495831 TCTGCTCTACTACTGCTTAGGGAGATAAGATCTGTGGTTTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGCGA
**
30495873 TTCCACTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
1 -TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * * *
30495914 TCTGCTCTACTACTGCTTAGGGAGATAAGATCTGTGGTTCTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGC-GA
* **
30495957 TCAGCTCCACTACAACTTCAGGGAGATAAGA-TTGAT
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGAT
30495993 TTTTTTTGTC
Statistics
Matches: 130, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
40 53 0.41
41 12 0.09
42 11 0.08
43 42 0.32
44 12 0.09
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:30495891 original size:43 final size:43
Alignment explanation
Indices: 30495839--30495988 Score: 164
Period size: 43 Copynumber: 3.5 Consensus size: 43
30495829 GATCTGCTCT
*
30495839 ACTACTGCTTAGGGAGATAAGATCTGTGGTTTTATTCCACTCC
1 ACTACTGCTTAGGGAGATAAGATCTGTGGTTCTATTCCACTCC
* * * ** *
30495882 ACTACTGCTTAGGGAGATAAGA-CT-TGATGCGA-TCTGCTCT
1 ACTACTGCTTAGGGAGATAAGATCTGTGGTTCTATTCCACTCC
*
30495922 ACTACTGCTTAGGGAGATAAGATCTGTGGTTCTAAT-CAGCTCC
1 ACTACTGCTTAGGGAGATAAGATCTGTGGTTCTATTCCA-CTCC
**
30495965 ACTACAACTTCAGGGAGATAAGAT
1 ACTACTGCTT-AGGGAGATAAGAT
30495989 TGATTTTTTT
Statistics
Matches: 87, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
40 27 0.31
41 6 0.07
42 7 0.08
43 34 0.39
44 13 0.15
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (43 bp):
ACTACTGCTTAGGGAGATAAGATCTGTGGTTCTATTCCACTCC
Found at i:30495905 original size:83 final size:83
Alignment explanation
Indices: 30495794--30496030 Score: 311
Period size: 83 Copynumber: 2.8 Consensus size: 83
30495784 TTTTCTGTCT
*
30495794 GCTCCACTACTGCTCAGGGA-AGTAAGACTTGATGCGATCTGCTCTACTACTGCTTAGGGAGATA
1 GCTCCACTACTGCTTAGGGAGA-TAAGACTTGATGCGATCTGCTCTACTACTGCTTAGGGAGATA
* *
30495858 AGATCTGTGGTTTTATTCCA
65 AGATCTGTGGTTCTAAT-CA
30495878 -CTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTACTGCTTAGGGAGATAA
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTACTGCTTAGGGAGATAA
30495942 GATCTGTGGTTCTAATCA
66 GATCTGTGGTTCTAATCA
** **
30495960 GCTCCACTACAACTTCAGGGAGATAAGA-TTGATTTTTTTTG-TCTGCTCTACTACTGCTTAGGG
1 GCTCCACTACTGCTT-AGGGAGATAAGACTTGA-----TGCGATCTGCTCTACTACTGCTTAGGG
30496023 AGATAAGA
60 AGATAAGA
30496031 CCTGCTATCT
Statistics
Matches: 138, Mismatches: 7, Indels: 13
0.87 0.04 0.08
Matches are distributed among these distances:
82 2 0.01
83 91 0.66
84 13 0.09
87 30 0.22
88 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (83 bp):
GCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTACTGCTTAGGGAGATAA
GATCTGTGGTTCTAATCA
Found at i:30496094 original size:45 final size:45
Alignment explanation
Indices: 30496027--30496228 Score: 318
Period size: 45 Copynumber: 4.5 Consensus size: 45
30496017 TTAGGGAGAT
*
30496027 AAGACCTGCTATCTTC-GATCTACTTCGCTGCCAATACAGGAAGAC
1 AAGACTTGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGAC
30496072 AAGACTTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
1 AAGACTTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
* *
30496117 AAGACTTGCTATCTTCAATCTACTTTGCTGCCAATACAGGAAGAC
1 AAGACTTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
* *
30496162 AAGACTTGCTATCTTCAATCTACTTCACTGCCAATACAGGAAGAC
1 AAGACTTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
*
30496207 AAGA-TCTGTTATCTTCAGTCTA
1 AAGACT-TGCTATCTTCAGTCTA
30496229 ATTAACTGCA
Statistics
Matches: 148, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
44 1 0.01
45 146 0.99
46 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (45 bp):
AAGACTTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGAC
Found at i:30496354 original size:99 final size:99
Alignment explanation
Indices: 30496230--30497331 Score: 1326
Period size: 99 Copynumber: 11.1 Consensus size: 99
30496220 TTCAGTCTAA
* * * * * * * *
30496230 TTAACTGCAATGTCGGGGAA-TAAGATTCGCTGTTGTAGCTTCAATCTGTTCTACTACACTACCA
1 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCA-TGCCA
* **
30496294 GAGAAGTAAGATTCGCTATTGCGGCTTCAAT-TTT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* * * * *
30496328 TTCATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCAC-GCACCGCCA
1 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCA-TGCCA
** * *
30496392 GAAAAGTAAGATTCGTCGTTGCAGCTTCAATCTTT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* *
30496427 TTAATTGCAATGTTC-GGGAA-CAAGATTCACCGTTGTAGCTTCAATCTGATCCACTGCAT-CAC
1 TTAATTGCAATG-TCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCATGC-C
*
30496489 TAGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTT
64 -AGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* **
30496526 TTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCCCCACTGCATTGCCA
1 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCA-TGCCA
**
30496591 GGGAAGTAAGATTCATCGTTGCGGCTTCAATCTTT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* * * * *
30496626 TTAATTGCAATATCGGGGAA-CAAGATTTGCCGTTGTAGCTTCAATTTGATCTACTGCATTGCCA
1 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCA-TGCCA
* * * *
