Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 97 of 144
Found at i:22757951 original size:58 final size:57
Alignment explanation
Indices: 22757812--22758004 Score: 230
Period size: 58 Copynumber: 3.4 Consensus size: 57
22757802 CATTGCTTGC
* * * * * *
22757812 CAAACATCC-AAAAAATCTTTTTAAATCT-AGGAAAAGTGGTGTATGTCATTGGGTGG
1 CAAACACCCAAAAAAATATTTTTAAATCTGA-GAAAGGTGGTGTAGGCCATTGGGTGA
* * * * *
22757868 CAAACACCTAAAAACATATTTTTAAATATGAGAAAGGTGATGTAGGCCATTGGATGA
1 CAAACACCCAAAAAAATATTTTTAAATCTGAGAAAGGTGGTGTAGGCCATTGGGTGA
*
22757925 CAAACACCCCAAAAAAATATTTTTAAATCTGAGAAAGGTGGTGTAGACCATTGGGTGA
1 CAAACA-CCCAAAAAAATATTTTTAAATCTGAGAAAGGTGGTGTAGGCCATTGGGTGA
*
22757983 CAAACACTC-AAAAAATATTTTT
1 CAAACACCCAAAAAAATATTTTT
22758005 TTGTTCGTAT
Statistics
Matches: 116, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
56 20 0.17
57 44 0.38
58 52 0.45
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (57 bp):
CAAACACCCAAAAAAATATTTTTAAATCTGAGAAAGGTGGTGTAGGCCATTGGGTGA
Found at i:22758716 original size:30 final size:31
Alignment explanation
Indices: 22758680--22758744 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 31
22758670 TTTTTCCTAA
22758680 TTTTTAA-TAAAACTTAAAT-ATCTTTTAT-AC
1 TTTTTAATTAAAA-TTAAATAAT-TTTTATAAC
*
22758710 TTTTTAATTAAAATTTAATAATTTTTATAAC
1 TTTTTAATTAAAATTAAATAATTTTTATAAC
22758741 TTTT
1 TTTT
22758745 ATTGTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTTTAATTAAAATTAAATAATTTTTATAAC
Found at i:22767952 original size:32 final size:29
Alignment explanation
Indices: 22767787--22767958 Score: 100
Period size: 29 Copynumber: 5.9 Consensus size: 29
22767777 TTCTAATAAC
* * *
22767787 AAATCATAAAAATTTATAAAAATATTAAA
1 AAATTATAAAAACTTATAAAAATATAAAA
** * * * *
22767816 ATTTTAGATATACTTATAAAATTTATAAAA
1 AAATTATAAAAACTTATAAAA-ATATAAAA
* ** *
22767846 AAATCATAAAAA-TT-TTGAAA-ATACAA
1 AAATTATAAAAACTTATAAAAATATAAAA
* * **
22767872 AAA-TACAACTAAATTTATAAAAATATTTAA
1 AAATTATAA--AAACTTATAAAAATATAAAA
*
22767902 AAATTATATAAACTTATAAAAATATAAAA
1 AAATTATAAAAACTTATAAAAATATAAAA
22767931 TAAATTCATAAAAAACTTATAAAAATAT
1 -AAATT-AT-AAAAACTTATAAAAATAT
22767959 GATTTTTAAA
Statistics
Matches: 102, Mismatches: 31, Indels: 17
0.68 0.21 0.11
Matches are distributed among these distances:
25 3 0.03
26 8 0.08
27 3 0.03
28 5 0.05
29 37 0.36
30 24 0.24
31 5 0.05
32 17 0.17
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.33
Consensus pattern (29 bp):
AAATTATAAAAACTTATAAAAATATAAAA
Found at i:22777816 original size:17 final size:15
Alignment explanation
Indices: 22777794--22777835 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
22777784 TTAATTAGTT
22777794 TAATCTTAATTAAACA
1 TAATCTTAATT-AACA
22777810 CTAATCTTCAATTAACA
1 -TAATCTT-AATTAACA
22777827 TAAT-TTAAT
1 TAATCTTAAT
22777836 GAAATCCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 2 0.08
16 4 0.17
17 11 0.46
18 4 0.17
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATCTTAATTAACA
Found at i:22782502 original size:12 final size:12
Alignment explanation
Indices: 22782474--22782537 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
22782464 TAACTTAATC
*
22782474 GAACATGTTCAC
1 GAACATGTTCAT
*
22782486 AAACATGTTCAT
1 GAACATGTTCAT
* *
22782498 GAACAT-ATAATT
1 GAACATGTTCA-T
22782510 GAACATGTTCAT
1 GAACATGTTCAT
*
22782522 GAACAATGTTAAT
1 GAAC-ATGTTCAT
22782535 GAA
1 GAA
22782538 TAATAAACAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
11 2 0.05
12 27 0.66
13 12 0.29
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (12 bp):
GAACATGTTCAT
Found at i:22782551 original size:4 final size:4
Alignment explanation
Indices: 22782542--22782567 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
22782532 AATGAATAAT
22782542 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
22782568 TAAGTACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:22790504 original size:18 final size:16
Alignment explanation
Indices: 22790472--22790507 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
22790462 ATGGAATAAG
22790472 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
22790488 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
22790506 AA
1 AA
22790508 ATTTTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:22792404 original size:174 final size:175
Alignment explanation
Indices: 22792114--22792466 Score: 636
Period size: 174 Copynumber: 2.0 Consensus size: 175
22792104 TTATTTTTAA
22792114 ATCACTTCACAATAACTATTATATATTTTCCAAAAATAACTTATTACAGTTTTCAAAAGAATTAT
1 ATCACTTCACAATAACTATTATATATTTTCCAAAAATAACTTATTACAGTTTTCAAAAGAATTAT
*
22792179 TTTTAAAATTAAATAATTTCTCTATTAATTAAATTTTGATATTAATTTCAAATCACTTCATAATA
66 TTTTAAAATTAAATAATTTCTCTATTAATTAAAATTTGATATTAATTTCAAATCACTTCATAATA
22792244 ATT-TTACATACTTAAATAATATCACCCAAAGAAAAATTGAGTAT
131 ATTATTACATACTTAAATAATATCACCCAAAGAAAAATTGAGTAT
* * *
22792288 ATCACTTCACAATAACTATTATATATTTTCCAAAAATAATTTATTATAGTTTTTAAAAGAATTAT
1 ATCACTTCACAATAACTATTATATATTTTCCAAAAATAACTTATTACAGTTTTCAAAAGAATTAT
* *
22792353 TTTTTAAATTAAATAATTTCTGTATTAATTAAAATTTGATATTAATTTCAAATCACTTCATAATA
66 TTTTAAAATTAAATAATTTCTCTATTAATTAAAATTTGATATTAATTTCAAATCACTTCATAATA
*
22792418 ATTATTATATACTTAAATAATATCACCCAAAGAAAAATTGAGTAT
131 ATTATTACATACTTAAATAATATCACCCAAAGAAAAATTGAGTAT
22792463 ATCA
1 ATCA
22792467 TAAATATCAT
Statistics
Matches: 171, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
174 127 0.74
175 44 0.26
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (175 bp):
ATCACTTCACAATAACTATTATATATTTTCCAAAAATAACTTATTACAGTTTTCAAAAGAATTAT
TTTTAAAATTAAATAATTTCTCTATTAATTAAAATTTGATATTAATTTCAAATCACTTCATAATA
ATTATTACATACTTAAATAATATCACCCAAAGAAAAATTGAGTAT
Found at i:22798766 original size:19 final size:20
Alignment explanation
Indices: 22798731--22798772 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
22798721 TTTTTATTTT
22798731 AATTTTTTATAACATGTATA
1 AATTTTTTATAACATGTATA
*
22798751 AATTTTTTAT-ATATGTATA
1 AATTTTTTATAACATGTATA
22798770 AAT
1 AAT
22798773 AGACAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (20 bp):
AATTTTTTATAACATGTATA
Found at i:22799379 original size:14 final size:14
Alignment explanation
Indices: 22799360--22799411 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
22799350 TGATCAAATC
22799360 AAAATTACATGTAT
1 AAAATTACATGTAT
***
22799374 AAAATTACACAAAAT
1 AAAATTACA-TGTAT
22799389 CAAAATT-CATGTAT
1 -AAAATTACATGTAT
22799403 AAAATTACA
1 AAAATTACA
22799412 CATTAAACCA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
13 6 0.21
14 13 0.45
15 4 0.14
16 6 0.21
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.29
Consensus pattern (14 bp):
AAAATTACATGTAT
Found at i:22799400 original size:29 final size:30
Alignment explanation
Indices: 22799355--22799413 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
22799345 GAATTTGATC
22799355 AAATCAAAATTACATGTATAAAATTACACA
1 AAATCAAAATTACATGTATAAAATTACACA
22799385 AAATCAAAATT-CATGTATAAAATTACACA
1 AAATCAAAATTACATGTATAAAATTACACA
22799414 TTAAACCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATCAAAATTACATGTATAAAATTACACA
Found at i:22799502 original size:23 final size:24
Alignment explanation
Indices: 22799444--22799502 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 24
22799434 TAATTTCGAG
*
22799444 ATTTAAATAAAATTATGAATTATAT
1 ATTTAAATAAAATTA-GAATTACAT
* * * *
22799469 ATTGAACTAAACTTA-CATTACAT
1 ATTTAAATAAAATTAGAATTACAT
22799492 ATTTAAATAAA
1 ATTTAAATAAA
22799503 TAATTTGACA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 15 0.56
25 12 0.44
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (24 bp):
ATTTAAATAAAATTAGAATTACAT
Found at i:22803203 original size:25 final size:24
Alignment explanation
Indices: 22803153--22803208 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 24
22803143 TTTAAGCCCC
* **
22803153 ATATTATTTTTTTAAAATTTTTTA
1 ATATTATTATTTTAAAATTTAATA
*
22803177 ATATATATTATTTTAATATTTAATA
1 ATAT-TATTATTTTAAAATTTAATA
*
22803202 ATTTTAT
1 ATATTAT
22803209 ACATGTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATTATTATTTTAAAATTTAATA
Found at i:22804825 original size:16 final size:16
Alignment explanation
Indices: 22804804--22804906 Score: 73
Period size: 16 Copynumber: 5.8 Consensus size: 16
22804794 ACACAACTTT
22804804 TAGGCTTTGTGCCTAG
1 TAGGCTTTGTGCCTAG
*
22804820 TAGGCTTCGTGCCGGT-G
1 TAGGCTTTGTGCC--TAG
22804837 TTTTCAGGCTTTGTGCCTAG
1 ---T-AGGCTTTGTGCCTAG
*
22804857 TAGGCTTTGTGCCAGTATTT
1 TAGGCTTTGTGCC--TA--G
22804877 TCAGGCTTTGTGCCTAG
1 T-AGGCTTTGTGCCTAG
*
22804894 TAGGCTTCGTGCC
1 TAGGCTTTGTGCC
22804907 GGTGTTTTCA
Statistics
Matches: 70, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
16 35 0.50
17 3 0.04
18 3 0.04
19 3 0.04
20 3 0.04
21 23 0.33
ACGTcount: A:0.11, C:0.21, G:0.30, T:0.38
Consensus pattern (16 bp):
TAGGCTTTGTGCCTAG
Found at i:22804855 original size:37 final size:37
Alignment explanation
Indices: 22804801--22804964 Score: 240
Period size: 37 Copynumber: 4.5 Consensus size: 37
22804791 CTTACACAAC
22804801 TTTT-AGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
* * *
22804837 TTTTCAGGCTTTGTGCCTAGTAGGCTTTGTGCCAGTA
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
22804874 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
* * **
22804911 TTTTCAGACTTTGTGCCTAGTAGGATTTATGCCGGTG
1 TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
* *
22804948 TTTTCAAGCTTCGTGCC
1 TTTTCAGGCTTTGTGCC
22804965 GGTGTTTTTA
Statistics
Matches: 114, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 4 0.04
37 110 0.96
ACGTcount: A:0.12, C:0.20, G:0.29, T:0.40
Consensus pattern (37 bp):
TTTTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
Found at i:22804884 original size:21 final size:21
Alignment explanation
Indices: 22804821--22804895 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
22804811 TGTGCCTAGT
* * *
22804821 AGGCTTCGTGCCGGTGTTTTC
1 AGGCTTTGTGCCAGTATTTTC
*
22804842 AGGCTTTGTGCC--TA--GT-
1 AGGCTTTGTGCCAGTATTTTC
22804858 AGGCTTTGTGCCAGTATTTTC
1 AGGCTTTGTGCCAGTATTTTC
22804879 AGGCTTTGTGCCTAGTA
1 AGGCTTTGTGCC-AGTA
22804896 GGCTTCGTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
16 12 0.27
17 1 0.02
18 2 0.05
19 1 0.02
20 1 0.02
21 23 0.52
22 4 0.09
ACGTcount: A:0.12, C:0.20, G:0.29, T:0.39
Consensus pattern (21 bp):
AGGCTTTGTGCCAGTATTTTC
Found at i:22814813 original size:39 final size:40
Alignment explanation
Indices: 22814768--22815114 Score: 168
Period size: 42 Copynumber: 8.5 Consensus size: 40
22814758 GTTTGAAACG
* *
22814768 AAAACGCCACAAAAGGTAAAGCAATAGCGGCG-TTTCCCA
1 AAAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTCCCA
* * * *
22814807 TAAACGCCGTAAAAAGTAAAGCAATAGCATCGTTTTCCCA
1 AAAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTCCCA
* * * ***
22814847 AAAAC-CCTGCAAAAGGTAAAGGAAAAG-TGACGTTTATGGGA
1 AAAACGCC-GCAAAAGGTAAAGCAATAGCAG-CGTTT-TCCCA
* * ***
22814888 AAAACGCCGCAAAAGGTAAAGAGCAATAACGGCGTTTAT-GGG
1 AAAACGCCGCAAAAGGT-AA-AGCAATAGCAGCGTTT-TCCCA
* * ** *
22814930 AAAATGTCGCAAAAGGTAAAGAGCAATAGTGGCGTTTAT--GA
1 AAAACGCCGCAAAAGGT-AA-AGCAATAGCAGCGTTT-TCCCA
* * *
22814971 GAAAACGCCGGAAAAGGTAAAG-TATAGCAGCGTTTTACCA
1 -AAAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTCCCA
* * * * ***
22815011 TAAACGCCACAAAAGGTAAAACAATAGCAGTGTTTATGGAA
1 AAAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTT-TCCCA
* * * *
22815052 AAAATGCCGCAAAAGGTAAAGAGCATTAGCGGCATTTTCCCCA
1 AAAACGCCGCAAAAGGT-AA-AGCAATAGCAGCGTTTT-CCCA
* **
22815095 TAAACGCCGTTAAAGGTAAA
1 AAAACGCCGCAAAAGGTAAA
22815115 TTGCAAAACC
Statistics
Matches: 235, Mismatches: 57, Indels: 30
0.73 0.18 0.09
Matches are distributed among these distances:
38 1 0.00
39 55 0.23
40 45 0.19
41 36 0.15
42 60 0.26
43 37 0.16
44 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (40 bp):
