Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 144 of 230
Found at i:42462238 original size:32 final size:30
Alignment explanation
Indices: 42462193--42462253 Score: 95
Period size: 32 Copynumber: 2.0 Consensus size: 30
42462183 TGGGTTATTG
*
42462193 GGCTTGTTTGGGTTGAGGGTTAATTGGGCT
1 GGCTTGTTTGGGTTGAGAGTTAATTGGGCT
42462223 GGCTTGTAATTGGGTTGAGAGTTAATTGGGC
1 GGCTTGT--TTGGGTTGAGAGTTAATTGGGC
42462254 CCAAGCATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 7 0.25
32 21 0.75
ACGTcount: A:0.15, C:0.07, G:0.41, T:0.38
Consensus pattern (30 bp):
GGCTTGTTTGGGTTGAGAGTTAATTGGGCT
Found at i:42462248 original size:16 final size:16
Alignment explanation
Indices: 42462200--42462252 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
42462190 TTGGGCTTGT
*
42462200 TTGGGTTGAGGGTTAA
1 TTGGGTTGAGAGTTAA
* **
42462216 TTGGGCTG-GCTTGTAA
1 TTGGGTTGAGAGT-TAA
42462232 TTGGGTTGAGAGTTAA
1 TTGGGTTGAGAGTTAA
42462248 TTGGG
1 TTGGG
42462253 CCCAAGCATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 25 0.86
17 2 0.07
ACGTcount: A:0.17, C:0.04, G:0.42, T:0.38
Consensus pattern (16 bp):
TTGGGTTGAGAGTTAA
Found at i:42462674 original size:44 final size:43
Alignment explanation
Indices: 42462606--42462808 Score: 216
Period size: 44 Copynumber: 4.7 Consensus size: 43
42462596 GATGCGATCT
*
42462606 ACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
1 ACTCCACTGCAACTTCAGAGAGATAAGAT-TGTGGTTTTAATCC
* * *
42462650 ACTCCACTGCAACTTCAGAGAGATAGGATTAGT-TTCTTTAATCT
1 ACTCCACTGCAACTTCAGAGAGATAAGATT-GTGGT-TTTAATCC
* *** *
42462694 ACTCCACTGCAACTTCAGGGAGATAAGATTG-GG-TACGATCT
1 ACTCCACTGCAACTTCAGAGAGATAAGATTGTGGTTTTAATCC
* * *
42462735 GCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
1 ACTCCACTGCAACTTCAGAGAGATAAGAT-TGTGGTTTTAATCC
*
42462779 ACTCCACTGCAACTTCATG-GAGATAGGATT
1 ACTCCACTGCAACTTCA-GAGAGATAAGATT
42462809 TGCTATCTTC
Statistics
Matches: 130, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
41 30 0.23
42 2 0.02
43 6 0.05
44 91 0.70
45 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (43 bp):
ACTCCACTGCAACTTCAGAGAGATAAGATTGTGGTTTTAATCC
Found at i:42462957 original size:45 final size:45
Alignment explanation
Indices: 42462908--42463083 Score: 280
Period size: 45 Copynumber: 3.9 Consensus size: 45
42462898 TTTGATTTGT
* * *
42462908 TTCGCTGCTAGTACAGGAAGACAAGATCTACTATCTTTGATCTAC
1 TTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCTAC
42462953 TTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCTAC
1 TTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCTAC
* * *
42462998 TTTGCTACCAGTACAGGAAGACAAGATCTGCTAACTTCGATCTAC
1 TTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCTAC
* *
42463043 TTCGCTGCCAATACAGGAAGACAAGATCTGCTACCTTCGAT
1 TTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGAT
42463084 GATTTGTTCT
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 121 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (45 bp):
TTCGCTGCCAGTACAGGAAGACAAGATCTGCTATCTTCGATCTAC
Found at i:42471549 original size:9 final size:9
Alignment explanation
Indices: 42471532--42471562 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42471522 AGGGTCTTTT
*
42471532 AATGCAATG
1 AATGAAATG
42471541 AATGAAATG
1 AATGAAATG
42471550 AATGAAATG
1 AATGAAATG
42471559 AATG
1 AATG
42471563 CAAAAAAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.23
Consensus pattern (9 bp):
AATGAAATG
Found at i:42475398 original size:9 final size:9
Alignment explanation
Indices: 42475368--42475396 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
42475358 ATAAATAAAT
42475368 AAATTAACA
1 AAATTAACA
42475377 AAATTAACA
1 AAATTAACA
42475386 AAATT-ACA
1 AAATTAACA
42475394 AAA
1 AAA
42475397 ATCTAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATTAACA
Found at i:42475851 original size:3 final size:3
Alignment explanation
Indices: 42475843--42475905 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
42475833 AAAATAAAAT
* * *
42475843 TAA TAA TAA CTAA TAA AAA TGA TAA TAA TAA AAA TAA TAA TAA -AA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42475888 TAA TTAA CTAAA TAA TAA
1 TAA -TAA -T-AA TAA TAA
42475906 AATTGCTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 2 0.04
3 37 0.76
4 8 0.16
5 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:42475873 original size:15 final size:15
Alignment explanation
Indices: 42475844--42475907 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
42475834 AAATAAAATT
42475844 AATAATAACTAATAAA
1 AATAATAA-TAATAAA
*
42475860 AATGATAATAATAAA
1 AATAATAATAATAAA
42475875 AATAATAATAA-AATA
1 AATAATAATAATAA-A
*
42475890 ATTAACTAAATAATAAA
1 AATAA-T-AATAATAAA
42475907 A
1 A
42475908 TTGCTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 2 0.05
15 22 0.54
16 8 0.20
17 7 0.17
18 2 0.05
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:42475879 original size:12 final size:12
Alignment explanation
Indices: 42475835--42475905 Score: 51
Period size: 12 Copynumber: 5.9 Consensus size: 12
42475825 ATAAAAGGAA
*
42475835 AATAAAATTAAT
1 AATAAAAATAAT
*
42475847 AAT--AACTAAT
1 AATAAAAATAAT
*
42475857 AA-AAATGATAAT
1 AATAAA-AATAAT
42475869 AATAAAAATAAT
1 AATAAAAATAAT
42475881 AAT-AAAATAATT
1 AATAAAAATAA-T
42475893 AACTAAATAATAA
1 AA-TAAA-AATAA
42475906 AATTGCTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
10 8 0.17
11 8 0.17
12 20 0.43
13 4 0.09
14 2 0.04
15 5 0.11
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:42478468 original size:16 final size:16
