Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 202 of 218
Found at i:59829220 original size:194 final size:193
Alignment explanation
Indices: 59828910--59829359 Score: 580
Period size: 194 Copynumber: 2.3 Consensus size: 193
59828900 CGACAAACAG
* * * *
59828910 ATTCCCATTCTTAAAAGTCATTTTTCTTCGACTCTTGAAAAACTCAAAAGCAATATATAGCAACA
1 ATTCCCATTCTTAAAAAT-ATTTCTCTTCGACTTTTGAAAAACTCAAAAGCAATATACAGCAACA
* *
59828975 AACAACATATATCAACAATCATAAACACAAATCCAGCAGAAACATTAAGGAATCAAGATTTCATA
65 AACAACATATATCAACAACCATAAACACAAATCCAGCAGAAACAGTAAGGAATCAAGATTTCATA
* * * * * * *
59829040 GCTTCGGATATGTCATAAAATGGGGTTTTGTTGAGAAGAAATTCG-GACAGTTAAACAACACCTG
130 ACGTCAGAAATGTCATAAAAT-GGGTTTTGTCGAGAAGAAATT-GAGACAGTTAAACAAAACCCG
59829104 A
193 A
* *
59829105 ATTCCCATTCTTAAAAATGTTTCTCTTCGACTTTTGTAAAACTCAAAAGCAATATACAGCAACAA
1 ATTCCCATTCTTAAAAATATTTCTCTTCGACTTTTGAAAAACTCAAAAGCAATATACAGCAACAA
* * * * *
59829170 ACAGCATATATCGACAACCATAAACACAAATTCAGCAGAATCAGTAAGGAATCAAGATTTTATAA
66 ACAACATATATCAACAACCATAAACACAAATCCAGCAGAAACAGTAAGGAATCAAGATTTCATAA
** * * *
59829235 CGTCAGAAATGTTGTAAACTGGGTTTTGTCGAGAAGCAATTGAGACAGTTAAACAAAACCCGT
131 CGTCAGAAATGTCATAAAATGGGTTTTGTCGAGAAGAAATTGAGACAGTTAAACAAAACCCGA
* * * * *
59829298 ATTCCCGTTTTTCAAAGACATTTCTCTTCGATTTTTGAAAAACTC-AAAGCAATATACAGCAA
1 ATTCCCATTCTT-AAAAATATTTCTCTTCGACTTTTGAAAAACTCAAAAGCAATATACAGCAA
59829360 TATTTCCAAT
Statistics
Matches: 221, Mismatches: 32, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
192 1 0.00
193 63 0.29
194 140 0.63
195 17 0.08
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (193 bp):
ATTCCCATTCTTAAAAATATTTCTCTTCGACTTTTGAAAAACTCAAAAGCAATATACAGCAACAA
ACAACATATATCAACAACCATAAACACAAATCCAGCAGAAACAGTAAGGAATCAAGATTTCATAA
CGTCAGAAATGTCATAAAATGGGTTTTGTCGAGAAGAAATTGAGACAGTTAAACAAAACCCGA
Found at i:59839593 original size:22 final size:21
Alignment explanation
Indices: 59839568--59839609 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
59839558 AGAAAAAAAT
*
59839568 TTTAATTTTCCTATTATTATTA
1 TTTAATTTTACTATT-TTATTA
59839590 TTTAATTTTACTATTTTATT
1 TTTAATTTTACTATTTTATT
59839610 TTATTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTAATTTTACTATTTTATTA
Found at i:59840220 original size:12 final size:13
Alignment explanation
Indices: 59840203--59840231 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
59840193 CTAAGTACAA
59840203 AAATAAAT-AAAT
1 AAATAAATAAAAT
59840215 AAATAAATAAAAT
1 AAATAAATAAAAT
59840228 AAAT
1 AAAT
59840232 TAGGGGTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:59845910 original size:20 final size:19
Alignment explanation
Indices: 59845873--59845915 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
59845863 AATTATTTTG
59845873 TAATAGTTTAAAAAAATTAT
1 TAATAGTTTAAAAAAATT-T
* * *
59845893 TAATAGTTTTAGAGAATTT
1 TAATAGTTTAAAAAAATTT
59845912 TAAT
1 TAAT
59845916 TAAATAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (19 bp):
TAATAGTTTAAAAAAATTT
Found at i:59846901 original size:14 final size:14
Alignment explanation
Indices: 59846882--59846911 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
59846872 CTATCGGCAC
59846882 ATTGTTCTTGAGAT
1 ATTGTTCTTGAGAT
59846896 ATTGTTCTTGAGAT
1 ATTGTTCTTGAGAT
59846910 AT
1 AT
59846912 AAGAACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50
Consensus pattern (14 bp):
ATTGTTCTTGAGAT
Found at i:59847418 original size:24 final size:25
Alignment explanation
Indices: 59847378--59847424 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
59847368 CAACTTCTAA
*
59847378 AGAAAACTCTAGAGAGAATTCTGGG
1 AGAAAACTCAAGAGAGAATTCTGGG
59847403 AGAAAACTCAAG-GAGAATTCTG
1 AGAAAACTCAAGAGAGAATTCTG
59847425 CACTTAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.19
Consensus pattern (25 bp):
AGAAAACTCAAGAGAGAATTCTGGG
Found at i:59862673 original size:23 final size:23
Alignment explanation
Indices: 59862647--59862695 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
59862637 ATGCCTATTT
*
59862647 ATAGGATTGTAAA-CCTTATTCTA
1 ATAGGAGTG-AAACCCTTATTCTA
59862670 ATAGGAGTGAAACTCCTTATTCTA
1 ATAGGAGTGAAAC-CCTTATTCTA
59862694 AT
1 AT
59862696 CAATATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 3 0.13
23 8 0.35
24 12 0.52
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (23 bp):
ATAGGAGTGAAACCCTTATTCTA
Found at i:59863865 original size:23 final size:23
Alignment explanation
Indices: 59863821--59863875 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
59863811 TTATCTTTAA
* *
59863821 AATTTT-AATTATATTTCAAAATT
1 AATTTTAAATAATATATCAAAA-T
59863844 AATTTTAAATAATATATC-AAAT
1 AATTTTAAATAATATATCAAAAT
59863866 ATATTTTAAA
1 A-ATTTTAAA
59863876 ATTTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 2 0.07
23 17 0.61
24 9 0.32
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTTAAATAATATATCAAAAT
Found at i:59867830 original size:18 final size:19
Alignment explanation
Indices: 59867799--59867841 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
59867789 TTAAAAAGTT
59867799 AAAATAAAATTTAAT-TTA
1 AAAATAAAATTTAATATTA
59867817 AAAAT-AAATATTAATATTA
1 AAAATAAAAT-TTAATATTA
*
59867836 CAAATA
1 AAAATA
59867842 TATTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATAAAATTTAATATTA
Found at i:59869101 original size:19 final size:19
Alignment explanation
Indices: 59869077--59869116 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
59869067 CTTGAGAGTG
*
59869077 TTAGCACACTTAACTTGAT
1 TTAGCACACTCAACTTGAT
59869096 TTAGCACACTCAACTTGAT
1 TTAGCACACTCAACTTGAT
59869115 TT
1 TT
59869117 TGACCATAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (19 bp):
TTAGCACACTCAACTTGAT
Found at i:59874863 original size:42 final size:43
Alignment explanation
Indices: 59874772--59874924 Score: 123
Period size: 43 Copynumber: 3.6 Consensus size: 43
59874762 AATGGCATAT
* * ** * * * **
59874772 CCCAGATATGGTCTTACATGTTATCACATATGGATGTCACTGT
1 CCCAGACATGGTCTTACACGAAATCTCATATCGATGCCACTAC
*
59874815 CCCAGACA-GAGTCTTATACGAAA--TCATATACGATGCCACTAC
1 CCCAGACATG-GTCTTACACGAAATCTCATAT-CGATGCCACTAC
* * **
59874857 CCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGT
1 CCCAGACATGGTCTTACACGAAATCTCATATCGATGCCACTAC
* *
59874900 CTCAAACATGGTCTTACACGAAATC
1 CCCAGACATGGTCTTACACGAAATC
59874925 AAACCTCAAG
Statistics
Matches: 87, Mismatches: 18, Indels: 10
0.76 0.16 0.09
Matches are distributed among these distances:
41 5 0.06
42 28 0.32
43 48 0.55
44 6 0.07
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (43 bp):
CCCAGACATGGTCTTACACGAAATCTCATATCGATGCCACTAC
Found at i:59877489 original size:27 final size:28
Alignment explanation
Indices: 59877459--59877512 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
59877449 AGCTAGACTG
59877459 TTAAAGAAGTTAG-CTGTTAAAAAGCTA
1 TTAAAGAAGTTAGTCTGTTAAAAAGCTA
* *
59877486 TTAAAGAAGTTAGTTTGTTAAATAGCT
1 TTAAAGAAGTTAGTCTGTTAAAAAGCT
59877513 TAGCAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.35
Consensus pattern (28 bp):
TTAAAGAAGTTAGTCTGTTAAAAAGCTA
Found at i:59886285 original size:43 final size:43
Alignment explanation
Indices: 59886215--59886694 Score: 653
Period size: 43 Copynumber: 11.2 Consensus size: 43
59886205 AGTGTCGCTA
* * *
59886215 ACCTTTA-CGGCGTTTATTTCTAAAAACGCCGCTAAAGAACAAG
1 ACCTTTAGCGGCGCTT-TTTCCACAAACGCCGCTAAAGAACAAG
59886258 ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
1 ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
*
59886301 ACCTTTAGCGGCGCTTTTTTCACAAACGCCGCTAAAGAACAAG
1 ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
* * * * *
59886344 ACCTTTAACGGTGCTTCTTT-CACAAATGCCACTAAAGAATAAG
1 ACCTTTAGCGGCGCTT-TTTCCACAAACGCCGCTAAAGAACAAG
59886387 ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
1 ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
* *
59886430 ACCTTTAGCGGCGCTTTTTTCACAAATGCCGCTAAAGAACAAG
1 ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
* * * * *
59886473 ACCTTTAACGGTGCTTCTTT-CACAAATGCCACTAAAGAATAAG
1 ACCTTTAGCGGCGCTT-TTTCCACAAACGCCGCTAAAGAACAAG
*
59886516 ACCTTTAGCGACGCTTTTT-CACAAACGCCGCTAAAGAACAAG
1 ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
* *
59886558 ACCTTTAGCAGCGCTTTTTCCACAAACGCCGCTAAAGAACAAC
1 ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
* * *
59886601 ACCTTTTAGCGGCTCTTTTTCCACAAACACCGCTATAGAACAAG
1 ACC-TTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
* * * * *
59886645 ACCTTTTGCGACGCTTTTCCCAAAAACGCCGCTAAAGAACATG
1 ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
59886688 ACCTTTA
1 ACCTTTA
59886695 AAAAAATATT
Statistics
Matches: 388, Mismatches: 43, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
42 43 0.11
43 294 0.76
44 51 0.13
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACAAG
Found at i:59886875 original size:12 final size:13
Alignment explanation
Indices: 59886860--59886889 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
59886850 TAAAAATTAA
59886860 TAAATTT-AAATT
1 TAAATTTAAAATT
59886872 TAAATTTAAAATT
1 TAAATTTAAAATT
59886885 TAAAT
1 TAAAT
59886890 ATTATGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:59886885 original size:7 final size:6
Alignment explanation
Indices: 59886860--59886889 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
59886850 TAAAAATTAA
59886860 TAAATT TAAATT TAAATT TAAAATT TAAAT
1 TAAATT TAAATT TAAATT T-AAATT TAAAT
59886890 ATTATGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:59890168 original size:106 final size:106
Alignment explanation
Indices: 59890011--59890868 Score: 1000
Period size: 106 Copynumber: 8.1 Consensus size: 106
59890001 TTTTATTTTG
*
59890011 TTTTTTT-ATAAATTGA--T-TTAT-TTTTGTGGCGCTTTTATAAAAAACGCCGCAAAAAAATTA
1 TTTTTTTAATAAATTGATTTATTATCTTTTGCGGCGCTTTTATAAAAAACGCCGCAAAAAAATTA
* *
59890071 TTTCGTTTTGAACAAAATGACGCTGTTTTGATATGCT-AAT
66 TTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAT
* * * *
59890111 TTTTTTAAAATAAATTGATTTATTATCTTTTGCGGCGTTTTTATGAAAAACGTCGC-AAAAAATT
1 TTTTTT-TAATAAATTGATTTATTATCTTTTGCGGCGCTTTTATAAAAAACGCCGCAAAAAAATT
* *
59890175 ATTTCAG-TTTGAA-AAAATGACGTCGTTTTGCTGTGCTAAAAT
65 ATTTC-GTTTTGAACAAAATGACGCCGTTTTGCTATGCT-AAAT
** *** * *
59890217 TTTTTTATTGTTTTTTTATAAATTGATTTAT-TTTTGCGGCGCTTTTATAAAAAACGCCG-GAAA
1 TTTTTT-TAATAAATTGAT---TT-A-TTATCTTTTGCGGCGCTTTTATAAAAAACGCCGCAAAA
* *
59890280 AAATTATTTCGTTTTGAACAAAATGACGCCGTTTTGCTAAGCTAAAA
60 AAATTATTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAT
59890327 TTTTTTTAATAAATTGATTTATTATCTTTTGCGGCGCTTTTATAAAAAACGCCGCAAAAAAATTA
1 TTTTTTTAATAAATTGATTTATTATCTTTTGCGGCGCTTTTATAAAAAACGCCGCAAAAAAATTA
* * *
59890392 TTTCGTTTTGAACAAAATGACGCCGTTTTGCTAAGTTAAAA
66 TTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAT
*
59890433 TTTTTTTAATAAATTGATTTATTATCTTTTGCGGTGCTTTTATAAAAAACGCCGCAAAAAAAATT
1 TTTTTTTAATAAATTGATTTATTATCTTTTGCGGCGCTTTTATAAAAAACGCCGC-AAAAAAATT
*
59890498 ATTTCGTTTTGAACAAAATGACGCCATTTTGCTATGCTAAAAT
65 ATTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCT-AAAT
* * * *
59890541 TTTTTTTAATAAATTGATTTATTATCTTTTGTGGCGTTTTTTATGACAAACGCCGC-AAAAAATT
1 TTTTTTTAATAAATTGATTTATTATCTTTTGCGGCG-CTTTTATAAAAAACGCCGCAAAAAAATT
* *
59890605 ATTTCAG-TTTGAA-AAAATGACGCCATTTTGCTGTGCTAAAAATTTTTT
65 ATTTC-GTTTTGAACAAAATGACGCCGTTTTGCTATGCT--AAA-----T
* * *
59890653 ATTTTTTTTATAAATTGA--T-TTAT-TTTTGCTGTGCTTTTATAAAAAACGCCGCAAAAAAATT
1 -TTTTTTTAATAAATTGATTTATTATCTTTTGCGGCGCTTTTATAAAAAACGCCGCAAAAAAATT
* *
59890714 ATTTCATTTTGAAAAAAATGACGCCGTTTTGCTATGCTAAAT
65 ATTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAT
* *
59890756 TTTTTTTAATAAATTGATTTATTATCTTTTGCGGCG-TTTTACATAAAAACGCCAC-AAAAAATT
1 TTTTTTTAATAAATTGATTTATTATCTTTTGCGGCGCTTTTATA-AAAAACGCCGCAAAAAAATT
* ** * *