AAAACGCCGCAAAAGGTAAAGCAATAGCAGCGTTTTCCCA
Found at i:22814844 original size:40 final size:39
Alignment explanation
Indices: 22814768--22814851 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
22814758 GTTTGAAACG
* *
22814768 AAAACGCCACAAAAGGTAAAGCAATAGCGGCGTTTCCCA
1 AAAACGCCACAAAAAGTAAAGCAATAGCAGCGTTTCCCA
* ** *
22814807 TAAACGCCGTAAAAAGTAAAGCAATAGCATCGTTTTCCCA
1 AAAACGCCACAAAAAGTAAAGCAATAGCAGCG-TTTCCCA
22814847 AAAAC
1 AAAAC
22814852 CCTGCAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 26 0.70
40 11 0.30
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.17
Consensus pattern (39 bp):
AAAACGCCACAAAAAGTAAAGCAATAGCAGCGTTTCCCA
Found at i:22814950 original size:42 final size:42
Alignment explanation
Indices: 22814877--22815076 Score: 169
Period size: 42 Copynumber: 4.8 Consensus size: 42
22814867 GGAAAAGTGA
22814877 CGTTTATGGGAAAAACGCCGCAAAAGGTAAAGAGCAATAACGG
1 CGTTTATGGG-AAAACGCCGCAAAAGGTAAAGAGCAATAACGG
* * **
22814920 CGTTTATGGGAAAATGTCGCAAAAGGTAAAGAGCAATAGTGG
1 CGTTTATGGGAAAACGCCGCAAAAGGTAAAGAGCAATAACGG
* * * * *
22814962 CGTTTATGAGAAAACGCCGGAAAAGGT-AA-AG-TATAGCAG
1 CGTTTATGGGAAAACGCCGCAAAAGGTAAAGAGCAATAACGG
*** * * *
22815001 CGTTT-TACCATAAACGCCACAAAAGGTAAA-A-CAATAGCAG
1 CGTTTATGGGA-AAACGCCGCAAAAGGTAAAGAGCAATAACGG
* * *
22815041 TGTTTATGGAAAAAATGCCGCAAAAGGTAAAGAGCA
1 CGTTTATGG-GAAAACGCCGCAAAAGGTAAAGAGCA
22815077 TTAGCGGCAT
Statistics
Matches: 127, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
38 2 0.02
39 24 0.19
40 16 0.13
41 20 0.16
42 53 0.42
43 12 0.09
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (42 bp):
CGTTTATGGGAAAACGCCGCAAAAGGTAAAGAGCAATAACGG
Found at i:22815101 original size:123 final size:123
Alignment explanation
Indices: 22814889--22815114 Score: 278
Period size: 122 Copynumber: 1.8 Consensus size: 123
22814879 TTTATGGGAA
* * * *
22814889 AAACGCCGCAAAAGGTAAAGAGCAATAACGGCGTTTATGGGAAAATGTCGCAAAAGGTAAAGAGC
1 AAACGCCACAAAAGGTAAAGAGCAATAACAGCGTTTATGGAAAAATGCCGCAAAAGGTAAAGAGC
* * * *
22814954 AATAGTGGCGTTTATGAGAAAACGCCGGAAAAGGTAAAGTATAGCAGCGTTTTACCAT
66 AATAGCGGCATTTATCACAAAACGCCGGAAAAGGTAAAGTATAGCAGCGTTTTACCAT
* *
22815012 AAACGCCACAAAAGGTAAA-A-CAATAGCAGTGTTTATGGAAAAAATGCCGCAAAAGGTAAAGAG
1 AAACGCCACAAAAGGTAAAGAGCAATAACAGCGTTTATGG-AAAAATGCCGCAAAAGGTAAAGAG
* * **
22815075 CATTAGCGGCATTT-TCCCCATAAACGCCGTTAAAGGTAAA
65 CAATAGCGGCATTTAT-CACA-AAACGCCGGAAAAGGTAAA
22815115 TTGCAAAACC
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
121 16 0.19
122 35 0.41
123 35 0.41
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (123 bp):
AAACGCCACAAAAGGTAAAGAGCAATAACAGCGTTTATGGAAAAATGCCGCAAAAGGTAAAGAGC
AATAGCGGCATTTATCACAAAACGCCGGAAAAGGTAAAGTATAGCAGCGTTTTACCAT
Found at i:22823446 original size:15 final size:15
Alignment explanation
Indices: 22823426--22823458 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
22823416 ATTTGAAGTT
*
22823426 ATTGGTTGGATTTGA
1 ATTGGTTAGATTTGA
22823441 ATTGGTTAGATTTGA
1 ATTGGTTAGATTTGA
22823456 ATT
1 ATT
22823459 TACAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
ATTGGTTAGATTTGA
Found at i:22823622 original size:42 final size:40
Alignment explanation
Indices: 22823550--22823791 Score: 261
Period size: 42 Copynumber: 5.8 Consensus size: 40
22823540 GGAAAAAACC
**
22823550 CCGCTAAAGACCATGTTCTATAGCAACGTTTGTGAGAAAAA
1 CCGCTAAAGACCATGTTCTATAGCGGCGTTTGTG-GAAAAA
**
22823591 CGCTGCTAAAGA-CATGTTCTATAGCGGCGTTTGTGGGCAAGCA
1 C-C-GCTAAAGACCATGTTCTATAGCGGCGTTTGT-GG-AAAAA
* * *
22823634 CCGATAAAGACCATGTTCTATAGCGGTGTTCGTGGAAAAACA
1 CCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGG-AAAA-A
*
22823676 CCGCTAAAGACCATGTTCTATAGTGGCGTTTGTGGAAAAGTA
1 CCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGAAAA--A
** *
22823718 CCGCTAAAGACCATGTTCTATAATGGCGTTTGTGGGAAAAG
1 CCGCTAAAGACCATGTTCTATAGCGGCGTTTGT-GGAAAAA
*
22823759 CGTCGCTAAAGATCATGTTCTATAGCGGCGTTT
1 C--CGCTAAAGACCATGTTCTATAGCGGCGTTT
22823792 TCCTACATAA
Statistics
Matches: 171, Mismatches: 20, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
41 17 0.10
42 108 0.63
43 46 0.27
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (40 bp):
CCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGAAAAA
Found at i:22823689 original size:126 final size:126
Alignment explanation
Indices: 22823543--22823786 Score: 332
Period size: 126 Copynumber: 1.9 Consensus size: 126
22823533 TGCTTTTGGA
*
22823543 AAAAACCCCGCTAAAGACCATGTTCTATAGCAACGTTTGTGAGAAAA-ACGCTGCTAAAGA-CAT
1 AAAAACACCGCTAAAGACCATGTTCTATAGCAACGTTTGTG-GAAAAGAC-C-GCTAAAGACCAT
* *
22823606 GTTCTATAGCGGCGTTTGTGGG-CAAGCACCGATAAAGACCATGTTCTATAGCGGTGTTCGTGG
63 GTTCTATAACGGCGTTTGTGGGAAAAGCACCGATAAAGACCATGTTCTATAGCGGTGTTCGTGG
***
22823669 AAAAACACCGCTAAAGACCATGTTCTATAGTGGCGTTTGTGGAAAAGTACCGCTAAAGACCATGT
1 AAAAACACCGCTAAAGACCATGTTCTATAGCAACGTTTGTGGAAAAG-ACCGCTAAAGACCATGT
* ** * *
22823734 TCTATAATGGCGTTTGTGGGAAAAGCGTCGCTAAAGATCATGTTCTATAGCGG
65 TCTATAACGGCGTTTGTGGGAAAAGCACCGATAAAGACCATGTTCTATAGCGG
22823787 CGTTTTCCTA
Statistics
Matches: 103, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
125 13 0.13
126 61 0.59
127 29 0.28
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (126 bp):
AAAAACACCGCTAAAGACCATGTTCTATAGCAACGTTTGTGGAAAAGACCGCTAAAGACCATGTT
CTATAACGGCGTTTGTGGGAAAAGCACCGATAAAGACCATGTTCTATAGCGGTGTTCGTGG
Found at i:22823695 original size:84 final size:83
Alignment explanation
Indices: 22823554--22823791 Score: 305
Period size: 84 Copynumber: 2.8 Consensus size: 83
22823544 AAAACCCCGC
** *
22823554 TAAAGACCATGTTCTATAGCAACGTTTGTGAGAAAAACGCTGCTAAAGACATGTTCTATAGCGGC
1 TAAAGACCATGTTCTATAGCGGCGTTTGTG-GAAAAACGCCGCTAAAGACATGTTCTATAGCGGC
**
22823619 GTTTGTGGGCAAGCACCGA
65 GTTTGTGGAAAAGCACCGA
* * * *
22823638 TAAAGACCATGTTCTATAGCGGTGTTCGTGGAAAAACACCGCTAAAGACCATGTTCTATAGTGGC
1 TAAAGACCATGTTCTATAGCGGCGTTTGTGGAAAAACGCCGCTAAAGA-CATGTTCTATAGCGGC
* *
22823703 GTTTGTGGAAAAGTACCGC
65 GTTTGTGGAAAAGCACCGA
** * *
22823722 TAAAGACCATGTTCTATAATGGCGTTTGTGGGAAAAGCGTCGCTAAAGATCATGTTCTATAGCGG
1 TAAAGACCATGTTCTATAGCGGCGTTTGT-GGAAAAACGCCGCTAAAGA-CATGTTCTATAGCGG
22823787 CGTTT
64 CGTTT
22823792 TCCTACATAA
Statistics
Matches: 132, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
83 16 0.12
84 81 0.61
85 35 0.27
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (83 bp):
TAAAGACCATGTTCTATAGCGGCGTTTGTGGAAAAACGCCGCTAAAGACATGTTCTATAGCGGCG
TTTGTGGAAAAGCACCGA
Found at i:22828521 original size:40 final size:40
Alignment explanation
Indices: 22828403--22828521 Score: 139
Period size: 40 Copynumber: 3.0 Consensus size: 40
22828393 ATGTTGGAAT
*
22828403 AAACTCAAGCTACGGCTTAGCAGGCTATGAGTCGGTGTCA
1 AAACTCAAGCTACGGCTTAGCAGGCTATGAGCCGGTGTCA
* * * * *
22828443 AAACTCAAGCAACGGCATAGCATGCAATGAGCTGGTGTCA
1 AAACTCAAGCTACGGCTTAGCAGGCTATGAGCCGGTGTCA
* * * * *
22828483 AAACTCAAGGTACAGCTTAGAAGGCTTTGAGCCAGTGTC
1 AAACTCAAGCTACGGCTTAGCAGGCTATGAGCCGGTGTC
22828522 TAATTTCAAG
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (40 bp):
AAACTCAAGCTACGGCTTAGCAGGCTATGAGCCGGTGTCA
Found at i:22828595 original size:65 final size:65
Alignment explanation
Indices: 22828469--22828597 Score: 156
Period size: 65 Copynumber: 2.0 Consensus size: 65
22828459 ATAGCATGCA
* * * *
22828469 ATGAGCTGGTGTCAAAACTCAAGGTACAGCTTAGAAGGCTTTGAGCCAGTGTCTAATTTCAAGCT
1 ATGAGCTGGTGACAAAACTCAAGCTACAGCTTAGAAGGCTATGAGCCAGTGTCTAAATTCAAGCT
* *
22828534 ATGAGCTGGTGACTAAACTCAAGCTATC-GCTTAGCAA-GCTATGAGCCGGTGT-TGAAATTCAA
1 ATGAGCTGGTGACAAAACTCAAGCTA-CAGCTTAG-AAGGCTATGAGCCAGTGTCT-AAATTCAA
22828596 GC
63 GC
22828598 CAGGTTATGG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
64 1 0.02
65 51 0.93
66 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (65 bp):
ATGAGCTGGTGACAAAACTCAAGCTACAGCTTAGAAGGCTATGAGCCAGTGTCTAAATTCAAGCT
Found at i:22831680 original size:19 final size:19
Alignment explanation
Indices: 22831643--22831681 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
22831633 TGAAGGAAAT
*
22831643 AAAAACTTAATATAATAAA
1 AAAAACTTAATAAAATAAA
22831662 AAAAAC-TAATAAAACTAAA
1 AAAAACTTAATAAAA-TAAA
22831681 A
1 A
22831682 CTCTAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAACTTAATAAAATAAA
Found at i:22834004 original size:3 final size:3
Alignment explanation
Indices: 22833996--22834026 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
22833986 CAAATGAAAT
22833996 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
22834027 GAATGCGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:22835738 original size:15 final size:16
Alignment explanation
Indices: 22835714--22835752 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
22835704 AAGTAGCCTA
*
22835714 TCTTTTTTCCTT-CTT
1 TCTTTCTTCCTTCCTT
22835729 TCTTTCTTCCTTCCTT
1 TCTTTCTTCCTTCCTT
22835745 TC-TTCTTC
1 TCTTTCTTC
22835753 TTGTTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
TCTTTCTTCCTTCCTT
Found at i:22844249 original size:20 final size:19
Alignment explanation
Indices: 22844220--22844259 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
22844210 AACTTCGAAT
22844220 AATAAGGAAAAACAAAGATA
1 AATAAGGAAAAA-AAAGATA
* *
22844240 AATAATGAAATAAAAGATA
1 AATAAGGAAAAAAAAGATA
22844259 A
1 A
22844260 GAAGTGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.70, C:0.03, G:0.12, T:0.15
Consensus pattern (19 bp):
AATAAGGAAAAAAAAGATA
Found at i:22849434 original size:235 final size:235
Alignment explanation
Indices: 22849154--22849789 Score: 612
Period size: 233 Copynumber: 2.7 Consensus size: 235
22849144 TGAAATTTGC
* * * * *
22849154 ATTACGAACCAACTTCCACTAACAAAGTGAATTCATCACAGAGGTTCATGATAACC-TATT-AAC
1 ATTACGAACCAACTTCCTCTAAGAAAGCGAATTCATGAAAGAGGTTCATGAT-ACCATATTAAAC
* * *
22849217 CTTTTAAAACCAAAGTAAATAAAAAAAATTAACCGTGAATAAACCTCACAGCAGCTATGAAGCTC
65 CTTTAAAAACCAAAGCAAA-AAAAAAAATTAACCGTGAATAAACCTCACAGCAGCTAGGAAGCTC
* * *
22849282 ACTCGAATTAAGTAATTCAATTGAACTTCAAAAAA-AAACGAC-TAAAACTTGCATAGTTTCTTC
129 ACTCGAATTAAGTAATTCAATTGAACTTCAAAAAATAAA-GACGGAAAACTTACAAAG-TTCTTC
* *
22849345 TACAGATACCCTAATTCAACCAAATTTC-TAGAACCTCGCATCTA
192 TACACATACCCTAATTCAACCAAATTTCAT-GAAACTCGCATCTA
* * * * ** *
22849389 ATTACGAACTAACTTCCTCTAAGAAAGCGATTTAATGAAAGAGGTTTATGACGCCGTATTAAAAC
1 ATTACGAACCAACTTCCTCTAAGAAAGCGAATTCATGAAAGAGGTTCATGATACCATATT-AAAC
* * * * * *** ** *
22849454 C--CAAAATCCTAAGGAAAGAAAAGGCTTAAGTGCGAGA-AAACCTCACAG--GCTAGGAAGCTC
65 CTTTAAAAACCAAAGCAAAAAAAAAAATTAACCGTGA-ATAAACCTCACAGCAGCTAGGAAGCTC
* * *
22849514 GCTCAAATTAAGTAATTCAATTGAACTTTCAAAAAATAAAGACGGAAAACTTACAAAGTTCTTGT
129 ACTCGAATTAAGTAATTCAATTGAAC-TTCAAAAAATAAAGACGGAAAACTTACAAAGTTCTTCT
22849579 ACACATACCCTAATTCAACCAAATTTCATGAAACTCGCATCTA
193 ACACATACCCTAATTCAACCAAATTTCATGAAACTCGCATCTA
* * *
22849622 ATTACGAACCAACTTCCTCT-GGCAAAGCGAATTCATAGAAAAGAGGTTCACGATACCATTTTAA
1 ATTACGAACCAACTTCCTCTAAG-AAAGCGAATTCAT-G-AAAGAGGTTCATGATACCATATTAA
* * * *
22849686 AACTAAAAATACTAAGAAAACACA-CAAAAAAAAAAAACCTTAATCGTGAATAAACCTCACAGCA
63 ACCT-----T--TAA-AAACCAAAGC-AAAAAAAAAAA--TTAACCGTGAATAAACCTCACAGCA
*
22849750 ACTAGGAAGCTCACTCGAATTAAGTAATTCAATTGAACTT
117 GCTAGGAAGCTCACTCGAATTAAGTAATTCAATTGAACTT
22849790 TTTAAGAAAA
Statistics
Matches: 315, Mismatches: 59, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
232 36 0.11
233 87 0.28
234 44 0.14
235 75 0.24
237 4 0.01
243 2 0.01
244 11 0.03
245 1 0.00
246 18 0.06
247 2 0.01
248 35 0.11
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (235 bp):
ATTACGAACCAACTTCCTCTAAGAAAGCGAATTCATGAAAGAGGTTCATGATACCATATTAAACC
TTTAAAAACCAAAGCAAAAAAAAAAATTAACCGTGAATAAACCTCACAGCAGCTAGGAAGCTCAC
TCGAATTAAGTAATTCAATTGAACTTCAAAAAATAAAGACGGAAAACTTACAAAGTTCTTCTACA
CATACCCTAATTCAACCAAATTTCATGAAACTCGCATCTA
Found at i:22852021 original size:13 final size:15
Alignment explanation