Alignment explanation
Indices: 42478447--42478526 Score: 54
Period size: 17 Copynumber: 4.8 Consensus size: 16
42478437 ATATTTTAAA
42478447 TTAAAAATAAAAAATT
1 TTAAAAATAAAAAATT
* * *
42478463 TTAAAAA-ATTATAATC
1 TTAAAAATA-AAAAATT
* *
42478479 TAAAAAATTCAAAAATT
1 TTAAAAA-TAAAAAATT
*
42478496 ATAAAAAATAAAAAATAT
1 -TTAAAAATAAAAAAT-T
*
42478514 TTAAAATTAAAAA
1 TTAAAAATAAAAA
42478527 TTAAAAACAA
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
15 1 0.02
16 17 0.35
17 22 0.46
18 8 0.17
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAATAAAAAATT
Found at i:42478501 original size:9 final size:8
Alignment explanation
Indices: 42478444--42478533 Score: 55
Period size: 8 Copynumber: 11.2 Consensus size: 8
42478434 TTCATATTTT
42478444 AAATT-AA
1 AAATTAAA
42478451 AAA-TAAA
1 AAATTAAA
42478458 AAATTTTAAA
1 AAA--TTAAA
42478468 AAATT--A
1 AAATTAAA
*
42478474 TAATCTAAA
1 AAAT-TAAA
*
42478483 AAATTCAA
1 AAATTAAA
42478491 AAATTATAA
1 AAATTA-AA
*
42478500 AAAATAAA
1 AAATTAAA
**
42478508 AAATATTTA
1 AAAT-TAAA
42478517 AAATT-AA
1 AAATTAAA
42478524 AAATTAAA
1 AAATTAAA
42478532 AA
1 AA
42478534 CAATTTTTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 19
0.70 0.10 0.21
Matches are distributed among these distances:
6 5 0.08
7 15 0.23
8 20 0.31
9 17 0.27
10 7 0.11
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (8 bp):
AAATTAAA
Found at i:42478507 original size:25 final size:24
Alignment explanation
Indices: 42478448--42478533 Score: 68
Period size: 25 Copynumber: 3.5 Consensus size: 24
42478438 TATTTTAAAT
42478448 TAAAAATAAAAAATTTTAAAAAATTA
1 TAAAAATAAAAAA--TTAAAAAATTA
** *
42478474 T-AATCTAAAAAATTCAAAAATTA
1 TAAAAATAAAAAATTAAAAAATTA
**
42478497 TAAAAAATAAAAAATATTTAAAATTA
1 T-AAAAATAAAAAAT-TAAAAAATTA
*
42478523 -AAAATTAAAAA
1 TAAAAATAAAAA
42478534 CAATTTTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
23 11 0.22
24 10 0.20
25 19 0.39
26 9 0.18
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
TAAAAATAAAAAATTAAAAAATTA
Found at i:42480265 original size:124 final size:124
Alignment explanation
Indices: 42480056--42480418 Score: 541
Period size: 124 Copynumber: 2.9 Consensus size: 124
42480046 GGTCCGGGAA
** * * *
42480056 GAAATAATTTTGAGTTGACATTTCTGATCAAATAGAATAAAATCGCTTCTAGCAAGATGCTATTT
1 GAAATAATTTT-TTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTT
* ** *
42480121 GAGAAGAATTTGTGAAATCGCGCCCTCGTGGATACGGTTTTGCTACAGTAGGTCATGGAT
65 GAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAT
42480181 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTG
1 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTG
* *
42480246 AGAAGAATTTGTAAAATCGCGCCCTTGTGGACGCGCTTTTGCTAAAGTAGGTCATGGAT
66 AGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAT
* * * *
42480305 AAAAT-A-TTTTTTTGACGTTTTTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTA
1 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTG
* *
42480368 AGAAGAATTTGTAAAAATCGCGCCCTCGTGGGCGCGTTTTTGCTACAGTAG
66 AGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
42480419 CATGTTTGGG
Statistics
Matches: 218, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
122 66 0.30
123 35 0.16
124 106 0.49
125 11 0.05
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (124 bp):
GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTG
AGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAT
Found at i:42486273 original size:20 final size:20
Alignment explanation
Indices: 42486226--42486274 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
42486216 TTTTCCTTTT
42486226 AATTTTCTTTTATTGCACCAC
1 AATTTTC-TTTATTGCACCAC
* * * *
42486247 AAATTTCTTTCTTGTACTAC
1 AATTTTCTTTATTGCACCAC
42486267 AATTTTCT
1 AATTTTCT
42486275 AACAGAGGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (20 bp):
AATTTTCTTTATTGCACCAC
Found at i:42489143 original size:29 final size:30
Alignment explanation
Indices: 42489088--42489144 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
42489078 TTTTGTTCTT
*
42489088 TCTTTTGTTTTTCTCTGTTTCCCTTTGCTC
1 TCTTTTCTTTTTCTCTGTTTCCCTTTGCTC
*
42489118 TCTTTTCTTCTTTCT-T-TTTCCTTTTGC
1 TCTTTTCTT-TTTCTCTGTTTCCCTTTGC
42489145 GATTGAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 9 0.38
31 5 0.21
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (30 bp):
TCTTTTCTTTTTCTCTGTTTCCCTTTGCTC
Found at i:42490484 original size:3 final size:3
Alignment explanation
Indices: 42490476--42490505 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42490466 TATGTTAACT
42490476 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42490506 ATAAAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42494984 original size:65 final size:65
Alignment explanation
Indices: 42494872--42495014 Score: 153
Period size: 65 Copynumber: 2.2 Consensus size: 65
42494862 GTCGTACCAT
* * ** * * ** *
42494872 AGCTCTTTATGAACGTCTTATTATATGATCGGTTGTGATCTTGCATATATTGGGGACACAAATAC
1 AGCTCTTTGTGAGCGTCTTATTATATGATCAATTGTGATCTTACATATATCGCAGACACAAACAC
* * *
42494937 AGCTCTTTGTGAGCGTCTTGTTTTATGATCAATTGTGATGC-TACATATGTCGCAGACACAAACA
1 AGCTCTTTGTGAGCGTCTTATTATATGATCAATTGTGAT-CTTACATATATCGCAGACACAAACA
42495001 C
65 C
*
42495002 AACTCTTTGTGAG
1 AGCTCTTTGTGAG
42495015 TGTCCTGATA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 63 0.98
66 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (65 bp):
AGCTCTTTGTGAGCGTCTTATTATATGATCAATTGTGATCTTACATATATCGCAGACACAAACAC
Found at i:42495098 original size:26 final size:26
Alignment explanation