59890819 ATTTCATTTCCAACAAAATGACGCCGTTTTGCTATGATAAAA
65 ATTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAT
*
59890861 ATTTTTTA
1 TTTTTTTA
59890869 TTTTGCTTTT
Statistics
Matches: 657, Mismatches: 63, Indels: 71
0.83 0.08 0.09
Matches are distributed among these distances:
100 6 0.01
102 25 0.04
103 1 0.00
104 26 0.04
105 114 0.17
106 187 0.28
107 67 0.10
108 57 0.09
109 51 0.08
110 80 0.12
111 26 0.04
112 1 0.00
113 16 0.02
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (106 bp):
TTTTTTTAATAAATTGATTTATTATCTTTTGCGGCGCTTTTATAAAAAACGCCGCAAAAAAATTA
TTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAT
Found at i:59890362 original size:215 final size:216
Alignment explanation
Indices: 59889928--59890910 Score: 1348
Period size: 215 Copynumber: 4.5 Consensus size: 216
59889918 AAACTTGAGG
* *
59889928 GTTTTTAATAAAAAAAGCCGCAAAAAATTATTTCAGTTTGAAAAAATGACGTCGTTTTGCTGTGC
1 GTTTTT-ATAAAAAACGCCGCAAAAAATTATTTCAGTTTGAAAAAATGACGCCGTTTTGCTGTGC
* *
59889993 TAAAAATTTTTTATTTTGTTTTTTTATAAATTGATTTATTTTTGTGGCGCTTTTATAAAAAACGC
65 T-AAAATTTTTT-TATTGTTTTTTTATAAATTGATTTATTTTTGCGGCGCTTTTATAAAAAACGC
* *
59890058 CGCAAAAAAATTATTTCGTTTTGAACAAAATGACGCTGTTTTGATATGCT--AATTTTTTTAAAA
128 CGCAAAAAAATTATTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAATTTTTTT--AA
59890121 TAAATTGATTTATTATCTTTTGCGGC
191 TAAATTGATTTATTATCTTTTGCGGC
* * *
59890147 GTTTTTATGAAAAACGTCGCAAAAAATTATTTCAGTTTGAAAAAATGACGTCGTTTTGCTGTGCT
1 GTTTTTATAAAAAACGCCGCAAAAAATTATTTCAGTTTGAAAAAATGACGCCGTTTTGCTGTGCT
59890212 AAAATTTTTTTATTGTTTTTTTATAAATTGATTTATTTTTGCGGCGCTTTTATAAAAAACGCCG-
66 AAAATTTTTTTATTGTTTTTTTATAAATTGATTTATTTTTGCGGCGCTTTTATAAAAAACGCCGC
* *
59890276 GAAAAAATTATTTCGTTTTGAACAAAATGACGCCGTTTTGCTAAGCTAAAATTTTTTTAATAAAT
131 AAAAAAATTATTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAATTTTTTTAATAAAT
59890341 TGATTTATTATCTTTTGCGGC
196 TGATTTATTATCTTTTGCGGC
* **
59890362 GCTTTTATAAAAAACGCCGCAAAAAAATTATTTC-GTTTTGAACAAAATGACGCCGTTTTGCTAA
1 GTTTTTATAAAAAACGCCGC-AAAAAATTATTTCAG-TTTGAA-AAAATGACGCCGTTTTGCTGT
* * *** * *
59890426 GTTAAAATTTTTTTA--ATAAATTGAT---TT-A-TTATCTTTTGCGGTGCTTTTATAAAAAACG
63 GCTAAAATTTTTTTATTGTTTTTTTATAAATTGATTTAT-TTTTGCGGCGCTTTTATAAAAAACG
*
59890484 CCGCAAAAAAAATTATTTCGTTTTGAACAAAATGACGCCATTTTGCTATGCTAAAATTTTTTTTA
127 CCGC-AAAAAAATTATTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAA-TTTTTTTA
*
59890549 ATAAATTGATTTATTATCTTTTGTGGC
190 ATAAATTGATTTATTATCTTTTGCGGC
* * *
59890576 GTTTTTTATGACAAACGCCGCAAAAAATTATTTCAGTTTGAAAAAATGACGCCATTTTGCTGTGC
1 G-TTTTTATAAAAAACGCCGCAAAAAATTATTTCAGTTTGAAAAAATGACGCCGTTTTGCTGTGC
* * *
59890641 TAAAAATTTTTTA-T-TTTTTTTATAAATTGATTTATTTTTGCTGTGCTTTTATAAAAAACGCCG
65 TAAAATTTTTTTATTGTTTTTTTATAAATTGATTTATTTTTGCGGCGCTTTTATAAAAAACGCCG
* * *
59890704 CAAAAAAATTATTTCATTTTGAAAAAAATGACGCCGTTTTGCTATGCTAAATTTTTTTTAATAAA
130 CAAAAAAATTATTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAATTTTTTTAATAAA
59890769 TTGATTTATTATCTTTTGCGGC
195 TTGATTTATTATCTTTTGCGGC
* * * *
59890791 G-TTTTACATAAAAACGCCACAAAAAATTATTTCA-TTTCCAACAAAATGACGCCGTTTTGCTAT
1 GTTTTTATA-AAAAACGCCGCAAAAAATTATTTCAGTTT-GAA-AAAATGACGCCGTTTTGCTGT
* * *
59890854 GATAAAAATTTTTTATTTTGCTTTTTTTATAAATTGATTTATTTTTGCGGCGTTTTT
63 GCT-AAAATTTTTT-TATTG-TTTTTTTATAAATTGATTTATTTTTGCGGCGCTTTT
59890911 TGAACAAAAT
Statistics
Matches: 682, Mismatches: 57, Indels: 49
0.87 0.07 0.06
Matches are distributed among these distances:
210 4 0.01
211 28 0.04
212 2 0.00
213 92 0.13
214 79 0.12
215 167 0.24
216 129 0.19
217 81 0.12
218 61 0.09
219 6 0.01
220 33 0.05
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (216 bp):
GTTTTTATAAAAAACGCCGCAAAAAATTATTTCAGTTTGAAAAAATGACGCCGTTTTGCTGTGCT
AAAATTTTTTTATTGTTTTTTTATAAATTGATTTATTTTTGCGGCGCTTTTATAAAAAACGCCGC
AAAAAAATTATTTCGTTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAATTTTTTTAATAAAT
TGATTTATTATCTTTTGCGGC
Found at i:59891000 original size:187 final size:184
Alignment explanation
Indices: 59890720--59891081 Score: 636
Period size: 187 Copynumber: 2.0 Consensus size: 184
59890710 AATTATTTCA
59890720 TTTTGAAAAAAATGACGCCGTTTTGCTATGCTAAATTTTTTTTAATAAATTGATTTATTATCTTT
1 TTTTGAAAAAAATGACGCCGTTTTGCTATGCTAAATTTTTTTTAATAAATTGATTTATTATCTTT
59890785 TGCGGCGTTTTACATAAAAACGCCACAAAAAATTATTTCATTTCCAACAAAATGACGCCGTTTTG
66 TGCGGCGTTTTACATAAAAACGCCACAAAAAATTATTTCATTTCCAACAAAATGACGCCGTTTTG
59890850 CTATGATAAAAATTTTTTATTTTGCTTTTTTTATAAATTGATTTATTTTTGCGGCGTT
131 CTATGATAAAAA-TTTTTATTTTG--TTTTTTATAAATTGATTT-TTTTTGCGGCGTT
* *
59890908 TTTTGAACAAAATGACGCCGTTTTGCTATGCTAAA-TTTTTTTAATATATTGATTTATTATCTTT
1 TTTTGAAAAAAATGACGCCGTTTTGCTATGCTAAATTTTTTTTAATAAATTGATTTATTATCTTT
* *
59890972 TGCGGCGTTTTTCATAAAAACGCCACAAAAAATTATTTCATTTTCAACAAAATGACGCCGTTTTG
66 TGCGGCGTTTTACATAAAAACGCCACAAAAAATTATTTCATTTCCAACAAAATGACGCCGTTTTG
*
59891037 CTATGCTAAAAATTTTTATTTTGTTTTTTATAAATTGATTTTTTT
131 CTATGATAAAAATTTTTATTTTGTTTTTTATAAATTGATTTTTTT
59891082 ATAAAATAAA
Statistics
Matches: 169, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
183 4 0.02
184 18 0.11
186 11 0.07
187 102 0.60
188 34 0.20
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.46
Consensus pattern (184 bp):
TTTTGAAAAAAATGACGCCGTTTTGCTATGCTAAATTTTTTTTAATAAATTGATTTATTATCTTT
TGCGGCGTTTTACATAAAAACGCCACAAAAAATTATTTCATTTCCAACAAAATGACGCCGTTTTG
CTATGATAAAAATTTTTATTTTGTTTTTTATAAATTGATTTTTTTTGCGGCGTT
Found at i:59891648 original size:15 final size:14
Alignment explanation
Indices: 59891593--59891702 Score: 57
Period size: 14 Copynumber: 7.7 Consensus size: 14
59891583 CCTAAATCAG
59891593 TAAACCTTAAATCCC
1 TAAACCTT-AATCCC
59891608 T-AACTCTTAA-CCC
1 TAAAC-CTTAATCCC
* *
59891621 TTAACGTCTAATCCC
1 TAAACCT-TAATCCC
59891636 TAAACCTTAAAT--C
1 TAAACCTT-AATCCC
*
59891649 TAAACCCTTAATCCA
1 TAAA-CCTTAATCCC
* * * *
59891664 TAATCCCTAATTCA
1 TAAACCTTAATCCC
* *
59891678 TAAATCCATACTCCC
1 TAAA-CCTTAATCCC
59891693 TAAACCTTAA
1 TAAACCTTAA
59891703 AATATGAACT
Statistics
Matches: 72, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
13 13 0.18
14 31 0.43
15 28 0.39
ACGTcount: A:0.37, C:0.32, G:0.01, T:0.30
Consensus pattern (14 bp):
TAAACCTTAATCCC
Found at i:59891703 original size:22 final size:22
Alignment explanation
Indices: 59891648--59891703 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
59891638 AACCTTAAAT
59891648 CTAAACCCTT-AATCCATAATCC
1 CTAAA-CCTTAAATCCATAATCC
** * *
59891670 CTAATTCATAAATCCATACTCC
1 CTAAACCTTAAATCCATAATCC
59891692 CTAAACCTTAAA
1 CTAAACCTTAAA
59891704 ATATGAACTC
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (22 bp):
CTAAACCTTAAATCCATAATCC
Found at i:59891903 original size:15 final size:15
Alignment explanation
Indices: 59891883--59891942 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
59891873 CCCTAACTTT
59891883 TAACCCCTAAACCTC
1 TAACCCCTAAACCTC
*
59891898 TAACCCTCT-AACCCC
1 TAACCC-CTAAACCTC
* * *
59891913 AAAACCTCTAACCCTC
1 -TAACCCCTAAACCTC
*
59891929 TAACCCTTAAACCT
1 TAACCCCTAAACCT
59891943 TAAATCCCAA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
15 23 0.70
16 10 0.30
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.22
Consensus pattern (15 bp):
TAACCCCTAAACCTC
Found at i:59891909 original size:23 final size:23
Alignment explanation
Indices: 59891883--59891942 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
59891873 CCCTAACTTT
59891883 TAACCCCTAAACCTCTAACCCTC
1 TAACCCCTAAACCTCTAACCCTC
*
59891906 TAACCCCAAAACCTCTAACCCTC
1 TAACCCCTAAACCTCTAACCCTC
*
59891929 TAACCCTTAAACCT
1 TAACCCCTAAACCT
59891943 TAAATCCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.22
Consensus pattern (23 bp):
TAACCCCTAAACCTCTAACCCTC
Found at i:59891935 original size:8 final size:8
Alignment explanation
Indices: 59891883--59891935 Score: 65
Period size: 8 Copynumber: 6.9 Consensus size: 8
59891873 CCCTAACTTT
59891883 TAACCC-C
1 TAACCCTC
*
59891890 TAAACCTC
1 TAACCCTC
59891898 TAACCCTC
1 TAACCCTC
59891906 TAACCC-C
1 TAACCCTC
* *
59891913 AAAACCTC
1 TAACCCTC
59891921 TAACCCTC
1 TAACCCTC
59891929 TAACCCT
1 TAACCCT
59891936 TAAACCTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
7 10 0.26
8 28 0.74
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (8 bp):
TAACCCTC
Found at i:59891943 original size:7 final size:8
Alignment explanation
Indices: 59891884--59891946 Score: 51
Period size: 8 Copynumber: 8.2 Consensus size: 8
59891874 CCTAACTTTT
*
59891884 AACCCCTA
1 AACCTCTA
59891892 AACCTCTA
1 AACCTCTA
*
59891900 ACCCTCT-
1 AACCTCTA
* *
59891907 AACCCCAA
1 AACCTCTA
59891915 AACCTCTA
1 AACCTCTA
*
59891923 ACCCTCTA
1 AACCTCTA
*
59891931 ACCCT-TA
1 AACCTCTA
59891938 AACCT-TA
1 AACCTCTA
59891945 AA
1 AA
59891947 TCCCAACCCT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
7 14 0.31
8 31 0.69
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.21
Consensus pattern (8 bp):
AACCTCTA
Found at i:59892241 original size:44 final size:44
Alignment explanation
Indices: 59892176--59892288 Score: 108
Period size: 44 Copynumber: 2.6 Consensus size: 44
59892166 ACCCCTGAAT
* * * *
59892176 CCCTAAA-CCCTAAATCCCTAACTATTAACCCTT-AATGTCTAAC
1 CCCTAAACCCCTAAACCCCTAACCATTAAACCTTAAATCTC-AAC
*
59892219 CCCTAAACCCCT-AACCCTCTAACCCTTAAACCTTAAATCTCAAC
1 CCCTAAACCCCTAAACCC-CTAACCATTAAACCTTAAATCTCAAC
* *
59892263 CCTTAAA-CCCTAAAACCCTAATCCAT
1 CCCTAAACCCCTAAACCCCTAA-CCAT
59892289 ACTCCCTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
43 19 0.33
44 33 0.58
45 5 0.09
ACGTcount: A:0.35, C:0.39, G:0.01, T:0.25
Consensus pattern (44 bp):
CCCTAAACCCCTAAACCCCTAACCATTAAACCTTAAATCTCAAC
Found at i:59892302 original size:15 final size:15
Alignment explanation
Indices: 59892278--59892313 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
59892268 AACCCTAAAA
59892278 CCCT-AATCCATACT
1 CCCTAAATCCATACT
59892292 CCCTAAATCCATACT
1 CCCTAAATCCATACT
59892307 CCCTAAA
1 CCCTAAA
59892314 CCTTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.33, C:0.42, G:0.00, T:0.25
Consensus pattern (15 bp):
CCCTAAATCCATACT
Found at i:59892534 original size:15 final size:15
Alignment explanation
Indices: 59892499--59892573 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
59892489 CCCTAACTTT
*
59892499 TAACCCCTAATACGTC
1 TAACCCCTAA-ACCTC
59892515 T-ACCCCTAAACCTC
1 TAACCCCTAAACCTC
*
59892529 TAACCCTCT-AACCCC
1 TAACCC-CTAAACCTC
* * *
59892544 AAAACCTCTAACCCTC
1 -TAACCCCTAAACCTC
*
59892560 TAACCCTTAAACCT
1 TAACCCCTAAACCT
59892574 TAAATCCCAA
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
14 5 0.11
15 29 0.64
16 11 0.24
ACGTcount: A:0.32, C:0.44, G:0.01, T:0.23
Consensus pattern (15 bp):
TAACCCCTAAACCTC
Found at i:59892536 original size:8 final size:8
Alignment explanation
Indices: 59892516--59892566 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
59892506 TAATACGTCT
59892516 ACCC-CTA
1 ACCCTCTA
*
59892523 AACCTCTA
1 ACCCTCTA
59892531 ACCCTCTA
1 ACCCTCTA
*
59892539 ACCC-CAA
1 ACCCTCTA
*
59892546 AACCTCTA
1 ACCCTCTA
59892554 ACCCTCTA
1 ACCCTCTA
59892562 ACCCT
1 ACCCT
59892567 TAAACCTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
7 8 0.22
8 28 0.78
ACGTcount: A:0.31, C:0.49, G:0.00, T:0.20
Consensus pattern (8 bp):
ACCCTCTA
Found at i:59892571 original size:23 final size:23
Alignment explanation
Indices: 59892516--59892573 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
59892506 TAATACGTCT
59892516 ACCCCTAAACCTCTAACCCTCTA
1 ACCCCTAAACCTCTAACCCTCTA
*
59892539 ACCCCAAAACCTCTAACCCTCTA
1 ACCCCTAAACCTCTAACCCTCTA
*
59892562 ACCCTTAAACCT
1 ACCCCTAAACCT
59892574 TAAATCCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.21
Consensus pattern (23 bp):
ACCCCTAAACCTCTAACCCTCTA