Indices: 22851987--22852023 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
22851977 TAAATATCAC
22851987 TTAATTAATATTAAAG
1 TTAATT-ATATTAAAG
22852003 TTAATTATATT-AA-
1 TTAATTATATTAAAG
22852016 TTAATTAT
1 TTAATTAT
22852024 TATTTTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 2 0.10
15 5 0.24
16 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAATTATATTAAAG
Found at i:22852682 original size:15 final size:15
Alignment explanation
Indices: 22852646--22852683 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
22852636 GGTTGCTCTC
*
22852646 CATAATT-TTTTTTT
1 CATAATTATTCTTTT
22852660 CATAAATTATTCTTTT
1 CAT-AATTATTCTTTT
22852676 CATAATTA
1 CATAATTA
22852684 AATTGATCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.43
16 9 0.43
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (15 bp):
CATAATTATTCTTTT
Found at i:22854928 original size:30 final size:30
Alignment explanation
Indices: 22854892--22854948 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
22854882 ACCAATCTCA
22854892 AATAAGGCAAAG-AAGCATTCAAAGAAGACG
1 AATAAGGCAAAGAAAGCATT-AAAGAAGACG
*
22854922 AATAAGGTAAAGAAAGCATTAAAGAAG
1 AATAAGGCAAAGAAAGCATTAAAGAAG
22854949 GCAAACTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.56, C:0.09, G:0.23, T:0.12
Consensus pattern (30 bp):
AATAAGGCAAAGAAAGCATTAAAGAAGACG
Found at i:22872937 original size:30 final size:31
Alignment explanation
Indices: 22872886--22872952 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
22872876 TTGAAAATTT
*
22872886 AGAATTT-AGTTCTTATATTTTT-ATTTTCA
1 AGAATTTAAGTTCTTATATTTTTAAATTTCA
*
22872915 AGAATTTAATTTCTT-TATTTTTTAAATTTCA
1 AGAATTTAAGTTCTTATA-TTTTTAAATTTCA
22872946 A-AATTTA
1 AGAATTTA
22872953 GGCCTAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 9 0.27
30 17 0.52
31 7 0.21
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (31 bp):
AGAATTTAAGTTCTTATATTTTTAAATTTCA
Found at i:22873130 original size:30 final size:30
Alignment explanation
Indices: 22873103--22873163 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
22873093 GATTAAATTT
*
22873103 TAAAATATGAAAAGTAAA-GTGACTAAATTCC
1 TAAAA-ATAAAAAGTAAATG-GACTAAATTCC
*
22873134 TAAAAATAAAAAGTACATGGACTAAATTCC
1 TAAAAATAAAAAGTAAATGGACTAAATTCC
22873164 AAATTTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (30 bp):
TAAAAATAAAAAGTAAATGGACTAAATTCC
Found at i:22873199 original size:30 final size:31
Alignment explanation
Indices: 22873143--22873200 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
22873133 CTAAAAATAA
**
22873143 AAAGTACATGGACTAAATTCCAAATTTTTGT
1 AAAGTACATGGACTAAATGACAAATTTTTGT
*
22873174 AAAGTACATGGACT-TATGACAAATTTT
1 AAAGTACATGGACTAAATGACAAATTTT
22873201 AATTGGTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (31 bp):
AAAGTACATGGACTAAATGACAAATTTTTGT
Found at i:22873468 original size:16 final size:17
Alignment explanation
Indices: 22873449--22873490 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
22873439 TACATGTGAA
22873449 AAATAATAAAATAAA-T
1 AAATAATAAAATAAATT
*
22873465 AAATAATAAATTAAATT
1 AAATAATAAAATAAATT
*
22873482 AAAAAATAA
1 AAATAATAA
22873491 CTTTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAATAAAATAAATT
Found at i:22879708 original size:17 final size:17
Alignment explanation
Indices: 22879686--22879719 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22879676 ACTTTTAAGA
22879686 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
22879703 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
22879720 CAATTTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:22882894 original size:28 final size:24
Alignment explanation
Indices: 22882854--22882910 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 24
22882844 AACTTTTAGC
22882854 TTTATTCATATAAACAATGCAATTAAAA
1 TTTATTCATATAAA-AAT-C-A-TAAAA
22882882 TTTATTC-TAATAAAAATCATAAAA
1 TTTATTCAT-ATAAAAATCATAAAA
22882906 TTTAT
1 TTTAT
22882911 CACTATGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 10 0.36
25 1 0.04
26 1 0.04
27 4 0.14
28 12 0.43
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTATTCATATAAAAATCATAAAA
Found at i:22884227 original size:29 final size:28
Alignment explanation
Indices: 22884195--22884294 Score: 85
Period size: 28 Copynumber: 3.5 Consensus size: 28
22884185 TGGTGAAATC
*
22884195 GAGGTTAAAAATGGGATTTAGGGAAGTTT
1 GAGGTT-AAAATGGGATTTAGGGAAGATT
* * **
22884224 GAGGGTAAAATGGTAATTTTAATGAA-ATT
1 GAGGTTAAAATGG-GA-TTTAGGGAAGATT
*
22884253 GGGGTTTAAAATGGGATTTAGGGAAGATT
1 GAGG-TTAAAATGGGATTTAGGGAAGATT
* *
22884282 GGGGGTAAAATGG
1 GAGGTTAAAATGG
22884295 TAATTTTGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
28 22 0.39
29 19 0.34
30 15 0.27
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (28 bp):
GAGGTTAAAATGGGATTTAGGGAAGATT
Found at i:22884238 original size:59 final size:58
Alignment explanation
Indices: 22884167--22884303 Score: 202
Period size: 58 Copynumber: 2.3 Consensus size: 58
22884157 GGATACCCGG
* *
22884167 GGGTAAAATGGTAGATTTTGGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAGTTTGA
1 GGGTAAAATGGTA-ATTTTGATGAAATCGAGGTTAAAAATGGGATTTAGGGAAGATTGA
* * * * *
22884226 GGGTAAAATGGTAATTTTAATGAAATTGGGGTTTAAAATGGGATTTAGGGAAGATTGG
1 GGGTAAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGGATTTAGGGAAGATTGA
22884284 GGGTAAAATGGTAATTTTGA
1 GGGTAAAATGGTAATTTTGA
22884304 AAGTTTCGGG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 57 0.81
59 13 0.19
ACGTcount: A:0.34, C:0.01, G:0.33, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGGATTTAGGGAAGATTGA
Found at i:22884257 original size:28 final size:30
Alignment explanation
Indices: 22884211--22884301 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
22884201 AAAAATGGGA
* * *
22884211 TTTAGGGAAGTTTGAGGGTAAAATGGTAAT
1 TTTAAGGAAGATTGGGGGTAAAATGGTAAT
* * *
22884241 TTTAATGAA-ATTGGGGTTTAAAATGG-GA-
1 TTTAAGGAAGATTGGGG-GTAAAATGGTAAT
*
22884269 TTTAGGGAAGATTGGGGGTAAAATGGTAAT
1 TTTAAGGAAGATTGGGGGTAAAATGGTAAT
22884299 TTT
1 TTT
22884302 GAAAGTTTCG
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
28 15 0.32
29 14 0.30
30 18 0.38
ACGTcount: A:0.33, C:0.00, G:0.32, T:0.35
Consensus pattern (30 bp):
TTTAAGGAAGATTGGGGGTAAAATGGTAAT
Found at i:22884300 original size:29 final size:28
Alignment explanation
Indices: 22884165--22884300 Score: 96
Period size: 29 Copynumber: 4.7 Consensus size: 28
22884155 TTGGATACCC
* *
22884165 GGGGGTAAAATGGTAGATTTTGGTGAAATC
1 GGGGGTAAAATGGTA-ATTTAGG-GAAATT
* * * *
22884195 GAGGTTAAAAATGG-GATTTAGGGAAGTTT
1 GGGGGT-AAAATGGTAATTTAGGGAA-ATT
* **
22884224 GAGGGTAAAATGGTAATTTTAATGAAATT
1 GGGGGTAAAATGGTAA-TTTAGGGAAATT
* *
22884253 GGGGTTTAAAATGG-GATTTAGGGAAGATT
1 GGGG-GTAAAATGGTAATTTAGGGAA-ATT
22884282 GGGGGTAAAATGGTAATTT
1 GGGGGTAAAATGGTAATTT
22884301 TGAAAGTTTC
Statistics
Matches: 81, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
28 25 0.31
29 30 0.37
30 19 0.23
31 7 0.09
ACGTcount: A:0.34, C:0.01, G:0.34, T:0.32
Consensus pattern (28 bp):
GGGGGTAAAATGGTAATTTAGGGAAATT
Found at i:22884372 original size:30 final size:30
Alignment explanation
Indices: 22884338--22884600 Score: 291
Period size: 30 Copynumber: 8.8 Consensus size: 30
22884328 TTTTTGGAAA
*
22884338 TTTTAGGGTCAAAATATGATTTTAGAAAAG
1 TTTTAGGGTCAAAATATAATTTTAGAAAAG
* *
22884368 TTTTAGGGTTAAAATGTAATTTTAGAAAAG
1 TTTTAGGGTCAAAATATAATTTTAGAAAAG
* * * *
22884398 TTTTGGGGTTAAAATGTAATTTTGGAAAAG
1 TTTTAGGGTCAAAATATAATTTTAGAAAAG
* *
22884428 TTTTAGGGTTAAAATGTAATTTCTAG-AAAG
1 TTTTAGGGTCAAAATATAATTT-TAGAAAAG
* * * *
22884458 TTTTGGGGTTAAAATAAAATTTCAGAAAAG
1 TTTTAGGGTCAAAATATAATTTTAGAAAAG
*
22884488 TTTT-GAGGTCAAAATATAATTTTGGAAAAG
1 TTTTAG-GGTCAAAATATAATTTTAGAAAAG
* *
22884518 -TTTAGGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTA-GGGTCAAAATATAATTTTAGAAAAG
*
22884548 TTTTGGGGTCAAAATATAATTTTTA-AAAAG
1 TTTTAGGGTCAAAATATAA-TTTTAGAAAAG
* *
22884578 TTTTGGGGTCAAAATGTAATTTT
1 TTTTAGGGTCAAAATATAATTTT
22884601 TGGACAATTT
Statistics
Matches: 206, Mismatches: 20, Indels: 15
0.85 0.08 0.06
Matches are distributed among these distances:
29 10 0.05
30 186 0.90
31 10 0.05
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (30 bp):
TTTTAGGGTCAAAATATAATTTTAGAAAAG
Found at i:22884419 original size:90 final size:89
Alignment explanation
Indices: 22884329--22884610 Score: 372
Period size: 90 Copynumber: 3.1 Consensus size: 89
22884319 AAAAAAAATT
* * * *
22884329 TTTTGG-AAATTTTAGGGTCAAAATATGATTTTAGAAAAGTTTTAGGGTTAAAATGTAATTTTAG
1 TTTTGGAAAATTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTTAAAATATAATTTTAG
*
22884393 AAAAGTTTTGGGGTTAAAATGTAA
66 AAAAGTTTTGGGGTCAAAATGTAA
* * *
22884417 TTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTCTAG-AAAGTTTTGGGGTTAAAATAAAATTTC
1 TTTTGGAAAA-TTTTAGGGTCAAAATGTAATTT-TAGAAAAGTTTTGGGGTTAAAATATAATTTT
* *
22884481 AGAAAAGTTTTGAGGTCAAAATATAA
64 AGAAAAGTTTTGGGGTCAAAATGTAA
* * *
22884507 TTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTT
1 TTTTGGAAAATTTTA-GGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTTAAAATATAA-TTTT
22884572 A-AAAAGTTTTGGGGTCAAAATGTAA
64 AGAAAAGTTTTGGGGTCAAAATGTAA
*
22884597 TTTTTGGACAATTT
1 -TTTTGGAAAATTT
22884611 AAGGACTTAC
Statistics
Matches: 167, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
88 6 0.04
89 9 0.05
90 134 0.80
91 18 0.11
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (89 bp):
TTTTGGAAAATTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTTAAAATATAATTTTAG
AAAAGTTTTGGGGTCAAAATGTAA
Found at i:22884420 original size:60 final size:60
Alignment explanation
Indices: 22884338--22884600 Score: 325
Period size: 60 Copynumber: 4.4 Consensus size: 60
22884328 TTTTTGGAAA
* * * * *
22884338 TTTTAGGGTCAAAATATGATTTTAGAAAAGTTTTAGGGTTAAAATGTAATTTTAGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTCAAAATATAATTTTAGAAAAG
* * * *
22884398 TTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTCTAG-AAAG
1 TTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTCAAAATATAATTT-TAGAAAAG
* ** * *
22884458 TTTTGGGGTTAAAATAAAATTTCAGAAAAGTTTT-GAGGTCAAAATATAATTTTGGAAAAG
1 TTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTTAG-GGTCAAAATATAATTTTAGAAAAG
* * *
22884518 TTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTTA-AAAAG
1 TTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTCAAAATATAA-TTTTAGAAAAG
22884578 TTTTGGGGTCAAAATGTAATTTT
1 TTTTGGGGTCAAAATGTAATTTT
22884601 TGGACAATTT
Statistics
Matches: 178, Mismatches: 20, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
59 3 0.02
60 167 0.94
61 8 0.04
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (60 bp):
TTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTTAGGGTCAAAATATAATTTTAGAAAAG
Found at i:22885727 original size:22 final size:22
Alignment explanation
Indices: 22885683--22885733 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
22885673 CGACGTACGA
* ** *
22885683 GCGAAACTCCGGCGGTGGTGGT
1 GCGAGACTCCGGCCATGGCGGT
22885705 GCGAGACTCCGGCCATGGCGGT
1 GCGAGACTCCGGCCATGGCGGT
22885727 GCGAGAC
1 GCGAGAC
22885734 AGGGAAGCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.43, T:0.14
Consensus pattern (22 bp):
GCGAGACTCCGGCCATGGCGGT
Found at i:22886583 original size:6 final size:6
Alignment explanation
Indices: 22886551--22886599 Score: 62
Period size: 6 Copynumber: 7.5 Consensus size: 6
22886541 AACATTGGAC
22886551 TTTTAA TTTTTAA TGTTTAGTA TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA -TTTTAA T-TTTA--A TTTTAA TTTTAA TTTTAA TTTTAA TTT
22886600 AAAGTAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 23 0.59
7 10 0.26
8 4 0.10
9 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:22886613 original size:6 final size:6
Alignment explanation
Indices: 22886572--22886654 Score: 59