Indices: 42495069--42495120 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
42495059 GAAGCTCTTA
* *
42495069 ATTAAAGGCTCTTCGTGAGCTTCCTG
1 ATTAAAAGCTCTTCGTGAACTTCCTG
* *
42495095 ATTAAAAGTTCTTTGTGAACTTCCTG
1 ATTAAAAGCTCTTCGTGAACTTCCTG
42495121 CTTATGCCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (26 bp):
ATTAAAAGCTCTTCGTGAACTTCCTG
Found at i:42510117 original size:26 final size:26
Alignment explanation
Indices: 42510087--42510144 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
42510077 TTGGAGCTCT
*
42510087 TGATTAAAAGCTCTTCATGAGCTTCC
1 TGATTAAAAGCTCTTCATGAACTTCC
* **
42510113 TGATTAAAAGTTCTTTGTGAACTTCC
1 TGATTAAAAGCTCTTCATGAACTTCC
42510139 TGATTA
1 TGATTA
42510145 TGCCTCTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (26 bp):
TGATTAAAAGCTCTTCATGAACTTCC
Found at i:42510229 original size:26 final size:26
Alignment explanation
Indices: 42510193--42510249 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
42510183 TTTCCCGATA
*
42510193 GGCTCTTTGTGAGCTTCATGATTA-AT
1 GGCTCATTGTGAGCTTCATG-TTATAT
* *
42510219 GGCTCATTGTGAGTTTCCTGTTATAT
1 GGCTCATTGTGAGCTTCATGTTATAT
42510245 GGCTC
1 GGCTC
42510250 GAGAGAGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.42
Consensus pattern (26 bp):
GGCTCATTGTGAGCTTCATGTTATAT
Found at i:42515195 original size:44 final size:44
Alignment explanation
Indices: 42515046--42515195 Score: 126
Period size: 44 Copynumber: 3.4 Consensus size: 44
42515036 TAGGGGTAAG
* * * * **
42515046 ATATGTTATGCTATGATATGTGATAAGAAAAGTTTCGATATG-C
1 ATATGATATGCTATGATATGTAATAAGATATGTCCCGATATGAC
* * * * *
42515089 AATATGATATGCTATGACATGTTACTAAG-TAT-ACTCCAATATGAA
1 -ATATGATATGCTATGATATG-TAATAAGATATGTC-CCGATATGAC
* * *
42515134 ATTTGATATGATGTGATATGTAATAAGATATGTCCCGATATGAC
1 ATATGATATGCTATGATATGTAATAAGATATGTCCCGATATGAC
42515178 ATATGATATGCTATGATA
1 ATATGATATGCTATGATA
42515196 CATTCCGTTA
Statistics
Matches: 79, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
43 6 0.08
44 67 0.85
45 6 0.08
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (44 bp):
ATATGATATGCTATGATATGTAATAAGATATGTCCCGATATGAC
Found at i:42517844 original size:39 final size:36
Alignment explanation
Indices: 42517750--42517847 Score: 92
Period size: 37 Copynumber: 2.6 Consensus size: 36
42517740 TGGGTGAATT
* * *
42517750 TTACTTCGGACGTTCCGATAAGTGCTAGGCACAATAT
1 TTACTTC-GACGTTCCGATGAGTGCTAGGCAAAATAA
42517787 TTACTTC-A-GTTATACCGATGAGTGCTAGGCATAAATTAA
1 TTACTTCGACG-T-T-CCGATGAGTGCTAGGCA-AAA-TAA
42517826 TTACTTCGAACGTTCCGATGAG
1 TTACTTCG-ACGTTCCGATGAG
42517848 GTACCGAGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
34 1 0.02
35 2 0.04
36 1 0.02
37 23 0.46
38 2 0.04
39 17 0.34
40 1 0.02
41 2 0.04
42 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (36 bp):
TTACTTCGACGTTCCGATGAGTGCTAGGCAAAATAA
Found at i:42520507 original size:34 final size:34
Alignment explanation
Indices: 42520464--42520531 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
42520454 ATACAAGTAT
42520464 GCAAATACAACCAAATTCAAGGTGTGATATGTAA
1 GCAAATACAACCAAATTCAAGGTGTGATATGTAA
42520498 GCAAATACAACCAAATTCAAGGTGTGATATGTAA
1 GCAAATACAACCAAATTCAAGGTGTGATATGTAA
42520532 TTGAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (34 bp):
GCAAATACAACCAAATTCAAGGTGTGATATGTAA
Found at i:42521707 original size:13 final size:13
Alignment explanation
Indices: 42521691--42521728 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
42521681 TTATCAGAAG
*
42521691 CACTTTTTCACAA
1 CACTTTTTCAAAA
*
42521704 CACTTTTTAAAAA
1 CACTTTTTCAAAA
42521717 CA-TTTTTCAAAA
1 CACTTTTTCAAAA
42521729 GTAATGCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (13 bp):
CACTTTTTCAAAA
Found at i:42524908 original size:47 final size:46
Alignment explanation
Indices: 42524839--42524930 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 46
42524829 CTGCCAATTA
*
42524839 ATAATATTATGGACAAGCCACCACTTTTGTAGATAAACTACCACTTT
1 ATAATATTATAGACAAGCCACCAC-TTTGTAGATAAACTACCACTTT
* * *
42524886 ATAATATTGTAGACAAGCCACCACTTTGTATATAAACTGCCACTT
1 ATAATATTATAGACAAGCCACCACTTTGTAGATAAACTACCACTT
42524931 CTTGCTCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 19 0.46
47 22 0.54
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (46 bp):
ATAATATTATAGACAAGCCACCACTTTGTAGATAAACTACCACTTT
Found at i:42525009 original size:20 final size:21
Alignment explanation
Indices: 42524976--42525016 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
42524966 ATATGGCCAC
*
42524976 AAAAATTTACTTTTTCACTTT
1 AAAAATTTAATTTTTCACTTT
42524997 AAAAA-TTAATTTTTCACTTT
1 AAAAATTTAATTTTTCACTTT
42525017 GGCATGGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAAATTTAATTTTTCACTTT
Found at i:42526371 original size:21 final size:20
Alignment explanation
Indices: 42526347--42526395 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
42526337 TCGGCTCCAT
42526347 TAGATTGA-AGCCTCTTAGTAA
1 TAGATTGAGA-CCTC-TAGTAA
*
42526368 TAGACTTGCGACCTCTAGTAA
1 TAGA-TTGAGACCTCTAGTAA
42526389 TAGATTG
1 TAGATTG
42526396 GCCTCTGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 14 0.56
22 7 0.28
23 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (20 bp):
TAGATTGAGACCTCTAGTAA
Found at i:42533646 original size:51 final size:52
Alignment explanation
Indices: 42533548--42533646 Score: 114
Period size: 53 Copynumber: 1.9 Consensus size: 52
42533538 TAAGTTTTTC
* * *
42533548 TATATATTTTTTATATTTTTAAACATTTTAAAGTTTTTTAAAATTTTTATGTA
1 TATATATTTTTCATATTTTCAAACATTTTAAAG-TTTTGAAAATTTTTATGTA
*
