Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 177 of 187
Found at i:54183270 original size:31 final size:31
Alignment explanation
Indices: 54183229--54183290 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
54183219 AGATAATTTT
54183229 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
*
54183260 AAAGATTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
54183291 TAATTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:54183848 original size:9 final size:9
Alignment explanation
Indices: 54183825--54183886 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 9
54183815 CTTATTCTTT
*
54183825 AAAAAAAAC
1 AAAAAAAGC
54183834 AGAAAAAAGC
1 A-AAAAAAGC
*
54183844 AAAAAACGC
1 AAAAAAAGC
54183853 AAAAAAAG-
1 AAAAAAAGC
*
54183861 AAGAAGAAGC
1 AA-AAAAAGC
**
54183871 AAAAAGCGC
1 AAAAAAAGC
54183880 AAAAAAA
1 AAAAAAA
54183887 AAGTTGCCTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
8 2 0.05
9 29 0.71
10 10 0.24
ACGTcount: A:0.74, C:0.11, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAGC
Found at i:54183870 original size:27 final size:25
Alignment explanation
Indices: 54183827--54183886 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 25
54183817 TATTCTTTAA
54183827 AAAAAACAGAAAAAAGCAAAAAACGC
1 AAAAAA-AGAAAAAAGCAAAAAACGC
*
54183853 AAAAAAAGAAGAAGAAGCAAAAAGCGC
1 AAAAAAAGAA-AA-AAGCAAAAAACGC
54183880 AAAAAAA
1 AAAAAAA
54183887 AAGTTGCCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 4 0.13
26 8 0.26
27 19 0.61
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (25 bp):
AAAAAAAGAAAAAAGCAAAAAACGC
Found at i:54184474 original size:31 final size:31
Alignment explanation
Indices: 54184436--54184497 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
54184426 AGGCAAATTA
54184436 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
54184467 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
54184498 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:54185272 original size:16 final size:16
Alignment explanation
Indices: 54185251--54185281 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54185241 TATCCAATTC
*
54185251 TCACATTTGCACATTA
1 TCACATTTACACATTA
54185267 TCACATTTACACATT
1 TCACATTTACACATT
54185282 GTTGACAACA
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:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (16 bp):
TCACATTTACACATTA
Found at i:54185927 original size:107 final size:107
Alignment explanation
Indices: 54185741--54185947 Score: 344
Period size: 107 Copynumber: 1.9 Consensus size: 107
54185731 AAGTTTTAAG
54185741 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTTTCTCGA
* * *
54185806 ATTTACAAACGCAAAACATTGCCTCGTTTTGAAATTATTGAA
66 ATTTACAAAAGCAAAACACTGCCTCGTTTTCAAATTATTGAA
* *
54185848 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGTACATTTTCTCG-
1 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTTTCTCGA
*
54185912 ATTTTCTAAAAGCAAAACACTGCCTCGTTTTCAAAT
66 ATTTAC-AAAAGCAAAACACTGCCTCGTTTTCAAAT
54185948 ATTTCCCTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
106 5 0.05
107 88 0.95
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (107 bp):
AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTTTCTCGA
ATTTACAAAAGCAAAACACTGCCTCGTTTTCAAATTATTGAA
Found at i:54186629 original size:15 final size:15
Alignment explanation
Indices: 54186602--54186636 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54186592 AAATATTTTA
54186602 ATAT-AGATAATAAT
1 ATATAAGATAATAAT
*
54186616 ATATAAGATGATAAT
1 ATATAAGATAATAAT
54186631 ATATAA
1 ATATAA
54186637 ATTTAAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (15 bp):
ATATAAGATAATAAT
Found at i:54187547 original size:13 final size:13
Alignment explanation
Indices: 54187529--54187553 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54187519 AGATACGTAG
54187529 ATAAATAAATGAA
1 ATAAATAAATGAA
54187542 ATAAATAAATGA
1 ATAAATAAATGA
54187554 TAAATGATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATAAATAAATGAA
Found at i:54187953 original size:17 final size:17
Alignment explanation
Indices: 54187933--54187970 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
54187923 ATTTAGGTAG
54187933 TGGGTT-TATTTTTGTTT
1 TGGGTTGTATTTTT-TTT
54187950 TGGGTTGTATTTTTTTT
1 TGGGTTGTATTTTTTTT
54187967 TGGG
1 TGGG
54187971 CCAGCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.05, C:0.00, G:0.29, T:0.66
Consensus pattern (17 bp):
TGGGTTGTATTTTTTTT
Found at i:54188344 original size:44 final size:44
Alignment explanation
Indices: 54188206--54188347 Score: 126
Period size: 44 Copynumber: 3.1 Consensus size: 44
54188196 ATGGGGATGA
* * * *
54188206 GATTTGTGGATTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
1 GATTTATGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAG
* *
54188250 GACTTGTCATGGTAAATTTAATCTGAC-CTACTGCAACTTCAGAGG-TATAG
1 GA-TT-T-ATGGT---TTTAATCTG-CTCCACTGCAACTTCAG-GGAGATAG
* *
54188300 GATTTATGGTTTTAATCCGCTCCACTGCAACTTAAGGGAGATAG
1 GATTTATGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAG
54188344 GATT
1 GATT
54188348 GGTCTCTTCT
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
43 3 0.04
44 31 0.40
45 2 0.03
46 1 0.01
47 8 0.10
48 1 0.01
49 2 0.03
50 27 0.35
51 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (44 bp):
GATTTATGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAG
Found at i:54189113 original size:108 final size:108
Alignment explanation
Indices: 54188924--54189119 Score: 392
Period size: 108 Copynumber: 1.8 Consensus size: 108
54188914 GAAAAATGCT
54188924 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
1 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
54188989 TAATCAAGATAGCAAATTTTGCTGAGATACGAGATGTATAAGA
66 TAATCAAGATAGCAAATTTTGCTGAGATACGAGATGTATAAGA
54189032 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
1 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
54189097 TAATCAAGATAGCAAATTTTGCT
66 TAATCAAGATAGCAAATTTTGCT
54189120 AGAATACAAA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 88 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
TAATCAAGATAGCAAATTTTGCTGAGATACGAGATGTATAAGA
Found at i:54189472 original size:19 final size:17
Alignment explanation
Indices: 54189448--54189487 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 17
54189438 GGCCTCTCCT
54189448 TTTTCTTTTTTCGTTCTTC
1 TTTTCTTTTTTC-TT-TTC
54189467 TTTTCTTTTTTCTTTTC
1 TTTTCTTTTTTCTTTTC
54189484 TTTT
1 TTTT
54189488 TGTGTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.33
18 2 0.10
19 12 0.57
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTTC
Found at i:54189479 original size:12 final size:12
Alignment explanation
Indices: 54189464--54189501 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54189454 TTTTTCGTTC
54189464 TTCTTTTCTTTT
1 TTCTTTTCTTTT
54189476 TTCTTTTCTTTT
1 TTCTTTTCTTTT
*
54189488 TGT-GTTTCTTTT
1 T-TCTTTTCTTTT
54189500 TT
1 TT
54189502 TCAAGTGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (12 bp):
TTCTTTTCTTTT
Found at i:54189482 original size:24 final size:24
Alignment explanation
Indices: 54189446--54189501 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
54189436 TTGGCCTCTC
*
54189446 CTTTTTCTTTTTTCGTTCTTCT-TTT
1 CTTTTT-TCTTTTC-TTCTTCTGTTT
* *
54189471 CTTTTTTCTTTTCTTTTTGTGTTT
1 CTTTTTTCTTTTCTTCTTCTGTTT
54189495 CTTTTTT
1 CTTTTTT
54189502 TCAAGTGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 5 0.19
24 16 0.59
25 6 0.22
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (24 bp):
CTTTTTTCTTTTCTTCTTCTGTTT
Found at i:54189950 original size:10 final size:10
Alignment explanation
Indices: 54189935--54189983 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
54189925 CCCAATAGAG
54189935 GTTTTTTTTT
1 GTTTTTTTTT
54189945 GTTTTTTTTT
1 GTTTTTTTTT
*
54189955 GTCTCTTTTGTT
1 GT-T-TTTTTTT
*
54189967 CTTTTTTTTT
1 GTTTTTTTTT
*
54189977 GTGTTTT
1 GTTTTTT
54189984 CGGTTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
10 23 0.72
11 2 0.06
12 7 0.22
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (10 bp):
GTTTTTTTTT
Found at i:54194179 original size:22 final size:21
Alignment explanation
Indices: 54194151--54194192 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
54194141 TCATCCATCG
54194151 GCCTCTTCCTGTTTCACTTTCA
1 GCCTCTTCCTGTTTCA-TTTCA
54194173 GCCTCTTCCTGTTTCATTTC
1 GCCTCTTCCTGTTTCATTTC
54194193 TTGCACCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.07, C:0.36, G:0.10, T:0.48
Consensus pattern (21 bp):
GCCTCTTCCTGTTTCATTTCA
Found at i:54195999 original size:20 final size:20
Alignment explanation
Indices: 54195963--54196001 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54195953 AATTTTTTAA
*
54195963 AAATATATTTATAATATAAT
1 AAATATATTAATAATATAAT
54195983 AAATATA-TAATACATATAA
1 AAATATATTAATA-ATATAA
54196002 ATTTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATTAATAATATAAT
Found at i:54198131 original size:11 final size:11
Alignment explanation
Indices: 54198115--54198141 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
54198105 TAAAAATTAG
54198115 TTTGTGAAACT
1 TTTGTGAAACT
54198126 TTTGTGAAACT
1 TTTGTGAAACT
54198137 TTTGT
1 TTTGT
54198142 ATTGTACTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:54199685 original size:91 final size:91
Alignment explanation
Indices: 54199538--54199745 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
54199528 TTGATTTTAG
* *
54199538 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
54199603 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
54199630 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
54199695 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
54199721 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
