Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 15 of 79
Found at i:5026357 original size:30 final size:30
Alignment explanation
Indices: 5026289--5026376 Score: 151
Period size: 31 Copynumber: 2.9 Consensus size: 30
5026279 GAATATAAAC
5026289 TATA-TTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTTATTTTTAAAATACACTACA
5026318 TATATTTTTTTTATTTTTAAAATACACTACA
1 TATA-TTTTTTTATTTTTAAAATACACTACA
*
5026349 TATATTTTTTAATTTTTAAAATACACTA
1 TATATTTTTTTATTTTTAAAATACACTA
5026377 ATACAGTGCA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
29 4 0.07
30 23 0.41
31 29 0.52
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (30 bp):
TATATTTTTTTATTTTTAAAATACACTACA
Found at i:5028949 original size:21 final size:21
Alignment explanation
Indices: 5028925--5028997 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
5028915 CAAAAAATAG
* *
5028925 GGGAGAAACCAGCAAAAACGA
1 GGGAGAAACCAGCAAGAACAA
* *
5028946 GGGACAAACCAACAAGAACAA
1 GGGAGAAACCAGCAAGAACAA
5028967 GGGAGAAACCAGCAAGAACAA
1 GGGAGAAACCAGCAAGAACAA
5028988 GGGGAGAAAC
1 -GGGAGAAAC
5028998 TGCTGTTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
21 36 0.80
22 9 0.20
ACGTcount: A:0.52, C:0.19, G:0.29, T:0.00
Consensus pattern (21 bp):
GGGAGAAACCAGCAAGAACAA
Found at i:5031624 original size:14 final size:14
Alignment explanation
Indices: 5031591--5031617 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5031581 AATGCCTTTA
5031591 AAAATAATAGTAAC
1 AAAATAATAGTAAC
5031605 AAAATAATAGTAA
1 AAAATAATAGTAA
5031618 TATAATAGTA
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:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAATAATAGTAAC
Found at i:5034373 original size:204 final size:203
Alignment explanation
Indices: 5033997--5034598 Score: 839
Period size: 204 Copynumber: 3.0 Consensus size: 203
5033987 AAGGTTTAAT
* *
5033997 GTGTAAAACCATA-TCTCGACTATGGA-AACCAATAGAGTCTGCTAGGATATTAAACATGGGGTT
1 GTGTAAGACCATAGT-TCGACTAT-GACAACCAATAGAGTCTGC-AGGACATTAAACATGGGGTT
* * * * ** *
5034060 ATAAGGTGTAAGACCATAGCTCAACTATGGCAACTAATGGAGTCTGCCAAGACATTAAACATGGG
63 ATAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGG
*
5034125 GTTACAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACAT
128 GTTACAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACGTTAAACAT
5034190 GAAGTTACAAA
193 GAAGTTACAAA
* * *
5034201 GTGTAAGACCATAGTTCGGCTATGACAACCAATAGGGTCCGTCAGGACATTAAACATGGGGTTAT
1 GTGTAAGACCATAGTTCGACTATGACAACCAATAGAGTCTG-CAGGACATTAAACATGGGGTTAT
* *
5034266 AAGGTGTAAGACCATAGCTCGGCTATAACAACCAATAGAGTCCACCAAAACATTAAACATGGGGT
65 AAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGGGT
* * * *
5034331 TACAAGGTGTAAGACCATAGCTTGTCTATGACAACCAATAGAGTTTGCCAGGACGTTAAACATAA
130 TACAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACGTTAAACATGA
*
5034396 AGTTACAAG
195 AGTTACAAA
* * * * * * * *
5034405 GTGTAAGACTATAGCTCGTCTATGGCAACCAATAGAGTTTGCCAGGACGTTAAACATGGAGTTAC
1 GTGTAAGACCATAGTTCGACTATGACAACCAATAGAGTCTG-CAGGACATTAAACATGGGGTTAT
*
5034470 AAGGTGTAAGACCATAGCTTGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGGGT
65 AAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGGGT
* * * * *
5034535 TATAAGGTGTAAGACCATAGCTCGGCTATGGCAACCAATAGAGTCTGCTAGGACGTTAAGCATG
130 TACAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACGTTAAACATG
5034599 GGCTTAGACT
Statistics
Matches: 353, Mismatches: 42, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
203 2 0.01
204 349 0.99
205 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (203 bp):
GTGTAAGACCATAGTTCGACTATGACAACCAATAGAGTCTGCAGGACATTAAACATGGGGTTATA
AGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGGGTT
ACAAGGTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACGTTAAACATGAA
GTTACAAA
Found at i:5034625 original size:68 final size:68
Alignment explanation
Indices: 5033997--5034600 Score: 751
Period size: 68 Copynumber: 8.9 Consensus size: 68
5033987 AAGGTTTAAT
* * * *
5033997 GTGTAAAACCATATCTCGACTATGGA-AACCAATAGAGTCTGCTAGGATATTAAACATGGGGTTA
1 GTGTAAGACCATAGCTCGACTAT-GACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTA
*
5034061 TAAG
65 CAAG
* * * * *
5034065 GTGTAAGACCATAGCTCAACTATGGCAACTAATGGAGTCTGCCAAGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
5034130 AAG
66 AAG
**
5034133 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGAAGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
*
5034198 AAA
66 AAG
* * * * * *
5034201 GTGTAAGACCATAGTTCGGCTATGACAACCAATAGGGTCCGTCAGGACATTAAACATGGGGTTAT
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
5034266 AAG
66 AAG
* * ** **
5034269 GTGTAAGACCATAGCTCGGCTATAACAACCAATAGAGTCCACCAAAACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
5034334 AAG
66 AAG
* * * * ***
5034337 GTGTAAGACCATAGCTTGTCTATGACAACCAATAGAGTTTGCCAGGACGTTAAACATAAAGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
5034402 AAG
66 AAG
* * * * * *
5034405 GTGTAAGACTATAGCTCGTCTATGGCAACCAATAGAGTTTGCCAGGACGTTAAACATGGAGTTAC
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
5034470 AAG
66 AAG
* ** ** *
5034473 GTGTAAGACCATAGCTTGACTATGACAACCAATAGAGTCCACCAAAACATTAAACATGGGGTTAT
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
5034538 AAG
66 AAG
* * * * *
5034541 GTGTAAGACCATAGCTCGGCTATGGCAACCAATAGAGTCTGCTAGGACGTTAAGCATGGG
1 GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGG
5034601 CTTAGACTGT
Statistics
Matches: 461, Mismatches: 74, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
67 1 0.00
68 460 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (68 bp):
GTGTAAGACCATAGCTCGACTATGACAACCAATAGAGTCTGCCAGGACATTAAACATGGGGTTAC
AAG
Found at i:5036915 original size:21 final size:21
Alignment explanation
Indices: 5036847--5036915 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
5036837 CACAAAAGCA
* *
5036847 CATAAGTGCCAAACAGAAACC
1 CATAAGAGCTAAACAGAAACC
* * * *
5036868 CATAAGGGTTGAAC-GAAAGCT
1 CATAAGAGCTAAACAGAAA-CC
*
5036889 CGTAAGAGCTAAACAGAAACC
1 CATAAGAGCTAAACAGAAACC
5036910 CATAAG
1 CATAAG
5036916 GGTTATACTG
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
20 4 0.11
21 27 0.77
22 4 0.11
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (21 bp):
CATAAGAGCTAAACAGAAACC
Found at i:5036930 original size:42 final size:41
Alignment explanation
Indices: 5036857--5036974 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 41
5036847 CATAAGTGCC
**
5036857 AAACAGAAACCCATAAGGGTTGAACGAAAGCTCGTAAGAGCT
1 AAACAGAAACCCATAAGGGTT-AACGAAAGCTCAAAAGAGCT
*
5036899 AAACAGAAACCCATAAGGGTTATACTG-AAGCTTAAAAGAGCT
1 AAACAGAAACCCATAAGGGTTA-AC-GAAAGCTCAAAAGAGCT
* * * * *
5036941 GAATAAAAACCCATTAGGGTTAAACGAAAACTCA
1 AAACAGAAACCCATAAGGGTT-AACGAAAGCTCA
5036975 TATGAGTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
41 2 0.03
42 59 0.94
43 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.17
Consensus pattern (41 bp):
AAACAGAAACCCATAAGGGTTAACGAAAGCTCAAAAGAGCT
Found at i:5049511 original size:22 final size:22
Alignment explanation
Indices: 5049486--5049527 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5049476 TAACTAATTA
*
5049486 AATTAATGAAATAAATAATAAT
1 AATTAATGAAATAAAAAATAAT
*
5049508 AATTATTGAAATAAAAAATA
1 AATTAATGAAATAAAAAATA
5049528 TTGGGTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
AATTAATGAAATAAAAAATAAT
Found at i:5049855 original size:20 final size:20
Alignment explanation
Indices: 5049826--5049874 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5049816 AAGTAGTGAA
*
5049826 TTTATATTCTTA-GAATAAAT
1 TTTATTTTCTTAGGAAT-AAT
5049846 TTTATTTTC-TAGGAATAAT
1 TTTATTTTCTTAGGAATAAT
*
5049865 ATTATTTTCT
1 TTTATTTTCT
5049875 GGTTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (20 bp):
TTTATTTTCTTAGGAATAAT
Found at i:5053879 original size:2 final size:2
Alignment explanation
Indices: 5053872--5053899 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5053862 AAACAGAATT
5053872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5053900 ATTTGCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5058903 original size:7 final size:7
Alignment explanation
Indices: 5058866--5058893 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
5058856 AGACTCGAAT
5058866 TTAAAAA
1 TTAAAAA
5058873 TTAAAAA
1 TTAAAAA
5058880 TTAAAAA
1 TTAAAAA
5058887 TTAAAAA
1 TTAAAAA
5058894 AATTACAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:5063631 original size:20 final size:22
Alignment explanation
Indices: 5063594--5063633 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5063584 TATTTTTAAA
*
5063594 AATATAAATTGTGTAACTACTT
1 AATAAAAATTGTGTAACTACTT
5063616 AATAAAAATT-TG-AACTAC
1 AATAAAAATTGTGTAACTAC
5063634 CAAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (22 bp):
AATAAAAATTGTGTAACTACTT
Found at i:5063639 original size:20 final size:22
Alignment explanation
Indices: 5063593--5063639 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
5063583 ATATTTTTAA
* *
5063593 AAATATAAATTGTGTAACTACT
1 AAATAAAAATTGTGTAACTACC
*
5063615 TAATAAAAATT-TG-AACTACC
1 AAATAAAAATTGTGTAACTACC
5063635 AAATA
1 AAATA
5063640 TATATAGAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (22 bp):
AAATAAAAATTGTGTAACTACC
Found at i:5067200 original size:98 final size:98
Alignment explanation
Indices: 5067031--5067220 Score: 335
Period size: 98 Copynumber: 1.9 Consensus size: 98
5067021 ATATAAAAAT
*
5067031 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACGATCCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATCCC
5067096 TTTAGAATCCCAAACTCGGAATATTTCTTTTAA
66 TTTAGAATCCCAAACTCGGAATATTTCTTTTAA
* * *
5067129 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATCCC
*
5067194 TTTAGAATCTCAAACTCGGAATATTTC
66 TTTAGAATCCCAAACTCGGAATATTTC
5067221 CTTCATGATT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.27
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATCCC
TTTAGAATCCCAAACTCGGAATATTTCTTTTAA
Found at i:5067502 original size:12 final size:12
Alignment explanation
Indices: 5067485--5067509 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5067475 AACGAGCAAC
5067485 ATAATATAAATG
1 ATAATATAAATG
5067497 ATAATATAAATG
1 ATAATATAAATG
5067509 A
1 A
5067510 AAGCACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAATATAAATG
Found at i:5067753 original size:2 final size:2
Alignment explanation
Indices: 5067694--5067740 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
5067684 AAAAATACTA
*
5067694 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5067736 AT AT A
1 AT AT A
5067741 AGAGAATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5069093 original size:14 final size:14
Alignment explanation
Indices: 5069074--5069106 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5069064 GCCATGTTTG
*
5069074 TTTGGGCTACTGAA
1 TTTGGGCCACTGAA
5069088 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
5069102 TTTGG
1 TTTGG
5069107 TTTTGGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.36
Consensus pattern (14 bp):
TTTGGGCCACTGAA
Found at i:5078611 original size:19 final size:19
Alignment explanation
Indices: 5078587--5078625 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5078577 GTATCAGCAG
*
5078587 CTGGTCATTGTTAACATAT
1 CTGGTCATTATTAACATAT
*
5078606 CTGGTCGTTATTAACATAT
1 CTGGTCATTATTAACATAT
5078625 C
1 C
5078626 CAGTCATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (19 bp):
CTGGTCATTATTAACATAT
Found at i:5085254 original size:14 final size:14
Alignment explanation
Indices: 5085235--5085267 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
5085225 GCCATGTTTG
5085235 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
5085249 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
5085263 TTTGG
1 TTTGG
5085268 TTTTGGGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (14 bp):
TTTGGGCCACTGAA
