Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 72 of 97
Found at i:28793771 original size:24 final size:23
Alignment explanation
Indices: 28793744--28794302 Score: 88
Period size: 24 Copynumber: 23.4 Consensus size: 23
28793734 TCTCCATCAC
28793744 CACCACCTCCTTACTATTACAAGT
1 CACCACCTCC-TACTATTACAAGT
* * * *
28793768 CACCACCACCTCCT-TCACCTAGT
1 CACCACCTCCTACTATTA-CAAGT
*
28793791 CCACCACCTCCATACTACTACAAGT
1 -CACCACCTCC-TACTATTACAAGT
* ** * *
28793816 CACCACCTCC-ACCATCCCCTAGCC
1 CACCACCTCCTACTAT-TACAAG-T
* * *
28793840 CACCACCACCATACTACTACAAAT
1 CACCACCTCC-TACTATTACAAGT
* * * * *
28793864 CCCCTCCACCTCCT-TT-GAAGT
1 CACCACCTCCTACTATTACAAGT
*
28793885 CACCACCTCCATATTATTACAAGT
1 CACCACCTCC-TACTATTACAAGT
* * *
28793909 CACCACCTCC-ACCATCTCCTAGT
1 CACCACCTCCTACTAT-TACAAGT
* * *
28793932 CCCCCACCACCATATTATTACAAGT
1 -CACCACCTCC-TACTATTACAAGT
* * * *
28793957 CACCACC-CCCACCATCTCCATCA-C
1 CACCACCTCCTACTAT-TACA--AGT
* *
28793981 CACCACCTCTTTACTACTACAAGT
1 CACCACCTC-CTACTATTACAAGT
* * *
28794005 CACCACCTCCT-CCATCTCCTAGT
1 CACCACCTCCTACTAT-TACAAGT
* * * *
28794028 CCCCCACCACCATACAACTACAAGT
1 -CACCACCTCC-TACTATTACAAGT
* * * *
28794053 CACCACC-CCCACCATCTCCATCA-C
1 CACCACCTCCTACTAT-TACA--AGT
*
28794077 CACCACCTCCTTACTACTACAAGT
1 CACCACCTCC-TACTATTACAAGT
* * * *
28794101 CACCACCTCC-GCCATCTCCTAGT
1 CACCACCTCCTACTAT-TACAAGT
* * *
28794124 CCCCCACCACCATACTACTACAAGT
1 -CACCACCTCC-TACTATTACAAGT
* * * *
28794149 CACCACCTCC-GCCATCTCCTAGT
1 CACCACCTCCTACTAT-TACAAGT
* * *
28794172 CCCCCACCACCATACTACTACAAGT
1 -CACCACCTCC-TACTATTACAAGT
* * * *
28794197 CACCACC-CCCACCATCTCCATCA-C
1 CACCACCTCCTACTAT-TACA--AGT
*
28794221 CACCACCTCCTTATTATTACAAGT
1 CACCACCTCC-TACTATTACAAGT
* * *
28794245 CACCACCACC-ACCT-TCACCCAGT
1 CACCACCTCCTA-CTATTA-CAAGT
*
28794268 CCACCACCACCATACTATTACAAGT
1 -CACCACCTCC-TACTATTACAAGT
28794293 CACCACCTCC
1 CACCACCTCC
28794303 ACCATCCCCT
Statistics
Matches: 361, Mismatches: 123, Indels: 102
0.62 0.21 0.17
Matches are distributed among these distances:
21 10 0.03
22 29 0.08
23 59 0.16
24 185 0.51
25 53 0.15
26 25 0.07
ACGTcount: A:0.27, C:0.48, G:0.04, T:0.20
Consensus pattern (23 bp):
CACCACCTCCTACTATTACAAGT
Found at i:28793778 original size:27 final size:26
Alignment explanation
Indices: 28793740--28793822 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 26
28793730 ACCATCTCCA
28793740 TCACCACCACCTCCTTACTATTACAAG
1 TCACCACCACCTCCTTACTA-TACAAG
* *
28793767 TCACCACCACCTCCTT-C-A-CCTAG
1 TCACCACCACCTCCTTACTATACAAG
*
28793790 T--CCACCACCTCCATACTACTACAAG
1 TCACCACCACCTCCTTACTA-TACAAG
28793815 TCACCACC
1 TCACCACC
28793823 TCCACCATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 12 0.27
22 1 0.02
23 5 0.11
25 5 0.11
26 1 0.02
27 21 0.47
ACGTcount: A:0.28, C:0.47, G:0.04, T:0.22
Consensus pattern (26 bp):
TCACCACCACCTCCTTACTATACAAG
Found at i:28798241 original size:48 final size:48
Alignment explanation
Indices: 28798085--28798306 Score: 198
Period size: 48 Copynumber: 4.7 Consensus size: 48
28798075 TCTCCGTTGT
* * * * * *
28798085 CACCTCCTGCTTATGTCTATAAATCCCCTCCACCTCCACCACCCTCAC
1 CACCTCCTCCATATGTCTATAAATCCCCACCACCACCATCACCATCAC
** * * * * * * * **
28798133 TGCCACCTCCATATTTTTACAAGTCTCCACCCCCACCATCACCATTGC
1 CACCTCCTCCATATGTCTATAAATCCCCACCACCACCATCACCATCAC
*
28798181 CACCTCCT---TATGTCTATAATTCCCCACCACCACCATCACCATCAC
1 CACCTCCTCCATATGTCTATAAATCCCCACCACCACCATCACCATCAC
* * * *
28798226 CTCCTCCTCCATATGTCTATAAATCTCCACCTCCACAATCACCATCAC
1 CACCTCCTCCATATGTCTATAAATCCCCACCACCACCATCACCATCAC
* * *
28798274 CACCTCCTCCAAATGTCTACAAGTCCCCACCAC
1 CACCTCCTCCATATGTCTATAAATCCCCACCAC
28798307 ATCCTTCTCC
Statistics
Matches: 132, Mismatches: 39, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
45 36 0.27
48 96 0.73
ACGTcount: A:0.25, C:0.46, G:0.04, T:0.25
Consensus pattern (48 bp):
CACCTCCTCCATATGTCTATAAATCCCCACCACCACCATCACCATCAC
Found at i:28798253 original size:93 final size:92
Alignment explanation
Indices: 28798039--28798281 Score: 254
Period size: 93 Copynumber: 2.6 Consensus size: 92
28798029 AAGATATCCA
* * * * *
28798039 CCTCCTACATATTCTTACAAATCTCCACCCCCTCCATCTCCGTTGTCACCTCCTGCTTATGTCTA
1 CCTCCTCCATATTC-TACAAATCTCCACCCCCACCATCACCATTGCCACCT-C--CTTATGTCTA
* * *
28798104 TAAATCCCCTCCACCTCCACCACCCTCACTG
62 TAAATCCCCACCACCACCACCACCATCACTG
* * *
28798135 CCACCTCCATATTTTTACAAGTCTCCACCCCCACCATCACCATTGCCACCTCCTTATGTCTATAA
1 CCTCCTCCATA-TTCTACAAATCTCCACCCCCACCATCACCATTGCCACCTCCTTATGTCTATAA
* *
28798200 TTCCCCACCACCACCATCACCATCACCT-
65 ATCCCCACCACCACCACCACCATCA-CTG
* * * **
28798228 CCTCCTCCATATGTCTATAAATCTCCACCTCCACAATCACCATCACCACCTCCT
1 CCTCCTCCATAT-TCTACAAATCTCCACCCCCACCATCACCATTGCCACCTCCT
28798282 CCAAATGTCT
Statistics
Matches: 123, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
92 1 0.01
93 77 0.63
94 2 0.02
95 1 0.01
96 40 0.33
97 2 0.02
ACGTcount: A:0.23, C:0.46, G:0.04, T:0.27
Consensus pattern (92 bp):
CCTCCTCCATATTCTACAAATCTCCACCCCCACCATCACCATTGCCACCTCCTTATGTCTATAAA
TCCCCACCACCACCACCACCATCACTG
Found at i:28798497 original size:21 final size:21
Alignment explanation
Indices: 28798473--28798517 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28798463 ATGTCTATAA
*
28798473 ATCCCCACCACCACCATCACC
1 ATCCCAACCACCACCATCACC
* *
28798494 ATCCCAACCACCTCCTTCACC
1 ATCCCAACCACCACCATCACC
28798515 ATC
1 ATC
28798518 ACCTCCCCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.58, G:0.00, T:0.16
Consensus pattern (21 bp):
ATCCCAACCACCACCATCACC
Found at i:28799169 original size:51 final size:50
Alignment explanation
Indices: 28799076--28799171 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 50
28799066 AGGCACATTG
* *
28799076 CAACACACCATAGGGGAAAAACAACACAGCTCCCCATGAAGAACACACAA
1 CAACACACCATAGGGGAAAAACAACACAACTCCCCATCAAGAACACACAA
* * *
28799126 CAACATACCATAGGTGAGAAAACAACACAACATCTCC-TCAAGAACA
1 CAACACACCATAGGGGA-AAAACAACACAAC-TCCCCATCAAGAACA
28799172 GACTCAACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 15 0.38
51 20 0.51
52 4 0.10
ACGTcount: A:0.48, C:0.30, G:0.12, T:0.09
Consensus pattern (50 bp):
CAACACACCATAGGGGAAAAACAACACAACTCCCCATCAAGAACACACAA
Found at i:28810567 original size:26 final size:27
Alignment explanation
Indices: 28810512--28810568 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
28810502 ATGGTTTTAC
**
28810512 TTTTCAAAAAAAAATCATGCATTTTGT
1 TTTTCAAAAAAAAATCATGCATTTAAT
*
28810539 TTTTCAAAAAAAATAT-AT-CGTTTAAT
1 TTTTCAAAAAAAA-ATCATGCATTTAAT
28810565 TTTT
1 TTTT
28810569 AATAAGCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 9 0.35
27 15 0.58
28 2 0.08
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (27 bp):
TTTTCAAAAAAAAATCATGCATTTAAT
Found at i:28811826 original size:23 final size:23
Alignment explanation
Indices: 28811796--28811841 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28811786 ATTTATTTCT
28811796 CATCATATTACTATACTAGTTAA
1 CATCATATTACTATACTAGTTAA
28811819 CATCATATTACTATACTAGTTAA
1 CATCATATTACTATACTAGTTAA
28811842 GTTGTTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.39
Consensus pattern (23 bp):
CATCATATTACTATACTAGTTAA
Found at i:28814194 original size:37 final size:37
Alignment explanation
Indices: 28814130--28814217 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
28814120 CCAGTCGATG
* * *
28814130 GAATCAAATCACGCATAGTACCAAAGTAACTAATGGA
1 GAATCAAATCACACAGAGTACCAAAGTAACTAATAGA
* **
28814167 GAATCAAATCACACACGA-TACCCAAGTAACTGGTAGA
1 GAATCAAATCACACA-GAGTACCAAAGTAACTAATAGA
*
28814204 GAGTCAAATCACAC
1 GAATCAAATCACAC
28814218 TTAATGTTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 42 0.98
38 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (37 bp):
GAATCAAATCACACAGAGTACCAAAGTAACTAATAGA
Found at i:28814283 original size:37 final size:37
Alignment explanation
Indices: 28814205--28814288 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
28814195 ACTGGTAGAG
* * *
28814205 AGTCAAATCACACTTAATGTTGAAGCAAATGACGGAG
1 AGTCAAATCACACTTAATGCTGAAGCAAATGACGCAA
* * *
28814242 AGTCAAATCACGCTTAGTGCTGAAGC-AATCGATGCAA
1 AGTCAAATCACACTTAATGCTGAAGCAAAT-GACGCAA
28814279 AGTCAAATCA
1 AGTCAAATCA
28814289 TGTATGGTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
36 3 0.08
37 37 0.93
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (37 bp):
AGTCAAATCACACTTAATGCTGAAGCAAATGACGCAA
Found at i:28817277 original size:15 final size:15
Alignment explanation
Indices: 28817259--28817287 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28817249 TTAAAATTAT
28817259 ATTATTTATATTAAC
1 ATTATTTATATTAAC
28817274 ATTATTTATATTAA
1 ATTATTTATATTAA
28817288 TATTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATTTATATTAAC
Found at i:28817603 original size:17 final size:17
Alignment explanation
Indices: 28817581--28817615 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28817571 GATCAAAAAA
28817581 AATTATACTCTTTAGAT
1 AATTATACTCTTTAGAT
*
28817598 AATTATATTCTTTAGAT
1 AATTATACTCTTTAGAT
28817615 A
1 A
28817616 GATTTAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (17 bp):
AATTATACTCTTTAGAT
Found at i:28818893 original size:8 final size:8
Alignment explanation
Indices: 28818880--28818923 Score: 70
Period size: 8 Copynumber: 5.4 Consensus size: 8
28818870 CTTTCATTAT
28818880 TTTTGTTA
1 TTTTGTTA
28818888 TTTTGTTA
1 TTTTGTTA
*
28818896 TTANTGTTA
1 TT-TTGTTA
28818905 TTTTGTTA
1 TTTTGTTA
28818913 TTTTGTTA
1 TTTTGTTA
28818921 TTT
1 TTT
28818924 ATTATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
8 26 0.79
9 7 0.21
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.73
Consensus pattern (8 bp):
TTTTGTTA
Found at i:28818903 original size:17 final size:16
Alignment explanation
Indices: 28818880--28818923 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 16
28818870 CTTTCATTAT
28818880 TTTTGTTATTTTGTTA
1 TTTTGTTATTTTGTTA
*
28818896 TTANTGTTATTTTGTTA
1 TT-TTGTTATTTTGTTA
28818913 TTTTGTTATTT
1 TTTTGTTATTT
28818924 ATTATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.73
Consensus pattern (16 bp):
TTTTGTTATTTTGTTA
Found at i:28820715 original size:48 final size:48
Alignment explanation
Indices: 28820499--28821120 Score: 453
Period size: 48 Copynumber: 13.0 Consensus size: 48
28820489 CTACACATCT
* * * *
28820499 TTGGAAAAAACTCATCATCTTTAAATGAGGCTACGCAA-TTTAAAATGA
1 TTGG-AAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTTAAAATGA
* * * * * *
28820547 TTAGAAAAGCTCCTTATCTCTAAACAAGGTTACACAACTTTAAAAAGA
1 TTGGAAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTTAAAATGA
* * * * * *
28820595 TTGAAAAAAACTCCTCATCTCTGAATGAGGCCACGCAACTTTAAAATAAA
1 TTG-GAAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTTAAAAT-GA
* *
28820645 TT-G-AAAGCTCCTCATCAT-TAAACGAGACTACGTAACTTTAAAATGA
1 TTGGAAAAGCTCCTCATC-TCTAAACGAGGCTACGCAACTTTAAAATGA
* * * * *
28820691 TTGGAAAAACTCCTCATATATAAAC-AAGCTACACAA----AAAATGA
1 TTGGAAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTTAAAATGA
* * * ** *
28820734 TTGGAAATGTTCCTCATCCCTAAATAAGGTTACGCAACTTTAAAATGA
1 TTGGAAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTTAAAATGA
** * * * *
28820782 TTGGAAAAGCTAATCATCTCTAAACGAGACTACACAATTTTAAAAATAA
1 TTGGAAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTT-AAAATGA
* * * ** *
28820831 TTGGAAAAGCTCATCATCTCTAAATGAAGCTACAAAATTTTAAAATGA
1 TTGGAAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTTAAAATGA
* * ** *
28820879 TTGGAAAGGCTCCTCATCT-TAGAACAAGGCTACATAACTTTAAAATAA
1 TTGGAAAAGCTCCTCATCTCTA-AACGAGGCTACGCAACTTTAAAATGA
* * * * * *
28820927 TGGGAAAAGCTCTTCATCCCTAAACCAGACTACGCAACTTTAAAAAT-T
1 TTGGAAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTT-AAAATGA
*** * * * *
28820975 TTGGGAAAATAACTTCATCTTTAAATGAGGCTACGTAA-TTTAAAAT-A
1 TT-GGAAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTTAAAATGA
* * * *
28821022 GTTGGAAAAACTCCTCATCTCTAAACAAGGTTACACAACTTTAAAATGA
1 -TTGGAAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTTAAAATGA
* * * *
28821071 TTGGAAAAGATCCTCGT-TACTAAACGAGGCTACTCAACTTTAAAACGA
1 TTGGAAAAGCTCCTCATCT-CTAAACGAGGCTACGCAACTTTAAAATGA
28821119 TT
1 TT
28821121 AAGAATTTTC
Statistics
Matches: 444, Mismatches: 109, Indels: 42
0.75 0.18 0.07
Matches are distributed among these distances:
43 25 0.06
44 8 0.02
46 3 0.01
47 100 0.23
48 196 0.44
49 109 0.25
50 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (48 bp):
TTGGAAAAGCTCCTCATCTCTAAACGAGGCTACGCAACTTTAAAATGA
Found at i:28820873 original size:97 final size:96
Alignment explanation
Indices: 28820772--28820950 Score: 243
Period size: 97 Copynumber: 1.9 Consensus size: 96
28820762 GTTACGCAAC
* * *
28820772 TTTAAAATGATTGGAAAAGCTAATCATCTCTA-AACGAGACTACACAATTTTAAAAATAATTGGA
1 TTTAAAATGATTGGAAAAGCTAATCATCT-TAGAACAAGACTACACAACTTT-AAAATAATGGGA
*
28820836 AAAGCTCATCATCTCTAAATGAAGCTACAAAAT
64 AAAGCTCATCATCCCTAAATGAAGCTACAAAAT
* ** * *
28820869 TTTAAAATGATTGGAAAGGCTCCTCATCTTAGAACAAGGCTACATAACTTTAAAATAATGGGAAA
1 TTTAAAATGATTGGAAAAGCTAATCATCTTAGAACAAGACTACACAACTTTAAAATAATGGGAAA
*
28820934 AGCTCTTCATCCCTAAA
66 AGCTCATCATCCCTAAA
28820951 CCAGACTACG
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
96 30 0.42
97 41 0.58
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (96 bp):
TTTAAAATGATTGGAAAAGCTAATCATCTTAGAACAAGACTACACAACTTTAAAATAATGGGAAA
AGCTCATCATCCCTAAATGAAGCTACAAAAT
Found at i:28820933 original size:145 final size:143
Alignment explanation
Indices: 28820727--28821079 Score: 404
Period size: 145 Copynumber: 2.4 Consensus size: 143
28820717 AGCTACACAA
* * * * *
28820727 AAAATGATTGGAAATGTTCCTCATCCCTAAATAAGGTTACGCAACTTTAAAATGATTGGAAAAGC
1 AAAATGATTGGAAAAGCTCCTCAT-CTTAAACAAGGTTACACAACTTTAAAATGATTGGAAAAGC
* * * **
28820792 TAATCATCTCTAAACGAGACTACACAATTTTAAAAATAATT-GGAAAAGCTCATCATCTCTAAAT
65 TAATCATCCCTAAACCAGACTACACAACTTTAAAAAT-ATTGGGAAAAGAACATCATCTCTAAAT
28820856 GAAGCTACAAAATTTT
129 GAAGCTACAAAA-TTT
* * * * *
28820872 AAAATGATTGGAAAGGCTCCTCATCTTAGAACAAGGCTACATAACTTTAAAATAATGGGAAAAGC
1 AAAATGATTGGAAAAGCTCCTCATCTTA-AACAAGGTTACACAACTTTAAAATGATTGGAAAAGC
** * * * * *
28820937 TCTTCATCCCTAAACCAGACTACGCAACTTTAAAAATTTTGGGAAAATAACTTCATCTTTAAATG
65 TAATCATCCCTAAACCAGACTACACAACTTTAAAAATATTGGGAAAAGAACATCATCTCTAAATG
* **
28821002 AGGCTACGTAATTT
130 AAGCTACAAAATTT
*
28821016 AAAAT-AGTTGGAAAAACTCCTCATCTCTAAACAAGGTTACACAACTTTAAAATGATTGGAAAAG
1 AAAATGA-TTGGAAAAGCTCCTCATCT-TAAACAAGGTTACACAACTTTAAAATGATTGGAAAAG
28821080 ATCCTCGTTA
Statistics
Matches: 174, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
143 1 0.01
144 61 0.35
145 112 0.64
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (143 bp):
AAAATGATTGGAAAAGCTCCTCATCTTAAACAAGGTTACACAACTTTAAAATGATTGGAAAAGCT
AATCATCCCTAAACCAGACTACACAACTTTAAAAATATTGGGAAAAGAACATCATCTCTAAATGA
AGCTACAAAATTT
Found at i:28837669 original size:22 final size:22
Alignment explanation
Indices: 28837644--28837697 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
28837634 TTTCAGCACC
28837644 AAAATCAGCCATA-ATAACCTCA
1 AAAATCAGCCA-ACATAACCTCA
28837666 AAAATTCCAG-CAACATAACCTCA
1 AAAA-T-CAGCCAACATAACCTCA
*
28837689 AAATTCAGC
1 AAAATCAGC
28837698 TTTCTTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
21 3 0.11
22 6 0.22
23 15 0.56
24 3 0.11
ACGTcount: A:0.48, C:0.28, G:0.06, T:0.19
Consensus pattern (22 bp):
AAAATCAGCCAACATAACCTCA
Found at i:28837931 original size:47 final size:47
Alignment explanation
Indices: 28837798--28837914 Score: 218
Period size: 47 Copynumber: 2.5 Consensus size: 47
28837788 TTCTCTTTTC
28837798 TCTTCCTCTCCCACGGTTCTTTCTCTCCCTTTTTCTCTTCATTTCTT
1 TCTTCCTCTCCCACGGTTCTTTCTCTCCCTTTTTCTCTTCATTTCTT
*
28837845 TCTTCCTCTCCCACGATTCTTTCTCTCCCTTTTTCTCTTCATTTCTT
1 TCTTCCTCTCCCACGGTTCTTTCTCTCCCTTTTTCTCTTCATTTCTT
28837892 TCTTCCTCTCCCACGGTT-TTTCT
1 TCTTCCTCTCCCACGGTTCTTTCT
28837915 TTCCTTTATT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
46 5 0.07
47 63 0.93
ACGTcount: A:0.05, C:0.38, G:0.04, T:0.52
Consensus pattern (47 bp):
TCTTCCTCTCCCACGGTTCTTTCTCTCCCTTTTTCTCTTCATTTCTT
Found at i:28838152 original size:20 final size:20
Alignment explanation
Indices: 28838127--28838164 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28838117 TGACTTTTCT
28838127 TCATTCCCATCCAAACCATA
1 TCATTCCCATCCAAACCATA
*
28838147 TCATTCCCATTCAAACCA
1 TCATTCCCATCCAAACCA
28838165 CATTCACACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.26
Consensus pattern (20 bp):
TCATTCCCATCCAAACCATA
Found at i:28842234 original size:5 final size:5
Alignment explanation
Indices: 28842196--28842230 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
28842186 TGTGGCCCCT
* *
28842196 AGTTA GGTTA AGTTA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
28842231 GGTTGAATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (5 bp):
AGTTA
Found at i:28845247 original size:5 final size:5
Alignment explanation
Indices: 28845239--28845263 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28845229 CTATTCAACC
28845239 TAACT TAACT TAACT TAACT TAACT
1 TAACT TAACT TAACT TAACT TAACT
28845264 AGGGGCCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
TAACT
Found at i:28845324 original size:22 final size:22
Alignment explanation
Indices: 28845299--28845342 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28845289 TTAAAACGAC
*
28845299 TTTAAAACTAAAAACTCTGATA
1 TTTAAAACCAAAAACTCTGATA
* *
28845321 TTTAAAACCAAAAGCTTTGATA
1 TTTAAAACCAAAAACTCTGATA
28845343 CCAATCGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.32
Consensus pattern (22 bp):
TTTAAAACCAAAAACTCTGATA
Found at i:28849396 original size:2 final size:2
Alignment explanation
Indices: 28849389--28849414 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28849379 TTTACGTCTA
28849389 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
28849415 TTCAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28849931 original size:25 final size:24
Alignment explanation
Indices: 28849903--28849964 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
28849893 TCATTTATTT
28849903 TTATTTCATATTGGGCCATGCCCAC
1 TTATTTC-TATTGGGCCATGCCCAC
* *
28849928 TTATTTTCTATTGGGTCATGCCCAT
1 TTA-TTTCTATTGGGCCATGCCCAC
28849953 TTATTTTCTATT
1 TTA-TTTCTATT
28849965 TCTTTTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 30 0.88
26 4 0.12
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.48
Consensus pattern (24 bp):
TTATTTCTATTGGGCCATGCCCAC
Found at i:28850307 original size:34 final size:34
Alignment explanation
Indices: 28850190--28850309 Score: 143
Period size: 34 Copynumber: 3.5 Consensus size: 34
28850180 CTTCCCAATT
*
28850190 TTGGCAGCACAA-AGCTGTCCAATTTTTTTGCACAAA
1 TTGGCAGCA-AACAGC--TCCAATTTTTCTGCACAAA
* ** *
28850226 CTACCAGCAAACAACTCCAATTTTTCTGCACAAA
1 TTGGCAGCAAACAGCTCCAATTTTTCTGCACAAA
* *
28850260 TTGACAGCAAACAGCTCCAATTTTTCTACACAAA
1 TTGGCAGCAAACAGCTCCAATTTTTCTGCACAAA
28850294 TTGGCAGCAAACAGCT
1 TTGGCAGCAAACAGCT
28850310 TAAATTTTCA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
34 62 0.86
35 2 0.03
36 8 0.11
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (34 bp):
TTGGCAGCAAACAGCTCCAATTTTTCTGCACAAA
Found at i:28850444 original size:22 final size:22
Alignment explanation
Indices: 28850418--28850471 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
28850408 TTTCAGCACC
28850418 AAAATCAGCCATA-ATAACCTCA
1 AAAATCAGCCA-ACATAACCTCA
28850440 AAAATTTCAG-CAACATAACCTCA
1 AAAA--TCAGCCAACATAACCTCA
*
28850463 AAATTCAGC
1 AAAATCAGC
28850472 TTTCTTACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
21 4 0.15
22 5 0.19
23 14 0.52
24 4 0.15
ACGTcount: A:0.48, C:0.26, G:0.06, T:0.20
Consensus pattern (22 bp):
AAAATCAGCCAACATAACCTCA
Found at i:28859486 original size:142 final size:142
Alignment explanation
Indices: 28859321--28859597 Score: 545
Period size: 142 Copynumber: 2.0 Consensus size: 142
28859311 CACTTTCTAG
28859321 AAGTGAAATTTATTTATAATAATTGTTGTTAACAGGTACTGGTTTGTTAGTAGTGGTACCTCTTA
1 AAGTGAAATTTATTTATAATAATTGTTGTTAACAGGTACTGGTTTGTTAGTAGTGGTACCTCTTA
28859386 TGAGAACCAAACTAGTGTCTGTTTGTGACGTGTATAGAATAAACAAATCACTTACAAGATTGTCC
66 TGAGAACCAAACTAGTGTCTGTTTGTGACGTGTATAGAATAAACAAATCACTTACAAGATTGTCC
28859451 AAATCTAATAGA
131 AAATCTAATAGA
28859463 AAGTGAAATTTATTTATAATAATTGTTGTTAACAGGTACTGGTTTGTTAGTAGTGGTACCTCTTA
1 AAGTGAAATTTATTTATAATAATTGTTGTTAACAGGTACTGGTTTGTTAGTAGTGGTACCTCTTA
*
28859528 TGAGAACCAAACTAGTGTCTGTTTGTGATGTGTATAGAATAAACAAATCACTTACAAGATTGTCC
66 TGAGAACCAAACTAGTGTCTGTTTGTGACGTGTATAGAATAAACAAATCACTTACAAGATTGTCC
28859593 AAATC
131 AAATC
28859598 GAAAAGTGCT
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 134 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (142 bp):
AAGTGAAATTTATTTATAATAATTGTTGTTAACAGGTACTGGTTTGTTAGTAGTGGTACCTCTTA
TGAGAACCAAACTAGTGTCTGTTTGTGACGTGTATAGAATAAACAAATCACTTACAAGATTGTCC
AAATCTAATAGA
Found at i:28870943 original size:19 final size:19
Alignment explanation
Indices: 28870919--28870956 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28870909 AGGCACCTTG
28870919 TTTTTTTTCACTTAATTAA
1 TTTTTTTTCACTTAATTAA
* *
28870938 TTTTTTTTGATTTAATTAA
1 TTTTTTTTCACTTAATTAA
28870957 CCAACTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTTTTTCACTTAATTAA
Found at i:28871705 original size:24 final size:24
Alignment explanation
Indices: 28871660--28871712 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
28871650 GAGAGACTGA
* *
28871660 AGGTTACTTGTAATATGGTGGTGG
1 AGGTGACTTGTAATATGATGGTGG
*
28871684 TGGTGACTTGTAA-ATGTATGGTGG
1 AGGTGACTTGTAATATG-ATGGTGG
28871708 AGGTG
1 AGGTG
28871713 GAGGTGACGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.21, C:0.04, G:0.40, T:0.36
Consensus pattern (24 bp):
AGGTGACTTGTAATATGATGGTGG
Found at i:28871763 original size:60 final size:60
Alignment explanation
Indices: 28871679--28872482 Score: 739
Period size: 60 Copynumber: 13.5 Consensus size: 60