30496690 GGAAAGTAAGATTCGCCCTTG-TGATTCAATCTTT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* * * **
30496724 TTAATTGCAATGTCGGGGAAGCAAAATTCGTCGTCGTAGCTTTAAGATGATCCACTGCATTGCCA
1 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCA-TGCCA
** * * *
30496789 GAAAAGTAAGATTCACCGTTGCGACTTTAATC-TT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
** * * * *
30496823 TTAATTGTGATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCA
1 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCA-TGCCA
* **
30496888 GGAAAGTAAGATTCGCCGTTGAAGCTTCAATCTTT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* * * *
30496923 TTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTTCACTGCATCGCCA
1 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCAT-GCCA
* *
30496988 AGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* *
30497023 TTAATTGCAATGTTGGGGAA-CAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTACATCGCCA
1 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCAT-GCCA
30497087 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* * * *
30497122 TTAATTGCAATGTTGGGGAA-CAAGATTCGCCGCTGTAGCTTCAATCTGATCCACTACATCGCCA
1 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCAT-GCCA
*
30497186 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
* * ** *
30497221 TTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGTTTTAATCTGCCCCACTGCATCGCTA
1 TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCAT-GCCA
* *
30497286 GGGAAGTAAGATTCACTGTTGCGGCTTCAATCTTT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
30497321 TTAATTGCAAT
1 TTAATTGCAAT
30497332 CTCAGAGGTA
Statistics
Matches: 882, Mismatches: 107, Indels: 28
0.87 0.11 0.03
Matches are distributed among these distances:
97 1 0.00
98 114 0.13
99 474 0.54
100 290 0.33
101 2 0.00
102 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (99 bp):
TTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCATGCCAG
GGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
Found at i:30496648 original size:199 final size:199
Alignment explanation
Indices: 30496230--30497331 Score: 1428
Period size: 199 Copynumber: 5.6 Consensus size: 199
30496220 TTCAGTCTAA
* * * * * * *
30496230 TTAACTGCAATGTCGGGGAATAAGATTCGCTGTTGTAGCTTCAATCTGTTCTACTACA-CTACCA
1 TTAATTGCAATGTCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGCATC-GCCA
* ** *
30496294 GAGAAGTAAGATTCGCTATTGCGGCTTCAAT-TTTTTCATTGCAATGTCGGGGAAGCAAGATTCA
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* ** ** *
30496358 CCGTCGTAGCTTTAATCTGCTCCAC-GCACCGCCAGAAAAGTAAGATTCGTCGTTGCAGCTTCAA
130 CCGTCGTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAA
30496422 TCTTT
195 TCTTT
* * *
30496427 TTAATTGCAATGTTC-GGGAACAAGATTCACCGTTGTAGCTTCAATCTGATCCACTGCATCACTA
1 TTAATTGCAATG-TCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCCA
*
30496491 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * * *
30496556 CCGTTGTAGCTTTAATCTGCCCCACTGCATTGCCAGGGAAGTAAGATTCATCGTTGCGGCTTCAA
130 CCGTCGTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAA
30496621 TCTTT
195 TCTTT
* * * * *
30496626 TTAATTGCAATATCGGGGAACAAGATTTGCCGTTGTAGCTTCAATTTGATCTACTGCATTGCCAG
1 TTAATTGCAATGTCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAG
* * * * * **
30496691 GAAAGTAAGATTCGCCCTTG-TGATTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAAATTCGT
66 GGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
** * * ** * *
30496755 CGTCGTAGCTTTAAGATGATCCACTGCATTGCCAGAAAAGTAAGATTCACCGTTGCGACTTTAAT
131 CGTCGTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAAT
30496820 C-TT
196 CTTT
** * * * * *
30496823 TTAATTGTGATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCA
1 TTAATTGCAATGTCGGGGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCCA
* **
30496888 GGAAAGTAAGATTCGCCGTTGAAGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * * *
30496953 CCGTCGTAGCTTTAATCTGCTTCACTGCATCGCCAAGGAAGTAAGATTCGCCGTTGTGGCTTCAA
130 CCGTCGTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAA
30497018 TCTTT
195 TCTTT
* * *
30497023 TTAATTGCAATGTTGGGGAACAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTACATCGCCAG
1 TTAATTGCAATGTCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAG
* *
30497088 GGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGAA-CAAGATTCGC
66 GGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
* * *
30497152 CG-CTGTAGCTTCAATCTGATCCACTACATCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAA
131 CGTC-GTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAA
30497216 TCTTT
195 TCTTT
* * * ** *
30497221 TTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGTTTTAATCTGCCCCACTGCATCGCTA
1 TTAATTGCAATGTCGGGGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCCA
* *
30497286 GGGAAGTAAGATTCACTGTTGCGGCTTCAATCTTTTTAATTGCAAT
65 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAAT
30497332 CTCAGAGGTA
Statistics
Matches: 789, Mismatches: 106, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
197 98 0.12
198 297 0.38
199 375 0.48
200 19 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (199 bp):
TTAATTGCAATGTCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAG
GGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
CGTCGTAGCTTTAATCTGCTCCACTGCATCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAAT
CTTT
Found at i:30496753 original size:49 final size:50
Alignment explanation
Indices: 30496399--30497268 Score: 213
Period size: 50 Copynumber: 17.5 Consensus size: 50
30496389 CCAGAAAAGT
* * * *
30496399 AAGATTCGTCGTTGCAGCTTCAATCTTTTTAATTGCAATGTTC-GGGAA-C
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATG-TCGGGGAAGC
* * * ** ** * ** * *
30496448 AAGATTCACCGTTGTAGCTTCAATCTGATCCACTGC-ATCACTAGGGAAGT
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTC-GGGGAAGC
* * ** *
30496498 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGC
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
* * * * ***** * * * * *
30496548 AAGATTCACCGTTGTAGCTTTAATCTGCCCCACTGCATTGCCAGGGAAGT
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
** * ** * *
30496598 AAGATTCATCGTTGCGGCTTCAATCTTTTTAATTGCAATATCGGGGAA-C
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
* * * * * * * * * *
30496647 AAGATTTGCCGTTGTAGCTTCAAT-TTGATCT-ACTGCATTGCCAGGAAAGT
1 AAGATTCGCCCTTGTAGATTCAATCTT--TTTAATTGCAATGTCGGGGAAGC
30496697 AAGATTCGCCCTTGT-GATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
* * * * * * ** ** ** * * * * ** *
30496746 AAAATTCGTCGTCGTAGCTTTAAGATGATCCACTGCATTGCCAGAAAAGT
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
* * * * **
30496796 AAGATTCACCGTTG-CGACTTTAATC-TTTTAATTGTGATGTCGGGGAAGC
1 AAGATTCGCCCTTGTAGA-TTCAATCTTTTTAATTGCAATGTCGGGGAAGC
* * * * * ** ** * ** * * * *
30496845 AAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCAGGAAAGT
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
* * *
30496895 AAGATTCGCCGTTGAAGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGC
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
* * * * * ** * * * ** *
30496945 AAGATTCACCGTCGTAGCTTTAATCTGCTTCACTGC-ATCGCCAAGGAAGT
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAAT-GTCGGGGAAGC
* * * *
30496995 AAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTGGGGAA-C
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
* * * ** ** * * * * *
30497044 AAGATTCGCCGTTGTAGCTTTAATCTGATCCACTAC-ATCGCCAGGGAAGT
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAAT-GTCGGGGAAGC
* ** * *
30497094 AAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGAA-C
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
* ** ** * * * * *
30497143 AAGATTCGCCGC-TGTAGCTTCAATCTGATCCACTAC-ATCGCCAGGGAAGT
1 AAGATTCGCC-CTTGTAGATTCAATCTTTTTAATTGCAAT-GTCGGGGAAGC
* * ** * *
30497193 AAGATTCACCGTTGCGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
* * *
30497243 AAGATTCGCCGTTGTAGTTTTAATCT
1 AAGATTCGCCCTTGTAGATTCAATCT
30497269 GCCCCACTGC
Statistics
Matches: 574, Mismatches: 224, Indels: 45
0.68 0.27 0.05
Matches are distributed among these distances:
47 1 0.00
48 10 0.02
49 194 0.34
50 360 0.63
51 9 0.02
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (50 bp):
AAGATTCGCCCTTGTAGATTCAATCTTTTTAATTGCAATGTCGGGGAAGC
Found at i:30497108 original size:298 final size:297
Alignment explanation
Indices: 30496230--30497331 Score: 1381
Period size: 298 Copynumber: 3.7 Consensus size: 297
30496220 TTCAGTCTAA
* * * * * * * **
30496230 TTAACTGCAATGTCGGGGAATAAGATTCGCTGTTGTAGCTTCAATCTGTTCTACTACACTACCA-
1 TTAATTGCAATGTCGGGGAACAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCCAG
* ** *
30496294 GAGAAGTAAGATTCGCTATTGCGGCTTCAAT-TTTTTCATTGCAATGTCGGGGAAGCAAGATTCA
66 GA-AAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * * *
30496358 CCGTCGTAGCTTTAATCTGCTCCAC-GCACCGCCAGAAAAGTAAGATTCGTCGTTGCAGCTTCAA
130 CCGTCGTAGCTTTAATCTGCTCCACTGCATCGCCAG-GAAGTAAGATTCGCCGTTGCGGCTTCAA
* * *
30496422 TCTTTTTAATTGCAATGTTCGGGAACAAGATTCACCGTTGTAGCTTCAATCTGATCCACTGCATC
194 TCTTTTTAATTGCAATGTTGGGGAACAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCATC
* *
30496487 ACTAGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTT
259 GCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTT
* * * * **
30496526 TTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGCCCCACTGCATTGCCA
1 TTAATTGCAATGTCGGGGAA-CAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCCA
* * * **
30496591 GGGAAGTAAGATTCATCGTTGCGGCTTCAATCTTTTTAATTGCAATATCGGGGAA-CAAGATTTG
65 GGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * * * * * * * *
30496655 CCGTTGTAGCTTCAATTTGATCTACTGCATTGCCAGGAAAGTAAGATTCGCCCTTG-TGATTCAA
130 CCGTCGTAGCTTTAATCTGCTCCACTGCATCGCCAGG-AAGTAAGATTCGCCGTTGCGGCTTCAA
* * * * **
30496719 TCTTTTTAATTGCAATGTCGGGGAAGCAAAATTCGTCGTCGTAGCTTTAAGATGATCCACTGCAT
194 TCTTTTTAATTGCAATGTTGGGGAA-CAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCAT
* ** * *
30496784 TGCCAGAAAAGTAAGATTCACCGTTGCGACTTTAATC-TT
258 CGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTT
** * *
30496823 TTAATTGTGATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGCACCGCCA
1 TTAATTGCAATGTCGGGGAA-CAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCCA
* **
30496888 GGAAAGTAAGATTCGCCGTTGAAGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