54199746 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:54199714 original size:26 final size:28
Alignment explanation
Indices: 54199660--54199720 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
54199650 TATTATCAAG
* *
54199660 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
54199688 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
54199714 AATTATA
1 AATTATA
54199721 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:54199720 original size:44 final size:43
Alignment explanation
Indices: 54199578--54199720 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
54199568 GAATTTTATG
* *
54199578 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
54199622 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
54199669 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
54199713 AAATTATA
1 AAATTATA
54199721 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:54199838 original size:59 final size:57
Alignment explanation
Indices: 54199772--54200080 Score: 184
Period size: 66 Copynumber: 5.2 Consensus size: 57
54199762 ATTTTATTAA
54199772 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
54199831 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
54199892 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
* * ** * *
54199951 ATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
54200012 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
54200071 ATCATATATT
1 ATCATATATT
54200081 ATGATTTCAG
Statistics
Matches: 185, Mismatches: 37, Indels: 56
0.67 0.13 0.20
Matches are distributed among these distances:
54 28 0.15
55 14 0.08
56 10 0.05
57 6 0.03
59 30 0.16
60 16 0.09
61 20 0.11
63 7 0.04
64 10 0.05
65 13 0.07
66 31 0.17
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:54199885 original size:120 final size:120
Alignment explanation
Indices: 54199761--54200173 Score: 738
Period size: 120 Copynumber: 3.4 Consensus size: 120
54199751 AATTATTTTA
* * * * *
54199761 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
54199825 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
54199881 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
54199946 ATAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
54200001 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
* *
54200066 ATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTATTTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
54200121 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
54200174 TAAATATGAT
Statistics
Matches: 283, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
120 281 0.99
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:54199921 original size:15 final size:15
Alignment explanation
Indices: 54199886--54200057 Score: 62
Period size: 15 Copynumber: 11.6 Consensus size: 15
54199876 TTAAGAATTT
*
54199886 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54199900 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54199914 TATTTAATAATAAT-
1 TATTTAATTATAATA
54199928 TATGTTAATT-T-ATA
1 TAT-TTAATTATAATA
* *
54199942 T-TTTATAGTATCATA
1 TATTTA-ATTATAATA
* *
54199957 TATTATGATT-TGAGTA
1 TATT-TAATTAT-AATA
* *
54199973 -AATTAA-TATAAGA
1 TATTTAATTATAATA
*
54199986 -ATATTAATTATTAAGA
1 TAT-TTAATTA-TAATA
* *
54200002 -ATTTTATTAAATTATA
1 TATTTAATT--ATAATA
54200018 TATTTTAATTATAATA
1 TA-TTTAATTATAATA
*
54200034 TATTTAATAATAAT-
1 TATTTAATTATAATA
54200048 TATGTTAATT
1 TAT-TTAATT
54200058 TATATTTTAT
Statistics
Matches: 119, Mismatches: 20, Indels: 37
0.68 0.11 0.21
Matches are distributed among these distances:
12 3 0.03
13 17 0.14
14 21 0.18
15 46 0.39
16 23 0.19
17 3 0.03
18 6 0.05
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54200156 original size:16 final size:16
Alignment explanation
Indices: 54200135--54200176 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
54200125 TTATTAAATT
*
54200135 ATATATTTTAATTATA
1 ATATATTTTAATAATA
54200151 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
54200166 AT-TATGTTTAA
1 ATATAT-TTTAA
54200177 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:54200161 original size:15 final size:15
Alignment explanation
Indices: 54200126--54200167 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54200116 TTAAGAATTT
*
54200126 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54200140 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54200154 TATTTAATAATAAT
1 TATTTAATTATAAT
54200168 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54200411 original size:16 final size:16
Alignment explanation
Indices: 54200390--54200443 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
54200380 TTGATTTGTT
*
54200390 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
54200406 ATTACACCTCTATTTC
1 ATTACACCTCTATTCC
54200422 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
54200438 AATACA
1 ATTACA
54200444 ACGAACCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:54202874 original size:13 final size:14
Alignment explanation
Indices: 54202841--54202885 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
54202831 AGGATAAATA
**
54202841 AATAATTAGTTAAT
1 AATAATTAAATAAT
54202855 AAT-ATTAAA-AAT
1 AATAATTAAATAAT
54202867 AATAATTAAATAA-
1 AATAATTAAATAAT
54202880 AATAAT
1 AATAAT
54202886 AATGGTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.22
13 16 0.59
14 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AATAATTAAATAAT
Found at i:54224375 original size:24 final size:24
Alignment explanation
Indices: 54224312--54224375 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
54224302 TGTGCCAAGC
54224312 AAAAGAAAAATACAAAAGAAACAGA
1 AAAAGAAAAATA-AAAAGAAACAGA
* * * * *
54224337 AAAATAAGAAGAAAAAG-TACTTGA
1 AAAAGAAAAATAAAAAGAAAC-AGA
54224361 AAAAGAAAAATAAAA
1 AAAAGAAAAATAAAA
54224376 GCATTTGTGA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
23 2 0.07
24 19 0.63
25 9 0.30
ACGTcount: A:0.73, C:0.05, G:0.12, T:0.09
Consensus pattern (24 bp):
AAAAGAAAAATAAAAAGAAACAGA
Found at i:54227975 original size:135 final size:134
Alignment explanation
Indices: 54227768--54228038 Score: 515
Period size: 135 Copynumber: 2.0 Consensus size: 134
54227758 TAAGCACAAA
*
54227768 GTGCTTACCCTGTTTCTTTTTCCCTGTTTTGTAGTGTTAAGAGCTTGGAGGTCGGATTCGGTCAG
1 GTGCTTACCCTGTTTCTTTTTCCCTGTTTTGTAGTGTTAAGAGCTCGGAGGTCGGATTCGGTCAG
*
54227833 AGACGTATCATACTATCAACCTCAAGATCTCGGTATATAAAGAAACTTTATTTTGGAAATCAATG
66 AGACGTATCACACTATCAACCTCAAGATCTCGGTATATAAAGAAACTTTATTTTGGAAATCAATG
54227898 GCAT
131 GCAT
54227902 GTGCTTACCCTGTTTCTTTTTCCCCTGTTTTGTAGTGTTAAGAGCTCGGAGGTCGGATTCGGTCA
1 GTGCTTACCCTGTTTCTTTTT-CCCTGTTTTGTAGTGTTAAGAGCTCGGAGGTCGGATTCGGTCA
54227967 GAGACGTATCACACTATCAACCTCAAGATCTCGGTATATAAAGAAACTTTATTTTGGAAATCAAT
65 GAGACGTATCACACTATCAACCTCAAGATCTCGGTATATAAAGAAACTTTATTTTGGAAATCAAT
54228032 GGCAT
130 GGCAT
54228037 GT
1 GT
54228039 ATAAGCTAGT
Statistics
Matches: 134, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
134 21 0.16
135 113 0.84
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (134 bp):
GTGCTTACCCTGTTTCTTTTTCCCTGTTTTGTAGTGTTAAGAGCTCGGAGGTCGGATTCGGTCAG
AGACGTATCACACTATCAACCTCAAGATCTCGGTATATAAAGAAACTTTATTTTGGAAATCAATG
GCAT
Found at i:54228642 original size:45 final size:45
Alignment explanation
Indices: 54228578--54228673 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 45
54228568 GCTATCACCC
*
54228578 ACACAACCAATCATAGCCTCCAAACACAA-ATAATTTACCCTCCAA
1 ACACAACCAATCATAGCCTCCAAACACAACA-AATATACCCTCCAA
*
54228623 ACACAACCAAAT-ATAGCCTCCCAACACAACCAAATATACCCTCCAA
1 ACACAACC-AATCATAGCCTCCAAACACAA-CAAATATACCCTCCAA
54228669 ACACA
1 ACACA
54228674 TCCTCTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
45 24 0.52
46 21 0.46
47 1 0.02
ACGTcount: A:0.46, C:0.38, G:0.02, T:0.15
Consensus pattern (45 bp):
ACACAACCAATCATAGCCTCCAAACACAACAAATATACCCTCCAA
Found at i:54228648 original size:23 final size:23
Alignment explanation
Indices: 54228578--54228673 Score: 117
Period size: 23 Copynumber: 4.2 Consensus size: 23
54228568 GCTATCACCC
*
54228578 ACACAACC-AATCATAGCCTCCAA
1 ACACAACCAAAT-ATACCCTCCAA
*
54228601 ACACAA--ATAATTTACCCTCCAA
1 ACACAACCA-AATATACCCTCCAA
* *
54228623 ACACAACCAAATATAGCCTCCCA
1 ACACAACCAAATATACCCTCCAA
54228646 ACACAACCAAATATACCCTCCAA
1 ACACAACCAAATATACCCTCCAA
54228669 ACACA
1 ACACA
54228674 TCCTCTTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
22 15 0.24
23 46 0.74
24 1 0.02
ACGTcount: A:0.46, C:0.38, G:0.02, T:0.15
Consensus pattern (23 bp):
ACACAACCAAATATACCCTCCAA
Found at i:54228828 original size:41 final size:41
Alignment explanation
Indices: 54228736--54228829 Score: 95
Period size: 41 Copynumber: 2.3 Consensus size: 41
54228726 AACTCATGTT
*
54228736 CATATCACATTTTCAAGTCTCATATCATATTCAATCCTAAA
1 CATATCACATTTTCAAGTCTCATATCATATACAATCCTAAA
* * * *
54228777 CACATAACATTTTC-ATTGTCATATCAATATAC-ATCAC-ATAA
1 CATATCACATTTTCAAGTCTCATATC-ATATACAATC-CTA-AA
54228818 CATATCACATTT
1 CATATCACATTT
54228830 AAGCATCATT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
40 13 0.30
41 30 0.70
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (41 bp):
CATATCACATTTTCAAGTCTCATATCATATACAATCCTAAA
Found at i:54233180 original size:50 final size:50
Alignment explanation
Indices: 54233105--54233200 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
54233095 TGAGGTTATG
* *
54233105 AGAGGTCCCACATAAGACAATGTCTGGGACATGGCGTTGGCACCGAGATT
1 AGAGGTCCCACATAAGACAATGTCTGGGACATGGCATGGGCACCGAGATT
* * *
54233155 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 AGAGGTCCCACATAAGACAATGTCTGGGACATGGCATGGGCACCGA
54233201 TATGAAAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.26, C:0.25, G:0.31, T:0.18
Consensus pattern (50 bp):