28871669 GTAATATGGT
* * * * * *
28871679 GGTGGTGGTGACTTGTAAATGTATGGTGGAGGTGGAGGTGACGTGTACACGTATGGAGGT
1 GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * * ** *
28871739 GGTGGTGGTGACTTGTACATGTATGGTGGAGGTGGAGGTGACTTGTAAATGTATGGAAGA
1 GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * * * * * *
28871799 GGAGGAGGTGAGTTATAC-TCGTATGGTGGAGGTGGTGGTGATTTGTACACGTATGGAGGA
1 GGTGGTGGTGACTTATACAT-GTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * * * * ** *
28871859 GGAGGTGGTGATTTATAAATGTATGGAGGAGGTGGAGGTGACTTATAAATGTATGGAGGT
1 GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * *
28871919 GGTGGTGGTGACTTGTAC-TCATATGGAGGAGGTGGGGGTGACTTGTACACATATGGAGGA
1 GGTGGTGGTGACTTATACAT-GTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * * *
28871979 GGTGGTGGTGATTTATAAATGTATGGAGGAGGTGGAGGTGAC-T-TATA-A-ATGTATGGA
1 GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTTGTACACATATGGA-GGA
* * *
28872036 ---GGTGGTGACTTGTAC-TCATATGGAGGAGGTGGAGGTGACTTGTAAACATATGGAGGA
1 GGTGGTGGTGACTTATACAT-GTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * *
28872093 GGTGGTGGTGATTTATAAATGTATGGAGGAGGTGGAGGTGA-TTCGTATACATATGGAGGA
1 GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTT-GTACACATATGGAGGA
* * * *
28872153 GGTGGAGGTGACTTATAAATGTATGGAGGTGGTGGTGGTGACTTGTACACATATGGAGGA
1 GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * * * ** **
28872213 GGTGGTGGCGACTCATACTTATATGGAGGAGGTGGAGGTGACTCATACTTATATGGAGGA
1 GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * * * ** **
28872273 GGTGGTGGGGACTCATACTTATATGGAGGAGGTGGAGGTGACTCATACTTATATGGAGGA
1 GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * * * * * *
28872333 GGTGGTGGTGACTCATACTTATATGGAGGTGGTGGTGGTGACTTGTATACATATGGAGGT
1 GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * * * * ** * * * **
28872393 GGAGGAGGTGATTTGTAAACATATGGAGGAGGAGGTGGTGACTTATACTTATATGGAGGA
1 GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
* * * *
28872453 GGTGGAGGTGACATGTACATGTACGGAGGA
1 GGTGGTGGTGACTTATACATGTATGGAGGA
28872483 AGATTCGGCG
Statistics
Matches: 625, Mismatches: 103, Indels: 32
0.82 0.14 0.04
Matches are distributed among these distances:
53 1 0.00
54 33 0.05
55 1 0.00
56 7 0.01
57 8 0.01
58 7 0.01
59 5 0.01
60 558 0.89
61 5 0.01
ACGTcount: A:0.25, C:0.07, G:0.40, T:0.28
Consensus pattern (60 bp):
GGTGGTGGTGACTTATACATGTATGGAGGAGGTGGAGGTGACTTGTACACATATGGAGGA
Found at i:28871787 original size:90 final size:90
Alignment explanation
Indices: 28871679--28872482 Score: 755
Period size: 90 Copynumber: 9.0 Consensus size: 90
28871669 GTAATATGGT
* * * * * * *
28871679 GGTGGTGGTGACTTGTAAATGTATGGTGGAGGTGGAGGTGACGTGTACACGTATGGAGGTGGTGG
1 GGTGGAGGTGACTTGTAAATATATGGAGGAGGTGGAGGTGACTTATACATGTATGGAGGAGGTGG
*
28871744 TGGTGACTTGTACATGTATGGTGGA
66 TGGTGACTTGTACATGTATGGAGGA
* * * * *
28871769 GGTGGAGGTGACTTGTAAATGTATGGAAGAGGAGGAGGTGAGTTATAC-TCGTATGGTGGAGGTG
1 GGTGGAGGTGACTTGTAAATATATGGAGGAGGTGGAGGTGACTTATACAT-GTATGGAGGAGGTG
* *
28871833 GTGGTGATTTGTACACGTATGGAGGA
65 GTGGTGACTTGTACATGTATGGAGGA
* * * * * * *
28871859 GGAGGTGGTGATTTATAAATGTATGGAGGAGGTGGAGGTGACTTATAAATGTATGGAGGTGGTGG
1 GGTGGAGGTGACTTGTAAATATATGGAGGAGGTGGAGGTGACTTATACATGTATGGAGGAGGTGG
*
28871924 TGGTGACTTGTAC-TCATATGGAGGA
66 TGGTGACTTGTACAT-GTATGGAGGA
* * * * * *
28871949 GGTGGGGGTGACTTGTACACATATGGAGGAGGTGGTGGTGATTTATAAATGTATGGAGGAGGTGG
1 GGTGGAGGTGACTTGTAAATATATGGAGGAGGTGGAGGTGACTTATACATGTATGGAGGAGGTGG
* * *
28872014 AGGTGACTTATAAATGTAT---GGA
66 TGGTGACTTGTACATGTATGGAGGA
* * * **
28872036 GGT---GGTGACTTGT-ACTCATATGGAGGAGGTGGAGGTGACTTGTAAACATATGGAGGAGGTG
1 GGTGGAGGTGACTTGTAAAT-ATATGGAGGAGGTGGAGGTGACTTATACATGTATGGAGGAGGTG
* * *
28872097 GTGGTGATTTATAAATGTATGGAGGA
65 GTGGTGACTTGTACATGTATGGAGGA
* * * *
28872123 GGTGGAGGTGA-TTCGTATACATATGGAGGAGGTGGAGGTGACTTATAAATGTATGGAGGTGGTG
1 GGTGGAGGTGACTT-GTAAATATATGGAGGAGGTGGAGGTGACTTATACATGTATGGAGGAGGTG
**
28872187 GTGGTGACTTGTACACATATGGAGGA
65 GTGGTGACTTGTACATGTATGGAGGA
* * ** ** * * *
28872213 GGTGGTGGCGACTCATACTTATATGGAGGAGGTGGAGGTGACTCATACTTATATGGAGGAGGTGG
1 GGTGGAGGTGACTTGTAAATATATGGAGGAGGTGGAGGTGACTTATACATGTATGGAGGAGGTGG
* ** * *
28872278 TGGGGACTCATACTTATATGGAGGA
66 TGGTGACTTGTACATGTATGGAGGA
** ** * * * * *
28872303 GGTGGAGGTGACTCATACTTATATGGAGGAGGTGGTGGTGACTCATACTTATATGGAGGTGGTGG
1 GGTGGAGGTGACTTGTAAATATATGGAGGAGGTGGAGGTGACTTATACATGTATGGAGGAGGTGG
* ** *
28872368 TGGTGACTTGTATACATATGGAGGT
66 TGGTGACTTGTACATGTATGGAGGA
* * * * * * *
28872393 GGAGGAGGTGATTTGTAAACATATGGAGGAGGAGGTGGTGACTTATACTTATATGGAGGAGGTGG
1 GGTGGAGGTGACTTGTAAATATATGGAGGAGGTGGAGGTGACTTATACATGTATGGAGGAGGTGG
* * *
28872458 AGGTGACATGTACATGTACGGAGGA
66 TGGTGACTTGTACATGTATGGAGGA
28872483 AGATTCGGCG
Statistics
Matches: 593, Mismatches: 107, Indels: 28
0.81 0.15 0.04
Matches are distributed among these distances:
84 67 0.11
87 12 0.02
89 2 0.00
90 509 0.86
91 3 0.01
ACGTcount: A:0.25, C:0.07, G:0.40, T:0.28
Consensus pattern (90 bp):
GGTGGAGGTGACTTGTAAATATATGGAGGAGGTGGAGGTGACTTATACATGTATGGAGGAGGTGG
TGGTGACTTGTACATGTATGGAGGA
Found at i:28872095 original size:24 final size:24
Alignment explanation
Indices: 28872012--28872096 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 24
28872002 TGGAGGAGGT
* **
28872012 GGAGGTGACTTATAAATGTATGGA
1 GGAGGTGACTTGTAAACATATGGA
* **
28872036 GGTGGTGACTTGTACTCATATGGAGGA
1 GGAGGTGACTTGTAAACATAT---GGA
28872063 GGTGGAGGTGACTTGTAAACATATGGA
1 ---GGAGGTGACTTGTAAACATATGGA
28872090 GGAGGTG
1 GGAGGTG
28872097 GTGGTGATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
24 22 0.48
27 6 0.13
30 18 0.39
ACGTcount: A:0.27, C:0.07, G:0.39, T:0.27
Consensus pattern (24 bp):
GGAGGTGACTTGTAAACATATGGA
Found at i:28872481 original size:30 final size:30
Alignment explanation
Indices: 28871679--28872482 Score: 649
Period size: 30 Copynumber: 27.0 Consensus size: 30
28871669 GTAATATGGT
* * * *
28871679 GGTGGTGGTGACTTGTAAATGTATGGTGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * * ** *
28871709 GGTGGAGGTGACGTGTACACGTATGGAGGT
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * *
28871739 GGTGGTGGTGACTTGTACATGTATGGTGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * * * *
28871769 GGTGGAGGTGACTTGTAAATGTATGGAAGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * * * *
28871799 GGAGGAGGTGAGTTATAC-TCGTATGGTGGA
1 GGTGGTGGTGACTTATACAT-ATATGGAGGA
* * **
28871829 GGTGGTGGTGATTTGTACACGTATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * * *
28871859 GGAGGTGGTGATTTATAAATGTATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * * *
28871889 GGTGGAGGTGACTTATAAATGTATGGAGGT
1 GGTGGTGGTGACTTATACATATATGGAGGA
*
28871919 GGTGGTGGTGACTTGTAC-TCATATGGAGGA
1 GGTGGTGGTGACTTATACAT-ATATGGAGGA
* * *
28871949 GGTGGGGGTGACTTGTACACATATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * *
28871979 GGTGGTGGTGATTTATAAATGTATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * *
28872009 GGTGGAGGTGACTTATAAATGTAT---GGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
*
28872036 ---GGTGGTGACTTGTAC-TCATATGGAGGA
1 GGTGGTGGTGACTTATACAT-ATATGGAGGA
* * * *
28872063 GGTGGAGGTGACTTGTAAACATATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * *
28872093 GGTGGTGGTGATTTATAAATGTATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* *
28872123 GGTGGAGGTGATTCGTATAC--ATATGGAGGA
1 GGTGGTGGTGA--CTTATACATATATGGAGGA
* * * *
28872153 GGTGGAGGTGACTTATAAATGTATGGAGGT
1 GGTGGTGGTGACTTATACATATATGGAGGA
* *
28872183 GGTGGTGGTGACTTGTACACATATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * *
28872213 GGTGGTGGCGACTCATACTTATATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * *
28872243 GGTGGAGGTGACTCATACTTATATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * *
28872273 GGTGGTGGGGACTCATACTTATATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * *
28872303 GGTGGAGGTGACTCATACTTATATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * *
28872333 GGTGGTGGTGACTCATACTTATATGGAGGT
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * * *
28872363 GGTGGTGGTGACTTGTATACATATGGAGGT
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * * * * *
28872393 GGAGGAGGTGATTTGTAAACATATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* *
28872423 GGAGGTGGTGACTTATACTTATATGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
* * * * *
28872453 GGTGGAGGTGACATGTACATGTACGGAGGA
1 GGTGGTGGTGACTTATACATATATGGAGGA
28872483 AGATTCGGCG
Statistics
Matches: 645, Mismatches: 113, Indels: 32
0.82 0.14 0.04
Matches are distributed among these distances:
23 1 0.00
24 15 0.02
27 6 0.01
28 5 0.01
29 2 0.00
30 612 0.95
32 4 0.01
ACGTcount: A:0.25, C:0.07, G:0.40, T:0.28
Consensus pattern (30 bp):
GGTGGTGGTGACTTATACATATATGGAGGA
Found at i:28878441 original size:18 final size:18
Alignment explanation
Indices: 28878420--28878464 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
28878410 AATCCACAAG
* * *
28878420 AAGTGGATAACTCATCAT
1 AAGTGGATAACCCACCAA
*
28878438 AAGTGGATCACCCACCAA
1 AAGTGGATAACCCACCAA
28878456 AAGTGGATA
1 AAGTGGATA
28878465 GATACTTGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (18 bp):
AAGTGGATAACCCACCAA
Found at i:28881383 original size:2 final size:2
Alignment explanation
Indices: 28881376--28881408 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28881366 AGCATCCATA
*
28881376 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28881409 AATGACTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:28885592 original size:59 final size:59
Alignment explanation
Indices: 28885382--28885839 Score: 551
Period size: 60 Copynumber: 7.7 Consensus size: 59
28885372 GAACAAATTC
*
28885382 AATTAAAATTTCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAACAA
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTT--A-AA
* * *
28885444 AATTGAAATTTCTAAACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTT-AA
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAA
*
28885502 AATTGAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAA
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAA
* *
28885561 AATTAAAATTCCTAGACTTAATCTAGACTCGACCTATCTCACAACAAGTTCGATTTAAA
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAA
* * * *
28885620 AATTAAAATTTCTAGACTTAATTTAGGCTCGACCTATCTCATAAATAGGTTCGATTTAAAA
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCA-CAACAGGTTCGATTT-AAA
* * * * *
28885681 AATTAAAATTCCTAGATTTGATCTCGGCTCGACCTATCTTAAAACAGGTTCGATTTTAAA
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGA-TTTAAA
* * * * * * * * * *
28885741 AATTGAAGTTCCTAAACTTGATCTAGGCTTGACCTATTTTAAAATAGGTTCGATTTTGAGA
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGA-TTT-AAA
* * ** *
28885802 AA-TGAAATTTCTAGACTCGATCTAGGCTCGACTTATCT
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCT
28885840 TAAAATGGGT
Statistics
Matches: 355, Mismatches: 36, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