65 GGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* *
30496953 CCGTCGTAGCTTTAATCTGCTTCACTGCATCGCCAAGGAAGTAAGATTCGCCGTTGTGGCTTCAA
130 CCGTCGTAGCTTTAATCTGCTCCACTGCATCGCC-AGGAAGTAAGATTCGCCGTTGCGGCTTCAA
*
30497018 TCTTTTTAATTGCAATGTTGGGGAACAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTACATC
194 TCTTTTTAATTGCAATGTTGGGGAACAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCATC
*
30497083 GCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
259 GCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTT
* * * *
30497122 TTAATTGCAATGTTGGGGAACAAGATTCGCCG-CTGTAGCTTCAATCTGATCCACTACATCGCCA
1 TTAATTGCAATGTCGGGGAACAAGATTCACCGTC-GTAGCTTCAATCTGCTCCACTACACCGCCA
* * *
30497186 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCG
65 GGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * * * * *
30497251 CCGTTGTAGTTTTAATCTGCCCCACTGCATCGCTAGGGAAGTAAGATTCACTGTTGCGGCTTCAA
130 CCGTCGTAGCTTTAATCTGCTCCACTGCATCGCCA-GGAAGTAAGATTCGCCGTTGCGGCTTCAA
30497316 TCTTTTTAATTGCAAT
194 TCTTTTTAATTGCAAT
30497332 CTCAGAGGTA
Statistics
Matches: 687, Mismatches: 107, Indels: 22
0.84 0.13 0.03
Matches are distributed among these distances:
296 19 0.03
297 226 0.33
298 390 0.57
299 52 0.08
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (297 bp):
TTAATTGCAATGTCGGGGAACAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCCAG
GAAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
CGTCGTAGCTTTAATCTGCTCCACTGCATCGCCAGGAAGTAAGATTCGCCGTTGCGGCTTCAATC
TTTTTAATTGCAATGTTGGGGAACAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCATCGC
CAGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTT
Found at i:30498244 original size:15 final size:15
Alignment explanation
Indices: 30498224--30498259 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
30498214 TTCTTTTTCA
*
30498224 TTTTTCTTTTCTTTT
1 TTTTTCGTTTCTTTT
30498239 TTTTTCGTTTCTTTT
1 TTTTTCGTTTCTTTT
30498254 TTTTTC
1 TTTTTC
30498260 AAGTGAAGTA
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:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTCGTTTCTTTT
Found at i:30503246 original size:15 final size:15
Alignment explanation
Indices: 30503222--30503255 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30503212 AACAATTATG
* *
30503222 ATAATGCGAGTAAAA
1 ATAATACGAGCAAAA
30503237 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
30503252 ATAA
1 ATAA
30503256 CAAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.18
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:30503840 original size:2 final size:2
Alignment explanation
Indices: 30503833--30503878 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
30503823 NNNNNNNNNN
30503833 AT 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 AT
30503875 AT AT
1 AT AT
30503879 CATAACTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30507620 original size:16 final size:16
Alignment explanation
Indices: 30507599--30507629 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30507589 TATACTTAAT
*
30507599 TTTCATATTATATAAA
1 TTTCATAATATATAAA
30507615 TTTCATAATATATAA
1 TTTCATAATATATAA
30507630 GAAAATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTCATAATATATAAA
Found at i:30509549 original size:49 final size:49
Alignment explanation
Indices: 30509487--30509644 Score: 165
Period size: 49 Copynumber: 3.2 Consensus size: 49
30509477 GGCAACCTGG
* * *
30509487 GATGGTAGGATATGCAAACAGTGAAAGCCATCATT-TTCGAGCCACCCAA
1 GATGGTAGAATATGCAAATAGTGAAAACCATCATTGTT-GAGCCACCCAA
* * * * ***
30509536 GATGGTAGAATATGAAAATTGTGAAAACCATCATTGTTGGGTCACCTGG
1 GATGGTAGAATATGCAAATAGTGAAAACCATCATTGTTGAGCCACCCAA
* * * **
30509585 GATGGTAGAATATGCAAATAGTGAAAATCATCATTGTTGGGCCACTCGG
1 GATGGTAGAATATGCAAATAGTGAAAACCATCATTGTTGAGCCACCCAA
30509634 GATGGTAGAAT
1 GATGGTAGAAT
30509645 TATTGGAAAA
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
49 90 0.98
50 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (49 bp):
GATGGTAGAATATGCAAATAGTGAAAACCATCATTGTTGAGCCACCCAA
Found at i:30510340 original size:20 final size:19
Alignment explanation
Indices: 30510293--30510342 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
30510283 CAAGATAAAC
30510293 ATTAAATT-A-AATTTAAT
1 ATTAAATTAATAATTTAAT
30510310 ATTAAGA-TAATAATTTTAAT
1 ATTAA-ATTAATAA-TTTAAT
30510330 ATTAAATTAATAA
1 ATTAAATTAATAA
30510343 AATACTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.21
18 2 0.07
19 3 0.11
20 17 0.61
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAT
Found at i:30510374 original size:68 final size:71
Alignment explanation
Indices: 30510252--30510382 Score: 187
Period size: 68 Copynumber: 1.9 Consensus size: 71
30510242 ACTTAATCAC
* *
30510252 TTTAATATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAGA
1 TTTAATATTAAATTAATAAAATATCTATCTA-AAGATAAACATTAAATTAAATTTAATATTAAGA
30510317 TAATAAT
65 TAATAAT
** *
30510324 TTTAATATTAAATTAATAAAATA-CTAT-T-AAGATAAGTATTAAATTTAATTTAATATTAA
1 TTTAATATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTAAATTTAATATTAA
30510383 ATCTATTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 28 0.52
70 1 0.02
71 3 0.06
72 22 0.41
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (71 bp):
TTTAATATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTAAATTTAATATTAAGAT
AATAAT
Found at i:30514748 original size:24 final size:24
Alignment explanation
Indices: 30514720--30514777 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
30514710 TAGTCATTCA
* *
30514720 TTTAAATTTTCACTTTTTT-TAAT
1 TTTAAATTTTCAATTTTTTGAAAT
* *
30514743 CTTTAATTTTTGAATTTTTTGAAAT
1 -TTTAAATTTTCAATTTTTTGAAAT
30514768 TTTAAATTTT
1 TTTAAATTTT
30514778 AAAAATCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (24 bp):
TTTAAATTTTCAATTTTTTGAAAT
Found at i:30523961 original size:15 final size:13
Alignment explanation
Indices: 30523928--30523970 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 13
30523918 CACGCCAATC
30523928 ACAGATACAAAAT
1 ACAGATACAAAAT
30523941 ACAGATACAGAAAT
1 ACAGATACA-AAAT
30523955 AACAGATACAATAAT
1 -ACAGATACAA-AAT
30523970 A
1 A
30523971 TCATGCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
14 6 0.22
15 12 0.44
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.16
Consensus pattern (13 bp):
ACAGATACAAAAT
Found at i:30527997 original size:114 final size:113
Alignment explanation
Indices: 30527822--30528147 Score: 505
Period size: 114 Copynumber: 2.9 Consensus size: 113
30527812 CAAATAAGCA
* * * *
30527822 TTAGCGGCGTTTTTGAGAAAGCGCCGC--AAAAACCTAATCCCAACGACGTCGTTTCCCGAGCTT
1 TTAGCGGCGTTTTTG-GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
30527885 TCGGGGATTTAGCGGCGTTTTTAAGTAAA-CGCCGCTAATGCTCAGGGCT
65 TCGGGGATTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAATGCTCAGGGAT
*
30527934 TTAGCGGCGTTTTTCGTAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTT-GGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
30527999 TCGAGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGAT
65 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGAT
30528048 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTT-GGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
**
30528113 TCGGGGATTTAGCGGCGTTTTTGGGAAAGCGCCGC
65 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
30528148 AAAAAAACCT
Statistics
Matches: 196, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
112 24 0.12
113 4 0.02
114 168 0.86
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGAT
Found at i:30528193 original size:72 final size:73
Alignment explanation
Indices: 30528043--30528225 Score: 341
Period size: 73 Copynumber: 2.5 Consensus size: 73
30528033 CTAATGCTCA
30528043 GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
1 GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
30528108 AGCTTTCG
66 AGCTTTCG
30528116 GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCG-TTTCTG
1 GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
30528180 AGCTTTCG
66 AGCTTTCG
* *
30528188 GGGATTTAGCGGCGTTTTTGGAAAAGCGCCGCTAAAAA
1 GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAA
30528226 TATTTTATCT
Statistics
Matches: 108, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
72 50 0.46
73 58 0.54
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (73 bp):
GGGATTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
AGCTTTCG
Found at i:30528609 original size:14 final size:14
Alignment explanation
Indices: 30528590--30528623 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
30528580 GTTTGGGGGT
30528590 TTAGGGGTT-AGATG
1 TTAGGGGTTAAGA-G
30528604 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
30528618 TTAGGG
1 TTAGGG
30528624 ATTTAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:30528610 original size:23 final size:23
Alignment explanation
Indices: 30528564--30528610 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
30528554 TGGGATTTAA
*
30528564 GGTTTAGGGGTTAGTGGTTTGGG
1 GGTTTAGGGGTTAGTGGTTAGGG
30528587 GGTTTAGGGGTTAGAT-GTTAGGG
1 GGTTTAGGGGTTAG-TGGTTAGGG
30528610 G
1 G
30528611 TTAAGAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.13, C:0.00, G:0.51, T:0.36
Consensus pattern (23 bp):
GGTTTAGGGGTTAGTGGTTAGGG
Found at i:30528946 original size:146 final size:147
Alignment explanation
Indices: 30528720--30529341 Score: 1054
Period size: 146 Copynumber: 4.3 Consensus size: 147
30528710 ATATAATTGT
30528720 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTACAA
1 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTACAA
30528785 AAACGCCGCAAAAAATAAATCAACTTATAAAAA-AATAAAAAAATTTTAGAATAGCAAAACGGCG
66 AAACGCCGCAAAAAATAAATCAACTTATAAAAATAATAAAAAAATTTTAGAATAGCAAAACGGCG
30528849 TCGTTTTGTTCAAAATG
131 TCGTTTTGTTCAAAATG
* *
30528866 AAAAAATTTTGTGGCGCTTTATAAGAAGCGCCACTAAAGGTAAGCAATAGCGGCGTTTTCTACAA
1 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTACAA
*
30528931 AAACGCCGCAAAAAATAAATCAACTTATAAAAA-AATAAAAATATTTTAGAATAGCAAAACGGCG
66 AAACGCCGCAAAAAATAAATCAACTTATAAAAATAATAAAAAAATTTTAGAATAGCAAAACGGCG
* *** *
30528995 TCCTTCCCTTCAAAATA
131 TCGTTTTGTTCAAAATG
* * * *
30529012 AAAAAAATTTGCGCCCCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTA-GA
1 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTACAA
*
30529076 AAACGCCGCAAAAAATAAATCAATTTATAAAAATAATAAAAAAATTTTAGAATAGCAAAACGGCG