Period size: 6 Copynumber: 14.2 Consensus size: 6
22886562 AATGTTTAGT
* * * * *
22886572 ATTTTA ATTTTA ATTTTA ATTTTA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
22886621 ATTTAA GA--TAA ATTTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
22886655 ATCAATTTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 16
0.78 0.04 0.19
Matches are distributed among these distances:
4 5 0.08
5 7 0.11
6 47 0.71
7 1 0.02
8 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:22886656 original size:17 final size:16
Alignment explanation
Indices: 22886604--22886654 Score: 79
Period size: 16 Copynumber: 3.2 Consensus size: 16
22886594 TAATTTAAAG
22886604 TAAATTTAAAT-AA-T
1 TAAATTTAAATAAATT
22886618 TAAATTTAAGATAAATT
1 TAAATTTAA-ATAAATT
22886635 TAAATTTAAATAAATT
1 TAAATTTAAATAAATT
22886651 TAAA
1 TAAA
22886655 ATCAATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.26
15 2 0.06
16 13 0.38
17 10 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TAAATTTAAATAAATT
Found at i:22886672 original size:27 final size:27
Alignment explanation
Indices: 22886595--22886672 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 27
22886585 TTTTAATTTT
* *
22886595 AATTTAAAGTAAATTTAAAT--AATTA
1 AATTTAAAATAAATTTAAATCCAAATA
* **
22886620 AATTTAAGATAAATTTAAATTTAAATA
1 AATTTAAAATAAATTTAAATCCAAATA
* *
22886647 AATTTAAAATCAATTTAACTCCAAAT
1 AATTTAAAATAAATTTAAATCCAAAT
22886673 TAAAACAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 18 0.42
27 25 0.58
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (27 bp):
AATTTAAAATAAATTTAAATCCAAATA
Found at i:22887078 original size:76 final size:76
Alignment explanation
Indices: 22886951--22887740 Score: 977
Period size: 76 Copynumber: 10.8 Consensus size: 76
22886941 TGCTCTTTAG
* * *
22886951 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
22887016 ACTTCAATTTC
66 ACTTCAATTTC
*
22887027 AGAGATAAAGACATGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCT-TT
1 AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
22887091 --TT--ACTTC
66 ACTTCAATTTC
* *
22887098 ------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
22887157 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
22887168 AGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAGGACAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
22887233 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
22887244 AGAGATAAAGACGTGTTATCAAACTCTACTTCAATTTCAAGAGGAT--G--ACG---TTGCTCTT
1 AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
22887302 ACTTCAATTTC
66 ACTTCAATTTC
* * *
22887313 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
22887378 ACTTCAATTTC
66 ACTTCAATTTC
*
22887389 AGAGATAAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCT-TT
1 AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
22887453 --TT--ACTTC
66 ACTTCAATTTC
* *
22887460 ------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
22887519 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
22887530 AGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAGGACAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
22887595 ACTTCAATTTC
66 ACTTCAATTTC
* * *
22887606 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT--G--ACG---TTGCTCTT
1 AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
22887664 ACTTCAATTTC
66 ACTTCAATTTC
* * ** * *
22887675 AGAGATAAAGACTTGTTATCCACTCTACTTTTTTTCAATTTCAAGCGGACAGGAAAAGATCTTGC
1 AGAGATAAAGACGTGATATCCA----ACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGC
22887740 T
62 T
22887741 GTGGTCTGAT
Statistics
Matches: 631, Mismatches: 43, Indels: 76
0.84 0.06 0.10
Matches are distributed among these distances:
65 109 0.17
66 4 0.01
68 4 0.01
69 103 0.16
70 8 0.01
71 9 0.01
72 4 0.01
73 25 0.04
74 2 0.00
75 5 0.01
76 351 0.56
77 2 0.00
80 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTC
Found at i:22887211 original size:141 final size:145
Alignment explanation
Indices: 22886957--22887651 Score: 804
Period size: 141 Copynumber: 4.8 Consensus size: 145
22886947 TTAGAGAGAT
* * * *
22886957 AAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTTACTTCA
1 AAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCA
*
22887022 ATTTCAGAGATAAAGACATGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
66 ATTTCAGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
*
22887087 CT-TT-TT-ACTTC-
131 CTCTTATTAATTTCA
*
22887098 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCA
1 AAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCA
* * * *
22887163 ATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAGGACAGGAAATGATCTTG
66 ATTTCAGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
22887228 CTCTTACTTCAATTTCAGAGA
131 CTCTTA-TT-AATTTC----A
* * * * *
22887249 TAAAGACGTGTTATCAAACTCTACTTCAATTTCAAGAGGAT--G--ACG---TTGCTCTTACTTC
1 -AAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTC
* * *
22887307 AATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTT
65 AATTTCAGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTT
22887372 GCTCTTACTTCAATTTCAGAGA
130 GCTCTTA-TT-AATTTC----A
22887394 TAAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCT-TT--TT-
1 -AAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTC
* * *
22887455 -ACTTC------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTT
65 AATTTCAGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTT
22887513 GCTCTTACTTCAATTTCAGAGA
130 GCTCTTA-TT-AATTTC----A
* * *
22887535 TAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAGGACAGGAAATGATCTTGCTCTTACTTC
1 -AAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTC
* *
22887600 AATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
65 AATTTCAGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGAT
22887652 GACGTTGCTC
Statistics
Matches: 485, Mismatches: 40, Indels: 47
0.85 0.07 0.08
Matches are distributed among these distances:
141 249 0.51
142 4 0.01
144 4 0.01
145 130 0.27
146 8 0.02
147 5 0.01
148 2 0.00
149 4 0.01
150 1 0.00
151 2 0.00
152 76 0.16
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (145 bp):
AAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCA
ATTTCAGAGATAAAGACGTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
CTCTTATTAATTTCA
Found at i:22887334 original size:145 final size:144
Alignment explanation
Indices: 22887098--22887704 Score: 657
Period size: 145 Copynumber: 4.2 Consensus size: 144
22887088 TTTTTACTTC
* * *
22887098 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCA
1 AAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT-------GA-CTTGCTCTTACTTCA
* * * * *
22887163 ATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAGGACAGGAAATGATCTTG
58 ATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
22887228 CTCTTACTTCAATTTCAGAGAT
123 CTCTTACTTCAATTTCAGAGAT
* *
22887250 AAAGACGTGTTATCAAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCAG
1 AAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATGAC-TTGCTCTTACTTCAATTTCAG
* *
22887315 AGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTTAC
65 AGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTAC
22887380 TTCAATTTCAGAGAT
130 TTCAATTTCAGAGAT
* * *** * *
22887395 AAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTT---TTT--
1 AAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGAT--GACTTGCTCTTACTTCAATTTCA
** * * *
22887455 -ACTTCAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
64 GAGAT-AAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
22887519 ACTTCAATTTCAGAGAT
128 ACTTCAATTTCAGAGAT
* * *
22887536 AAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAGGACAGGAAATGATCTTGCTCTTACTTCA
1 AAAGACGTGATATCCAACTCTACTTCAATTTC-A-A-G--AGG--ATGA-CTTGCTCTTACTTCA
* *
22887601 ATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT--G--ACG---TTG
58 ATTTCAGAGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
22887659 CTCTTACTTCAATTTCAGAGAT
123 CTCTTACTTCAATTTCAGAGAT
* *
22887681 AAAGACTTGTTATCC-ACTCTACTT
1 AAAGACGTGATATCCAACTCTACTT
22887705 TTTTTCAATT
Statistics
Matches: 392, Mismatches: 45, Indels: 44
0.81 0.09 0.09
Matches are distributed among these distances:
140 2 0.01
141 102 0.26
142 1 0.00
143 4 0.01
144 9 0.02
145 170 0.43
146 13 0.03
147 10 0.03
148 4 0.01
150 4 0.01
152 71 0.18
153 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (144 bp):
AAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATGACTTGCTCTTACTTCAATTTCAGA
GATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACT
TCAATTTCAGAGAT
Found at i:22887616 original size:362 final size:362
Alignment explanation
Indices: 22886951--22887740 Score: 1447
Period size: 362 Copynumber: 2.2 Consensus size: 362
22886941 TGCTCTTTAG
* * * *
22886951 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
22887016 ACTTCAATTTCAGAGATAAAGACATGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAG
66 ACTTCAATTTCAGAGATAAAGACATGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAG
22887081 ATCTTGCTTTTTACTTCAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAG
131 ATCTTGCTTTTTACTTCAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAG
22887146 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAG
196 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAG
22887211 GACAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCAAACTCTACTTC
261 GACAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCAAACTCTACTTC
22887276 AATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTC
326 AATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTC
*
22887313 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
* *
22887378 ACTTCAATTTCAGAGATAAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAG
66 ACTTCAATTTCAGAGATAAAGACATGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAG
22887443 ATCTTGCTTTTTACTTCAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAG
131 ATCTTGCTTTTTACTTCAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAG
22887508 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAG
196 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAG
*
22887573 GACAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTC
261 GACAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCAAACTCTACTTC
22887638 AATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTC
326 AATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTC
*
22887675 AGAGATAAAGACTTGTTATCC-ACTCTACTTTTTTTCAATTTCAAGCGGACAGGAAAAGATCTTG
1 AGAGATAAAGACTTGTTATCCAACTCTAC-----TTCAATTTCAAGCGGATAGGAAAAGATCTTG
22887739 CT
61 CT
22887741 GTGGTCTGAT
Statistics
Matches: 413, Mismatches: 10, Indels: 6
0.96 0.02 0.01
Matches are distributed among these distances:
361 7 0.02
362 374 0.91
366 32 0.08
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (362 bp):
AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTCAGAGATAAAGACATGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAG
ATCTTGCTTTTTACTTCAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAG
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAG
GACAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCAAACTCTACTTC
AATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTC
Found at i:22887636 original size:38 final size:35
Alignment explanation
Indices: 22887518--22887704 Score: 118
Period size: 38 Copynumber: 5.1 Consensus size: 35
22887508 ATCTTGCTCT
*
22887518 TACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTT
1 TACTTCAATTTCAGAGATAAAGA-CTG-TATCCA-CTC
* **
22887556 TACTTCAATTTCAAGAGGACAGGAA-A-TG-ATCTTGCTC
1 TACTTCAATTTC-AGA-GATA--AAGACTGTATC-CACTC
22887593 TTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTC
1 -TACTTCAATTTCAGAGATAAAGAC-TG-TATCC-ACTC