58 56 0.16
59 96 0.27
60 104 0.29
61 45 0.13
62 54 0.15
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (59 bp):
AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAA
Found at i:28885594 original size:179 final size:179
Alignment explanation
Indices: 28885382--28885856 Score: 591
Period size: 179 Copynumber: 2.6 Consensus size: 179
28885372 GAACAAATTC
*
28885382 AATTAAAATTTCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAACAAAAT
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTT--A-AAAAT
* * *
28885447 TGAAATTTCTAAACTTAATCTAGGCTCGACCTATCTCA-CAACAGGTTCGATTT-AAAATTGAAA
63 TGAAATTTCTAGACTTAATCTAGGCTCGACCTATCTCATAAACAGGTTCGATTTAAAAATTAAAA
*
28885510 TTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGA-TTTAAA
128 TTCCTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTTAAA
* * *
28885561 AATTAAAATTCCTAGACTTAATCTAGACTCGACCTATCTCACAACAAGTTCGATTTAAAAATTAA
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGA
* *
28885626 AATTTCTAGACTTAATTTAGGCTCGACCTATCTCATAAATAGGTTCGATTTAAAAAATTAAAATT
66 AATTTCTAGACTTAATCTAGGCTCGACCTATCTCATAAACAGGTTCGATTT-AAAAATTAAAATT
* * * *
28885691 CCTAGATTTGATCTCGGCTCGACCTATCTTAAAACAGGTTCGATTTTAAA
130 CCTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTTAAA
* * * * * * * * * *
28885741 AATTGAAGTTCCTAAACTTGATCTAGGCTTGACCTATTTTAAAATAGGTTCGATTTTGAGAAA-T
1 AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGA-TTT-AAAAATT
** * * **
28885805 GAAATTTCTAGACTCGATCTAGGCTCGACTTATCTTA-AAATGGGTTCGATTT
64 GAAATTTCTAGACTTAATCTAGGCTCGACCTATCTCATAAACAGGTTCGATTT
28885857 GATTCACTGA
Statistics
Matches: 257, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
176 40 0.16
177 14 0.05
179 102 0.40
180 62 0.24
181 35 0.14
182 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (179 bp):
AATTAAAATTCCTAGACTTAATCTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGA
AATTTCTAGACTTAATCTAGGCTCGACCTATCTCATAAACAGGTTCGATTTAAAAATTAAAATTC
CTAGACTTAATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTTAAA
Found at i:28897776 original size:31 final size:30
Alignment explanation
Indices: 28897698--28897773 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
28897688 ATCACCTTAT
* * *
28897698 TTATATATTTATTTT-GTCATTTTTATGGA
1 TTATTTATTTATTTTATTAATTTTTATGGA
*
28897727 TTATTTATTTATTTTATTANATTTTTATGTA
1 TTATTTATTTATTTTATTA-ATTTTTATGGA
28897758 TT-TTTA--TATTTTATTA
1 TTATTTATTTATTTTATTA
28897774 TTATTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 10 0.24
29 14 0.34
30 5 0.12
31 12 0.29
ACGTcount: A:0.25, C:0.01, G:0.05, T:0.67
Consensus pattern (30 bp):
TTATTTATTTATTTTATTAATTTTTATGGA
Found at i:28897783 original size:31 final size:30
Alignment explanation
Indices: 28897716--28897781 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
28897706 TTATTTTGTC
* *
28897716 ATTTTTATGGATTATTTATTTATTTTATTAN
1 ATTTTTATGTATT-TTTATTTATTTTATTAT
28897747 ATTTTTATGTATTTTTA--TATTTTATTATT
1 ATTTTTATGTATTTTTATTTATTTTATTA-T
28897776 ATTTTT
1 ATTTTT
28897782 TTTGTTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 10 0.31
29 6 0.19
30 4 0.12
31 12 0.38
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (30 bp):
ATTTTTATGTATTTTTATTTATTTTATTAT
Found at i:28904899 original size:30 final size:26
Alignment explanation
Indices: 28904776--28904912 Score: 77
Period size: 27 Copynumber: 5.2 Consensus size: 26
28904766 CTTTCTTTTC
* * *
28904776 TCTTTTCTCTCTTTT-TCTTTTTTTT
1 TCTTTACTTTCTTTTATCTTTTTTAT
* * *
28904801 TATTTTC-TTCTTTTCTCCATTTTTCT-T
1 TCTTTACTTTCTTTTAT-C-TTTTT-TAT
* * *
28904828 TCTTTCCTATCTTTTTTCTTTTTT-T
1 TCTTTACTTTCTTTTATCTTTTTTAT
*
28904853 TCCCTTA-TTTCTTTTATCCTTTGTTCTAT
1 T-CTTTACTTTCTTTTAT-CTTT-TT-TAT
28904882 TCTTTACTTTCTATTTATCTTTTTTAT
1 TCTTTACTTTCT-TTTATCTTTTTTAT
28904909 TCTT
1 TCTT
28904913 AAAGACTATA
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
24 6 0.07
25 18 0.20
26 13 0.15
27 21 0.24
28 15 0.17
29 11 0.12
30 5 0.06
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.72
Consensus pattern (26 bp):
TCTTTACTTTCTTTTATCTTTTTTAT
Found at i:28917844 original size:16 final size:16
Alignment explanation
Indices: 28917805--28917844 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28917795 AGACACCTAA
*
28917805 AAAAAAAAATTAAAAT
1 AAAATAAAATTAAAAT
* *
28917821 TAATTAAAATTAAAAT
1 AAAATAAAATTAAAAT
28917837 AAAATAAA
1 AAAATAAA
28917845 TAAATAATTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATAAAATTAAAAT
Found at i:28950026 original size:48 final size:48
Alignment explanation
Indices: 28949956--28950167 Score: 244
Period size: 48 Copynumber: 4.4 Consensus size: 48
28949946 TATCCTAACA
* * * * * * *
28949956 TAGACATATGGTGGTGGAGGTGATGGAGATGGAGGCGGTGGCGATTTA
1 TAGACATAAGGAGGAGGTGGTGATGGAGATGGAGGAGGTGGAGATTTG
* * *
28950004 TAGACATAAGGAGGAGGTGGTGAGGGAGATGGCGGAGGTGGGGATTTG
1 TAGACATAAGGAGGAGGTGGTGATGGAGATGGAGGAGGTGGAGATTTG
* * * *
28950052 TAGACATAGGGAGGAGGTGGTGATGGAGATGGTGGGGGTGGAGACTTG
1 TAGACATAAGGAGGAGGTGGTGATGGAGATGGAGGAGGTGGAGATTTG
* * * *
28950100 TAGATATAAGGAGGAGGCGGTGAAGGAGATGGGGGAGGTGGAGATTTG
1 TAGACATAAGGAGGAGGTGGTGATGGAGATGGAGGAGGTGGAGATTTG
* *
28950148 TAGGCATAAGGTGGAGGTGG
1 TAGACATAAGGAGGAGGTGG
28950168 GGACTTGTAG
Statistics
Matches: 138, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 138 1.00
ACGTcount: A:0.25, C:0.04, G:0.50, T:0.21
Consensus pattern (48 bp):
TAGACATAAGGAGGAGGTGGTGATGGAGATGGAGGAGGTGGAGATTTG
Found at i:28950075 original size:96 final size:96
Alignment explanation
Indices: 28949956--28950167 Score: 280
Period size: 96 Copynumber: 2.2 Consensus size: 96
28949946 TATCCTAACA
* * * * *
28949956 TAGACATATGGTGGTGGAGGTGATGGAGATGGAGGCGGTGGCGATTTATAGACATAAGGAGGAGG
1 TAGACATAAGGTGGAGGTGGTGATGGAGATGGAGGCGGTGGAGACTTATAGACATAAGGAGGAGG
* * *
28950021 TGGTGAGGGAGATGGCGGAGGTGGGGATTTG
66 CGGTGAAGGAGATGGCGGAGGTGGAGATTTG
* * * * * *
28950052 TAGACATAGGGAGGAGGTGGTGATGGAGATGGTGGGGGTGGAGACTTGTAGATATAAGGAGGAGG
1 TAGACATAAGGTGGAGGTGGTGATGGAGATGGAGGCGGTGGAGACTTATAGACATAAGGAGGAGG
*
28950117 CGGTGAAGGAGATGGGGGAGGTGGAGATTTG
66 CGGTGAAGGAGATGGCGGAGGTGGAGATTTG
*
28950148 TAGGCATAAGGTGGAGGTGG
1 TAGACATAAGGTGGAGGTGG
28950168 GGACTTGTAG
Statistics
Matches: 99, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 99 1.00
ACGTcount: A:0.25, C:0.04, G:0.50, T:0.21
Consensus pattern (96 bp):
TAGACATAAGGTGGAGGTGGTGATGGAGATGGAGGCGGTGGAGACTTATAGACATAAGGAGGAGG
CGGTGAAGGAGATGGCGGAGGTGGAGATTTG
Found at i:28950163 original size:27 final size:27
Alignment explanation
Indices: 28950133--28950284 Score: 94
Period size: 27 Copynumber: 6.1 Consensus size: 27
28950123 AGGAGATGGG
* *
28950133 GGAGGTGGAGATTTGTAGGCATAAGGT
1 GGAGGTGGAGACTTGTAGACATAAGGT
*
28950160 GGAGGTGGGGACTTGTAGACATAAGGT
1 GGAGGTGGAGACTTGTAGACATAAGGT
* ** * *
28950187 TGA-G-GG-G--TTG-AGGGAGATGGT
1 GGAGGTGGAGACTTGTAGACATAAGGT
* * *
28950208 GGAGGTGGGGACTTGTAAACATAAGGG
1 GGAGGTGGAGACTTGTAGACATAAGGT
* *
28950235 GGAGGTGGTGA--TG--GAGAT--GGT
1 GGAGGTGGAGACTTGTAGACATAAGGT
*
28950256 GGAGGTGGAGACTTGTAAACATAAGGT
1 GGAGGTGGAGACTTGTAGACATAAGGT
28950283 GG
1 GG
28950285 TGGAGGTGAT
Statistics
Matches: 91, Mismatches: 22, Indels: 24
0.66 0.16 0.18
Matches are distributed among these distances:
21 21 0.23
22 4 0.04
23 7 0.08
24 2 0.02
25 7 0.08
26 4 0.04
27 46 0.51
ACGTcount: A:0.26, C:0.05, G:0.47, T:0.22
Consensus pattern (27 bp):
GGAGGTGGAGACTTGTAGACATAAGGT
Found at i:28950167 original size:75 final size:75
Alignment explanation
Indices: 28950082--28950242 Score: 198
Period size: 75 Copynumber: 2.1 Consensus size: 75
28950072 TGATGGAGAT
* * *
28950082 GGTGGGGGTGGAGACTTGTAGATATAAGGAGGAGGCGG-TGAAGGAGATGGGGGAGGTGGAGATT
1 GGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGG-GGTTGAAGGAGATGGGGGAGGTGGAGACT
**
28950146 TGTAGGCATAA
65 TGTAAACATAA
* ** * * *
28950157 GGTGGAGGTGGGGACTTGTAGACATAAGGTTGAGGGGTTGAGGGAGATGGTGGAGGTGGGGACTT
1 GGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGGGTTGAAGGAGATGGGGGAGGTGGAGACTT
28950222 GTAAACATAA
66 GTAAACATAA
*
28950232 GGGGGAGGTGG
1 GGTGGAGGTGG
28950243 TGATGGAGAT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
74 2 0.03
75 71 0.97
ACGTcount: A:0.25, C:0.04, G:0.50, T:0.20
Consensus pattern (75 bp):
GGTGGAGGTGGAGACTTGTAGACATAAGGAGGAGGGGTTGAAGGAGATGGGGGAGGTGGAGACTT
GTAAACATAA
Found at i:28950176 original size:123 final size:123
Alignment explanation
Indices: 28950037--28950284 Score: 336
Period size: 123 Copynumber: 2.0 Consensus size: 123
28950027 GGGAGATGGC
* * * *
28950037 GGAGGTGGGGATTTGTAGACATAGGGAGGAGGTGG-TGATGGAGATGGTGGGGGTGGAGACTTGT
1 GGAGGTGGGGACTTGTAGACATAAGGAGGAGG-GGTTGAGGGAGATGGTGGAGGTGGAGACTTGT
* * * **
28950101 AGATATAAGGAGGAGGCGGTGAAGGAGATGGGGGAGGTGGAGATTTGTAGGCATAAGGT
65 AAACATAAGGAGGAGGCGGTGAAGGAGATGGGGGAGGTGGAGACTTGTAAACATAAGGT
** *
28950160 GGAGGTGGGGACTTGTAGACATAAGGTTGAGGGGTTGAGGGAGATGGTGGAGGTGGGGACTTGTA
1 GGAGGTGGGGACTTGTAGACATAAGGAGGAGGGGTTGAGGGAGATGGTGGAGGTGGAGACTTGTA
* * * *
28950225 AACATAAGGGGGAGGTGGTGATGGAGATGGTGGAGGTGGAGACTTGTAAACATAAGGT
66 AACATAAGGAGGAGGCGGTGAAGGAGATGGGGGAGGTGGAGACTTGTAAACATAAGGT
28950283 GG
1 GG
28950285 TGGAGGTGAT
Statistics
Matches: 108, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
122 2 0.02
123 106 0.98
ACGTcount: A:0.25, C:0.04, G:0.49, T:0.21
Consensus pattern (123 bp):
GGAGGTGGGGACTTGTAGACATAAGGAGGAGGGGTTGAGGGAGATGGTGGAGGTGGAGACTTGTA
AACATAAGGAGGAGGCGGTGAAGGAGATGGGGGAGGTGGAGACTTGTAAACATAAGGT
Found at i:28950209 original size:48 final size:48
Alignment explanation
Indices: 28950157--28950311 Score: 206
Period size: 48 Copynumber: 3.2 Consensus size: 48
28950147 GTAGGCATAA
* *
28950157 GGTGGAGGTGGGGACTTGTAGACATAAGGTTGAGG-GGTTGAGGGAGAT
1 GGTGGAGGTGGGGACTTGTAAACATAAGGTGGAGGAGG-TGAGGGAGAT
* * *
28950205 GGTGGAGGTGGGGACTTGTAAACATAAGGGGGAGGTGGTGATGGAGAT
1 GGTGGAGGTGGGGACTTGTAAACATAAGGTGGAGGAGGTGAGGGAGAT
* *
28950253 GGTGGAGGTGGAGACTTGTAAACATAAGGTGGTGGAGGTGATGGG-GAT
1 GGTGGAGGTGGGGACTTGTAAACATAAGGTGGAGGAGGTGA-GGGAGAT
*
28950301 GGTGGTGGTGG
1 GGTGGAGGTGG
28950312 TGGGGACTTA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
48 91 0.96
49 4 0.04
ACGTcount: A:0.23, C:0.04, G:0.51, T:0.23
Consensus pattern (48 bp):
GGTGGAGGTGGGGACTTGTAAACATAAGGTGGAGGAGGTGAGGGAGAT
Found at i:28950305 original size:18 final size:18
Alignment explanation
Indices: 28950282--28950317 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28950272 AAACATAAGG
28950282 TGGTGGAGGTGATGGGGA
1 TGGTGGAGGTGATGGGGA
* *
28950300 TGGTGGTGGTGGTGGGGA
1 TGGTGGAGGTGATGGGGA
28950318 CTTATAGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.64, T:0.25
Consensus pattern (18 bp):
TGGTGGAGGTGATGGGGA
Found at i:28950377 original size:129 final size:126
Alignment explanation
Indices: 28950206--28950677 Score: 438
Period size: 129 Copynumber: 3.7 Consensus size: 126
28950196 GAGGGAGATG
* *
28950206 GTGGAGGTGGGGACTTGTAAACATAAGGG-GGAGGTGGTGATGGAGATGGTGGAGGTGGAGACTT