66 AAACGCCGCAAAAAATAAATCAACTTATAAAAATAATAAAAAAATTTTAGAATAGCAAAACGGCG
30529141 TCGTTTTGTTCAAAATG
131 TCGTTTTGTTCAAAATG
*
30529158 AAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATA
1 -AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTACA
* *
30529223 AAAACGCCGCCAAAAATAAATCAATTTATAAAAATAATAAAAAAATTTTAGAATAGCAAAACGGC
65 AAAACGCCGCAAAAAATAAATCAACTTATAAAAATAATAAAAAAATTTTAGAATAGCAAAACGGC
30529288 GTCGTTTTGTTCAAAATG
130 GTCGTTTTGTTCAAAATG
*
30529306 AAAAAATTTTGCGGCGC-TTATAGGAAGCGCCGCTAA
1 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAA
30529342 NNNNNNNNNN
Statistics
Matches: 446, Mismatches: 27, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
145 33 0.07
146 255 0.57
147 76 0.17
148 82 0.18
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (147 bp):
AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTACAA
AAACGCCGCAAAAAATAAATCAACTTATAAAAATAATAAAAAAATTTTAGAATAGCAAAACGGCG
TCGTTTTGTTCAAAATG
Found at i:30529254 original size:293 final size:293
Alignment explanation
Indices: 30528720--30529341 Score: 1052
Period size: 293 Copynumber: 2.1 Consensus size: 293
30528710 ATATAATTGT
30528720 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTACAA
1 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTACAA
30528785 AAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGT
66 AAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGT
*
30528850 CGTTTTGTTCAAAATGAAAAAATTTTGTGGCGCTTTATAAGAAGCGCCACTAAAGGTAAGCAATA
131 CGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCACTAAAGGTAAGCAATA
*
30528915 GCGGCGTTTTCTACAAAAACGCCGCAAAAAATAAATCAACTTATAAAAA-AATAAAAATATTTTA
196 GCGGCGTTTTCTACAAAAACGCCGCAAAAAATAAATCAACTTATAAAAATAATAAAAAAATTTTA
30528979 GAATAGCAAAACGGCGTCCTTCCCTTCAAAATA
261 GAATAGCAAAACGGCGTCCTTCCCTTCAAAATA
* * * *
30529012 AAAAAAATTTGCGCCCCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTA-GA
1 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTACAA
*
30529076 AAACGCCGCAAAAAATAAATCAATTTATAAAAATAATAAAAAAATTTTAGAATAGCAAAACGGCG
66 AAACGCCGCAAAAAATAAATCAACTTATAAAAA-AATAAAAAAATTTTAGAATAGCAAAACGGCG
*
30529141 TCGTTTTGTTCAAAATGAAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAA
130 TCGTTTTGTTCAAAATG-AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCACTAAAGGTAAGCAA
* * *
30529206 TAGCGGCGTTTTCTATAAAAACGCCGCCAAAAATAAATCAATTTATAAAAATAATAAAAAAATTT
194 TAGCGGCGTTTTCTACAAAAACGCCGCAAAAAATAAATCAACTTATAAAAATAATAAAAAAATTT
* *** *
30529271 TAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
259 TAGAATAGCAAAACGGCGTCCTTCCCTTCAAAATA
*
30529306 AAAAAATTTTGCGGCGC-TTATAGGAAGCGCCGCTAA
1 AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAA
30529342 NNNNNNNNNN
Statistics
Matches: 307, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
291 33 0.11
292 107 0.35
293 111 0.36
294 56 0.18
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (293 bp):
AAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTACAA
AAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGT
CGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCACTAAAGGTAAGCAATA
GCGGCGTTTTCTACAAAAACGCCGCAAAAAATAAATCAACTTATAAAAATAATAAAAAAATTTTA
GAATAGCAAAACGGCGTCCTTCCCTTCAAAATA
Found at i:30532959 original size:21 final size:21
Alignment explanation
Indices: 30532916--30532962 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
30532906 TTAAATTTGA
* *
30532916 AATTTTACAATTTAATCATCT
1 AATTTTACAATATAATCAACT
* *
30532937 AATTTTACAATATCATTAACT
1 AATTTTACAATATAATCAACT
30532958 AATTT
1 AATTT
30532963 AAATAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTACAATATAATCAACT
Found at i:30533325 original size:28 final size:28
Alignment explanation
Indices: 30533266--30533319 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
30533256 NNNNNNNNNN
* ***
30533266 CTATAATTCATGCCTTGTCTTTTAATCG
1 CTATAATTCATGCCATGTCTGCAAATCG
30533294 CTATAATTCATGCCATGTCTGCAAAT
1 CTATAATTCATGCCATGTCTGCAAAT
30533320 GACTATGGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (28 bp):
CTATAATTCATGCCATGTCTGCAAATCG
Found at i:30533697 original size:53 final size:54
Alignment explanation
Indices: 30533640--30533774 Score: 120
Period size: 53 Copynumber: 2.5 Consensus size: 54
30533630 TATATAATTC
* *
30533640 ACATAATAACTTACATAACTGAACAACTTAACAACTCACATAATTTACATAAT-
1 ACATAATAACTTACATAACTCAACAACTTAACAACTCACATAATTCACATAATA
* * * *
30533693 ACATATATATA-TGT-CAT-AC-CATATAACTTAATAACTTATATAATTCACATAATA
1 ACATA-ATA-ACT-TACATAACTCA-ACAACTTAACAACTCACATAATTCACATAATA
* *
30533747 ACTTAATAACTTA-ATAACTTAACAACTT
1 ACATAATAACTTACATAACTCAACAACTT
30533775 GCATAATTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
52 5 0.08
53 45 0.70
54 12 0.19
55 2 0.03
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.33
Consensus pattern (54 bp):
ACATAATAACTTACATAACTCAACAACTTAACAACTCACATAATTCACATAATA
Found at i:30533728 original size:8 final size:8
Alignment explanation
Indices: 30533715--30533797 Score: 66
Period size: 8 Copynumber: 10.5 Consensus size: 8
30533705 GTCATACCAT
30533715 ATAACTTA
1 ATAACTTA
30533723 ATAACTTA
1 ATAACTTA
*
30533731 TATAA-TTC
1 -ATAACTTA
*
30533739 A-CA-T-A
1 ATAACTTA