AGAGGTCCCACATAAGACAATGTCTGGGACATGGCATGGGCACCGAGATT
Found at i:54234114 original size:17 final size:17
Alignment explanation
Indices: 54234092--54234124 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54234082 ACGCAAAAGA
54234092 ATTTTATATTTT-GTGAT
1 ATTTTA-ATTTTAGTGAT
54234109 ATTTTAATTTTAGTGA
1 ATTTTAATTTTAGTGA
54234125 GACAGGGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (17 bp):
ATTTTAATTTTAGTGAT
Found at i:54240886 original size:22 final size:23
Alignment explanation
Indices: 54240843--54240886 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
54240833 GTAAGTTTAG
** *
54240843 TTGTGTTTTAGGATTTTCCATTA
1 TTGTGTTTTAGGAAATTACATTA
54240866 TTGT-TTTTAGGAAATTACATT
1 TTGTGTTTTAGGAAATTACATT
54240887 GAAGAGCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.55
Consensus pattern (23 bp):
TTGTGTTTTAGGAAATTACATTA
Found at i:54241151 original size:8 final size:8
Alignment explanation
Indices: 54241140--54241179 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
54241130 AGAGGAAAAA
54241140 ATCATGGG
1 ATCATGGG
*
54241148 ATCATGAG
1 ATCATGGG
54241156 ATCATGGG
1 ATCATGGG
54241164 ATCATGGG
1 ATCATGGG
*
54241172 ATAATGGG
1 ATCATGGG
54241180 CCTACTCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.30, C:0.10, G:0.35, T:0.25
Consensus pattern (8 bp):
ATCATGGG
Found at i:54242935 original size:16 final size:17
Alignment explanation
Indices: 54242909--54242950 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 17
54242899 CTTTGCGAAC
54242909 AAGGTTCTTAAAACAAT
1 AAGGTTCTTAAAACAAT
54242926 AAGG-TCTTAAAACAAAAT
1 AAGGTTCTTAAAAC--AAT
54242944 AAGGTTC
1 AAGGTTC
54242951 GCATACTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 7 0.32
19 2 0.09
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (17 bp):
AAGGTTCTTAAAACAAT
Found at i:54244374 original size:30 final size:30
Alignment explanation
Indices: 54244265--54244439 Score: 139
Period size: 30 Copynumber: 6.0 Consensus size: 30
54244255 GGCATTCATG
* *
54244265 TAATTGAGATAGCCACAAAGGTAT-CTTTT
1 TAATAGAGATAGCCACAAAGGCATCCTTTT
* * *
54244294 TAATAGAGATAGTCATAAATGCATCCTTTT
1 TAATAGAGATAGCCACAAAGGCATCCTTTT
* *
54244324 TAACAGAGATAGCCACAAGGGCATCCTTTT
1 TAATAGAGATAGCCACAAAGGCATCCTTTT
* *
54244354 TAATAGAGATAGCCA-TAAGGGATTCC--TT
1 TAATAGAGATAGCCACAAAGGCA-TCCTTTT
* * * *
54244382 TAAGAGAGATCA-CCACAAAAGC-TTC-ATT
1 TAATAGAGAT-AGCCACAAAGGCATCCTTTT
* *
54244410 TAATAGAGATTAGACACAAAGGCTTCCTTT
1 TAATAGAGA-TAGCCACAAAGGCATCCTTT
54244440 AACAAAGATA
Statistics
Matches: 113, Mismatches: 24, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
27 2 0.02
28 25 0.22
29 36 0.32
30 49 0.43
31 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (30 bp):
TAATAGAGATAGCCACAAAGGCATCCTTTT
Found at i:54244381 original size:60 final size:59
Alignment explanation
Indices: 54244270--54244459 Score: 169
Period size: 57 Copynumber: 3.3 Consensus size: 59
54244260 TCATGTAATT
* * *
54244270 GAGATAGCCACAAAGGTATCTTTTTAATAGAGATAGTCATAAATGCATCCTTTTTAACA
1 GAGATAGCCACAAAGGCATCTTTTTAATAGAGATAGCCATAAAGGCATCCTTTTTAACA
* * *
54244329 GAGATAGCCACAAGGGCATCCTTTTTAATAGAGATAGCCAT-AAGGGATTCC--TTTAAGA
1 GAGATAGCCACAAAGGCAT-CTTTTTAATAGAGATAGCCATAAAGGCA-TCCTTTTTAACA
* * * * * *
54244387 GAGATCA-CCACAAAAGCTTC-ATTTAATAGAGATTAGACACAAAGGCTTCC--TTTAACA
1 GAGAT-AGCCACAAAGGCATCTTTTTAATAGAGA-TAGCCATAAAGGCATCCTTTTTAACA
* *
54244444 AAGATATCCACAAAGG
1 GAGATAGCCACAAAGG
54244460 TTCACTTTTA
Statistics
Matches: 108, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
56 12 0.11
57 27 0.25
58 24 0.22
59 22 0.20
60 23 0.21
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (59 bp):
GAGATAGCCACAAAGGCATCTTTTTAATAGAGATAGCCATAAAGGCATCCTTTTTAACA
Found at i:54244440 original size:29 final size:29
Alignment explanation
Indices: 54244265--54244467 Score: 107
Period size: 30 Copynumber: 7.0 Consensus size: 29
54244255 GGCATTCATG
* *
54244265 TAATTGAGA-TAGCCACAAAGG-TATCTTTT
1 TAATAGAGATTAGCCACAAAGGCT-TC-CTT
* * * *
54244294 TAATAGAGA-TAGTCATAAATGCATCCTTTT
1 TAATAGAGATTAGCCACAAAGGCTTCC--TT
* * *
54244324 TAACAGAGA-TAGCCACAAGGGCATCCTTTT
1 TAATAGAGATTAGCCACAAAGGCTTCC--TT
* * *
54244354 TAATAGAGA-TAGCCATAAGGGATTCCTT
1 TAATAGAGATTAGCCACAAAGGCTTCCTT
* * * *
54244382 TAAGAGAGATCA-CCACAAAAGCTTCATT
1 TAATAGAGATTAGCCACAAAGGCTTCCTT
*
54244410 TAATAGAGATTAGACACAAAGGCTTCCTT
1 TAATAGAGATTAGCCACAAAGGCTTCCTT
* * *
54244439 TAACAAAGA-TATCCACAAAGG-TTCACTT
1 TAATAGAGATTAGCCACAAAGGCTTC-CTT
54244467 T
1 T
54244468 TACAAAAATT
Statistics
Matches: 137, Mismatches: 31, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
27 3 0.02
28 45 0.33
29 40 0.29
30 49 0.36
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (29 bp):
TAATAGAGATTAGCCACAAAGGCTTCCTT
Found at i:54252208 original size:27 final size:27
Alignment explanation
Indices: 54252178--54252235 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
54252168 TAAAAACAGG
* **
54252178 AATGATCCTAGTTTCAATGAAAATCCA
1 AATGATCCTAGTCTCAACCAAAATCCA
* **
54252205 AATGGTTGTAGTCTCAACCAAAATCCA
1 AATGATCCTAGTCTCAACCAAAATCCA
54252232 AATG
1 AATG
54252236 GCCAAGATGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (27 bp):
AATGATCCTAGTCTCAACCAAAATCCA
Found at i:54271338 original size:40 final size:39
Alignment explanation
Indices: 54271301--54271392 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
54271291 GCTACTCGTT
*
54271301 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
54271341 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
54271380 CAAATGCCTTCGG
1 CAAATGCCTTCGG
54271393 ATCTTAGTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:54271372 original size:39 final size:40
Alignment explanation
Indices: 54271282--54271445 Score: 167
Period size: 40 Copynumber: 4.1 Consensus size: 40
54271272 CGGAATTTAA
** *
54271282 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
54271322 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54271361 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
54271401 CTGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54271441 CCGGA
1 CCGGA
54271446 CATCATTCGA
Statistics
Matches: 103, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.31
40 56 0.54
41 12 0.12
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54272691 original size:56 final size:56
Alignment explanation
Indices: 54272624--54272743 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
54272614 TATTAGTTTA
54272624 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
54272680 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
54272736 TTGCCCAT
1 TTGCCCAT
54272744 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:54279948 original size:27 final size:27
Alignment explanation
Indices: 54279884--54279945 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
54279874 ATTATACTTT
*
54279884 TTATTATTAATATTTTATTAAAAATAC
1 TTATTATTAATATTTTAATAAAAATAC
54279911 TT-TCTATTAATATTTTAATAATAAATA-
1 TTAT-TATTAATATTTTAATAA-AAATAC
54279938 TATATTAT
1 T-TATTAT
54279946 AATTTATAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 1 0.03
27 19 0.63
28 9 0.30
29 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATTATTAATATTTTAATAAAAATAC
Found at i:54292132 original size:26 final size:27
Alignment explanation
Indices: 54292096--54292148 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
54292086 TAAACTAAAC
*
54292096 TTTTCAAAAGTACTTCTCAAAATCAAT
1 TTTTCAAAAGTACTTCTCAAAAGCAAT
*
54292123 TTTTC-AAAGTCCTTCTCAAAAGCAAT
1 TTTTCAAAAGTACTTCTCAAAAGCAAT
54292149 ACTAAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (27 bp):
TTTTCAAAAGTACTTCTCAAAAGCAAT
Found at i:54292980 original size:10 final size:10
Alignment explanation
Indices: 54292965--54293016 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
54292955 AAGAGAATGA
54292965 AAAAAAAAAG
1 AAAAAAAAAG
54292975 AAAAAAAAAGG
1 AAAAAAAAA-G
**
54292986 AAAGCTAAAAG
1 AAA-AAAAAAG
* *
54292997 AATATAAAAG
1 AAAAAAAAAG
54293007 AAAAAAAAAG
1 AAAAAAAAAG
54293017 TAAATTGCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 23 0.68
11 7 0.21
12 4 0.12
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:54295058 original size:20 final size:20
Alignment explanation
Indices: 54295020--54295058 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54295010 TAAATTGTGT
54295020 ATATTTATATGTTTGAATTGA
1 ATATTTATATG-TTGAATTGA
54295041 ATATTGTATATG-TGAATT
1 ATATT-TATATGTTGAATT
54295059 ATGTATATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (20 bp):
ATATTTATATGTTGAATTGA
Found at i:54295066 original size:22 final size:21
Alignment explanation
Indices: 54295012--54295066 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 21
54295002 CGTGTAACTA
54295012 AATTGTGTATATTTATATGTTTG
1 AATT-TGTATATTTATATG-TTG
*
54295035 AA-TTGAATATTGTATATG-TG
1 AATTTGTATATT-TATATGTTG
54295055 AATTATGTATAT
1 AATT-TGTATAT
54295067 GCCATGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
20 4 0.15
21 8 0.30
22 13 0.48
23 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AATTTGTATATTTATATGTTG
Found at i:54295235 original size:24 final size:23
Alignment explanation
Indices: 54295207--54295290 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 23
54295197 ACAGCTTGAA
*
54295207 AGAGCGTCCCGTTATTAGCTCTC
1 AGAGCTTCCCGTTATTAGCTCTC
*
54295230 ATGAGCTTCCCGTTATATAGTTCTTGC
1 A-GAGCTTCCCGTTAT-TAGCTC-T-C
*
54295257 -GAGCTTCCCGTTAATAGCTCTTC
1 AGAGCTTCCCGTTATTAGCTC-TC
*
54295280 AGAGCATCCCG
1 AGAGCTTCCCG
54295291 ATTGGTTGTG
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
23 2 0.04
24 29 0.57
25 18 0.35
26 1 0.02
27 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (23 bp):
AGAGCTTCCCGTTATTAGCTCTC
Found at i:54295381 original size:25 final size:25