1 GTGGAGGTGGGGACTTGTAAACAT-AGGGAGG-GATGGTGATGGAGATGGTGGAGGGGGAGACTT
28950270 GTAAACATAAGGTGGTGGAGGTGATGGGGATGGTGGTGGTGGTGGGGACTTATAGACATATGGAA
64 GTAAACATAAGGTGGTGGAGGTGATGGGGAT--TGGTGGTGGTGGGGACTTATAGACATATGGAA
* *
28950335 GTGGAGGTGGGGACTTGTACACATAGGGAGCGGATGGTGATGGGGATGGTGGAGGGGGAGACTTG
1 GTGGAGGTGGGGACTTGTAAACATAGGGAG-GGATGGTGATGGAGATGGTGGAGGGGGAGACTTG
* * * * * ** * * ** * ** *
28950400 TAGATATATGGTGGTGGAGGTGGTGGTGATTTATAGAT-ATAAGGA--GA-AGGAGGTGAGGGAG
65 TAAACATAAGGTGGTGGAGGTGATGGGGATTGGT-GGTGGTGGGGACTTATA-GACAT-ATGGA-
28950461 A
126 A
* * *
28950462 TGGTGGAGGTGGGG-CTT-TATAGACATAAGGAGGTAGTGGTGATGGAGATGGTGGAGGTGGAGA
1 --GTGGAGGTGGGGACTTGTA-A-ACATAGGGAGGGA-TGGTGATGGAGATGGTGGAGGGGGAGA
* * * *
28950525 CTTGTAGACATATGGTGGTGGAGGTGATGGGGA-TGGCGGTGGTGGGGACTTATAAACATATGGA
61 CTTGTAAACATAAGGTGGTGGAGGTGATGGGGATTGGTGGTGGTGGGGACTTATAGACATATGGA
*
28950589 G
126 A
* * * *
28950590 GTGGAGGTGGGGACTTGTATACATAGGGAGGTGGTGGTGAGGGAGATGGTGGAGGGGGTGACTTG
1 GTGGAGGTGGGGACTTGTAAACATAGGGAGG-GATGGTGATGGAGATGGTGGAGGGGGAGACTTG
** * *
28950655 TAAATGTAAGGAGGTGGTGGTGA
65 TAAACATAAGGTGGTGGAGGTGA
28950678 CGAAGATGGT
Statistics
Matches: 272, Mismatches: 53, Indels: 39
0.75 0.15 0.11
Matches are distributed among these distances:
124 1 0.00
125 4 0.01
126 71 0.26
127 14 0.05
128 18 0.07
129 159 0.58
130 4 0.01
131 1 0.00
ACGTcount: A:0.24, C:0.04, G:0.48, T:0.24
Consensus pattern (126 bp):
GTGGAGGTGGGGACTTGTAAACATAGGGAGGGATGGTGATGGAGATGGTGGAGGGGGAGACTTGT
AAACATAAGGTGGTGGAGGTGATGGGGATTGGTGGTGGTGGGGACTTATAGACATATGGAA
Found at i:28950425 original size:81 final size:81
Alignment explanation
Indices: 28950254--28950422 Score: 204
Period size: 81 Copynumber: 2.1 Consensus size: 81
28950244 GATGGAGATG
* * *
28950254 GTGGAGGTGGAGACTTGTAAACATAAGGTGGTGGAGGTGATGGGGATGGTGGTGGTGGTGGGGAC
1 GTGGAGGTGGAGACTTGTAAACATAAGGTGGCGGAGGTGATGGGGATGGTGGTAGTGGTGGAGAC
28950319 TTATAGACATATGGAA
66 TTATAGACATATGGAA
* *
28950335 GTGGAGGTGGGGACTTGTACACAT-AGG-GAGCGGATGGTGATGGGGATGGTGG-AG-GG-GGAG
1 GTGGAGGTGGAGACTTGTAAACATAAGGTG-GCGGA-GGTGATGGGGATGGTGGTAGTGGTGGAG
* * **
28950395 ACTTGTAGATATATGGTG
64 ACTTATAGACATATGGAA
28950413 GTGGAGGTGG
1 GTGGAGGTGG
28950423 TGGTGATTTA
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
78 27 0.35
79 3 0.04
80 8 0.10
81 39 0.51
ACGTcount: A:0.22, C:0.05, G:0.49, T:0.24
Consensus pattern (81 bp):
GTGGAGGTGGAGACTTGTAAACATAAGGTGGCGGAGGTGATGGGGATGGTGGTAGTGGTGGAGAC
TTATAGACATATGGAA
Found at i:28950587 original size:27 final size:27
Alignment explanation
Indices: 28950557--28950626 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 27
28950547 GGTGATGGGG
*
28950557 ATGGCGGTGGTGGGGACTTATAAACAT
1 ATGGAGGTGGTGGGGACTTATAAACAT
* *
28950584 ATGGAGGTGGAGGTGGGGACTTGTATACAT
1 ATGGAGGT---GGTGGGGACTTATAAACAT
*
28950614 AGGGAGGTGGTGG
1 ATGGAGGTGGTGG
28950627 TGAGGGAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 12 0.33
30 24 0.67
ACGTcount: A:0.23, C:0.07, G:0.46, T:0.24
Consensus pattern (27 bp):
ATGGAGGTGGTGGGGACTTATAAACAT
Found at i:28950593 original size:48 final size:48
Alignment explanation
Indices: 28950411--28950598 Score: 182
Period size: 48 Copynumber: 3.9 Consensus size: 48
28950401 AGATATATGG
* * * **
28950411 TGGTGGAGGTGGTGGTGATTTATAGATATAAGGAGAAGGAGGTGA-GGGAGA
1 TGGTGGAGGT-G-GG-GACTTATAGACATATGGAGGTGGAGGTGATGGG-GA
* * * *
28950462 TGGTGGAGGTGGGG-CTTTATAGACATAAGGAGGTAGTGGTGATGGAGA
1 TGGTGGAGGTGGGGAC-TTATAGACATATGGAGGTGGAGGTGATGGGGA
* * *
28950510 TGGTGGAGGTGGAGACTTGTAGACATATGGTGGTGGAGGTGATGGGGA
1 TGGTGGAGGTGGGGACTTATAGACATATGGAGGTGGAGGTGATGGGGA
* * *
28950558 TGGCGGTGGTGGGGACTTATAAACATATGGAGGTGGAGGTG
1 TGGTGGAGGTGGGGACTTATAGACATATGGAGGTGGAGGTG
28950599 GGGACTTGTA
Statistics
Matches: 114, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
48 98 0.86
49 5 0.04
50 1 0.01
51 10 0.09
ACGTcount: A:0.24, C:0.04, G:0.47, T:0.24
Consensus pattern (48 bp):
TGGTGGAGGTGGGGACTTATAGACATATGGAGGTGGAGGTGATGGGGA
Found at i:28950601 original size:30 final size:30
Alignment explanation
Indices: 28950565--28950633 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
28950555 GGATGGCGGT
*
28950565 GGTGGGGACTTATAAACATATGGAGGTGGA
1 GGTGGGGACTTATAAACATAGGGAGGTGGA
* * *
28950595 GGTGGGGACTTGTATACATAGGGAGGTGGT
1 GGTGGGGACTTATAAACATAGGGAGGTGGA
28950625 GGTGAGGGA
1 GGTG-GGGA
28950634 GATGGTGGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.25, C:0.06, G:0.46, T:0.23
Consensus pattern (30 bp):
GGTGGGGACTTATAAACATAGGGAGGTGGA
Found at i:28950653 original size:78 final size:78
Alignment explanation
Indices: 28950511--28950676 Score: 192
Period size: 78 Copynumber: 2.1 Consensus size: 78
28950501 TGATGGAGAT
* * *
28950511 GGTGGAGGTGGAGACTTGTAGACATATGGTGGTGGAGGTGATGGGGATGGCGGTGGTGGGGACTT
1 GGTGGAGGTGGAGACTTGTAGACATAGGGAGGTGGAGGTGATGGGGATGGCGGAGGTGGGGACTT
*
28950576 ATAAACATATGGA
66 ATAAACATAAGGA
* * * *
28950589 GGTGGAGGTGGGGACTTGTATACATAGGGAGGTGGTGGTGA-GGGAGATGGTGGAGG-GGGTGAC
1 GGTGGAGGTGGAGACTTGTAGACATAGGGAGGTGGAGGTGATGGG-GATGGCGGAGGTGGG-GAC
* **
28950652 TTGTAAATGTAAGGA
64 TTATAAACATAAGGA
*
28950667 GGTGGTGGTG
1 GGTGGAGGTG
28950677 ACGAAGATGG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
77 6 0.08
78 68 0.92
ACGTcount: A:0.22, C:0.05, G:0.49, T:0.24
Consensus pattern (78 bp):
GGTGGAGGTGGAGACTTGTAGACATAGGGAGGTGGAGGTGATGGGGATGGCGGAGGTGGGGACTT
ATAAACATAAGGA
Found at i:28950716 original size:48 final size:48
Alignment explanation
Indices: 28950589--28950717 Score: 147
Period size: 48 Copynumber: 2.7 Consensus size: 48
28950579 AACATATGGA
* ** * * *
28950589 GGTGGAGGTGGG-GACTTGTATACATAGGGAGGTGGTGGTGAGGGAGAT
1 GGTGGAGG-GGGTGACTTGTAAATGTAAGGAGGTGGTGGTGACGAAGAT
28950637 GGTGGAGGGGGTGACTTGTAAATGTAAGGAGGTGGTGGTGACGAAGAT
1 GGTGGAGGGGGTGACTTGTAAATGTAAGGAGGTGGTGGTGACGAAGAT
*
28950685 GGTGG-GGGAGGTGACTTGTAGAA-GTATGGAGGT
1 GGTGGAGGG-GGTGACTTGTA-AATGTAAGGAGGT
28950718 AAAGGTGAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
47 6 0.08
48 63 0.89
49 2 0.03
ACGTcount: A:0.22, C:0.04, G:0.50, T:0.23
Consensus pattern (48 bp):
GGTGGAGGGGGTGACTTGTAAATGTAAGGAGGTGGTGGTGACGAAGAT
Found at i:28950724 original size:126 final size:125
Alignment explanation
Indices: 28950468--28950724 Score: 266
Period size: 126 Copynumber: 2.0 Consensus size: 125
28950458 GAGATGGTGG
* * *
28950468 AGGTGGGGCTTTATAGACATAAGGAGGTAGTGGTGATGGAGATGGTGGAGGTGGAGACTTGTAGA
1 AGGTGGGGCTTTATA-ACATAAGGAGGTAGTGGTGAGGGAGATGGTGGAGGGGGAGACTTGTAAA
* * * ** * * **
28950533 CATATGGTGGTGGAGGTGATGGGGATGGCGGTGGTGGGGACTTATAAACATATGGAGGTGG
65 CATAAGGAGGTGGAGGTGACGAAGATGGCGGGGGAGGGGACTTATAAACATATGGAGGTAA
* * *
28950594 AGGTGGGGACTTGTAT-ACATAGGGAGGTGGTGGTGAGGGAGATGGTGGAGGGGGTGACTTGTAA
1 AGGTGGGG-CTT-TATAACATAAGGAGGTAGTGGTGAGGGAGATGGTGGAGGGGGAGACTTGTAA
** * * * * *
28950658 ATGTAAGGAGGTGGTGGTGACGAAGATGGTGGGGGAGGTGACTTGTAGAA-GTATGGAGGTAA
64 ACATAAGGAGGTGGAGGTGACGAAGATGGCGGGGGAGGGGACTTATA-AACATATGGAGGTAA
28950720 AGGTG
1 AGGTG
28950725 AAGGGTACCG
Statistics
Matches: 106, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
126 98 0.92
127 5 0.05
128 3 0.03
ACGTcount: A:0.24, C:0.05, G:0.47, T:0.24
Consensus pattern (125 bp):
AGGTGGGGCTTTATAACATAAGGAGGTAGTGGTGAGGGAGATGGTGGAGGGGGAGACTTGTAAAC
ATAAGGAGGTGGAGGTGACGAAGATGGCGGGGGAGGGGACTTATAAACATATGGAGGTAA
Found at i:28953720 original size:30 final size:30
Alignment explanation
Indices: 28953684--28953747 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
28953674 CAAGAAGTTA
*
28953684 ATGAAGAGATTCAAAATTATCATAAAAATC
1 ATGAAGAGATTCAAAATGATCATAAAAATC
28953714 ATGAAGAGATTCAAAATGATCATAAAAATC
1 ATGAAGAGATTCAAAATGATCATAAAAATC
28953744 ATGA
1 ATGA
28953748 TGAAGAGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (30 bp):
ATGAAGAGATTCAAAATGATCATAAAAATC
Found at i:28954032 original size:26 final size:26
Alignment explanation
Indices: 28954003--28954056 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
28953993 ATGTTAATTG
*
28954003 CTCCAGAAGAAAGAAGTTTTTCAAAA
1 CTCCAAAAGAAAGAAGTTTTTCAAAA
28954029 CTCCAAAAGAAAGAAGTTTTTCAAAA
1 CTCCAAAAGAAAGAAGTTTTTCAAAA
28954055 CT
1 CT
28954057 AAAATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (26 bp):
CTCCAAAAGAAAGAAGTTTTTCAAAA
Found at i:28958714 original size:9 final size:9
Alignment explanation
Indices: 28958697--28958774 Score: 68
Period size: 9 Copynumber: 8.6 Consensus size: 9
28958687 CCCATTTAAT
28958697 AAAAATAAA
1 AAAAATAAA
*
28958706 AATAATAAA
1 AAAAATAAA
28958715 AAAAATAAA
1 AAAAATAAA
28958724 AACAAATAAA
1 AA-AAATAAA
***
28958734 TCTAATAAGA
1 AAAAATAA-A
*
28958744 ATAAA-AAA
1 AAAAATAAA
*
28958752 TAAAATAAA
1 AAAAATAAA
*
28958761 AAAAAGAAA
1 AAAAATAAA
28958770 AAAAA
1 AAAAA
28958775 GAATAAAGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
8 4 0.07
9 40 0.74
10 10 0.19
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (9 bp):
AAAAATAAA
Found at i:28958790 original size:46 final size:49
Alignment explanation
Indices: 28958697--28958791 Score: 110
Period size: 48 Copynumber: 2.0 Consensus size: 49
28958687 CCCATTTAAT
* *
28958697 AAAAATAAAAATAATAAAAAAAATAAAAACAAATAAATCTAATAAGAATA
1 AAAAATAAAAATAATAAAAAAAATAAAAACAAATAAA-CGAAGAAGAATA
28958747 AAAAAT-AAAATAA-AAAAAAGAA-AAAAA-AGAATAAA-GAAGAAGAAT
1 AAAAATAAAAATAATAAAAAA-AATAAAAACA-AATAAACGAAGAAGAAT
28958792 CTAGAGACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
46 8 0.20
47 1 0.02
48 17 0.41
49 9 0.22
50 6 0.15
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (49 bp):
AAAAATAAAAATAATAAAAAAAATAAAAACAAATAAACGAAGAAGAATA
Found at i:28959387 original size:12 final size:12
Alignment explanation
Indices: 28959372--28959405 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
28959362 GTGGCGGCAA
28959372 GAGAGAGAAAGT
1 GAGAGAGAAAGT
28959384 GAGAGAGGAAAGT
1 GAGAGA-GAAAGT
28959397 GAAGAGAGA
1 G-AGAGAGA
28959406 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 9 0.45
14 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.44, T:0.06
Consensus pattern (12 bp):
GAGAGAGAAAGT
Found at i:28959411 original size:16 final size:15
Alignment explanation
Indices: 28959370--28959409 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
28959360 GAGTGGCGGC
28959370 AAGAGAGAGAAAGTG
1 AAGAGAGAGAAAGTG
28959385 -AGAGAG-GAAAGTG
1 AAGAGAGAGAAAGTG
28959398 AAGAGAGAGAAA
1 AAGAGAGAGAAA
28959410 AGAAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.30
14 12 0.52
15 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.40, T:0.05
Consensus pattern (15 bp):
AAGAGAGAGAAAGTG
Found at i:28964736 original size:30 final size:29
Alignment explanation
Indices: 28964700--28964761 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
28964690 CTTCTCTTTA
*
28964700 TATATAAATAAATATAATCATATAAAAATC
1 TATATAAATAAATACAATCATAT-AAAATC
28964730 TATATAAATAAATACAATCATATAAAATC
1 TATATAAATAAATACAATCATATAAAATC
28964759 TAT
1 TAT