30533744 ATAACTTA
1 ATAACTTA
30533752 ATAACTTA
1 ATAACTTA
30533760 ATAACTTA
1 ATAACTTA
* *
30533768 ACAACTTGC
1 ATAACTT-A
*
30533777 ATAATTTA
1 ATAACTTA
30533785 CATAACTTA
1 -ATAACTTA
30533794 ATAA
1 ATAA
30533798 TTTTAAAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
5 1 0.02
6 3 0.05
7 2 0.03
8 37 0.63
9 16 0.27
ACGTcount: A:0.48, C:0.14, G:0.01, T:0.36
Consensus pattern (8 bp):
ATAACTTA
Found at i:30533732 original size:29 final size:29
Alignment explanation
Indices: 30533708--30533763 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
30533698 TATATATGTC
30533708 ATAC-CAT-ATAACTTAATAACTTATATA
1 ATACACATAATAACTTAATAACTTATATA
*
30533735 ATTCACATAATAACTTAATAACTTA-ATA
1 ATACACATAATAACTTAATAACTTATATA
30533763 A
1 A
30533764 CTTAACAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 3 0.12
28 7 0.27
29 16 0.62
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (29 bp):
ATACACATAATAACTTAATAACTTATATA
Found at i:30533915 original size:17 final size:17
Alignment explanation
Indices: 30533893--30533964 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
30533883 ATAACTCACA
30533893 TAATAACTTACATAACT
1 TAATAACTTACATAACT
*
30533910 TAATAACTTATATATA-T
1 TAATAACTTACATA-ACT
**
30533927 GCATAACTTA-ATAACT
1 TAATAACTTACATAACT
* * *
30533943 CATATTATTTACATAACT
1 TA-ATAACTTACATAACT
30533961 TAAT
1 TAAT
30533965 CATTGTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 30 0.70
18 8 0.19
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (17 bp):
TAATAACTTACATAACT
Found at i:30533937 original size:25 final size:26
Alignment explanation
Indices: 30533901--30533964 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
30533891 CATAATAACT
*
30533901 TACATAACTTAATAACTTATA-TATA
1 TACATAACTTAATAACTCATATTATA
* *
30533926 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTCATATTATA
30533952 TACATAACTTAAT
1 TACATAACTTAAT
30533965 CATTGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.41
Consensus pattern (26 bp):
TACATAACTTAATAACTCATATTATA
Found at i:30534530 original size:43 final size:43
Alignment explanation
Indices: 30534470--30534734 Score: 431
Period size: 43 Copynumber: 6.2 Consensus size: 43
30534460 CACCAAACAA
* *
30534470 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGACCTT
* * *
30534513 TAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGGCCTT
1 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGACCTT
* *
30534556 TAGTGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGGCCTT
1 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGACCTT
* * *
30534599 TAGCGGCATTTGCGGAAAAAGCGCCGCTAAAGAACATGGCCTT
1 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGACCTT
*
30534642 TAGCGGCGTTTTCGGGAAAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGACCTT
30534685 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGACCTT
30534728 TAGCGGC
1 TAGCGGC
30534735 ATTTATTTTT
Statistics
Matches: 208, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 208 1.00
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (43 bp):
TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGACCTT
Found at i:30535517 original size:24 final size:22
Alignment explanation
Indices: 30535476--30535537 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
30535466 TGCATTTCTT
30535476 AAATAATAAAAAAATATTTATA
1 AAATAATAAAAAAATATTTATA
*
30535498 AAATAATCAAAAATATTATTTAT-
1 AAATAAT-AAAAA-AATATTTATA
30535521 AAATAAATAAAACAAAT
1 AAAT-AATAAAA-AAAT
30535538 GGATAAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 7 0.21
23 15 0.44
24 12 0.35
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATAATAAAAAAATATTTATA
Found at i:30538583 original size:15 final size:16
Alignment explanation
Indices: 30538563--30538599 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
30538553 CTTAGGGTGA
30538563 GGTATTGGTACCTA-G
1 GGTATTGGTACCTAGG
30538578 GGTATTGGTACCTAGG
1 GGTATTGGTACCTAGG
30538594 GGTATT
1 GGTATT
30538600 ACCCCTAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.19, C:0.11, G:0.35, T:0.35
Consensus pattern (16 bp):
GGTATTGGTACCTAGG
Found at i:30543403 original size:26 final size:26
Alignment explanation
Indices: 30543374--30543425 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
30543364 TTATGGATGA
*
30543374 AAGGGTTTGACAAGTTTCCTTCTACT
1 AAGGGTTTGACAAGCTTCCTTCTACT
* *
30543400 AAGGGTTTGGCAAGCTTCTTTCTACT
1 AAGGGTTTGACAAGCTTCCTTCTACT
30543426 TTCTTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (26 bp):
AAGGGTTTGACAAGCTTCCTTCTACT
Found at i:30553843 original size:21 final size:21
Alignment explanation
Indices: 30553819--30553863 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
30553809 TTACAGCTAT
*
30553819 ATTACATTACAACTCTATTCC
1 ATTACAATACAACTCTATTCC
* * *
30553840 ATTACAATCCTATTCTATTCC
1 ATTACAATACAACTCTATTCC
30553861 ATT
1 ATT
30553864 GAACCAAACG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTACAATACAACTCTATTCC
Found at i:30553854 original size:16 final size:16
Alignment explanation
Indices: 30553792--30553846 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
30553782 TGAATTACTG
*
30553792 ATTACAACTTTATTCC