Found at i:59892574 original size:7 final size:8
Alignment explanation
Indices: 59892520--59892577 Score: 50
Period size: 8 Copynumber: 7.6 Consensus size: 8
59892510 ACGTCTACCC
59892520 CTAAACCT
1 CTAAACCT
*
59892528 CTAACCCT
1 CTAAACCT
*
59892536 CT-AACCC
1 CTAAACCT
*
59892543 CAAAACCT
1 CTAAACCT
*
59892551 CTAACCCT
1 CTAAACCT
*
59892559 CTAACCCT
1 CTAAACCT
59892567 -TAAACCT
1 CTAAACCT
59892574 -TAAA
1 CTAAA
59892578 TCCCAACCCT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
7 14 0.34
8 27 0.66
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.22
Consensus pattern (8 bp):
CTAAACCT
Found at i:59892630 original size:15 final size:15
Alignment explanation
Indices: 59892594--59892636 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
59892584 CCCTTAAACA
*
59892594 ATAATCCCT-AATCC
1 ATAATCCCTAAACCC
59892608 ATAATCCCTAAACCC
1 ATAATCCCTAAACCC
*
59892623 ATACTCCCTAAACC
1 ATAATCCCTAAACC
59892637 TTAAAATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAATCCCTAAACCC
Found at i:59892838 original size:631 final size:616
Alignment explanation
Indices: 59891678--59893016 Score: 2378
Period size: 631 Copynumber: 2.1 Consensus size: 616
59891668 CCCTAATTCA
59891678 TAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAATCAGCCTTAAATCTTAAATTAATT
1 TAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAATCAGCCTTAAATCTTAAATTAATT
*
59891743 ATATACCCTAAACTAAAAATCCTAAACGAATTTATTATTATCTCTTTTACAATTATATAAGAACA
66 ATATACCCTAAACTAAAAATCCTAAACGAATTTATTATTATCTCTTTCACAATTATATAAGAACA
59891808 TATTTAAAATATAAATTAAAAAAATAATTAATCTAAACCTAAAACCCTAACCCGACCCCCTAAAT
131 TATTTAAAATATAAATTAAAAAAATAATTAATCTAAACCTAAAACCCTAACCCGACCCCCTAAAT
59891873 CCCTAACTTTTAACCCCTAAACCTCTAACCCTCTAACCCCAAAACCTCTAACCCTCTAACCCTTA
196 CCCTAACTTTTAACCCCTAAACCTCTAACCCTCTAACCCCAAAACCTCTAACCCTCTAACCCTTA
* *
59891938 AACCTTAAATCCCAACCCTTAAACAATTATCCCTAATCCATAATCTCTAAACCCATACTCCCTAA
261 AACCTTAAATCCCAACCCTTAAACAATAATCCCTAATCCATAATCCCTAAACCCATACTCCCTAA
59892003 ACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAATCATATACCCTAAACCAAAA
326 ACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAATCATATACCCTAAACCAAAA
59892068 CCCTAAATAAATTTATTATCATCTCTTTTCAATTATATAAGAACATATTTAAAATATAAATTAAA
391 CCCTAAATAAATTTATTATCATCTCTTTTCAATTATATAAGAACATATTTAAAATATAAATTAAA
59892133 AAAATTAATCTAAACGCCCAAAATCCTAACTCGACCCCTGAATCCCTAAACCCTAAATCCCTAAC
456 AAAATTAATCTAAACGCCCAAAATCCTAACTCGACCCCTGAATCCCTAAACCCTAAATCCCTAAC
*
59892198 TATTAACCCTTAATGTCTAACCCCTAAACCCCTAACCCTCTAACCCTTAAACCTTAAATCTCAAC
521 TATTAACCCTTAATGTCTAACCCCTAAACCACTAACCCTCTAACCCTTAAACCTTAAATCTCAAC
59892263 CCTTAAACCCTAAAACCCTAATCCATACTCCC
586 CCTTAAACCCTAAAA-CCTAATCCATACTCCC
59892295 TAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAATCAGCCTTAAATCTTAAATTAATT
1 TAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAATCAGCCTTAAATCTTAAATTAATT
59892360 ATATACCCTAAACTAAAAATCCTAAACGAATTTATTATTATCTCTTTCACAATTATATAAGAACA
66 ATATACCCTAAACTAAAAATCCTAAACGAATTTATTATTATCTCTTTCACAATTATATAAGAACA
59892425 TATTTAAAATATAAATTAAAAAAATAATTAATCTAAACCTAAAACCCTAACCCGA-CCCCTAAAT
131 TATTTAAAATATAAATTAAAAAAATAATTAATCTAAACCTAAAACCCTAACCCGACCCCCTAAAT
59892489 CCCTAACTTTTAACCCCTAATACGTCTACCCCTAAACCTCTAACCCTCTAACCCCAAAACCTCTA
196 CCCTAAC--TT------T--TA-----ACCCCTAAACCTCTAACCCTCTAACCCCAAAACCTCTA
59892554 ACCCTCTAACCCTTAAACCTTAAATCCCAACCCTTAAACAATAATCCCTAATCCATAATCCCTAA
246 ACCCTCTAACCCTTAAACCTTAAATCCCAACCCTTAAACAATAATCCCTAATCCATAATCCCTAA
*
59892619 ACCCATACTCCCTAAACCTTAAAATATGAACTCCTAAATCGGCCTTAAATCTTAAATAAATCATA
311 ACCCATACTCCCTAAACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAATCATA
59892684 TACCCTAAACCAAAACCCTAAATAAATTTATTATCATCTCTTTTCAATTATATAAGAACATATTT
376 TACCCTAAACCAAAACCCTAAATAAATTTATTATCATCTCTTTTCAATTATATAAGAACATATTT
59892749 AAAATATAAATTAAAAAAATTAATCTAAACGCCCAAAATCCTAACTCGACCCCTGAATCCCTAAA
441 AAAATATAAATTAAAAAAATTAATCTAAACGCCCAAAATCCTAACTCGACCCCTGAATCCCTAAA
*
59892814 CCTTAAATCCCTAACTATTAACCCTTAATGTCTAACCCCTAAACCACTAACCCTCTAACCCTTAA
506 CCCTAAATCCCTAACTATTAACCCTTAATGTCTAACCCCTAAACCACTAACCCTCTAACCCTTAA
*
59892879 ACCTTAAATCTCAACCCTTAAACCTTAAAACCTAATCCATACTCCC
571 ACCTTAAATCTCAACCCTTAAACCCTAAAACCTAATCCATACTCCC
* *
59892925 TAAAACCATACTCCCTAAACCTTAAAATA-GTAACTCCTAAA-CAGGCCTTAAATCTTAAATAAA
1 TAAATCCATACTCCCTAAACCTTAAAATATG-AACTCCTAAATCA-GCCTTAAATCTTAAATTAA
* * * *
59892988 TCATATACCCCAAACCAAAAACCCTAAAC
64 TTATATACCCTAAACTAAAAATCCTAAAC
59893017 TATAGTGAAA
Statistics
Matches: 692, Mismatches: 13, Indels: 21
0.95 0.02 0.03
Matches are distributed among these distances:
616 16 0.02
617 184 0.27
618 2 0.00
624 1 0.00
626 2 0.00
629 3 0.00
630 97 0.14
631 387 0.56
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.28
Consensus pattern (616 bp):
TAAATCCATACTCCCTAAACCTTAAAATATGAACTCCTAAATCAGCCTTAAATCTTAAATTAATT
ATATACCCTAAACTAAAAATCCTAAACGAATTTATTATTATCTCTTTCACAATTATATAAGAACA
TATTTAAAATATAAATTAAAAAAATAATTAATCTAAACCTAAAACCCTAACCCGACCCCCTAAAT
CCCTAACTTTTAACCCCTAAACCTCTAACCCTCTAACCCCAAAACCTCTAACCCTCTAACCCTTA
AACCTTAAATCCCAACCCTTAAACAATAATCCCTAATCCATAATCCCTAAACCCATACTCCCTAA
ACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAATCATATACCCTAAACCAAAA
CCCTAAATAAATTTATTATCATCTCTTTTCAATTATATAAGAACATATTTAAAATATAAATTAAA
AAAATTAATCTAAACGCCCAAAATCCTAACTCGACCCCTGAATCCCTAAACCCTAAATCCCTAAC
TATTAACCCTTAATGTCTAACCCCTAAACCACTAACCCTCTAACCCTTAAACCTTAAATCTCAAC
CCTTAAACCCTAAAACCTAATCCATACTCCC
Found at i:59892935 original size:15 final size:15
Alignment explanation
Indices: 59892915--59892943 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59892905 AAAACCTAAT
59892915 CCATACTCCCTAAAA
1 CCATACTCCCTAAAA
59892930 CCATACTCCCTAAA
1 CCATACTCCCTAAA
59892944 CCTTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (15 bp):
CCATACTCCCTAAAA
Found at i:59892944 original size:14 final size:14
Alignment explanation
Indices: 59892909--59892945 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
59892899 AACCTTAAAA
*
59892909 CCTAATCCATACTC
1 CCTAAACCATACTC
59892923 CCTAAAACCATACTC
1 CCT-AAACCATACTC
59892938 CCTAAACC
1 CCTAAACC
59892946 TTAAAATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTAAACCATACTC
Found at i:59893384 original size:42 final size:40
Alignment explanation
Indices: 59893290--59893448 Score: 246
Period size: 41 Copynumber: 3.9 Consensus size: 40
59893280 TAAAATATTT
*
59893290 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCAGCA
1 TTAGCAGCGCTTTTCCAAAAACGCCGCTAAAGCCCCAGCA
*
59893330 TTAGCGGCGCTTTTCCAAAAAACGCCGCTAAAGCCCTCAGCA
1 TTAGCAGCGCTTTTCC-AAAAACGCCGCTAAAGCCC-CAGCA
*
59893372 TTAGCAGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAAGCA
1 TTAGCAGCGCTTTTCCAAAAACGCCGCTAAAGCCCC-AGCA
* *
59893413 TTAGCAGCGCTTTTTCAAAAAAGCCGCTAAAGCCCC
1 TTAGCAGCGCTTTTCCAAAAACGCCGCTAAAGCCCC
59893449 GAAAGGTAAC
Statistics
Matches: 113, Mismatches: 3, Indels: 5
0.93 0.02 0.04
Matches are distributed among these distances:
40 17 0.15
41 77 0.68
42 19 0.17
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (40 bp):
TTAGCAGCGCTTTTCCAAAAACGCCGCTAAAGCCCCAGCA
Found at i:59899245 original size:3 final size:3
Alignment explanation
Indices: 59899237--59899271 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
59899227 TAACAAGCTT
59899237 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
59899272 TAAAGAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:59899760 original size:14 final size:14
Alignment explanation
Indices: 59899733--59899777 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
59899723 TTAATATGTA
*
59899733 AAATATACACATAT
1 AAATATATACATAT
* *
59899747 AAGTATGTACATAT
1 AAATATATACATAT
*
59899761 AAATATATACTTAT
1 AAATATATACATAT
59899775 AAA
1 AAA
59899778 AATTTAGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.33
Consensus pattern (14 bp):
AAATATATACATAT
Found at i:59899824 original size:43 final size:41
Alignment explanation
Indices: 59899749--59899833 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 41
59899739 ACACATATAA
*
59899749 GTATGTACATATAAATATATACTTATAAAAATTTAGAAAATAT
1 GTATGTACATATAAATATATA-GTATAAAAA-TTAGAAAATAT
* *
59899792 GTATGTAGATATAAATATAT-GTATACACAAATTATAAAATAT
1 GTATGTACATATAAATATATAGTATA-A-AAATTAGAAAATAT
59899834 ATATAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 4 0.11
42 11 0.30
43 22 0.59
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (41 bp):
GTATGTACATATAAATATATAGTATAAAAATTAGAAAATAT
Found at i:59899932 original size:22 final size:22
Alignment explanation
Indices: 59899907--59899967 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
59899897 ATATATATAC
* *
59899907 ATATATGTGTATATAATAAGAT
1 ATATATATATATATAATAAGAT
59899929 ATATATATATATATAATAAGAT
1 ATATATATATATATAATAAGAT
*
59899951 ATA-A-AGATATATAATAA
1 ATATATATATATATAATAA
59899968 TTATAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 12 0.33
21 1 0.03
22 23 0.64
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (22 bp):
ATATATATATATATAATAAGAT
Found at i:59899952 original size:10 final size:10
Alignment explanation
Indices: 59899917--59899976 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
59899907 ATATATGTGT
59899917 ATATAATAAG
1 ATATAATAAG
*
59899927 ATATATATATAT
1 ATATA-ATA-AG
59899939 ATATAATAAG
1 ATATAATAAG
*
59899949 ATATAA-AGAT
1 ATATAATA-AG
59899959 ATATAATAA-
1 ATATAATAAG
*
59899968 TTATAATAA
1 ATATAATAA
59899977 TAATAACAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
9 9 0.21
10 20 0.48
11 7 0.17
12 6 0.14
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (10 bp):
ATATAATAAG
Found at i:59899952 original size:20 final size:21
Alignment explanation
Indices: 59899916--59899967 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
59899906 CATATATGTG
* *
59899916 TATATAATAAGATATATATATA
1 TATATAATAAGA-ATATAAAGA
59899938 TATATAATAAG-ATATAAAGA
1 TATATAATAAGAATATAAAGA
59899958 TATATAATAA
1 TATATAATAA
59899968 TTATAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 17 0.61
22 11 0.39
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (21 bp):
TATATAATAAGAATATAAAGA
Found at i:59899998 original size:26 final size:25
Alignment explanation
Indices: 59899969--59900029 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
59899959 ATATAATAAT
59899969 TATAATAATAA-TAACAATAAGACAAA
1 TATAATAATAATTAA-AATAAGA-AAA
*
59899995 TATAATCAA-AATTTAAATAAGAAAA
1 TATAAT-AATAATTAAAATAAGAAAA
59900020 TATAA-AATAA
1 TATAATAATAA
59900030 AAATATAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 8 0.26
26 15 0.48
27 4 0.13
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (25 bp):
TATAATAATAATTAAAATAAGAAAA
Found at i:59900344 original size:40 final size:40
Alignment explanation
Indices: 59900300--59900436 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 40
59900290 GCGTTTGGAT
* *
59900300 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGTGCTTTAG
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTAC
* * * * * *
59900340 AAAAAACGCCACTAAAGATCTAGTATTAGCGGCGTTTTCC
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTAC
* * * *
59900380 AAAAAACGCCGTTAAAAAT-GAGCATTAGCGGCGTTTTCC
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTAC
* *
59900419 AAAAAGCGCCGCAAAAAA
1 AAAAAACGCCGCTAAAAA
59900437 CCTAAGCACA
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
39 33 0.41
40 48 0.59
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTAC
Found at i:59901234 original size:15 final size:15
Alignment explanation
Indices: 59901214--59901258 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
59901204 GGTAATTTTT
59901214 GGGATTATGTGTTTA
1 GGGATTATGTGTTTA
*
59901229 GGGATTATG-GATTA
1 GGGATTATGTGTTTA
*
59901243 TGGATTATGTGGTTTA
