Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 15 of 344
Found at i:5444517 original size:14 final size:14
Alignment explanation
Indices: 5444498--5444553 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
5444488 GAGTTACCTA
5444498 TTATATAATAACTC
1 TTATATAATAACTC
5444512 TTATATAATAACTC
1 TTATATAATAACTC
* * **
5444526 TT-GA-ACTTCCTC
1 TTATATAATAACTC
5444538 TTATATAATAACTC
1 TTATATAATAACTC
5444552 TT
1 TT
5444554 CGAAGTTACC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
12 7 0.22
13 2 0.06
14 23 0.72
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.45
Consensus pattern (14 bp):
TTATATAATAACTC
Found at i:5444553 original size:40 final size:42
Alignment explanation
Indices: 5444465--5444553 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
5444455 TTACCAGTCC
* *
5444465 AACTCTTATATAATAACTCTTCGGAGTTACCTATTATATAAT
1 AACTCTTATATAATAACTCTTCGAACTTACCTATTATATAAT
*
5444507 AACTCTTATATAATAACTCTT-GAACTT-CCTCTTATATAAT
1 AACTCTTATATAATAACTCTTCGAACTTACCTATTATATAAT
5444547 AACTCTT
1 AACTCTT
5444554 CGAAGTTACC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 19 0.43
41 4 0.09
42 21 0.48
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (42 bp):
AACTCTTATATAATAACTCTTCGAACTTACCTATTATATAAT
Found at i:5450246 original size:10 final size:9
Alignment explanation
Indices: 5450209--5450294 Score: 68
Period size: 10 Copynumber: 9.0 Consensus size: 9
5450199 GGTGTTTTAT
5450209 AATTA-AAA
1 AATTATAAA
5450217 TAATT-TAAA
1 -AATTATAAA
* *
5450226 ATTTATTAA
1 AATTATAAA
5450235 AATTATAGAA
1 AATTATA-AA
5450245 AACTTATAGAA
1 AA-TTATA-AA
5450256 AATTATAAA
1 AATTATAAA
5450265 ATATTATAAAA
1 A-ATTAT-AAA
*
5450276 AACTATTAAA
1 AATTA-TAAA
5450286 AATTATAAA
1 AATTATAAA
5450295 TATATATAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
8 3 0.05
9 22 0.34
10 24 0.38
11 15 0.23
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
AATTATAAA
Found at i:5450319 original size:36 final size:34
Alignment explanation
Indices: 5450272--5450349 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 34
5450262 AAAATATTAT
5450272 AAAAAACTATTAAAAAT-TATAAATATATATAAGTG
1 AAAAAACTATTAAAAATAT-TAAA-ATATATAAGTG
*
5450307 CAAAAAATTATTAAAAATATTAAAATATATAAGTG
1 -AAAAAACTATTAAAAATATTAAAATATATAAGTG
5450342 AAAAAACT
1 AAAAAACT
5450350 CATGAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 7 0.18
35 11 0.28
36 20 0.51
37 1 0.03
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (34 bp):
AAAAAACTATTAAAAATATTAAAATATATAAGTG
Found at i:5450898 original size:21 final size:21
Alignment explanation
Indices: 5450872--5450925 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
5450862 AAATTTTAAT
5450872 TTTTTTAATAATTTAT-ATAAA
1 TTTTTT-ATAATTTATAATAAA
5450893 TTTTTTATAATTTATAATAAA
1 TTTTTTATAATTTATAATAAA
*
5450914 TTTTATA-AATTT
1 TTTTTTATAATTT
5450926 TTAGTCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTTATAATTTATAATAAA
Found at i:5450902 original size:20 final size:22
Alignment explanation
Indices: 5450872--5450917 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
5450862 AAATTTTAAT
5450872 TTTTTTAATAATTTAT-ATAAA
1 TTTTTTAATAATTTATAATAAA
5450893 TTTTTT-ATAATTTATAATAAA
1 TTTTTTAATAATTTATAATAAA
5450914 TTTT
1 TTTT
5450918 ATAAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTTTAATAATTTATAATAAA
Found at i:5450911 original size:30 final size:29
Alignment explanation
Indices: 5450877--5450946 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 29
5450867 TTAATTTTTT
5450877 TAATAATTTATATAAATTTTTTA-TAATTTA
1 TAATAATTT-TATAAA-TTTTTAGTAATTTA
*
5450907 TAATAAATTTTATAAATTTTTAGTCATTTA
1 TAAT-AATTTTATAAATTTTTAGTAATTTA
5450937 TAATAATTTT
1 TAATAATTTT
5450947 TTTTATAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 12 0.32
30 20 0.54
31 5 0.14
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (29 bp):
TAATAATTTTATAAATTTTTAGTAATTTA
Found at i:5450924 original size:20 final size:20
Alignment explanation
Indices: 5450874--5450925 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
5450864 ATTTTAATTT
5450874 TTTTA-ATAATTTATATAAA
1 TTTTATATAATTTATATAAA
*
5450893 TTTTTTATAATTTATAATAAA
1 TTTTATATAATTTAT-ATAAA
5450914 TTTTATA-AATTT
1 TTTTATATAATTT
5450926 TTAGTCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTATATAATTTATATAAA
Found at i:5450990 original size:22 final size:20
Alignment explanation
Indices: 5450965--5451006 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5450955 TCTTTTTGCA
5450965 CTTTTATATATTTTTACATATT
1 CTTTTATA-ATTTTTA-ATATT
*
5450987 CTTTTGTAATTTTTAATATT
1 CTTTTATAATTTTTAATATT
5451007 TTAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 7 0.37
22 7 0.37
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (20 bp):
CTTTTATAATTTTTAATATT
Found at i:5453841 original size:25 final size:27
Alignment explanation
Indices: 5453807--5453857 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
5453797 GAAATAATTT
* *
5453807 TTTTGGGAG-AAAGTAAAAA-GAAAAG
1 TTTTGAGAGAAAAATAAAAAGGAAAAG
5453832 TTTTGAGAGAAAAATAAAAAGGAAAA
1 TTTTGAGAGAAAAATAAAAAGGAAAA
5453858 AAAATTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 9 0.41
27 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.20
Consensus pattern (27 bp):
TTTTGAGAGAAAAATAAAAAGGAAAAG
Found at i:5470324 original size:46 final size:46
Alignment explanation
Indices: 5470170--5470337 Score: 239
Period size: 46 Copynumber: 3.7 Consensus size: 46
5470160 CAAATCAGTT
*
5470170 GATTGAAGAAGATATAAATCCTATACCCCTGAGTTACAGTGGGATG
1 GATTGAAGAAGATACAAATCCTATACCCCTGAGTTACAGTGGGATG
* **
5470216 GATTGAAGATA-ATACAAATCCTACACCCCTGAGTTGTAGTGGGATG
1 GATTGAAGA-AGATACAAATCCTATACCCCTGAGTTACAGTGGGATG
* *
5470262 GATTGAAGATGATACAAATCCTATACCCCTGAGCTACAGTGGGATG
1 GATTGAAGAAGATACAAATCCTATACCCCTGAGTTACAGTGGGATG
* * *
5470308 GATTGAAGAAGTTACAAATCTTGTACCCCT
1 GATTGAAGAAGATACAAATCCTATACCCCT
5470338 AAATTGCAAA
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
46 106 0.99
47 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (46 bp):
GATTGAAGAAGATACAAATCCTATACCCCTGAGTTACAGTGGGATG
Found at i:5470413 original size:68 final size:68
Alignment explanation
Indices: 5470276--5470403 Score: 166
Period size: 68 Copynumber: 1.9 Consensus size: 68
5470266 GAAGATGATA
* * ** * *
5470276 CAAATCCTATACCCCTGAGCTACAGTGGGATGGATTGAAGAAGTTACAAATCTTGTACCCCTAAA
1 CAAATCCTATACCCCTGAGCTACAGTAGGATAGATTGAAGAAGACACAAATCCTATACCCCTAAA
5470341 TTG
66 TTG
* * * *
5470344 CAAATCCTATACCTCTGAGTTGCAGTAGGATAGATTGAAGATGACACAAATCCTATACCC
1 CAAATCCTATACCCCTGAGCTACAGTAGGATAGATTGAAGAAGACACAAATCCTATACCC
5470404 TTGAGTTGCA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 50 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (68 bp):
CAAATCCTATACCCCTGAGCTACAGTAGGATAGATTGAAGAAGACACAAATCCTATACCCCTAAA
TTG
Found at i:5470438 original size:46 final size:46
Alignment explanation
Indices: 5470344--5470440 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 46
5470334 CCCTAAATTG
* *
5470344 CAAATCCTATACCTCTGAGTTGCAGTAGGATAGATTGAAGATGACA
1 CAAATCCTATACCTCTGAGTTGCAGTAGGATAGATAGAAGATAACA
* * *
5470390 CAAATCCTATACC-CTTGAGTTGCAGTGGGGTGGATAGAAGA-AACCA
1 CAAATCCTATACCTC-TGAGTTGCAGTAGGATAGATAGAAGATAA-CA
5470436 CAAAT
1 CAAAT
5470441 TTTATCTCTC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
45 2 0.05
46 42 0.95
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (46 bp):
CAAATCCTATACCTCTGAGTTGCAGTAGGATAGATAGAAGATAACA
Found at i:5470454 original size:114 final size:114
Alignment explanation
Indices: 5470230--5470440 Score: 296
Period size: 114 Copynumber: 1.9 Consensus size: 114
5470220 GAAGATAATA
* * * *
5470230 CAAATCCTACACCCCTGAGTTGTAGTGGGATGGATTGAAGATGATACAAATCCTATACCCCTGAG
1 CAAATCCTACACCCCTGAGTTGCAGTAGGATAGATTGAAGATGACACAAATCCTATACCCCTGAG
* ***
5470295 CTACAGTGGGATGGATTGAAGAAGTTACAAATCTTGTACCCCTAAATTG
66 CTACAGTGGGATGGATAGAAGAAACCACAAATCTTGTACCCCTAAATTG
* * *
5470344 CAAATCCTATACCTCTGAGTTGCAGTAGGATAGATTGAAGATGACACAAATCCTATACCCTTGAG
1 CAAATCCTACACCCCTGAGTTGCAGTAGGATAGATTGAAGATGACACAAATCCTATACCCCTGAG
* * *
5470409 TTGCAGTGGGGTGGATAGAAGAAACCACAAAT
66 CTACAGTGGGATGGATAGAAGAAACCACAAAT
5470441 TTTATCTCTC
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
114 83 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (114 bp):
CAAATCCTACACCCCTGAGTTGCAGTAGGATAGATTGAAGATGACACAAATCCTATACCCCTGAG
CTACAGTGGGATGGATAGAAGAAACCACAAATCTTGTACCCCTAAATTG
Found at i:5471002 original size:87 final size:88
Alignment explanation
Indices: 5470829--5471186 Score: 273
Period size: 87 Copynumber: 4.1 Consensus size: 88
5470819 ATCATGGCCA
* * * *
5470829 ATCTTATCTCCTTAAAGTTGCAGTGGAGCAGATTGAAACCACAAGTCTTATCTTCCTAAAGTTGT
1 ATCTTATCTCCTTGAAGTTGCAGTGAAGCAGACTGAAA-CACAAGTCTTATCTTCCTAAAGTTGC
* **
5470894 AGTGGAGTAGACTAAAGATAGCA-
65 AATGGAACAGACTAAAGATAGCAG
** *
5470917 AGTCTTATCTCCTTGAAGTTGCAGTGAAGCAGACTGAAA-GTAAGTCTTATCTTCCTGAAGTTGC
1 A-TCTTATCTCCTTGAAGTTGCAGTGAAGCAGACTGAAACACAAGTCTTATCTTCCTAAAGTTGC
*
5470981 AATGGAACAGACTGAAGATAGCAG
65 AATGGAACAGACTAAAGATAGCAG
* * * * *
5471005 ATCTTATCTCCCTGAAGTTGTAGTGGAGTAGA-TCGAAAC-CATATTCTTTATC-TCTCTAAAGT
1 ATCTTATCTCCTTGAAGTTGCAGTGAAGCAGACT-GAAACACA-AGTC-TTATCTTC-CTAAAGT
* * * * *
5471067 TGCAGTAGAGCAGGA-TAAAAATA-CAA
62 TGCAATGGAACA-GACTAAAGATAGCAG
* * * ** ** * *
5471093 ACCTTATCTCCCTAAAGTTGCAGT-AGAGCAGGTTGAAGTAGCAAGTCTTATCTCCCTGAAGTTG