Found at i:5088562 original size:21 final size:22
Alignment explanation
Indices: 5088519--5088564 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
5088509 TTGCTTTAAG
5088519 TATTAGACTAACATGTAAATTAT
1 TATTAGACTAACATG-AAATTAT
5088542 TATT-GACTGAACATG-AATTAT
1 TATTAGACT-AACATGAAATTAT
5088563 TA
1 TA
5088565 AATTTCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 8 0.36
22 4 0.18
23 10 0.45
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (22 bp):
TATTAGACTAACATGAAATTAT
Found at i:5091472 original size:36 final size:36
Alignment explanation
Indices: 5091423--5091495 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 36
5091413 CATTCACTTA
5091423 GCTTCTCTACATCTATGGCCTTTACTGAA-GTCAAGG
1 GCTTCTCTACATCTATGGCCTTTACT-AATGTCAAGG
*
5091459 GCTTCTCTTCATCTATGGCCTTTACTAATGTCAAGG
1 GCTTCTCTACATCTATGGCCTTTACTAATGTCAAGG
5091495 G
1 G
5091496 ACACTTCACG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 2 0.06
36 33 0.94
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (36 bp):
GCTTCTCTACATCTATGGCCTTTACTAATGTCAAGG
Found at i:5093776 original size:3 final size:3
Alignment explanation
Indices: 5093768--5093822 Score: 65
Period size: 3 Copynumber: 17.3 Consensus size: 3
5093758 TCATTGTCAC
* *
5093768 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CCAT CACT CTTT CTT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT -CAT CA-T C-AT CAT CAT
5093816 CAT CAT C
1 CAT CAT C
5093823 TACTACCACT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 40 0.85
4 7 0.15
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.36
Consensus pattern (3 bp):
CAT
Found at i:5093848 original size:15 final size:15
Alignment explanation
Indices: 5093824--5093853 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5093814 ATCATCATCT
5093824 ACTACCACTACCACC
1 ACTACCACTACCACC
*
5093839 ACTACTACTACCACC
1 ACTACCACTACCACC
5093854 GTGGATTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (15 bp):
ACTACCACTACCACC
Found at i:5105477 original size:547 final size:548
Alignment explanation
Indices: 5104432--5105527 Score: 2185
Period size: 547 Copynumber: 2.0 Consensus size: 548
5104422 TATATAATTT
5104432 TTTATTAAAATTTTAAATATTTTTAATACTTATATTAGAGTATTATATATTTACTTCTCATATAA
1 TTTATTAAAATTTTAAATATTTTTAATACTTATATTAGAGTATTATATATTTACTTCTCATATAA
5104497 TATAAAGATCAAATTTTGCTACTAGTCCTTGTATCATGCGTAAATCGTGGACTTAATCCATATAC
66 TATAAAGATCAAATTTTGCTACTAGTCCTTGTATCATGCGTAAATCGTGGACTTAATCCATATAC
5104562 TCTAATTAATTTAATTTTAATTCCTATATTTTTAAAATTTTGGAATATCAGTTTTGGTTCAAATG
131 TCTAATTAATTTAATTTTAATTCCTATATTTTTAAAATTTTGGAATATCAGTTTTGGTTCAAATG
5104627 GTAGCAGTTAGCTCTGCTAAGTCAAATTCTACTATCAATCCTGCACTATGTACAAGTTGTGGATT
196 GTAGCAGTTAGCTCTGCTAAGTCAAATTCTACTATCAATCCTGCACTATGTACAAGTTGTGGATT
5104692 TAATCATTGTTCCCCATTTTGATCATTTTTAATCTCCATACTTTTTAATTTTTTTGAAATTGCAA
261 TAATCATTGTTCCCCATTTTGATCATTTTTAATCTCCATACTTTTTAATTTTTTTGAAATTGCAA
5104757 CCCTAACTCAAACGATAGCCATTAATTCCATTAAATAAAATAACATGGTTTTTTTTGTGAGTATC
326 CCCTAACTCAAACGATAGCCATTAATTCCATTAAATAAAATAACATGGTTTTTTTTGTGAGTATC
5104822 ATGTGGAAATGACAATCTCATATGATATTGCACATATGATAATGAGTTTGTGTTAGGATTGAAAT
391 ATGTGGAAATGACAATCTCATATGATATTGCACATATGATAATGAGTTTGTGTTAGGATTGAAAT
5104887 CTCAAATCTTGAAAAGTGTAAGGACTAAAAAAAATACTAAATTAAAATACAAGGTTTAAATCCGA
456 CTCAAATCTTGAAAAGTGTAAGGACTAAAAAAAATACTAAATTAAAATACAAGGTTTAAATCCGA
5104952 ATCTTATGCATTGTACAAAGACTAATAG
521 ATCTTATGCATTGTACAAAGACTAATAG
5104980 TTTATTAAAA-TTTAAATATTTTTAATACTTATATTAGAGTATTATATATTTACTTCTCATATAA
1 TTTATTAAAATTTTAAATATTTTTAATACTTATATTAGAGTATTATATATTTACTTCTCATATAA
5105044 TATAAAGATCAAATTTTGCTACTAGTCCTTGTATCATGCGTAAATCGTGGACTTAATCCATATAC
66 TATAAAGATCAAATTTTGCTACTAGTCCTTGTATCATGCGTAAATCGTGGACTTAATCCATATAC
5105109 TCTAATTAATTTAATTTTAATTCCTATATTTTTAAAATTTTGGAATATCAGTTTTGGTTCAAATG
131 TCTAATTAATTTAATTTTAATTCCTATATTTTTAAAATTTTGGAATATCAGTTTTGGTTCAAATG
5105174 GTAGCAGTTAGCTCTGCTAAGTCAAATTCTACTATCAATCCTGCACTATGTACAAGTTGTGGATT
196 GTAGCAGTTAGCTCTGCTAAGTCAAATTCTACTATCAATCCTGCACTATGTACAAGTTGTGGATT
5105239 TAATCATTGTTCCCCATTTTGATCATTTTTAATCTCCATACTTTTTAATTTTTTTGAAATTGCAA
261 TAATCATTGTTCCCCATTTTGATCATTTTTAATCTCCATACTTTTTAATTTTTTTGAAATTGCAA
5105304 CCCTAACTCAAACGATAGCCATTAATTCCATTAAATAAAATAACATGGTTTTTTTTGTGAGTATC
326 CCCTAACTCAAACGATAGCCATTAATTCCATTAAATAAAATAACATGGTTTTTTTTGTGAGTATC
5105369 ATGTGGAAATGACAATCTCATATGATATTGCACATATGATAATGAGTTTGTGTTAGGATTGAAAT
391 ATGTGGAAATGACAATCTCATATGATATTGCACATATGATAATGAGTTTGTGTTAGGATTGAAAT
5105434 CTCAAATCTTGAAAAGTGTAAGGACTAAAAAAAATACTAAATTAAAATACAAGGTTTAAATCCGA
456 CTCAAATCTTGAAAAGTGTAAGGACTAAAAAAAATACTAAATTAAAATACAAGGTTTAAATCCGA
5105499 ATCTTATGCATTGTACAAAGACTAATAG
521 ATCTTATGCATTGTACAAAGACTAATAG
5105527 T
1 T
5105528 AGAATTTCAA
Statistics
Matches: 548, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
547 538 0.98
548 10 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (548 bp):
TTTATTAAAATTTTAAATATTTTTAATACTTATATTAGAGTATTATATATTTACTTCTCATATAA
TATAAAGATCAAATTTTGCTACTAGTCCTTGTATCATGCGTAAATCGTGGACTTAATCCATATAC
TCTAATTAATTTAATTTTAATTCCTATATTTTTAAAATTTTGGAATATCAGTTTTGGTTCAAATG
GTAGCAGTTAGCTCTGCTAAGTCAAATTCTACTATCAATCCTGCACTATGTACAAGTTGTGGATT
TAATCATTGTTCCCCATTTTGATCATTTTTAATCTCCATACTTTTTAATTTTTTTGAAATTGCAA
CCCTAACTCAAACGATAGCCATTAATTCCATTAAATAAAATAACATGGTTTTTTTTGTGAGTATC
ATGTGGAAATGACAATCTCATATGATATTGCACATATGATAATGAGTTTGTGTTAGGATTGAAAT
CTCAAATCTTGAAAAGTGTAAGGACTAAAAAAAATACTAAATTAAAATACAAGGTTTAAATCCGA
ATCTTATGCATTGTACAAAGACTAATAG
Found at i:5107741 original size:113 final size:114
Alignment explanation
Indices: 5107550--5108217 Score: 489
Period size: 113 Copynumber: 5.9 Consensus size: 114
5107540 TTACCACAAT
* * * * * * *
5107550 GCGCCGCTAAATCTCTTAACCAAAACGCTGTGTTTTCGTCTTGATGTATCTTAAAAGTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATCTTAGAATTAGTGGCG
* * * *
5107615 TT-TACGCAAAACGCCGTTAAAGGACAGTAATAGCGGCGCTTTTTGGAA
66 TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTTATGGAA
* * *
5107663 ACGCCGCAAAATAGCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATCTTAGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATCTTAGAATTAGTGGCG
* * *
5107727 TTTATAGG-AAAACGCCGTTAAAGTACAGTAATAGCGGCGCTTCACGGAA
66 -TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTTATGGAA
* * * * ** * * *
5107776 GCGCCGCAAACTATCTGAACCGAAACACATCGTTTTGGTCTTGATTTATAC-TACAACTAGTGGC
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTAT-CTTAGAATTAGTGGC
* * * * * * * * **
5107840 G-CATACGGTCAAACGCCGGTAAAGAATAGTATTAGCGGCGATTTGTGTCTA
65 GTTATA-GGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTTATG-GAA
* * * * * * *
5107891 GCGCCGCAAAATATCTTAACAAAAACGCAGTGTTGTGATCTTAATGTAT-ATAAAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATCTTAGAATTAGTGGCG
* ** * * * *
5107955 CTTAT-GGTAAACCGCCGCGAACG-ATATTAATAGCGGCGCTTTGTGAGAA
66 -TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTTATG-GAA
* * * * * * **
5108004 GCGCCGCAAAATATATTAACCAAAACGCATAATTTCGGCCTCGATGTATAGTAGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATCTTAGAATTAGTGGCG
* * * * * * **
5108069 CT-TA-GTGAAACGCCGTTAAAGCATAGT-ATTGCGGTGCTTGGATAAAA
66 TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTT-TATGGAA
* * * ** *
5108116 GCGCCACCAAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTT-GATTTAGTGGC
1 GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTAT-CTTAGAATTAGTGGC
* * *
5108180 GATT-TCGGTAAAACGCCGCTAAAGCACAGTATTAGCGG
65 G-TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGG
5108218 TGATTTGTTG
Statistics
Matches: 428, Mismatches: 109, Indels: 34
0.75 0.19 0.06
Matches are distributed among these distances:
112 107 0.25
113 158 0.37
114 116 0.27
115 45 0.11
116 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (114 bp):
GCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATCTTAGAATTAGTGGCG
TTATAGGTAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTTATGGAA
Found at i:5108067 original size:228 final size:225
Alignment explanation
Indices: 5107664--5108102 Score: 479
Period size: 228 Copynumber: 1.9 Consensus size: 225
5107654 TTTTTGGAAA
* * * * * *
5107664 CGCCGCAAAATAGCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATCTTAGAATTAGTGGCGTT
1 CGCCGCAAAATAGCTTAACAAAAACGCAGAGTTTGATCTTAAGGTATCATAAAATTAGTGGCGCT
** * *
5107729 TATAGGAAAACGCCGTTAAAGTACAGTAATAGCGGCGCTTCACGGAAGCGCCGCAAACTATCTGA
66 TATAGGAAAACGCCGCGAAAGTACAGTAATAGCGGCGCTTCACGGAAGCGCCGCAAAATATATGA
* ** * * * *
5107794 ACCGAAACACATCGTTTTGGTCTTGATTTATACTACAACTAGTGGCGCATACGGTCAAACGCCGG
131 ACCAAAACACATAATTTCGGCCTCGATGTATACTACAACTAGTGGCGCATA--GTCAAACGCCGG
5107859 TAAAGAATAGTATTAGCGGCGATTTGTGTCTAG
194 TAAAGAATAGTATT-GCGGCGATTTGTGTCTAG
* * *
5107892 CGCCGCAAAATATCTTAACAAAAACGCAGTGTTGTGATCTTAATGTAT-ATAAAATTAGTGGCGC
1 CGCCGCAAAATAGCTTAACAAAAACGCAGAGTT-TGATCTTAAGGTATCATAAAATTAGTGGCGC
* * * * ***
5107956 TTAT-GGTAAACCGCCGCGAACG-ATATTAATAGCGGCGCTTTGTGAGAAGCGCCGCAAAATATA
65 TTATAGG-AAAACGCCGCGAAAGTACAGTAATAGCGGCGCTTCACG-GAAGCGCCGCAAAATATA
* * * * * * *
5108019 TTAACCAAAACGCATAATTTCGGCCTCGATGTATAGTAGAATTAGTGGCGCTTAGTGAAACGCCG
128 TGAACCAAAACACATAATTTCGGCCTCGATGTATACTACAACTAGTGGCGCATAGTCAAACGCCG
* *
5108084 TTAAAGCATAGTATTGCGG
193 GTAAAGAATAGTATTGCGG
5108103 TGCTTGGATA
Statistics
Matches: 172, Mismatches: 36, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
225 4 0.02
226 23 0.13
227 19 0.11
228 115 0.67
229 11 0.06
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (225 bp):
CGCCGCAAAATAGCTTAACAAAAACGCAGAGTTTGATCTTAAGGTATCATAAAATTAGTGGCGCT
TATAGGAAAACGCCGCGAAAGTACAGTAATAGCGGCGCTTCACGGAAGCGCCGCAAAATATATGA
ACCAAAACACATAATTTCGGCCTCGATGTATACTACAACTAGTGGCGCATAGTCAAACGCCGGTA
AAGAATAGTATTGCGGCGATTTGTGTCTAG
Found at i:5108149 original size:340 final size:340
Alignment explanation
Indices: 5107642--5108298 Score: 790
Period size: 340 Copynumber: 1.9 Consensus size: 340
5107632 TAAAGGACAG
* * * * *
5107642 TAATAGCGGCGCTTTTTGGAAACGCCGCAAAATAGCTTAACCAAAACGCAGAGTTTGGTCTTGAG
1 TAATAGCGGCGCTTTGTGGAAACGCCGCAAAATAGATTAACCAAAACGCAGAATTTGGCCTCGAG
** * *
5107707 GTATCTTAGAATTAGTGGCGTTTATAGGAAAACGCCGTTAAAGTACAGTAATAGCGGCGCTTCAC
66 GTATAGTAGAATTAGTGGCGCTTATA-GAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTCAC
** * * *
5107772 GGAAGCGCCGCAAACTATCTGAACCGAAACACATCGTTTTGGTCTTGATTTATACTACAACTAGT
130 AAAAGCGCCCCAAACTATCTGAACCAAAACACATCGTTTTGGTCTTGATGTATACTACAACTAGT
* * *
5107837 GGCGCA-TACGGTCAAACGCCGGTAAAGAATAGTATTAGCGGCGATTTG-TGTCTAGCGCCGCAA
195 GGCG-ATTACGGTAAAACGCCGCTAAAGAACAGTATTAGCGGCGATTTGTTG-CTAGCGCCGCAA
* * **
5107900 AATATC-TTAACAAAAACGCAGTGTTGTGATCTTAATGTATA-TAAAATTAGTGGCGCTTATGGT
258 AATACCATAAAC-AAAACGCAACGTTGTGATCTTAATGTATACTAAAATTAGTGGCGCTTATGGT
5107963 AAACCGCCGCGAACGATAT
322 AAACCGCCGCGAACGATAT
* * *
5107982 TAATAGCGGCGCTTTGTGAGAAGCGCCGCAAAATATATTAACCAAAACGCATAATTTCGGCCTCG
1 TAATAGCGGCGCTTTGTG-GAAACGCCGCAAAATAGATTAACCAAAACGCAGAATTT-GGCCTCG
* * * *
5108047 ATGTATAGTAGAATTAGTGGCGCTTAGT-G-AAACGCCGTTAAAGCATAGT-ATTGCGGTGCTTG
64 AGGTATAGTAGAATTAGTGGCGCTTA-TAGAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTT-
* * * ** **
5108109 GATAAAAGCGCCACCAAA-TATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTTGATT
127 CACAAAAGCGCC-CCAAACTATCTGAACCAAAACACATCGTTTTGGTCTTGATGTATACTACAAC
* * *
5108173 TAGTGGCGATTTCGGTAAAACGCCGCTAAAGCACAGTATTAGCGGTGATTTGTTGCTAGCGCCGC
191 TAGTGGCGATTACGGTAAAACGCCGCTAAAGAACAGTATTAGCGGCGATTTGTTGCTAGCGCCGC
* * * * *
5108238 GACATACCATAAACAAAACGCAACGTTTTGGTCTTAATTTATACTAAAATTAGTGGCGCTT
256 AAAATACCATAAACAAAACGCAACGTTGTGATCTTAATGTATACTAAAATTAGTGGCGCTT
5108299 TGTTGAAAGC
Statistics
Matches: 265, Mismatches: 43, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
339 11 0.04
340 165 0.62
341 61 0.23
342 27 0.10
343 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (340 bp):
TAATAGCGGCGCTTTGTGGAAACGCCGCAAAATAGATTAACCAAAACGCAGAATTTGGCCTCGAG