28964762 GTATGTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (29 bp):
TATATAAATAAATACAATCATATAAAATC
Found at i:28964752 original size:18 final size:18
Alignment explanation
Indices: 28964701--28964755 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
28964691 TTCTCTTTAT
*
28964701 ATATAAATAAATATAATC
1 ATATAAATAAATACAATC
28964719 ATAT-AA-AAAT-C--T-
1 ATATAAATAAATACAATC
28964731 ATATAAATAAATACAATC
1 ATATAAATAAATACAATC
28964749 ATATAAA
1 ATATAAA
28964756 ATCTATGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
12 4 0.13
13 3 0.10
14 4 0.13
15 1 0.03
16 4 0.13
17 3 0.10
18 11 0.37
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (18 bp):
ATATAAATAAATACAATC
Found at i:28985504 original size:15 final size:15
Alignment explanation
Indices: 28985484--28985521 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
28985474 ATTTGTTCTG
*
28985484 TAAGGTTTATTATGA
1 TAAGGTTTACTATGA
28985499 TAAGGTTTACTATGA
1 TAAGGTTTACTATGA
*
28985514 TGAGGTTT
1 TAAGGTTT
28985522 TTAATGAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.45
Consensus pattern (15 bp):
TAAGGTTTACTATGA
Found at i:28989298 original size:2 final size:2
Alignment explanation
Indices: 28989293--28989325 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28989283 GAATTACTTA
28989293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28989326 GAGAGAGANN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28989899 original size:19 final size:19
Alignment explanation
Indices: 28989877--28989940 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 19
28989867 AATTAAAAAT
28989877 AAAAAATTAAAAAATTTAG
1 AAAAAATTAAAAAATTTAG
*
28989896 AAAATAA--AAGAAAATTTAAA
1 AAAA-AATTAA-AAAATTT-AG
*
28989916 ACATAAAATTAAAAAATGTAG
1 A-A-AAAATTAAAAAATTTAG
28989937 AAAA
1 AAAA
28989941 TAAGAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
18 2 0.06
19 13 0.37
20 5 0.14
21 5 0.14
22 8 0.23
23 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAAAATTAAAAAATTTAG
Found at i:28989924 original size:41 final size:41
Alignment explanation
Indices: 28989842--28989943 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
28989832 ATTTTTATAT
* * *
28989842 AATTAAAAAATGTA-TAAA-AAAATAAAATTAAAAATAAAA
1 AATTAAAAAATGTAGAAAATAAAAGAAAATTAAAAACAAAA
* * *
28989881 AATTAAAAAATTTAGAAAATAAAAGAAAATTTAAAACATAA
1 AATTAAAAAATGTAGAAAATAAAAGAAAATTAAAAACAAAA
28989922 AATTAAAAAATGTAGAAAATAA
1 AATTAAAAAATGTAGAAAATAA
28989944 GAAAAGAGAG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 13 0.24
40 3 0.06
41 38 0.70
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.24
Consensus pattern (41 bp):
AATTAAAAAATGTAGAAAATAAAAGAAAATTAAAAACAAAA
Found at i:28992476 original size:72 final size:73
Alignment explanation
Indices: 28992353--28992546 Score: 225
Period size: 72 Copynumber: 2.7 Consensus size: 73
28992343 TGAGAAACAA
* * * * * *
28992353 AACCGACTTAGTTGACCAAGATGTGAGTTAGTCGACTAGATGCTTTATGCCAAAATCT-AGACT-
1 AACCAACTTAGTCGACCAAGATGTAAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTGAGA-TA
*
28992416 TCAAGACAG
65 ACAAGACAG
*
28992425 AACCAACTTAGTC-AGCCAAGATGTAAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTGCGATA
1 AACCAACTTAGTCGA-CCAAGATGTAAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTGAGATA
*
28992489 AGAAGACAG
65 ACAAGACAG
* * *
28992498 AACCAATTTAGTCGACCAAGAAGAAAGTTAGTCGACTAAGA-GCTCTCTG
1 AACCAACTTAGTCGACCAAGATGTAAGTTAGTCGACTAA-ATGCTCTCTG
28992547 TCTGCAATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
71 1 0.01
72 51 0.49
73 51 0.49
74 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (73 bp):
AACCAACTTAGTCGACCAAGATGTAAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTGAGATAA
CAAGACAG
Found at i:29005257 original size:77 final size:77
Alignment explanation
Indices: 29005123--29005284 Score: 256
Period size: 77 Copynumber: 2.1 Consensus size: 77
29005113 TACCATCTAT
* *
29005123 TTTAATTTTGGGTGATCCATAAAAAATAAGAAATTGTTTCGTACTTTAAAAGCAATTCCTAAAAT
1 TTTAATTTTGGGTGATCCATAAAAAATAAGAAATTGTTTCCTACTTTAAAAGAAATTCCTAAAAT
29005188 TAAGGATAG-AA
66 TAAGGATAGTAA
*
29005199 TTTAATTTTGGGTGATTCATAAAAAA-ATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
1 TTTAATTTTGGGTGATCCATAAAAAATA-AG-AAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
*
29005263 ATTAAGGATAGTAT
64 ATTAAGGATAGTAA
29005277 TTTAATTT
1 TTTAATTT
29005285 GAAAAATTCA
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
75 1 0.01
76 27 0.34
77 42 0.53
78 9 0.11
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (77 bp):
TTTAATTTTGGGTGATCCATAAAAAATAAGAAATTGTTTCCTACTTTAAAAGAAATTCCTAAAAT
TAAGGATAGTAA
Found at i:29009328 original size:33 final size:33
Alignment explanation
Indices: 29009282--29009356 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
29009272 TATTGAACAT
**
29009282 AACTCTTTAAATAGTTATATTGTGAAAGAAAAC
1 AACTCTTTAAATAGTTATATAATGAAAGAAAAC
* *
29009315 AACTGTTTGAATAGTTATATAATGAAAGAAAAC
1 AACTCTTTAAATAGTTATATAATGAAAGAAAAC
29009348 AACTCTTTA
1 AACTCTTTA
29009357 CATTGAAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (33 bp):
AACTCTTTAAATAGTTATATAATGAAAGAAAAC
Found at i:29010095 original size:72 final size:73
Alignment explanation
Indices: 29009956--29010143 Score: 197
Period size: 72 Copynumber: 2.6 Consensus size: 73
29009946 TTAAAGTTTC
* * * * ** * *
29009956 ACAAAAAGATTTTAATCGATTAACCT-ACATTTTAATCGATTAAAATAACATTGGAATGGACTTT
1 ACAAAAAGATTTTAATCGATTAACATAAGATTTTAATCGATTAAAACAACACTAAAATGCACTCT
29010020 GAGA-AAG
66 GAGACAAG
* *
29010027 ACAAAAAGGTTTTAATCAATTAACATAAGATTTTAATCGATTAAAACAACACTAAAATGCA-TAC
1 ACAAAAAGATTTTAATCGATTAACATAAGATTTTAATCGATTAAAACAACACTAAAATGCACT-C
29010091 TGAGACAAG
65 TGAGACAAG
* * * * *
29010100 -CAAAGAGATTATAATCGATTAACACAAG-GTTTAATCAATTAAAA
1 ACAAAAAGATTTTAATCGATTAACATAAGATTTTAATCGATTAAAA
29010144 TGGTATTGGA
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
71 38 0.39
72 56 0.58
73 3 0.03
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (73 bp):
ACAAAAAGATTTTAATCGATTAACATAAGATTTTAATCGATTAAAACAACACTAAAATGCACTCT
GAGACAAG
Found at i:29016120 original size:33 final size:33
Alignment explanation
Indices: 29016078--29016142 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
29016068 AATATAACTC
*
29016078 TTTGAATAGTTATATTATGAAAGGAAACAATTA
1 TTTGAATAGTTATATTATGAAACGAAACAATTA
29016111 TTTGAATAGTTATATTATGAAACGAAACAATT
1 TTTGAATAGTTATATTATGAAACGAAACAATT
29016143 CTTTACATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.37
Consensus pattern (33 bp):
TTTGAATAGTTATATTATGAAACGAAACAATTA
Found at i:29018686 original size:28 final size:29
Alignment explanation
Indices: 29018628--29018689 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
29018618 GCAAATTTTT
* * *
29018628 AAAAATTACACTTTTGCCCCCATAAAGTG
1 AAAAATTACACTTTTGACCCCAAAAACTG
* *
29018657 AAAAATTACA-TTTTTACCTCAAAAACTG
1 AAAAATTACACTTTTGACCCCAAAAACTG
29018685 AAAAA
1 AAAAA
29018690 CTGCCCATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.27
Consensus pattern (29 bp):
AAAAATTACACTTTTGACCCCAAAAACTG
Found at i:29019481 original size:35 final size:32
Alignment explanation
Indices: 29019426--29019543 Score: 110
Period size: 35 Copynumber: 3.4 Consensus size: 32
29019416 GCTCCGTTTA
* *
29019426 TTCTAATTGTTCTGTGTGAAGTGATATTTCACTTG
1 TTCTAGTTGTTC--TGTGAAGT-ATGTTTCACTTG
*
29019461 TTGTAGTTGTTCTGCATGAAGTAATGTTTCACTTG
1 TTCTAGTTGTTCTG--TGAAGT-ATGTTTCACTTG
* *
29019496 ATCTAGTTGCTCTCTGTGAAGTAGTGCTTCACTTG
1 TTCTAGTTG-T-TCTGTGAAGTA-TGTTTCACTTG
29019531 TTCTAGTTGTTCT
1 TTCTAGTTGTTCT
29019544 TAATATTCTC
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
33 5 0.07
34 2 0.03
35 58 0.83
36 1 0.01
37 4 0.06
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.47
Consensus pattern (32 bp):
TTCTAGTTGTTCTGTGAAGTATGTTTCACTTG
Found at i:29024634 original size:35 final size:34
Alignment explanation
Indices: 29024595--29024682 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 34
29024585 GAAATAGTGC
** *
29024595 TTCACTTGTTGTAGTTGTTCTGTATTAAGTAGTAT
1 TTCACTTGTT-TAGTTGTTCTACATGAAGTAGTAT
* *
29024630 TTCACTTGATCTAGTTGTTCTACATGAATTAGTAT
1 TTCACTTG-TTTAGTTGTTCTACATGAAGTAGTAT
*
29024665 TTTACTTGCTTTAGTTGT
1 TTCACTTG-TTTAGTTGT
29024683 CATCAATATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 43 0.98
36 1 0.02
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.51
Consensus pattern (34 bp):
TTCACTTGTTTAGTTGTTCTACATGAAGTAGTAT
Found at i:29025228 original size:2 final size:2
Alignment explanation
Indices: 29025221--29025261 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29025211 AATATCCCAC
29025221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29025262 GTAAACAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29028861 original size:19 final size:19
Alignment explanation
Indices: 29028825--29028862 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
29028815 ATAAAGATTT
* *
29028825 ATTTAAAAATTTTTAAATA
1 ATTTAAAAATGTTCAAATA
29028844 ATTTAAAAATGTTCAAATA
1 ATTTAAAAATGTTCAAATA
29028863 TTATACCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTTAAAAATGTTCAAATA
Found at i:29035199 original size:20 final size:19
Alignment explanation
Indices: 29035174--29035227 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 19
29035164 TACAATTATT
29035174 TATTTTTTTATTATCATTAA
1 TATTTTTTTATTATCATT-A
*
29035194 TATTTTTTTATTTTC-TTA
1 TATTTTTTTATTATCATTA
*
29035212 TA-TATTTTATTATCAT
1 TATTTTTTTATTATCAT
29035228 ATTTCCTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 10 0.33
18 4 0.13
19 2 0.07
20 14 0.47
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTTTTATTATCATTA
Found at i:29035401 original size:16 final size:14
Alignment explanation
Indices: 29035362--29035419 Score: 61
Period size: 15 Copynumber: 4.4 Consensus size: 14
29035352 GTAAGCAAAA
29035362 ATTATATA-TTTTT
1 ATTATATATTTTTT
29035375 ATTATACTATTTTTT
1 ATTATA-TATTTTTT
* *
29035390 ATTTTATATATTTT
1 ATTATATATTTTTT
29035404 -TT-TATA-TTTTT
1 ATTATATATTTTTT
29035415 ATTAT
1 ATTAT
29035420 TTACACATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.11
12 6 0.16
13 9 0.24
14 9 0.24
15 10 0.26
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTATATATTTTTT
Found at i:29035589 original size:4 final size:4
Alignment explanation
Indices: 29035576--29035606 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
29035566 ATTAGTTATT
29035576 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
29035607 ATGTCATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:29048206 original size:22 final size:22
Alignment explanation
Indices: 29048178--29048250 Score: 128
Period size: 22 Copynumber: 3.3 Consensus size: 22
29048168 CTTTTGGCCA
29048178 GCCTCTCAACTACCGTCGGTCG
1 GCCTCTCAACTACCGTCGGTCG
*
29048200 GCCTCTCAACTACCGTCAGTCG
1 GCCTCTCAACTACCGTCGGTCG
29048222 GCCTCTCAACTACCGTCGGTCG
1 GCCTCTCAACTACCGTCGGTCG
*
29048244 GCTTCTC