1 ATCTTATCTCCTTGAAGTTGCAGTGA-AGCAGACTGAAACA-CAAGTCTTATCTTCCTAAAGTTG
* * * *
5471157 CAGTGGAGCAGACTGAAGACAGCAG
64 CAATGGAACAGACTAAAGATAGCAG
5471182 ATCTT
1 ATCTT
5471187 CTCCCTGAAA
Statistics
Matches: 214, Mismatches: 41, Indels: 29
0.75 0.14 0.10
Matches are distributed among these distances:
86 1 0.00
87 74 0.35
88 64 0.30
89 71 0.33
90 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (88 bp):
ATCTTATCTCCTTGAAGTTGCAGTGAAGCAGACTGAAACACAAGTCTTATCTTCCTAAAGTTGCA
ATGGAACAGACTAAAGATAGCAG
Found at i:5471174 original size:44 final size:44
Alignment explanation
Indices: 5470830--5471254 Score: 275
Period size: 44 Copynumber: 9.7 Consensus size: 44
5470820 TCATGGCCAA
* * * **
5470830 TCTTATCTCCTTAAAGTTGCAGTGGAGCAGATTGAAACCA-CAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AAGTAGCAAG
* * * * *
5470874 TCTTATCTTCCTAAAGTTGTAGTGGAGTAGACTAAAGATAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-TAGCAAG
* * *
5470919 TCTTATCTCCTTGAAGTTGCAGTGAAGCAGACTGAA--AGTAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGCAAG
* * *
5470961 TCTTATCTTCCTGAAGTTGCAATGGAACAGACTGAAGATAGC-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-TAGCAAG
* * * *
5471005 ATCTTATCTCCCTGAAGTTGTAGTGGAGTAGA-TCGAA--ACCATAT
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGTAGCA-AG
* * * * * *
5471049 TCTTTATCTCTCTAAAGTTGCAGTAGAGCAGGA-TAAAAATA-CAAA
1 TC-TTATCTCCCTGAAGTTGCAGTGGAGCA-GACT-GAAGTAGCAAG
* * * **
5471094 CCTTATCTCCCTAAAGTTGCAGTAGAGCAGGTTGAAGTAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGCAAG
*
5471138 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGC-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-TAGCAAG
* * * * **
5471182 ATC-T-TCTCCCTGAAATTACATTGGAGCAGACCGAACCCA-CAA-
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-GTAGCAAG
* *
5471224 TCCTTATCTCTCTGAAGTTGCAGTAGAGCAG
1 T-CTTATCTCCCTGAAGTTGCAGTGGAGCAG
5471255 GATAAAAATA
Statistics
Matches: 300, Mismatches: 59, Indels: 44
0.74 0.15 0.11
Matches are distributed among these distances:
41 1 0.00
42 40 0.13
43 40 0.13
44 140 0.47
45 76 0.25
46 2 0.01
47 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGCAAG
Found at i:5471244 original size:175 final size:178
Alignment explanation
Indices: 5470829--5471324 Score: 535
Period size: 175 Copynumber: 2.8 Consensus size: 178
5470819 ATCATGGCCA
* * **
5470829 ATCTTATCT-CCTTAAAGTTGCAGTGGAGCAGATTGAAACCACAAGT-CTTATCT-TCCTAAAGT
1 ATCTTATCTCCCTGAAA-TTACAGTGGAGCAGACCGAAACCACAA-TCCTTATCTCT-CTAAAGT
* * * * * ** * **
5470891 TGTAGTGGAGTA-GACTAAAGATAGCAAGTCTTATCTCCTTGAAGTTGCAGT-GAAGCAGACTGA
63 TGCAGTAGAGCAGGA-TAAAAATAACAAACCTTATCTCCCTGAAGTTGCAGTAG-AGCAGGTTGA
* * *
5470954 A--AGTAAGTCTTATCTTCCTGAAGTTGCAATGGAACAGACTGAAGATAGCAG
126 AGTAGCAAGTCTTATCTCCCTGAAGTTGCAATGGAACAGACTGAAGACAGCAG
* ** * * * * *
5471005 ATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATCGAAACCATATTCTTTATCTCTCTAAAGTTGC
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGACCGAAACCACAATCCTTATCTCTCTAAAGTTGC
*
5471070 AGTAGAGCAGGATAAAAAT-ACAAACCTTATCTCCCTAAAGTTGCAGTAGAGCAGGTTGAAGTAG
66 AGTAGAGCAGGATAAAAATAACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTAG
* *
5471134 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGCAG
131 CAAGTCTTATCTCCCTGAAGTTGCAATGGAACAGACTGAAGACAGCAG
* * *
5471182 ATC-T-TCTCCCTGAAATTACATTGGAGCAGACCGAACCCACAATCCTTATCTCTCTGAAGTTGC
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGACCGAAACCACAATCCTTATCTCTCTAAAGTTGC
* * *
5471245 AGTAGAGCAGGATAAAAATACACAAACCTTACCTCCCTGAAGTTGCAGTAGAGCTGGTTAAAGTT
66 AGTAGAGCAGGATAAAAATA-ACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAG-T
* *
5471310 ACCAATTCTTATCTC
129 AGCAAGTCTTATCTC
5471325 TTTTAAGTTC
Statistics
Matches: 269, Mismatches: 41, Indels: 18
0.82 0.12 0.05
Matches are distributed among these distances:
175 100 0.37
176 61 0.23
177 94 0.35
178 14 0.05
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (178 bp):
ATCTTATCTCCCTGAAATTACAGTGGAGCAGACCGAAACCACAATCCTTATCTCTCTAAAGTTGC
AGTAGAGCAGGATAAAAATAACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTAG
CAAGTCTTATCTCCCTGAAGTTGCAATGGAACAGACTGAAGACAGCAG
Found at i:5471688 original size:15 final size:16
Alignment explanation
Indices: 5471668--5471700 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5471658 CCAATTTTAG
*
5471668 AATTACAA-AACCCAA
1 AATTACAATAAACCAA
5471683 AATTACAATAAACCAA
1 AATTACAATAAACCAA
5471699 AA
1 AA
5471701 CCCAAACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.15
Consensus pattern (16 bp):
AATTACAATAAACCAA
Found at i:5490482 original size:14 final size:14
Alignment explanation
Indices: 5490463--5490509 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
5490453 TTACCTTACC
5490463 ATTTTAGTTTATAT
1 ATTTTAGTTTATAT
*
5490477 ATTTTAATTTA-AT
1 ATTTTAGTTTATAT
* *
5490490 ATTTTTTGTTTTTAT
1 A-TTTTAGTTTATAT
5490505 ATTTT
1 ATTTT
5490510 TAAAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 3 0.11
14 21 0.78
15 3 0.11
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (14 bp):
ATTTTAGTTTATAT
Found at i:5501748 original size:21 final size:21
Alignment explanation
Indices: 5501722--5501762 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5501712 ATGGCCTCAC
* *
5501722 AGATCATTATGAGTTATAAAG
1 AGATCATTACGAGTGATAAAG
5501743 AGATCATTACGAGTGATAAA
1 AGATCATTACGAGTGATAAA
5501763 CATTCCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (21 bp):
AGATCATTACGAGTGATAAAG
Found at i:5502375 original size:3 final size:3
Alignment explanation
Indices: 5502357--5502390 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5502347 GATTGAGTTT
*
5502357 TTG TTT TTG TTG -TG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
5502391 TTTTTGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:5504241 original size:16 final size:16
Alignment explanation
Indices: 5504220--5504252 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5504210 TGACATGTGG
5504220 TAAAAAGTT-ATAAAAA
1 TAAAAA-TTAATAAAAA
5504236 TAAAAATTAATAAAAA
1 TAAAAATTAATAAAAA
5504252 T
1 T
5504253 TATAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
TAAAAATTAATAAAAA
Found at i:5504250 original size:9 final size:9
Alignment explanation
Indices: 5504235--5504316 Score: 58
Period size: 10 Copynumber: 8.8 Consensus size: 9
5504225 AGTTATAAAA
5504235 ATAAAAATT
1 ATAAAAATT
5504244 AATAAAAATT
1 -ATAAAAATT
*
5504254 ATAAAAATG
1 ATAAAAATT
**
5504263 ATTAAATTTT
1 A-TAAAAATT
5504273 ATTAAAAA-T
1 A-TAAAAATT
*
5504282 ATAAAAAAT
1 ATAAAAATT
* *
5504291 ATTAAATTT
1 ATAAAAATT
5504300 ATAAAAAATT
1 AT-AAAAATT
*
5504310 GTAAAAA
1 ATAAAAA
5504317 ACTATAATAT
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
8 6 0.11
9 25 0.44
10 26 0.46
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:5504287 original size:28 final size:27
Alignment explanation
Indices: 5504246--5504317 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
5504236 TAAAAATTAA
5504246 TAAAAAT-TATAAAAATGATTAAATTTTAT
1 TAAAAATATA-AAAAAT-ATTAAA-TTTAT
5504275 TAAAAATATAAAAAATATTAAATTTAT
1 TAAAAATATAAAAAATATTAAATTTAT
* *
5504302 AAAAAATTGTAAAAAA
1 TAAAAA-TATAAAAAA
5504318 CTATAATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.26
28 14 0.36
29 13 0.33
30 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (27 bp):
TAAAAATATAAAAAATATTAAATTTAT
Found at i:5504293 original size:18 final size:18
Alignment explanation
Indices: 5504272--5504308 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5504262 GATTAAATTT
5504272 TATTAAAAATATAAAAAA
1 TATTAAAAATATAAAAAA
**
5504290 TATTAAATTTATAAAAAA
1 TATTAAAAATATAAAAAA
5504308 T
1 T
5504309 TGTAAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATTAAAAATATAAAAAA
Found at i:5505633 original size:22 final size:21
Alignment explanation
Indices: 5505583--5505633 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
5505573 TTTTGTTTAC
**
5505583 AATTTT-TTATAATTTCTTCT
1 AATTTTATTATAATTTCAACT
**
5505603 AATAATATTATTAATTTCAACT
1 AATTTTATTA-TAATTTCAACT
5505625 AATTTTATT
1 AATTTTATT
5505634 TCAATTATCC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 4 0.17
21 3 0.13
22 16 0.70
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTTATTATAATTTCAACT
Found at i:5505699 original size:21 final size:21
Alignment explanation
Indices: 5505675--5505715 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5505665 TTTATAATTT
*
5505675 TTTCTAGATTATGTATATATA
1 TTTCTAAATTATGTATATATA
* *
5505696 TTTCTAAATTTTTTATATAT
1 TTTCTAAATTATGTATATAT
5505716 TTATTTCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTCTAAATTATGTATATATA
Found at i:5505726 original size:21 final size:22
Alignment explanation
Indices: 5505688--5505739 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
5505678 CTAGATTATG
*
5505688 TATATATATTTCTAAATTTTTTA
1 TATATTTATTTC-AAATTTTTTA
5505711 TATATTTATTTC-AATTTTTTA
1 TATATTTATTTCAAATTTTTTA
*
5505732 TATTTTTA
1 TATATTTA
5505740 ATGTGTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 16 0.59
23 11 0.41
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (22 bp):
TATATTTATTTCAAATTTTTTA
Found at i:5513725 original size:46 final size:46
Alignment explanation
Indices: 5513568--5513787 Score: 193
Period size: 46 Copynumber: 4.7 Consensus size: 46
5513558 TTATTTGTGT
*