GTATAGTAGAATTAGTGGCGCTTATAGAAAACGCCGTTAAAGCACAGTAATAGCGGCGCTTCACA
AAAGCGCCCCAAACTATCTGAACCAAAACACATCGTTTTGGTCTTGATGTATACTACAACTAGTG
GCGATTACGGTAAAACGCCGCTAAAGAACAGTATTAGCGGCGATTTGTTGCTAGCGCCGCAAAAT
ACCATAAACAAAACGCAACGTTGTGATCTTAATGTATACTAAAATTAGTGGCGCTTATGGTAAAC
CGCCGCGAACGATAT
Found at i:5108543 original size:90 final size:90
Alignment explanation
Indices: 5108392--5108764 Score: 721
Period size: 90 Copynumber: 4.1 Consensus size: 90
5108382 AATCATATTT
*
5108392 GGTTTA-GGTATAGGGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAA
1 GGTTTAGGGT-TAGAGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAA
5108456 GTTTAAAGTTTAGGGTTTACGATGTA
65 GTTTAAAGTTTAGGGTTTACGATGTA
5108482 GGTTTAGGGTTAGAGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAAG
1 GGTTTAGGGTTAGAGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAAG
5108547 TTTAAAGTTTAGGGTTTACGATGTA
66 TTTAAAGTTTAGGGTTTACGATGTA
5108572 GGTTTAGGGTTAGAGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAAG
1 GGTTTAGGGTTAGAGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAAG
5108637 TTTAAAGTTTAGGGTTTACGATGTA
66 TTTAAAGTTTAGGGTTTACGATGTA
5108662 GGTTTAGGGTTAGAGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAAG
1 GGTTTAGGGTTAGAGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAAG
5108727 TTTAAAGTTTAGGGTTTACGATGTA
66 TTTAAAGTTTAGGGTTTACGATGTA
5108752 GGTTTAGGGTTAG
1 GGTTTAGGGTTAG
5108765 GGTGTTAATT
Statistics
Matches: 281, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
90 278 0.99
91 3 0.01
ACGTcount: A:0.27, C:0.03, G:0.26, T:0.43
Consensus pattern (90 bp):
GGTTTAGGGTTAGAGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAAG
TTTAAAGTTTAGGGTTTACGATGTA
Found at i:5108743 original size:7 final size:7
Alignment explanation
Indices: 5108733--5108851 Score: 50
Period size: 7 Copynumber: 17.0 Consensus size: 7
5108723 AAAGTTTAAA
5108733 GTTTAGG
1 GTTTAGG
*
5108740 GTTTACG
1 GTTTAGG
* *
5108747 ATGTA-G
1 GTTTAGG
5108753 GTTTAGG
1 GTTTAGG
5108760 G-TTAGG
1 GTTTAGG
5108766 GTGTTA--
1 GT-TTAGG
*
5108772 ATTTAGG
1 GTTTAGG
5108779 G-TTAGG
1 GTTTAGG
5108785 GTATTAGGG
1 GT-TTA-GG
*
5108794 TGTTTTGG
1 -GTTTAGG
*
5108802 GTTTAAG
1 GTTTAGG
5108809 GTTTAGG
1 GTTTAGG
* *
5108816 AGTCTGGG
1 -GTTTAGG
* *
5108824 GTATAAG
1 GTTTAGG
*
5108831 GTTTAAG
1 GTTTAGG
*
5108838 GTTTGGG
1 GTTTAGG
5108845 GTTTAGG
1 GTTTAGG
5108852 CTACTTTACT
Statistics
Matches: 82, Mismatches: 20, Indels: 20
0.67 0.16 0.16
Matches are distributed among these distances:
5 3 0.04
6 17 0.21
7 43 0.52
8 13 0.16
9 4 0.05
10 2 0.02
ACGTcount: A:0.18, C:0.02, G:0.39, T:0.40
Consensus pattern (7 bp):
GTTTAGG
Found at i:5108926 original size:14 final size:14
Alignment explanation
Indices: 5108909--5108936 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5108899 TCTGGTTGTT
5108909 GGTTTTAGGGTTTA
1 GGTTTTAGGGTTTA
5108923 GGTTTTAGGGTTTA
1 GGTTTTAGGGTTTA
5108937 ACGATTTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (14 bp):
GGTTTTAGGGTTTA
Found at i:5115046 original size:16 final size:17
Alignment explanation
Indices: 5115008--5115050 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
5114998 TAAATTAAGG
*
5115008 TTTATTTTTTAATTTAA
1 TTTATTATTTAATTTAA
* *
5115025 TGTATTATTT-ATTTAT
1 TTTATTATTTAATTTAA
5115041 TTTATTATTT
1 TTTATTATTT
5115051 TCCACATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTATTATTTAATTTAA
Found at i:5115979 original size:24 final size:24
Alignment explanation
Indices: 5115946--5115995 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
5115936 ATTAGCACAA
5115946 TTTTAAAAAAATA-AAAATTATAAT
1 TTTTAAAAAAATACAAAATTA-AAT
*
5115970 TTTTATAAAAATATCAAAATTAAAT
1 TTTTAAAAAAATA-CAAAATTAAAT
5115995 T
1 T
5115996 AGCACAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 12 0.52
25 4 0.17
26 7 0.30
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TTTTAAAAAAATACAAAATTAAAT
Found at i:5116154 original size:19 final size:18
Alignment explanation
Indices: 5116130--5116174 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
5116120 AAATGTGTAC
*
5116130 TTATAATTTGTTTATTAAA
1 TTATAATTTATTT-TTAAA
5116149 TTATAA-TTATTTTTAAA
1 TTATAATTTATTTTTAAA
5116166 TGTATAATT
1 T-TATAATT
5116175 ATCAAAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 10 0.43
19 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
TTATAATTTATTTTTAAA
Found at i:5116172 original size:37 final size:38
Alignment explanation
Indices: 5116099--5116174 Score: 93
Period size: 43 Copynumber: 1.9 Consensus size: 38
5116089 AAAACAATAA
5116099 TTATTAATTATAATTATTTTTAAATGTGTACTTATAATTTGT
1 TTATTAATTATAATTATTTTTAAA-GTG---TTATAATTTGT
5116141 TTATTAAATTATAATTATTTTTAAA-TG-TATAATT
1 TTATT-AATTATAATTATTTTTAAAGTGTTATAATT
5116175 ATCAAAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
37 7 0.21
41 2 0.06
42 5 0.15
43 19 0.58
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (38 bp):
TTATTAATTATAATTATTTTTAAAGTGTTATAATTTGT
Found at i:5129818 original size:126 final size:127
Alignment explanation
Indices: 5129674--5129925 Score: 479
Period size: 126 Copynumber: 2.0 Consensus size: 127
5129664 CAATAGCATC
5129674 AAAGATAAGATAAATAAAAAGGACAAATCAACGACATACAAGATAACAAGCATAAGCAAATGAGA
1 AAAGATAAGATAAATAAAAAGGACAAATCAACGACATACAAGATAACAAGCATAAGCAAATGAGA
*
5129739 TTAAAACATTTTAAAATAATGATGAAAATGTAAATAAATAAAATTATAAAGAATGTAAGAAA
66 TTAAAACATTTTAAAATAATGATGAAAATGGAAATAAATAAAATTATAAAGAATGTAAGAAA
5129801 AAAGATAAGA-AAATAAAAAGGACAAATCAACGACATACAAGATAACAAGCATAAGCAAATGAGA
1 AAAGATAAGATAAATAAAAAGGACAAATCAACGACATACAAGATAACAAGCATAAGCAAATGAGA
*
5129865 TTAAAACATTTTAAAATAATGATGAAAATGGAAATAGATAAAATTATAAAGAATGTAAGAA
66 TTAAAACATTTTAAAATAATGATGAAAATGGAAATAAATAAAATTATAAAGAATGTAAGAA
5129926 GATATATATG
Statistics
Matches: 123, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
126 113 0.92
127 10 0.08
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (127 bp):
AAAGATAAGATAAATAAAAAGGACAAATCAACGACATACAAGATAACAAGCATAAGCAAATGAGA
TTAAAACATTTTAAAATAATGATGAAAATGGAAATAAATAAAATTATAAAGAATGTAAGAAA
Found at i:5136494 original size:26 final size:27
Alignment explanation
Indices: 5136446--5136509 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
5136436 AGCTATAAAA
5136446 TATAAAA-A-ATATGTATATGTATGAAT
1 TATAAAATATATATGTATA-GTATGAAT
*
5136472 TATAAAATATATATGTATA-TATGTAT
1 TATAAAATATATATGTATAGTATGAAT
*
5136498 TTTAAAAT-TATA
1 TATAAAATATATA
5136510 AAACCTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 4 0.12
26 20 0.59
27 1 0.03
28 9 0.26
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (27 bp):
TATAAAATATATATGTATAGTATGAAT
Found at i:5141839 original size:26 final size:26
Alignment explanation
Indices: 5141796--5141845 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5141786 TTTTTCAACT
* *
5141796 TTTTTTTTTTTAATTTAAAGATTTGA
1 TTTTTTTTTATAAATTAAAGATTTGA
*
5141822 TTTTTTTTTATAAATTAAATATTT
1 TTTTTTTTTATAAATTAAAGATTT
5141846 CTTTAAAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTTTTTTTATAAATTAAAGATTTGA
Found at i:5144409 original size:14 final size:14
Alignment explanation
Indices: 5144390--5144419 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5144380 CACAATCTAC
5144390 AAGAAAAGAAAGAA
1 AAGAAAAGAAAGAA
5144404 AAGAAAAGAAAGAA
1 AAGAAAAGAAAGAA
5144418 AA
1 AA
5144420 CCTGTAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAGAA
Found at i:5147890 original size:28 final size:28
Alignment explanation
Indices: 5147848--5147903 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
5147838 GAATTGGATT
5147848 AAATCAAAATTTCATGTATAAAATATATA
1 AAATCAAAATTTCATGTATAAAAT-TATA
5147877 AAATCAAAA-TTCATGTATAAAATTATA
1 AAATCAAAATTTCATGTATAAAATTATA
5147904 CATTTAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 4 0.15
28 14 0.52
29 9 0.33
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (28 bp):
AAATCAAAATTTCATGTATAAAATTATA
Found at i:5150694 original size:23 final size:24
Alignment explanation
Indices: 5150667--5150717 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
5150657 ATATATATAT
*
5150667 ATATATGTTAA-TA-TTTTGTCAAA
1 ATATA-GTTAAGTATTTTTCTCAAA
5150690 ATATAGTTAAGTTATTTTTCTCAAA
1 ATATAGTTAAG-TATTTTTCTCAAA
5150715 ATA
1 ATA
5150718 AATTTATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
23 5 0.21
24 2 0.08
25 12 0.50
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (24 bp):
ATATAGTTAAGTATTTTTCTCAAA
Found at i:5152219 original size:24 final size:23
Alignment explanation
Indices: 5152192--5152238 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
5152182 TTATTTTTCC
5152192 ATTTCAAA-AAATATTAATTAATTA
1 ATTT-AAAGAAAT-TTAATTAATTA
5152216 ATTTAAAGTAAATTTAATTAATT
1 ATTTAAAG-AAATTTAATTAATT
5152239 CCATAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTTAAAGAAATTTAATTAATTA
Found at i:5154257 original size:9 final size:9
Alignment explanation
Indices: 5154245--5154310 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 9
5154235 GAGATAAGGA
5154245 TAATAATAT
1 TAATAATAT
5154254 TAATAATA-
1 TAATAATAT
*
5154262 -AATAATAA
1 TAATAATAT
*
5154270 TGATGCAATA-
1 TAAT--AATAT
5154280 TAATAATAT
1 TAATAATAT
*
5154289 TAATAATGT
1 TAATAATAT
5154298 TAA-AATAAT
1 TAATAAT-AT
5154307 TAAT
1 TAAT
5154311 TTAACCGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
7 7 0.15
8 7 0.15
9 25 0.54
10 3 0.07
11 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (9 bp):
TAATAATAT
Found at i:5158574 original size:1 final size:1
Alignment explanation
Indices: 5158563--5158596 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
5158553 TCTATAACCT
*
5158563 CCCCCCTCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
5158597 TCTTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:5171219 original size:17 final size:16
Alignment explanation
Indices: 5171189--5171222 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5171179 AATACCAAAC
*
5171189 ATTTTTTTATTTTTTA
1 ATTTTTTTAGTTTTTA
5171205 ATTTTCTTTAGTTTTTA
1 ATTTT-TTTAGTTTTTA
5171222 A
1 A
5171223 AATTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
ATTTTTTTAGTTTTTA
Found at i:5175163 original size:17 final size:17
Alignment explanation
Indices: 5175141--5175175 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5175131 ATATAATTTT
5175141 ATTTTTACT-AATTTAAA
1 ATTTTTA-TAAATTTAAA
5175158 ATTTTTATAAATTTAAA
1 ATTTTTATAAATTTAAA
5175175 A
1 A
5175176 GGTGTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTTATAAATTTAAA
Found at i:5176439 original size:4 final size:4
Alignment explanation
Indices: 5176430--5176454 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5176420 CTTTTAAAAT
5176430 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
5176455 AGAGATGAAT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:5177773 original size:19 final size:19
Alignment explanation
Indices: 5177749--5177861 Score: 154
Period size: 19 Copynumber: 5.8 Consensus size: 19
5177739 AATTTTTGAG
5177749 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
5177768 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
*
5177787 GATATATGCAATCTTAGACAT
1 G--ATATGCAATCTTAGATAT
5177808 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
5177827 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
5177846 GATATGCAATATTAGA
1 GATATGCAATCTTAGA
5177862 ATATATGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 65 0.80
21 16 0.20
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5177794 original size:40 final size:40
Alignment explanation
Indices: 5177750--5177855 Score: 171
Period size: 40 Copynumber: 2.7 Consensus size: 40
5177740 ATTTTTGAGG
5177750 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
* **
5177790 ATATGCAATCTTAGACATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
5177830 ATAT--AATCTTAGATATGATATGCAAT
1 ATATGCAATCTTAGATATGATATGCAAT