1 GGGATTATGT-GTTTA
59901259 AGGGTTGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 9 0.36
16 4 0.16
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (15 bp):
GGGATTATGTGTTTA
Found at i:59901947 original size:15 final size:14
Alignment explanation
Indices: 59901926--59901974 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
59901916 ATGATTTTAA
59901926 GGTTTAGGGATTAT
1 GGTTTAGGGATTAT
*
59901940 GTGTTTAGGGATTAG
1 G-GTTTAGGGATTAT
*
59901955 GGATTAGGGATTAT
1 GGTTTAGGGATTAT
59901969 GGTTTA
1 GGTTTA
59901975 TAGTTTAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:59901956 original size:7 final size:7
Alignment explanation
Indices: 59901929--59901967 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
59901919 ATTTTAAGGT
59901929 TTAGGGA
1 TTAGGGA
* *
59901936 TTATGTGT
1 TTA-GGGA
59901944 TTAGGGA
1 TTAGGGA
59901951 TTAGGGA
1 TTAGGGA
59901958 TTAGGGA
1 TTAGGGA
59901965 TTA
1 TTA
59901968 TGGTTTATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 22 0.81
8 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (7 bp):
TTAGGGA
Found at i:59901985 original size:29 final size:30
Alignment explanation
Indices: 59901921--59901985 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 30
59901911 ATTAAATGAT
* *
59901921 TTTAA-GGTTTAGGGATTATGTGTTTAGGG
1 TTTAAGGGATTAGGGATTATGTGTTTAGAG
* *
59901950 ATT-AGGGATTAGGGATTATG-GTTTATAG
1 TTTAAGGGATTAGGGATTATGTGTTTAGAG
59901978 TTTAAGGG
1 TTTAAGGG
59901986 TTGGGGTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.42
Consensus pattern (30 bp):
TTTAAGGGATTAGGGATTATGTGTTTAGAG
Found at i:59902010 original size:17 final size:17
Alignment explanation
Indices: 59901983--59902029 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
59901973 TATAGTTTAA
59901983 GGGTT-GGGGTTATAAG
1 GGGTTAGGGGTTATAAG
59901999 GGGTTAGGGGTTATAAG
1 GGGTTAGGGGTTATAAG
59902016 GGGTTAGGGGTTAT
1 GGGTTAGGGGTTAT
59902030 GGGGTTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.19, C:0.00, G:0.49, T:0.32
Consensus pattern (17 bp):
GGGTTAGGGGTTATAAG
Found at i:59902655 original size:23 final size:25
Alignment explanation
Indices: 59902616--59902665 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
59902606 AATTTTACTT
* *
59902616 TAAAATAATTTTTAGCA-GACAAAA
1 TAAAATAAATTTTAGCATAACAAAA
59902640 TAAAA-AAATTTTAGCATAACAAAA
1 TAAAATAAATTTTAGCATAACAAAA
59902664 TA
1 TA
59902666 GCGTCGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (25 bp):
TAAAATAAATTTTAGCATAACAAAA
Found at i:59907182 original size:43 final size:42
Alignment explanation
Indices: 59907114--59907259 Score: 159
Period size: 43 Copynumber: 3.4 Consensus size: 42
59907104 AATATTATGT
* * * *
59907114 TTTTAGCGACATTTTTGCTAGAAGCGTCGCTAAAGGTTTGGG
1 TTTTAGCGGCATTTGTGATAAAAGCGTCGCTAAAGGTTTGGG
* *
59907156 TTTATAGCGGCATTTGTGATAAAAGCGCCGCTAAAGGTTTCGG
1 TTT-TAGCGGCATTTGTGATAAAAGCGTCGCTAAAGGTTTGGG
* *
59907199 TCTTTAGCGGCATTTATGGA-AAAAGCATCGCTAAAGGTCTTGGG
1 T-TTTAGCGGCATTTGT-GATAAAAGCGTCGCTAAAGGT-TTGGG
* *
59907243 CTTTAGCGGCGTTTGTG
1 TTTTAGCGGCATTTGTG
59907260 GGAAAAGTGC
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
42 4 0.05
43 75 0.86
44 8 0.09
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.33
Consensus pattern (42 bp):
TTTTAGCGGCATTTGTGATAAAAGCGTCGCTAAAGGTTTGGG
Found at i:59907266 original size:43 final size:42
Alignment explanation
Indices: 59907135--59907284 Score: 160
Period size: 43 Copynumber: 3.5 Consensus size: 42
59907125 TTTTTGCTAG
*
59907135 AAGCGTCGCTAAAGGTTTGGGTTTATAGCGGCATTTGT-GATAA
1 AAGCGTCGCTAAAGGTTTGGGCTT-TAGCGGCATTTGTGGA-AA
* * *
59907178 AAGCGCCGCTAAAGGTTTCGGTCTTTAGCGGCATTTATGGAAA
1 AAGCGTCGCTAAAGGTTT-GGGCTTTAGCGGCATTTGTGGAAA
* * *
59907221 AAGCATCGCTAAAGGTCTTGGGCTTTAGCGGCGTTTGTGGGAA
1 AAGCGTCGCTAAAGGT-TTGGGCTTTAGCGGCATTTGTGGAAA
*
59907264 AAGTG-CTGCTAAAGGTCTTGG
1 AAGCGTC-GCTAAAGGT-TTGG
59907285 AGAAGCGCCG
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.01
43 82 0.90
44 8 0.09
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.29
Consensus pattern (42 bp):
AAGCGTCGCTAAAGGTTTGGGCTTTAGCGGCATTTGTGGAAA
Found at i:59908080 original size:5 final size:5
Alignment explanation
Indices: 59908070--59908110 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
59908060 AAAACAAACA
59908070 AAAAT AAAAT AAAAT AAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT -AAAAT AAA
59908111 GAAAATACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:59908094 original size:6 final size:6
Alignment explanation
Indices: 59908069--59908110 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
59908059 TAAAACAAAC
59908069 AAAAAT -AAAAT -AAAAT -AAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
59908111 GAAAATACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 15 0.43
6 20 0.57
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:59912468 original size:35 final size:35
Alignment explanation
Indices: 59912419--59912488 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
59912409 ATTTGAAAAA
*
59912419 GGGATCATGTCCAGTAAGTTAGGACACAATCTTTT
1 GGGATCATGCCCAGTAAGTTAGGACACAATCTTTT
*
59912454 GGGATCATGCCCAGTAAGTTAGGACACGATCTTTT
1 GGGATCATGCCCAGTAAGTTAGGACACAATCTTTT
59912489 CTTAATTCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (35 bp):
GGGATCATGCCCAGTAAGTTAGGACACAATCTTTT
Found at i:59913139 original size:25 final size:27
Alignment explanation
Indices: 59913071--59913150 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 27
59913061 GAAAAGATAT
*
59913071 ATAATTATATAATAATAATATATAATAAG
1 ATAAATATA-AATAA-AATATATAATAAG
** *
59913100 ATAAATATATTTAAAATTTA-AATAAG
1 ATAAATATAAATAAAATATATAATAAG
59913126 -TAAATATAAATAAAATATAGTAATA
1 ATAAATATAAATAAAATATA-TAATA
59913151 GTAATACTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
25 16 0.38
26 6 0.14
27 9 0.21
28 3 0.07
29 8 0.19
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (27 bp):
ATAAATATAAATAAAATATATAATAAG
Found at i:59915812 original size:8 final size:8
Alignment explanation
Indices: 59915801--59915849 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
59915791 TTAAATTTTA
59915801 ATAAAAAT
1 ATAAAAAT
59915809 ATAAAAAT
1 ATAAAAAT
*
59915817 AGAAAACAT
1 ATAAAA-AT
59915826 ATAAAATAT
1 ATAAAA-AT
*
59915835 ATAGAAAT
1 ATAAAAAT
59915843 ATAAAAA
1 ATAAAAA
59915850 AATTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
8 21 0.60
9 14 0.40
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (8 bp):
ATAAAAAT
Found at i:59915829 original size:17 final size:16
Alignment explanation
Indices: 59915803--59915849 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
59915793 AAATTTTAAT
59915803 AAAAATATAAAAATAG
1 AAAAATATAAAAATAG
*
59915819 AAAACATATAAAATATAT
1 AAAA-ATATAAAA-ATAG
*
59915837 AGAAATATAAAAA
1 AAAAATATAAAAA
59915850 AATTATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 16 0.59
18 6 0.22
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (16 bp):
AAAAATATAAAAATAG
Found at i:59915844 original size:10 final size:9
Alignment explanation
Indices: 59915801--59915860 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 9
59915791 TTAAATTTTA
59915801 ATAAAA-AT
1 ATAAAATAT
59915809 ATAAAA-AT
1 ATAAAATAT
* *
59915817 AGAAAACAT
1 ATAAAATAT
59915826 ATAAAATAT
1 ATAAAATAT
59915835 ATAGAAATAT
1 ATA-AAATAT
*
59915845 A-AAAAAATT
1 ATAAAATA-T
59915854 ATAAAAT
1 ATAAAAT
59915861 TTTATAAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
8 17 0.40
9 15 0.35
10 11 0.26
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (9 bp):
ATAAAATAT
Found at i:59915880 original size:29 final size:30
Alignment explanation
Indices: 59915844--59915927 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
59915834 TATAGAAATA
*
59915844 TAAAAAAATTATAAAATTTTATAAAGTT-G
1 TAAAAAAATTATAAAATTTTATAAAATTCG
* **
59915873 TAAGAAAATTAT-AAATAAATATAAAATTCG
1 TAAAAAAATTATAAAAT-TTTATAAAATTCG
59915903 TAAAAAAATTATAAAAATTATTATA
1 TAAAAAAATTAT-AAAATT-TTATA
59915928 CCAAAAGAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
28 4 0.09
29 19 0.44
30 12 0.28
32 8 0.19
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.35
Consensus pattern (30 bp):
TAAAAAAATTATAAAATTTTATAAAATTCG
Found at i:59915918 original size:9 final size:9
Alignment explanation
Indices: 59915779--59915923 Score: 57
Period size: 10 Copynumber: 15.4 Consensus size: 9
59915769 TCAATAGAAG
59915779 TTATAAAAA
1 TTATAAAAA
**
59915788 TTATTAAATT
1 TTA-TAAAAA
59915798 TTAATAAAAA
1 TT-ATAAAAA
59915808 -TATAAAAA
1 TTATAAAAA
*
59915816 -TAGAAAACA
1 TTATAAAA-A
59915825 -TAT-AAAA
1 TTATAAAAA
*
59915832 TATATAGAAA
1 T-TATAAAAA
*
59915842 TATAAAAAAA
1 T-TATAAAAA
59915852 TTAT-AAAA
1 TTATAAAAA
* *
59915860 TTTTATAAAG
1 TTATA-AAAA
*
59915870 TTGTAAGAAAA
1 TTAT-A-AAAA
59915881 TTATAAATAA
1 TTATAAA-AA
* *
59915891 ATATAAAAT
1 TTATAAAAA
*
59915900 TCGTAAAAAAA
1 T--TATAAAAA
59915911 TTATAAAAA
1 TTATAAAAA
59915920 TTAT
1 TTAT
59915924 TATACCAAAA
Statistics
Matches: 102, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
7 1 0.01
8 23 0.23
9 26 0.25
10 37 0.36
11 15 0.15
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:59916114 original size:27 final size:26
Alignment explanation
Indices: 59916071--59916123 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
59916061 TATTTATTCT
59916071 AATTTTAATAAATTTTAAATACTTTTA
1 AATTTTAATAAATTTTAAA-ACTTTTA
*
59916098 AATTTTAAT-AATATTTATAACTTTTA
1 AATTTTAATAAAT-TTTAAAACTTTTA
59916124 TTGATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
AATTTTAATAAATTTTAAAACTTTTA
Found at i:59916448 original size:10 final size:10
Alignment explanation
Indices: 59916429--59916515 Score: 56
Period size: 10 Copynumber: 8.8 Consensus size: 10
59916419 GCCCCTACTC
59916429 TTATAAAAAA
1 TTATAAAAAA
*
59916439 TTAGAAAAAAAA
1 TT--ATAAAAAA
59916451 TTATAAAAAA
1 TTATAAAAAA
*
59916461 TCAT-AAAAA
1 TTATAAAAAA
59916470 --ATAAAAAA
1 TTATAAAAAA
* **
59916478 TTGTAAAATT
1 TTATAAAAAA
*
59916488 TTAT-AATAA
1 TTATAAAAAA
*
59916497 TCATTAAAAAA
1 TTA-TAAAAAA
59916508 TTATAAAA
1 TTATAAAA
59916516 TGCATTGCTT
Statistics
Matches: 57, Mismatches: 13, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
7 2 0.04
8 5 0.09
9 9 0.16
10 26 0.46
11 6 0.11
12 9 0.16
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:59916455 original size:22 final size:22
Alignment explanation
Indices: 59916429--59916470 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
59916419 GCCCCTACTC
*
59916429 TTATAAAAAATTAGAAAAAAAA
1 TTATAAAAAATCAGAAAAAAAA
*
59916451 TTATAAAAAATCATAAAAAA
1 TTATAAAAAATCAGAAAAAA
59916471 TAAAAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
TTATAAAAAATCAGAAAAAAAA
Found at i:59918690 original size:18 final size:19
Alignment explanation
Indices: 59918667--59918708 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
59918657 TGATAATTTT
**
59918667 AAAAATT-CAAAAATTAAA
1 AAAAATTGCAAAAAACAAA
59918685 AAAAATTGCAAAAAACAAA
1 AAAAATTGCAAAAAACAAA
59918704 AAAAA
1 AAAAA
59918709 ATGAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAATTGCAAAAAACAAA
Found at i:59920277 original size:132 final size:132
Alignment explanation
Indices: 59920141--59921655 Score: 2323
Period size: 132 Copynumber: 11.5 Consensus size: 132
59920131 AAATAGGGTA
* * * * *
59920141 ACTGGCTTCAATGTACTCCACTGTAAACACAGGGAGGTAAAATCCACTATCTTTAATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
* * *
59920206 CCACTGCTTAGAGAGACAAGATCTGAAATCTTCAACCTATTCCACTGCTGCCCAGGG-AGATAGA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGA
59920270 ATT
130 ATT
* *
59920273 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAACCCGCCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