5513568 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAT--A-TTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-TCGAGATAT-A-A
* * * * *
5513614 GCCAGTGTAAGATCATGTCTGGGACGTGGCATTGGCATTGAGACGATAA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGA-TATAA
* * *
5513663 -CTAGTGTAAGATATGTCTGGGACATGCATCAGCCTCGAGATATAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATAA
* *
5513708 GCCAGTGTAAGACATGTCTGGAACATGCATCGG-CTACAAGATAT--
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATATAA
* *
5513752 GTCAGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
5513788 ATGAATATGT
Statistics
Matches: 142, Mismatches: 21, Indels: 21
0.77 0.11 0.11
Matches are distributed among these distances:
44 11 0.08
45 18 0.13
46 65 0.46
47 26 0.18
48 17 0.12
49 2 0.01
50 1 0.01
51 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATAA
Found at i:5513805 original size:94 final size:94
Alignment explanation
Indices: 5513570--5513839 Score: 245
Period size: 94 Copynumber: 2.9 Consensus size: 94
5513560 ATTTGTGTGC
* *
5513570 CAGTGTAAGACATGTCTGGGACATGCATCGGCCAT-ATTA-TGAGAGCCAGTGTAAGATCATGTC
1 CAGTGTAAGACATGTCTGGGACATGCATCGG-CATGAATATTGAGAGCCAGTGTAAGACCATGTC
* * * *
5513633 TGGGACGTGGCATTGGCATTGAGACGATAACT
65 T-GGACATGGCATCGGCA-TGACAAGATAACT
* * *
5513665 -AGTGTAAGATATGTCTGGGACATGCATCAGCCTCGAGATA-T-A-AGCCAGTGTAAGA-CATGT
1 CAGTGTAAGACATGTCTGGGACATGCATCGGCAT-GA-ATATTGAGAGCCAGTGTAAGACCATGT
**
5513725 CTGGAACAT-GCATCGGC-T-ACAAGATATGT
64 CTGG-ACATGGCATCGGCATGACAAGATAACT
* * *
5513754 CAGTGTAAGACCATGTCTAGGACATGGCATCGGCATGAATATGTGAGAGCCATTGTAAAACCATG
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATGAATAT-TGAGAGCCAGTGTAAGACCATG
*
5513819 TCTCGGACATGGCATCAGCAT
63 TCT-GGACATGGCATCGGCAT
5513840 TATACCCTAT
Statistics
Matches: 143, Mismatches: 17, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
89 7 0.05
90 13 0.09
91 14 0.10
92 18 0.13
93 13 0.09
94 52 0.36
95 13 0.09
96 12 0.08
97 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (94 bp):
CAGTGTAAGACATGTCTGGGACATGCATCGGCATGAATATTGAGAGCCAGTGTAAGACCATGTCT
GGACATGGCATCGGCATGACAAGATAACT
Found at i:5513811 original size:140 final size:142
Alignment explanation
Indices: 5513568--5513837 Score: 302
Period size: 140 Copynumber: 1.9 Consensus size: 142
5513558 TTATTTGTGT
* * * *
5513568 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCCAGTGTAAGATCATGTC
1 GCCAGTGTAAGACATGTCTGGAACATGCATCGGCCATATCAAGAGAGCCAGTGTAAGACCATGTC
* * * * * * *
5513633 TGGGACGTGGCATTGGCATTGAGACGATAACTAGTGTAAGA-TATGTCTGGGACAT-GCATCAGC
66 TAGGACATGGCATCGGCATTGAGACGATAACCAGTGTAAAACCATGTCTCGGACATGGCATCAGC
5513696 CTCGAGATATAA
131 CTCGAGATATAA
* *
5513708 GCCAGTGTAAGACATGTCTGGAACATGCATCGG-C-TA-CAAGATATGTCAGTGTAAGACCATGT
1 GCCAGTGTAAGACATGTCTGGAACATGCATCGGCCATATCAAGAGA-GCCAGTGTAAGACCATGT
* * *
5513770 CTAGGACATGGCATCGGCA-TGAATATG-TGAGAGCCATTGTAAAACCATGTCTCGGACATGGCA
65 CTAGGACATGGCATCGGCATTG-AGACGAT-A-A-CCAGTGTAAAACCATGTCTCGGACATGGCA
5513833 TCAGC
126 TCAGC
5513838 ATTATACCCT
Statistics
Matches: 107, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
137 7 0.07
138 38 0.36
139 2 0.02
140 40 0.37
141 12 0.11
142 8 0.07
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (142 bp):
GCCAGTGTAAGACATGTCTGGAACATGCATCGGCCATATCAAGAGAGCCAGTGTAAGACCATGTC
TAGGACATGGCATCGGCATTGAGACGATAACCAGTGTAAAACCATGTCTCGGACATGGCATCAGC
CTCGAGATATAA
Found at i:5514166 original size:28 final size:28
Alignment explanation
Indices: 5514126--5514182 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
5514116 TGCTTATGAG
*
5514126 AATGATTTTGTGATGACCTTGTGATTAT
1 AATGATTTTGTGATGACCTGGTGATTAT
5514154 AATGATTTTGTGATGACCTGGTGATTAT
1 AATGATTTTGTGATGACCTGGTGATTAT
5514182 A
1 A
5514183 GGTCTATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (28 bp):
AATGATTTTGTGATGACCTGGTGATTAT
Found at i:5515042 original size:22 final size:23
Alignment explanation
Indices: 5515017--5515062 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5515007 CAACCAAATC
5515017 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
5515039 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
5515062 A
1 A
5515063 GATAACGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:5525608 original size:29 final size:27
Alignment explanation
Indices: 5525552--5525608 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
5525542 ACAAAAATGA
* *
5525552 TCATTATTTTATATTTAGAATATGTTT
1 TCATTATTTAATATTTAAAATATGTTT
5525579 TCATTACTTTAATATTTATAAATATGTTT
1 TCATTA-TTTAATATTTA-AAATATGTTT
5525608 T
1 T
5525609 ATATACATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 6 0.23
28 10 0.38
29 10 0.38
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (27 bp):
TCATTATTTAATATTTAAAATATGTTT
Found at i:5528564 original size:23 final size:23
Alignment explanation
Indices: 5528518--5528564 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5528508 TTTAGCCCAG
* *
5528518 TTAGTTTACTTAACAATTTAATT
1 TTAGTTTACTAAACAAATTAATT
5528541 TTAGTTTA-TAAACAAATTATATT
1 TTAGTTTACTAAACAAATTA-ATT
5528564 T
1 T
5528565 GAATTTGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.51
Consensus pattern (23 bp):
TTAGTTTACTAAACAAATTAATT
Found at i:5534847 original size:21 final size:20
Alignment explanation
Indices: 5534818--5534870 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
5534808 CGTTCTTGTC
*
5534818 TGTGACTTTCTGTTATTTTAT
1 TGTGGCTTTCT-TTATTTTAT
* *
5534839 TGTGGCTTTCTTTGTTTTCT
1 TGTGGCTTTCTTTATTTTAT
*
5534859 TATGGC-TTCTTT
1 TGTGGCTTTCTTT
5534871 TGGCATAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 6 0.21
20 12 0.43
21 10 0.36
ACGTcount: A:0.08, C:0.13, G:0.17, T:0.62
Consensus pattern (20 bp):
TGTGGCTTTCTTTATTTTAT
Found at i:5536277 original size:25 final size:25
Alignment explanation
Indices: 5536243--5536345 Score: 106
Period size: 25 Copynumber: 4.1 Consensus size: 25
5536233 CATCGAGAGA
5536243 GTTTGGTGAATAATGTAACCTATTT
1 GTTTGGTGAATAATGTAACCTATTT
5536268 GTTTGGTGAATAATGTAACCTA--T
1 GTTTGGTGAATAATGTAACCTATTT
* * * *
5536291 -TTTGTTGAATAGTTAGTGACAT-TGATT
1 GTTTGGTGAATA-AT-GTAACCTAT--TT
5536318 GTTTGGTGAATAATGTAACCTATTT
1 GTTTGGTGAATAATGTAACCTATTT
5536343 GTT
1 GTT
5536346 GACCGAAAGA
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
22 10 0.16
23 2 0.03
24 5 0.08
25 27 0.44
26 5 0.08
27 3 0.05
28 10 0.16
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.45
Consensus pattern (25 bp):
GTTTGGTGAATAATGTAACCTATTT
Found at i:5539257 original size:43 final size:43
Alignment explanation
Indices: 5539210--5539349 Score: 158
Period size: 43 Copynumber: 3.3 Consensus size: 43
5539200 TGAGATTATA
* * *
5539210 TGTAAGACCATGTCTGAGACATTGGCATTG-TATTGTGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTA-TATGATTACG
* *
5539253 TGTAAGACCATGTCTGGGACATTGACATCGTTATATGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTATATGATTACG
* * * * *
5539296 TGTAGGACCATGTCTGGGACATTGGGATCGATATGA-GATAACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTAT-ATGATTACG
5539339 TGTAAGACCAT
1 TGTAAGACCAT
5539350 ATCTAGGATA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 79 0.96
44 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTTATATGATTACG
Found at i:5548248 original size:18 final size:18
Alignment explanation
Indices: 5548225--5548293 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 18
5548215 TCCTCAAATG
5548225 CAGCAGCCACAGCAACAT
1 CAGCAGCCACAGCAACAT
5548243 CAGCAG-CAGCAGC-A-A-
1 CAGCAGCCA-CAGCAACAT
* * * *
5548258 CAGCAACTACTGCAACAA
1 CAGCAGCCACAGCAACAT
*
5548276 CAGCAGCTACAGCAACAT
1 CAGCAGCCACAGCAACAT
5548294 GCTCAACAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
15 8 0.20
16 3 0.08
17 4 0.10
18 25 0.62
ACGTcount: A:0.41, C:0.35, G:0.17, T:0.07
Consensus pattern (18 bp):
CAGCAGCCACAGCAACAT
Found at i:5549086 original size:20 final size:20
Alignment explanation
Indices: 5549063--5549105 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5549053 AAAAGTGAAA
*
5549063 AAATATTCAAAATAATA-ATT
1 AAATAGTCAAAAT-ATAGATT
*
5549083 AAATAGTGAAAATATAGATT
1 AAATAGTCAAAATATAGATT
5549103 AAA
1 AAA
5549106 GTAAAGTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (20 bp):
AAATAGTCAAAATATAGATT
Found at i:5563195 original size:29 final size:27
Alignment explanation
Indices: 5563118--5563199 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 27
5563108 TAAATAAATT
*
5563118 TTAAATTTTAAATTAAAAAATAAAGGAA
1 TTAAATTTTAAATT-AAAAATATAGGAA
*
5563146 TTAAATTTTTAAAAATAAAAATATA-GAGA
1 TTAAA-TTTT-AAATTAAAAATATAGGA-A
5563175 TTAAATTTTAAATGTAGAAAATATA
1 TTAAATTTTAAAT-TA-AAAATATA
5563200 ATAAATCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 3 0.07
28 13 0.28
29 26 0.57
30 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (27 bp):
TTAAATTTTAAATTAAAAATATAGGAA
Found at i:5568661 original size:21 final size:22
Alignment explanation
Indices: 5568625--5568672 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
5568615 TATTTGTCTA
*
5568625 TTATTTTTTCATTGTTTTACTG
1 TTATTTTTTCACTGTTTTACTG
*
5568647 TTATTTTTT-ACTGTTTTGCTG
1 TTATTTTTTCACTGTTTTACTG
5568668 TTATT
1 TTATT
5568673 AACACTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.12, C:0.08, G:0.10, T:0.69
Consensus pattern (22 bp):
TTATTTTTTCACTGTTTTACTG
Found at i:5583213 original size:44 final size:42
Alignment explanation
Indices: 5583135--5583290 Score: 133
Period size: 44 Copynumber: 3.6 Consensus size: 42