5177856 ATTAGAATAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 21 0.34
40 41 0.66
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
Found at i:5184001 original size:29 final size:29
Alignment explanation
Indices: 5183959--5184016 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5183949 TCTAGGTGGG
5183959 AGCATTTGATTCATTTTGATCATGCCATC
1 AGCATTTGATTCATTTTGATCATGCCATC
5183988 AGCATTTGATTCATTTTGATCATGCCATC
1 AGCATTTGATTCATTTTGATCATGCCATC
5184017 CTAATCATTA
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:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (29 bp):
AGCATTTGATTCATTTTGATCATGCCATC
Found at i:5184998 original size:44 final size:41
Alignment explanation
Indices: 5184950--5185151 Score: 142
Period size: 44 Copynumber: 4.7 Consensus size: 41
5184940 CCGATAATCC
*
5184950 TATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCT
1 TATCTTCCTGAAGTTGCAGTGGAGCAGA-TAAAATCA-AG-TCT
* *** *
5184994 TATC-TCTCTGAAGTTGCAGT-GAACAGATCGCATCTAGTCT
1 TATCTTC-CTGAAGTTGCAGTGGAGCAGATAAAATCAAGTCT
* *
5185034 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTTCCTGAAGTTGCAGTGGAGCAGA-TAA--AATCAAGTCT
* * *
5185078 TATCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAATCT
1 TATCTTCCTGAAGTTGCAGTGGA-GCAGA-T-AAAAT--CAAGTCT
* *
5185123 TATC-TCTTCAAAGTTGCAGTGGAGCAGAT
1 TATCTTCCT-GAAGTTGCAGTGGAGCAGAT
5185152 TAAAGCTGAT
Statistics
Matches: 126, Mismatches: 20, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
40 20 0.16
41 9 0.07
42 5 0.04
43 10 0.08
44 53 0.42
45 27 0.21
46 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (41 bp):
TATCTTCCTGAAGTTGCAGTGGAGCAGATAAAATCAAGTCT
Found at i:5185328 original size:44 final size:44
Alignment explanation
Indices: 5185203--5185640 Score: 356
Period size: 44 Copynumber: 10.0 Consensus size: 44
5185193 GGTAAAAATA
* * * *
5185203 GCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAT
1 GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT
* * * * *
5185246 AGCA-AGTCCTATCTTCGTATATTAGTAGG-G-AGTGGATCGAAGAT
1 -GCAGA-TCTTGTCTTCCTATATTGGT-GGCGAAGTAGATCGAAGAT
* * *
5185290 GCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAA
1 GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAG-AT
* * * *
5185335 GCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAT
1 GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT
* * * * *
5185378 AGCAGATCCTGTCTTCCTATGTTGTTAG-GAAGTGGATCGAAGAT
1 -GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT
* * * *
5185422 GCAGATCTTGTC-TCCCATACTAGTGGCGAAGTAGATCGAAGAAA
1 GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAG-AT
* * * * *
5185466 GCAGATCTTGTCTTCATGTATTAG-CGTGAAGTAGATCGAAGAT
1 GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT
* * * *
5185509 AGCAGATCCTATCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT
1 -GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT
* * * *
5185554 GCAGATCTTGTC-TCCCATACTAGTGGCGAAGTAGATCGAAGAAA
1 GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAG-AT
* * * *
5185598 GCAGATCTTGTCTTCATGTATTGGT-GTGAAGAAGATCGAAGAT
1 GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT
5185641 AGCAAATTTT
Statistics
Matches: 309, Mismatches: 69, Indels: 33
0.75 0.17 0.08
Matches are distributed among these distances:
42 10 0.03
43 70 0.23
44 175 0.57
45 53 0.17
46 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (44 bp):
GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT
Found at i:5185361 original size:132 final size:130
Alignment explanation
Indices: 5185202--5185644 Score: 753
Period size: 132 Copynumber: 3.4 Consensus size: 130
5185192 AGGTAAAAAT
*
5185202 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCA-AGTCCTATCTTCGTAT
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGA-TCCTATCTTCCTAT
* *
5185266 ATTAGTAGGGAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
65 ATT-GTAGGAAGTGGATCGAAGATGCAGATCTTGTC-TCCCATACTAGTGGCGAAGTAGATCGAA
5185331 GAA
128 GAA
* *
5185334 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATG
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATA
5185399 TTGTTAGGAAGTGGATCGAAGATGCAGATCTTGTCTCCCATACTAGTGGCGAAGTAGATCGAAGA
66 TTG-TAGGAAGTGGATCGAAGATGCAGATCTTGTCTCCCATACTAGTGGCGAAGTAGATCGAAGA
5185464 A
130 A
*
5185465 AGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATA
5185530 TTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTCCCATACTAGTGGCGAAGTAGATCGAAG
66 TT-GTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTCCCATACTAGTGGCGAAGTAGATCGAAG
5185595 AA
129 AA
* *
5185597 AGCAGATCTTGTCTTCATGTATTGGTGTGAAGAAGATCGAAGATAGCA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCA
5185645 AATTTTGTTC
Statistics
Matches: 296, Mismatches: 11, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
131 98 0.33
132 197 0.67
133 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (130 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATA
TTGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTCCCATACTAGTGGCGAAGTAGATCGAAGAA
Found at i:5185945 original size:19 final size:19
Alignment explanation
Indices: 5185921--5185997 Score: 82
Period size: 19 Copynumber: 3.8 Consensus size: 19
5185911 AATTTTTGAC
5185921 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
5185940 GATATGCAATCCAAGATATGATT
1 GATATGCAATCTTAG--AT-A-T
**
5185963 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5185982 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
5185998 ATATATGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
19 28 0.61
20 1 0.02
21 4 0.09
22 1 0.02
23 12 0.26
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5188571 original size:3 final size:3
Alignment explanation
Indices: 5188563--5188598 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5188553 GAATATACGT
5188563 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5188599 CAGTAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5189826 original size:3 final size:3
Alignment explanation
Indices: 5189765--5189807 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
5189755 CAACAAAAAC
* *
5189765 TAA TAA TAA TAA CAA TAA TAA TAA TAA TGA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5189808 TTATCAGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5192172 original size:149 final size:150
Alignment explanation
Indices: 5191992--5192293 Score: 597
Period size: 149 Copynumber: 2.0 Consensus size: 150
5191982 TTTTTGGTAT
5191992 ATTTAACCATTTTAATAATAAAAATATTATATTAATAAAAATTTTCAAACCATAATTAATGTGTG
1 ATTTAACCATTTTAATAATAAAAATATTATATTAATAAAAATTTTCAAACCATAATTAATGTGTG
5192057 AATGAAAATCAAACATTTTTGTGATTTTTTAAGCTACTATTTTAATAAAAATCCTTAAGGGTATG
66 AATGAAAATCAAACATTTTTGTGATTTTTTAAGCTACTATTTTAATAAAAATCCTTAAGGGTATG
5192122 TTTGTAAAATAACTTGAGTA
131 TTTGTAAAATAACTTGAGTA
5192142 ATTTAACCATTTT-ATAATAAAAATATTATATTAATAAAAATTTTCAAACCATAATTAATGTGTG
1 ATTTAACCATTTTAATAATAAAAATATTATATTAATAAAAATTTTCAAACCATAATTAATGTGTG
5192206 AATGAAAATCAAACATTTTTGTGATTTTTTAAGCTACTATTTTAATAAAAATCCTTAAGGGTATG
66 AATGAAAATCAAACATTTTTGTGATTTTTTAAGCTACTATTTTAATAAAAATCCTTAAGGGTATG
5192271 TTTGTAAAATAACTTGAGTA
131 TTTGTAAAATAACTTGAGTA
5192291 ATT
1 ATT
5192294 ACACATGTAT
Statistics
Matches: 152, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
149 139 0.91
150 13 0.09
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.40
Consensus pattern (150 bp):
ATTTAACCATTTTAATAATAAAAATATTATATTAATAAAAATTTTCAAACCATAATTAATGTGTG
AATGAAAATCAAACATTTTTGTGATTTTTTAAGCTACTATTTTAATAAAAATCCTTAAGGGTATG
TTTGTAAAATAACTTGAGTA
Found at i:5193716 original size:27 final size:27
Alignment explanation
Indices: 5193677--5193730 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
5193667 ATTTGTCAAA
*
5193677 AATTTAATTATTTAAAATAA-TTAATTT
1 AATTTAATAATTT-AAATAATTTAATTT
* *
5193704 AATTTACTAATTTATATAATTTAATTT
1 AATTTAATAATTTAAATAATTTAATTT
5193731 TAAATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
AATTTAATAATTTAAATAATTTAATTT
Found at i:5195736 original size:3 final size:3
Alignment explanation
Indices: 5195728--5195760 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5195718 GTTATTTTTG
*
5195728 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5195761 AATTGCTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5195809 original size:22 final size:21
Alignment explanation
Indices: 5195769--5195827 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
5195759 ATAATTGCTC
*
5195769 TTATATATATACGAGTAT-TTCT
1 TTATATATATAC-A-TATATTTT
5195791 TTATATATATACATATATTTT
1 TTATATATATACATATATTTT
*
5195812 TCTATATATTTACATA
1 T-TATATATATACATA
5195828 CATACATACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 25 0.76
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (21 bp):
TTATATATATACATATATTTT
Found at i:5199341 original size:17 final size:18
Alignment explanation
Indices: 5199319--5199355 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5199309 TTATTCTTTT
5199319 ATTCTTTCATCCA-AATC
1 ATTCTTTCATCCATAATC
*
5199336 ATTCTTTCATTCATAATC
1 ATTCTTTCATCCATAATC
5199354 AT
1 AT
5199356 ACAGTGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCTTTCATCCATAATC
Found at i:5200095 original size:11 final size:10
Alignment explanation
Indices: 5200075--5200125 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 10
5200065 TCAGACTAAA
5200075 AAAAATAAAAC
1 AAAAA-AAAAC
5200086 AAAAACAAAAAC
1 -AAAA-AAAAAC
5200098 AAAATAAAAAC
1 AAAA-AAAAAC
5200109 AAAAAAAATA-
1 AAAAAAAA-AC
5200119 AAAAAAA
1 AAAAAAA
5200126 TCAGAGTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
10 11 0.31
11 15 0.42
12 9 0.25
13 1 0.03
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.06
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:5200101 original size:17 final size:17
Alignment explanation
Indices: 5200075--5200113 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5200065 TCAGACTAAA
*
5200075 AAAAATAAAACAAAAAC
1 AAAAACAAAACAAAAAC
*
5200092 AAAAACAAAATAAAAAC
1 AAAAACAAAACAAAAAC
5200109 AAAAA
1 AAAAA
5200114 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.85, C:0.10, G:0.00, T:0.05
Consensus pattern (17 bp):
AAAAACAAAACAAAAAC
Found at i:5200122 original size:6 final size:6
Alignment explanation
Indices: 5200081--5200113 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5200071 TAAAAAAAAT
*
5200081 AAAACA AAAACA AAAAC- AAAATA AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
5200114 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAACA
Found at i:5200123 original size:17 final size:17
Alignment explanation
Indices: 5200072--5200124 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
5200062 AGTTCAGACT
5200072 AAAAAAAATAAAACAAAAAC
1 AAAAAAAAT--AA-AAAAAC
*
5200092 AAAAACAAA-ATAAAAAC
1 AAAAA-AAATAAAAAAAC
5200109 AAAAAAAATAAAAAAA
1 AAAAAAAATAAAAAAA
5200125 ATCAGAGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 3 0.10
17 17 0.59
18 1 0.03
20 5 0.17
21 3 0.10
ACGTcount: A:0.87, C:0.08, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAAATAAAAAAAC
Found at i:5200156 original size:10 final size:10
Alignment explanation
Indices: 5200143--5200181 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
5200133 CAAAAATAGG
5200143 AGAAAAAGAA
1 AGAAAAAGAA
5200153 AGAAGAAA-AA
1 AGAA-AAAGAA
5200163 AGAAAAAGAA
1 AGAAAAAGAA
*
5200173 AAAAAAAGA
1 AGAAAAAGA
5200182 GGTCAAGGCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 20 0.77
11 3 0.12
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:5200161 original size:13 final size:13
Alignment explanation
Indices: 5200143--5200181 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
5200133 CAAAAATAGG
5200143 AGAAAAAGAAAGA
1 AGAAAAAGAAAGA
5200156 AGAAAAAAGAAA-A
1 AG-AAAAAGAAAGA
*
5200169 AGAAAAAAAAAGA
1 AGAAAAAGAAAGA