** * * *
22887632 TACTTCAATTTCA-AGAGGATGAC-GT-TGCTCT-
1 TACTTCAATTTCAGAGATAAAGACTGTATCCACTC
22887663 TACTTCAATTTCAGAGATAAAGACTTGTTATCCACTC
1 TACTTCAATTTCAGAGATAAAGAC-TG-TATCCACTC
22887700 TACTT
1 TACTT
22887705 TTTTTCAATT
Statistics
Matches: 114, Mismatches: 17, Indels: 37
0.68 0.10 0.22
Matches are distributed among these distances:
31 13 0.11
32 9 0.08
33 2 0.02
34 4 0.04
35 3 0.03
36 7 0.06
37 22 0.19
38 37 0.32
39 11 0.10
40 3 0.03
41 1 0.01
42 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (35 bp):
TACTTCAATTTCAGAGATAAAGACTGTATCCACTC
Found at i:22899548 original size:58 final size:59
Alignment explanation
Indices: 22899451--22899578 Score: 186
Period size: 58 Copynumber: 2.2 Consensus size: 59
22899441 GGATATCCGG
* * *
22899451 GGGTAAAATGGTAGATTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTTAA
1 GGGTAAAATGGCAGATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAGTTTAA
* * **
22899510 GGGTAAAATGGCA-ATTTTAGTGAAATCGAGGTTTAAAATGGGATTTTGGGAAGTTTGG
1 GGGTAAAATGGCAGATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAGTTTAA
22899568 GGGTAAAATGG
1 GGGTAAAATGG
22899579 TAATATTTGA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 50 0.81
59 12 0.19
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.30
Consensus pattern (59 bp):
GGGTAAAATGGCAGATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAGTTTAA
Found at i:22899622 original size:30 final size:30
Alignment explanation
Indices: 22899560--22899853 Score: 332
Period size: 30 Copynumber: 9.9 Consensus size: 30
22899550 GGATTTTGGG
*
22899560 AAGTTTGGGGGT-AAAATGGTAATATTT-G-A
1 AAGTTTTGGGGTCAAAAT-GTAAT-TTTAGAA
* *
22899589 AAGTTTT-GGGTAAAAATGTAATTTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAA-TTTTAGAA
* *
22899619 AAGTTTTAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* *
22899649 AAGTTTTGGTGTCAAAATGTAATTTCCAG-A
1 AAGTTTTGGGGTCAAAATGTAATTT-TAGAA
* *
22899679 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* * *
22899709 AAGTTTTGGGGTTAAAATATAATTTTAAAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* *
22899739 AAGTTTTAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* *
22899769 AAATTTTGGGGTCAAAATGTAATTTCAG-A
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* *
22899798 AAGTTTTAGGGTCAAAATATAATTTTTAG-A
1 AAGTTTTGGGGTCAAAATGTAA-TTTTAGAA
22899828 AAGTTTTGGGGTCAAAATGTAATTTT
1 AAGTTTTGGGGTCAAAATGTAATTTT
22899854 TAGATAATTT
Statistics
Matches: 229, Mismatches: 28, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
28 11 0.05
29 38 0.17
30 166 0.72
31 14 0.06
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTAGAA
Found at i:22899652 original size:60 final size:60
Alignment explanation
Indices: 22899568--22899857 Score: 367
Period size: 60 Copynumber: 4.9 Consensus size: 60
22899558 GGAAGTTTGG
* *
22899568 GGGT-AAAATGGTAATATTT-G-AAAGTTTT-GGGTAAAAATGTAATTTTTGGAAAAGTTTTA
1 GGGTCAAAAT-GTAAT-TTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAG-AAAGTTTTA
* ** *
22899627 GGGTCAAAATGTAATTTTGGAAAAGTTTTGGTGTCAAAATGTAATTTCCAGAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAGTTTTA
* * * * *
22899687 GGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTTAAAATATAATTTTAAAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAGTTTTA
* *
22899747 GGGTCAAAATGTAATTTTGGAAAAATTTTGGGGTCAAAATGTAA-TTTCAGAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAGTTTTA
* *
22899806 GGGTCAAAATATAATTTT-TAGAAAGTTTTGGGGTCAAAATGTAATTTTTAGA
1 GGGTCAAAATGTAATTTTGGA-AAAGTTTTGGGGTCAAAATGTAATTTTTAGA
22899858 TAATTTAGGG
Statistics
Matches: 201, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
58 4 0.02
59 62 0.31
60 119 0.59
61 16 0.08
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (60 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAGTTTTA
Found at i:22900716 original size:16 final size:15
Alignment explanation
Indices: 22900692--22900733 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
22900682 CCTCCCTTCC
22900692 TTTTCTTTTCTTTATT
1 TTTTCTTTTCTTT-TT
*
22900708 TTTTGTTTTC-TTTT
1 TTTTCTTTTCTTTTT
22900722 TTTTC-TTTCTTT
1 TTTTCTTTTCTTT
22900734 ATTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
15 2 0.09
16 9 0.39
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTCTTTTT
Found at i:22900724 original size:13 final size:13
Alignment explanation
Indices: 22900691--22900733 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
22900681 TCCTCCCTTC
22900691 CTTTTCTTTTCTTT
1 CTTTT-TTTTCTTT
* *
22900705 ATTTTTTGT-TTT
1 CTTTTTTTTCTTT
22900717 CTTTTTTTTCTTT
1 CTTTTTTTTCTTT
22900730 CTTT
1 CTTT
22900734 ATTATAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 10 0.42
13 10 0.42
14 4 0.17
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (13 bp):
CTTTTTTTTCTTT
Found at i:22900972 original size:22 final size:22
Alignment explanation
Indices: 22900928--22900978 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
22900918 CGACGTACGA
* ** *
22900928 GCGAAACTCCGGCGGTGGTGGT
1 GCGAGACTCCGGCCATGGCGGT
22900950 GCGAGACTCCGGCCATGGCGGT
1 GCGAGACTCCGGCCATGGCGGT
22900972 GCGAGAC
1 GCGAGAC
22900979 AGGGAAGCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.43, T:0.14
Consensus pattern (22 bp):
GCGAGACTCCGGCCATGGCGGT
Found at i:22901824 original size:6 final size:6
Alignment explanation
Indices: 22901813--22901901 Score: 89
Period size: 6 Copynumber: 15.2 Consensus size: 6
22901803 AAGGTTTAGT
* * *
22901813 ATTTTA ATTTTA ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
22901862 ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
22901902 ATCAATTTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
4 5 0.07
5 7 0.10
6 53 0.74
7 1 0.01
8 6 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:22901835 original size:11 final size:11
Alignment explanation
Indices: 22901815--22901911 Score: 70
Period size: 11 Copynumber: 8.5 Consensus size: 11
22901805 GGTTTAGTAT
*
22901815 TTTAATTTTAA
1 TTTAAATTTAA
22901826 TTTAAATTTAAA
1 TTTAAATTT-AA
* *
22901838 TTTAAAGTAAA
1 TTTAAATTTAA
22901849 TTTAAATAATTAAA
1 TTTAAAT--TT-AA
22901863 TTTAAATTTAA
1 TTTAAATTTAA
**
22901874 GATAAATTTAAA
1 TTTAAATTT-AA
*
22901886 TTTAAA-TAAA
1 TTTAAATTTAA
* *
22901896 TTTAAAATCAA
1 TTTAAATTTAA
22901907 TTTAA
1 TTTAA
22901912 CTCCAAATTA
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
10 8 0.12
11 34 0.49
12 17 0.25
13 1 0.01
14 9 0.13
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:22901841 original size:17 final size:16
Alignment explanation
Indices: 22901815--22901901 Score: 97
Period size: 17 Copynumber: 5.4 Consensus size: 16
22901805 GGTTTAGTAT
*
22901815 TTTAATTTTAATTTAAA
1 TTTAAATTTAA-TTAAA
*
22901832 TTTAAATTTAAAGTAAA
1 TTTAAATTT-AATTAAA
22901849 TTTAAA--TAATTAAA
1 TTTAAATTTAATTAAA
*
22901863 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-TTAAA
*
22901880 TTTAAATTTAAATAAA
1 TTTAAATTTAATTAAA
22901896 TTTAAA
1 TTTAAA
22901902 ATCAATTTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
14 12 0.19
15 1 0.02
16 14 0.23
17 33 0.53
18 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:22901870 original size:37 final size:37
Alignment explanation
Indices: 22901824--22901894 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
22901814 TTTTAATTTT
22901824 AATTTAAATTTAA-ATTTAAA-GTAAATTTAAATAATTA
1 AATTTAAATTTAAGA--TAAATGTAAATTTAAATAATTA
*
22901861 AATTTAAATTTAAGATAAATTTAAATTTAAATAA
1 AATTTAAATTTAAGATAAATGTAAATTTAAATAA
22901895 ATTTAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 4 0.13
37 26 0.84
38 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (37 bp):
AATTTAAATTTAAGATAAATGTAAATTTAAATAATTA
Found at i:22901903 original size:17 final size:16
Alignment explanation
Indices: 22901828--22901901 Score: 107
Period size: 17 Copynumber: 4.6 Consensus size: 16
22901818 AATTTTAATT
22901828 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
22901844 GTAAATTTAAA--TAAT
1 -TAAATTTAAATTTAAA
22901859 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAA-A
22901876 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
22901892 TAAATTTAAA
1 TAAATTTAAA
22901902 ATCAATTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
14 10 0.19
15 3 0.06
16 14 0.27
17 25 0.48
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:22901919 original size:27 final size:27
Alignment explanation
Indices: 22901865--22901919 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
22901855 TAATTAAATT
* **
22901865 TAAATTTAAGATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCCAAA
* *
22901892 TAAATTTAAAATCAATTTAACTCCAAA
1 TAAATTTAAAATAAATTTAAATCCAAA
22901919 T
1 T
22901920 TAAAACAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCCAAA
Found at i:22909810 original size:26 final size:25
Alignment explanation
Indices: 22909780--22909929 Score: 156
Period size: 22 Copynumber: 6.2 Consensus size: 25
22909770 GAAGTGCATA
* *
22909780 AGTGCTGGGAAACAGTAGGCACCCAC
1 AGTGCTGGGAAACAG-AAGCACACAC
22909806 AGTGCT--G-AACAGAAGCACACAC
1 AGTGCTGGGAAACAGAAGCACACAC
*
22909828 AGTGCT--G-ATCAGAAGCACACAC
1 AGTGCTGGGAAACAGAAGCACACAC
*
22909850 AGTGCTGGGGAAACAGAAGCGCACAC
1 AGTGCT-GGGAAACAGAAGCACACAC
22909876 AGTGCTGGGGAAACAGAAGCACACAC
1 AGTGCT-GGGAAACAGAAGCACACAC
* *
22909902 AGTGCT--G-AATAGAAGCACACAT
1 AGTGCTGGGAAACAGAAGCACACAC
22909924 AGTGCT
1 AGTGCT
22909930 AAACAGTAGG
Statistics
Matches: 112, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
22 54 0.48
23 6 0.05
24 1 0.01
25 1 0.01
26 50 0.45
ACGTcount: A:0.36, C:0.24, G:0.28, T:0.12
Consensus pattern (25 bp):
AGTGCTGGGAAACAGAAGCACACAC
Found at i:22909897 original size:24 final size:25
Alignment explanation
Indices: 22909845--22909908 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 25
22909835 ATCAGAAGCA
22909845 CACACAGTGCTGGGGAAACAGAAGCG
1 CACACAGTGCTGGGGAAACAGAA-CG
*
22909871 CACACAGTGCTGGGGAAACAGAAGCA
1 CACACAGTGCTGGGGAAACAGAA-CG
22909897 CACACAGTGCTG
1 CACACAGTGCTG
22909909 AATAGAAGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.34, C:0.25, G:0.31, T:0.09
Consensus pattern (25 bp):
CACACAGTGCTGGGGAAACAGAACG
Found at i:22909916 original size:48 final size:47
Alignment explanation
Indices: 22909780--22909929 Score: 171
Period size: 48 Copynumber: 3.1 Consensus size: 47
22909770 GAAGTGCATA
* *
22909780 AGTGCTGGGAAACAGTAGGCACCCACAGTGCTGAACAGAAGCACACAC
1 AGTGCTGGGAAACAG-AAGCACACACAGTGCTGAACAGAAGCACACAC
* *
22909828 AGTGCT--G-ATCAGAAGCACACACAGTGCTGGGGAAACAGAAGCGCACAC
1 AGTGCTGGGAAACAGAAGCACACACAGTGCT---G-AACAGAAGCACACAC
* *
22909876 AGTGCTGGGGAAACAGAAGCACACACAGTGCTGAATAGAAGCACACAT
1 AGTGCT-GGGAAACAGAAGCACACACAGTGCTGAACAGAAGCACACAC
22909924 AGTGCT
1 AGTGCT
22909930 AAACAGTAGG
Statistics
Matches: 86, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
44 14 0.16
45 4 0.05
46 1 0.01
47 1 0.01
48 44 0.51
49 1 0.01
51 1 0.01
52 20 0.23
ACGTcount: A:0.36, C:0.24, G:0.28, T:0.12
Consensus pattern (47 bp):
AGTGCTGGGAAACAGAAGCACACACAGTGCTGAACAGAAGCACACAC
Found at i:22920272 original size:18 final size:18
Alignment explanation
Indices: 22920245--22920298 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
22920235 TTTTAGAGAA
*
22920245 AAGAACAATGAGAGAAGC
1 AAGAAGAATGAGAGAAGC
*
22920263 AAGAAGAATGTGAGAAAG-
1 AAGAAGAATGAGAG-AAGC
*
22920281 GAGAAGAATGAGAGAAGC
1 AAGAAGAATGAGAGAAGC
22920299 TCAGGTTCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.54, C:0.06, G:0.33, T:0.07
Consensus pattern (18 bp):
AAGAAGAATGAGAGAAGC
Found at i:22920436 original size:28 final size:28
Alignment explanation
Indices: 22920403--22920507 Score: 129
Period size: 28 Copynumber: 3.8 Consensus size: 28
22920393 TTGCAACGAT
* *
22920403 CATATTGTAATGGTCAGATTCCAACAGC
1 CATATTGTAATGGTCAGATTTCAACGGC
* * * *