Alignment explanation
Indices: 54295365--54295436 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
54295355 CTCTTCGAAA
54295365 CTTCCCGATTAAAGGCTCTTTCATGAG
1 CTTCCCGATTAAAGGCTC-TTCA-GAG
* *
54295392 CTTCTCGATTAATGGCTC-TCTAGAG
1 CTTCCCGATTAAAGGCTCTTC-AGAG
*
54295417 CTTCCCAATTAAAGGCTCTT
1 CTTCCCGATTAAAGGCTCTT
54295437 TTATGAGCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
25 20 0.53
26 2 0.05
27 16 0.42
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (25 bp):
CTTCCCGATTAAAGGCTCTTCAGAG
Found at i:54295400 original size:27 final size:26
Alignment explanation
Indices: 54295365--54295473 Score: 105
Period size: 27 Copynumber: 4.2 Consensus size: 26
54295355 CTCTTCGAAA
*
54295365 CTTCCCGATTAAAGGCTCTTTCATGAG
1 CTTCCCAATTAAAGGCTCTTT-ATGAG
* * * *
54295392 CTTCTCGATTAATGGCTCTCTA-GAG
1 CTTCCCAATTAAAGGCTCTTTATGAG
54295417 CTTCCCAATTAAAGGCTCTTTTATGAG
1 CTTCCCAATTAAAGGCTC-TTTATGAG
** * *
54295444 CTTCTTAATTAATGGCTCTCTA-GAG
1 CTTCCCAATTAAAGGCTCTTTATGAG
54295469 CTTCC
1 CTTCC
54295474 TGATATGGCT
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
25 25 0.37
26 7 0.10
27 36 0.53
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (26 bp):
CTTCCCAATTAAAGGCTCTTTATGAG
Found at i:54295407 original size:52 final size:53
Alignment explanation
Indices: 54295351--54295462 Score: 156
Period size: 52 Copynumber: 2.2 Consensus size: 53
54295341 ATCTAGATAT
* *
54295351 ATGGCTCTTCGA-AACTTCCCGATTAAAGGCTCTTTCATGAGCTTCTCGATTA
1 ATGGCTCTTCGAGAACTTCCCAATTAAAGGCTCTTTCATGAGCTTCTCAATTA
* * * *
54295403 ATGGCTC-TCTAGAGCTTCCCAATTAAAGGCTCTTTTATGAGCTTCTTAATTA
1 ATGGCTCTTCGAGAACTTCCCAATTAAAGGCTCTTTCATGAGCTTCTCAATTA
54295455 ATGGCTCT
1 ATGGCTCT
54295463 CTAGAGCTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
51 3 0.06
52 49 0.94
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (53 bp):
ATGGCTCTTCGAGAACTTCCCAATTAAAGGCTCTTTCATGAGCTTCTCAATTA
Found at i:54295463 original size:52 final size:52
Alignment explanation
Indices: 54295365--54295473 Score: 182
Period size: 52 Copynumber: 2.1 Consensus size: 52
54295355 CTCTTCGAAA
* *
54295365 CTTCCCGATTAAAGGCTCTTTCATGAGCTTCTCGATTAATGGCTCTCTAGAG
1 CTTCCCAATTAAAGGCTCTTTCATGAGCTTCTCAATTAATGGCTCTCTAGAG
* *
54295417 CTTCCCAATTAAAGGCTCTTTTATGAGCTTCTTAATTAATGGCTCTCTAGAG
1 CTTCCCAATTAAAGGCTCTTTCATGAGCTTCTCAATTAATGGCTCTCTAGAG
54295469 CTTCC
1 CTTCC
54295474 TGATATGGCT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (52 bp):
CTTCCCAATTAAAGGCTCTTTCATGAGCTTCTCAATTAATGGCTCTCTAGAG
Found at i:54295530 original size:25 final size:25
Alignment explanation
Indices: 54295501--54295575 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
54295491 CTTCCTAATT
54295501 ATGGCTCTA-ATGAGCTTCCCGTTAC
1 ATGGCTC-ACATGAGCTTCCCGTTAC
* * *
54295526 ATGGCTCACATGAGTTTCCCATTAT
1 ATGGCTCACATGAGCTTCCCGTTAC
* *
54295551 ATGGCTCGAGAGAGAGCTTCCCGTT
1 ATGGCTC-ACA-TGAGCTTCCCGTT
54295576 TATGTGCTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.03
25 27 0.68
26 2 0.05
27 10 0.25
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (25 bp):
ATGGCTCACATGAGCTTCCCGTTAC
Found at i:54297272 original size:21 final size:21
Alignment explanation
Indices: 54297243--54297282 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54297233 TTATGGCAAA
54297243 AAATATATTTTTTTTATAAAT
1 AAATATATTTTTTTTATAAAT
*
54297264 AAATGTATTTTTTTTATAA
1 AAATATATTTTTTTTATAA
54297283 TATATAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
AAATATATTTTTTTTATAAAT
Found at i:54310415 original size:34 final size:34
Alignment explanation
Indices: 54310347--54310428 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
54310337 TTATTGTATC
* * * *
54310347 TATT-AAAAAATAAATAAGTTCATTTTATTTTAT
1 TATTAAAAAAATAAATAAATTAATTTTAGTATAT
54310380 TATTAAAAAAATAAATAAATTAATCTTT-GTATAT
1 TATTAAAAAAATAAATAAATTAAT-TTTAGTATAT
*
54310414 TAGATAAAAAAATAA
1 TA-TTAAAAAAATAA
54310429 GTTGGTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 4 0.10
34 23 0.56
35 14 0.34
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (34 bp):
TATTAAAAAAATAAATAAATTAATTTTAGTATAT
Found at i:54311084 original size:18 final size:18
Alignment explanation
Indices: 54311061--54311120 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
54311051 TTAATATATT
54311061 ATTTTATACTTAAATTTA
1 ATTTTATACTTAAATTTA
* *
54311079 ATTTTA-ATGTTCAATTTA
1 ATTTTATA-CTTAAATTTA
* *
54311097 GTATTTGATACCTAAATTTA
1 --ATTTTATACTTAAATTTA
54311117 ATTT
1 ATTT
54311121 CAATATTCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 1 0.03
18 18 0.56
20 12 0.38
21 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (18 bp):
ATTTTATACTTAAATTTA
Found at i:54311102 original size:38 final size:38
Alignment explanation
Indices: 54311060--54311138 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
54311050 ATTAATATAT
* * * *
54311060 TATTTTATACTTAAATTTAATTTTAATGTTCAATTTAG
1 TATTTGATACCTAAATTTAATTTCAATATTCAATTTAG
*
54311098 TATTTGATACCTAAATTTAATTTCAATATTCAATTTTG
1 TATTTGATACCTAAATTTAATTTCAATATTCAATTTAG
54311136 TAT
1 TAT
54311139 CAAAACCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (38 bp):
TATTTGATACCTAAATTTAATTTCAATATTCAATTTAG
Found at i:54321202 original size:41 final size:41
Alignment explanation
Indices: 54321157--54321342 Score: 221
Period size: 41 Copynumber: 4.5 Consensus size: 41
54321147 GGCTCGATGC
* * * *
54321157 CTAGCAGGGTTAATGCCGGTGAATTATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAGT
* * * * *
54321198 CTAGCAAGCTTAATGCCGGTGAATTATTTCAGACTTCATGT
1 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAGT
* * *
54321239 CTAGCAGGCTTAAGGCTGGTGAAATAATTCGGACTTTAAGT
1 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAGT
* *
54321280 CTAGCAGGCTTAAGGCCGGTGAAATAATTCGGACTTTAAGT
1 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAGT
*
54321321 CTGGCAGGC-TAAGTGCCGGTGA
1 CTAGCAGGCTTAA-TGCCGGTGA
54321343 TCTGAATCAG
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 3 0.02
41 127 0.98
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAGT
Found at i:54321369 original size:41 final size:41
Alignment explanation
Indices: 54321324--54321424 Score: 166
Period size: 41 Copynumber: 2.5 Consensus size: 41
54321314 TTTAAGTCTG
*
54321324 GCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCTA
1 GCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAACCTA
* *
54321365 GCAGGCTAAGTGCTGGTGATCTGAATCAGGCTATAAGCCTA
1 GCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAACCTA
*
54321406 GCAGACTAAGTGCCGGTGA
1 GCAGGCTAAGTGCCGGTGA
54321425 ATATGTTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (41 bp):
GCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAACCTA
Found at i:54322789 original size:16 final size:17
Alignment explanation
Indices: 54322768--54322801 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54322758 ACAAAATTAT
*
54322768 TAGTAA-AAGGTTAATA
1 TAGTAATAAGGTAAATA
54322784 TAGTAATAAGGTAAATA
1 TAGTAATAAGGTAAATA
54322801 T
1 T
54322802 TAACTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (17 bp):
TAGTAATAAGGTAAATA
Found at i:54323728 original size:42 final size:42
Alignment explanation
Indices: 54323672--54323771 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
54323662 CTATATGAAC
*
54323672 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
* *
54323714 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGTATAACG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
54323756 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
54323772 TACCGAGAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.27
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
Found at i:54328041 original size:215 final size:217
Alignment explanation
Indices: 54327670--54328108 Score: 765
Period size: 215 Copynumber: 2.0 Consensus size: 217
54327660 AAATAAATCA
* *
54327670 TACATTCTCGCTGTCAAATACAACATATGTCAATGAACAAACTTCCTTTAGATCAATATCATTAA
1 TACATTCTCCCTGTCAAATACAACATAAGTCAATGAACAAACTTCCTTTAGATCAATATCATTAA
* *
54327735 TAATCAATATATCTTTTAATTCATTCACATAGATCTTTTACCAATTCTTACTGAATTGAGGAACG
66 TAATCAATATATCTTTCAATTCATTCACATAGATCTTTTACCAATTCTTACTGAATCGAGGAACG
*
54327800 ACTTACGGGTATGAGTACATCG-TTTTTTTTGGGCCATAGTCCAACTATGGTCTTACACA-GCAT
131 ACTTACGGGTATGAGTACATCGTTTTTTTTTGGGCCATAATCCAACTATGGTCTTACACATGCAT
*
54327863 TGCCATGACCCAGCCATGGTCT
196 TGCCATGACCCAGCCAAGGTCT
*
54327885 TACATTCTCCCTGTCAAATACAACATAAGTCAATGAACAGACTTCCTTTAGATCAATATCATTAA
1 TACATTCTCCCTGTCAAATACAACATAAGTCAATGAACAAACTTCCTTTAGATCAATATCATTAA
*
54327950 TAATCAATATATCTTTCAATTCATTCACATAGGTCTTTTACCAATTCTTACTGAATCGAGGAACG
66 TAATCAATATATCTTTCAATTCATTCACATAGATCTTTTACCAATTCTTACTGAATCGAGGAACG
* *
54328015 ACTTACGGGTATGAGTACATCGTTTTTTTTTGTGCCATAATCCAACTATGGTTTTACACATGCAT
131 ACTTACGGGTATGAGTACATCGTTTTTTTTTGGGCCATAATCCAACTATGGTCTTACACATGCAT
*
54328080 TGCCATGGCCCAGCCAAGGTCT
196 TGCCATGACCCAGCCAAGGTCT
54328102 TACATTC
1 TACATTC
54328109 GTAGTGTCAT
Statistics
Matches: 211, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
215 146 0.69
216 34 0.16
217 31 0.15
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (217 bp):
TACATTCTCCCTGTCAAATACAACATAAGTCAATGAACAAACTTCCTTTAGATCAATATCATTAA
TAATCAATATATCTTTCAATTCATTCACATAGATCTTTTACCAATTCTTACTGAATCGAGGAACG
ACTTACGGGTATGAGTACATCGTTTTTTTTTGGGCCATAATCCAACTATGGTCTTACACATGCAT
TGCCATGACCCAGCCAAGGTCT
Found at i:54328164 original size:33 final size:34
Alignment explanation
Indices: 54328111--54328270 Score: 123
Period size: 33 Copynumber: 4.8 Consensus size: 34
54328101 TTACATTCGT
* * * *
54328111 AGTGTCATAACCCAGTTATGGTCTTATCATCAGA
1 AGTGCCATAGCCCAGCTATGGTCTTATCATCAAA
* *
54328145 A-TGCCATAGCCTAGCTATGGTCTTACTTAT-AAA
1 AGTGCCATAGCCCAGCTATGGTCTTA-TCATCAAA
* * * * *