5583125 TTATTGCTAT
* *
5583135 TATTATTATGTTTCTATT-TGTATTTATTTTTTTATTCTAATAC
1 TATTATTATATTTCTATTAT-TATTTATTTATTTATT-TAATAC
* **
5583178 TATTATTAT-TTATCTAATTATTATTTATCTATTTATATTTCTAC
1 TATTATTATATT-TCT-ATTATTATTTATTTATTTAT-TTAATAC
5583222 TATTATTATATTTCTATTTATTATATT-TTTATTTCTATTTATATAC
1 TATTATTATATTTCTA-TTATTAT-TTATTTA-TT-TATTTA-ATAC
*
5583268 TAATATTAT-TTTC-ATTATTATTT
1 TATTATTATATTTCTATTATTATTT
5583291 TTCTCATATA
Statistics
Matches: 95, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
42 4 0.04
43 20 0.21
44 43 0.45
45 14 0.15
46 14 0.15
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (42 bp):
TATTATTATATTTCTATTATTATTTATTTATTTATTTAATAC
Found at i:5583246 original size:15 final size:15
Alignment explanation
Indices: 5583137--5583255 Score: 67
Period size: 15 Copynumber: 8.1 Consensus size: 15
5583127 ATTGCTATTA
*
5583137 TTATTATGTTTCTATT
1 TTATTATATTTCTA-T
5583153 TGTATT-TATTT-T-T
1 T-TATTATATTTCTAT
* * *
5583166 TTATTCTAATACTA-
1 TTATTATATTTCTAT
*
5583180 TTATTAT-TTATCTAA
1 TTATTATATT-TCTAT
5583195 TTATTAT-TTATCTA-
1 TTATTATATT-TCTAT
5583209 -T-TTATATTTCTACT
1 TTATTATATTTCTA-T
5583223 ATTATTATATTTCTAT
1 -TTATTATATTTCTAT
*
5583239 TTATTATATTTTTAT
1 TTATTATATTTCTAT
5583254 TT
1 TT
5583256 CTATTTATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 25
0.72 0.06 0.22
Matches are distributed among these distances:
12 12 0.14
13 9 0.11
14 10 0.12
15 31 0.37
16 7 0.08
17 15 0.18
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (15 bp):
TTATTATATTTCTAT
Found at i:5583254 original size:29 final size:30
Alignment explanation
Indices: 5583123--5583245 Score: 92
Period size: 29 Copynumber: 4.2 Consensus size: 30
5583113 TATTTTAATA
** *
5583123 TATTATTGCTATTATTATTATGTTTCTATT
1 TATTATTTATATTATTATTATATTTCTATT
* * * * * *
5583153 T-GTATTTATTTTTTTATTCTAATACTA-T
1 TATTATTTATATTATTATTATATTTCTATT
* *
5583181 TATTATTTATCTAATTATTAT-TTATCTATT
1 TATTATTTATATTATTATTATATT-TCTATT
* *
5583211 TA-TATTTCTACTATTATTATATTTCTATT
1 TATTATTTATATTATTATTATATTTCTATT
5583240 TATTAT
1 TATTAT
5583246 ATTTTTATTT
Statistics
Matches: 68, Mismatches: 20, Indels: 10
0.69 0.20 0.10
Matches are distributed among these distances:
28 3 0.04
29 56 0.82
30 9 0.13
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.63
Consensus pattern (30 bp):
TATTATTTATATTATTATTATATTTCTATT
Found at i:5583297 original size:15 final size:14
Alignment explanation
Indices: 5583177--5583294 Score: 75
Period size: 15 Copynumber: 8.1 Consensus size: 14
5583167 TATTCTAATA
*
5583177 CTATTATTATTTAT
1 CTATTATTATTTTT
*
5583191 CTAATTATTATTTAT
1 CT-ATTATTATTTTT
*
5583206 CTATT-TATATTTCTA
1 CTATTAT-TATTT-TT
*
5583221 CTATTATTATATTT
1 CTATTATTATTTTT
5583235 CTATTTATTATATTTT
1 CTA-TTATTAT-TTTT
5583251 -TATT-TCTATTTATAT
1 CTATTAT-TATTT-T-T
*
5583266 ACTAATATTA-TTTT
1 -CTATTATTATTTTT
5583280 C-ATTATTATTTTT
1 CTATTATTATTTTT
5583293 CT
1 CT
5583295 CATATATGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 28
0.70 0.06 0.24
Matches are distributed among these distances:
12 6 0.07
13 10 0.12
14 21 0.25
15 34 0.41
16 6 0.07
17 5 0.06
18 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (14 bp):
CTATTATTATTTTT
Found at i:5583337 original size:4 final size:4
Alignment explanation
Indices: 5583328--5583352 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5583318 ATTAACATTC
5583328 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
5583353 TACATTTTTT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:5583432 original size:25 final size:25
Alignment explanation
Indices: 5583404--5583498 Score: 66
Period size: 25 Copynumber: 3.7 Consensus size: 25
5583394 CTCATTTCAA
5583404 ATTTTTATACATTATTTATTTTAAT
1 ATTTTTATACATTATTTATTTTAAT
* * * *
5583429 ATTTTCATATATTATGTATTTCAAACT
1 ATTTTTATACATTATTTATTT-TAA-T
* * *
5583456 TTTTTTCACACATTATATATTTTGAAT
1 ATTTTT-ATACATTATTTATTTT-AAT
* *
5583483 -TGTTTATATATTATTT
1 ATTTTTATACATTATTT
5583499 TTAAAGAGTT
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
25 26 0.50
26 6 0.12
27 6 0.12
28 14 0.27
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (25 bp):
ATTTTTATACATTATTTATTTTAAT
Found at i:5584949 original size:20 final size:18
Alignment explanation
Indices: 5584909--5584951 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5584899 TATTAATTAC
*
5584909 ATTAATATTTTTTTAATA
1 ATTAATATTTTTTTAAAA
5584927 ATTAATATTCTTTTTAAAAA
1 ATTAATATT-TTTTT-AAAA
5584947 ATTAA
1 ATTAA
5584952 AACTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 5 0.23
20 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAATATTTTTTTAAAA
Found at i:5585477 original size:13 final size:13
Alignment explanation
Indices: 5585461--5585490 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
5585451 TTAGTCGTTG
5585461 ATTTAAAAATTTT
1 ATTTAAAAATTTT
5585474 ATTT-AAAATTTT
1 ATTTAAAAATTTT
5585486 ATTTA
1 ATTTA
5585491 TATTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTAAAAATTTT
Found at i:5595493 original size:22 final size:22
Alignment explanation
Indices: 5595465--5595509 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5595455 GGTTGTTGTG
5595465 TAGGAATAT-TCTGTAAATATTT
1 TAGGAATATCT-TGTAAATATTT
*
5595487 TAGGAATATCTTGTAGATATTT
1 TAGGAATATCTTGTAAATATTT
5595509 T
1 T
5595510 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATCTTGTAAATATTT
Found at i:5600093 original size:22 final size:22
Alignment explanation
Indices: 5600065--5600109 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5600055 AGGGGGAGTG
5600065 TAGGAATAT-TCTGTAAATATTT
1 TAGGAATATCT-TGTAAATATTT
*
5600087 TAGGAATATCTTGTAGATATTT
1 TAGGAATATCTTGTAAATATTT
5600109 T
1 T
5600110 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATCTTGTAAATATTT
Found at i:5601665 original size:19 final size:19
Alignment explanation
Indices: 5601641--5601678 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5601631 AATGAATTTC
5601641 CATAGCTACCAAGAGACAA
1 CATAGCTACCAAGAGACAA
5601660 CATAGCTACCAAGAGACAA
1 CATAGCTACCAAGAGACAA
5601679 AAATGTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.26, G:0.16, T:0.11
Consensus pattern (19 bp):
CATAGCTACCAAGAGACAA
Found at i:5603687 original size:46 final size:46
Alignment explanation
Indices: 5603635--5603898 Score: 377
Period size: 46 Copynumber: 5.7 Consensus size: 46
5603625 AGTGTGCTCT
5603635 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
5603681 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCACGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
5603727 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
5603773 CTAATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * ** **
5603819 GTGACATGAAAAGAATAAGACCACAGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
5603865 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGA
5603899 CACTACGGCA
Statistics
Matches: 200, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.00
46 199 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:5604214 original size:23 final size:25
Alignment explanation
Indices: 5604169--5604215 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5604159 AATAAATATA
*
5604169 CATAAAATATATAGAAATGATGAAG
1 CATAAAATATATAGAAATAATGAAG
*
5604194 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATAGAAATAATGAA
5604216 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.28
Consensus pattern (25 bp):
CATAAAATATATAGAAATAATGAAG
Found at i:5607062 original size:24 final size:24
Alignment explanation
Indices: 5607030--5607080 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5607020 TTAGGACTAG
* *
5607030 TTTAGCATTGTTTTTGAGAAGTGT
1 TTTAACATTATTTTTGAGAAGTGT
*
5607054 TTTAACATTATTTTTGTGAAGTGT
1 TTTAACATTATTTTTGAGAAGTGT
5607078 TTT
1 TTT
5607081 TAAAAAGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.20, T:0.55
Consensus pattern (24 bp):
TTTAACATTATTTTTGAGAAGTGT
Found at i:5607370 original size:100 final size:101
Alignment explanation
Indices: 5607236--5607446 Score: 343
Period size: 100 Copynumber: 2.1 Consensus size: 101
5607226 TCAAATTAGT
* *
5607236 TAATATTATGATATTTTAATAAGAATATAAAAATAATTTATTATAATTTGTTGTTAATACTTTAA
1 TAATATTA-AATATCTTAATAAGAATATAAAAATAATTTATTATAATTTGTTGTTAATACTTTAA
*
5607301 CATATGAAATATAAATTTTAAAT-TTTTTTAAAAAAA
65 CATATAAAATATAAATTTTAAATATTTTTTAAAAAAA
* * *
5607337 TAATATTAAATATCTTAGTAAGAATATAAAAATAATTTATTATAATTTGTTGTTAATATTTTAAT
1 TAATATTAAATATCTTAATAAGAATATAAAAATAATTTATTATAATTTGTTGTTAATACTTTAAC
*
5607402 ATATAAAATATAAATTTTAAATATTTTTTAAAAAAT
66 ATATAAAATATAAATTTTAAATATTTTTTAAAAAAA
5607438 TAATATTAA
1 TAATATTAA
5607447 TTATTTATAA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 73 0.72
101 29 0.28
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (101 bp):
TAATATTAAATATCTTAATAAGAATATAAAAATAATTTATTATAATTTGTTGTTAATACTTTAAC
ATATAAAATATAAATTTTAAATATTTTTTAAAAAAA
Found at i:5607434 original size:25 final size:25
Alignment explanation
Indices: 5607405--5607452 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5607395 TTTTAATATA
* *
5607405 TAAAATATAAATTTTAAATATTTTT
1 TAAAAAATAAATATTAAATATTTTT
* *
5607430 TAAAAAATTAATATTAATTATTT
1 TAAAAAATAAATATTAAATATTT
5607453 ATAAATTTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAAAAATAAATATTAAATATTTTT
Found at i:5607494 original size:19 final size:20
Alignment explanation