22920431 CATATTGTAATGGTTAGATTTTAATGGT
1 CATATTGTAATGGTCAGATTTCAACGGC
*
22920459 CATATTGTAATGGTTAGATTTCAACGGC
1 CATATTGTAATGGTCAGATTTCAACGGC
* *
22920487 CATATTGTAACGGTCATATTT
1 CATATTGTAATGGTCAGATTT
22920508 TTGCATTACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (28 bp):
CATATTGTAATGGTCAGATTTCAACGGC
Found at i:22920504 original size:14 final size:14
Alignment explanation
Indices: 22920383--22920506 Score: 70
Period size: 14 Copynumber: 8.9 Consensus size: 14
22920373 CAAAAAATTC
* *
22920383 AACGGGCATATTGC
1 AACGGTCATATTGT
*
22920397 AACGATCATATTGT
1 AACGGTCATATTGT
* * **
22920411 AATGGTCAGATTCC
1 AACGGTCATATTGT
* *
22920425 AACAGCCATATTGT
1 AACGGTCATATTGT
* * * *
22920439 AATGGTTAGATTTT
1 AACGGTCATATTGT
*
22920453 AATGGTCATATTGT
1 AACGGTCATATTGT
* * *
22920467 AATGGTTAGATT-T
1 AACGGTCATATTGT
*
22920480 CAACGGCCATATTGT
1 -AACGGTCATATTGT
22920495 AACGGTCATATT
1 AACGGTCATATT
22920507 TTTGCATTAC
Statistics
Matches: 78, Mismatches: 30, Indels: 4
0.70 0.27 0.04
Matches are distributed among these distances:
13 1 0.01
14 76 0.97
15 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (14 bp):
AACGGTCATATTGT
Found at i:22920508 original size:56 final size:56
Alignment explanation
Indices: 22920402--22920508 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
22920392 ATTGCAACGA
* *
22920402 TCATATTGTAATGGTCAGATTCCAACAGCCATATTGTAATGGTTAGATTTTAATGG
1 TCATATTGTAATGGTCAGATTCCAACAGCCATATTGTAACGGTCAGATTTTAATGG
* * * *
22920458 TCATATTGTAATGGTTAGATTTCAACGGCCATATTGTAACGGTCATATTTT
1 TCATATTGTAATGGTCAGATTCCAACAGCCATATTGTAACGGTCAGATTTT
22920509 TGCATTACCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (56 bp):
TCATATTGTAATGGTCAGATTCCAACAGCCATATTGTAACGGTCAGATTTTAATGG
Found at i:22924250 original size:26 final size:26
Alignment explanation
Indices: 22924221--22924351 Score: 190
Period size: 26 Copynumber: 5.0 Consensus size: 26
22924211 CTGGAGAAAT
*
22924221 TACTAAACTGGATCGTAAGAGCGATA
1 TACTAAACTGGCTCGTAAGAGCGATA
*
22924247 TACTGAACTGGCTCGTAAGAGCGATA
1 TACTAAACTGGCTCGTAAGAGCGATA
*
22924273 TAATAAACTGGCTCGTAAGAGCGATA
1 TACTAAACTGGCTCGTAAGAGCGATA
* * *
22924299 TACTGAACTAGCTCGTAAGAGTGATA
1 TACTAAACTGGCTCGTAAGAGCGATA
* *
22924325 TACTAAAATGGCTCGTAAGAACGATA
1 TACTAAACTGGCTCGTAAGAGCGATA
22924351 T
1 T
22924352 CCTGACTAGG
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 92 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (26 bp):
TACTAAACTGGCTCGTAAGAGCGATA
Found at i:22924302 original size:52 final size:52
Alignment explanation
Indices: 22924224--22924374 Score: 205
Period size: 52 Copynumber: 2.9 Consensus size: 52
22924214 GAGAAATTAC
*
22924224 TAAACTGGATCGTAAGAGCGATATACTGAACTGGCTCGTAAGAGCGATATAA
1 TAAACTGGCTCGTAAGAGCGATATACTGAACTGGCTCGTAAGAGCGATATAA
* * *
22924276 TAAACTGGCTCGTAAGAGCGATATACTGAACTAGCTCGTAAGAGTGATATAC
1 TAAACTGGCTCGTAAGAGCGATATACTGAACTGGCTCGTAAGAGCGATATAA
* * * * *
22924328 TAAAATGGCTCGTAAGAACGATATCCTG-ACTAGGCTCATATGAGCGA
1 TAAACTGGCTCGTAAGAGCGATATACTGAACT-GGCTCGTAAGAGCGA
22924375 AATTTACTAG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 3 0.03
52 84 0.97
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (52 bp):
TAAACTGGCTCGTAAGAGCGATATACTGAACTGGCTCGTAAGAGCGATATAA
Found at i:22924363 original size:26 final size:26
Alignment explanation
Indices: 22924233--22924374 Score: 139
Period size: 26 Copynumber: 5.5 Consensus size: 26
22924223 CTAAACTGGA
22924233 TCGTAAGAGCGATATACTGAACT-GGC
1 TCGTAAGAGCGATATACTG-ACTAGGC
* *
22924259 TCGTAAGAGCGATATAATAAACT-GGC
1 TCGTAAGAGCGATATACT-GACTAGGC
22924285 TCGTAAGAGCGATATACTGAACTA-GC
1 TCGTAAGAGCGATATACTG-ACTAGGC
* **
22924311 TCGTAAGAGTGATATACT-AAAATGGC
1 TCGTAAGAGCGATATACTGACTA-GGC
* *
22924337 TCGTAAGAACGATATCCTGACTAGGC
1 TCGTAAGAGCGATATACTGACTAGGC
* *
22924363 TCATATGAGCGA
1 TCGTAAGAGCGA
22924375 AATTTACTAG
Statistics
Matches: 95, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
24 2 0.02
26 91 0.96
27 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (26 bp):
TCGTAAGAGCGATATACTGACTAGGC
Found at i:22929755 original size:52 final size:52
Alignment explanation
Indices: 22929672--22929960 Score: 406
Period size: 52 Copynumber: 5.6 Consensus size: 52
22929662 TAAATGACAA
* * *
22929672 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTCATGGGTTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
22929724 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
22929776 AGGTCCGATGAC--TGTGTCATCGTAAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
22929826 AGGTCTGATGACTATGTGCCATCGTGAGTATATGAATCCTTTACGGATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
22929878 AGGTCCGATGATTATGTGTCATCGTGAGCATAT-AGATCCTTTTATGGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGA-ATCC-TTTACGGATTATG
* *
22929930 AGGTCCGATAACTTTGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
22929961 TAAATGGGAA
Statistics
Matches: 212, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
50 48 0.23
51 1 0.00
52 154 0.73
53 9 0.04
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:22929862 original size:102 final size:102
Alignment explanation
Indices: 22929672--22929960 Score: 386
Period size: 102 Copynumber: 2.8 Consensus size: 102
22929662 TAAATGACAA
* *
22929672 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTCATGGGTTATGAGGT-TCGATGAC
1 AGGTCCGATGAC--TGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTCT-GATGAC
*
22929736 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
63 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
* *
22929776 AGGTCCGATGACTGTGTCATCGTAAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACTAT
1 AGGTCCGATGACTGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTCTGATGACTAT
*
22929841 GTGCCATCGTGAGTATATGAATCCTTTACGGATTAAG
66 GTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
* * * * *
22929878 AGGTCCGATGATTATGTGTCATCGTGAGCATAT-AGATCCTTTTATGGATT-TAAGGTCCGATAA
1 AGGTCCGATGA--CTGTGTCATCGTGAGTATATGA-ATCC-TTTATGGATTATGAGGTCTGATGA
*
22929941 CTTTGTGTCATCGTGAGTAT
62 CTATGTGTCATCGTGAGTAT
22929961 TAAATGGGAA
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
102 93 0.56
103 2 0.01
104 61 0.37
105 9 0.05
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (102 bp):
AGGTCCGATGACTGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTCTGATGACTAT
GTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
Found at i:22931990 original size:18 final size:18
Alignment explanation
Indices: 22931969--22932026 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
22931959 TTTTAGAGAA
*
22931969 AAGAAGAATGAGAGAAGC
1 AAGAAGAATGAGAGAAAC
*
22931987 AAGAA-AAGTGAGAGAAAT
1 AAGAAGAA-TGAGAGAAAC
*
22932005 GAGAAGAATGAGAGAAATC
1 AAGAAGAATGAGAGAAA-C
22932024 AAG
1 AAG
22932027 TTTGTTGCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.06
18 26 0.81
19 4 0.12
ACGTcount: A:0.57, C:0.03, G:0.31, T:0.09
Consensus pattern (18 bp):
AAGAAGAATGAGAGAAAC
Found at i:22938325 original size:131 final size:129
Alignment explanation
Indices: 22938190--22938440 Score: 376
Period size: 131 Copynumber: 1.9 Consensus size: 129
22938180 CCTAGTATAG
* * * * *
22938190 GCGTGTTTTTATTTTTGAGATATTTTTCACTTTAATCCTTTCGTATTTTTATGGTGTTACAATTT
1 GCGTGTTTTTATTTATGAGATATTTTCCACTTTAATCCTTCCGCATTTTTATGGTATTACAATTT
* ** * *
22938255 AGTATTTTTTTATTTTTAATTATTTTAATTTGGCCCATTAATTATAATTTCTTTACAGTTCGGTC
66 AGTACTTTTACATTTTTAATTATTTTAA--TAGCCCATTAATTATAAGTTCTTTACAGTTCGGTC
22938320 C
129 C
*
22938321 GCGTGTTTTTATTTATGAGATATTTTCCACTTTAATCCTTCCGCATTTTTGTGGTATTACAATTT
1 GCGTGTTTTTATTTATGAGATATTTTCCACTTTAATCCTTCCGCATTTTTATGGTATTACAATTT
*
22938386 AGTACTTTTACATTTTTAATTATTTTAATAGCCCATTAATTCTAAGTTCTTTACA
66 AGTACTTTTACATTTTTAATTATTTTAATAGCCCATTAATTATAAGTTCTTTACA
22938441 ATTCAATCCT
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
129 24 0.22
131 84 0.78
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.53
Consensus pattern (129 bp):
GCGTGTTTTTATTTATGAGATATTTTCCACTTTAATCCTTCCGCATTTTTATGGTATTACAATTT
AGTACTTTTACATTTTTAATTATTTTAATAGCCCATTAATTATAAGTTCTTTACAGTTCGGTCC
Found at i:22938554 original size:16 final size:15
Alignment explanation
Indices: 22938533--22938562 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
22938523 TGATCTCACT
22938533 TTTTATTTGTGTATTG
1 TTTTATTTGT-TATTG
22938549 TTTTATTTGTTATT
1 TTTTATTTGTTATT
22938563 TAATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (15 bp):
TTTTATTTGTTATTG
Found at i:22941917 original size:12 final size:12
Alignment explanation
Indices: 22941900--22941924 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22941890 AAAAATGCCA
22941900 TTGAAGCAGATT
1 TTGAAGCAGATT
22941912 TTGAAGCAGATT
1 TTGAAGCAGATT
22941924 T
1 T
22941925 CCATCAGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TTGAAGCAGATT
Found at i:22944775 original size:23 final size:22
Alignment explanation
Indices: 22944749--22944884 Score: 130
Period size: 23 Copynumber: 6.0 Consensus size: 22
22944739 TTACCGTTCA
*
22944749 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCCTACTGTTT
* *
22944771 CGCACTTTGTGTGCTTACTGTTTT
1 -GCACTGTGTGTGCCTACTG-TTT
*
22944795 GCACT-TCATGTGCCTACTGATTT
1 GCACTGT-GTGTGCCTACTG-TTT
* * * *
22944818 GCGCTATGTGGGCCTACTGATT
1 GCACTGTGTGTGCCTACTGTTT
*
22944840 GCACTGTGTGTGCCTACTGGATT
1 GCACTGTGTGTGCCTACT-GTTT
*
22944863 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCCTACTGTTT
22944885 CCCCAGCACT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
22 21 0.22
23 71 0.74
24 4 0.04
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.41
Consensus pattern (22 bp):
GCACTGTGTGTGCCTACTGTTT
Found at i:22950519 original size:16 final size:16
Alignment explanation
Indices: 22950491--22950532 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
22950481 ATACTATTTT
22950491 TAATATGATATAGA-CA
1 TAATAT-ATATAGATCA
*
22950507 TAATATATGATAGATTA
1 TAATATAT-ATAGATCA
22950524 TAATATATA
1 TAATATATA
22950533 CAATCTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 12 0.52
17 9 0.39
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (16 bp):
TAATATATATAGATCA
Found at i:22950822 original size:15 final size:16
Alignment explanation
Indices: 22950789--22950823 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
22950779 ATCAAAATTG
*
22950789 ATTTAAACATGAGAAA
1 ATTTAAACATGAAAAA
22950805 ATTTAAACAT-AAAAA
1 ATTTAAACATGAAAAA
22950820 ATTT
1 ATTT
22950824 CAAAAGAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (16 bp):
ATTTAAACATGAAAAA
Found at i:22950861 original size:15 final size:15
Alignment explanation
Indices: 22950840--22950882 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
22950830 AGTCCAAGCT
22950840 CAAAAAAACTAA-TC
1 CAAAAAAACTAAGTC
*
22950854 CGAAAAAACTTAAGTC
1 CAAAAAAAC-TAAGTC
22950870 CAAAAAAATCTAA
1 CAAAAAAA-CTAA
22950883 ACCCGAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 8 0.33
15 3 0.12
16 12 0.50
17 1 0.04
ACGTcount: A:0.60, C:0.19, G:0.05, T:0.16
Consensus pattern (15 bp):
CAAAAAAACTAAGTC
Found at i:22956012 original size:9 final size:9
Alignment explanation
Indices: 22955998--22956112 Score: 59
Period size: 9 Copynumber: 11.8 Consensus size: 9
22955988 GTTTAAATTT
22955998 TTTTTATAA
1 TTTTTATAA
22956007 TTTTTATAAA
1 TTTTTAT-AA
* * *
22956017 ATTTTACGAT
1 TTTTTA-TAA
22956027 TTTTTATAA
1 TTTTTATAA
*
22956036 TTTTTTTAA
1 TTTTTATAA
22956045 TTTTTAATAA
1 TTTTT-ATAA
** *
22956055 AATTTAAATA
1 TTTTTATA-A
*
22956065 TTTTTTTACA
1 TTTTTATA-A
22956075 TTTTCTTATTAAA
1 -TTT-TTA-T-AA
* *
22956088 ATTTAATAA
1 TTTTTATAA
22956097 TTTTTATAA
1 TTTTTATAA
22956106 TTTTTAT
1 TTTTTAT
22956113 TTATTACAAT
Statistics
Matches: 77, Mismatches: 21, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
9 39 0.51
10 26 0.34
11 5 0.06
12 4 0.05