42533601 TATATATTTTTCAT-TTTTCATAA-ATTTTAATA-TTTTGAAACTTTTT
1 TATATATTTTTCATATTTTCA-AACATTTTAA-AGTTTTGAAAATTTTT
42533647 TTTACAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
51 12 0.30
52 12 0.30
53 16 0.40
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (52 bp):
TATATATTTTTCATATTTTCAAACATTTTAAAGTTTTGAAAATTTTTATGTA
Found at i:42533730 original size:10 final size:10
Alignment explanation
Indices: 42533696--42533763 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 10
42533686 CCCTTTTTTT
42533696 TAATTTTT-A
1 TAATTTTTAA
* *
42533705 CAATTTTACAA
1 TAATTTT-TAA
42533716 T-ATTTTTAA
1 TAATTTTTAA
*
42533725 TAATTTCTTTA
1 TAATTT-TTAA
*
42533736 TAATTTTTTA
1 TAATTTTTAA
42533746 TAATGTTTTAGA
1 TAAT-TTTTA-A
42533758 TAATTT
1 TAATTT
42533764 AATTTTCTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
9 9 0.19
10 17 0.36
11 16 0.34
12 5 0.11
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:42533738 original size:11 final size:10
Alignment explanation
Indices: 42533717--42533755 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
42533707 ATTTTACAAT
*
42533717 ATTTTTAATA
1 ATTTTTTATA
42533727 ATTTCTTTATA
1 ATTT-TTTATA
42533738 ATTTTTTATA
1 ATTTTTTATA
*
42533748 ATGTTTTA
1 ATTTTTTA
42533756 GATAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:42540903 original size:19 final size:19
Alignment explanation
Indices: 42540879--42540917 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
42540869 CAGTTGAGGG
* *
42540879 TAATTAGTGATTTAATTGA
1 TAATTAGGGATTTAAATGA
42540898 TAATTAGGGATTTAAATGA
1 TAATTAGGGATTTAAATGA
42540917 T
1 T
42540918 CATAGGCCGA
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:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (19 bp):
TAATTAGGGATTTAAATGA
Found at i:42540984 original size:18 final size:18
Alignment explanation
Indices: 42540958--42540996 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
42540948 AGGAATAAGA
42540958 AATTCAATTAGGTTAATT
1 AATTCAATTAGGTTAATT
* *
42540976 AATTTAATTAGTTTAATT
1 AATTCAATTAGGTTAATT
42540994 AAT
1 AAT
42540997 ACTTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (18 bp):
AATTCAATTAGGTTAATT
Found at i:42542590 original size:16 final size:16
Alignment explanation
Indices: 42542569--42542614 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
42542559 AAGGGCTTAT
42542569 ATTTTAATTTGTTTTA
1 ATTTTAATTTGTTTTA
42542585 ATTTTAATTT-TCTTTA
1 ATTTTAATTTGT-TTTA
* *
42542601 TTTTTCATTTGTTT
1 ATTTTAATTTGTTT
42542615 GTTTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (16 bp):
ATTTTAATTTGTTTTA
Found at i:42547973 original size:24 final size:24
Alignment explanation
Indices: 42547941--42547988 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42547931 GTGACAAAAT
42547941 TTTTGATTTATTTGAGAAATTAAA
1 TTTTGATTTATTTGAGAAATTAAA
42547965 TTTTGATTTATTTGAGAAATTAAA
1 TTTTGATTTATTTGAGAAATTAAA
42547989 CTTTAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (24 bp):
TTTTGATTTATTTGAGAAATTAAA
Found at i:42548001 original size:24 final size:24
Alignment explanation
Indices: 42547950--42548001 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42547940 TTTTTGATTT
* * ***
42547950 ATTTGAGAAATTAAATTTTGATTT
1 ATTTGAGAAATTAAACTTTAAAAC
42547974 ATTTGAGAAATTAAACTTTAAAAC
1 ATTTGAGAAATTAAACTTTAAAAC
42547998 ATTT
1 ATTT
42548002 TTATAAAATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (24 bp):
ATTTGAGAAATTAAACTTTAAAAC
Found at i:42554491 original size:19 final size:19
Alignment explanation
Indices: 42554432--42554491 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
42554422 GAAAAATTTA
**
42554432 TTTATATTAATTTAGCCATT
1 TTTATATTAATTTA-AAATT
**
42554452 TTTATATTAATTTAATGTT
1 TTTATATTAATTTAAAATT
*
42554471 TTTATTTTAATTTAAAATT
1 TTTATATTAATTTAAAATT
42554490 TT
1 TT
42554492 ACATTCTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTATATTAATTTAAAATT
Found at i:42557350 original size:24 final size:25
Alignment explanation
Indices: 42557309--42557358 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
42557299 ATTTCATATT
42557309 ATTTTAAAAAATATTTGAAAAAGAA
1 ATTTTAAAAAATATTTGAAAAAGAA
*
42557334 ATTTTGAAAAAA-A-TTGAAAATGAA
1 ATTTT-AAAAAATATTTGAAAAAGAA
42557358 A
1 A
42557359 GAAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 11 0.48
25 6 0.26
26 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (25 bp):
ATTTTAAAAAATATTTGAAAAAGAA
Found at i:42557408 original size:21 final size:22
Alignment explanation
Indices: 42557384--42557426 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42557374 GATTTTTTTT
42557384 GAAAAA-AATTGGAAAAAAAAA
1 GAAAAATAATTGGAAAAAAAAA
* *
42557405 GAAAAATATTTTGAAAAAAAAA
1 GAAAAATAATTGGAAAAAAAAA
42557427 TTCAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (22 bp):
GAAAAATAATTGGAAAAAAAAA
Found at i:42557846 original size:6 final size:6
Alignment explanation
Indices: 42557835--42557880 Score: 74
Period size: 6 Copynumber: 7.5 Consensus size: 6
42557825 TTGTCTTTTA
*
42557835 TTTATT TTTATT TTTATT TTTATT TTTATT CTTATT ATTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT -TTTATT TTT
42557881 TCTTCCTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 32 0.86
7 5 0.14
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:42557858 original size:18 final size:19
Alignment explanation
Indices: 42557828--42557880 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 19
42557818 TTTCTTATTG
42557828 TCTT-TTATTTATTTTTAT
1 TCTTATTATTTATTTTTAT
*
42557846 TTTTATT-TTTATTTTTAT