*
59920338 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGTCCAGGGAAGTAGAA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
59920403 TT
131 TT
* * * *
59920405 ATTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
*
59920470 CTACTGCTTAGGGAGAAAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
59920535 TT
131 TT
* *
59920537 ACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
**
59920602 CTACTGCTTAGGGAGACAAGATCCAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
59920667 TT
131 TT
* * * *
59920669 ACTGGCTTCAATGTACTCCACTGCAACCTCAGTGAGGTAAAATTCACCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
* *
59920734 CTATTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
59920799 TT
131 TT
* * *
59920801 ACTGGCTTCAATGTTCTCCACTGTAACCACAGGGAGGTAAAATTCGCCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
** *
59920866 CTACTGCTTAGGGAGACAAGATCCAAAATCTTCAATCTATTCCACTGCTGTCCAGGGAAGTAGAA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
59920931 TT
131 TT
* * * * *
59920933 ATTGGCTTCAATGTACTCCACTGCAGCCTCAGGGAGGTAAAATCTGGCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
** *
59920998 CTACTGCTTAGGGAGACAAGATCCAAAATCTTCAATCTATTCCACTGCTGCCCAGGAAAGTAGAA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
59921063 TT
131 TT
* * * * * *
59921065 ATTGGCTTCAATGTACTCTACTGTAACCACAGGGAGGTAAAATCTGTCATTTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
* * *
59921130 CTACTGCGTAGGGAGGA-AATATCTGAAATCTTCAATCTATTCCACTGCTGCCTAGGGAAGTAGA
66 CTACTGCTTAGGGA-GACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGA
59921194 ATT
130 ATT
* *
59921197 ACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
* ** *
59921262 CTACTGCTTAGGGAGAAAAGATCCAAAATCTTCAATCTATTCCACTGCTGCCTAGGGAAGTAGAA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
59921327 TT
131 TT
* * * * * *
59921329 ATTGGCTTCAATGTAATCCATTGCAACCTCAGGAAGGTAAAATCTGCCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
** *
59921394 CTACTGCTTAGGGAGACAAGATCCAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAAAA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
59921459 TT
131 TT
* * * *
59921461 ATTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATATTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
* * *
59921526 CTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCCATTCCGCTGCTGCCCAGGGAAGTAGAA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
59921591 TT
131 TT
* * * *
59921593 ACTGGCTTCAATGTTCTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTC
1 ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTC
59921656 TGCTGTCTAT
Statistics
Matches: 1281, Mismatches: 99, Indels: 6
0.92 0.07 0.00
Matches are distributed among these distances:
131 2 0.00
132 1275 1.00
133 4 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
ACTGGCTTCAATGTACTCCACTGCAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCA
CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
TT
Found at i:59920527 original size:44 final size:43
Alignment explanation
Indices: 59920226--59921319 Score: 124
Period size: 44 Copynumber: 24.9 Consensus size: 43
59920216 GAGAGACAAG
* *
59920226 ATCTGAAATCTTCAACCTATTCCACTGCTGCCCAGGGAGATAGAA
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGAGA-A-AA
* * * * *
59920271 TTACTG---GCTTCAATGTACTCCACTG-TAACCACAGGGAGGTAAA
1 AT-CTGAAATCTTCAATCTACTCCACTGCT-GCC-CAGGGA-GAAAA
* * ** ** * * ** *
59920314 ACCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAG
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGAGA-AAA
* * * *
59920358 ATCTGAAATCTTCAATCTATTCCACTGCTGTCCAGGGAAGTAGA
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGG-AGAAAA
* * ** *
59920402 AT-T--ATTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAA
1 ATCTGAAAT--CTTCAATCTACTCCACTGCTGCC-CAGGGA-GAAAA
* * ** * * **
59920446 AT-TCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGAAAA
1 ATCTGA-AATCTTCAATCTACTCCACTGCTGCCCAGGGAGAAAA
* *
59920489 GATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
1 -ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGG-AG-AAAA
* * * ** *
59920535 TTACTG---GCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAA
1 AT-CTGAAATCTTCAATCTACTCCACTGCTGCC-CAGGGA-GAAAA
** ** * * ** *
59920578 ATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAG
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGAGA-AAA
** * *
59920622 ATCCAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGG-AG-AAAA
* * * ** * *
59920667 TTACTG---GCTTCAATGTACTCCACTGCAACCTCAGTGAGGTAAA
1 AT-CTGAAATCTTCAATCTACTCCACTGCTGCC-CAGGGA-GAAAA
* * ** * ** ** *
59920710 AT-TCACCATCTTTGATCTGCTCCACTATTGCTTAGGGAGACAAG
1 ATCTGA-AATCTTCAATCTACTCCACTGCTGCCCAGGGAGA-AAA
* * *
59920754 ATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAA
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGG-AG-AAAA
* * * * * *
59920799 TTACTG---GCTTCAATGTTCTCCACTG-TAACCACAGGGAGGTAAA
1 AT-CTGAAATCTTCAATCTACTCCACTGCT-GCC-CAGGGA-GAAAA
** ** * * ** *
59920842 AT-TCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAG
1 ATCT-GAAATCTTCAATCTACTCCACTGCTGCCCAGGGAGA-AAA
** * * * *
59920886 ATCCAAAATCTTCAATCTATTCCACTGCTGTCCAGGGAAGTAGA
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGG-AGAAAA
* * * *
59920930 AT-T--ATTGGCTTCAATGTACTCCACTGCAGCCTCAGGGAGGTAAA
1 ATCTGAAAT--CTTCAATCTACTCCACTGCTGCC-CAGGGA-GAAAA
** ** * * ** *
59920974 ATCTGGCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAG
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGAGA-AAA
** * * * *
59921018 ATCCAAAATCTTCAATCTATTCCACTGCTGCCCAGGAAAGTAGA
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGG-GAGAAAA
* * * * *
59921062 AT-T--ATTGGCTTCAATGTACTCTACTG-TAACCACAGGGAGGTAAA
1 ATCTGAAAT--CTTCAATCTACTCCACTGCT-GCC-CAGGGA-GAAAA
** * ** * * ** *
59921106 ATCTGTCATTTTTGATCTGCTCCACTACTGCGTAGGGAGGAAAT
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGA-GAAAA
* * *
59921150 ATCTGAAATCTTCAATCTATTCCACTGCTGCCTAGGGAAGTAGAA
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGG-AG-AAAA
* * * ** *
59921195 TTACTG---GCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAA
1 AT-CTGAAATCTTCAATCTACTCCACTGCTGCC-CAGGGA-GAAAA
** ** * * **
59921238 ATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGAAAA
1 ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGAGAAAA
** * *
59921281 GATCCAAAATCTTCAATCTATTCCACTGCTGCCTAGGGA
1 -ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGA
59921320 AGTAGAATTA
Statistics
Matches: 696, Mismatches: 273, Indels: 161
0.62 0.24 0.14
Matches are distributed among these distances:
41 8 0.01
42 12 0.02
43 179 0.26
44 329 0.47
45 144 0.21
46 21 0.03
47 3 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (43 bp):
ATCTGAAATCTTCAATCTACTCCACTGCTGCCCAGGGAGAAAA
Found at i:59923012 original size:7 final size:7
Alignment explanation
Indices: 59923002--59923044 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
59922992 TCCATTTTAC
59923002 TTTTTCA
1 TTTTTCA
59923009 TTTTTCA
1 TTTTTCA
*
59923016 GTTTTCA
1 TTTTTCA
59923023 -TTTTCA
1 TTTTTCA
59923029 CTTTTTCA
1 -TTTTTCA
59923037 TTTTTCA
1 TTTTTCA
59923044 T
1 T
59923045 CTCATCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
6 6 0.18
7 21 0.64
8 6 0.18
ACGTcount: A:0.14, C:0.16, G:0.02, T:0.67
Consensus pattern (7 bp):
TTTTTCA
Found at i:59927732 original size:18 final size:19
Alignment explanation
Indices: 59927709--59927750 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
59927699 TGATAATTTT
**
59927709 AAAAATT-CAAAAATTAAA
1 AAAAATTGCAAAAAACAAA
59927727 AAAAATTGCAAAAAACAAA
1 AAAAATTGCAAAAAACAAA
59927746 AAAAA
1 AAAAA
59927751 ATGAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAATTGCAAAAAACAAA
Found at i:59930207 original size:3 final size:3
Alignment explanation
Indices: 59930199--59930270 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
59930189 AACATGCATG
59930199 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
59930247 AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
59930271 GCAAATGACA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:59933314 original size:17 final size:18
Alignment explanation
Indices: 59933270--59933314 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
59933260 TATGAAATTT
59933270 TGATATGAAATGTGAGTA
1 TGATATGAAATGTGAGTA
*
59933288 TGAT-TAAAATGATGA-TA
1 TGATATGAAATG-TGAGTA
59933305 T-ATATGAAAT
1 TGATATGAAAT
59933315 ATATGATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (18 bp):
TGATATGAAATGTGAGTA
Found at i:59933818 original size:3 final size:3
Alignment explanation
Indices: 59933798--59933890 Score: 75
Period size: 3 Copynumber: 30.3 Consensus size: 3
59933788 TTTAGCAATT
* * *
59933798 TTA TTA TTTA GTTG TTA TTA TTG TTA TTA TTA TTA TTA GTA TTA TTA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
59933845 GTA TT- TCTA TTA TTA TT- TATA TTA TTG TTA CTTA TTA -TA TTA TTA
1 TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA TTA TTA
59933890 T
1 T
59933891 CATATGATAG
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
2 4 0.06
3 58 0.81
4 10 0.14
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:59934011 original size:24 final size:24
Alignment explanation
Indices: 59933956--59934012 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
59933946 TCCTTTTTAG
59933956 ACTTATTTAATATATATATATAAATA
1 ACTT-TTT-ATATATATATATAAATA
* * *
59933982 CCTTTTTATATGTATATATATATA
1 ACTTTTTATATATATATATAAATA
*
59934006 AGTTTTT
1 ACTTTTT
59934013 TTTCCTTTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 20 0.77
25 3 0.12
26 3 0.12
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (24 bp):
ACTTTTTATATATATATATAAATA
Found at i:59934158 original size:15 final size:15
Alignment explanation
Indices: 59934140--59934179 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
59934130 CACATATACA
59934140 TTTTTTATATATATT
1 TTTTTTATATATATT
* *
59934155 TTTTATGTATATATT
1 TTTTTTATATATATT
*
59934170 TTTTTAATAT
1 TTTTTTATAT
59934180 TTATATGAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTTTATATATATT
Found at i:59934165 original size:13 final size:13
Alignment explanation
Indices: 59934073--59934181 Score: 60
Period size: 13 Copynumber: 8.1 Consensus size: 13
59934063 ATATGGTTTC
*
59934073 TTTTATATCTATT
1 TTTTATATATATT
*
59934086 TATATATATATATT
1 T-TTTATATATATT
* *
59934100 TATTTATCTTATTTT
1 T-TTTAT-ATATATT
* *
59934115 ATTTTTTATATATC
1 -TTTTATATATATT
*** *
59934129 TCACATATACATT
1 TTTTATATATATT
59934142 TTTTATATATATT
1 TTTTATATATATT
59934155 TTTTATGTATATATT
1 TTTTA--TATATATT
59934170 TTTT-TA-ATATT
1 TTTTATATATATT
59934181 T
1 T
59934182 ATATGAATTT
Statistics
Matches: 72, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
11 6 0.08
12 2 0.03
13 22 0.31
14 20 0.28
15 21 0.29
16 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (13 bp):
TTTTATATATATT
Found at i:59939769 original size:24 final size:23
Alignment explanation
Indices: 59939742--59939786 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
59939732 AAGTAACTCA
*
59939742 TAATATGATATTAATCTCTAATGT
1 TAATATAATATTAATC-CTAATGT
* *
59939766 TAATCTAATATTTATCCTAAT
1 TAATATAATATTAATCCTAAT
59939787 ATTGTCATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (23 bp):
TAATATAATATTAATCCTAATGT
Found at i:59948353 original size:42 final size:42
Alignment explanation
Indices: 59948260--59948437 Score: 212
Period size: 42 Copynumber: 4.4 Consensus size: 42
59948250 TGATTCGGGA
*
59948260 AATCAGCACTTAGCAACCCCTTTCACATTCAAAAATACGGTGG
1 AATCAGCACTTAGCAACCCCTTTCACATT-TAAAATACGGTGG