54328178 TATTGCCATGGTCCAACCATGGTCTTA-CATTC-AA
1 -AGTGCCATAGCCCAGCTATGGTCTTATCA-TCAAA
* * * *
54328212 AGTGCCATAACCCAGTTATGGTCTTTTCATTAAA
1 AGTGCCATAGCCCAGCTATGGTCTTATCATCAAA
54328246 A-TGCCATAGCCCAGCTATGGTCTTA
1 AGTGCCATAGCCCAGCTATGGTCTTA
54328271 CATATAAACA
Statistics
Matches: 95, Mismatches: 24, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
33 63 0.66
34 13 0.14
35 19 0.20
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (34 bp):
AGTGCCATAGCCCAGCTATGGTCTTATCATCAAA
Found at i:54328206 original size:101 final size:101
Alignment explanation
Indices: 54328077--54328295 Score: 321
Period size: 101 Copynumber: 2.2 Consensus size: 101
54328067 TTTACACATG
* * ** *
54328077 CATTGCCATGGCCCAGCCAAGGTCTTACATTCGTAGTGTCATAACCCAGTTATGGTCTTATCATC
1 CATTGCCATGGTCCAACCAAGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATC
* * *
54328142 AGAATGCCATAGCCTAGCTATGGTCTTACTTATAAA
66 AAAATGCCATAGCCCAGCTATGGTCTTACATATAAA
* * * *
54328178 TATTGCCATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTTTCATT
1 CATTGCCATGGTCCAACCAAGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATC
54328243 AAAATGCCATAGCCCAGCTATGGTCTTACATATAAA
66 AAAATGCCATAGCCCAGCTATGGTCTTACATATAAA
*
54328279 CATTTCCATGGTCCAAC
1 CATTGCCATGGTCCAAC
54328296 GGTCTTATCC
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 104 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (101 bp):
CATTGCCATGGTCCAACCAAGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATC
AAAATGCCATAGCCCAGCTATGGTCTTACATATAAA
Found at i:54335694 original size:101 final size:101
Alignment explanation
Indices: 54335451--54335709 Score: 265
Period size: 101 Copynumber: 2.6 Consensus size: 101
54335441 GTTTTCTTTG
* * * *
54335451 TGTCATAGCCCAACTAAGATCTTACACAT--AC-CTTGCCATGAG-CCAGCCATGGTCTTACATT
1 TGTCATAGCCCAGCTATGATCTTACATATAAACAC-TGCCATG-GTCCAACCATGGTCTTACATT
** *
54335512 CGTAGTGCCATAACCCAGTTATGGTCGTATCATCAGAA
64 CAAAGTGCCATAACCCAGTTATGGTCGTATCATCAAAA
* * * ** * * * *
54335550 TGTCATAGCCTAGCTATGGTCTTACTTATGCATACTGCCATGGTCTAACCATGGTCTTACGTTTA
1 TGTCATAGCCCAGCTATGATCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACATTCA
* * * *
54335615 AAGTGCCATAACCCAGTTATGGTCTTTTTATTAAAA
66 AAGTGCCATAACCCAGTTATGGTCGTATCATCAAAA
* * *
54335651 TGTCATAGCCCAGCTATGATCTTACATATAAACATTGCGATGGTCCAACCATGGCCTTA
1 TGTCATAGCCCAGCTATGATCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTA
54335710 TCCGTCAATT
Statistics
Matches: 128, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
99 23 0.18
100 1 0.01
101 103 0.80
102 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (101 bp):
TGTCATAGCCCAGCTATGATCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACATTCA
AAGTGCCATAACCCAGTTATGGTCGTATCATCAAAA
Found at i:54344301 original size:28 final size:26
Alignment explanation
Indices: 54344260--54344360 Score: 71
Period size: 28 Copynumber: 3.7 Consensus size: 26
54344250 ATACGAAATT
* *
54344260 AAATATATAAAAATCAAAGAATAGTA
1 AAATAAATAAAAATCAAACAATAGTA
* *
54344286 AGCAATAAATAAAAAT-ATAATTCAA-AATT
1 A--AATAAATAAAAATCA-AA--CAATAGTA
*
54344315 AAATAAATAAAAATCAAATAATAGTAAA
1 AAATAAATAAAAATCAAACAATAGT--A
*
54344343 AAATAAATAAAAAACAAA
1 AAATAAATAAAAATCAAA
54344361 ATTCAAAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
25 2 0.03
26 3 0.05
27 16 0.28
28 32 0.55
29 3 0.05
30 2 0.03
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.22
Consensus pattern (26 bp):
AAATAAATAAAAATCAAACAATAGTA
Found at i:54344325 original size:55 final size:56
Alignment explanation
Indices: 54344255--54344382 Score: 186
Period size: 55 Copynumber: 2.3 Consensus size: 56
54344245 AAGTAATACG
* ** * *
54344255 AAATTAAATATATAAAAATCAAAGAATAGTAAGCAATAAAT-AAAAATATAATTCA
1 AAATTAAATAAATAAAAATCAAAGAATAGTAAAAAATAAATAAAAAACAAAATTCA
*
54344310 AAATTAAATAAATAAAAATCAAATAATAGTAAAAAATAAATAAAAAACAAAATTCA
1 AAATTAAATAAATAAAAATCAAAGAATAGTAAAAAATAAATAAAAAACAAAATTCA
54344366 AAATTAAATAAAATAAA
1 AAATTAAAT-AAATAAA
54344383 CCCAATTGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
55 37 0.57
56 21 0.32
57 7 0.11
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (56 bp):
AAATTAAATAAATAAAAATCAAAGAATAGTAAAAAATAAATAAAAAACAAAATTCA
Found at i:54344348 original size:13 final size:11
Alignment explanation
Indices: 54344289--54344356 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
54344279 AATAGTAAGC
54344289 AATAAATAAAA
1 AATAAATAAAA
* *
54344300 ATATAATTCAAA
1 A-ATAAATAAAA
* *
54344312 ATTAAATAAAT
1 AATAAATAAAA
*
54344323 AA-AAATCAAAT
1 AATAAAT-AAAA
*
54344334 AAT-AGTAAAA
1 AATAAATAAAA
54344344 AATAAATAAAA
1 AATAAATAAAA
54344355 AA
1 AA
54344357 CAAAATTCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
10 10 0.23
11 24 0.56
12 9 0.21
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:54344374 original size:28 final size:28
Alignment explanation
Indices: 54344289--54344382 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
54344279 AATAGTAAGC
* *
54344289 AATAAAT-AAAAATATAATTCAAAATTA
1 AATAAATAAAAAACAAAATTCAAAATTA
* *
54344316 AATAAATAAAAATCAAATAAT-AGTAAA--A
1 AATAAATAAAAAACAAA-ATTCA--AAATTA
54344344 AATAAATAAAAAACAAAATTCAAAATTA
1 AATAAATAAAAAACAAAATTCAAAATTA
54344372 AATAAAATAAA
1 AAT-AAATAAA
54344383 CCCAATTGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
26 3 0.06
27 9 0.17
28 29 0.55
29 9 0.17
30 3 0.06
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.23
Consensus pattern (28 bp):
AATAAATAAAAAACAAAATTCAAAATTA
Found at i:54345523 original size:12 final size:13
Alignment explanation
Indices: 54345506--54345537 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54345496 CTAGGGACAC
54345506 GCCCGTGT-CTCA
1 GCCCGTGTCCTCA
54345518 GCCCGTGTCCTCA
1 GCCCGTGTCCTCA
54345531 -CCCGTGT
1 GCCCGTGT
54345538 AACTCTCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.06, C:0.44, G:0.25, T:0.25
Consensus pattern (13 bp):
GCCCGTGTCCTCA
Found at i:54352873 original size:27 final size:27
Alignment explanation
Indices: 54352826--54352882 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
54352816 ATTTTAAACA
54352826 TTTTTCATAATATTTACAATTTTTTAT
1 TTTTTCATAATATTTACAATTTTTTAT
* *
54352853 TTTTTCTTAAT-TTATATAATTTTTTAT
1 TTTTTCATAATATT-TACAATTTTTTAT
54352880 TTT
1 TTT
54352883 GCTAGTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTTCATAATATTTACAATTTTTTAT
Found at i:54352939 original size:12 final size:12
Alignment explanation
Indices: 54352898--54352930 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
54352888 TTTCTTTTAT
54352898 AATTTTTTTGCA
1 AATTTTTTTGCA
54352910 AATTTTTTTGCA
1 AATTTTTTTGCA
54352922 AATTTTTTT
1 AATTTTTTT
54352931 TATAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (12 bp):
AATTTTTTTGCA
Found at i:54380165 original size:44 final size:44
Alignment explanation
Indices: 54380116--54380370 Score: 351
Period size: 44 Copynumber: 5.9 Consensus size: 44
54380106 ATAAATCGAG
* * *
54380116 AGGATAGATACATGGCAAAAACGGGAGCAAGATAACTTTTAATC
1 AGGATAGATACAAGGCAAAAACTGGAGCAAGATAGCTTTTAATC
* *
54380160 AGGATAGACACAAGGCAAAAACTGGAGCAAGATGGCTTTTAATC
1 AGGATAGATACAAGGCAAAAACTGGAGCAAGATAGCTTTTAATC
*
54380204 AGGATAGACACAAGGC--AAACTGGAGCAAGATAGCTTTTAATC
1 AGGATAGATACAAGGCAAAAACTGGAGCAAGATAGCTTTTAATC
* *
54380246 GGGATAGATACATA-GCAAAAACTGGAGCAAGATTGCTTTTAATC
1 AGGATAGATACA-AGGCAAAAACTGGAGCAAGATAGCTTTTAATC
* *
54380290 AGGATAGATACAAGGC--AAAGTAGAGCAAGATAGCTTTTAATC
1 AGGATAGATACAAGGCAAAAACTGGAGCAAGATAGCTTTTAATC
*
54380332 AGGATAGATACATA-GCAAAAACTGGAGCAAGATTGCTTT
1 AGGATAGATACA-AGGCAAAAACTGGAGCAAGATAGCTTT
54380371 AAACCAAAGA
Statistics
Matches: 188, Mismatches: 16, Indels: 14
0.86 0.07 0.06
Matches are distributed among these distances:
42 74 0.39
43 3 0.02
44 111 0.59
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (44 bp):
AGGATAGATACAAGGCAAAAACTGGAGCAAGATAGCTTTTAATC
Found at i:54380241 original size:86 final size:86
Alignment explanation
Indices: 54380116--54380370 Score: 395
Period size: 86 Copynumber: 2.9 Consensus size: 86
54380106 ATAAATCGAG
* * * *
54380116 AGGATAGATACATGGCAAAAACGGGAGCAAGATAACTTTTAATCAGGATAGACACA-AGGCAAAA
1 AGGATAGATACAAGGC--AAACTGGAGCAAGATAGCTTTTAATCAGGATAGATACATA-GCAAAA
*
54380180 ACTGGAGCAAGATGGCTTTTAATC
63 ACTGGAGCAAGATTGCTTTTAATC
* *
54380204 AGGATAGACACAAGGCAAACTGGAGCAAGATAGCTTTTAATCGGGATAGATACATAGCAAAAACT
1 AGGATAGATACAAGGCAAACTGGAGCAAGATAGCTTTTAATCAGGATAGATACATAGCAAAAACT
54380269 GGAGCAAGATTGCTTTTAATC
66 GGAGCAAGATTGCTTTTAATC
* *
54380290 AGGATAGATACAAGGCAAAGTAGAGCAAGATAGCTTTTAATCAGGATAGATACATAGCAAAAACT
1 AGGATAGATACAAGGCAAACTGGAGCAAGATAGCTTTTAATCAGGATAGATACATAGCAAAAACT
54380355 GGAGCAAGATTGCTTT
66 GGAGCAAGATTGCTTT
54380371 AAACCAAAGA
Statistics
Matches: 155, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
86 140 0.90
87 1 0.01
88 14 0.09
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (86 bp):
AGGATAGATACAAGGCAAACTGGAGCAAGATAGCTTTTAATCAGGATAGATACATAGCAAAAACT
GGAGCAAGATTGCTTTTAATC
Found at i:54380354 original size:130 final size:129
Alignment explanation
Indices: 54380117--54380370 Score: 368
Period size: 130 Copynumber: 2.0 Consensus size: 129
54380107 TAAATCGAGA
*
54380117 GGATAGATACATGGCAAAAACGGGAGCAAGATAACTTTTAATCAGGATAGACACAAGGCAAAAAC
1 GGATAGATACATAGCAAAAACGGGAGCAAGATAACTTTTAATCAGGATAGACACAAGGC-AAAAC
* *
54380182 TGGAGCAAGATGGCTTTTAATCAGGATAGACACAAGGCAAACTGGAGCAAGATAGCTTTTAATCG
65 TAGAGCAAGATAGCTTTTAATCAGGATAGACACAAGGCAAACTGGAGCAAGATAGCTTTTAATCG
* ** * *
54380247 GGATAGATACATAGCAAAAACTGGAGCAAGATTGCTTTTAATCAGGATAGATACAAGGC-AAAGT
1 GGATAGATACATAGCAAAAACGGGAGCAAGATAACTTTTAATCAGGATAGACACAAGGCAAAACT
* *
54380311 AGAGCAAGATAGCTTTTAATCAGGATAGATACATA-GCAAAAACTGGAGCAAGATTGCTTT
66 AGAGCAAGATAGCTTTTAATCAGGATAGACACA-AGGC--AAACTGGAGCAAGATAGCTTT
54380371 AAACCAAAGA