1 ATTACAACTCTATTCC
* * *
30553808 ATTACAGCTATATTAC
1 ATTACAACTCTATTCC
30553824 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
30553840 ATTACAA
1 ATTACAA
30553847 TCCTATTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:30559849 original size:39 final size:39
Alignment explanation
Indices: 30559795--30560044 Score: 331
Period size: 39 Copynumber: 6.4 Consensus size: 39
30559785 GCTATCGGGA
* *
30559795 GTACCAAAGCACAACAAGGGCACGTAAGTGCGTTCAGGG
1 GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
*
30559834 GTACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGG
1 GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
** *
30559873 GTACCAAAGTACAAC-AGGAGCACACAAGTGCATTTAGGG
1 GTACCAAAGTACAACAAGG-GCACGTAAGTGCATTCAGGG
** * * *
30559912 GTACTGAAGTGCAACAGGGGCACATAAGTGCATTCAGGG
1 GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
*
30559951 GTACCAAAGTACAACAAGGGCGCGTAAGTGCATTCAGGG
1 GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
** * *
30559990 GTACTGAAGTACAACAAGGGCATGTAAGTGCATCCAGGG
1 GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
*
30560029 GTACCGAAGTACAACA
1 GTACCAAAGTACAACA
30560045 GTTTTCTACT
Statistics
Matches: 184, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
38 2 0.01
39 180 0.98
40 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.30, T:0.16
Consensus pattern (39 bp):
GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
Found at i:30566979 original size:39 final size:39
Alignment explanation
Indices: 30566925--30567171 Score: 271
Period size: 39 Copynumber: 6.3 Consensus size: 39
30566915 TAGAAAACTA
* * **
30566925 TTGTACTTCGGTACCCCTGAATTCACTTACGTGCCTTTG
1 TTGTACTTCAGTACCCCTGAATGCACTTACGTGCCCCTG
* *
30566964 TTGTACTTCAGTACCCCTAAATGCACTTACGTGCCCCTA
1 TTGTACTTCAGTACCCCTGAATGCACTTACGTGCCCCTG
* * * * * *
30567003 TTGTACTTCGGTACCCCT-AATTGCAGTTATGTACACGTG
1 TTGTACTTCAGTACCCCTGAA-TGCACTTACGTGCCCCTG
* ** * * * *
30567042 TTGTCCTTTGGTACCACTGAATGTACTTGCGTGCCCCTA
1 TTGTACTTCAGTACCCCTGAATGCACTTACGTGCCCCTG
* *
30567081 TTGTACTTCAGTACCCCTGAATGCACTTAGGTGCCCTTG
1 TTGTACTTCAGTACCCCTGAATGCACTTACGTGCCCCTG
* *
30567120 TTGTACTTTAGTACCCCTGAATGCACTTACGTGCCCATG
1 TTGTACTTCAGTACCCCTGAATGCACTTACGTGCCCCTG
30567159 TTGTACTTCAGTA
1 TTGTACTTCAGTA
30567172 ATCTTGGTAG
Statistics
Matches: 169, Mismatches: 37, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
38 2 0.01
39 165 0.98
40 2 0.01
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (39 bp):
TTGTACTTCAGTACCCCTGAATGCACTTACGTGCCCCTG
Found at i:30567019 original size:19 final size:20
Alignment explanation
Indices: 30566964--30567025 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
30566954 CGTGCCTTTG
*
30566964 TTGTACTTCAGTACCCCTAA
1 TTGTACTTCGGTACCCCTAA
* * *
30566984 ATGCACTTAC-GTGCCCCT-A
1 TTGTACTT-CGGTACCCCTAA
30567003 TTGTACTTCGGTACCCCTAA
1 TTGTACTTCGGTACCCCTAA
30567023 TTG
1 TTG
30567026 CAGTTATGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.42
20 17 0.52
21 1 0.03
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.34
Consensus pattern (20 bp):
TTGTACTTCGGTACCCCTAA
Found at i:30567147 original size:20 final size:20
Alignment explanation
Indices: 30567085--30567147 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
30567075 CCCCTATTGT
*
30567085 ACTTCAGTACCCCTGAATGC
1 ACTTTAGTACCCCTGAATGC
* * * *
30567105 AC-TTAGGTGCCCTTG-TTGT
1 ACTTTA-GTACCCCTGAATGC
30567124 ACTTTAGTACCCCTGAATGC
1 ACTTTAGTACCCCTGAATGC
30567144 ACTT
1 ACTT
30567148 ACGTGCCCAT
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (20 bp):
ACTTTAGTACCCCTGAATGC
Found at i:30567168 original size:78 final size:78
Alignment explanation
Indices: 30566922--30567171 Score: 313
Period size: 78 Copynumber: 3.2 Consensus size: 78
30566912 TAGTAGAAAA
* * * * *
30566922 CTATTGTACTTCGGTACCCCTGAATTCACTTACGTGCCTTTGTTGTACTTCAGTACCCCTAAATG
1 CTATTGTACTTCAGTACCCCTGAATGCACTTACGTGCCCTTGTTGTACTTTAGTACCCCTGAATG
30566987 CACTTACGTGCCC
66 CACTTACGTGCCC
* * * * * * * * *
30567000 CTATTGTACTTCGGTACCCCT-AATTGCAGTTATGTACACGTGTTGTCCTTTGGTACCACTGAAT
1 CTATTGTACTTCAGTACCCCTGAA-TGCACTTACGTGCCCTTGTTGTACTTTAGTACCCCTGAAT
* *
30567064 GTACTTGCGTGCCC
65 GCACTTACGTGCCC
*
30567078 CTATTGTACTTCAGTACCCCTGAATGCACTTAGGTGCCCTTGTTGTACTTTAGTACCCCTGAATG
1 CTATTGTACTTCAGTACCCCTGAATGCACTTACGTGCCCTTGTTGTACTTTAGTACCCCTGAATG
30567143 CACTTACGTGCCC
66 CACTTACGTGCCC
* *
30567156 ATGTTGTACTTCAGTA
1 CTATTGTACTTCAGTA
30567172 ATCTTGGTAG
Statistics
Matches: 143, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
77 2 0.01
78 139 0.97
79 2 0.01
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (78 bp):
CTATTGTACTTCAGTACCCCTGAATGCACTTACGTGCCCTTGTTGTACTTTAGTACCCCTGAATG
CACTTACGTGCCC
Found at i:30568400 original size:26 final size:26
Alignment explanation
Indices: 30568364--30568416 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
30568354 GAAAAAAATT
30568364 TGCCTTTTTCTAAAAAATTTCATATG
1 TGCCTTTTTCTAAAAAATTTCATATG
30568390 TGCCTTTTTCTAAAAAATTTCATATG
1 TGCCTTTTTCTAAAAAATTTCATATG
30568416 T
1 T
30568417 TTTCGGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (26 bp):
TGCCTTTTTCTAAAAAATTTCATATG
Done.