5200182 GGTCAAGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 8 0.35
13 6 0.26
14 9 0.39
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAGA
Found at i:5200172 original size:16 final size:16
Alignment explanation
Indices: 5200151--5200181 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5200141 GGAGAAAAAG
*
5200151 AAAGAAGAAAAAAGAA
1 AAAGAAAAAAAAAGAA
5200167 AAAGAAAAAAAAAGA
1 AAAGAAAAAAAAAGA
5200182 GGTCAAGGCG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAAGAA
Found at i:5201502 original size:44 final size:44
Alignment explanation
Indices: 5201454--5201680 Score: 157
Period size: 44 Copynumber: 5.2 Consensus size: 44
5201444 AGACACAAAC
* *
5201454 CTTGCCTCTCTCAGTTGTGATGGAGTTGGTTGAAGATAAAAGAT
1 CTTGCCTCTCTCAGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
* * * * *
5201498 CTTGCCT-TC-CTGTAT-TGACAGCGAAG-TAGGTCGAAGACACAA-AC
1 CTTGCCTCTCTCAGT-TGTGA-TG-G-AGCT-GGTTGAAGACAAAAGAT
* *
5201542 CTTGCGTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCAGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
** * * * * *
5201586 CTTGCCATC-CTGCA-TTGACATTGAAGCAGGTCGAAGACACAA-AC
1 CTTGCC-TCTCT-CAGTTGTGA-TGGAGCTGGTTGAAGACAAAAGAT
*
5201630 CTTGCGTCTCTC-GATTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCAG-TTGTGATGGAGCTGGTTGAAGACAAAAGAT
5201674 CTTGCCT
1 CTTGCCT
5201681 TCCTGCGTTA
Statistics
Matches: 136, Mismatches: 30, Indels: 34
0.68 0.15 0.17
Matches are distributed among these distances:
42 6 0.04
43 38 0.28
44 49 0.36
45 37 0.27
46 6 0.04
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (44 bp):
CTTGCCTCTCTCAGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
Found at i:5201767 original size:87 final size:86
Alignment explanation
Indices: 5201405--5201986 Score: 609
Period size: 87 Copynumber: 6.7 Consensus size: 86
5201395 AATGAAGTTG
* * * * * *
5201405 CAGATCTTGCCTTTCTGCATTGACAGTGAAGCAGGTCGAAGACACAAA-CCTTGCCTCTCTCAGT
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTC-CTCGGT
* * *
5201469 TGTGATGGAGTTGGTTGAAGATAA
63 TGAGATGGAGCTGGTTAAAGATAA
* ** * * * *
5201493 AAGATCTTGCCTTCCTGTATTGACAGCGAAGTAGGTCGAAGACACAAA-CCTTGCGTCTCTCGGT
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTC-CTCGGT
* * *
5201557 TGTGATGGAGCTGGTTGAAGACAA
63 TGAGATGGAGCTGGTTAAAGATAA
* * * * ** * * *
5201581 AAGATCTTGCCATCCTGCATTGACATTGAAGCAGGTCGAAGACACAAA-CCTTGCGTCTCTCGAT
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTC-CTCGGT
* * *
5201645 TGTGATGGAGCTGGTTGAAGACAA
63 TGAGATGGAGCTGGTTAAAGATAA
* *
5201669 AAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGACTTGCCTCCATCGGTTG
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC-TCGGTTG
5201734 CAG-TGGAGCTGGTTAAAGATAA
65 -AGATGGAGCTGGTTAAAGATAA
**
5201756 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATATAAAACAAAGCCTTGCCTCCATCGGTTG
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC-TCGGTTG
*
5201821 CAG-TGGAGCTGGTTAAAGATAG
65 -AGATGGAGCTGGTTAAAGATAA
* *
5201843 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGTAGATCGAAAACAAAGCCTTGCCTCCATCAGTTG
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC-TCGGTTG
*
5201908 CAG-TGGAGCTGGTTAAAGATAG
65 -AGATGGAGCTGGTTAAAGATAA
* * *
5201930 CAGATCTTACCTTCCTGCGTTAACATCGAAGCAGATCAAAAACAAAGCCTTGCCTCC
1 CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCC
5201987 CTAAGCGGTA
Statistics
Matches: 451, Mismatches: 40, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
86 6 0.01
87 249 0.55
88 196 0.43
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (86 bp):
CAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCTCGGTTGA
GATGGAGCTGGTTAAAGATAA
Found at i:5201810 original size:43 final size:42
Alignment explanation
Indices: 5201674--5201984 Score: 118
Period size: 42 Copynumber: 7.2 Consensus size: 42
5201664 GACAAAAGAT
* *
5201674 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGA
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGAT-TAAAACAAAGC
* * * * * * *
5201717 CTTGCC-TCCAT-CGGTT-GCAGTGGAGCTGGTTAAAGATAACAGAT
1 CTTGCCTTCC-TGC-GTTAACAGCGAAGCAGATTAAA-ACAA-AG-C
5201761 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATATAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGAT-TAAAACAAAGC
* * * * * * * *
5201804 CTTGCC-TCCAT-CGGTT-GCAGTGGAGCTGGTTAAAGATAGCAGAT
1 CTTGCCTTCC-TGC-GTTAACAGCGAAGCAGATTAAA-ACA-AAG-C
* *
5201848 CTTGCCTTCCTGCGTTAACAGCGAAGTAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGAT-TAAAACAAAGC
* * * * * * * *
5201891 CTTGCC-TCCAT-CAGTT-GCAGTGGAGCTGGTTAAAGATAGCAGAT
1 CTTGCCTTCC-TGC-GTTAACAGCGAAGCAGATTAAA-ACA-AAG-C
* * *
5201935 CTTACCTTCCTGCGTTAACATCGAAGCAGATCAAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGAT-TAAAACAAAGC
5201978 CTTGCCT
1 CTTGCCT
5201985 CCCTAAGCGG
Statistics
Matches: 186, Mismatches: 55, Indels: 54
0.63 0.19 0.18
Matches are distributed among these distances:
41 10 0.05
42 45 0.24
43 42 0.23
44 35 0.19
45 44 0.24
46 10 0.05
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (42 bp):
CTTGCCTTCCTGCGTTAACAGCGAAGCAGATTAAAACAAAGC
Found at i:5212566 original size:23 final size:25
Alignment explanation
Indices: 5212532--5212592 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
5212522 ATCCTTCTAA
*
5212532 GATTTCCTTTCCTTTTTC-TCTTCC-
1 GATTT-CTTTCCTTTTTCTTCTCCCT
*
5212556 GATTTCTTTCCCTTTTCTTCTCCCT
1 GATTTCTTTCCTTTTTCTTCTCCCT
5212581 GA-TTCTTTCCTT
1 GATTTCTTTCCTT
5212593 GCTCTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 11 0.34
24 19 0.59
25 2 0.06
ACGTcount: A:0.05, C:0.33, G:0.05, T:0.57
Consensus pattern (25 bp):
GATTTCTTTCCTTTTTCTTCTCCCT
Found at i:5214192 original size:11 final size:12
Alignment explanation
Indices: 5214176--5214208 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5214166 CATGACTTGA
5214176 TAAAATAT-TTT
1 TAAAATATATTT
5214187 TAAAATATATTT
1 TAAAATATATTT
5214199 TATAAATATA
1 TA-AAATATA
5214209 GTTCTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 5 0.25
13 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAAATATATTT
Found at i:5217459 original size:17 final size:16
Alignment explanation
Indices: 5217414--5217461 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
5217404 GTATTTTTCA
5217414 TTTATTTTATT-TTAAG
1 TTTA-TTTATTATTAAG
*
5217430 TTTATTTATTTATTTAG
1 TTTATTTA-TTATTAAG
5217447 TTTATGTTATTATTA
1 TTTAT-TTATTATTA
5217462 TTAAAGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 6 0.22
17 14 0.52
18 3 0.11
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTATTTATTATTAAG
Found at i:5217935 original size:114 final size:112
Alignment explanation
Indices: 5217760--5218403 Score: 642
Period size: 114 Copynumber: 5.7 Consensus size: 112
5217750 TATATGTAAG
* * * * * ** * * *
5217760 CGCCGCAAAA-ATTGTTAGCCAAAATGCATCGTTTGTTCCCGAGGTATATTAGATTTGGTGGCGT
1 CGCCGCAAAATA-TCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGC
* * * * * *
5217824 TTATGGAAAACACCGCTATAGTATATTATTAGCGGCATTTTTTAGTAAA
65 TTATGGAAAACGCCACTATAGCAGAGTATTAGCGGCCTTTTTTAG-AAA
* * * *
5217873 CGCCACAAAATATCTTAACAAAAAACACAGCGTTTGGTCTTGAGGCATATTAGAATTAGTGGCGC
1 CGCCGCAAAATATCTTAAC-CAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGC
* * * * * *
5217938 TTATGTAAAAACGCCGCTATAGCACAGTATTAGCAGCGTTTTATAGAAA
65 TTATG-GAAAACGCCACTATAGCAGAGTATTAGCGGCCTTTTTTAGAAA
* * *
5217987 GCGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATAAGAATTAGTGGCGG
1 -CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGC
* * * * *
5218052 TTACGGAAAAACGCCACTAAAGGAGAGTATTAGAGGCGCTTTTTAAGAAA
65 TTATGG-AAAACGCCACTATAGCAGAGTATTAGCGGC-CTTTTTTAGAAA
** * * *
5218102 CGTTGCAAAATATCTTAACCAAAACGTAGCGTTTGGTCTTAATGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * * * *
5218167 TGTGGAAAAACGCCACTATAGCATAGTATTGGCGGCGTTTTGTATGAAA
66 TATGG-AAAACGCCACTATAGCAGAGTATTAGCGGCCTTTTTTA-GAAA
* * * * * * *
5218216 CGCCGCAAGATATCTTAACCAAAACGCATCGTTTGGTCTTGATGAATATAAAAATTAGTGGCGGT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * * * * * *
5218281 TACGGAAAAAAGCCACTAAAGCAGAGTATTAGAGGCGCTTTGTAAGAAT
66 TATGG-AAAACGCCACTATAGCAGAGTATTAGCGGC-CTTTTTTAGAAA
*
5218330 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCT
1 CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
*
5218395 TATGTAAAA
66 TATGGAAAA
5218404 ATGCATGTAG
Statistics
Matches: 435, Mismatches: 88, Indels: 16
0.81 0.16 0.03
Matches are distributed among these distances:
113 23 0.05
114 349 0.80
115 63 0.14
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (112 bp):
CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
TATGGAAAACGCCACTATAGCAGAGTATTAGCGGCCTTTTTTAGAAA
Found at i:5218135 original size:228 final size:228
Alignment explanation
Indices: 5217870--5218404 Score: 829
Period size: 228 Copynumber: 2.3 Consensus size: 228
5217860 ATTTTTTAGT
* * * * *
5217870 AAACGCCACAAAATATCTTAACAAAAAACACAGCGTTTGGTCTTGAGGCATATTAGAATTAGTGG
1 AAACGCCGCAAAATATCTTAAC-CAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGG
*
5217935 CGCTTATGTAAAAACGCCGCTATAGCACAGTATTAGCAGCGTTTTATA-GAAAGCGCCGCAAAAT
65 CGCTTATGTAAAAACGCCACTATAGCACAGTATTAGCAGCGTTTTATATGAAA-CGCCGCAAAAT
* * *
5217999 ATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATAAGAATTAGTGGCGGTTACGGAAAAAC
129 ATCTTAACCAAAACGCATCGTTTGGTCTTGAGGAATATAAAAATTAGTGGCGGTTACGGAAAAAA
* *
5218064 GCCACTAAAGGAGAGTATTAGAGGCGCTTTTTAAG
194 GCCACTAAAGCAGAGTATTAGAGGCGCTTTGTAAG
** * *
5218099 AAACGTTGCAAAATATCTTAACCAAAACGTAGCGTTTGGTCTTAATGTATATTAGAATTAGTGGC
1 AAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
* * * * * * *
5218164 GCTTGTGGAAAAACGCCACTATAGCATAGTATTGGCGGCGTTTTGTATGAAACGCCGCAAGATAT
66 GCTTATGTAAAAACGCCACTATAGCACAGTATTAGCAGCGTTTTATATGAAACGCCGCAAAATAT
*
5218229 CTTAACCAAAACGCATCGTTTGGTCTTGATGAATATAAAAATTAGTGGCGGTTACGGAAAAAAGC
131 CTTAACCAAAACGCATCGTTTGGTCTTGAGGAATATAAAAATTAGTGGCGGTTACGGAAAAAAGC
5218294 CACTAAAGCAGAGTATTAGAGGCGCTTTGTAAG
196 CACTAAAGCAGAGTATTAGAGGCGCTTTGTAAG
*
5218327 AATCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
1 AAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
5218392 GCTTATGTAAAAA
66 GCTTATGTAAAAA
5218405 TGCATGTAGG
Statistics
Matches: 275, Mismatches: 30, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
228 252 0.92
229 23 0.08
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (228 bp):
AAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
GCTTATGTAAAAACGCCACTATAGCACAGTATTAGCAGCGTTTTATATGAAACGCCGCAAAATAT
CTTAACCAAAACGCATCGTTTGGTCTTGAGGAATATAAAAATTAGTGGCGGTTACGGAAAAAAGC
CACTAAAGCAGAGTATTAGAGGCGCTTTGTAAG
Found at i:5218404 original size:114 final size:114
Alignment explanation
Indices: 5217870--5218404 Score: 680
Period size: 114 Copynumber: 4.7 Consensus size: 114
5217860 ATTTTTTAGT
* * * * *
5217870 AAACGCCACAAAATATCTTAACAAAAAACACAGCGTTTGGTCTTGAGGCATATTAGAATTAGTGG
1 AAACGCCGCAAAATATCTTAAC-CAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGG
* * * *
5217935 CGCTTATGTAAAAACGCCGCTATAGCACAGTATTAGCA-GCG-TTT-TATAG
65 CGCTTATGGAAAAACGCCACTAAAGCAGAGTATTAG-AGGCGCTTTGTA-AG
* * *
5217984 AAAGCGCCGCAAAATATCTTAACCAAAACGCATCGTTTGGTCTTGAGGTATATAAGAATTAGTGG
1 AAA-CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGG
* * * *
5218049 CGGTTACGGAAAAACGCCACTAAAGGAGAGTATTAGAGGCGCTTTTTAAG
65 CGCTTATGGAAAAACGCCACTAAAGCAGAGTATTAGAGGCGCTTTGTAAG
** * *
5218099 AAACGTTGCAAAATATCTTAACCAAAACGTAGCGTTTGGTCTTAATGTATATTAGAATTAGTGGC
1 AAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
* * * * * * *
5218164 GCTTGTGGAAAAACGCCACTATAGCATAGTATTGGCGGCGTTTTGTATG
66 GCTTATGGAAAAACGCCACTAAAGCAGAGTATTAGAGGCGCTTTGTAAG
* * * * *
5218213 AAACGCCGCAAGATATCTTAACCAAAACGCATCGTTTGGTCTTGATGAATATAAAAATTAGTGGC
1 AAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
* * *
5218278 GGTTACGGAAAAAAGCCACTAAAGCAGAGTATTAGAGGCGCTTTGTAAG
66 GCTTATGGAAAAACGCCACTAAAGCAGAGTATTAGAGGCGCTTTGTAAG
*