1 TCTTATTATTTATTTTTAT
42557864 TCTTATTATTTATTTTT
1 TCTTATTATTTATTTTT
42557881 TCTTCCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 20 0.65
19 11 0.35
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (19 bp):
TCTTATTATTTATTTTTAT
Found at i:42559050 original size:16 final size:16
Alignment explanation
Indices: 42559029--42559061 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42559019 TGTACTTTTA
42559029 TTTTTATTTTTAGTTG
1 TTTTTATTTTTAGTTG
*
42559045 TTTTTATTTTTATTTG
1 TTTTTATTTTTAGTTG
42559061 T
1 T
42559062 GAGAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (16 bp):
TTTTTATTTTTAGTTG
Found at i:42559052 original size:22 final size:23
Alignment explanation
Indices: 42559002--42559059 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
42558992 TTTGCTTTAG
* *
42559002 TTATTTTTACTTTTGGTTGTACTT
1 TTATTTTTATTTTTAGTTGTA-TT
42559026 TTATTTTTATTTTTAGTTGT-TT
1 TTATTTTTATTTTTAGTTGTATT
42559048 TTATTTTTATTT
1 TTATTTTTATTT
42559060 GTGAGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 14 0.44
24 18 0.56
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (23 bp):
TTATTTTTATTTTTAGTTGTATT
Found at i:42564582 original size:47 final size:48
Alignment explanation
Indices: 42564517--42564610 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 48
42564507 TCGCATATCA
* * * *
42564517 CACACCGTAGCCATATCCCGGCTATGGTTTTACACGGAAA-CACATAT
1 CACACCGTAGCCATATCCCAGATATGGTCTTACAAGGAAATCACATAT
42564564 CACACCG-ATGCCATATCCCAGATATGGTCTTACAAGGAAATCACATA
1 CACACCGTA-GCCATATCCCAGATATGGTCTTACAAGGAAATCACATA
42564611 ATCATATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
46 1 0.02
47 34 0.83
48 6 0.15
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (48 bp):
CACACCGTAGCCATATCCCAGATATGGTCTTACAAGGAAATCACATAT
Found at i:42567647 original size:9 final size:9
Alignment explanation
Indices: 42567633--42567657 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42567623 AATTTATCAT
42567633 AAGATATTA
1 AAGATATTA
42567642 AAGATATTA
1 AAGATATTA
42567651 AAGATAT
1 AAGATAT
42567658 CCTATGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (9 bp):
AAGATATTA
Found at i:42585918 original size:19 final size:20
Alignment explanation
Indices: 42585882--42585925 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
42585872 TGTCAACATT
42585882 CCAAATACCATAATCACAA-
1 CCAAATACCATAATCACAAG
42585901 CCAAGATACCATAA-CACAAG
1 CCAA-ATACCATAATCACAAG
42585921 CCAAA
1 CCAAA
42585926 CCATATGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.52, C:0.32, G:0.05, T:0.11
Consensus pattern (20 bp):
CCAAATACCATAATCACAAG
Found at i:42588652 original size:24 final size:24
Alignment explanation
Indices: 42588607--42588653 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42588597 CATTAAAGTC
* **
42588607 CATAATTCAACCATTTTGTATACT
1 CATAATTCAACCAATTCATATACT
42588631 CATAATTCAACCAATTCATATAC
1 CATAATTCAACCAATTCATATAC
42588654 GTTTGCATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (24 bp):
CATAATTCAACCAATTCATATACT
Found at i:42589045 original size:26 final size:26
Alignment explanation
Indices: 42589009--42589062 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
42588999 TGTTGAATTG
42589009 ATAGTTAATTAAGGTACATAGACCAA
1 ATAGTTAATTAAGGTACATAGACCAA
42589035 ATAGTTAATTAAGGTACATAGACCAA
1 ATAGTTAATTAAGGTACATAGACCAA
42589061 AT
1 AT
42589063 TGTAAAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (26 bp):
ATAGTTAATTAAGGTACATAGACCAA
Found at i:42590368 original size:17 final size:19
Alignment explanation
Indices: 42590336--42590373 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
42590326 ACTGATAACC
42590336 TAACACAAATATATATATT
1 TAACACAAATATATATATT
42590355 TAACACAAATATATATATT
1 TAACACAAATATATATATT
42590374 CAACTCGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (19 bp):
TAACACAAATATATATATT
Found at i:42594149 original size:47 final size:47
Alignment explanation
Indices: 42594083--42594560 Score: 785
Period size: 47 Copynumber: 10.1 Consensus size: 47
42594073 GAAATGATAG
*
42594083 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
42594130 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
42594179 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
42594226 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
42594273 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
42594322 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
42594369 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
42594416 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
42594463 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
42594510 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
42594557 TAAG
1 TAAG
42594561 TCCCGAAGGG
Statistics
Matches: 404, Mismatches: 23, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 310 0.77
49 94 0.23
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:42594341 original size:143 final size:143
Alignment explanation
Indices: 42594083--42594560 Score: 816
Period size: 143 Copynumber: 3.4 Consensus size: 143
42594073 GAAATGATAG
42594083 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
42594148 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
42594213 TGTATATACGTGA
131 TGTATATACGTGA
*
42594226 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
42594291 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
42594356 TGTATATACGTGA
131 TGTATATACGTGA
* *
42594369 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