**
59948303 AATCAGCACTTAGCAACCCCTTTCACATTTACGATACGGTGG
1 AATCAGCACTTAGCAACCCCTTTCACATTTAAAATACGGTGG
* * * *
59948345 GATCAGCACTTAGCAACCAC---CA-A--T--AATTCAG-GG
1 AATCAGCACTTAGCAACCCCTTTCACATTTAAAATACGGTGG
*
59948378 AATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGG
1 AATCAGCACTTAGCAACCCCTTTCACATTTAAAATACGGTGG
59948420 AATCAGCACTTAGCAACC
1 AATCAGCACTTAGCAACC
59948438 ACCAATGATT
Statistics
Matches: 114, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
33 20 0.18
34 4 0.04
36 3 0.03
37 1 0.01
38 1 0.01
39 3 0.03
41 5 0.04
42 48 0.42
43 29 0.25
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (42 bp):
AATCAGCACTTAGCAACCCCTTTCACATTTAAAATACGGTGG
Found at i:59948388 original size:33 final size:33
Alignment explanation
Indices: 59948346--59948470 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 33
59948336 ATACGGTGGG
*
59948346 ATCAGCACTTAGCAACCACCAATAATTCAGGGA
1 ATCAGCACTTAGCAACCACCAATAATTCGGGGA
* *
59948379 ATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGA
1 ATCAGCACTTAGCAA-CCAC--CA-A--T--AATTCGG-GGA
*
59948421 ATCAGCACTTAGCAACCACCAATGATTCGGGGA
1 ATCAGCACTTAGCAACCACCAATAATTCGGGGA
*
59948454 ATCAGTACTTAGCAACC
1 ATCAGCACTTAGCAACC
59948471 CCCTTTATAT
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
33 34 0.45
34 8 0.11
36 3 0.04
37 1 0.01
38 1 0.01
39 3 0.04
41 8 0.11
42 18 0.24
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (33 bp):
ATCAGCACTTAGCAACCACCAATAATTCGGGGA
Found at i:59948390 original size:75 final size:75
Alignment explanation
Indices: 59948301--59948475 Score: 287
Period size: 75 Copynumber: 2.3 Consensus size: 75
59948291 AAAATACGGT
* ** *
59948301 GGAATCAGCACTTAGCAACCCCTTTCACATTTACGATACGGTGGGATCAGCACTTAGCAACCACC
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACC
59948366 AATAATTCAG
66 AATAATTCAG
59948376 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACC
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACC
* *
59948441 AATGATTCGG
66 AATAATTCAG
*
59948451 GGAATCAGTACTTAGCAACCCCCTT
1 GGAATCAGCACTTAGCAACCCCCTT
59948476 TATATTCAAT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 93 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (75 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACC
AATAATTCAG
Found at i:59954734 original size:21 final size:23
Alignment explanation
Indices: 59954686--59954736 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
59954676 CATATGATTT
59954686 TATATTTTTAATTTATTAAATAA
1 TATATTTTTAATTTATTAAATAA
59954709 TATATTTTATAA-TT-TTAAAT-A
1 TATATTTT-TAATTTATTAAATAA
59954730 TATATTT
1 TATATTT
59954737 ATGCTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.30
22 6 0.22
23 10 0.37
24 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATTTTTAATTTATTAAATAA
Found at i:59968477 original size:18 final size:19
Alignment explanation
Indices: 59968431--59968470 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
59968421 AAAATGAACT
*
59968431 AATACATATACAACTATTAA
1 AATA-ATATACAAATATTAA
59968451 AATAATATACAAAT-TTAA
1 AATAATATACAAATATTAA
59968469 AA
1 AA
59968471 CTATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAATATACAAATATTAA
Found at i:59973231 original size:19 final size:19
Alignment explanation
Indices: 59973207--59973268 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
59973197 TTTGGTTCAG
59973207 ACTTTCAATTGGTTGCTTT
1 ACTTTCAATTGGTTGCTTT
* *
59973226 ACTTTCAA-TGGCTTTGGTTGAC
1 ACTTTCAATTGG--TTGCTT--T
59973248 ACTTTCAATTGGTTGCTTT
1 ACTTTCAATTGGTTGCTTT
59973267 AC
1 AC
59973269 ATTTAAGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 3 0.09
19 10 0.29
20 5 0.15
21 5 0.15
22 8 0.24
23 3 0.09
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (19 bp):
ACTTTCAATTGGTTGCTTT
Found at i:59973236 original size:41 final size:41
Alignment explanation
Indices: 59973191--59973268 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
59973181 AGGCAATTCT
*
59973191 AATGGCTTTGGTTCAGACTTTCAATTGGTTGCTTTACTTTC
1 AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTACTTTC
*
59973232 AATGGCTTTGGTTGACACTTTCAATTGGTTGCTTTAC
1 AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTAC
59973269 ATTTAAGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.45
Consensus pattern (41 bp):
AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTACTTTC
Found at i:59973757 original size:39 final size:39
Alignment explanation
Indices: 59973623--59973758 Score: 137
Period size: 40 Copynumber: 3.4 Consensus size: 39
59973613 GTTTAGACAA
* * *
59973623 AAAACGCCGCTAAAAATCGATCATTAGCGGCGCATTACGT
1 AAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTAAGT
* * * *
59973663 AAAACGCCGCTAAAGATTGAGCATTAGCGGCACTTTCAGG
1 AAAACGCCGCTAAA-AATGAGCATTAGCGGCGCTTTAAGT
* * **
59973703 AAAGCGCCGCTAAAAATGAGCATTAGCGGCGTTTTTTTGT
1 AAAACGCCGCTAAAAATGAGCATTAGCGGCG-CTTTAAGT
*
59973743 AAAACGCCGCAAAAAA
1 AAAACGCCGCTAAAAA
59973759 CCTAAGCCCA
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 15 0.19
40 61 0.78
41 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTAAGT
Found at i:59973872 original size:41 final size:42
Alignment explanation
Indices: 59973795--59974066 Score: 303
Period size: 41 Copynumber: 6.7 Consensus size: 42
59973785 CCTTTCGGGG
** *
59973795 CTTTAGCGGCGTTTTTAAAAAAAGCGCTGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAATGCTCAGAT
* *
59973837 CTTTAGCGGCGTTTTT-GACAAAGCGCCGCTAATGCTTAGAT
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAATGCTCAGAT
* *
59973878 CTTTAGCGGCGTTTTT-CAAAAAGCGCCGCTAATTCTCAGAT
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAATGCTCAGAT
* * *
59973919 CTTTAGCGTCGTTTTT-GAAAAAGCGTCGCT-A---TCAAAT
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAATGCTCAGAT
* * * *
59973956 CTTTAGCAGTGTTTTTGG-AAAAGCGCCGTTAATACTCAGAT
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAATGCTCAGAT
* **
59973997 CTTTAGCGGCGTTTTTGG-AAAAGCGCCGCTAATGCTCGGGG
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAATGCTCAGAT
* *
59974038 CTTTAGCGGCGTTTTT-TAAAAAGTGCCGC
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGC
59974067 AAAAACATTT
Statistics
Matches: 197, Mismatches: 27, Indels: 13
0.83 0.11 0.05
Matches are distributed among these distances:
37 28 0.14
38 2 0.01
40 1 0.01
41 150 0.76
42 16 0.08
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAATGCTCAGAT
Found at i:59973999 original size:78 final size:80
Alignment explanation
Indices: 59973795--59974032 Score: 291
Period size: 78 Copynumber: 3.0 Consensus size: 80
59973785 CCTTTCGGGG
* * * * *
59973795 CTTTAGCGGCGTTTTTAAAAAAAGCGCTGCTAATGCTCAGATCTTTAGCGGCGTTTTTGACAAAG
1 CTTTAGCAGCGTTTTT-CAAAAAGCGCCGCTAATACTCAGATCTTTAGCGGCGTTTTTGAAAAAG
*
59973860 CGCCGCTAATGCTTAGAT
65 CGCCGCT-ATGC-TAAAT
* * *
59973878 CTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATTCTCAGATCTTTAGCGTCGTTTTTGAAAAAGC
1 CTTTAGCAGCGTTTTTCAAAAAGCGCCGCTAATACTCAGATCTTTAGCGGCGTTTTTGAAAAAGC
*
59973943 GTCGCTAT-C-AAAT
66 GCCGCTATGCTAAAT
* ** * *
59973956 CTTTAGCAGTGTTTTTGGAAAAGCGCCGTTAATACTCAGATCTTTAGCGGCGTTTTTGGAAAAGC
1 CTTTAGCAGCGTTTTTCAAAAAGCGCCGCTAATACTCAGATCTTTAGCGGCGTTTTTGAAAAAGC
59974021 GCCGCTAATGCT
66 GCCGCT-ATGCT
59974033 CGGGGCTTTA
Statistics
Matches: 136, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
78 65 0.48
79 2 0.01
80 2 0.01
81 2 0.01
82 49 0.36
83 16 0.12
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (80 bp):
CTTTAGCAGCGTTTTTCAAAAAGCGCCGCTAATACTCAGATCTTTAGCGGCGTTTTTGAAAAAGC
GCCGCTATGCTAAAT
Found at i:59974011 original size:119 final size:119
Alignment explanation
Indices: 59973794--59974060 Score: 322
Period size: 119 Copynumber: 2.2 Consensus size: 119
59973784 ACCTTTCGGG
* * *
59973794 GCTTTAGCGGCGTTTTTAAAAAAAGCG-CTGCTAATGCTCAGATCTTTAGCGGCGTTTTTGACAA
1 GCTTTAGCGGCGTTTTT-GAAAAAGCGTC-GCT-A---TCAAATCTTTAGCAGCGTTTTTGACAA
* * *
59973858 AGCGCCGCTAATGCTTAGATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATTCTCAGA
60 AGCGCCGCTAATACTCAGATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAGA
* * *
59973918 TCTTTAGCGTCGTTTTTGAAAAAGCGTCGCTATCAAATCTTTAGCAGTGTTTTTGGA-AAAGCGC
1 GCTTTAGCGGCGTTTTTGAAAAAGCGTCGCTATCAAATCTTTAGCAGCGTTTTT-GACAAAGCGC
* ** * *
59973982 CGTTAATACTCAGATCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCGGG
65 CGCTAATACTCAGATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAGA
*
59974037 GCTTTAGCGGCGTTTTTTAAAAAG
1 GCTTTAGCGGCGTTTTTGAAAAAG
59974061 TGCCGCAAAA
Statistics
Matches: 124, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
119 94 0.76
120 2 0.02
122 1 0.01
123 11 0.09
124 16 0.13
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (119 bp):
GCTTTAGCGGCGTTTTTGAAAAAGCGTCGCTATCAAATCTTTAGCAGCGTTTTTGACAAAGCGCC
GCTAATACTCAGATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAGA
Found at i:59974211 original size:26 final size:26
Alignment explanation
Indices: 59974163--59974213 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
59974153 AAAATGGATA
* * *
59974163 AATTTGAAATAATAACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
*
59974189 AATTTGAAATAAAAAAATATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
59974214 AATATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.61, C:0.04, G:0.10, T:0.25
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:59974507 original size:14 final size:15
Alignment explanation
Indices: 59974474--59974507 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
59974464 TAAGGTTTAT
59974474 AGATTATGGAATTAG
1 AGATTATGGAATTAG
59974489 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
59974503 GGATT
1 AGATT
59974508 TTGATTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:59974557 original size:14 final size:14
Alignment explanation
Indices: 59974538--59974564 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
59974528 TAAGGTTTAT
59974538 GGGTTAGAGGTTAG
1 GGGTTAGAGGTTAG
59974552 GGGTTAGAGGTTA
1 GGGTTAGAGGTTA
59974565 AGAGTTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.48, T:0.30
Consensus pattern (14 bp):
GGGTTAGAGGTTAG
Found at i:59974767 original size:22 final size:22
Alignment explanation
Indices: 59974739--59974791 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
59974729 TATATCAAAT
59974739 AAGGTTTAGGGGTTAGTGTCTA
1 AAGGTTTAGGGGTTAGTGTCTA
* *
59974761 AGGGTTT-GGGGTTAGTGTTTA
1 AAGGTTTAGGGGTTAGTGTCTA
59974782 AAGGTTTAGG
1 AAGGTTTAGG
59974792 ATTAAGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.21, C:0.02, G:0.40, T:0.38
Consensus pattern (22 bp):
AAGGTTTAGGGGTTAGTGTCTA
Found at i:59975219 original size:43 final size:43
Alignment explanation
Indices: 59975182--59975434 Score: 398
Period size: 43 Copynumber: 5.9 Consensus size: 43
59975172 CGTTTGTAAT
59975182 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
* * *
59975225 AAAAGTGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTTTGGG
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
* * * *
59975268 AGAAGTGTCGCTAAAGGTATTGGTCTTTAGTGGCGTTTGTGGG
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
* * *
59975311 AGAAGCGCTGCTAAAGGTCTTAGTCTTTAGCGGCGCTTGTGGG
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
59975354 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
* *
59975397 AGACGCACCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
59975435 TTTTCTATAA
Statistics
Matches: 190, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 190 1.00
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.30
Consensus pattern (43 bp):
AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
Found at i:59975555 original size:22 final size:22
Alignment explanation