13 2 0.03
14 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:22956038 original size:10 final size:10
Alignment explanation
Indices: 22955997--22956110 Score: 58
Period size: 10 Copynumber: 11.5 Consensus size: 10
22955987 TGTTTAAATT
22955997 TTTTTTATAA
1 TTTTTTATAA
22956007 -TTTTTATAA
1 TTTTTTATAA
** **
22956016 AATTTTACGA
1 TTTTTTATAA
22956026 TTTTTTATAA
1 TTTTTTATAA
22956036 TTTTTT-TAA
1 TTTTTTATAA
*
22956045 TTTTTAATAA
1 TTTTTTATAA
**
22956055 -AATTTA-AA
1 TTTTTTATAA
*
22956063 TATTTTTTTACA
1 T-TTTTTATA-A
22956075 TTTTCTTATTAA
1 TTTT-TTA-TAA
** *
22956087 AATTTAATAA
1 TTTTTTATAA
22956097 -TTTTTATAA
1 TTTTTTATAA
22956106 TTTTT
1 TTTTT
22956111 ATTTATTACA
Statistics
Matches: 75, Mismatches: 20, Indels: 18
0.66 0.18 0.16
Matches are distributed among these distances:
8 2 0.03
9 27 0.36
10 31 0.41
11 6 0.08
12 7 0.09
13 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:22956068 original size:39 final size:39
Alignment explanation
Indices: 22955997--22956083 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 39
22955987 TGTTTAAATT
* *
22955997 TTTTTTATAATTTTTATAAAATTTTACGATTTTTTATA-A
1 TTTTTTATAATTTTTATAAAATTTAAAGATTTTTT-TACA
*
22956036 TTTTTT-TAATTTTTAATAAAATTTAAATATTTTTTTACA
1 TTTTTTATAATTTTT-ATAAAATTTAAAGATTTTTTTACA
22956075 TTTTCTTAT
1 TTTT-TTAT
22956084 TAAAATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 10 0.24
39 28 0.68
40 2 0.05
41 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (39 bp):
TTTTTTATAATTTTTATAAAATTTAAAGATTTTTTTACA
Found at i:22956093 original size:32 final size:30
Alignment explanation
Indices: 22956032--22956110 Score: 99
Period size: 32 Copynumber: 2.6 Consensus size: 30
22956022 ACGATTTTTT
22956032 ATAATTTTTTTAA-TTTTTAATAAAATTTA
1 ATAATTTTTTTAATTTTTTAATAAAATTTA
*
22956061 A-ATATTTTTTTACATTTTCTTATTAAAATTTA
1 ATA-ATTTTTTTA-ATTTT-TTAATAAAATTTA
*
22956093 ATAATTTTTATAATTTTT
1 ATAATTTTTTTAATTTTT
22956111 ATTTATTACA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
28 1 0.02
29 10 0.23
30 2 0.05
31 8 0.19
32 21 0.49
33 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
ATAATTTTTTTAATTTTTTAATAAAATTTA
Found at i:22983498 original size:12 final size:12
Alignment explanation
Indices: 22983477--22983513 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
22983467 TGAAGATAAC
*
22983477 TAAAGTTGAAGA
1 TAAAGATGAAGA
22983489 TAAAGATGAAGA
1 TAAAGATGAAGA
*
22983501 TGAAGATGAAGA
1 TAAAGATGAAGA
22983513 T
1 T
22983514 GAAGGCTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (12 bp):
TAAAGATGAAGA
Found at i:22983500 original size:6 final size:6
Alignment explanation
Indices: 22983483--22983517 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
22983473 TAACTAAAGT
*
22983483 TGAAGA TAAAGA TGAAGA TGAAGA TGAAGA TGAAG
1 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAG
22983518 GCTTTGCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
TGAAGA
Found at i:22984173 original size:17 final size:18
Alignment explanation
Indices: 22984151--22984210 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
22984141 TGAACTATGG
*
22984151 GCTCACCAAATA-TGCGA
1 GCTCACCAAAAACTGCGA
* *
22984168 GCTCACCAAAAAGTGTGA
1 GCTCACCAAAAACTGCGA
* * *
22984186 ACTCACCAAAGACCGCGA
1 GCTCACCAAAAACTGCGA
22984204 GCTCACC
1 GCTCACC
22984211 TAGACTATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
17 11 0.32
18 23 0.68
ACGTcount: A:0.35, C:0.33, G:0.18, T:0.13
Consensus pattern (18 bp):
GCTCACCAAAAACTGCGA
Found at i:22988630 original size:59 final size:59
Alignment explanation
Indices: 22988570--22988867 Score: 429
Period size: 59 Copynumber: 5.1 Consensus size: 59
22988560 TCCGAGTGTA
* * * *
22988570 AAAAT-GTAATTTTTGGTGAAAGTAG-GGTCAAAAATGAAATCTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAA-TCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* *
22988628 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* *
22988687 AAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* *
22988746 AAAATGGTTATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* * * * * *
22988805 AAAATGGTGAGTTTTGGTAAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
22988864 AAAA
1 AAAA
22988868 ATATAATTTA
Statistics
Matches: 217, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
58 7 0.03
59 210 0.97
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
Found at i:22988671 original size:30 final size:30
Alignment explanation
Indices: 22988628--22988789 Score: 135
Period size: 30 Copynumber: 5.5 Consensus size: 30
22988618 GTTTGGGGGT
22988628 AAAATGGTAATTTTTGGTGAAATCGAGGTTA
1 AAAATGGTAATTTTT-GTGAAATCGAGGTTA
* ** *
22988659 AAAATGG-GA-TTTTG-GAAAGTTTAGGGGT-
1 AAAATGGTAATTTTTGTGAAA-TCGA-GGTTA
22988687 AAAATGGTAATTTTTAGTGAAATCGAGGTTA
1 AAAATGGTAATTTTT-GTGAAATCGAGGTTA
* *
22988718 AAAATGG-AA-TTTTG-GAAAGTTCGGGGGT-
1 AAAATGGTAATTTTTGTGAAA--TCGAGGTTA
*
22988746 AAAATGGTTATTTTTGGTGAAATCGAGGTTA
1 AAAATGGTAATTTTT-GTGAAATCGAGGTTA
22988777 AAAATGG-AATTTT
1 AAAATGGTAATTTT
22988790 GGAAAGTTTA
Statistics
Matches: 103, Mismatches: 14, Indels: 29
0.71 0.10 0.20
Matches are distributed among these distances:
27 8 0.08
28 18 0.17
29 19 0.18
30 25 0.24
31 25 0.24
32 8 0.08
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (30 bp):
AAAATGGTAATTTTTGTGAAATCGAGGTTA
Found at i:22988689 original size:29 final size:29
Alignment explanation
Indices: 22988594--22988891 Score: 120
Period size: 29 Copynumber: 10.1 Consensus size: 29
22988584 GGTGAAAGTA
* * *
22988594 GGGTCAAAAATGAAATCTTGGAAAGTTTGG
1 GGGT-AAAAATGGAATTTTGGAAAGTTTAG
**
22988624 GGGT-AAAATGGTAATTTTTGGTGAAA-TCGA-
1 GGGTAAAAATGG-AA-TTTT-G-GAAAGTTTAG
* *
22988654 GGTTAAAAATGGGATTTTGGAAAGTTTAG
1 GGGTAAAAATGGAATTTTGGAAAGTTTAG
**
22988683 GGGT-AAAATGGTAATTTTTAGTGAAA-TCGA-
1 GGGTAAAAATGG-AA-TTTT-G-GAAAGTTTAG
* **
22988713 GGTTAAAAATGGAATTTTGGAAAGTTCGG
1 GGGTAAAAATGGAATTTTGGAAAGTTTAG
* **
22988742 GGGT-AAAATGGTTATTTTTGGTGAAA-TCGA-
1 GGGTAAAAATGG--AATTTT-G-GAAAGTTTAG
*
22988772 GGTTAAAAATGGAATTTTGGAAAGTTTAG
1 GGGTAAAAATGGAATTTTGGAAAGTTTAG
* * *
22988801 GGGT-AAAATGGTGAGTTTTGGTAAA--ATCG
1 GGGTAAAAAT-G-GAATTTTGG-AAAGTTTAG
*
22988830 GGGTTAAAAATAGAATTTTGGAAAGTTT-G
1 GGG-TAAAAATGGAATTTTGGAAAGTTTAG
**
22988859 AGGGTAAAAATATAATTTAT-GAATAGTTTAG
1 -GGGTAAAAATGGAATTT-TGGAA-AGTTTAG
22988890 GG
1 GG
22988892 ACCTTTTAGC
Statistics
Matches: 202, Mismatches: 34, Indels: 64
0.67 0.11 0.21
Matches are distributed among these distances:
27 12 0.06
28 36 0.18
29 56 0.28
30 49 0.24
31 37 0.18
32 12 0.06
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:22988838 original size:30 final size:30
Alignment explanation
Indices: 22988622--22988838 Score: 105
Period size: 30 Copynumber: 7.3 Consensus size: 30
22988612 TGGAAAGTTT
* * *
22988622 GGGGGTAAAATGGTAATTTTTGGTGAAATC
1 GGGGTTAAAATGGTGATTTTTGGTAAAATC
* * *
22988652 GAGGTTAAAAATGG-GA-TTTTGG-AAAGTTTA
1 GGGGTT-AAAATGGTGATTTTTGGTAAA--ATC
* * *
22988682 GGGG-TAAAATGGTAATTTTTAGTGAAATC
1 GGGGTTAAAATGGTGATTTTTGGTAAAATC
* * *
22988711 GAGGTTAAAAAT-G-GAATTTTGG-AAAGTTC
1 GGGGTT-AAAATGGTGATTTTTGGTAAA-ATC
* * *
22988740 GGGGGTAAAATGGTTATTTTTGGTGAAATC
1 GGGGTTAAAATGGTGATTTTTGGTAAAATC
* * * *
22988770 GAGGTTAAAAAT-G-GAATTTTGG-AAAGTTTA
1 GGGGTT-AAAATGGTGATTTTTGGTAAA--ATC
*
22988800 GGGG-TAAAATGGTGAGTTTTGGTAAAATC
1 GGGGTTAAAATGGTGATTTTTGGTAAAATC
22988829 GGGGTTAAAA
1 GGGGTTAAAA
22988839 ATAGAATTTT
Statistics
Matches: 133, Mismatches: 35, Indels: 38
0.65 0.17 0.18
Matches are distributed among these distances:
28 23 0.17
29 39 0.29
30 47 0.35
31 24 0.18
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (30 bp):
GGGGTTAAAATGGTGATTTTTGGTAAAATC
Found at i:22989979 original size:23 final size:21
Alignment explanation
Indices: 22989933--22989980 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
22989923 TTTCTTTTTA
*
22989933 ATTA-TTATTAAATTAATAAT
1 ATTATTTATTAAATTAATAAC
*
22989953 ATTATTTATTAATATTTAATACC
1 ATTATTTATTAA-A-TTAATAAC
22989976 ATTAT
1 ATTAT
22989981 CACTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 7 0.30
22 1 0.04
23 11 0.48
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATTTATTAAATTAATAAC
Found at i:22990918 original size:43 final size:43
Alignment explanation
Indices: 22990837--22991038 Score: 325
Period size: 43 Copynumber: 4.7 Consensus size: 43
22990827 AGAACATGGC
* * * *
22990837 CTTTAGCGGCGCTTT-CCCATAAGTGCCGCTGAAGGCCATGTA
1 CTTTAGCGGCGCTTTATCCACAAGCGCCGCTGAAGGCCATGTT
*
22990879 CTTTAGCGGCGCTTTTTCCACAAGCGCCGCTGAAGGCCATGTT
1 CTTTAGCGGCGCTTTATCCACAAGCGCCGCTGAAGGCCATGTT
*
22990922 CTTTCGCGGCGCTTTATCCACAAGCGCCGCTGAAGGCCATGTT
1 CTTTAGCGGCGCTTTATCCACAAGCGCCGCTGAAGGCCATGTT
*
22990965 CTTTCGCGGCGCTTTATCCACAAGCGCCGCTGAAGGCCATGTT
1 CTTTAGCGGCGCTTTATCCACAAGCGCCGCTGAAGGCCATGTT
*
22991008 CTTTAGCGGCGCTTTATCCAAAAGCGCCGCT
1 CTTTAGCGGCGCTTTATCCACAAGCGCCGCT
22991039 AATATAACAG
Statistics
Matches: 151, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
42 15 0.10
43 136 0.90
ACGTcount: A:0.17, C:0.31, G:0.25, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTATCCACAAGCGCCGCTGAAGGCCATGTT
Found at i:22991505 original size:65 final size:66
Alignment explanation
Indices: 22991356--22991512 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 66
22991346 CTTCGCTTGC
* * * * *
22991356 CTCGCTGCTGCCTCCACTTTAAGTTGTATGTGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTC
1 CTCGATGCAGCCTCCTCTTTAAGTTGTATGTGGAGTTCATCATATTTTTTTTAAGACTCTGCTTC
22991421 T
66 T
* * * *
22991422 CTCAATGCAACCTCCTCTTTAAGTTTTA-GATGGAGTTCATCATA-TTTTTTTAAGCCTCTGCTT
1 CTCGATGCAGCCTCCTCTTTAAGTTGTATG-TGGAGTTCATCATATTTTTTTTAAGACTCTGCTT
22991485 CT
65 CT
*
22991487 CTCGTTGCAGCCTCCTCTTTAAGTTG
1 CTCGATGCAGCCTCCTCTTTAAGTTG
22991513 AGCAATTTGC
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
65 42 0.55
66 35 0.45
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (66 bp):
CTCGATGCAGCCTCCTCTTTAAGTTGTATGTGGAGTTCATCATATTTTTTTTAAGACTCTGCTTC
T
Found at i:22997033 original size:18 final size:18
Alignment explanation
Indices: 22997010--22997295 Score: 136
Period size: 18 Copynumber: 17.1 Consensus size: 18
22997000 CTGTTTTTAT
*
22997010 TAATTAAATAATTAAATA
1 TAATTAAATAATTTAATA
22997028 TAATTAAATATTTAATTTAATA
1 TAATT-AA-A--TAATTTAATA
*** *
22997050 TAATTTTTTACTTTAATA
1 TAATTAAATAATTTAATA
22997068 TAATTAAATAA-TTAA-A
1 TAATTAAATAATTTAATA
* *
22997084 T-CTT---TAACTTAATA
1 TAATTAAATAATTTAATA
** * *
22997098 TAATTATTTACTTTAACA
1 TAATTAAATAATTTAATA
22997116 TAATTAAATAA-TTAA-A
1 TAATTAAATAATTTAATA
* * *
22997132 T-CTT--TTAACTTAATA
1 TAATTAAATAATTTAATA
** *
22997147 TAATTATTTACTTTAATA
1 TAATTAAATAATTTAATA
22997165 TAATTAAATAA-TTAA-A
1 TAATTAAATAATTTAATA
22997181 T-ATT---TAATTTAATA
1 TAATTAAATAATTTAATA
** *
22997195 TAATTATTTACTTTAATA
1 TAATTAAATAATTTAATA
22997213 TAATTAAATAA-TTAA-A
1 TAATTAAATAATTTAATA
22997229 T-ATT---TAATTTAATA
1 TAATTAAATAATTTAATA
** *
22997243 TAATTATTTACTTTAATA
1 TAATTAAATAATTTAATA
*
22997261 TAATT--ATACTTTAATA
1 TAATTAAATAATTTAATA
*
22997277 TAATTAAATAATTAAATA
1 TAATTAAATAATTTAATA
22997295 T
1 T
22997296 TTAATTATGT
Statistics
Matches: 206, Mismatches: 33, Indels: 58
0.69 0.11 0.20
Matches are distributed among these distances:
12 9 0.04
13 15 0.07
14 10 0.05
15 20 0.10
16 25 0.12
17 16 0.08
18 94 0.46
19 2 0.01
20 1 0.00
22 14 0.07
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTAAATAATTTAATA
Found at i:22997033 original size:22 final size:22
Alignment explanation
Indices: 22997008--22997054 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
22996998 GGCTGTTTTT
*
22997008 ATTAATTAAATAATTAAATATA
1 ATTAAATAAATAATTAAATATA
** *
22997030 ATTAAATATTTAATTTAATATA
1 ATTAAATAAATAATTAAATATA
22997052 ATT
1 ATT