Indices: 5607452--5607501 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
5607442 ATTAATTATT
*
5607452 TATAAATT-TAATTTGAATA
1 TATAAATTATAATTTAAATA
*
5607471 TATAAATTATATTTTAAATA
1 TATAAATTATAATTTAAATA
*
5607491 -ATAAAATATAA
1 TATAAATTATAA
5607502 CCAATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TATAAATTATAATTTAAATA
Found at i:5607935 original size:16 final size:16
Alignment explanation
Indices: 5607914--5607978 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 16
5607904 TTAGAATTTC
5607914 TATATATTAATATACA
1 TATATATTAATATACA
*
5607930 TATATATT--TA-AGA
1 TATATATTAATATACA
* *
5607943 -ATTTAATAAT-TAC-
1 TATATATTAATATACA
5607956 -ATATATTAATATACA
1 TATATATTAATATACA
5607971 TATATATT
1 TATATATT
5607979 TTTTAGTGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
12 5 0.14
13 10 0.27
14 7 0.19
16 15 0.41
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (16 bp):
TATATATTAATATACA
Found at i:5618732 original size:22 final size:22
Alignment explanation
Indices: 5618700--5618742 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5618690 CTCTATAAAC
*
5618700 ATATTAATTAATAGATTAAAAT
1 ATATTAATTAATAAATTAAAAT
*
5618722 ATATTATTTAATAAATTAAAA
1 ATATTAATTAATAAATTAAAA
5618743 AATAACTACG
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:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATTAATTAATAAATTAAAAT
Found at i:5618894 original size:23 final size:22
Alignment explanation
Indices: 5618855--5618902 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
5618845 ATAAATACAA
5618855 ATATTTTTAATAATTTATCAAT
1 ATATTTTTAATAATTTATCAAT
*
5618877 ATATATTTTAA-AAGTTTATTAAT
1 ATAT-TTTTAATAA-TTTATCAAT
5618900 ATA
1 ATA
5618903 ATTAACGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTTTTAATAATTTATCAAT
Found at i:5620390 original size:208 final size:206
Alignment explanation
Indices: 5620030--5620564 Score: 885
Period size: 208 Copynumber: 2.6 Consensus size: 206
5620020 TTAATACTCG
*
5620030 GTTTTATTAGGTATAAGTATTTAAAATTTTGTTTTTGTAATGTGATACATGCGTAAATATATATA
1 GTTTTATTAGGTATAAGTATTT-AAATTTT-TTTTTGTAATGTGATACATGCGT--GTATATATA
* * * *
5620095 TATAATCATATTAGTGAATTTGCTAATATATACTTCATCCAGGTAAAGTATACATTATTAAAATT
62 TATAATCATATTAGTGAATCTGCTAATACATACTTCATCCAGGTAAAGTATGCATTTTTAAAATT
5620160 AAATTAAAATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAACTATTAT
127 AAATTAAAATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAACTATTAT
5620225 TGTAATGAGATACAT
192 TGTAATGAGATACAT
5620240 GTTTTATTAGGTATAAGTATTTAAATTTTTATTTTTGTAATGTGATACATGCGTGTATATATATA
1 GTTTTATTAGGTATAAGTATTTAAA-TTTT-TTTTTGTAATGTGATACATGCGTGTATATATATA
*
5620305 TAATCATATTAGTGAATCTGCTAATACATACTTCATTCAGGTAAAGTATGCATTTTTAAAATTAA
64 TAATCATATTAGTGAATCTGCTAATACATACTTCATCCAGGTAAAGTATGCATTTTTAAAATTAA
*
5620370 ATTAAAATGTTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAACTATTATTG
129 ATTAAAATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAACTATTATTG
5620435 TAATGAGATACAT
194 TAATGAGATACAT
* * * *
5620448 GTTTTATTAGGTATAAGCATTTAAAATTTTTTTTGTAATGTGATACAT-C-CGTAAATATATATA
1 GTTTTATTAGGTATAAGTATTTAAATTTTTTTTTGTAATGTGATACATGCGTGTATATATATATA
* *
5620511 ATCATATTAGTAAATCTGCTAATACATACTTCATCCAGATAAAGTATGCATTTT
66 ATCATATTAGTGAATCTGCTAATACATACTTCATCCAGGTAAAGTATGCATTTT
5620565 AATAACACAT
Statistics
Matches: 309, Mismatches: 15, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
204 63 0.20
205 1 0.00
206 19 0.06
207 3 0.01
208 171 0.55
209 3 0.01
210 49 0.16
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (206 bp):
GTTTTATTAGGTATAAGTATTTAAATTTTTTTTTGTAATGTGATACATGCGTGTATATATATATA
ATCATATTAGTGAATCTGCTAATACATACTTCATCCAGGTAAAGTATGCATTTTTAAAATTAAAT
TAAAATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAACTATTATTGTA
ATGAGATACAT
Found at i:5625533 original size:20 final size:18
Alignment explanation
Indices: 5625508--5625557 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 18
5625498 TGGCTTAAAA
5625508 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTG--G
5625528 TTGGTAGTGGATTGTTGG
1 TTGGTAGTGGATTGTTGG
5625546 -TGGTAGTGGATT
1 TTGGTAGTGGATT
5625558 AGTGGATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.40
18 1 0.03
20 17 0.57
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (18 bp):
TTGGTAGTGGATTGTTGG
Found at i:5625544 original size:17 final size:17
Alignment explanation
Indices: 5625508--5625557 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
5625498 TGGCTTAAAA
5625508 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGA---TTGTTG
5625528 TTGGTAGTGGATTGTTG
1 TTGGTAGTGGATTGTTG
*
5625545 GTGGTAGTGGATT
1 TTGGTAGTGGATT
5625558 AGTGGATGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 18 0.62
20 11 0.38
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (17 bp):
TTGGTAGTGGATTGTTG
Found at i:5630172 original size:20 final size:20
Alignment explanation
Indices: 5630147--5630196 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
5630137 TGGCTTAAAA
5630147 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
5630167 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
5630184 GTGGTAGTGGATT
1 TTGGTAGTGGATT
5630197 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:5633100 original size:13 final size:13
Alignment explanation
Indices: 5633082--5633109 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5633072 CTTCATACTT
5633082 AACTATAACAAAA
1 AACTATAACAAAA
5633095 AACTATAACAAAA
1 AACTATAACAAAA
5633108 AA
1 AA
5633110 GAGGAAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (13 bp):
AACTATAACAAAA
Found at i:5640342 original size:41 final size:41
Alignment explanation
Indices: 5640285--5640367 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
5640275 CTGAAGATCA
5640285 ATAGCATGCTCGCAATAATACTACTGTTTCTTTTGTTTTCG
1 ATAGCATGCTCGCAATAATACTACTGTTTCTTTTGTTTTCG
5640326 ATAGCATGCTCGCAATAATACTACTGTTTCTTTTGTTTTCG
1 ATAGCATGCTCGCAATAATACTACTGTTTCTTTTGTTTTCG
5640367 A
1 A
5640368 CTTGCTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.43
Consensus pattern (41 bp):
ATAGCATGCTCGCAATAATACTACTGTTTCTTTTGTTTTCG
Found at i:5657397 original size:46 final size:45
Alignment explanation
Indices: 5657372--5657631 Score: 224
Period size: 46 Copynumber: 5.4 Consensus size: 45
5657362 GATCAAGTGA
* * *
5657372 CAAGTGGA-AAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGAT
1 CAAGT-GACAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGAT
* *
5657417 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTATAGCTACACTTATCTGAT
*
5657463 CAAGTGACAAGTGGA-AAGTGATAAG-TATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGACAAGT-GATAAGTGAT-AGCTATA------GCTACACTTATCTGAT
*
5657514 CAAGTGACAAAGTGATAAGTGATAGCT-TCGGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGAT
*
5657560 CAAGTGACAAGTGAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGAC------AAGTGATAAGTGATAGCTATAGCTACACTTATCTGAT
*
5657611 CAAGAGACAAAGTGATAAGTG
1 CAAGTGAC-AAGTGATAAGTG
5657632 GCTACACTTA
Statistics
Matches: 183, Mismatches: 11, Indels: 41
0.78 0.05 0.17
Matches are distributed among these distances:
44 2 0.01
45 18 0.10
46 79 0.43
47 1 0.01
51 70 0.38
52 13 0.07
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
CAAGTGACAAGTGATAAGTGATAGCTATAGCTACACTTATCTGAT
Found at i:5657515 original size:51 final size:51
Alignment explanation
Indices: 5657425--5657631 Score: 282
Period size: 51 Copynumber: 4.1 Consensus size: 51
5657415 ATCAAGTGAC
* *
5657425 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
* *
5657477 AAAGTGATAAGT-ATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
5657522 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
5657573 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGTG
5657625 ATAAGTG
1 A-AAGTG
5657632 GCTACACTTA
Statistics
Matches: 139, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
45 12 0.09
46 32 0.23
51 72 0.52
52 18 0.13
53 5 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:5657558 original size:97 final size:98
Alignment explanation
Indices: 5657313--5657632 Score: 554
Period size: 97 Copynumber: 3.3 Consensus size: 98
5657303 TTTGAGTACT
5657313 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
5657378 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
5657411 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
5657476 GAAAGTGATAAGT-ATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* **
5657508 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* ** *
5657572 GAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
5657605 TCTGATCAAGAGACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
5657633 CTACACTTAT
Statistics
Matches: 213, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
96 13 0.06
97 122 0.57
98 78 0.37
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:5657639 original size:37 final size:37
Alignment explanation
Indices: 5657595--5657740 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
5657585 GATAGCTTTA
*
5657595 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
5657632 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
5657669 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
5657706 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
5657741 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:5659069 original size:58 final size:58
Alignment explanation