Indices: 59975527--59975569 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
59975517 TAGCGGCACT
*
59975527 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
59975549 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
59975570 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:59989398 original size:24 final size:23
Alignment explanation
Indices: 59989371--59989415 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
59989361 AAGTAAATCC
*
59989371 TAATATGATATTAATCTCTAATGT
1 TAATATAATATTAATC-CTAATGT
* *
59989395 TAATCTAATATTTATCCTAAT
1 TAATATAATATTAATCCTAAT
59989416 ATTGTCGTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (23 bp):
TAATATAATATTAATCCTAATGT
Found at i:59990801 original size:4 final size:4
Alignment explanation
Indices: 59990792--59990816 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
59990782 CTCACACTCG
59990792 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
59990817 GAAGGCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:59995698 original size:34 final size:35
Alignment explanation
Indices: 59995638--59995704 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
59995628 CAAACACCAG
*
59995638 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCAATTTACAGAAAAGT
* *
59995673 AAAATATTTTCCCG-AAATCAATTTACGGAAAA
1 AAAATATTTTCCAGTAAATCAATTTACAGAAAA
59995705 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCAATTTACAGAAAAGT
Found at i:59996687 original size:16 final size:16
Alignment explanation
Indices: 59996663--59996693 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59996653 ATCCTTACTT
59996663 TAAAAAGTATAATTAA
1 TAAAAAGTATAATTAA
*
59996679 TAAATAGTATAATTA
1 TAAAAAGTATAATTA
59996694 TTTTTCAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TAAAAAGTATAATTAA
Found at i:59997012 original size:12 final size:12
Alignment explanation
Indices: 59996992--59997021 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
59996982 TATACATGGA
*
59996992 TTTTGTTTTCCT
1 TTTTTTTTTCCT
59997004 TTTTTTTTTCCT
1 TTTTTTTTTCCT
59997016 TTTTTT
1 TTTTTT
59997022 GTTCTTGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTCCT
Found at i:60002495 original size:13 final size:13
Alignment explanation
Indices: 60002485--60002575 Score: 51
Period size: 13 Copynumber: 6.6 Consensus size: 13
60002475 GGTTAAATTT
60002485 ATTACTTAAATAC
1 ATTACTTAAATAC
60002498 ATTACTTACTAAAATAC
1 ATTAC-T--T-AAATAC
60002515 ATTACTTACTAA-A-
1 ATTACTTA--AATAC
** **
60002528 ATTTGTTTAAATTT
1 A-TTACTTAAATAC
*
60002542 ATTACTTAAATAT
1 ATTACTTAAATAC
*
60002555 GTTACTTAAATAC
1 ATTACTTAAATAC
60002568 ATTACTTA
1 ATTACTTA
60002576 CTAAAATTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
12 2 0.03
13 34 0.57
14 9 0.15
15 2 0.03
16 2 0.03
17 11 0.18
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (13 bp):
ATTACTTAAATAC
Found at i:60002512 original size:17 final size:17
Alignment explanation
Indices: 60002486--60002529 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
60002476 GTTAAATTTA
*
60002486 TTACTTAAATACATTAC
1 TTACTAAAATACATTAC
60002503 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
60002520 TTACTAAAAT
1 TTACTAAAAT
60002530 TTGTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (17 bp):
TTACTAAAATACATTAC
Found at i:60002539 original size:57 final size:53
Alignment explanation
Indices: 60002470--60002584 Score: 167
Period size: 53 Copynumber: 2.1 Consensus size: 53
60002460 TTTGTAAGTT
60002470 AATTTGGTTAAATTTATTACTTAAATACATTACTTACTAAAATACATTACTTACTAA
1 AATTTGGTTAAATTTATTACTTAAAT--A-T-CTTACTAAAATACATTACTTACTAA
* * *
60002527 AATTTGTTTAAATTTATTACTTAAATATGTTACTTAAATACATTACTTACTAA
1 AATTTGGTTAAATTTATTACTTAAATATCTTACTAAAATACATTACTTACTAA
60002580 AATTT
1 AATTT
60002585 AAGTATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
53 28 0.51
54 1 0.02
55 1 0.02
57 25 0.45
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (53 bp):
AATTTGGTTAAATTTATTACTTAAATATCTTACTAAAATACATTACTTACTAA
Found at i:60002941 original size:157 final size:157
Alignment explanation
Indices: 60002747--60003094 Score: 646
Period size: 157 Copynumber: 2.2 Consensus size: 157
60002737 TATTTATATA
60002747 AACTTACATAACTATCACAT-A-AACTTACATAATATATAACTTACATGTTACCTTACATAATAC
1 AACTTACATAA-TA--ACATAACAACTTACATAATATATAACTTACATGTTACCTTACATAATAC
60002810 ATAACTTATATAAAATTTTTATATAAACTTACATAATACATTATTTACATATTAACTTACATAAG
63 ATAACTTATATAAAATTTTTATATAAACTTACATAATACATTATTTACATATTAACTTACATAAG
*
60002875 TTATCTACAAGCTTGTGGTTAAACTTGCAT
128 TTATCTACAAGCTTGTGGTTAAACTGGCAT
60002905 AACTTACATAATAACATAACAACTTACATAATATATAACTTACATGTTACCTTACATAATACATA
1 AACTTACATAATAACATAACAACTTACATAATATATAACTTACATGTTACCTTACATAATACATA
60002970 ACTTATATAAAATTTTTATATAAACTTACATAATACATTATTTACATATTAACTTACATAAGTTA
66 ACTTATATAAAATTTTTATATAAACTTACATAATACATTATTTACATATTAACTTACATAAGTTA
60003035 TCTACAAGCTTGTGGTTAAACTGGCAT
131 TCTACAAGCTTGTGGTTAAACTGGCAT
60003062 AACTTACATAATAACATAACAACTTACATAATA
1 AACTTACATAATAACATAACAACTTACATAATA
60003095 CATAGCATAG
Statistics
Matches: 187, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
155 4 0.02
156 1 0.01
157 171 0.91
158 11 0.06
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.36
Consensus pattern (157 bp):
AACTTACATAATAACATAACAACTTACATAATATATAACTTACATGTTACCTTACATAATACATA
ACTTATATAAAATTTTTATATAAACTTACATAATACATTATTTACATATTAACTTACATAAGTTA
TCTACAAGCTTGTGGTTAAACTGGCAT
Found at i:60003071 original size:9 final size:9
Alignment explanation
Indices: 60003059--60003431 Score: 220
Period size: 9 Copynumber: 43.1 Consensus size: 9
60003049 GTTAAACTGG
60003059 CATAACTTA
1 CATAACTTA
*
60003068 CATAA-TAA
1 CATAACTTA
60003076 CATAACAACTTA
1 CAT---AACTTA
60003088 CATAA--TA
1 CATAACTTA
* *
60003095 CATAGCATA
1 CATAACTTA
*
60003104 GATAACTTA
1 CATAACTTA
60003113 CATAACTTA
1 CATAACTTA
60003122 CATAA--TA
1 CATAACTTA
*
60003129 CAAAACTTA
1 CATAACTTA
60003138 CATAACTTA
1 CATAACTTA
* *
60003147 AATATCTTA
1 CATAACTTA
*
60003156 CACAACTTA
1 CATAACTTA
*
60003165 CATAACGTA
1 CATAACTTA
60003174 CATAA--TA
1 CATAACTTA
60003181 CATAACTTA
1 CATAACTTA
60003190 CATAA--TA
1 CATAACTTA
*
60003197 CATAA-TAA
1 CATAACTTA
60003205 CTTATAACTTA
1 C--ATAACTTA
*
60003216 CATAACATA
1 CATAACTTA
* *
60003225 CATTACTTT
1 CATAACTTA
*
60003234 GATAACTTA
1 CATAACTTA
60003243 CATAACTTA
1 CATAACTTA
60003252 CATAA--TA
1 CATAACTTA
*
60003259 CACAACTT-
1 CATAACTTA
**
60003267 GTTAAGCTTA
1 CATAA-CTTA
*
60003277 CTTAA--TA
1 CATAACTTA
60003284 CATAACTTA
1 CATAACTTA
60003293 CATAA--TA
1 CATAACTTA
*
60003300 CATAA-TAA
1 CATAACTTA
60003308 CTTATAACTTA
1 C--ATAACTTA
*
60003319 CATAACATA
1 CATAACTTA
* *
60003328 CATTACTTT
1 CATAACTTA
*
60003337 GATAACTTA
1 CATAACTTA
60003346 CATAACTTA
1 CATAACTTA
60003355 CATAA--TA
1 CATAACTTA
*
60003362 CACAACTT-
1 CATAACTTA
**
60003370 GTTAAGCTTA
1 CATAA-CTTA
*
60003380 CTTAA--TA
1 CATAACTTA
60003387 CATAACTTA
1 CATAACTTA
60003396 CATAACTT-
1 CATAACTTA
*
60003404 -ATACACGTA
1 CATA-ACTTA
60003413 CATAACTTA
1 CATAACTTA
*
60003422 CATAATTTA
1 CATAACTTA
60003431 C
1 C
60003432 TTAATACATA
Statistics
Matches: 280, Mismatches: 51, Indels: 66
0.71 0.13 0.17
Matches are distributed among these distances:
7 60 0.21
8 16 0.06
9 172 0.61
10 19 0.07
11 8 0.03
12 5 0.02
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (9 bp):
CATAACTTA
Found at i:60003112 original size:25 final size:25
Alignment explanation
Indices: 60003059--60003426 Score: 207
Period size: 25 Copynumber: 14.6 Consensus size: 25
60003049 GTTAAACTGG
60003059 CATAACTTACATAA-T--A-ACATA
1 CATAACTTACATAACTACATACATA
*
60003080 -ACAACTTACATAA-TACATAGCATA
1 CATAACTTACATAACTACATA-CATA
*
60003104 GATAACTTACATAACTTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
* * *
60003129 CAAAACTTACATAACTTAAATATCTTA
1 CATAACTTACATAAC-TACATA-CATA
*
60003156 CACAACTTACATAACGTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
60003181 CATAACTTACATAA-TACATA-ATAA
1 CATAACTTACATAACTACATACAT-A
* *
60003205 CTTATAACTTACATAACATACATTACTTT
1 C--ATAACTTACATAAC-TACA-TACATA
*
60003234 GATAACTTACATAACTTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
* ** *
60003259 CACAACTT-GTTAAGCTTACTTA-ATA
1 CATAACTTACATAA-C-TACATACATA
60003284 CATAACTTACATAA-TACATA-ATAA
1 CATAACTTACATAACTACATACAT-A
* *
60003308 CTTATAACTTACATAACATACATTACTTT
1 C--ATAACTTACATAAC-TACA-TACATA
*
60003337 GATAACTTACATAACTTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
* ** *
60003362 CACAACTT-GTTAAGCTTACTTA-ATA
1 CATAACTTACATAA-C-TACATACATA
*
60003387 CATAACTTACATAACT-TATACACGTA
1 CATAACTTACATAACTACATACA--TA
60003413 CATAACTTACATAA
1 CATAACTTACATAA
60003427 TTTACTTAAT
Statistics
Matches: 275, Mismatches: 42, Indels: 55
0.74 0.11 0.15
Matches are distributed among these distances:
20 13 0.05
22 1 0.00
23 18 0.07
24 16 0.06
25 98 0.36
26 52 0.19
27 63 0.23
28 8 0.03
29 4 0.01
30 2 0.01
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (25 bp):
CATAACTTACATAACTACATACATA
Found at i:60003122 original size:34 final size:34
Alignment explanation
Indices: 60003082--60003427 Score: 185
Period size: 34 Copynumber: 10.4 Consensus size: 34
60003072 ATAACATAAC
*
60003082 AACTTACATAATACATAGCATAGATAACTTACAT
1 AACTTACATAATACATAACATAGATAACTTACAT
* * * *
60003116 AACTTACATAATACAAAACTTACATAACTTAAAT
1 AACTTACATAATACATAACATAGATAACTTACAT
* * * *
60003150 ATCTTACACAACTTACATAACGTACATAA--TACAT
1 AACTTACATAA--TACATAACATAGATAACTTACAT
60003184 AACTTAC---ATA-AT-ACATA-ATAACTT--AT
1 AACTTACATAATACATAACATAGATAACTTACAT
* * *
60003210 AACTTACATAACATACATTACTTTGATAACTTACAT
1 AACTTACAT-A-ATACATAACATAGATAACTTACAT
* * * *
60003246 AACTTACATAATACACAAC-TTGTTAAGCTTACTT
1 AACTTACATAATACATAACATAGATAA-CTTACAT
60003280 AA--TACATAACTTACATAATACATA-ATAACTT--AT
1 AACTTACATAA--TACAT-A-ACATAGATAACTTACAT
* * *
60003313 AACTTACATAACATACATTACTTTGATAACTTACAT
1 AACTTACAT-A-ATACATAACATAGATAACTTACAT
* * * *
60003349 AACTTACATAATACACAAC-TTGTTAAGCTTACTT
1 AACTTACATAATACATAACATAGATAA-CTTACAT
* *
60003383 AA--TACATAACTTACATAAC-T-TATACACGTACAT
1 AACTTACATAA--TACATAACATAGATA-ACTTACAT
60003416 AACTTACATAAT
1 AACTTACATAAT
60003428 TTACTTAATA
Statistics
Matches: 245, Mismatches: 34, Indels: 67
0.71 0.10 0.19
Matches are distributed among these distances:
26 13 0.05
27 4 0.02
28 3 0.01
29 2 0.01
31 4 0.02
32 16 0.07
33 31 0.13
34 105 0.43
35 23 0.09
36 42 0.17
37 2 0.01
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (34 bp):
AACTTACATAATACATAACATAGATAACTTACAT
Found at i:60003199 original size:16 final size:16
Alignment explanation
Indices: 60003059--60003369 Score: 138
Period size: 16 Copynumber: 19.5 Consensus size: 16
60003049 GTTAAACTGG
60003059 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
60003076 CATAACAACTTACATAATA
1 CAT---AACTTACATAATA
* * *
60003095 CATAGCATAGATAACTTA
1 CATAACTTACATAA--TA
60003113 CATAACTTACATAATA
1 CATAACTTACATAATA
*
60003129 CAAAACTTACATAACTTA
1 CATAACTTACATAA--TA
* * *
60003147 AATATCTTACACAACTTA
1 CATAACTTACATAA--TA
*
60003165 CATAACGTACATAATA
1 CATAACTTACATAATA
60003181 CATAACTTACATAATA
1 CATAACTTACATAATA
*
60003197 CATAA-TAAC-T--T-
1 CATAACTTACATAATA
60003208 -ATAACTTACATAACATA
1 CATAACTTACAT-A-ATA
* **
60003225 CATTACTTTGATAACTTA
1 CATAACTTACATAA--TA
60003243 CATAACTTACATAATA
1 CATAACTTACATAATA
* *
60003259 CACAACTT--GT--T-
1 CATAACTTACATAATA
* *
60003270 -A-AGCTTACTTAATA
1 CATAACTTACATAATA
60003284 CATAACTTACATAATA
1 CATAACTTACATAATA
*
60003300 CATAA-TAAC-T--T-
1 CATAACTTACATAATA
60003311 -ATAACTTACATAACATA
1 CATAACTTACAT-A-ATA
* **
60003328 CATTACTTTGATAACTTA
1 CATAACTTACATAA--TA
60003346 CATAACTTACATAATA
1 CATAACTTACATAATA
*
60003362 CACAACTT
1 CATAACTT
60003370 GTTAAGCTTA