5218327 AATCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
1 AAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
*
5218392 GCTTATGTAAAAA
66 GCTTATGGAAAAA
5218405 TGCATGTAGG
Statistics
Matches: 358, Mismatches: 59, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
113 1 0.00
114 329 0.92
115 26 0.07
116 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (114 bp):
AAACGCCGCAAAATATCTTAACCAAAACGCAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGC
GCTTATGGAAAAACGCCACTAAAGCAGAGTATTAGAGGCGCTTTGTAAG
Found at i:5218722 original size:22 final size:21
Alignment explanation
Indices: 5218695--5218745 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
5218685 TAGGTTTAGT
*
5218695 GTTTTGGGTTTAAGGTTTGGG
1 GTTTTGGGTTTAAGGGTTGGG
5218716 AGTTTTGGGTTTAAGGGTTGGG
1 -GTTTTGGGTTTAAGGGTTGGG
5218738 G-TTTGGGT
1 GTTTTGGGT
5218746 CGCTTTAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 7 0.25
21 1 0.04
22 20 0.71
ACGTcount: A:0.10, C:0.00, G:0.45, T:0.45
Consensus pattern (21 bp):
GTTTTGGGTTTAAGGGTTGGG
Found at i:5220542 original size:15 final size:16
Alignment explanation
Indices: 5220522--5220551 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5220512 GGCACATTAC
5220522 TTGGTATTCT-TTTTT
1 TTGGTATTCTGTTTTT
5220537 TTGGTATTCTGTTTT
1 TTGGTATTCTGTTTT
5220552 GGCACGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.70
Consensus pattern (16 bp):
TTGGTATTCTGTTTTT
Found at i:5222313 original size:30 final size:31
Alignment explanation
Indices: 5222265--5222329 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
5222255 ATCTTTGATA
* *
5222265 TATATATACTTACTTATTTTTT-ATATACTT
1 TATATATACATACATATTTTTTCATATACTT
* *
5222295 TATATGTACATACATATTTTTTCATATATTT
1 TATATATACATACATATTTTTTCATATACTT
5222326 TATA
1 TATA
5222330 ATTCATAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (31 bp):
TATATATACATACATATTTTTTCATATACTT
Found at i:5222454 original size:18 final size:18
Alignment explanation
Indices: 5222412--5222467 Score: 51
Period size: 20 Copynumber: 3.0 Consensus size: 18
5222402 ACATACTTTA
* *
5222412 TATTTTTTTATAATTTTGT
1 TATTTTTTTATTATTAT-T
5222431 TAATTTTTTTATTATTATT
1 T-ATTTTTTTATTATTATT
*
5222450 TATTTATGTT-TTATTATT
1 TATTT-TTTTATTATTATT
5222468 CTTTGAAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.38
19 6 0.19
20 14 0.44
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (18 bp):
TATTTTTTTATTATTATT
Found at i:5227659 original size:13 final size:12
Alignment explanation
Indices: 5227625--5227728 Score: 55
Period size: 13 Copynumber: 7.8 Consensus size: 12
5227615 AGATCTTTTC
5227625 AAAAAAAAATCA
1 AAAAAAAAATCA
*
5227637 AAAATCAAAATCA
1 AAAA-AAAAATCA
*
5227650 AAATAAAAAATGA
1 AAA-AAAAAATCA
**
5227663 GAGAAAAAGAAAGAA
1 -A-AAAAA-AAATCA
5227678 GAAAAAAAAATCTA
1 -AAAAAAAAATC-A
**
5227692 GATGAAAAAATCA
1 -AAAAAAAAATCA
5227705 AAATAAAAAATGACA
1 AAA-AAAAAAT--CA
5227720 AAAAAAAAA
1 AAAAAAAAA
5227729 AAAGGAGAGG
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
12 5 0.07
13 27 0.38
14 27 0.38
15 13 0.18
ACGTcount: A:0.75, C:0.06, G:0.09, T:0.11
Consensus pattern (12 bp):
AAAAAAAAATCA
Found at i:5228592 original size:7 final size:7
Alignment explanation
Indices: 5228582--5228663 Score: 91
Period size: 7 Copynumber: 12.0 Consensus size: 7
5228572 AAAAAAAGAA
5228582 AAAAATG
1 AAAAATG
5228589 AAAAATG
1 AAAAATG
*
5228596 -AGAATG
1 AAAAATG
5228602 AAAAAAATG
1 --AAAAATG
5228611 AAAAATG
1 AAAAATG
*
5228618 -AGAATG
1 AAAAATG
5228624 AAAAATG
1 AAAAATG
5228631 AAAAATG
1 AAAAATG
5228638 -AAAATG
1 AAAAATG
5228644 -AAAATG
1 AAAAATG
*
5228650 AAAAACG
1 AAAAATG
5228657 AAAAATG
1 AAAAATG
5228664 GAGAGGCTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
6 22 0.34
7 37 0.58
9 5 0.08
ACGTcount: A:0.68, C:0.01, G:0.17, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:5228601 original size:13 final size:13
Alignment explanation
Indices: 5228583--5228660 Score: 85
Period size: 13 Copynumber: 6.3 Consensus size: 13
5228573 AAAAAAGAAA
5228583 AAAATGAAAAATG
1 AAAATGAAAAATG
*
5228596 AGAATG--AAA--
1 AAAATGAAAAATG
5228605 AAAATGAAAAATG
1 AAAATGAAAAATG
*
5228618 AGAATGAAAAATG
1 AAAATGAAAAATG
5228631 AAAAATG-AAAATG
1 -AAAATGAAAAATG
*
5228644 AAAATGAAAAACG
1 AAAATGAAAAATG
5228657 AAAA
1 AAAA
5228661 ATGGAGAGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
9 5 0.09
11 6 0.11
12 6 0.11
13 32 0.59
14 5 0.09
ACGTcount: A:0.69, C:0.01, G:0.17, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:5228607 original size:22 final size:22
Alignment explanation
Indices: 5228579--5228647 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
5228569 TAAAAAAAAA
5228579 GAAAAAAATGAAAAATGAGAAT
1 GAAAAAAATGAAAAATGAGAAT
5228601 GAAAAAAATGAAAAATGAGAAT
1 GAAAAAAATGAAAAATGAGAAT
*
5228623 G--AAAAATGAAAAATGAAAAT
1 GAAAAAAATGAAAAATGAGAAT
5228643 GAAAA
1 GAAAA
5228648 TGAAAAACGA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
20 19 0.43
22 25 0.57
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (22 bp):
GAAAAAAATGAAAAATGAGAAT
Found at i:5228660 original size:6 final size:6
Alignment explanation
Indices: 5228583--5228653 Score: 67
Period size: 6 Copynumber: 11.7 Consensus size: 6
5228573 AAAAAAGAAA
* *
5228583 AAAATG AAAAATG AGAATG -AAA-- AAAATG AAAAATG AGAATG AAAAATG
1 AAAATG -AAAATG AAAATG AAAATG AAAATG -AAAATG AAAATG -AAAATG
5228631 AAAAATG AAAATG AAAATG AAAA
1 -AAAATG AAAATG AAAATG AAAA
5228654 ACGAAAAATG
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
4 3 0.05
5 2 0.04
6 26 0.47
7 24 0.44
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:5228663 original size:20 final size:20
Alignment explanation
Indices: 5228582--5228660 Score: 106
Period size: 22 Copynumber: 3.9 Consensus size: 20
5228572 AAAAAAAGAA
*
5228582 AAAAATGAAAAATGAGAATG
1 AAAAATGAAAAATGAAAATG
*
5228602 AAAAAAATGAAAAATGAGAATG
1 --AAAAATGAAAAATGAAAATG
5228624 AAAAATGAAAAATGAAAATG
1 AAAAATGAAAAATGAAAATG
*
5228644 -AAAATGAAAAACGAAAA
1 AAAAATGAAAAATGAAAA
5228661 ATGGAGAGGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
19 16 0.29
20 19 0.35
22 20 0.36
ACGTcount: A:0.70, C:0.01, G:0.16, T:0.13
Consensus pattern (20 bp):
AAAAATGAAAAATGAAAATG
Found at i:5229867 original size:15 final size:16
Alignment explanation
Indices: 5229847--5229876 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5229837 GGCACATTAC
5229847 TTGGTATTCT-TTTTT
1 TTGGTATTCTGTTTTT
5229862 TTGGTATTCTGTTTT
1 TTGGTATTCTGTTTT
5229877 GGCACAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.70
Consensus pattern (16 bp):
TTGGTATTCTGTTTTT
Found at i:5234473 original size:29 final size:30
Alignment explanation
Indices: 5234439--5234497 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
5234429 TAGTGGCATT
* * *
5234439 TTTGTACAAAAA-TGCCGCTAAAGAATATG
1 TTTGTAAAAAAAGAGCCGCAAAAGAATATG
*
5234468 TTTGTAAAAAAAGAGCCGCAAAAGATTATG
1 TTTGTAAAAAAAGAGCCGCAAAAGAATATG
5234498 ATCTCTAGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (30 bp):
TTTGTAAAAAAAGAGCCGCAAAAGAATATG
Found at i:5239271 original size:95 final size:95
Alignment explanation
Indices: 5239056--5239561 Score: 546
Period size: 95 Copynumber: 5.4 Consensus size: 95
5239046 AAGCTATAAG
* * * * *
5239056 TCTTATCTCCCTGAAGTTGCAGTGAAACAAATTAAATATAGCGAATATTATTTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAAG-TGC
* * * *
5239121 AATGGAATAGATTAAAGGTACAAGTTATAAA
65 AGTGGAACAGATTAAAGCTACAAGTTACAAA
* *
5239152 TCTTATCTCCCTGAAGATGTAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTGCA
* *
5239217 GTGGAACATATTGAAGCTACAAGTTACAAA
66 GTGGAACAGATTAAAGCTACAAGTTACAAA
* * ** * *
5239247 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGATTATAGCGAATCTTATTTCCCTGAATTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAA-GTGC
5239312 AGTGGAACAGATTAAAGCTACAAGTTACAAA
65 AGTGGAACAGATTAAAGCTACAAGTTACAAA
* * * * * *
5239343 T-TTATCTCTCTGAAGATGCAATAGAGCAGATTGAAGATAGCGAATCTTATTTCCCTAAAGTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTGCA
*
5239407 GTGGAACAGATTGAAGCTACAAGTTACAAA
66 GTGGAACAGATTAAAGCTACAAGTTACAAA
* * * ** * * * *
5239437 TCTTATCTCCCTAAAGTTACAATGGAGTAGATTAAAG-TCA-CAAATCTTATCTCCCTAAAGATG
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAT-AGCGAATCTTATTTCCCTGAAG-TG
* * * *
5239500 CAATGGAGCAGATTAAAG--A-TAG---CGAA
64 CAGTGGAACAGATTAAAGCTACAAGTTACAAA
*
5239526 TCTTATTTCCCTGAAG-TGCAGTGGAACAGATTGAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG
5239562 CTACAAGTTA
Statistics
Matches: 351, Mismatches: 55, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
88 15 0.04
89 17 0.05
92 2 0.01
93 1 0.00
94 52 0.15
95 178 0.51
96 86 0.25
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (95 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTGCA
GTGGAACAGATTAAAGCTACAAGTTACAAA
Found at i:5239422 original size:190 final size:191
Alignment explanation
Indices: 5239056--5239472 Score: 620
Period size: 190 Copynumber: 2.2 Consensus size: 191
5239046 AAGCTATAAG
* * * * *
5239056 TCTTATCTCCCTGAAGTTGCAGTGAAACAAATTAAATATAGCGAATATTATTTCCCTGAAGTTGC
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAATATAGCGAATATTATTTCCCTGAAGTTAC
* * * * * *
5239121 AATGGAATAGATTAAAGGTACAAGTTATAAATCTTATCTCCCTGAAGATGTAGTGGAACAGATTG
66 AATGGAACAGATTAAAGCTACAAGTTACAAATCTTATCTCCCTGAAGATGCAATAGAACAGATTG
* *
5239186 AAGATAGCGAATCTTATTTCCCTGAAGTGCAGTGGAACATATTGAAGCTACAAGTTACAAA
131 AAGATAGCGAATCTTATTTCCCTAAAGTGCAGTGGAACAGATTGAAGCTACAAGTTACAAA
* * * *
5239247 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGATTATAGCGAATCTTATTTCCCTGAATTTAC
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAATATAGCGAATATTATTTCCCTGAAGTTAC
* * *
5239312 AGTGGAACAGATTAAAGCTACAAGTTACAAAT-TTATCTCTCTGAAGATGCAATAGAGCAGATTG
66 AATGGAACAGATTAAAGCTACAAGTTACAAATCTTATCTCCCTGAAGATGCAATAGAACAGATTG
5239376 AAGATAGCGAATCTTATTTCCCTAAAGTGCAGTGGAACAGATTGAAGCTACAAGTTACAAA
131 AAGATAGCGAATCTTATTTCCCTAAAGTGCAGTGGAACAGATTGAAGCTACAAGTTACAAA
* * *
5239437 TCTTATCTCCCTAAAGTTACAATGGAGTAGATTAAA
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA
5239473 GTCACAAATC
Statistics
Matches: 201, Mismatches: 25, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
190 117 0.58
191 84 0.42
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (191 bp):
TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAATATAGCGAATATTATTTCCCTGAAGTTAC
AATGGAACAGATTAAAGCTACAAGTTACAAATCTTATCTCCCTGAAGATGCAATAGAACAGATTG
AAGATAGCGAATCTTATTTCCCTAAAGTGCAGTGGAACAGATTGAAGCTACAAGTTACAAA
Found at i:5239495 original size:44 final size:44
Alignment explanation
Indices: 5239427--5239828 Score: 371
Period size: 44 Copynumber: 9.0 Consensus size: 44
5239417 TTGAAGCTAC
* * * *
5239427 AAGTTACAAATCTTATCTCCCTAAAGTTACAATGGAGTAGATTA
1 AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA
* * * *
5239471 AAGTCACAAATCTTATCTCCCTAAAGATGCAATGGAGCAGATTA
1 AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA
* * * *
5239515 AAGAT-AGCGAATCTTATTTCCCTGAAG-TGCAGTGGAACAGATTGAAGCTA
1 AAG-TCA-CAAATCTTATCTCCCTGAAGTTGCAGTGG---AG-TAG-A-TTA
* *
5239565 CAAGTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTA
1 -AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA
* *
5239610 AAGTCACAAATCTTATCTCCCTGAAGTTGTAGTGGAGTATATTA
1 AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA
* * * * *
5239654 AAGTTACAAATCTCATCTCCCTGAAGTTACAATGGAGTAGATTG
1 AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA
* * * * * * * *
5239698 AAGAT-ACGAGTATCATCTCTCTGAAGTTGCAGTAGAGCAAATTA
1 AAG-TCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA
*
5239742 AAG-CTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTG
1 AAGTC-ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA
* * * *
5239786 AAGTCACAGATCTCATCTCCCTGAAGTTACAGTAGAGTAGATT
1 AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT
5239829 GAAGATTGAA
Statistics
Matches: 293, Mismatches: 50, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
44 230 0.78
45 22 0.08
46 1 0.00
47 4 0.01
48 3 0.01
49 1 0.00
50 20 0.07
51 12 0.04
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (44 bp):
AAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA
Found at i:5239580 original size:95 final size:95
Alignment explanation
Indices: 5239471--5239645 Score: 255
Period size: 95 Copynumber: 1.8 Consensus size: 95
5239461 GAGTAGATTA
* *
5239471 AAGTCACAAATCTTATCTCCCTAAAGATGCAATGGAGCAGATTAAAGAT-AGCGAATCTTATTTC
1 AAGTCACAAATCTTATCTCCCTAAAGATGCAATGGAGCAGATTAAAG-TCA-CAAATCTTATCTC
5239535 CCTGAAG-TGCAGTGGAACAGATTGAAGCTAC
64 CCTGAAGTTGCAGTGGAACAGATTGAAGCTAC
* * * *
5239566 AAGTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGTCACAAATCTTATCTCCC
1 AAGTCACAAATCTTATCTCCCTAAAGATGCAATGGAGCAGATTAAAGTCACAAATCTTATCTCCC
*
5239631 TGAAGTTGTAGTGGA
66 TGAAGTTGCAGTGGA
5239646 GTATATTAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
94 19 0.27
95 52 0.73
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (95 bp):
AAGTCACAAATCTTATCTCCCTAAAGATGCAATGGAGCAGATTAAAGTCACAAATCTTATCTCCC
TGAAGTTGCAGTGGAACAGATTGAAGCTAC
Found at i:5239646 original size:139 final size:140
Alignment explanation
Indices: 5238922--5239784 Score: 616
Period size: 139 Copynumber: 6.2 Consensus size: 140
5238912 CACCGTGATG
* * ** * * *
5238922 AATCTTATCTTCCTGAAGTGGCAGTGGAAAAGATTAAAG-TCA-CAAATTTTATCTCCCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAT-AGCGAATCTTATTTCCCTGAAGT
* * ** * * * * * *
5238985 TACAGCGGAGTAGATTGAAG--A-TAG---CAAATATTATCTCTCTGAAATTGTA-TAGAGCAGA
65 TGCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
*
5239043 TTAAAG-CTATA
130 TTAAAGTC-ACA
* * * * * *
5239054 AGTCTTATCTCCCTGAAGTTGCAGTGAAACAAATTAAATATAGCGAATATTATTTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCGAATCTTATTTCCCTGAAGTT
* * * * * * * *
5239119 GCAATGGAATAGATTAAAGGTACAAGTTATAAATCTTATCTCCCTGAAGATGTAGTGGAACAGAT
66 GCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
* *
5239184 TGAAGAT-AGCG
131 TAAAG-TCA-CA
* * * * * * *
5239195 AATCTTATTTCCCTGAAG-TGCAGTGGAACATATTGAAGCTACAAGTTACAAATCTTATCTCCCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--A-TAG---CGAATCTTATTTCCCT
* * * * * * * *
5239259 AAAGTTGCAGTGGAGCAGATTG-A-TTA-TAG---CGAATCTTATTTCCCTGAATTTACAGTGGA
60 GAAGTTGCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGA
*
5239318 ACAGATTAAAGCTACAAGTTACA
125 GCAGATTAAAG-T-C-----ACA
* * * * * *
5239341 AAT-TTATCTCTCTGAAGATGCAATAGAGCAGATTGAAGATAGCGAATCTTATTTCCCTAAAG-T
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCGAATCTTATTTCCCTGAAGTT
* * * *
5239404 GCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTATCTCCCTAAAGTTACAATGGAGTAGAT
66 GCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
5239469 TAAAGTCACA
131 TAAAGTCACA
* * *
5239479 AATCTTATCTCCCTAAAGATGCAATGGAGCAGATTAAAGATAGCGAATCTTATTTCCCTGAAG-T
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCGAATCTTATTTCCCTGAAGTT
* *
5239543 GCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGAT
66 GCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
5239608 TAAAGTCACA
131 TAAAGTCACA
* * * * * * *
5239618 AATCTTATCTCCCTGAAGTTGTAGTGGAGTATATTAAAGTTA-CAAATCTCATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCGAATCTTATTTCCCTGAAGTT
* * ** * * * * *
5239682 ACAATGGAGTAGATTGAAGATACGAG-T----ATC--ATCTCTCTGAAGTTGCAGTAGAGCAAAT
66 GCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
5239740 TAAAG-CTACA
131 TAAAGTC-ACA
*
5239750 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
5239785 GAAGTCACAG
Statistics
Matches: 594, Mismatches: 102, Indels: 70
0.78 0.13 0.09
Matches are distributed among these distances:
131 1 0.00
132 97 0.16
133 34 0.06
134 3 0.01
135 1 0.00
136 2 0.00
138 24 0.04
139 220 0.37
140 82 0.14
141 18 0.03
142 3 0.01
143 7 0.01
144 4 0.01
145 47 0.08
146 50 0.08
147 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (140 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCGAATCTTATTTCCCTGAAGTT
GCAGTGGAACAGATTGAAGCTACAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
TAAAGTCACA
Found at i:5253185 original size:20 final size:21
Alignment explanation
Indices: 5253148--5253189 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5253138 CAAAAAAAAT
*
5253148 GTTTTTCCTATAAAAATCCAA
1 GTTTTTACTATAAAAATCCAA
*
5253169 GTTTTTACTAT-AGAATCCAA
1 GTTTTTACTATAAAAATCCAA
5253189 G
1 G
5253190 GTAATTCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
GTTTTTACTATAAAAATCCAA
Found at i:5254397 original size:61 final size:59
Alignment explanation
Indices: 5254273--5254435 Score: 152
Period size: 57 Copynumber: 2.7 Consensus size: 59
5254263 TAAAAAGATA
** * *
5254273 ATTATTAAATTTAATTTAATAAAAATGAAAATAAATAATTTAATCATATTTTAACATAATT
1 ATTATTAAATACAATTTAATAAAAAT--AAATAAATAATTTAATAACATTTTAACATAATT
* *
5254334 ATTATTAAATACAATTTAAT-AAAAT-AATATATAATTTAATAACATTCTTAATATAATT
1 ATTATTAAATACAATTTAATAAAAATAAATAAATAATTTAATAACATT-TTAACATAATT
* * * *
5254392 TTTATTAAAGTATAAATTAA-AAAAATCATAATATATAATATTAA
1 ATTATTAAA-TACAATTTAATAAAAAT-A-AATAAATAAT-TTAA
5254436 AAAATAATAT
Statistics
Matches: 86, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
57 18 0.21
58 18 0.21
59 13 0.15
60 5 0.06
61 18 0.21
62 10 0.12
63 4 0.05
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (59 bp):
ATTATTAAATACAATTTAATAAAAATAAATAAATAATTTAATAACATTTTAACATAATT
Found at i:5254437 original size:23 final size:22
Alignment explanation
Indices: 5254402--5254448 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
5254392 TTTATTAAAG
*
5254402 TATAAATTAAAAAAATCATAATA
1 TATAAATTAAAAAAATAAT-ATA
5254425 TATAATATT-AAAAAATAATATA
1 TATAA-ATTAAAAAAATAATATA
5254447 TA
1 TA
5254449 ACCTAGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 14 0.64
24 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
TATAAATTAAAAAAATAATATA
Found at i:5262440 original size:2 final size:2
Alignment explanation
Indices: 5262433--5262463 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5262423 GTTATTTTAA
5262433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5262464 ATCATACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5265198 original size:3 final size:3
Alignment explanation
Indices: 5265190--5265218 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5265180 TTTCGATTCA
5265190 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5265219 TGCTCTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:5269052 original size:27 final size:27
Alignment explanation
Indices: 5268994--5269056 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
5268984 CATTATCGAG
* * *
5268994 GGGACCCGACATGAACCCTCTCTCGAT
1 GGGACCCGACATAAACCCTCTCTCCAA
* *
5269021 CGGACCCGACATAAACCCTCTTTCCAA
1 GGGACCCGACATAAACCCTCTCTCCAA
5269048 GGGACCCGA
1 GGGACCCGA
5269057 ACCTGGAACG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.38, G:0.21, T:0.16
Consensus pattern (27 bp):
GGGACCCGACATAAACCCTCTCTCCAA
Found at i:5273409 original size:26 final size:26
Alignment explanation
Indices: 5273350--5273410 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
5273340 TATTAATTAC
*
5273350 TAAATATTATTTAATTTTCAATAGTTT
1 TAAATATT-TTTAATTTTCAATAATTT
* *
5273377 T-ACTATTTTTTATTTT-AATAATATT
1 TAAATATTTTTAATTTTCAATAAT-TT
5273402 TAAATATTT
1 TAAATATTT
5273411 GTAAATAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
24 5 0.18
25 11 0.39
26 11 0.39
27 1 0.04
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (26 bp):
TAAATATTTTTAATTTTCAATAATTT
Found at i:5286108 original size:2 final size:2
Alignment explanation
Indices: 5286101--5286126 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5286091 TGATTCATAC
5286101 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5286127 TTACAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5295528 original size:26 final size:28
Alignment explanation
Indices: 5295449--5295529 Score: 114
Period size: 27 Copynumber: 3.0 Consensus size: 28
5295439 TCAGGCCAAT
*
5295449 TAAATTGGCGGCACCAAAGGTGCCAAA-
1 TAAATTGGCGGCACCAATGGTGCCAAAG
*
5295476 TAAATTGGTGGCACCAATGGTGCCAAAG
1 TAAATTGGCGGCACCAATGGTGCCAAAG
*
5295504 T-CATTGGCGGCACC-ATGGTGCCAAAG
1 TAAATTGGCGGCACCAATGGTGCCAAAG
5295530 GAAAAAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 12 0.24
27 36 0.73
28 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (28 bp):
TAAATTGGCGGCACCAATGGTGCCAAAG
Found at i:5295639 original size:18 final size:19
Alignment explanation
Indices: 5295603--5295672 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
5295593 TCAACTCATT
*
5295603 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
5295622 TTTTAATTTAATAA-TCTA
1 TTTTAATTTAATAACTCTA
* *
5295640 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
5295659 TTTTAATTTAATAA
1 TTTTAATTTAATAA
5295673 ACTATTAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
18 16 0.36
19 29 0.64
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:5295653 original size:37 final size:37
Alignment explanation
Indices: 5295608--5295678 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
5295598 TCATTTTTTT
*
5295608 ATTTAATAACTCTATTTTAATTTAATAATCTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
5295645 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
5295679 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:5296086 original size:19 final size:19
Alignment explanation
Indices: 5296017--5296085 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
5296007 NNNNNNNNNT
5296017 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* *
5296036 TTATTAAATGAGAATAGA-
1 TTATTAAATTAAAATAGAG
5296054 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
5296073 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
5296086 AAATGAGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
18 21 0.47
19 24 0.53
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:5296209 original size:27 final size:27
Alignment explanation
Indices: 5296160--5296237 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
5296150 CTTTTTTTTC
5296160 CTTTGGCACCA-TGGTGCCGCCAATGA
1 CTTTGGCACCATTGGTGCCGCCAATGA
* *
5296186 CTTTGGCACCATTGGTGCCACCAATTTA
1 CTTTGGCACCATTGGTGCCGCCAA-TGA
*
5296214 -TTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
5296238 TTAATTGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.26
27 32 0.70
28 2 0.04
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATGA
Found at i:5296238 original size:27 final size:26
Alignment explanation
Indices: 5296161--5296246 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 26
5296151 TTTTTTTTCC
* *
5296161 TTTGGCACCATGGTGCCGCCAA-TGA
1 TTTGGCACCTTGGTGCCGCCAATTTA
*
5296186 CTTTGGCACCATTGGTGCCACCAATTTA
1 -TTTGGCACC-TTGGTGCCGCCAATTTA
5296214 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACC-TTGGTGCCGCCAATTTA
*
5296241 ATTGGC
1 TTTGGC
5296247 CTGATCAGGC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 9 0.17
27 41 0.79
28 2 0.04
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (26 bp):
TTTGGCACCTTGGTGCCGCCAATTTA
Found at i:5302051 original size:20 final size:19
Alignment explanation
Indices: 5302007--5302052 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
5301997 ACTGTTTTTA
* *
5302007 AAAATTAAATAAAAATATT
1 AAAATTAAAAAAAAACATT
5302026 ATAAATTAAAAAAAAACATT
1 A-AAATTAAAAAAAAACATT
5302046 GAAAATT
1 -AAAATT
5302053 GGAATGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATTAAAAAAAAACATT
Found at i:5306766 original size:109 final size:110
Alignment explanation
Indices: 5306573--5306883 Score: 432
Period size: 110 Copynumber: 2.9 Consensus size: 110
5306563 GATTGAAATC
* * * * * * * *
5306573 AAAAGGATATTTGGCTATTTGTTTAAACGAG--AAATCGAAACCCAGCTCATTAGGGCACG-TTC