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
128 36 0.32
129 1 0.01
130 74 0.67
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (129 bp):
GGATAGATACATAGCAAAAACGGGAGCAAGATAACTTTTAATCAGGATAGACACAAGGCAAAACT
AGAGCAAGATAGCTTTTAATCAGGATAGACACAAGGCAAACTGGAGCAAGATAGCTTTTAATCG
Found at i:54380438 original size:18 final size:18
Alignment explanation
Indices: 54380415--54380461 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
54380405 ATTTAAATTG
*
54380415 CGGTCGCGGTCGCATTTT
1 CGGTCGCGGTCGCAGTTT
54380433 CGGTCGC-GTCGC-GTTT
1 CGGTCGCGGTCGCAGTTT
54380449 --GTCGCGGTCGCAG
1 CGGTCGCGGTCGCAG
54380462 ACATAACGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
16 4 0.15
17 5 0.19
18 7 0.27
ACGTcount: A:0.04, C:0.30, G:0.38, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCAGTTT
Found at i:54382032 original size:22 final size:22
Alignment explanation
Indices: 54381999--54382054 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
54381989 ATTTCCTCTC
54381999 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
54382022 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
54382044 AATTCTCTCAA
1 AATTCTCTCAA
54382055 ATCTATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:54382083 original size:51 final size:51
Alignment explanation
Indices: 54382026--54382141 Score: 205
Period size: 51 Copynumber: 2.3 Consensus size: 51
54382016 TTCCAAAATT
* *
54382026 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCTATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
54382077 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
*
54382128 TTCTCAATTTCCTT
1 CTCTCAATTTCCTT
54382142 TTTTAAAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:54382831 original size:53 final size:53
Alignment explanation
Indices: 54382767--54382872 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
54382757 CACGGTTTCG
*
54382767 GTTTCTATTTCTACGTCCTCGAGTGAACCACTCATATACATTCCCACTCATAA
1 GTTTCCATTTCTACGTCCTCGAGTGAACCACTCATATACATTCCCACTCATAA
54382820 GTTTCCATTTCTACGTCCTCGAGTGAACCACTCATATACATTCCCACTCATAA
1 GTTTCCATTTCTACGTCCTCGAGTGAACCACTCATATACATTCCCACTCATAA
54382873 CGAGGTAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.33
Consensus pattern (53 bp):
GTTTCCATTTCTACGTCCTCGAGTGAACCACTCATATACATTCCCACTCATAA
Found at i:54383773 original size:18 final size:18
Alignment explanation
Indices: 54383747--54383781 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54383737 AGGTGTGTTT
*
54383747 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
54383765 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
54383782 TCCTTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:54387570 original size:125 final size:124
Alignment explanation
Indices: 54387207--54387573 Score: 502
Period size: 125 Copynumber: 2.9 Consensus size: 124
54387197 CGCAAACATG
* *
54387207 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGGTTTCACAAATTCTTCTCAAATAGCATCCTGT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
54387272 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
66 TAGAAGAGATTTTATATTATTTTCTCAGAAAAGTCAAAAAAAATTATTTCTTACATGAC
* * * * *
54387331 CTACTGTAGCAAAAGCACG-CTGACGAGGCCGCAATTTCACAAATTCTTCTCAAATAGCATCCTA
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* * * * * *
54387395 CTAGAAGAGATTTTATACTATTTTCTCAGAAATGACAAAAAAAAAATATTTCTTTCGTGAC
65 CTAGAAGAGATTTTATATTATTTTCTCAGAAAAGTC-AAAAAAAATTATTTCTTACATGAC
* *
54387456 CTACTGTATCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * **
54387521 TAGAAGTGATTTTATATTATTTTATCAGAAAAGTCAACTCAAAATTATTTCTT
66 TAGAAGAGATTTTATATTATTTTCTCAGAAAAGTCAA-AAAAAATTATTTCTT
54387574 CCAGGACTTA
Statistics
Matches: 209, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
123 1 0.00
124 88 0.42
125 119 0.57
126 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGAGATTTTATATTATTTTCTCAGAAAAGTCAAAAAAAATTATTTCTTACATGAC
Found at i:54390005 original size:42 final size:42
Alignment explanation
Indices: 54389933--54390133 Score: 199
Period size: 42 Copynumber: 4.5 Consensus size: 42
54389923 ATAAAAAGTT
54389933 TTGA-GGTCCTTTCTTGAAGAGTTTTGTGGTTTTAAGGGAAA
1 TTGATGGTCCTTTCTTGAAGAGTTTTGTGGTTTTAAGGGAAA
* * * * *
54389974 TTGATTGTCCTTTCTTGAAGGGATTTCTGGTTTTAAGGGAAT
1 TTGATGGTCCTTTCTTGAAGAGTTTTGTGGTTTTAAGGGAAA
54390016 TTGATAAAAAGTTTTGAGATCCTTTCTTGAAGAGTTTTGTGGTTTTAAGGGAAA
1 TTG------A----TG-G-TCCTTTCTTGAAGAGTTTTGTGGTTTTAAGGGAAA
*
54390070 TTTATGGTCCTTTCTTGAAGAGCTTTT-TGGTTTTAAGGGAAA
1 TTGATGGTCCTTTCTTGAAGAG-TTTTGTGGTTTTAAGGGAAA
* *
54390112 TAGATGGTGCTTTCTTGAAGAG
1 TTGATGGTCCTTTCTTGAAGAG
54390134 CTCTTCTGTT
Statistics
Matches: 132, Mismatches: 14, Indels: 27
0.76 0.08 0.16
Matches are distributed among these distances:
41 4 0.03
42 84 0.64
43 5 0.04
44 2 0.02
48 2 0.02
52 1 0.01
53 1 0.01
54 33 0.25
ACGTcount: A:0.23, C:0.08, G:0.26, T:0.42
Consensus pattern (42 bp):
TTGATGGTCCTTTCTTGAAGAGTTTTGTGGTTTTAAGGGAAA
Found at i:54390040 original size:96 final size:96
Alignment explanation
Indices: 54389810--54390112 Score: 438
Period size: 96 Copynumber: 3.2 Consensus size: 96
54389800 TCAAGAAGGG
* *
54389810 TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCATTTCTTGAAGAGTGTTT-TAGTTT
1 TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGT-TTTGTGGTTT
* *
54389874 TAATGGAAATTGATGGTAC--TC---AAGAGC
65 TAAGGGAAATTGATGGTCCTTTCTTGAAGAGC
* *
54389901 TTTTTGGTTTCAAGGAAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGTTTTGTGGTTTT
1 TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGTTTTGTGGTTTT
* * *
54389966 AAGGGAAATTGATTGTCCTTTCTTGAAGGGA
66 AAGGGAAATTGATGGTCCTTTCTTGAAGAGC
* * *
54389997 TTTCTGGTTTTAAGGGAATTTGATAAAAAGTTTTGAGATCCTTTCTTGAAGAGTTTTGTGGTTTT
1 TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGTTTTGTGGTTTT
*
54390062 AAGGGAAATTTATGGTCCTTTCTTGAAGAGC
66 AAGGGAAATTGATGGTCCTTTCTTGAAGAGC
54390093 TTTTTGGTTTTAAGGGAAAT
1 TTTTTGGTTTTAAGGGAAAT
54390113 AGATGGTGCT
Statistics
Matches: 186, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
90 3 0.02
91 72 0.39
93 2 0.01
96 109 0.59
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (96 bp):
TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGTTTTGTGGTTTT
AAGGGAAATTGATGGTCCTTTCTTGAAGAGC
Found at i:54390145 original size:42 final size:42
Alignment explanation
Indices: 54390035--54390145 Score: 152
Period size: 42 Copynumber: 2.6 Consensus size: 42
54390025 AGTTTTGAGA
* * **
54390035 TCCTTTCTTGAAGAGTTTTGTGGTTTTAAGGGAAATTTATGG
1 TCCTTTCTTGAAGAGCTTTCTGGTTTTAAGGGAAATAGATGG
*
54390077 TCCTTTCTTGAAGAGCTTTTTGGTTTTAAGGGAAATAGATGG
1 TCCTTTCTTGAAGAGCTTTCTGGTTTTAAGGGAAATAGATGG
*
54390119 TGCTTTCTTGAAGAGCTCTTCT-GTTTT
1 TCCTTTCTTGAAGAGCT-TTCTGGTTTT
54390146 CTCATACTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 59 0.95
43 3 0.05
ACGTcount: A:0.20, C:0.11, G:0.24, T:0.45
Consensus pattern (42 bp):
TCCTTTCTTGAAGAGCTTTCTGGTTTTAAGGGAAATAGATGG
Found at i:54392113 original size:24 final size:24
Alignment explanation
Indices: 54392085--54392179 Score: 138
Period size: 24 Copynumber: 4.0 Consensus size: 24
54392075 TCTTTCTAGA
* *
54392085 ATATTTAGTATTTATTAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
54392109 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
*
54392133 ATATTTAACATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
*
54392157 ATATTT-GACATTTATTAGTATAA
1 ATATTTAG-CATTTATTAGCATAA
54392180 AAATCTTTGT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.48
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:54393806 original size:25 final size:25
Alignment explanation
Indices: 54393765--54393821 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
54393755 ACAATCCATG
** * *
54393765 TAAATCATGTATTTCATGTAACTTT
1 TAAATCATGTAAATCATATAACATT
54393790 TAAATCATGTAAATCATATAACATT
1 TAAATCATGTAAATCATATAACATT
*
54393815 TATATCA
1 TAAATCA
54393822 ATTTTTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (25 bp):
TAAATCATGTAAATCATATAACATT
Found at i:54394090 original size:23 final size:23
Alignment explanation
Indices: 54394068--54394159 Score: 121
Period size: 23 Copynumber: 3.9 Consensus size: 23
54394058 AAGCCATGAT
*
54394068 CGGTAAGCTCATTTCGAGCTGATAAA
1 CGGTAAGCTC-TATCGAGCTG--AAA
54394094 CGGTAAGCTCTATCGAGCTGAAA
1 CGGTAAGCTCTATCGAGCTGAAA
*
54394117 CGGTAAGCTCTATAGAGCTGAAA
1 CGGTAAGCTCTATCGAGCTGAAA
* *
54394140 CGGTAAGCTCTTTCAAGCTG
1 CGGTAAGCTCTATCGAGCTG
54394160 TAGTGAGTCC
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
23 42 0.69
25 9 0.15
26 10 0.16
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (23 bp):
CGGTAAGCTCTATCGAGCTGAAA
Found at i:54401892 original size:36 final size:34
Alignment explanation
Indices: 54401843--54401930 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 34
54401833 ATTTATAAAA
54401843 TTTT-AAATTAATAATAATAAAATTATATTTT-ATT
1 TTTTAAAATT-ATAATAATAAAATT-TATTTTAATT
54401877 TCTTTAAAA-T-TAAT-A-AAAATTTATTTTAATT
1 T-TTTAAAATTATAATAATAAAATTTATTTTAATT
*
54401908 TTTTAAAATTTATAAAAATAAAA
1 TTTTAAAA-TTATAATAATAAAA
54401931 ACTATTAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
30 13 0.29
31 10 0.22
32 2 0.04
33 7 0.16
34 2 0.04
35 8 0.18
36 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (34 bp):
TTTTAAAATTATAATAATAAAATTTATTTTAATT
Found at i:54401925 original size:30 final size:31
Alignment explanation
Indices: 54401857--54401926 Score: 101
Period size: 30 Copynumber: 2.3 Consensus size: 31
54401847 AAATTAATAA
54401857 TAAT-AAAATTATATTTTATTTCTTTAAAAT
1 TAATAAAAATTATATTTTATTTCTTTAAAAT
54401887 TAATAAAAATT-TATTTTAATTT-TTTAAAAT
1 TAATAAAAATTATATTTT-ATTTCTTTAAAAT
*
54401917 TTATAAAAAT
1 TAATAAAAAT
54401927 AAAAACTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
30 27 0.73
31 10 0.27