Statistics
Matches: 221, Mismatches: 39, Indels: 69
0.67 0.12 0.21
Matches are distributed among these distances:
9 4 0.02
10 9 0.04
11 7 0.03
12 5 0.02
13 1 0.00
14 3 0.01
15 7 0.03
16 83 0.38
17 5 0.02
18 81 0.37
19 4 0.02
20 12 0.05
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:60003227 original size:103 final size:103
Alignment explanation
Indices: 60003132--60003400 Score: 450
Period size: 103 Copynumber: 2.6 Consensus size: 103
60003122 CATAATACAA
* * ** * *
60003132 AACTTACATAACTTAAATATCTTACACAACTTACATAA-CGTACATAATACATAACTTACATAAT
1 AACTTACATAACTTACATA--ATACACAACTT-GTTAAGCTTACTTAATACATAACTTACATAAT
60003196 ACATAATAACTTATAACTTACATAACATACATTACTTTGAT
63 ACATAATAACTTATAACTTACATAACATACATTACTTTGAT
60003237 AACTTACATAACTTACATAATACACAACTTGTTAAGCTTACTTAATACATAACTTACATAATACA
1 AACTTACATAACTTACATAATACACAACTTGTTAAGCTTACTTAATACATAACTTACATAATACA
60003302 TAATAACTTATAACTTACATAACATACATTACTTTGAT
66 TAATAACTTATAACTTACATAACATACATTACTTTGAT
60003340 AACTTACATAACTTACATAATACACAACTTGTTAAGCTTACTTAATACATAACTTACATAA
1 AACTTACATAACTTACATAATACACAACTTGTTAAGCTTACTTAATACATAACTTACATAA
60003401 CTTATACACG
Statistics
Matches: 157, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
102 3 0.02
103 136 0.87
105 18 0.11
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.34
Consensus pattern (103 bp):
AACTTACATAACTTACATAATACACAACTTGTTAAGCTTACTTAATACATAACTTACATAATACA
TAATAACTTATAACTTACATAACATACATTACTTTGAT
Found at i:60008973 original size:21 final size:21
Alignment explanation
Indices: 60008947--60009017 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
60008937 CTACAACTTA
*
60008947 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
60008968 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
60008989 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
60009010 AAGCAGAG
1 AAGCAGAG
60009018 CAGACCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.31, C:0.20, G:0.46, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:60009455 original size:42 final size:43
Alignment explanation
Indices: 60009314--60009455 Score: 207
Period size: 42 Copynumber: 3.3 Consensus size: 43
60009304 ATCCCAAAAA
** *
60009314 TAGTGGCGTTTTTGTATAAAAACGCCGCTAAAGAACATGGTCTT
1 TAGTGGCGTTTTT-TACCAAAGCGCCGCTAAAGAACATGGTCTT
*
60009358 TAGTGGCG-TTTTTACCAAAGCGCCCCTAAAGAACATGGTCTT
1 TAGTGGCGTTTTTTACCAAAGCGCCGCTAAAGAACATGGTCTT
*
60009400 TAGTGGCGTTTTTTA-CTAAGCGCCGCTAAAGAACATGGTCTT
1 TAGTGGCGTTTTTTACCAAAGCGCCGCTAAAGAACATGGTCTT
*
60009442 TAGCGGCGTTTTTT
1 TAGTGGCGTTTTTT
60009456 TGTAAACGCT
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
42 72 0.80
43 10 0.11
44 8 0.09
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (43 bp):
TAGTGGCGTTTTTTACCAAAGCGCCGCTAAAGAACATGGTCTT
Found at i:60018499 original size:20 final size:20
Alignment explanation
Indices: 60018472--60018515 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
60018462 TTTTTAATGG
60018472 TTTTTAAAAT-TTTATAA-TA
1 TTTTTAAAATGTTT-TAACTA
60018491 TTTTCTAAAATGTTTTAACTA
1 TTTT-TAAAATGTTTTAACTA
60018512 TTTT
1 TTTT
60018516 GGTCGTCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 9 0.41
21 9 0.41
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTTAAAATGTTTTAACTA
Found at i:60023882 original size:20 final size:20
Alignment explanation
Indices: 60023859--60023908 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
60023849 TTTATAATTT
* *
60023859 ATATCTATATATCTATATAC
1 ATATCTATATATATATACAC
* *
60023879 ATATTTATACATATATACAC
1 ATATCTATATATATATACAC
*
60023899 ATACCTATAT
1 ATATCTATAT
60023909 GTTTTATATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATCTATATATATATACAC
Found at i:60024228 original size:39 final size:33
Alignment explanation
Indices: 60024151--60024215 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
60024141 TTGCTCATCT
60024151 TTATTTTTATGAAATGCTTTAGTTCTTTTTACA
1 TTATTTTTATGAAATGCTTTAGTTCTTTTTACA
60024184 TTATTTTTATGAAATGCTTTAGTTCTTTTTAC
1 TTATTTTTATGAAATGCTTTAGTTCTTTTTAC
60024216 TTACTCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58
Consensus pattern (33 bp):
TTATTTTTATGAAATGCTTTAGTTCTTTTTACA
Found at i:60029310 original size:97 final size:97
Alignment explanation
Indices: 60029203--60029392 Score: 244
Period size: 97 Copynumber: 2.0 Consensus size: 97
60029193 TTCATTTTGA
* **
60029203 ATCTTAGCAAAATTCGCTGT-TC-TGCTTAATTTATTTGTTTAGAGCTCTGCTCTCAATAAAATT
1 ATCTTAGCAAAATTCG-T-TATCTTGATTAATTTATTCATTTAGAGCTCTGCTCTCAATAAAATT
60029266 TCATCTT-TCCCACTA-TGATAATCTTTTTCATCTT
64 TCATCTTAT-CCA-TATTGATAATCTTTTTCATCTT
* * * * *
60029300 ATCTTAGCAAAATTTGTTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTTAATAAAATTTC
1 ATCTTAGCAAAATTCGTTATCTTGATTAATTTATTCATTTAGAGCTCTGCTCTCAATAAAATTTC
60029365 ATCTTATCCATATTGATAATCTTTTTCA
66 ATCTTATCCATATTGATAATCTTTTTCA
60029393 AGCATTTTAC
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
95 1 0.01
96 5 0.06
97 74 0.91
98 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (97 bp):
ATCTTAGCAAAATTCGTTATCTTGATTAATTTATTCATTTAGAGCTCTGCTCTCAATAAAATTTC
ATCTTATCCATATTGATAATCTTTTTCATCTT
Found at i:60030330 original size:46 final size:46
Alignment explanation
Indices: 60030277--60030764 Score: 659
Period size: 46 Copynumber: 10.7 Consensus size: 46
60030267 AGTGGACTAG
*
60030277 AGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGAAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
60030323 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* * *
60030369 AGATAGCGGATCTTGTTTTCCTGTATTTGGCAGC-AGAGTAGATCAT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGT
* * * *
60030415 AGATAGCAGATCTTGTCTTCTTATATTTGGCAGCGGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
*
60030461 AGATAGCAGATCTTGCCTTCCTGTATTTGGCAGCG-A--AG--CGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
** *
60030502 AGATAGCAGATCTTGTCTTTTTGTATTTAGCAGCGAAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* * * *
60030548 AGATAGCAGATCTTGTCTTCCTGTATTTGGTAGAGGAGTAGATCAT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* * *
60030594 AGATGGCAGATCTTGTCTTCCTGTATTTGGCAG-TAGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGT
* * * *
60030640 AGATAGCAGATATTGTCTTCCTATATTTGGCAGCGAAGTAGATTGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
**
60030686 AGATAGCAGATCTTGTCTTCCTGTATTTGGCA-ATAGAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGT
*
60030732 AGATAGTAGATCTTGTCTTCCTGTATTTGGCAG
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
60030765 TGGAGTTGGT
Statistics
Matches: 387, Mismatches: 44, Indels: 21
0.86 0.10 0.05
Matches are distributed among these distances:
41 33 0.09
42 1 0.00
43 2 0.01
44 2 0.01
45 3 0.01
46 345 0.89
47 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (46 bp):
AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
Found at i:60030668 original size:225 final size:225
Alignment explanation
Indices: 60030277--60030764 Score: 717
Period size: 225 Copynumber: 2.1 Consensus size: 225
60030267 AGTGGACTAG
*
60030277 AGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGAAGTAGATCGTAGATAGCAGATCTTGTCTT
1 AGATAGCAGATCTTATCTTCCTGTATTTAGCAGCGAAGTAGATCGTAGATAGCAGATCTTGTCTT
* * * *
60030342 CCTGTATTTGGCAGCGAAGTAGATCGTAGATAGCGGATCTTGTTTTCCTGTATTTGGCAGCAGAG
66 CCTGTATTTGGCAGAGAAGTAGATCATAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAG
* * *
60030407 TAGATCATAGATAGCAGATCTTGTCTTCTTATATTTGGCAGCGGAGTAGATCGAAGATAGCAGAT
131 TAGATCATAGATAGCAGATATTGTCTTCCTATATTTGGCAGCGAAGTAGATCGAAGATAGCAGAT
60030472 CTTGCCTTCCTGTATTTGGCAGCGAAGCGT
196 CTTGCCTTCCTGTATTTGGCAGCGAAGCGT
* **
60030502 AGATAGCAGATCTTGTCTTTTTGTATTTAGCAGCGAAGTAGATCGTAGATAGCAGATCTTGTCTT
1 AGATAGCAGATCTTATCTTCCTGTATTTAGCAGCGAAGTAGATCGTAGATAGCAGATCTTGTCTT
* * * *
60030567 CCTGTATTTGGTAGAGGAGTAGATCATAGATGGCAGATCTTGTCTTCCTGTATTTGGCAGTAGAG
66 CCTGTATTTGGCAGAGAAGTAGATCATAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAG
*
60030632 TAGATCGA-AGATAGCAGATATTGTCTTCCTATATTTGGCAGCGAAGTAGATTGAAGATAGCAGA
131 TAGATC-ATAGATAGCAGATATTGTCTTCCTATATTTGGCAGCGAAGTAGATCGAAGATAGCAGA
* * *
60030696 TCTTGTCTTCCTGTATTTGGCAATAGAGTAGATCGT
195 TCTTGCCTTCCTGTATTTGGC---AGCG-A-AGCGT
* * *
60030732 AGATAGTAGATCTTGTCTTCCTGTATTTGGCAG
1 AGATAGCAGATCTTATCTTCCTGTATTTAGCAG
60030765 TGGAGTTGGT
Statistics
Matches: 234, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
225 196 0.84
226 1 0.00
228 3 0.01
229 1 0.00
230 33 0.14
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (225 bp):
AGATAGCAGATCTTATCTTCCTGTATTTAGCAGCGAAGTAGATCGTAGATAGCAGATCTTGTCTT
CCTGTATTTGGCAGAGAAGTAGATCATAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAG
TAGATCATAGATAGCAGATATTGTCTTCCTATATTTGGCAGCGAAGTAGATCGAAGATAGCAGAT
CTTGCCTTCCTGTATTTGGCAGCGAAGCGT
Found at i:60036768 original size:22 final size:21
Alignment explanation
Indices: 60036730--60036770 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
60036720 AGATTATTAT
**
60036730 CTCTTTTTCTTCTTTTGTTGA
1 CTCTTTTTCTTAGTTTGTTGA
60036751 CTCTTTTTCATTAGTTTGTT
1 CTCTTTTTC-TTAGTTTGTT
60036771 ATTTCTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.07, C:0.17, G:0.10, T:0.66
Consensus pattern (21 bp):
CTCTTTTTCTTAGTTTGTTGA
Found at i:60037238 original size:23 final size:23
Alignment explanation
Indices: 60037211--60037262 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
60037201 CATATAATTT
*
60037211 TATATTTTTTAT-TTTTTAAATA
1 TATATTTTTTATAATTTTAAATA
60037233 -ATATATTTTTATAATTTTAAATA
1 TATAT-TTTTTATAATTTTAAATA
60037256 TATATTT
1 TATATTT
60037263 ATGCTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
23 11 0.42
24 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATATTTTTTATAATTTTAAATA
Found at i:60037244 original size:22 final size:22
Alignment explanation
Indices: 60037211--60037262 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
60037201 CATATAATTT
*
60037211 TATAT-TTTTTAT-TTTTTAAA
1 TATATATTTTTATAATTTTAAA
60037231 TAATATATTTTTATAATTTTAAA
1 T-ATATATTTTTATAATTTTAAA
60037254 TATATATTT
1 TATATATTT
60037263 ATGCTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.04
21 4 0.14
22 15 0.54
23 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATATATTTTTATAATTTTAAA
Found at i:60037270 original size:23 final size:23
Alignment explanation
Indices: 60037224--60037271 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
60037214 ATTTTTTATT
*
60037224 TTTTAAATAATATATTTTTATAA
1 TTTTAAATAATATATTTTGATAA
*
60037247 TTTTAAAT-ATATATTTATGCTAA
1 TTTTAAATAATATATTT-TGATAA
60037270 TT
1 TT
60037272 AAACGAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTTAAATAATATATTTTGATAA
Found at i:60038162 original size:28 final size:28
Alignment explanation
Indices: 60038098--60038162 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 28
60038088 TTTTATACTG
60038098 TTTAATATAACTTTAATAGTTTTTAATTT
1 TTTAA-ATAACTTTAATAGTTTTTAATTT
* * *
60038127 TTAAAAATAA-TTTTATATTTTTTGAATTT
1 TT-TAAATAACTTTAATAGTTTTT-AATTT
60038156 TTTAAAT
1 TTTAAAT
60038163 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
28 15 0.50
29 13 0.43
30 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTAAATAACTTTAATAGTTTTTAATTT
Found at i:60040921 original size:33 final size:33
Alignment explanation
Indices: 60040884--60040956 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
60040874 AACTATATGC
*
60040884 TTTTAAGGATAAAAAACAAAATTTCTATTAAAA
1 TTTTAACGATAAAAAACAAAATTTCTATTAAAA
**
60040917 TTTTAACTTTAAAAAACAAAATTTCTATTAAAA
1 TTTTAACGATAAAAAACAAAATTTCTATTAAAA
60040950 TTTTAAC
1 TTTTAAC
60040957 TTTAAAGCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (33 bp):
TTTTAACGATAAAAAACAAAATTTCTATTAAAA
Done.