42594434 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* *
42594497 TATATATATGTGA
131 TGTATATACGTGA
* * * * * * * * *
42594510 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGATAAG
42594561 TCCCGAAGGG
Statistics
Matches: 320, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
141 98 0.31
143 222 0.69
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.28
Consensus pattern (143 bp):
TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATACGTGA
Found at i:42594735 original size:37 final size:37
Alignment explanation
Indices: 42594679--42594757 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
42594669 CCGAGCTCTA
* * *
42594679 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
42594716 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
42594753 AAGAC
1 AAGAC
42594758 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:42596939 original size:16 final size:16
Alignment explanation
Indices: 42596918--42596950 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42596908 TTTGTTGTAT
42596918 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
42596934 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
42596950 T
1 T
42596951 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:42597518 original size:119 final size:120
Alignment explanation
Indices: 42597162--42597695 Score: 880
Period size: 119 Copynumber: 4.5 Consensus size: 120
42597152 ATTTAATCAT
*
42597162 ATTTAAACATAATTATTATT-AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
42597226 GTCAATATTGTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * * *
42597282 AATTAACATAATCATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
42597347 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
42597401 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAA-TTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
42597465 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
42597520 ATTTAACATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
42597584 TCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* *
42597639 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
42597696 TAAAATAATT
Statistics
Matches: 392, Mismatches: 18, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
118 66 0.17
119 221 0.56
120 105 0.27
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:42597562 original size:59 final size:57
Alignment explanation
Indices: 42597259--42597684 Score: 186
Period size: 54 Copynumber: 7.2 Consensus size: 57
42597249 CTCAAATCAT
* * *
42597259 AATATATGATACTATAAAATATAAATTAACATAATCATTATTAAATATATTATAATTAA
1 AATATATGATACTATAAAA-ATAATTTAA-ATAATAATTATTAAATATATTTTAATTAA
* * * * ** *
42597318 AATCTAT-A-A-TTTAATAA-AATTCTTAATAATTAA-TATTCTTATATGAATTTACTCAAATCA
1 AATATATGATACTATAAAAATAATT-TAAATAA-TAATTATT-AAATAT--ATTT--T--AATTA
*
42597378 T
57 A
* *
42597379 AATATATGATACTATAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAAATAATTTAA-ATAATAATTATTAAATATATTTTAATTAA
* * ** *
42597437 AATATAT-A-A-T-TAATAA-AATTCTTAATAATTAA-TATTCTTATATGAATTTACTCAAATCA
1 AATATATGATACTATAAAAATAATT-TAAATAA-TAATTATT-AAATAT--ATTT--T--AATTA
*
42597496 T
57 A
42597497 AATATATGATACTATAAAAGATAATTTAACATAATAATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAA-ATAATTTAA-ATAATAATTATTAAATATATTTTAATTAA
* * ** *
42597556 AATATAT-A-A-TTTAATAA-AATTCT-AATAATCAA-TATTCTTATATGAATTTACTAAAATCA
1 AATATATGATACTATAAAAATAATT-TAAATAAT-AATTATT-AAATAT--ATTT--T--AATTA
*
42597615 T
57 A
42597616 AATATATGATACTATAAAATATAATTTGAAATAATTAA-TATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAA-ATAATTT-AAATAA-TAATTATTAAATATATTTTAATTAA
42597675 AATATATGAT
1 AATATATGAT
42597685 TTAATAAAAT
Statistics
Matches: 271, Mismatches: 47, Indels: 98
0.65 0.11 0.24
Matches are distributed among these distances:
53 21 0.08
54 34 0.13
55 12 0.04
56 19 0.07
57 6 0.02
58 15 0.06
59 32 0.12
60 23 0.08
61 14 0.05
62 7 0.03
63 15 0.06
64 19 0.07
65 30 0.11
66 23 0.08
67 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (57 bp):
AATATATGATACTATAAAAATAATTTAAATAATAATTATTAAATATATTTTAATTAA
Found at i:42597563 original size:18 final size:17
Alignment explanation
Indices: 42597541--42597575 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42597531 TAATTATTAA
*
42597541 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42597559 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42597576 TCTAATAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42600059 original size:38 final size:38
Alignment explanation
Indices: 42599936--42600069 Score: 171
Period size: 46 Copynumber: 3.3 Consensus size: 38
42599926 GACAGAAACT
* *
42599936 GAGCAAATCGGCAGAAAAGAAAGGAAAAG-AATAGAGG
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
42599973 GAGCAAATCGGCAGAAAAGAAAAGAAAATAAACAGAGGAACAGAGG
1 GAGCAAATCGGCAGAAAAGAAAAG-----AAA-AGA--AACAGAGG
42600019 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
42600057 GAGCAAATCGGCA
1 GAGCAAATCGGCA
42600070 AAAGCTAGAA
Statistics
Matches: 86, Mismatches: 2, Indels: 17
0.82 0.02 0.16
Matches are distributed among these distances:
37 23 0.27
38 21 0.24
40 3 0.03
41 3 0.03
42 3 0.03
43 2 0.02
46 31 0.36
ACGTcount: A:0.54, C:0.11, G:0.30, T:0.04
Consensus pattern (38 bp):
GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAGAGG
Found at i:42603701 original size:13 final size:13
Alignment explanation
Indices: 42603683--42603711 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42603673 ATCTAACACC
42603683 TAATATTTTTCCA