1 GCCTCTC
29048251 CCCATTGCAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.14, C:0.41, G:0.21, T:0.25
Consensus pattern (22 bp):
GCCTCTCAACTACCGTCGGTCG
Found at i:29048993 original size:2 final size:2
Alignment explanation
Indices: 29048988--29049021 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
29048978 ATACACACAC
* *
29048988 AT AT AT AT AT AT AT AT AT AT AC AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29049022 TACTTATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:29052867 original size:19 final size:19
Alignment explanation
Indices: 29052843--29052885 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
29052833 TATTTTTTAA
*
29052843 ATATATTTTATATATAAAT
1 ATATATTTTATAAATAAAT
* *
29052862 ATATATTTTTTAAATATAT
1 ATATATTTTATAAATAAAT
29052881 ATATA
1 ATATA
29052886 CGATTAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATTTTATAAATAAAT
Found at i:29052872 original size:21 final size:21
Alignment explanation
Indices: 29052843--29052885 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29052833 TATTTTTTAA
*
29052843 ATATATTTTATATATAAATAT
1 ATATATTTTAAATATAAATAT
* *
29052864 ATATTTTTTAAATATATATAT
1 ATATATTTTAAATATAAATAT
29052885 A
1 A
29052886 CGATTAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATATTTTAAATATAAATAT
Found at i:29052880 original size:17 final size:17
Alignment explanation
Indices: 29052833--29052884 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
29052823 ATTAATAATG
29052833 TATTTTTTAAATATAT-
1 TATTTTTTAAATATATA
* *
29052849 T-TTATATATAA-ATATA
1 TATTTTTTA-AATATATA
29052865 TATTTTTTAAATATATA
1 TATTTTTTAAATATATA
29052882 TAT
1 TAT
29052885 ACGATTAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
15 9 0.32
16 6 0.21
17 13 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTTTAAATATATA
Found at i:29054095 original size:26 final size:26
Alignment explanation
Indices: 29054059--29054110 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
29054049 TGAAGAACTA
29054059 GTGCTTGCATTCACCTTATGATGGCT
1 GTGCTTGCATTCACCTTATGATGGCT
29054085 GTGCTTGCATTCACCTTATGATGGCT
1 GTGCTTGCATTCACCTTATGATGGCT
29054111 TAGCTAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
GTGCTTGCATTCACCTTATGATGGCT
Found at i:29064797 original size:23 final size:23
Alignment explanation
Indices: 29064767--29064835 Score: 138
Period size: 23 Copynumber: 3.0 Consensus size: 23
29064757 AAAAGTGTGC
29064767 TTAAATAATTGACATATATATAT
1 TTAAATAATTGACATATATATAT
29064790 TTAAATAATTGACATATATATAT
1 TTAAATAATTGACATATATATAT
29064813 TTAAATAATTGACATATATATAT
1 TTAAATAATTGACATATATATAT
29064836 ATATAATCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAAATAATTGACATATATATAT
Found at i:29078916 original size:21 final size:20
Alignment explanation
Indices: 29078892--29078939 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
29078882 ACTTACCTTT
* *
29078892 TTTTTCACTTGTTTCCTTGTA
1 TTTTTCACTT-TTCCCTTGAA
*
29078913 TTTTCACACTTTTCCCTTGAA
1 TTTT-TCACTTTTCCCTTGAA
29078934 TTTTTC
1 TTTTTC
29078940 CACCTAGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.12, C:0.23, G:0.06, T:0.58
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTGAA
Found at i:29082772 original size:20 final size:21
Alignment explanation
Indices: 29082734--29082772 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
29082724 TTTAGAAAAC
*
29082734 CATAGTCAAACCTAGAAGCAT
1 CATAGTCAAACCTACAAGCAT
*
29082755 CATAGTC-AACCTTCAAGC
1 CATAGTCAAACCTACAAGC
29082773 TTTAGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (21 bp):
CATAGTCAAACCTACAAGCAT
Found at i:29083716 original size:5 final size:5
Alignment explanation
Indices: 29083706--29083739 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
29083696 TGCTTATTTG
* *
29083706 TTTTA TTTTA TTTTA CTTTA TTTCA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
29083740 GCTTTCTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:29087132 original size:45 final size:45
Alignment explanation
Indices: 29087072--29087207 Score: 150
Period size: 45 Copynumber: 3.0 Consensus size: 45
29087062 TTCAGCTTAG
* * *
29087072 GGTTGTTTCTCCATTTCTTTTTCTTACTTATTCTCTTCTGTGGTT
1 GGTTCTTTCTCCATTTCTTTTTCTTACTCATTCTCTTCTATGGTT
* *
29087117 GGTTCTTTCTCCATTT-TTCTTTCTTTCTCATTCTCTTCTATGATT
1 GGTTCTTTCTCCATTTCTT-TTTCTTACTCATTCTCTTCTATGGTT
* * * * *
29087162 GATTCTTTTTCCATTCCTCTTTT-TTCCTCATTTTCTTCTATGGTT
1 GGTTCTTTCTCCATTTCT-TTTTCTTACTCATTCTCTTCTATGGTT
29087207 G
1 G
29087208 ATGTCTTTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
44 2 0.03
45 70 0.91
46 4 0.05
47 1 0.01
ACGTcount: A:0.08, C:0.23, G:0.10, T:0.60
Consensus pattern (45 bp):
GGTTCTTTCTCCATTTCTTTTTCTTACTCATTCTCTTCTATGGTT
Found at i:29088549 original size:14 final size:14
Alignment explanation
Indices: 29088529--29088565 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29088519 TCGGGTTTTG
29088529 AAGGAAAATAAGGA
1 AAGGAAAATAAGGA
* *
29088543 GAGGAAAATAGGGA
1 AAGGAAAATAAGGA
29088557 AAGGAAAAT
1 AAGGAAAAT
29088566 CTAAAGGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.08
Consensus pattern (14 bp):
AAGGAAAATAAGGA
Found at i:29094189 original size:26 final size:26
Alignment explanation
Indices: 29094129--29094190 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
29094119 ACCATATACC
*
29094129 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
29094155 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
29094181 TATCATCATC
1 CATCATCATC
29094191 TCATATGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.39, G:0.03, T:0.26
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:29094484 original size:42 final size:42
Alignment explanation
Indices: 29094425--29094547 Score: 210
Period size: 42 Copynumber: 2.9 Consensus size: 42
29094415 ACGGAGGGAA
* * * *
29094425 CAACGGCTTATGTGCACTTCTATTCACACATAGTCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
29094467 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
29094509 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
29094548 TCAAATCAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:29097793 original size:20 final size:20
Alignment explanation
Indices: 29097768--29097805 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29097758 TGTGTTCTTT
29097768 GCTCTAACAGATTACAAGAG
1 GCTCTAACAGATTACAAGAG
*
29097788 GCTCTAACTGATTACAAG
1 GCTCTAACAGATTACAAG
29097806 TTTTCTGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (20 bp):
GCTCTAACAGATTACAAGAG
Found at i:29103942 original size:40 final size:38
Alignment explanation
Indices: 29103849--29103951 Score: 134
Period size: 38 Copynumber: 2.7 Consensus size: 38
29103839 ATAGTGCCCG
* * *
29103849 TGTGCATGATGTGGGGGGATGTACACGATGGCACTGAT
1 TGTGCATGATGTGGGGGGATGCACACGATGACACGGAT
* *
29103887 TGTGCATGATGTGGGGGGATGCACACGATGACTTCGGCT
1 TGTGCATGATGTGGGGGGATGCACACGATGAC-ACGGAT
*
29103926 ATGTGCACGATGTGGGGGGATGCACA
1 -TGTGCATGATGTGGGGGGATGCACA
29103952 TGAGCTGGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 30 0.53
39 3 0.05
40 24 0.42
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (38 bp):
TGTGCATGATGTGGGGGGATGCACACGATGACACGGAT
Found at i:29104311 original size:91 final size:91
Alignment explanation
Indices: 29104172--29104359 Score: 322
Period size: 91 Copynumber: 2.1 Consensus size: 91
29104162 TGCTCTGTTT
* * *
29104172 CTCGCTGCAGTGAGAAACTCTCGAGTTTGAAGGCCTTCACCTGACCTGGTTCTCGTTGCAGCGAG
1 CTCGCTACAGTGAAAAACTCTCGAGTTTGAAGGCCTTCACCTGACCTGGTTCTCGCTGCAGCGAG
*
29104237 AAACTTTCTGTTTTGTCCAAGTGAAA
66 AAACTTTCTGTTTTGGCCAAGTGAAA
* *
29104263 CTCGCTACAGTGAAAAACTCTCGGGTTTGAGGGCCTTCACCTGACCTGGTTCTCGCTGCAGCGAG
1 CTCGCTACAGTGAAAAACTCTCGAGTTTGAAGGCCTTCACCTGACCTGGTTCTCGCTGCAGCGAG
29104328 AAACTTTCTGTTTTGGCCAAGTGAAA
66 AAACTTTCTGTTTTGGCCAAGTGAAA
29104354 CTCGCT
1 CTCGCT
29104360 GCAGCGAGAA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (91 bp):
CTCGCTACAGTGAAAAACTCTCGAGTTTGAAGGCCTTCACCTGACCTGGTTCTCGCTGCAGCGAG
AAACTTTCTGTTTTGGCCAAGTGAAA
Found at i:29105561 original size:29 final size:29
Alignment explanation
Indices: 29105529--29105600 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
29105519 CCTATTTTAA
29105529 CCTTAATTTTTAATTTTATTCTTGTATTT
1 CCTTAATTTTTAATTTTATTCTTGTATTT
29105558 CCTTAATTTTTAATTTTATTCTTGTATTT
1 CCTTAATTTTTAATTTTATTCTTGTATTT
29105587 CCTT-ATTTATTAAT
1 CCTTAATTT-TTAAT
29105601 CATTATTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 4 0.10
29 38 0.90
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.64
Consensus pattern (29 bp):
CCTTAATTTTTAATTTTATTCTTGTATTT
Found at i:29105592 original size:16 final size:16
Alignment explanation
Indices: 29105544--29105593 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
29105534 ATTTTTAATT
29105544 TTATTCTTGTATTTCC
1 TTATTCTTGTATTTCC
*
29105560 TTAATT-TT-TAATT--
1 TT-ATTCTTGTATTTCC
29105573 TTATTCTTGTATTTCC
1 TTATTCTTGTATTTCC
29105589 TTATT
1 TTATT
29105594 TATTAATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
12 3 0.11
13 4 0.15
14 4 0.15
15 4 0.15
16 9 0.33
17 3 0.11
ACGTcount: A:0.18, C:0.12, G:0.04, T:0.66
Consensus pattern (16 bp):
TTATTCTTGTATTTCC
Found at i:29106158 original size:26 final size:27
Alignment explanation
Indices: 29106121--29106176 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
29106111 ATGTTGAGTT
* **
29106121 GTTTTAATTTAAGTTG-TTTTTTTTTA
1 GTTTTAATTTAAATTGCTTTTAGTTTA
29106147 GTTTT-ATGTTAAATTGCTTTTAGTTTA
1 GTTTTAAT-TTAAATTGCTTTTAGTTTA
29106174 GTT
1 GTT
29106177 AGTATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 2 0.08
26 12 0.48
27 11 0.44
ACGTcount: A:0.20, C:0.02, G:0.14, T:0.64
Consensus pattern (27 bp):
GTTTTAATTTAAATTGCTTTTAGTTTA
Found at i:29106194 original size:21 final size:22
Alignment explanation
Indices: 29106143--29106196 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
29106133 GTTGTTTTTT
*
29106143 TTTAGTTTTATGTTAAATTGCT
1 TTTAGTTTTATGTTAAATTGCA
*
29106165 TTTAG-TTTA-GTTAGTATTG-A
1 TTTAGTTTTATGTTA-AATTGCA
29106185 TTTAGTTTTATG
1 TTTAGTTTTATG
29106197 CGTTTGTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 9 0.33
21 12 0.44
22 6 0.22
ACGTcount: A:0.22, C:0.02, G:0.17, T:0.59
Consensus pattern (22 bp):
TTTAGTTTTATGTTAAATTGCA
Found at i:29107584 original size:21 final size:22
Alignment explanation
Indices: 29107559--29107601 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
29107549 TTTAGCGTTG
29107559 TTATTATTATTA-TTATTTATT
1 TTATTATTATTATTTATTTATT
*
29107580 TTATTATTGTTATTTATTTATT
1 TTATTATTATTATTTATTTATT
29107602 AATGATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (22 bp):
TTATTATTATTATTTATTTATT
Found at i:29107585 original size:18 final size:17
Alignment explanation
Indices: 29107562--29107602 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
29107552 AGCGTTGTTA
29107562 TTATTATTATTATTTATT
1 TTATTATTATTATTTA-T
*
29107580 TTATTATTGTTATTTAT