1 AAAAGGATATTTAGCTATTTGCTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
*
5306635 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTGAGAA-TTTTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTT
* * *
5306679 AAAAGGATATTTAGCAATTTGCTTGAATGAGAAAAATCGACACCCAACACCTTAGGGCATGTTTT
1 AAAAGGATATTTAGCTATTTGCTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
*
5306744 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTT
* *
5306789 AAAAGGATATTAAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
1 AAAAGGATATTTAGCTATTTGCTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
* *
5306854 CTCGAATTTCCCAAACGCTAAATATTGCCT
66 CTCGAATTT-CCAAACGCAAAACATTGCCT
5306884 CAATTAGAAA
Statistics
Matches: 180, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
106 26 0.14
108 23 0.13
109 39 0.22
110 74 0.41
111 18 0.10
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (110 bp):
AAAAGGATATTTAGCTATTTGCTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTT
CTCGAATTTCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTT
Found at i:5309112 original size:83 final size:84
Alignment explanation
Indices: 5308972--5309139 Score: 329
Period size: 83 Copynumber: 2.0 Consensus size: 84
5308962 GGTTATCAAG
5308972 TGAATTATATATATATATTTTAAAATAAAATATCACTATAACGAATTTAACAAAAAAATTTAACC
1 TGAATTATATATATATATTTTAAAATAAAATATCACTATAACGAATTTAACAAAAAAATTTAACC
5309037 ATAACAATTGGACCTAAAT
66 ATAACAATTGGACCTAAAT
5309056 TGAATTATATA-ATATATTTTAAAATAAAATATCACTATAACGAATTTAACAAAAAAATTTAACC
1 TGAATTATATATATATATTTTAAAATAAAATATCACTATAACGAATTTAACAAAAAAATTTAACC
5309120 ATAACAATTGGACCTAAAT
66 ATAACAATTGGACCTAAAT
5309139 T
1 T
5309140 TTCAATTTTG
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 73 0.87
84 11 0.13
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (84 bp):
TGAATTATATATATATATTTTAAAATAAAATATCACTATAACGAATTTAACAAAAAAATTTAACC
ATAACAATTGGACCTAAAT
Found at i:5314764 original size:19 final size:19
Alignment explanation
Indices: 5314742--5314779 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5314732 ATTTTTTGAA
* *
5314742 TTTTTAAAATTTTTAAAAT
1 TTTTTAAAAATTTAAAAAT
5314761 TTTTTAAAAATTTAAAAAT
1 TTTTTAAAAATTTAAAAAT
5314780 AAAAAAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTAAAAATTTAAAAAT
Found at i:5314774 original size:27 final size:27
Alignment explanation
Indices: 5314725--5314777 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
5314715 TAAAAATAAA
* * **
5314725 TTTTATAATTTTTTGAATTTTTAAAAT
1 TTTTAAAATTTTTTAAAAATTTAAAAT
5314752 TTTTAAAATTTTTTAAAAATTTAAAA
1 TTTTAAAATTTTTTAAAAATTTAAAA
5314778 ATAAAAAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTAAAATTTTTTAAAAATTTAAAAT
Found at i:5316239 original size:12 final size:13
Alignment explanation
Indices: 5316216--5316248 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5316206 AATCTATTTT
*
5316216 ATAATTTTAATAA
1 ATAATTTAAATAA
5316229 AT-ATTTAAATAA
1 ATAATTTAAATAA
5316241 ATAATTTA
1 ATAATTTA
5316249 TTATTTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAATTTAAATAA
Found at i:5316874 original size:33 final size:34
Alignment explanation
Indices: 5316775--5316939 Score: 163
Period size: 34 Copynumber: 4.7 Consensus size: 34
5316765 TATTAAATCA
* *
5316775 CATATTATATAACATGTGGGTTTGCATACTATGT
1 CATATTATATAACATGAGGGTTCGCATACTATGT
* * * *
5316809 CAT-TCAATAGAACGTGAGGGTTCGCATTCTATGT
1 CATAT-TATATAACATGAGGGTTCGCATACTATGT
*
5316843 CATATTATATAACATG-GGGTTCACATACTATGT
1 CATATTATATAACATGAGGGTTCGCATACTATGT
* *
5316876 CATACTATATAACATGAGGGTTGGGTTCGCATACTATAT
1 CATATTATATAACATGA-----GGGTTCGCATACTATGT
* *
5316915 CATACTACATAACATGAGGGTTCGC
1 CATATTATATAACATGAGGGTTCGC
5316940 CTAACAGTTC
Statistics
Matches: 108, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
33 31 0.29
34 45 0.42
35 1 0.01
39 31 0.29
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (34 bp):
CATATTATATAACATGAGGGTTCGCATACTATGT
Found at i:5316918 original size:39 final size:39
Alignment explanation
Indices: 5316859--5316936 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
5316849 ATATAACATG
* *
5316859 GGGTTCACATACTATGTCATACTATATAACATGAGGGTT
1 GGGTTCACATACTATATCATACTACATAACATGAGGGTT
*
5316898 GGGTTCGCATACTATATCATACTACATAACATGAGGGTT
1 GGGTTCACATACTATATCATACTACATAACATGAGGGTT
5316937 CGCCTAACAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (39 bp):
GGGTTCACATACTATATCATACTACATAACATGAGGGTT
Found at i:5318465 original size:23 final size:23
Alignment explanation
Indices: 5318416--5318462 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
5318406 NNNNNAGGAT
*
5318416 TATTTTTTATATAAATTTTTTTA
1 TATTTTTTATATAAATTTTTATA
*
5318439 TATTTTTTAT-T-AATTTATATA
1 TATTTTTTATATAAATTTTTATA
5318460 TAT
1 TAT
5318463 ATTAATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 1 0.05
23 10 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TATTTTTTATATAAATTTTTATA
Found at i:5320650 original size:84 final size:84
Alignment explanation
Indices: 5320548--5320717 Score: 261
Period size: 84 Copynumber: 2.0 Consensus size: 84
5320538 CACAAAACAA
*
5320548 TTGATAAAATTCCATTTTTAATGGTACTATAATTTTGCTGAGTAGGA-TTCTAGTGTCTGGAAGT
1 TTGATAAAATTCCATTTTTAATAGTACTATAATTTTGCTGAGTAGGATTTC-AGTGTCTGGAAGT
*
5320612 AAATTGGAATATTTGCTCTT
65 AAACTGGAATATTTGCTCTT
* * * *
5320632 TTGATAAATTTTCTTTTTTAATAGTACTATAATTTTGCTGAGTAGGATTTCAGTGTTTGGAAGTA
1 TTGATAAAATTCCATTTTTAATAGTACTATAATTTTGCTGAGTAGGATTTCAGTGTCTGGAAGTA
*
5320697 AACTGGACTATTTGCTCTT
66 AACTGGAATATTTGCTCTT
5320716 TT
1 TT
5320718 CCTCCTTTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 75 0.96
85 3 0.04
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (84 bp):
TTGATAAAATTCCATTTTTAATAGTACTATAATTTTGCTGAGTAGGATTTCAGTGTCTGGAAGTA
AACTGGAATATTTGCTCTT
Found at i:5327559 original size:9 final size:9
Alignment explanation
Indices: 5327545--5327573 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
5327535 TTTCAAATCA
5327545 CAACCAATT
1 CAACCAATT
5327554 CAACCAATT
1 CAACCAATT
5327563 CAACCAATT
1 CAACCAATT
5327572 CA
1 CA
5327574 TTTCACATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (9 bp):
CAACCAATT
Found at i:5331602 original size:870 final size:868
Alignment explanation
Indices: 5329925--5331663 Score: 3460
Period size: 870 Copynumber: 2.0 Consensus size: 868
5329915 TCTATATATA
5329925 TATACATGCATTTTGATGTATAATTATAAAGTATGTACATGCCTACATTTTCTTAATATATATAC
1 TATACATGCATTTTGATGTATAATTATAAAGTATGTACATGCCTACATTTTCTTAATATATATAC
5329990 ATATATTACAATATATATATAAATATACATTTATCCTTTTATTATTATTTTATAACTTATGTACA
66 ATATATTACAATATATATATAAATATACATTTATCCTTTTATTATTATTTTATAACTTATGTACA
5330055 TATTTACGTATTTATATACCTTTTTAATATATATATTATATTTTTATACCTTATATCATTTATAT
131 TATTTACGTATTTATATACCTTTTTAATATATATATTATATTTTTATACCTTATATCATTTATAT
5330120 ATCTTTATATACACACTTTTAATTTTCATATATATATATATATATATACATGTTTGCATATTTCT
196 ATCTTTATATACACACTTTTAATTTTCATATATATATATATATATATACATGTTTGCATATTTCT
5330185 TATTATATCTTATACTTTATATACATATACATATATCCTATCGCATCTTTATAATTATAATTCAT
261 TATTATATCTTATACTTTATATACATATACATATATCCTATCGCATCTTTATAATTATAATTCAT
5330250 TTATTATCTATTCATTCACGCTTTCATTATTATTTTAAAAATGTTTCACTTTTATTTTGTTTATA
326 TTATTATCTATTCATTCACGCTTTCATTATTATTTTAAAAATGTTTCACTTTTATTTTGTTTATA
5330315 CACTCGTTATTCGGCCTGCTATTGATTCGTCATTTTTTTTATCTTATTTTTGTCACTATCGTTCG
391 CACTCGTTATTCGGCCTGCTATTGATTCGTCATTTTTTTTATCTTATTTTTGTCACTATCGTTCG
5330380 TATTACGTTACACTATCGTATTTATTATTGTTTCGCATGCGTATCCAATGTAATTTGTTTTCGCA
456 TATTACGTTACACTATCGTATTTATTATTGTTTCGCATGCGTATCCAATGTAATTTGTTTTCGCA
5330445 TTTTTCACGACATCATATTTTACTTTATTCAATATATCAAAACTCGTTTTTTTTTGTATTTCGAT
521 TTTTTCACGACATCATATTTTACTTTATTCAATATATCAAAACTCGTTTTTTTTTGTATTTCGAT
5330510 ATTCGAAAAATCGTACCTTAACTTACGGGGTTTCAATTTTCTCGACAAATCTAGATATGCGAATC
586 ATTCGAAAAATCGTACCTTAACTTACGGGGTTTCAATTTTCTCGACAAATCTAGATATGCGAATC
5330575 ATTTCAAACAAAAGTTTTATATGCTCTCAGGAATTAATGAAATATCGTGTTCTAACTCACGGGAC
651 ATTTCAAACAAAAGTTTTATATGCTCTCAGGAATTAATGAAATATCGTGTTCTAACTCACGGGAC
5330640 ATGATCTCTTTCCTAAACCCGAGATGATCAAATATCTTTCAAGATAAGTAAATTCTTTTTCGGTA
716 ATGATCTCTTTCCTAAACCCGAGATGATCAAATATCTTTCAAGATAAGTAAATTCTTTTTCGGTA
5330705 TTCATTTTCGCATCGGGAAATCGAGACATTGTGTCCTAACTTACGGGATATAATTTTTTTTCTCG
781 TTCATTTTCGCATCGGGAAATCGAGACATTGTGTCCTAACTTACGGGATATAATTTTTTTTCTCG
5330770 ATTAACGTGAAATATACCCCCTT
846 ATTAACGTGAAATATACCCCCTT
5330793 TATACATGCATTTTGATGTATAATTATAAAGTATGTACATGCCTACATTTTCTTAATATATATAC
1 TATACATGCATTTTGATGTATAATTATAAAGTATGTACATGCCTACATTTTCTTAATATATATAC
5330858 ATATATTACAATATATATATAAATATACATTTATCCTTTTATTATTATTTTATAACTTATGTACA
66 ATATATTACAATATATATATAAATATACATTTATCCTTTTATTATTATTTTATAACTTATGTACA
5330923 TATTTACGTATTTATATACCTTTTTAATATATATATTATATTTTTATACCTTATATCATTTATAT
131 TATTTACGTATTTATATACCTTTTTAATATATATATTATATTTTTATACCTTATATCATTTATAT
5330988 ATCTTTATATACACACTTTTAATTTTCATATATATATATATATATATATACATGTTTGCATATTT
196 ATCTTTATATACACACTTTTAATTTTC--ATATATATATATATATATATACATGTTTGCATATTT
5331053 CTTATTATATCTTATACTTTATATACATATACATATATCCTATCGCATCTTTATAATTATAATTC
259 CTTATTATATCTTATACTTTATATACATATACATATATCCTATCGCATCTTTATAATTATAATTC
5331118 ATTTATTATCTATTCATTCACGCTTTCATTATTATTTTAAAAATGTTTCACTTTTATTTTGTTTA
324 ATTTATTATCTATTCATTCACGCTTTCATTATTATTTTAAAAATGTTTCACTTTTATTTTGTTTA
5331183 TACACTCGTTATTCGGCCTGCTATTGATTCGTCATTTTTTTTATCTTATTTTTGTCACTATCGTT
389 TACACTCGTTATTCGGCCTGCTATTGATTCGTCATTTTTTTTATCTTATTTTTGTCACTATCGTT
5331248 CGTATTACGTTACACTATCGTATTTATTATTGTTTCGCATGCGTATCCAATGTAATTTGTTTTCG
454 CGTATTACGTTACACTATCGTATTTATTATTGTTTCGCATGCGTATCCAATGTAATTTGTTTTCG
5331313 CATTTTTCACGACATCATATTTTACTTTATTCAATATATCAAAACTCGTTTTTTTTTGTATTTCG
519 CATTTTTCACGACATCATATTTTACTTTATTCAATATATCAAAACTCGTTTTTTTTTGTATTTCG
5331378 ATATTCGAAAAATCGTACCTTAACTTACGGGGTTTCAATTTTCTCGACAAATCTAGATATGCGAA
584 ATATTCGAAAAATCGTACCTTAACTTACGGGGTTTCAATTTTCTCGACAAATCTAGATATGCGAA
5331443 TCATTTCAAACAAAAGTTTTATATGCTCTCAGGAATTAATGAAATATCGTGTTCTAACTCACGGG
649 TCATTTCAAACAAAAGTTTTATATGCTCTCAGGAATTAATGAAATATCGTGTTCTAACTCACGGG
5331508 ACATGATCTCTTTCCTAAACCCGAGATGATCAAATATCTTTCAAGATAAGTAAATTCTTTTTCGG
714 ACATGATCTCTTTCCTAAACCCGAGATGATCAAATATCTTTCAAGATAAGTAAATTCTTTTTCGG
5331573 TATTCATTTTCGCATCGGGAAATCGAGACATTGTGTCCTAACTTACGGGATATAATTTTTTTTCT
779 TATTCATTTTCGCATCGGGAAATCGAGACATTGTGTCCTAACTTACGGGATATAATTTTTTTTCT
5331638 CGATTAACGTGAAATATACCCCCTT
844 CGATTAACGTGAAATATACCCCCTT
5331663 T
1 T
5331664 TTCTTGAAAT
Statistics
Matches: 869, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
868 222 0.26
870 647 0.74
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (868 bp):
TATACATGCATTTTGATGTATAATTATAAAGTATGTACATGCCTACATTTTCTTAATATATATAC
ATATATTACAATATATATATAAATATACATTTATCCTTTTATTATTATTTTATAACTTATGTACA
TATTTACGTATTTATATACCTTTTTAATATATATATTATATTTTTATACCTTATATCATTTATAT
ATCTTTATATACACACTTTTAATTTTCATATATATATATATATATATACATGTTTGCATATTTCT
TATTATATCTTATACTTTATATACATATACATATATCCTATCGCATCTTTATAATTATAATTCAT
TTATTATCTATTCATTCACGCTTTCATTATTATTTTAAAAATGTTTCACTTTTATTTTGTTTATA
CACTCGTTATTCGGCCTGCTATTGATTCGTCATTTTTTTTATCTTATTTTTGTCACTATCGTTCG
TATTACGTTACACTATCGTATTTATTATTGTTTCGCATGCGTATCCAATGTAATTTGTTTTCGCA
TTTTTCACGACATCATATTTTACTTTATTCAATATATCAAAACTCGTTTTTTTTTGTATTTCGAT
ATTCGAAAAATCGTACCTTAACTTACGGGGTTTCAATTTTCTCGACAAATCTAGATATGCGAATC
ATTTCAAACAAAAGTTTTATATGCTCTCAGGAATTAATGAAATATCGTGTTCTAACTCACGGGAC
ATGATCTCTTTCCTAAACCCGAGATGATCAAATATCTTTCAAGATAAGTAAATTCTTTTTCGGTA
TTCATTTTCGCATCGGGAAATCGAGACATTGTGTCCTAACTTACGGGATATAATTTTTTTTCTCG
ATTAACGTGAAATATACCCCCTT
Found at i:5340717 original size:24 final size:24
Alignment explanation
Indices: 5340689--5340740 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5340679 TTAGTAAGTC
* *
5340689 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
5340713 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
5340737 AAAT
1 AAAT
5340741 TTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Done.