1 TAATATTTTTCCA
42603696 TAATATTTTTCCA
1 TAATATTTTTCCA
42603709 TAA
1 TAA
42603712 GAAAAGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATATTTTTCCA
Found at i:42612107 original size:25 final size:25
Alignment explanation
Indices: 42612072--42612138 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
42612062 TCTCGAGCCA
* **
42612072 TATAACAGGAAGCTCATGTAAGCTG
1 TATAACGGGAAGCTCATCCAAGCTG
* * *
42612097 TATAACGGGAAGCTTATCCAGGTTG
1 TATAACGGGAAGCTCATCCAAGCTG
42612122 TATAACGGGAAGCTCAT
1 TATAACGGGAAGCTCAT
42612139 AAGAGTCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (25 bp):
TATAACGGGAAGCTCATCCAAGCTG
Found at i:42612280 original size:25 final size:26
Alignment explanation
Indices: 42612249--42612319 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
42612239 GAGCCATATC
* *
42612249 GGAAGCTC-CGGAGAGCCATTAATTA
1 GGAAGCTCACGAAGAGCCATTAATCA
* *
42612274 GGAAGCTCACAAAGAGCCTTTAATCA
1 GGAAGCTCACGAAGAGCCATTAATCA
*
42612300 GGAAACTCACGAAGAGCCAT
1 GGAAGCTCACGAAGAGCCAT
42612320 ATATCGGGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 8 0.21
26 30 0.79
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACGAAGAGCCATTAATCA
Found at i:42631498 original size:30 final size:31
Alignment explanation
Indices: 42631429--42631506 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
42631419 GAATTATTCG
* * *
42631429 AAAGTTTTTATTTAAGTTATTGAACTATTTA
1 AAAGTTTTTATTTAAGTCAATGAACTAGTTA
42631460 AAAGTTTTTATTTAAGTCAATGAACT-GTTA
1 AAAGTTTTTATTTAAGTCAATGAACTAGTTA
** *
42631490 AATTTTTTTTTTTAAGT
1 AAAGTTTTTATTTAAGT
42631507 TCTGATAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 17 0.41
31 24 0.59
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (31 bp):
AAAGTTTTTATTTAAGTCAATGAACTAGTTA
Found at i:42640913 original size:11 final size:11
Alignment explanation
Indices: 42640897--42640923 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42640887 TAGAAATTAG
42640897 TTTGTGAAACT
1 TTTGTGAAACT
42640908 TTTGTGAAACT
1 TTTGTGAAACT
42640919 TTTGT
1 TTTGT
42640924 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:42642459 original size:92 final size:92
Alignment explanation
Indices: 42642323--42642516 Score: 286
Period size: 92 Copynumber: 2.1 Consensus size: 92
42642313 TTGATTTTAG
* *
42642323 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
*
42642387 TAT-TAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
42642414 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
42642479 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
42642507 CAAATTCATA
1 TAAATTCATA
42642517 AACTATAATC
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
91 17 0.18
92 43 0.46
93 30 0.32
94 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:42642564 original size:48 final size:52
Alignment explanation
Indices: 42642494--42642592 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
42642484 AATAATTATT
42642494 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
42642542 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
42642593 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:42642574 original size:17 final size:17
Alignment explanation
Indices: 42642549--42642582 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42642539 ATAATTTTAA
*
42642549 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
42642566 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
42642583 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:42642599 original size:17 final size:16
Alignment explanation
Indices: 42642554--42642601 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
42642544 TTTAAATTTT
42642554 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
42642571 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
42642585 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
42642602 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:42642673 original size:18 final size:17
Alignment explanation
Indices: 42642642--42642676 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42642632 ATTATTAAGA
42642642 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
42642659 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
42642677 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:42642742 original size:129 final size:129
Alignment explanation
Indices: 42642589--42642821 Score: 414
Period size: 129 Copynumber: 1.8 Consensus size: 129
42642579 ATATTAGTTA
*
42642589 TAATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* *
42642654 TATATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGTATCATATT
66 TATATATTTTAATTAAAATATATTT-ATAATAATTATGTTATTTTATATTTTACAGTATCATATT
*
42642719 TAATAATA-ATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
42642783 TATATATTTTAATTAAAATATATTTATAATAATTATGTT
66 TATATATTTTAATTAAAATATATTTATAATAATTATGTT
42642822 TAAATATGAT
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
128 14 0.14
129 78 0.79
130 7 0.07
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (129 bp):
TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
TATATATTTTAATTAAAATATATTTATAATAATTATGTTATTTTATATTTTACAGTATCATATT
Found at i:42642799 original size:18 final size:17
Alignment explanation
Indices: 42642771--42642805 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42642761 ATTATTAAGA
*
42642771 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
42642788 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