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
TAATAAAAATTATATTTTATTTCTTTAAAAT
Found at i:54402242 original size:29 final size:27
Alignment explanation
Indices: 54402209--54402274 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 27
54402199 TAATATGTTA
*
54402209 TATTTTTATAATAAAATTATTGAACACT
1 TATTTTTATAATAAAATAATTGAACA-T
* *
54402237 TGATTTTATATGATAAAATAATTGAATAT
1 T-ATTTT-TATAATAAAATAATTGAACAT
54402266 TATTTTTAT
1 TATTTTTAT
54402275 GCTAATAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 3 0.09
28 6 0.18
29 7 0.21
30 17 0.52
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (27 bp):
TATTTTTATAATAAAATAATTGAACAT
Found at i:54405047 original size:19 final size:19
Alignment explanation
Indices: 54405004--54405047 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
54404994 GGGACTAAAT
*
54405004 TGAAAAGTTATAAAATTCA
1 TGAAAAATTATAAAATTCA
* *
54405023 TGGAAAAATTATAAATTTTA
1 T-GAAAAATTATAAAATTCA
54405043 TGAAA
1 TGAAA
54405048 TACATGGGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.34
Consensus pattern (19 bp):
TGAAAAATTATAAAATTCA
Found at i:54405625 original size:24 final size:24
Alignment explanation
Indices: 54405549--54405630 Score: 60
Period size: 24 Copynumber: 3.4 Consensus size: 24
54405539 CAGCTCGAAA
* * *
54405549 GAGCGTCCCGTTATTAGCCCTCTC-
1 GAGCTTCCCGTTAATAGCTCT-TCG
* * *
54405573 GAGCTTCTCGTTATATGGTTCTT-G
1 GAGCTTCCCGTTA-ATAGCTCTTCG
54405597 CGAGCTTCCCGTTAATAGCTCTTCG
1 -GAGCTTCCCGTTAATAGCTCTTCG
*
54405622 GAGCATCCC
1 GAGCTTCCC
54405631 AATTGGTTGT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
24 27 0.61
25 17 0.39
ACGTcount: A:0.15, C:0.30, G:0.22, T:0.33
Consensus pattern (24 bp):
GAGCTTCCCGTTAATAGCTCTTCG
Found at i:54407387 original size:21 final size:22
Alignment explanation
Indices: 54407343--54407390 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
54407333 TTTCTTTTCA
** *
54407343 TTTTTTAGATTAGGTTTTACCT
1 TTTTTTAGAGAAGATTTTACCT
54407365 TTTTTTAGAGAAGATTTTA-CT
1 TTTTTTAGAGAAGATTTTACCT
54407386 TTTTT
1 TTTTT
54407391 GTTTTATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.60
Consensus pattern (22 bp):
TTTTTTAGAGAAGATTTTACCT
Found at i:54420138 original size:125 final size:125
Alignment explanation
Indices: 54419916--54420169 Score: 436
Period size: 125 Copynumber: 2.0 Consensus size: 125
54419906 ATTTCCCATC
* * *
54419916 ATCTCACTAGAAGACATGTGGCCAGCGCCCAACTTGACATGTTTGCTTGGCAAGGAAAGTACTAT
1 ATCTCACAAGAAGACATGTGGCCAACGCCCAACTTAACATGTTTGCTTGGCAAGGAAAGTACTAT
*
54419981 AAATAAAAAGGTTTGCCCATTTGAATAATCATATCTCAAAACACAATACAATCACATAAG
66 AAATAAAAAGGTTTGCCCATTTGAACAATCATATCTCAAAACACAATACAATCACATAAG
*
54420041 ATCTCACAAGAAGACATGTGGCCAACGCCCAACTTAACATGTTTGCTTGGCGAGGAAAGTACTAT
1 ATCTCACAAGAAGACATGTGGCCAACGCCCAACTTAACATGTTTGCTTGGCAAGGAAAGTACTAT
* * *
54420106 AAATAGAAGGGTTTGCCCATTTGAACAATCATATCTCAAAACACAATACAATCCCATAAG
66 AAATAAAAAGGTTTGCCCATTTGAACAATCATATCTCAAAACACAATACAATCACATAAG
54420166 ATCT
1 ATCT
54420170 TATCCATTTA
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 121 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (125 bp):
ATCTCACAAGAAGACATGTGGCCAACGCCCAACTTAACATGTTTGCTTGGCAAGGAAAGTACTAT
AAATAAAAAGGTTTGCCCATTTGAACAATCATATCTCAAAACACAATACAATCACATAAG
Found at i:54423480 original size:16 final size:17
Alignment explanation
Indices: 54423459--54423490 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54423449 TTGGTTGAGA
54423459 AAATTA-TTTAATTAAG
1 AAATTATTTTAATTAAG
54423475 AAATTATTTTAATTAA
1 AAATTATTTTAATTAA
54423491 TTAATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AAATTATTTTAATTAAG
Found at i:54440397 original size:35 final size:35
Alignment explanation
Indices: 54440351--54440422 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
54440341 CTAGAGTTAA
54440351 ATAAACGATGTCTTTAGAAGTATTAAATGTCAACT
1 ATAAACGATGTCTTTAGAAGTATTAAATGTCAACT
*
54440386 ATAAATGATGTCTTTAGAAGTATTAAATGTCAACT
1 ATAAACGATGTCTTTAGAAGTATTAAATGTCAACT
54440421 AT
1 AT
54440423 CTTTTGTGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (35 bp):
ATAAACGATGTCTTTAGAAGTATTAAATGTCAACT
Found at i:54443910 original size:6 final size:6
Alignment explanation
Indices: 54443899--54443929 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
54443889 CGGGGGAGGA
54443899 GTGGGG GTGGGG GTGGGG GTGGGG GTGGGG G
1 GTGGGG GTGGGG GTGGGG GTGGGG GTGGGG G
54443930 AATTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.84, T:0.16
Consensus pattern (6 bp):
GTGGGG
Found at i:54444010 original size:24 final size:23
Alignment explanation
Indices: 54443983--54444053 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
54443973 ATATTAATAT
*
54443983 AAAATTTAAATTTATTATTATTTC
1 AAAATTT-TATTTATTATTATTTC
* *
54444007 AAAATATTTGTTT-TTATATATTTG
1 AAAAT-TTTATTTATTAT-TATTTC
*
54444031 AAAATTTTATATATTATTATTTC
1 AAAATTTTATTTATTATTATTTC
54444054 TTGTCAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
23 14 0.37
24 22 0.58
25 2 0.05
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (23 bp):
AAAATTTTATTTATTATTATTTC
Found at i:54444255 original size:50 final size:51
Alignment explanation
Indices: 54444192--54444288 Score: 126
Period size: 50 Copynumber: 1.9 Consensus size: 51
54444182 ATTTCTTTGA
* * * *
54444192 ATTTTCTAGAATTAGGA-TCAAATTGATATCATTTGTAAATTTTGAGGGTTC
1 ATTTTCTAAAATTAGGACT-AAATTGATATAATATGTAAAATTTGAGGGTTC
*
54444243 ATTTT-TAAAATTATGACTAAATTGATATAATATGTAAAATTTGAGG
1 ATTTTCTAAAATTAGGACTAAATTGATATAATATGTAAAATTTGAGG
54444289 ACTAAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
50 34 0.85
51 6 0.15
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.42
Consensus pattern (51 bp):
ATTTTCTAAAATTAGGACTAAATTGATATAATATGTAAAATTTGAGGGTTC
Found at i:54446078 original size:16 final size:17
Alignment explanation
Indices: 54446042--54446078 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
54446032 ATATTTATAT
*
54446042 TAAAAATCATTAATAGC
1 TAAAAATAATTAATAGC
54446059 -AAAAATAATTAATA-C
1 TAAAAATAATTAATAGC
54446074 TAAAA
1 TAAAA
54446079 TTTTGTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (17 bp):
TAAAAATAATTAATAGC
Found at i:54447540 original size:26 final size:26
Alignment explanation
Indices: 54447510--54447561 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
54447500 CATGCATAAT
* *
54447510 AGGTTTGCAC-ATAGTGTTCTCACATA
1 AGGTTTGC-CTATAGGGTTCACACATA
54447536 AGGTTTGCCTATAGGGTTCACACATA
1 AGGTTTGCCTATAGGGTTCACACATA
54447562 CAGGGTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (26 bp):
AGGTTTGCCTATAGGGTTCACACATA
Found at i:54448515 original size:27 final size:27
Alignment explanation
Indices: 54448475--54448711 Score: 181
Period size: 27 Copynumber: 8.6 Consensus size: 27
54448465 AGTAAAATTT
*
54448475 TAAAAAATAGGGGCAAAACTATAAAATC
1 TAAAAAATA-GGGCAAAATTATAAAATC
* *
54448503 TAAAAAATAGGGCAAAATTTTAAAATT
1 TAAAAAATAGGGCAAAATTATAAAATC
* * *
54448530 TGAAAAATGTGGGCAAAATT-TAAAATA
1 TAAAAAAT-AGGGCAAAATTATAAAATC
* * * *
54448557 T-AAAAATAAGGCTAAGTTGTAAAATC
1 TAAAAAATAGGGCAAAATTATAAAATC
* * *
54448583 TGAAAAATAGGGGAAAATTGTAAAATC
1 TAAAAAATAGGGCAAAATTATAAAATC
* * *
54448610 TAAAAAAAAGTGGAAAAACTATAAAATC
1 TAAAAAATAG-GGCAAAATTATAAAATC
* * *
54448638 TAAAAAATAGTGGATAAAATTGTAAAATT
1 TAAAAAATAG-GG-CAAAATTATAAAATC
* * * *
54448667 TGAAAAATAGGGGCTAAACTATAAAATA
1 TAAAAAATA-GGGCAAAATTATAAAATC
* *
54448695 TGAAAAATAGGGGAAAA
1 TAAAAAATAGGGCAAAA
54448712 ATAAGGGCTA
Statistics
Matches: 170, Mismatches: 33, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
25 7 0.04
26 13 0.08
27 64 0.38
28 64 0.38
29 21 0.12
30 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.23
Consensus pattern (27 bp):
TAAAAAATAGGGCAAAATTATAAAATC
Found at i:54448544 original size:28 final size:28
Alignment explanation
Indices: 54448453--54448913 Score: 206
Period size: 28 Copynumber: 16.2 Consensus size: 28
54448443 TTGGTAAAGC
54448453 AGGGGACAAAA-TAGTAAAATTTTAAAAAAT
1 AGGGG-CAAAATTA-TAAAA-TTTAAAAAAT
* *
54448483 AGGGGCAAAACTATAAAATCTAAAAAAT
1 AGGGGCAAAATTATAAAATTTAAAAAAT
* *
54448511 A-GGGCAAAATTTTAAAATTTGAAAAAT
1 AGGGGCAAAATTATAAAATTTAAAAAAT
*
54448538 -GTGGGCAAAATT-TAAAATAT-AAAAAT
1 AG-GGGCAAAATTATAAAATTTAAAAAAT
* * * * * *
54448564 A-AGGCTAAGTTGTAAAATCTGAAAAAT
1 AGGGGCAAAATTATAAAATTTAAAAAAT
* * *
54448591 AGGGG-AAAATTGTAAAATCTAAAAAAA
1 AGGGGCAAAATTATAAAATTTAAAAAAT
* * * *
54448618 AGTGGAAAAACTATAAAATCTAAAAAAT
1 AGGGGCAAAATTATAAAATTTAAAAAAT
** * *
54448646 AGTGGATAAAATTGTAAAATTTGAAAAAT
1 AG-GGGCAAAATTATAAAATTTAAAAAAT
* * * *
54448675 AGGGGCTAAACTATAAAATATGAAAAAT
1 AGGGGCAAAATTATAAAATTTAAAAAAT
* *
54448703 AGGGGAAAAATAAGGGCTAAACTATAAAATCTAAAAAAT
1 AGGGGCAAAAT------T--A---TAAAATTTAAAAAAT
*
54448742 AGGGG-AAGAATTATAAAATTTGAAAAAT
1 AGGGGCAA-AATTATAAAATTTAAAAAAT
* * * * * *
54448770 ACGAGCAAAACTGTAAAATCTT-TAGAAT
1 AGGGGCAAAATTATAAAAT-TTAAAAAAT
* *
54448798 AGGGG-AAAATTGTAAAATCTGAAAAAAT
1 AGGGGCAAAATTATAAAAT-TTAAAAAAT
* * **
54448826 A-GGGCAAAAGTGTAAAATTTGGAAAAT
1 AGGGGCAAAATTATAAAATTTAAAAAAT
* * * **
54448853 AGGGGCAAAAGTGTAAAATCTGGAAAAT
1 AGGGGCAAAATTATAAAATTTAAAAAAT
** * * * *
54448881 ATTGGAAAAACTCTAAAATTTAATAAAT
1 AGGGGCAAAATTATAAAATTTAAAAAAT
54448909 AGGGG
1 AGGGG
54448914 ACACAAGACT
Statistics
Matches: 338, Mismatches: 67, Indels: 54
0.74 0.15 0.12
Matches are distributed among these distances:
25 7 0.02
26 13 0.04
27 82 0.24
28 167 0.49
29 35 0.10
30 7 0.02
31 1 0.00
33 1 0.00
34 1 0.00
36 1 0.00
38 2 0.01
39 21 0.06
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.23
Consensus pattern (28 bp):
AGGGGCAAAATTATAAAATTTAAAAAAT
Found at i:54448587 original size:53 final size:53
Alignment explanation
Indices: 54448459--54448713 Score: 181
Period size: 53 Copynumber: 4.6 Consensus size: 53