Indices: 5658992--5659159 Score: 237
Period size: 58 Copynumber: 3.0 Consensus size: 58
5658982 CATGTGAACA
5658992 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
5659051 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATA--
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
* * *
5659107 TGTG--A--T--TT-CGTGTAAGACCATAGTTGGGCTATGGCATCGGTATGTGATTTG
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
5659158 TG
1 TG
5659160 ATTACGTGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
49 38 0.37
50 2 0.02
51 2 0.02
52 1 0.01
54 1 0.01
56 4 0.04
58 51 0.49
59 5 0.05
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (58 bp):
TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
Found at i:5659101 original size:28 final size:28
Alignment explanation
Indices: 5659011--5659101 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
5659001 GTGATTCCGT
5659011 GTAAGACCATAGCTGGGCTATGGCATCG
1 GTAAGACCATAGCTGGGCTATGGCATCG
** * *
5659039 GTAAG-TGATATG-TGTGATATGTG-ATTCCG
1 GTAAGACCATA-GCTGGGCTATG-GCA-T-CG
5659068 TGTAAGACCATAGCTGGGCTATGGCATCG
1 -GTAAGACCATAGCTGGGCTATGGCATCG
5659097 GTAAG
1 GTAAG
5659102 TGATATGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 11 0.23
28 13 0.28
29 4 0.09
30 8 0.17
31 11 0.23
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
GTAAGACCATAGCTGGGCTATGGCATCG
Found at i:5659124 original size:49 final size:49
Alignment explanation
Indices: 5659052--5659194 Score: 232
Period size: 49 Copynumber: 2.9 Consensus size: 49
5659042 AGTGATATGT
* *
5659052 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
5659101 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
5659150 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
5659195 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:5662383 original size:46 final size:44
Alignment explanation
Indices: 5662358--5662729 Score: 307
Period size: 46 Copynumber: 8.5 Consensus size: 44
5662348 GATCAAGTGA
* * *
5662358 CAAGTGGA-AAGTGATAAGTAATAGCTTCGGCTATACTTATCTGAT
1 CAAGT-GACAAGTGATAAGTGATAGCTT-AGCTACACTTATCTGAT
* * * *
5662403 CAAGTGATAAAGTGATAAGTTATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGA-CAAGTGATAAGTGATAGCTT-AGCTACACTTATCTGAT
5662449 CAAGTGACAAAGTGATAAGTG-TAGCTTAGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTTAGCTACACTTATCTGAT
*
5662493 CAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
1 CAAGTGAC-------AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGAT
*
5662545 CAAGTGACAAAGTGATAAGTGATAGCTTCGGCTA-ACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGAT
* *
5662590 CAAGAGATAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGA-CAAGTGATAAGTGATAGC-TTAGCTACACTTATCTGAT
*
5662636 CAAGAGACAAAGTGATAA--G-T-G----GCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTTAGCTACACTTATCTGAT
* *
5662673 CAA--GA-AA--CA-AAGTGATAG--TGGCTACACTTATCTGAT
1 CAAGTGACAAGTGATAAGTGATAGCTTAGCTACACTTATCTGAT
*
5662709 C-AGGGACAAGTGATAAGTGAT
1 CAAGTGACAAGTGATAAGTGAT
5662730 CATACGTAAG
Statistics
Matches: 288, Mismatches: 12, Indels: 58
0.80 0.03 0.16
Matches are distributed among these distances:
30 2 0.01
31 1 0.00
32 1 0.00
33 3 0.01
34 1 0.00
35 3 0.01
36 17 0.06
37 21 0.07
38 2 0.01
40 1 0.00
41 7 0.02
42 1 0.00
43 1 0.00
44 26 0.09
45 49 0.17
46 109 0.38
50 13 0.05
51 6 0.02
52 24 0.08
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (44 bp):
CAAGTGACAAGTGATAAGTGATAGCTTAGCTACACTTATCTGAT
Found at i:5662384 original size:52 final size:48
Alignment explanation
Indices: 5662299--5662656 Score: 431
Period size: 46 Copynumber: 7.6 Consensus size: 48
5662289 TTTGAGTACT
* **
5662299 TCTGATCAAGTGAC--AAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
5662345 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGAC-A-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
5662397 TCTGATCAAGTG--ATAAAGTGATAAGTTATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
5662443 TCTGATCAAGTGAC--AAAGTGATAAGTG-TAGCTT-AGCTACACTTA
1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
5662487 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGAC-A-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
5662539 TCTGATCAAGTGAC--AAAGTGATAAGTGATAGCTTCGGCTA-ACTTA
1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
5662584 TCTGATCAA--GAGATAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
5662630 TCTGATCAAGAGAC--AAAGTGATAAGTG
1 TCTGATCAAGTGACATAAAGTGATAAGTG
5662657 GCTACACTTA
Statistics
Matches: 277, Mismatches: 14, Indels: 42
0.83 0.04 0.13
Matches are distributed among these distances:
43 2 0.01
44 23 0.08
45 44 0.16
46 122 0.44
48 3 0.01
49 1 0.00
50 13 0.05
51 6 0.02
52 63 0.23
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (48 bp):
TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:5662513 original size:142 final size:142
Alignment explanation
Indices: 5662299--5662645 Score: 597
Period size: 142 Copynumber: 2.4 Consensus size: 142
5662289 TTTGAGTACT
5662299 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGT-GTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* * *
5662364 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTTATAGC
65 GAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGC
5662429 TTCGGCTATACTTA
130 TTCGGCTA-ACTTA
5662443 TCTGATCAAGTGACAAAGTGATAAGTGTAGC-TTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
*
5662507 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
66 AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
5662572 TCGGCTAACTTA
131 TCGGCTAACTTA
* * *
5662584 TCTGATCAAGAGATAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGTGACAAAGTGATAAGTG-TAGCTTTAGCTACACTTATCTGATCAAGTGACAA
5662646 AGTGATAAGT
Statistics
Matches: 194, Mismatches: 7, Indels: 5
0.94 0.03 0.02
Matches are distributed among these distances:
141 30 0.15
142 105 0.54
143 33 0.17
144 26 0.13
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (142 bp):
TCTGATCAAGTGACAAAGTGATAAGTGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
TCGGCTAACTTA
Found at i:5662634 original size:187 final size:189
Alignment explanation
Indices: 5662313--5662656 Score: 539
Period size: 187 Copynumber: 1.8 Consensus size: 189
5662303 ATCAAGTGAC
* *
5662313 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-----GAAAGTGATAAGTA
* * * *
5662378 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTTATAGCTTCGGCTATACTTA
61 ATAGCTTCGGCTATACTTATCTGATCAAGAGATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
5662443 TCTGATCAAGTGACAAAGTGATAAGTGTAGCTTAGCTACACTTATCTGATCAAGTGACAAGTGG
126 TCTGATCAAGAGACAAAGTGATAAGTGTAGCTTAGCTACACTTATCTGATCAAGTGACAAGTGG
* *
5662507 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAAGTGATAAGTGATAGC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACGAAAGTGATAAGTAATAGC
*
5662571 TTCGGCTA-ACTTATCTGATCAAGAGATAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGA
66 TTCGGCTATACTTATCTGATCAAGAGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGA
5662635 TCAAGAGACAAAGTGATAAGTG
131 TCAAGAGACAAAGTGATAAGTG
5662657 GCTACACTTA
Statistics
Matches: 140, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
187 72 0.51
188 25 0.18
194 43 0.31
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (189 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACGAAAGTGATAAGTAATAGC
TTCGGCTATACTTATCTGATCAAGAGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGA
TCAAGAGACAAAGTGATAAGTGTAGCTTAGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:5662670 original size:37 final size:37
Alignment explanation
Indices: 5662620--5662727 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
5662610 GATAGCTTTA
5662620 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
5662657 GCTACACTTATCTGATCAAGAAACAAAGTGAT-AGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
5662693 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
5662728 ATCATACGTA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
34 7 0.10
35 8 0.12
36 21 0.31
37 31 0.46
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:5667623 original size:21 final size:20
Alignment explanation
Indices: 5667599--5667644 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
5667589 ATAATATTAT
5667599 TAAAAATTAT--TATCATATA
1 TAAAAATTATACTAT-ATATA
*
5667618 TATAAATTTATACTATATATA
1 TA-AAAATTATACTATATATA
5667639 TAAAAA
1 TAAAAA
5667645 CATTTTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.09
20 10 0.45
21 7 0.32
22 3 0.14
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAATTATACTATATATA
Found at i:5669843 original size:11 final size:11
Alignment explanation
Indices: 5669824--5669856 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5669814 GAAGATATGA
5669824 ATTTTAAAAAT
1 ATTTTAAAAAT
*
5669835 ATTTCAAAAA-
1 ATTTTAAAAAT
5669845 ATTTTAAAAAT
1 ATTTTAAAAAT
5669856 A
1 A
5669857 ATTATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:5674620 original size:24 final size:24
Alignment explanation
Indices: 5674592--5674640 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5674582 TCTCCATTGC
5674592 ACACATCCAAATTTTTTGCATGCA
1 ACACATCCAAATTTTTTGCATGCA
5674616 ACACATCCAAATTTTTTGCATGCA
1 ACACATCCAAATTTTTTGCATGCA
5674640 A
1 A
5674641 AATTCATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (24 bp):
ACACATCCAAATTTTTTGCATGCA
Found at i:5695721 original size:21 final size:21