1 TTATTATTATTATTTAT
29107597 TTATTA
1 TTATTA
29107603 ATGATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTATTATTATTTAT
Found at i:29113145 original size:29 final size:29
Alignment explanation
Indices: 29113088--29113145 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
29113078 TTTGTCTTCC
***
29113088 TTAATTTCAATAAAAAAAGTTTTATTTTT
1 TTAATTTCAATAAAAAAAGCCCTATTTTT
29113117 TTAATTTCAATAAAAAAAGACCCTATTTT
1 TTAATTTCAATAAAAAAAG-CCCTATTTT
29113146 GAATATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (29 bp):
TTAATTTCAATAAAAAAAGCCCTATTTTT
Found at i:29124959 original size:5 final size:5
Alignment explanation
Indices: 29124951--29124983 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
29124941 ACCTAACCTG
29124951 ACTTA ACTTA AC-TA ACTTA ACTTA ACTTA ACTT
1 ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTT
29124984 GAGCCACGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
ACTTA
Found at i:29124970 original size:14 final size:15
Alignment explanation
Indices: 29124951--29124983 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
29124941 ACCTAACCTG
29124951 ACTTAACTTAAC-TA
1 ACTTAACTTAACTTA
29124965 ACTTAACTTAACTTA
1 ACTTAACTTAACTTA
29124980 ACTT
1 ACTT
29124984 GAGCCACGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (15 bp):
ACTTAACTTAACTTA
Found at i:29125038 original size:15 final size:15
Alignment explanation
Indices: 29125018--29125068 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
29125008 TTCTTAAAAC
29125018 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
29125033 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
* *
29125048 AGCTTTAAAATCAAA
1 AACTTTAAAACCAAA
*
29125063 ATCTTT
1 AACTTT
29125069 GATCTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.90
16 2 0.06
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:29127625 original size:19 final size:19
Alignment explanation
Indices: 29127601--29127638 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29127591 CTGCCAAACC
*
29127601 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
29127620 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
29127639 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:29141023 original size:14 final size:15
Alignment explanation
Indices: 29140999--29141028 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29140989 TCAAAATTCC
29140999 TTTAGTTTTTTGGTT
1 TTTAGTTTTTTGGTT
29141014 TTTA-TTTTTTGGTT
1 TTTAGTTTTTTGGTT
29141028 T
1 T
29141029 AAGGTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.07, C:0.00, G:0.17, T:0.77
Consensus pattern (15 bp):
TTTAGTTTTTTGGTT
Found at i:29142238 original size:31 final size:31
Alignment explanation
Indices: 29142198--29142335 Score: 204
Period size: 31 Copynumber: 4.5 Consensus size: 31
29142188 GTGTTAGCGT
* *
29142198 TGGCATGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACATTATATGCA
*
29142229 TGGCGTGTTACAACATTTTACATTATAGGCA
1 TGGCGTGTTACAACATTTTACATTATATGCA
* * *
29142260 TAGCGTGTTATAACATTTTACGTTATATGCA
1 TGGCGTGTTACAACATTTTACATTATATGCA
*
29142291 TGGCGTGTTATAACATTTTACATTATATGCA
1 TGGCGTGTTACAACATTTTACATTATATGCA
*
29142322 TGTCGTGTTACAAC
1 TGGCGTGTTACAAC
29142336 GTGACTGACA
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 96 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (31 bp):
TGGCGTGTTACAACATTTTACATTATATGCA
Found at i:29146292 original size:31 final size:30
Alignment explanation
Indices: 29146222--29146299 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
29146212 AATGACATCT
*
29146222 TGTGGTGACACGCTGAGTGGAAGCAGATAC
1 TGTGGTGACACGCTGAGTGCAAGCAGATAC
* * *
29146252 T-TGACGTGACACGTTGAGTGCATGCAGATTTC
1 TGTG--GTGACACGCTGAGTGCAAGCAGA-TAC
29146284 TGTGGTGACACGCTGA
1 TGTGGTGACACGCTGA
29146300 CTTCTTGCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.05
30 1 0.03
31 31 0.79
32 3 0.08
33 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (30 bp):
TGTGGTGACACGCTGAGTGCAAGCAGATAC
Found at i:29146429 original size:118 final size:117
Alignment explanation
Indices: 29146221--29146614 Score: 601
Period size: 117 Copynumber: 3.4 Consensus size: 117
29146211 CAATGACATC
* *
29146221 TTGTGGTGACACGCTGAGTGGAAGCAGATACTTGACGTGACACGTTGAGTGCATGCAGATTTCT-
1 TTGTGGTGACACGCTGAGTGGAAGCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTT-TG
* * * * *
29146285 GTGGTGACACGCTGACTTCTTGCAGTATTGTGGGATGACATGGTACACCCCATC
65 GTGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTGACATGGCACACTCCA-A
* *
29146339 TTGTGGTGACACGCTGAGTGGAAACAGATACTTGGCGTGACATGCTGAGTGCATGCAGATTTTGG
1 TTGTGGTGACACGCTGAGTGGAAGCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTTGG
*
29146404 TGGTGACACGTTGACTTCTTACAGTATTGTGGGGTGACATGGCACACTCCAA
66 TGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTGACATGGCACACTCCAA
* *
29146456 TTGTGGTGACACGCTGAGTGGAAGCAGATACTTGGCCTGACACGCTAAGTGCATGCAGATTTTGG
1 TTGTGGTGACACGCTGAGTGGAAGCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTTGG
* *
29146521 TGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTGACACGGCACGCTCCAA
66 TGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTGACATGGCACACTCCAA
* * * *
29146573 TTGTGGTGACACGCTGAGTGGAAGTAAATATTTGGCATGACA
1 TTGTGGTGACACGCTGAGTGGAAGCAGATACTTGGCGTGACA
29146615 TGCTAACTTA
Statistics
Matches: 254, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
117 149 0.59
118 105 0.41
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.28
Consensus pattern (117 bp):
TTGTGGTGACACGCTGAGTGGAAGCAGATACTTGGCGTGACACGCTGAGTGCATGCAGATTTTGG
TGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTGACATGGCACACTCCAA
Found at i:29146528 original size:31 final size:32
Alignment explanation
Indices: 29146458--29146530 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
29146448 CACTCCAATT
* *
29146458 GTGGTGACACGCTGAGTGGAAGCAGATACTTG
1 GTGGTGACACGCTAAGTGCAAGCAGATACTTG
** * *
29146490 G-CCTGACACGCTAAGTGCATGCAGAT-TTTG
1 GTGGTGACACGCTAAGTGCAAGCAGATACTTG
29146520 GTGGTGACACG
1 GTGGTGACACG
29146531 TTGACTTCTT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
30 4 0.12
31 27 0.84
32 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23
Consensus pattern (32 bp):
GTGGTGACACGCTAAGTGCAAGCAGATACTTG
Found at i:29150002 original size:145 final size:145
Alignment explanation
Indices: 29149808--29150138 Score: 391
Period size: 145 Copynumber: 2.3 Consensus size: 145
29149798 AACATATGTG
* * * **
29149808 GAAA-TGTTGAACACAAACTGTTAAAACCGAT-CGTATC-GACGGGTCGTTAGCACTATGAGTCT
1 GAAATTGTTGAACACAAACTGTTAGAACCG-TCCTTA-CAGGCTCGTCGTTAGCACTATGAGTCT
* * * * * **
29149870 GAGGAAGATCTCTCAGTGGTTGAGGGGCTGTCGTTGCATGGTCCAACTGCAAACACAGATATGTT
64 AAGGAAGACCTCTCAGTGATTGAGGAGCTGTCATCACATGGTCCAACTGCAAACACAGATATGTT
29149935 ATTCGATAATCACATAT
129 ATTCGATAATCACATAT
* * * * *
29149952 GGAATTGTTGAACACAAA-TCGTTATAATCGTCCTTACAGGCTCGTCGTTAGCACTGTGAGTTTA
1 GAAATTGTTGAACACAAACT-GTTAGAACCGTCCTTACAGGCTCGTCGTTAGCACTATGAGTCTA
* * * * * *
29150016 AGGAGGACCTCTCGGTGATTGTGGAGCTGTTATCATATGGTCCAATTGCAAACACAGATATGTTA
65 AGGAAGACCTCTCAGTGATTGAGGAGCTGTCATCACATGGTCCAACTGCAAACACAGATATGTTA
29150081 TTCGATAATCACATAT
130 TTCGATAATCACATAT
*
29150097 GAAATTGTTGAACACAAACTGTTAGAACCGTCCTTACCGGCT
1 GAAATTGTTGAACACAAACTGTTAGAACCGTCCTTACAGGCT
29150139 TTTCACTGCC
Statistics
Matches: 156, Mismatches: 26, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
144 6 0.04
145 149 0.96
146 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (145 bp):
GAAATTGTTGAACACAAACTGTTAGAACCGTCCTTACAGGCTCGTCGTTAGCACTATGAGTCTAA
GGAAGACCTCTCAGTGATTGAGGAGCTGTCATCACATGGTCCAACTGCAAACACAGATATGTTAT
TCGATAATCACATAT
Found at i:29152302 original size:20 final size:21
Alignment explanation
Indices: 29152277--29152328 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
29152267 TAAACCCTGC
29152277 CGTGTCACAGA-TCTCCATGG
1 CGTGTCACAGATTCTCCATGG
*
29152297 CGTGTCATAGATTTTCTCCATGG
1 CGTGTCACAGA--TTCTCCATGG
*
29152320 CATGTCACA
1 CGTGTCACA
29152329 AACTTTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 10 0.38
23 16 0.62
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (21 bp):
CGTGTCACAGATTCTCCATGG
Found at i:29152365 original size:47 final size:47
Alignment explanation
Indices: 29152312--29152508 Score: 198
Period size: 47 Copynumber: 4.2 Consensus size: 47
29152302 CATAGATTTT
* ** * *
29152312 CTCCATGGCATGTCACAAACTTTGAATGCTACCGTGCCACAAATTCC
1 CTCCATGGCATGTCACAAACTCTGAACCCTACCGTGTCAGAAATTCC
** ** * *
29152359 CTCCATGGTGTGTCACAAACTCCAAACCCTGCCGTGTCAGAGATTCC
1 CTCCATGGCATGTCACAAACTCTGAACCCTACCGTGTCAGAAATTCC
* * *
29152406 CTCCATGGCATGTCACAAACTTTGAACCCTACCATGTCAGAGATTCC
1 CTCCATGGCATGTCACAAACTCTGAACCCTACCGTGTCAGAAATTCC
* * ** **
29152453 TTCCATGAG-GTGTCACAAACTCTGAATGCTGGCGTGTCAGAAATTCC
1 CTCCATG-GCATGTCACAAACTCTGAACCCTACCGTGTCAGAAATTCC
29152500 CTCCATGGC
1 CTCCATGGC
29152509 GTGTAGGGAT
Statistics
Matches: 120, Mismatches: 28, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
46 1 0.01
47 118 0.98
48 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (47 bp):
CTCCATGGCATGTCACAAACTCTGAACCCTACCGTGTCAGAAATTCC
Found at i:29152410 original size:94 final size:94
Alignment explanation
Indices: 29152297--29152508 Score: 264
Period size: 94 Copynumber: 2.3 Consensus size: 94
29152287 ATCTCCATGG
* ** ** *
29152297 CGTGTCATAGATTTTCTCCATGGCATGTCACAAACTTTGAATGCTACCGTGCCACAAATTCCCTC
1 CGTGTCAGAGATTCCCTCCATGGCATGTCACAAACTTTGAACCCTACCATGCCACAAATTCCCTC
29152362 CATG-GTGTGTCACAAACTCCAAACCCTGC
66 CATGAG-GTGTCACAAACTCCAAACCCTGC
* * * *
29152391 CGTGTCAGAGATTCCCTCCATGGCATGTCACAAACTTTGAACCCTACCATGTCAGAGATTCCTTC
1 CGTGTCAGAGATTCCCTCCATGGCATGTCACAAACTTTGAACCCTACCATGCCACAAATTCCCTC
** ** *
29152456 CATGAGGTGTCACAAACTCTGAATGCTGG
66 CATGAGGTGTCACAAACTCCAAACCCTGC
*
29152485 CGTGTCAGAAATTCCCTCCATGGC
1 CGTGTCAGAGATTCCCTCCATGGC
29152509 GTGTAGGGAT
Statistics
Matches: 101, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 100 0.99
95 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (94 bp):
CGTGTCAGAGATTCCCTCCATGGCATGTCACAAACTTTGAACCCTACCATGCCACAAATTCCCTC
CATGAGGTGTCACAAACTCCAAACCCTGC
Found at i:29153306 original size:23 final size:23
Alignment explanation
Indices: 29153276--29153400 Score: 79
Period size: 23 Copynumber: 5.4 Consensus size: 23
29153266 AACGCTGGCG
29153276 TGTCACAAATTCTCTCCATGACA
1 TGTCACAAATTCTCTCCATGACA
* *** *
29153299 TGTCACAAACTCTAAACACTGACC
1 TGTCACAAATTCTCTCCA-TGACA
* * *
29153323 TGTCACAAATTCCCTTCATGGCA
1 TGTCACAAATTCTCTCCATGACA
* ** * * *
29153346 TGTCACAAACTCTAACCCTGTCG
1 TGTCACAAATTCTCTCCATGACA
* * * *
29153369 TGTCACAGATTCCCTCCATGGCG
1 TGTCACAAATTCTCTCCATGACA
29153392 TGTCACAAA
1 TGTCACAAA
29153401 CTCTAAAGGC
Statistics
Matches: 73, Mismatches: 28, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
23 56 0.77
24 17 0.23
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (23 bp):
TGTCACAAATTCTCTCCATGACA
Done.