54448449 AAGCAGGGGA
* * * * *
54448459 CAAAATAGTAAAATTTTAAAAAATAGGGGCAAAACTATAAAATCTAAAAAATAGGG
1 CAAAATTGTAAAA-TCTGAAAAATAGGGGCAAAA-TTTAAAATCT-AAAAATAAGG
* * *
54448515 CAAAATTTTAAAATTTGAAAAAT-GTGGGCAAAATTTAAAATATAAAAATAAGG
1 CAAAATTGTAAAATCTGAAAAATAG-GGGCAAAATTTAAAATCTAAAAATAAGG
* * *
54448568 CTAAGTTGTAAAATCTGAAAAATAGGGG-AAAATTGTAAAATCTAAAAAAAAGTGG
1 CAAAATTGTAAAATCTGAAAAATAGGGGCAAAATT-TAAAATCTAAAAATAA--GG
* * * * ** * *
54448623 AAAAACTATAAAATCTAAAAAATAGTGGATAAAATTGTAAAATTTGAAAAATAGGGG
1 CAAAATTGTAAAATCTGAAAAATAG-GGGCAAAATT-TAAAATCT-AAAAATA-AGG
* * * * *
54448680 CTAAACTATAAAATATGAAAAATAGGGGAAAAAT
1 CAAAATTGTAAAATCTGAAAAATAGGGGCAAAAT
54448714 AAGGGCTAAA
Statistics
Matches: 162, Mismatches: 28, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
52 6 0.04
53 45 0.28
54 10 0.06
55 38 0.23
56 20 0.12
57 37 0.23
58 6 0.04
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.24
Consensus pattern (53 bp):
CAAAATTGTAAAATCTGAAAAATAGGGGCAAAATTTAAAATCTAAAAATAAGG
Found at i:54448713 original size:39 final size:39
Alignment explanation
Indices: 54448668--54448748 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
54448658 TGTAAAATTT
* *
54448668 GAAAAATAGGGGCTAAACTATAAAATATGAAAAATAGGG
1 GAAAAATAAGGGCTAAACTATAAAATATAAAAAATAGGG
*
54448707 GAAAAATAAGGGCTAAACTATAAAATCTAAAAAATAGGG
1 GAAAAATAAGGGCTAAACTATAAAATATAAAAAATAGGG
54448746 GAA
1 GAA
54448749 GAATTATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.17
Consensus pattern (39 bp):
GAAAAATAAGGGCTAAACTATAAAATATAAAAAATAGGG
Found at i:54448781 original size:95 final size:96
Alignment explanation
Indices: 54448625--54448806 Score: 258
Period size: 95 Copynumber: 1.9 Consensus size: 96
54448615 AAAAGTGGAA
* * * * *
54448625 AAACTATAAAATCTAAAAAATAGTGGATAAAATTGTAAAATTTGAAAAATAGGGGCTAAACTATA
1 AAACTATAAAATCTAAAAAATAGGGGATAAAATTATAAAATTTGAAAAATACGAGCAAAACTATA
54448690 AAATATGAAAAATAGGGGAAAAATAAGGGCT
66 AAATATGAAAAATAGGGGAAAAATAAGGGCT
* *
54448721 AAACTATAAAATCTAAAAAATAGGGGA-AGAATTATAAAATTTGAAAAATACGAGCAAAACTGTA
1 AAACTATAAAATCTAAAAAATAGGGGATAAAATTATAAAATTTGAAAAATACGAGCAAAACTATA
* ** *
54448785 AAATCTTTAGAATAGGGGAAAA
66 AAATATGAAAAATAGGGGAAAA
54448807 TTGTAAAATC
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
95 49 0.65
96 26 0.35
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (96 bp):
AAACTATAAAATCTAAAAAATAGGGGATAAAATTATAAAATTTGAAAAATACGAGCAAAACTATA
AAATATGAAAAATAGGGGAAAAATAAGGGCT
Found at i:54448814 original size:150 final size:150
Alignment explanation
Indices: 54448558--54448862 Score: 348
Period size: 150 Copynumber: 2.0 Consensus size: 150
54448548 TTTAAAATAT
** * * * *
54448558 AAAAATAAGGCTAAGTTGTAAAATCTGAAAAATAGGGGAAAATTGTAAAATCTAAAAAAAAGTGG
1 AAAAATAAGGCTAAACTATAAAATCTAAAAAATAGGGGAAAATTATAAAATCTAAAAAAAAGTAG
* * *
54448623 AAAAACTATAAAATCTAAAAAATAGTGGATAAAATTGTAAAATTTG-AAAAATAGGGGCTAAACT
66 AAAAACTATAAAATCTAAAAAATAGTGGAGAAAATTGTAAAATCTGAAAAAATA-GGGCAAAACT
54448687 ATAAAATATGAAAAATAGGGG
130 ATAAAATATGAAAAATAGGGG
* * *
54448708 AAAAATAAGGGCTAAACTATAAAATCTAAAAAATAGGGGAAGAATTATAAAATTTGAAAAATACG
1 AAAAATAA-GGCTAAACTATAAAATCTAAAAAATAGGGGAA-AATTATAAAATCT-AAAAAAAAG
* * ** *
54448773 -AGCAAAACTGTAAAATCTTTAGAATAG-GG-GAAAATTGTAAAATCTGAAAAAATAGGGCAAAA
63 TAGAAAAACTATAAAATCTAAAAAATAGTGGAGAAAATTGTAAAATCTGAAAAAATAGGGCAAAA
* * * *
54448835 GTGTAAAATTTGGAAAATAGGGG
128 CTATAAAATATGAAAAATAGGGG
*
54448858 CAAAA
1 AAAAA
54448863 GTGTAAAATC
Statistics
Matches: 129, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
150 53 0.41
151 37 0.29
152 32 0.25
153 7 0.05
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.22
Consensus pattern (150 bp):
AAAAATAAGGCTAAACTATAAAATCTAAAAAATAGGGGAAAATTATAAAATCTAAAAAAAAGTAG
AAAAACTATAAAATCTAAAAAATAGTGGAGAAAATTGTAAAATCTGAAAAAATAGGGCAAAACTA
TAAAATATGAAAAATAGGGG
Found at i:54448840 original size:55 final size:55
Alignment explanation
Indices: 54448737--54448881 Score: 168
Period size: 55 Copynumber: 2.6 Consensus size: 55
54448727 TAAAATCTAA
* * *
54448737 AAAATAGGGGAAGAATTATAAAATTTGAAAAATACGAGCAAAACTGTAAAATCTT-T
1 AAAATAGGGGAA-AATTGTAAAATCTGAAAAATACGAGCAAAACTGTAAAAT-TTGG
* * *
54448793 AGAATAGGGGAAAATTGTAAAATCTGAAAAAATA-GGGCAAAAGTGTAAAATTTGG
1 AAAATAGGGGAAAATTGTAAAATCTG-AAAAATACGAGCAAAACTGTAAAATTTGG
* *
54448848 AAAATAGGGGCAAAAGTGTAAAATCTGGAAAATA
1 AAAATAGGGG-AAAATTGTAAAATCTGAAAAATA
54448882 TTGGAAAAAC
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
54 2 0.03
55 42 0.55
56 33 0.43
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.22
Consensus pattern (55 bp):
AAAATAGGGGAAAATTGTAAAATCTGAAAAATACGAGCAAAACTGTAAAATTTGG
Found at i:54448889 original size:83 final size:83
Alignment explanation
Indices: 54448727--54448881 Score: 204
Period size: 83 Copynumber: 1.9 Consensus size: 83
54448717 GGCTAAACTA
* * *
54448727 TAAAATCTAAAAAATAGGGGAAGAATTATAAAATTTGAAAAATACGAGCAAAACTGTAAAATCTT
1 TAAAATCTAAAAAATAGGGCAAGAAGTATAAAATTTGAAAAATACGAGCAAAACTGTAAAATCTG
* *
54448792 TAGAATAGGGGAAAATTG
66 GAAAATAGGGGAAAATTG
* * * * *
54448810 TAAAATCTGAAAAAATAGGGCAA-AAGTGTAAAATTTGGAAAATAGGGGCAAAAGTGTAAAATCT
1 TAAAATCT-AAAAAATAGGGCAAGAAGTATAAAATTTGAAAAATACGAGCAAAACTGTAAAATCT
54448874 GGAAAATA
65 GGAAAATA
54448882 TTGGAAAAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
83 48 0.79
84 13 0.21
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.23
Consensus pattern (83 bp):
TAAAATCTAAAAAATAGGGCAAGAAGTATAAAATTTGAAAAATACGAGCAAAACTGTAAAATCTG
GAAAATAGGGGAAAATTG
Found at i:54448909 original size:83 final size:83
Alignment explanation
Indices: 54448721--54448912 Score: 197
Period size: 83 Copynumber: 2.3 Consensus size: 83
54448711 AATAAGGGCT
* * *
54448721 AAACTATAAAATCTAAAAAATAGGGGAAGAATTATAAAATTTGAAAAATACGAGCAAAACTGTAA
1 AAACTATAAAATTTAAAAAATAGGGCAAGAAGTATAAAATTTGAAAAATACGAGCAAAACTGTAA
** * *
54448786 AATCTTTAGAATAGGGGA
66 AATCTGGAAAATAGGGAA
* * * * * * * *
54448804 AAATTGTAAAATCTGAAAAAATAGGGCAA-AAGTGTAAAATTTGGAAAATAGGGGCAAAAGTGTA
1 AAACTATAAAAT-TTAAAAAATAGGGCAAGAAGTATAAAATTTGAAAAATACGAGCAAAACTGTA
*
54448868 AAATCTGGAAAATATTGGAA
65 AAATCTGGAAAATA-GGGAA
* *
54448888 AAACTCTAAAATTTAATAAATAGGG
1 AAACTATAAAATTTAAAAAATAGGG
54448913 GACACAAGAC
Statistics
Matches: 87, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
83 61 0.70
84 26 0.30
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (83 bp):
AAACTATAAAATTTAAAAAATAGGGCAAGAAGTATAAAATTTGAAAAATACGAGCAAAACTGTAA
AATCTGGAAAATAGGGAA
Found at i:54450034 original size:20 final size:20
Alignment explanation
Indices: 54449990--54450036 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
54449980 TATTGGTTAT
*
54449990 ATTTTA-ATATTTAAAATAT
1 ATTTTATATATTTAAAATAA
* *
54450009 AGTTTATATATTTAAATTAA
1 ATTTTATATATTTAAAATAA
54450029 ATTTTATA
1 ATTTTATA
54450037 AATAAATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTATATATTTAAAATAA
Found at i:54450288 original size:13 final size:13
Alignment explanation
Indices: 54450272--54450314 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
54450262 TTTAAATTAG
54450272 ACTTTTCAAAATC
1 ACTTTTCAAAATC
*
54450285 ACTTTTCCACAAT-
1 ACTTTT-CAAAATC
*
54450298 ACTTTTTAAAATC
1 ACTTTTCAAAATC
54450311 ACTT
1 ACTT
54450315 CTTAAAAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 4 0.16
13 16 0.64
14 5 0.20
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (13 bp):
ACTTTTCAAAATC
Found at i:54452112 original size:19 final size:20
Alignment explanation
Indices: 54452075--54452112 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54452065 TAGAATTGTA
54452075 ATTCTTAAAAAATATAATTT
1 ATTCTTAAAAAATATAATTT
54452095 ATTCTTAAAAAATA-AATT
1 ATTCTTAAAAAATATAATT
54452113 CTCACTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTCTTAAAAAATATAATTT
Found at i:54452261 original size:21 final size:24
Alignment explanation
Indices: 54452237--54452282 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 24
54452227 AATAAAATAC
54452237 AAATAATAT-TTATT-TAA-TAGA
1 AAATAATATCTTATTCTAAGTAGA
*
54452258 AAATAATGTCTTATTCTAAGTAGA
1 AAATAATATCTTATTCTAAGTAGA
54452282 A
1 A
54452283 TAGGGTGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 5 0.24
23 3 0.14
24 5 0.24
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (24 bp):
AAATAATATCTTATTCTAAGTAGA
Found at i:54455485 original size:5 final size:5
Alignment explanation
Indices: 54455475--54455502 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
54455465 TGAACATGTA
54455475 CATAT CATAT CATAT CATAT CATAT CAT
1 CATAT CATAT CATAT CATAT CATAT CAT
54455503 TGTACTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:54455743 original size:25 final size:25
Alignment explanation
Indices: 54455696--54455743 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
54455686 TCTCGAGCCA
* **
54455696 TATAACAGGAAGCTTATTCGAGCTG
1 TATAACAGGAAGCTCATAAGAGCTG
*
54455721 TATAATAGGAAGCTCATAAGAGC
1 TATAACAGGAAGCTCATAAGAGC
54455744 CATAATCGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (25 bp):
TATAACAGGAAGCTCATAAGAGCTG
Found at i:54455805 original size:48 final size:49
Alignment explanation
Indices: 54455690--54455806 Score: 123
Period size: 48 Copynumber: 2.4 Consensus size: 49
54455680 GCCCTCTCTC
* * * * *
54455690 GAGCCATATAACAGGAAGCTTATTCGAGCTGTATAATAGGAAGCTCATAA
1 GAGCCAT-TAACGGGAAGCTCATGCGAGCTGAATAACAGGAAGCTCATAA
* *
54455740 GAGCCA-TAATCGAGAAGCTCATGCGAGCT-AATAACAGGTAGCTC-TGAA
1 GAGCCATTAA-CGGGAAGCTCATGCGAGCTGAATAACAGGAAGCTCAT-AA
54455788 GAGCCATTAACGGGAAGCT
1 GAGCCATTAACGGGAAGCT
54455807 TCAGATAGCC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
47 1 0.02
48 31 0.55
49 18 0.32
50 6 0.11
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (49 bp):
GAGCCATTAACGGGAAGCTCATGCGAGCTGAATAACAGGAAGCTCATAA
Done.