Alignment explanation
Indices: 5695695--5695735 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5695685 ATCTGCTCAA
* *
5695695 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5695716 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5695736 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5708704 original size:12 final size:12
Alignment explanation
Indices: 5708689--5708719 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5708679 TTCTCTTTTA
5708689 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
5708701 TTTTTCTTTCTC
1 TTTTTCTTTCCC
5708713 TTTTTCT
1 TTTTTCT
5708720 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:5709995 original size:21 final size:20
Alignment explanation
Indices: 5709971--5710010 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5709961 ACTTGTTTAA
5709971 CTATCAACAACCATTCAAAAT
1 CTATCAACAACCA-TCAAAAT
* *
5709992 CTATCATCAATCATCAAAA
1 CTATCAACAACCATCAAAA
5710011 ATCATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (20 bp):
CTATCAACAACCATCAAAAT
Found at i:5711181 original size:27 final size:26
Alignment explanation
Indices: 5711144--5711258 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
5711134 AGCATGGCTG
* *
5711144 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
5711170 CCAGATACAGATAATCGTGGTAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
5711198 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
5711225 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
5711252 CCAGAAC
1 CCAGAAC
5711259 GCTTCCTCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
26 5 0.06
27 57 0.73
28 16 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5711203 original size:54 final size:54
Alignment explanation
Indices: 5711144--5711258 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
5711134 AGCATGGCTG
* *
5711144 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGTAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
5711198 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
5711252 CCAGAAC
1 CCAGAAC
5711259 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:5711424 original size:28 final size:26
Alignment explanation
Indices: 5711364--5711434 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 26
5711354 TTAACCCTAC
* * *
5711364 GGGTATAACGGTAATTTTGCACCTAG
1 GGGTATAACAGTAATTTTCCACATAG
5711390 GGGTATAACAGTAATTTTCCATACATAG
1 GGGTATAACAGTAATTTTCC--ACATAG
*
5711418 GGGTATAATAGTAATTT
1 GGGTATAACAGTAATTT
5711435 AGCTACTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 18 0.46
28 21 0.54
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (26 bp):
GGGTATAACAGTAATTTTCCACATAG
Found at i:5712912 original size:26 final size:26
Alignment explanation
Indices: 5712876--5712985 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
5712866 CATGAAATTC
5712876 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5712902 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
5712928 TTATCATGGAATATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
5712954 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5712980 TTATCA
1 TTATCA
5712986 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5727109 original size:58 final size:58
Alignment explanation
Indices: 5727036--5727154 Score: 220
Period size: 58 Copynumber: 2.1 Consensus size: 58
5727026 TATCTAAAGA
5727036 TGTTAGTGCCATTGATGATCTAAGCCTTCTCTTTTTGTAACGACCTGAAAGTGAATGG
1 TGTTAGTGCCATTGATGATCTAAGCCTTCTCTTTTTGTAACGACCTGAAAGTGAATGG
* *
5727094 TGTTAGTGTCGTTGATGATCTAAGCCTTCTCTTTTTGTAACGACCTGAAAGTGAATGG
1 TGTTAGTGCCATTGATGATCTAAGCCTTCTCTTTTTGTAACGACCTGAAAGTGAATGG
5727152 TGT
1 TGT
5727155 CAAAAAAAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.38
Consensus pattern (58 bp):
TGTTAGTGCCATTGATGATCTAAGCCTTCTCTTTTTGTAACGACCTGAAAGTGAATGG
Found at i:5728447 original size:106 final size:106
Alignment explanation
Indices: 5728320--5728529 Score: 384
Period size: 106 Copynumber: 2.0 Consensus size: 106
5728310 TGCTGCTTTG
* *
5728320 TGCATGGACTAATGAATTGATGATGAGATTGTGCTATAAATTGAGATATTGATGTATAAATGAAA
1 TGCATGGACTAATGAATTGATGACGAGATTGTGCTATAAATTGAGATATTGACGTATAAATGAAA
5728385 TTGAGAAATGGTTACCCTATTAATTGTTCAAGCAGGGTCTA
66 TTGAGAAATGGTTACCCTATTAATTGTTCAAGCAGGGTCTA
*
5728426 TGCATGGACTAATGAATTGATGACGATATTGTGCTATAAATTGAGATATTGACGTATAAATGAAA
1 TGCATGGACTAATGAATTGATGACGAGATTGTGCTATAAATTGAGATATTGACGTATAAATGAAA
*
5728491 TTGAGAAATGGTTACCCTATTAATTGTTCAGGCAGGGTC
66 TTGAGAAATGGTTACCCTATTAATTGTTCAAGCAGGGTC
5728530 AAGTATAATT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 100 1.00
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (106 bp):
TGCATGGACTAATGAATTGATGACGAGATTGTGCTATAAATTGAGATATTGACGTATAAATGAAA
TTGAGAAATGGTTACCCTATTAATTGTTCAAGCAGGGTCTA
Found at i:5737397 original size:27 final size:25
Alignment explanation
Indices: 5737372--5737419 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
5737362 TTTCTTTTAA
5737372 AACTACTGAAATTATATTTATATTT
1 AACTACTGAAATTATATTTATATTT
* *
5737397 AAGTGCTGAAATTATATTTATAT
1 AACTACTGAAATTATATTTATAT
5737420 ATATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (25 bp):
AACTACTGAAATTATATTTATATTT
Found at i:5743115 original size:20 final size:20
Alignment explanation
Indices: 5743090--5743127 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5743080 TGTTGGTTAG
*
5743090 ATATTTTAAAATTAAAAATA
1 ATATTTAAAAATTAAAAATA
5743110 ATATTTAAAAATTAAAAA
1 ATATTTAAAAATTAAAAA
5743128 AAAAAATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATTTAAAAATTAAAAATA
Found at i:5746818 original size:78 final size:78
Alignment explanation
Indices: 5746684--5746835 Score: 268
Period size: 78 Copynumber: 1.9 Consensus size: 78
5746674 GTCGTGACTT
*
5746684 GTAGGATATGATGCAACTCTTCAACCTTCATGTACAACTCATTGAACTTGTACACAAGAGACAAC
1 GTAGGAGATGATGCAACTCTTCAACCTTCATGTACAACTCATTGAACTTGTACACAAGAGACAAC
5746749 AACAATGCAACTC
66 AACAATGCAACTC
* *
5746762 GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAACTCATTGAACTTGTGCACAAGAGACAAC
1 GTAGGAGATGATGCAACTCTTCAACCTTCATGTACAACTCATTGAACTTGTACACAAGAGACAAC
*
5746827 AACTATGCA
66 AACAATGCA
5746836 GGGAGTACTC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.24
Consensus pattern (78 bp):
GTAGGAGATGATGCAACTCTTCAACCTTCATGTACAACTCATTGAACTTGTACACAAGAGACAAC
AACAATGCAACTC
Found at i:5749738 original size:6 final size:6
Alignment explanation
Indices: 5749727--5749760 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5749717 TGGAAGCCCC
5749727 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
5749761 CCTGTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:5751504 original size:30 final size:30
Alignment explanation
Indices: 5751460--5751521 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
5751450 ATATTATGTT
5751460 ATAAAATTATTATA-TTA-ATTATATATTTAA
1 ATAAAATTATTATATTTATATT-TATA-TTAA
5751490 ATAATAATTA-TATATTTATATTTATATTAA
1 ATAA-AATTATTATATTTATATTTATATTAA
5751520 AT
1 AT
5751522 CACTAACCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
30 14 0.48
31 12 0.41
32 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATAAAATTATTATATTTATATTTATATTAA
Found at i:5751518 original size:19 final size:18
Alignment explanation
Indices: 5751469--5751518 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
5751459 TATAAAATTA
5751469 TTATATTA-ATTATATAT
1 TTATATTATATTATATAT
* *
5751486 TTAAATAATAATTATATAT
1 TTATATTAT-ATTATATAT
5751505 TTATATTTATATTA
1 TTATA-TTATATTA
5751519 AATCACTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.23
19 17 0.65
20 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATATTATATTATATAT
Found at i:5753804 original size:10 final size:10
Alignment explanation
Indices: 5753789--5753818 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5753779 AAACAAACAC
5753789 ACATATATAT
1 ACATATATAT
5753799 ACATATATAT
1 ACATATATAT
*
5753809 ATATATATAT
1 ACATATATAT
5753819 TTTTCTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
ACATATATAT
Found at i:5755238 original size:3 final size:3
Alignment explanation
Indices: 5755230--5755378 Score: 87
Period size: 3 Copynumber: 50.0 Consensus size: 3
5755220 TAGTACCATG
* * * *
5755230 ATA ATA ATA ACA ATA ATA ATA ATA A-A ATA ATA AAA ATA ACA AT- ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* ** *
5755276 TTA CCA ATA ATA ATA ATAA ATAA ATA ATG ATA ATAA ATA TATA A-A ATA
1 ATA ATA ATA ATA ATA AT-A AT-A ATA ATA ATA AT-A ATA -ATA ATA ATA
* * *
5755324 ATA GTA ACA GTA ATA A-A ATA A-A TATA AT- ATA ATA A-A TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA ATA
*
5755367 ATA ATA ACA ATA
1 ATA ATA ATA ATA
5755379 TTTAAAAATA
Statistics
Matches: 112, Mismatches: 22, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
2 12 0.11
3 85 0.76
4 15 0.13
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:5755310 original size:13 final size:12
Alignment explanation
Indices: 5755282--5755372 Score: 62
Period size: 14 Copynumber: 7.1 Consensus size: 12
5755272 TATGTTACCA
5755282 ATAAT-AATAAT
1 ATAATAAATAAT
5755293 A-AATAAATAAT
1 ATAATAAATAAT
5755304 GATAATAAATATAT
1 -ATAATAAATA-AT
* *
5755318 AAAATAATAGTAAC
1 ATAATAA-A-TAAT
5755332 AGTAATAAAATAAAT
1 A-TAAT-AAAT-AAT
5755347 ATAATATAATAAAT
1 ATAATA-AAT-AAT
5755361 ATAAT-AATAAT
1 ATAATAAATAAT
5755372 A
1 A
5755373 ACAATATTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