22997055 TTTTACTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTAAATAAATAATTAAATATA
Found at i:22997096 original size:48 final size:48
Alignment explanation
Indices: 22997013--22997266 Score: 420
Period size: 48 Copynumber: 5.2 Consensus size: 48
22997003 TTTTTATTAA
*
22997013 TTAA-ATAATTAAATATAATTAAATATTTAATTTAATATAATTTTTTACT
1 TTAATATAATT-AA-ATAATTAAATATTTAATTTAATATAATTATTTACT
* *
22997062 TTAATATAATTAAATAATTAAATCTTTAACTTAATATAATTATTTACT
1 TTAATATAATTAAATAATTAAATATTTAATTTAATATAATTATTTACT
* * *
22997110 TTAACATAATTAAATAATTAAATCTTTTAACTTAATATAATTATTTACT
1 TTAATATAATTAAATAATTAAAT-ATTTAATTTAATATAATTATTTACT
22997159 TTAATATAATTAAATAATTAAATATTTAATTTAATATAATTATTTACT
1 TTAATATAATTAAATAATTAAATATTTAATTTAATATAATTATTTACT
22997207 TTAATATAATTAAATAATTAAATATTTAATTTAATATAATTATTTACT
1 TTAATATAATTAAATAATTAAATATTTAATTTAATATAATTATTTACT
22997255 TTAATATAATTA
1 TTAATATAATTA
22997267 TACTTTAATA
Statistics
Matches: 195, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
48 137 0.70
49 52 0.27
50 6 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (48 bp):
TTAATATAATTAAATAATTAAATATTTAATTTAATATAATTATTTACT
Found at i:22997177 original size:8 final size:8
Alignment explanation
Indices: 22997159--22997299 Score: 55
Period size: 8 Copynumber: 17.5 Consensus size: 8
22997149 ATTATTTACT
22997159 TTAATATAA
1 TTAA-ATAA
22997168 TTAAATAA
1 TTAAATAA
22997176 TTAAAT-A
1 TTAAATAA
*
22997183 TTTAAT--
1 TTAAATAA
22997189 TTAATATAA
1 TTAA-ATAA
** *
22997198 TTATTTACT
1 TTAAATA-A
22997207 TTAATATAA
1 TTAA-ATAA
22997216 TTAAATAA
1 TTAAATAA
22997224 TTAAAT-A
1 TTAAATAA
*
22997231 TTTAAT--
1 TTAAATAA
22997237 TTAATATAA
1 TTAA-ATAA
** *
22997246 TTATTTACT
1 TTAAATA-A
22997255 TTAATATAA
1 TTAA-ATAA
*
22997264 TT--ATACT
1 TTAAATA-A
22997271 TTAATATAA
1 TTAA-ATAA
22997280 TTAAATAA
1 TTAAATAA
*
22997288 TTAAATAT
1 TTAAATAA
22997296 TTAA
1 TTAA
22997300 TTATGTTAAG
Statistics
Matches: 99, Mismatches: 19, Indels: 29
0.67 0.13 0.20
Matches are distributed among these distances:
6 9 0.09
7 18 0.18
8 39 0.39
9 26 0.26
10 7 0.07
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (8 bp):
TTAAATAA
Found at i:22998875 original size:44 final size:43
Alignment explanation
Indices: 22998812--22998939 Score: 166
Period size: 44 Copynumber: 2.9 Consensus size: 43
22998802 GATCGGCTCA
* *
22998812 AGAAGCGGGTTCTGGGGGTGAAGAGCGAACGGAGTGAGGGGAAG
1 AGAAGCGGGTTTTGGGGGTGAAGAG-GAACGGAGTGAGGGGAAC
*
22998856 AGAAGCGGGTTTTGGGGGTGAAGAGGGAACGGGGTGAGGGGAAC
1 AGAAGCGGGTTTTGGGGGTGAAGA-GGAACGGAGTGAGGGGAAC
* ***
22998900 AGAAGTGGGTTTTACAGGTGAAGAGGCAACGGAGTGAGGG
1 AGAAGCGGGTTTTGGGGGTGAAGAGG-AACGGAGTGAGGG
22998940 AAATAAAAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 2 0.03
44 71 0.96
45 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.51, T:0.14
Consensus pattern (43 bp):
AGAAGCGGGTTTTGGGGGTGAAGAGGAACGGAGTGAGGGGAAC
Found at i:22998878 original size:23 final size:22
Alignment explanation
Indices: 22998812--22998880 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 22
22998802 GATCGGCTCA
22998812 AGAAGCGGGTTCTGGGGGTGAAG
1 AGAAGCGGGTT-TGGGGGTGAAG
*
22998835 AGCGAA-CGGAG--TGAGGG-GAAG
1 A--GAAGCGG-GTTTGGGGGTGAAG
22998856 AGAAGCGGGTTTTGGGGGTGAAG
1 AGAAGCGGG-TTTGGGGGTGAAG
22998879 AG
1 AG
22998881 GGAACGGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 16
0.67 0.04 0.30
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 5 0.14
22 10 0.28
23 7 0.19
24 3 0.08
25 4 0.11
ACGTcount: A:0.26, C:0.07, G:0.52, T:0.14
Consensus pattern (22 bp):
AGAAGCGGGTTTGGGGGTGAAG
Found at i:22998954 original size:44 final size:44
Alignment explanation
Indices: 22998828--22998958 Score: 147
Period size: 44 Copynumber: 3.0 Consensus size: 44
22998818 GGGTTCTGGG
* * ***
22998828 GGTGAAGA-GCGAACGGAGTGAGGGGAAGAGAAGCGGGTTTTGGG
1 GGTGAAGAGGC-AACGGAGTGAGGGGAACAGAAGAGGGTTTTACA
* * *
22998872 GGTGAAGAGGGAACGGGGTGAGGGGAACAGAAGTGGGTTTTACA
1 GGTGAAGAGGCAACGGAGTGAGGGGAACAGAAGAGGGTTTTACA
* * *
22998916 GGTGAAGAGGCAACGGAGTGAGGGAAATAAAAGAGGGTTTTAC
1 GGTGAAGAGGCAACGGAGTGAGGGGAACAGAAGAGGGTTTTAC
22998959 GATTTGAGAG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 72 0.99
45 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.47, T:0.15
Consensus pattern (44 bp):
GGTGAAGAGGCAACGGAGTGAGGGGAACAGAAGAGGGTTTTACA
Found at i:22998976 original size:25 final size:25
Alignment explanation
Indices: 22998946--22999015 Score: 86
Period size: 26 Copynumber: 2.8 Consensus size: 25
22998936 AGGGAAATAA
22998946 AAGAGGGTTTTACGATTTGAGAGTG
1 AAGAGGGTTTTACGATTTGAGAGTG
* * *
22998971 AAGAGGGGTATTACGATTTGGGGGTG
1 AAGA-GGGTTTTACGATTTGAGAGTG
* *
22998997 AAGAGGGTTCTGCGATTTG
1 AAGAGGGTTTTACGATTTG
22999016 GGGGTGATGC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 16 0.42
26 22 0.58
ACGTcount: A:0.24, C:0.06, G:0.40, T:0.30
Consensus pattern (25 bp):
AAGAGGGTTTTACGATTTGAGAGTG
Found at i:22999016 original size:25 final size:24
Alignment explanation
Indices: 22998946--22999022 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 24
22998936 AGGGAAATAA
* *
22998946 AAGAGGGTTTTACGATTTGAGAGTG
1 AAGAGGG-TTTACGATTTGGGGGTG
22998971 AAGAGGGGTATTACGATTTGGGGGTG
1 AAGA-GGGT-TTACGATTTGGGGGTG
*
22998997 AAGAGGGTTCTGCGATTTGGGGGTG
1 AAGAGGGTT-TACGATTTGGGGGTG
22999022 A
1 A
22999023 TGCATGCAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 1 0.02
25 24 0.52
26 21 0.46
ACGTcount: A:0.23, C:0.05, G:0.43, T:0.29
Consensus pattern (24 bp):
AAGAGGGTTTACGATTTGGGGGTG
Found at i:22999269 original size:41 final size:42
Alignment explanation
Indices: 22999133--22999486 Score: 237
Period size: 41 Copynumber: 8.4 Consensus size: 42
22999123 GCTTATAGAA
* **
22999133 AAGCGCCGCTAATG-CAC-ACCTTTAGCGGCGCTTAT-TAGAA
1 AAGCGCCGCTAATGACACGACCTTTAGCGGCGCTT-TGTGGGT
* * * * ***
22999173 AAGCGCCGCTAATAAC-CTGACCTTTACCGACGCTTTCTATAT
1 AAGCGCCGCTAATGACAC-GACCTTTAGCGGCGCTTTGTGGGT
* *
22999215 AAGAGTCGCTAATGACACGACCTTTAGCGGCG-TTTGTGGGT
1 AAGCGCCGCTAATGACACGACCTTTAGCGGCGCTTTGTGGGT
* * *
22999256 AAGCGCCGCTAATGACTCCACTTTTAGCGGCGCTTT-T-GGT
1 AAGCGCCGCTAATGACACGACCTTTAGCGGCGCTTTGTGGGT
* *
22999296 GAAGCGCCGCTAATGACTA-GACCATTAGCGCCGCTTCTGGATAAGCGCCGCT
1 -AAGCGCCGCTAATGAC-ACGACCTTTAGCGGCGCTT-T-G-T--G-G--G-T
** * * * **
22999348 ATCCAGCCGCTAATGACCCGACTTTTAGTGGCGC-TTGTGTCT
1 AAGC-GCCGCTAATGACACGACCTTTAGCGGCGCTTTGTGGGT
**
22999390 AAGCGCCGCTAATGAGTCGACCTTTAGCGGCGC-TTGTGGGT
1 AAGCGCCGCTAATGACACGACCTTTAGCGGCGCTTTGTGGGT
* *
22999431 AAAGCGCCGCTAAAGACCCGACCTTTAGCGGCGCTTTGT--GT
1 -AAGCGCCGCTAATGACACGACCTTTAGCGGCGCTTTGTGGGT
22999472 AAGCGCCGCTAATGA
1 AAGCGCCGCTAATGA
22999487 TTTACCTTTT
Statistics
Matches: 246, Mismatches: 45, Indels: 46
0.73 0.13 0.14
Matches are distributed among these distances:
40 31 0.13
41 97 0.39
42 79 0.32
43 5 0.02
45 1 0.00
46 1 0.00
48 1 0.00
49 2 0.01
50 1 0.00
51 4 0.02
52 24 0.10
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (42 bp):
AAGCGCCGCTAATGACACGACCTTTAGCGGCGCTTTGTGGGT
Found at i:22999424 original size:93 final size:94
Alignment explanation
Indices: 22999260--22999442 Score: 246
Period size: 93 Copynumber: 2.0 Consensus size: 94
22999250 GTGGGTAAGC
*
22999260 GCCGCTAATGACTCCACTTTTAGCGGCGCTTTTGGTGAAGCGCCGCTAATGACTAGACCATTAGC
1 GCCGCTAATGACTCCACTTTTAGCGGCGCTTGTGGTGAAGCGCCGCTAATGACTAGACCATTAGC
22999325 GCCGCTTCTGGAT-AAGCGCCGCTATCCA
66 GCCGCTTCTGGATAAAGCGCCGCTATCCA
* * * * *
22999353 GCCGCTAATGAC-CCGACTTTTAGTGGCGCTTGT-GTCTAAGCGCCGCTAATGAGTCGACCTTTA
1 GCCGCTAATGACTCC-ACTTTTAGCGGCGCTTGTGGT-GAAGCGCCGCTAATGACTAGACCATTA
* * *
22999416 GCGGCGCTTGTGGGTAAAGCGCCGCTA
64 GCGCCGCTTCTGGATAAAGCGCCGCTA
22999443 AAGACCCGAC
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
92 4 0.05
93 63 0.81
94 11 0.14
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.25
Consensus pattern (94 bp):
GCCGCTAATGACTCCACTTTTAGCGGCGCTTGTGGTGAAGCGCCGCTAATGACTAGACCATTAGC
GCCGCTTCTGGATAAAGCGCCGCTATCCA
Found at i:22999475 original size:134 final size:134
Alignment explanation
Indices: 22999221--22999482 Score: 348
Period size: 134 Copynumber: 2.0 Consensus size: 134
22999211 ATATAAGAGT
* * *
22999221 CGCTAATGACACGACCTTTAGCGGCGTTTGTGGGTAAGCGCCGCTAATGACTCCACTTTTAGCGG
1 CGCTAATGACACGACCTTTAGCGGCGCTTGTGGCTAAGCGCCGCTAATGACTCCACCTTTAGCGG
* * * *
22999286 CGCTTTTGGTGAAGCGCCGCTAATGACTAGACCATTAGCGCCGCTTCTGGATAAGCGCCGCTATC
66 CGCTTTGGGTAAAGCGCCGCTAAAGACCAGACCATTAGCGCCGCTTCTGGATAAGCGCCGCTATC
22999351 CAGC
131 CAGC
* * * * * *
22999355 CGCTAATGACCCGACTTTTAGTGGCGCTTGTGTCTAAGCGCCGCTAATGAGTCGACCTTTAGCGG
1 CGCTAATGACACGACCTTTAGCGGCGCTTGTGGCTAAGCGCCGCTAATGACTCCACCTTTAGCGG
* * *
22999420 CGCTTGTGGGTAAAGCGCCGCTAAAGACCCGACCTTTAGCGGCGCTT-TGTG-TAAGCGCCGCTA
66 CGCTT-TGGGTAAAGCGCCGCTAAAGACCAGACCATTAGCGCCGCTTCTG-GATAAGCGCCGCTA
22999483 ATGATTTACC
Statistics
Matches: 110, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 75 0.68
135 35 0.32
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (134 bp):
CGCTAATGACACGACCTTTAGCGGCGCTTGTGGCTAAGCGCCGCTAATGACTCCACCTTTAGCGG
CGCTTTGGGTAAAGCGCCGCTAAAGACCAGACCATTAGCGCCGCTTCTGGATAAGCGCCGCTATC
CAGC
Found at i:22999560 original size:81 final size:83
Alignment explanation
Indices: 22999353--22999564 Score: 229
Period size: 81 Copynumber: 2.6 Consensus size: 83
22999343 CCGCTATCCA
* * *
22999353 GCCGCTAATGACCCGACTTTTAGTGGCGC-TTGTGTCTAAGCGCCGCTAATGAGTCGACCTTTAG
1 GCCGCTAAAGACCCGACCTTTAGCGGCGCTTTGTGTC-AAGCGCCGCTAATGAGTCGACCTTTAG
* * *
22999417 CGGCGCTTGTGGGTAAAGC
65 CGGCGCATGTAGGAAAAGC
** *
22999436 GCCGCTAAAGACCCGACCTTTAGCGGCGCTTTGTGT-AAGCGCCGCTAATGA-TTTACCTTTTGC
1 GCCGCTAAAGACCCGACCTTTAGCGGCGCTTTGTGTCAAGCGCCGCTAATGAGTCGACCTTTAGC
22999499 GGCGCAT-TAGGAAAAGC
66 GGCGCATGTAGGAAAAGC
* * * * *
22999516 GCCGCTAATG-CTTC-ACCTTTTGCGGTGCTTTGTGTCCAAACGCCGCTAA
1 GCCGCTAAAGAC-CCGACCTTTAGCGGCGCTTTGTGT-CAAGCGCCGCTAA
22999565 AAATGCCGCT
Statistics
Matches: 111, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
79 20 0.18
80 18 0.16
81 26 0.23
82 15 0.14
83 26 0.23
84 6 0.05
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (83 bp):
GCCGCTAAAGACCCGACCTTTAGCGGCGCTTTGTGTCAAGCGCCGCTAATGAGTCGACCTTTAGC
GGCGCATGTAGGAAAAGC
Found at i:22999757 original size:27 final size:27
Alignment explanation
Indices: 22999743--22999805 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
22999733 GTTTAAAGTT
22999743 ATTTCAAATGTATTTAAATTTAAATAA
1 ATTTCAAATGTATTTAAATTTAAATAA
22999770 ATTTCAAATGTATTTAAATTTAAATAA
1 ATTTCAAATGTATTTAAATTTAAATAA
*
22999797 ATTTAAAAT
1 ATTTCAAAT
22999806 TAATTTCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (27 bp):
ATTTCAAATGTATTTAAATTTAAATAA
Found at i:22999822 original size:12 final size:11
Alignment explanation
Indices: 22999786--22999828 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
22999776 AATGTATTTA
*
22999786 AATTT-AAATA
1 AATTTAAAATT
22999796 AATTTAAAATT
1 AATTTAAAATT
*
22999807 AATTTCAAACTT
1 AATTT-AAAATT
22999819 AATTTAAAAT
1 AATTTAAAAT
22999829 CCAAGTTGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 10 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:23001274 original size:12 final size:12
Alignment explanation
Indices: 23001259--23001283 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23001249 CAAATTTTAA
23001259 TTTAATCGAAAT
1 TTTAATCGAAAT
23001271 TTTAATCGAAAT
1 TTTAATCGAAAT
23001283 T
1 T
23001284 CAAAATTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTAATCGAAAT
Found at i:23001731 original size:10 final size:11
Alignment explanation
Indices: 23001701--23001725 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23001691 GTTGATTAGG
23001701 TATCAATTTTT
1 TATCAATTTTT
23001712 TATCAATTTTT
1 TATCAATTTTT
23001723 TAT
1 TAT
23001726 TATTTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (11 bp):
TATCAATTTTT
Done.