10 3 0.05
11 11 0.17
12 4 0.06
13 15 0.23
14 22 0.33
15 9 0.14
16 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (12 bp):
ATAATAAATAAT
Found at i:5755378 original size:17 final size:16
Alignment explanation
Indices: 5755282--5755379 Score: 80
Period size: 17 Copynumber: 6.1 Consensus size: 16
5755272 TATGTTACCA
*
5755282 ATAATAATAATAAATAA
1 ATAATAATAATAAA-AT
*
5755299 ATAATGATAATAAATAT
1 ATAATAATAATAAA-AT
* *
5755316 ATAA-AATAATAGTAAC
1 ATAATAATAATA-AAAT
5755332 AGTAATAA-AAT-AAAT
1 A-TAATAATAATAAAAT
5755347 ATAAT-ATAAT-AAAT
1 ATAATAATAATAAAAT
5755361 ATAATAATAATAACAAT
1 ATAATAATAATAA-AAT
5755378 AT
1 AT
5755380 TTAAAAATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
13 1 0.01
14 16 0.24
15 8 0.12
16 9 0.13
17 31 0.46
18 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (16 bp):
ATAATAATAATAAAAT
Found at i:5755771 original size:17 final size:17
Alignment explanation
Indices: 5755749--5755787 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5755739 CATGGTGGCA
5755749 AGTGGGGTAATGG-GATT
1 AGTGGGGTAATGGAG-TT
*
5755766 AGTGGGGTGATGGAGTT
1 AGTGGGGTAATGGAGTT
5755783 AGTGG
1 AGTGG
5755788 CAAGTAGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.21, C:0.00, G:0.51, T:0.28
Consensus pattern (17 bp):
AGTGGGGTAATGGAGTT
Found at i:5756179 original size:21 final size:22
Alignment explanation
Indices: 5756139--5756181 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5756129 CTTTTTAATA
*
5756139 ATTTATAATATTCTAAAATATT
1 ATTTATAAAATTCTAAAATATT
*
5756161 ATTTTTAAAATTC-AAAATATT
1 ATTTATAAAATTCTAAAATATT
5756182 TTGAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTATAAAATTCTAAAATATT
Found at i:5757420 original size:29 final size:29
Alignment explanation
Indices: 5757387--5757444 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5757377 ATTATTTTAA
5757387 TTGCATAATAACAAGGTTATATGATACAC
1 TTGCATAATAACAAGGTTATATGATACAC
5757416 TTGCATAATAACAAGGTTATATGATACAC
1 TTGCATAATAACAAGGTTATATGATACAC
5757445 CAAGTATGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (29 bp):
TTGCATAATAACAAGGTTATATGATACAC
Found at i:5762405 original size:28 final size:27
Alignment explanation
Indices: 5762355--5762411 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
5762345 GCAAATGATT
**
5762355 AAGTATTGATAATATTCGTTCATCAAAA
1 AAGTATTGATAATATTCCATCAT-AAAA
*
5762383 AAGTATTGATACTATTCCATCATAAAA
1 AAGTATTGATAATATTCCATCATAAAA
5762410 AA
1 AA
5762412 TTTGGATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (27 bp):
AAGTATTGATAATATTCCATCATAAAA
Found at i:5762816 original size:31 final size:29
Alignment explanation
Indices: 5762778--5762851 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
5762768 TCTACCAAAA
**
5762778 TAGTCACTTATGTTTGCCTCAGGTTACATTT
1 TAGTCACTTATGTTTG--AAAGGTTACATTT
* *
5762809 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAAGGTTACATTT
5762838 TAGTCACTTATGTT
1 TAGTCACTTATGTT
5762852 ACTATTTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.59
31 16 0.41
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAAGGTTACATTT
Found at i:5763886 original size:31 final size:29
Alignment explanation
Indices: 5763817--5763888 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
5763807 ACAAAATAAT
*
5763817 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATTGCA
* *
5763846 AACATAAGTGACTAAAATGTAACCTGATGCA
1 AACATAAGTGACTAAAACGTAACAT--TGCA
*
5763877 AACAAAAGTGAC
1 AACATAAGTGAC
5763889 AATTTTTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 23 0.62
31 14 0.38
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATTGCA
Found at i:5765987 original size:20 final size:20
Alignment explanation
Indices: 5765953--5766001 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
5765943 TTTTGTTGAT
*
5765953 CTTATATTACATTTTAGTCA
1 CTTATGTTACATTTTAGTCA
*
5765973 -TTCATGTTACGTTTTAGTCA
1 CTT-ATGTTACATTTTAGTCA
5765993 CTTATGTTA
1 CTTATGTTA
5766002 TTGTTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.51
Consensus pattern (20 bp):
CTTATGTTACATTTTAGTCA
Found at i:5766823 original size:10 final size:11
Alignment explanation
Indices: 5766801--5766826 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5766791 AGTATGGGCC
5766801 AACTTTTTAAA
1 AACTTTTTAAA
5766812 AACTTTTTAAA
1 AACTTTTTAAA
5766823 AACT
1 AACT
5766827 CTTATAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (11 bp):
AACTTTTTAAA
Found at i:5767651 original size:18 final size:18
Alignment explanation
Indices: 5767625--5767659 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5767615 AAATTATTTT
*
5767625 CTTAAAATTAGAATTATG
1 CTTAAAATTACAATTATG
*
5767643 CTTATAATTACAATTAT
1 CTTAAAATTACAATTAT
5767660 TATATTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (18 bp):
CTTAAAATTACAATTATG
Found at i:5767766 original size:3 final size:3
Alignment explanation
Indices: 5767758--5767782 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5767748 ATCTAGTTTT
5767758 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
5767783 GCAATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5769344 original size:32 final size:32
Alignment explanation
Indices: 5769298--5769377 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
5769288 TGTCAATCAC
*
5769298 TTCAATATCCAACAAGCTT-AAAACATAATAAA
1 TTCAATATCCAACAA-ATTCAAAACATAATAAA
* * *
5769330 TTCAATATCTAACAAATTCAAGACATAATAAT
1 TTCAATATCCAACAAATTCAAAACATAATAAA
*
5769362 TTCAAAATCCAACAAA
1 TTCAATATCCAACAAA
5769378 CTAAAATTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 2 0.05
32 39 0.95
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.26
Consensus pattern (32 bp):
TTCAATATCCAACAAATTCAAAACATAATAAA
Found at i:5774754 original size:28 final size:29
Alignment explanation
Indices: 5774695--5774760 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
5774685 TCTAACGAAC
* *
5774695 AACAAGCATAAACTTTATGCAAAACCCAGA
1 AACAAACATAAACTCTA-GCAAAACCCAGA
*
5774725 AACAAACATAAACTCTA-CAAAATCCAGA
1 AACAAACATAAACTCTAGCAAAACCCAGA
5774753 AACAAACA
1 AACAAACA
5774761 GATTAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 18 0.55
30 15 0.45
ACGTcount: A:0.56, C:0.24, G:0.06, T:0.14
Consensus pattern (29 bp):
AACAAACATAAACTCTAGCAAAACCCAGA
Found at i:5785251 original size:3 final size:3
Alignment explanation
Indices: 5785243--5785433 Score: 95
Period size: 3 Copynumber: 65.0 Consensus size: 3
5785233 TGTCTAACAC
* * * *
5785243 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAC TAT TAT TAC TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * *
5785291 TTT TAT TAA CAT TAA CAT TAA CAT TAG TAT TAT TAT TTT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
5785338 T-T TAT TAT CAT TAT CAT TCT TGT AAT TAT TAT TAC TAT TCT T-T TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
5785384 TAT TAT TAT T-T AACA TAC TAT TAT TAC TAT T-G TAT TAT TAC TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5785428 TAT TAT
1 TAT TAT
5785434 ATTTTCATCT
Statistics
Matches: 131, Mismatches: 51, Indels: 12
0.68 0.26 0.06
Matches are distributed among these distances:
2 8 0.06
3 122 0.93
4 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:5785421 original size:14 final size:14
Alignment explanation
Indices: 5785402--5785428 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5785392 TTTAACATAC
5785402 TATTATTACTATTG
1 TATTATTACTATTG
5785416 TATTATTACTATT
1 TATTATTACTATT
5785429 ATTATATTTT
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:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (14 bp):
TATTATTACTATTG
Found at i:5785476 original size:15 final size:14
Alignment explanation
Indices: 5785456--5785490 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
5785446 GTTTATTTTA
5785456 TTATTTATCTAATTT
1 TTATTTATCT-ATTT
5785471 TTATTTATCTATTT
1 TTATTTATCTATTT
*
5785485 ATATTT
1 TTATTT
5785491 CTGTTATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTATCTATTT
Found at i:5785590 original size:18 final size:17
Alignment explanation
Indices: 5785546--5785592 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 17
5785536 GTATAAATAT
5785546 CATTATTTTATTATT-G
1 CATTATTTTATTATTAG
5785562 C--TATTTT-TTATTAG
1 CATTATTTTATTATTAG
5785576 CATTATATTTATTATTA
1 CATTAT-TTTATTATTA
5785593 TTATTTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.19
14 8 0.31
16 4 0.15
17 3 0.12
18 6 0.23
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (17 bp):
CATTATTTTATTATTAG
Found at i:5785828 original size:44 final size:44
Alignment explanation
Indices: 5785778--5785870 Score: 186
Period size: 44 Copynumber: 2.1 Consensus size: 44
5785768 TGTTTGTTTT
5785778 CATATTCTCGTATTCCTTATTGTCATTCATGCTAGCACATTTAC
1 CATATTCTCGTATTCCTTATTGTCATTCATGCTAGCACATTTAC
5785822 CATATTCTCGTATTCCTTATTGTCATTCATGCTAGCACATTTAC
1 CATATTCTCGTATTCCTTATTGTCATTCATGCTAGCACATTTAC
5785866 CATAT
1 CATAT
5785871 CGTTATGCGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.24, C:0.25, G:0.09, T:0.43
Consensus pattern (44 bp):
CATATTCTCGTATTCCTTATTGTCATTCATGCTAGCACATTTAC
Found at i:5791042 original size:6 final size:6
Alignment explanation
Indices: 5791031--5791055 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5791021 TTTTCTTTAT
5791031 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
5791056 GATATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Done.