42642806 TTATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:42642805 original size:16 final size:17
Alignment explanation
Indices: 42642771--42642812 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
42642761 ATTATTAAGA
42642771 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
42642788 ATTTTAATTAAA-ATAT
1 ATTTTAATTAAATATAT
42642804 ATTTATAAT
1 ATTT-TAAT
42642813 AATTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 9 0.39
18 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:42642915 original size:143 final size:147
Alignment explanation
Indices: 42642759--42643029 Score: 478
Period size: 143 Copynumber: 1.9 Consensus size: 147
42642749 ATAAGAATAT
*
42642759 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT-TATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
42642823 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
42642885 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
42642902 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
42642967 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
42643030 CAATAATCAT
Statistics
Matches: 120, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
143 48 0.40
144 42 0.35
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:42642942 original size:18 final size:17
Alignment explanation
Indices: 42642914--42642948 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42642904 ATTATTAAGA
*
42642914 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
42642931 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
42642949 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:42643159 original size:44 final size:45
Alignment explanation
Indices: 42643110--42643204 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
42643100 TTACACCTCT
* *
42643110 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
42643154 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
42643199 ATTACA
1 ATTACA
42643205 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:42643204 original size:16 final size:16
Alignment explanation
Indices: 42643183--42643215 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42643173 TTGATTTGCT
*
42643183 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
42643199 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
42643215 A
1 A
42643216 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:42643225 original size:21 final size:21
Alignment explanation
Indices: 42643196--42643238 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
42643186 ACACCTCTAT
*
42643196 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
42643217 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
42643238 T
1 T
42643239 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:42646657 original size:25 final size:25
Alignment explanation
Indices: 42646581--42646708 Score: 166
Period size: 25 Copynumber: 5.0 Consensus size: 25
42646571 ATTTTTCTTG
* *
42646581 AAATTTTACCAGGGGCAAAATTGTCA
1 AAATTTTA-CAAGGGTAAAATTGTCA
* **
42646607 AAATTTTACCAGAGACAAAATTGTCA
1 AAATTTTACAAG-GGTAAAATTGTCA
*
42646633 AAATTTTATAAGGGTAAAATTGTCA
1 AAATTTTACAAGGGTAAAATTGTCA
*
42646658 AAATTTTATAAGGGTAAAATTGTCA
1 AAATTTTACAAGGGTAAAATTGTCA
*
42646683 AAATTTTACAGGGGTAAAATTGTCA
1 AAATTTTACAAGGGTAAAATTGTCA
42646708 A
1 A
42646709 TTTTGTTGAG
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
25 62 0.67
26 30 0.33
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.31
Consensus pattern (25 bp):
AAATTTTACAAGGGTAAAATTGTCA
Found at i:42646720 original size:25 final size:24
Alignment explanation
Indices: 42646623--42646727 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 24
42646613 TACCAGAGAC
* *
42646623 AAAATTGTCAAAATTTTATAAGGGT
1 AAAATTGTC-AAATTTTTTAGGGGT
* *
42646648 AAAATTGTCAAAATTTTATAAGGGT
1 AAAATTGTC-AAATTTTTTAGGGGT
**
42646673 AAAATTGTCAAAATTTTACAGGGGT
1 AAAATTGTC-AAATTTTTTAGGGGT
42646698 AAAATTGTC-AATTTTGTTGAGGGGT
1 AAAATTGTCAAATTTT-TT-AGGGGT
42646723 AAAAT
1 AAAAT
42646728 AAGGACGGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
23 6 0.08
25 68 0.92
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (24 bp):
AAAATTGTCAAATTTTTTAGGGGT
Found at i:42659891 original size:27 final size:29
Alignment explanation
Indices: 42659854--42659920 Score: 111
Period size: 27 Copynumber: 2.3 Consensus size: 29
42659844 ACGATCGAAA
42659854 AAAATCAAGATTCACTTT-T-TTTTCAAG
1 AAAATCAAGATTCACTTTCTATTTTCAAG
42659881 AAAATCAAGATTCACTTTCGTATTTTCAAG
1 AAAATCAAGATTCACTTTC-TATTTTCAAG
42659911 AAAATCAAGA
1 AAAATCAAGA
42659921 AATTGAATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
27 18 0.49
29 1 0.03
30 18 0.49
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (29 bp):
AAAATCAAGATTCACTTTCTATTTTCAAG
Found at i:42667191 original size:29 final size:29
Alignment explanation
Indices: 42667149--42667207 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
42667139 TCACAGTCCC
*
42667149 TATGGGTATGATAACTCGACATTTACTAG
1 TATGGGTATGATAACTCAACATTTACTAG
42667178 TATGGGTATGATAACTCAACATTTACTAG
1 TATGGGTATGATAACTCAACATTTACTAG
42667207 T
1 T
42667208 CACTTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (29 bp):
TATGGGTATGATAACTCAACATTTACTAG
Found at i:42677464 original size:27 final size:29
Alignment explanation
Indices: 42677419--42677488 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 29
42677409 CACAAATTTG
42677419 AAATTTAGTCCATGCAC-TTT-AATTTTA
1 AAATTTAGTCCATGCACTTTTAAATTTTA
* * **
42677446 GAATTTAGTCCCTTTACTTTTTAAATTTTA
1 AAATTTAGTCCATGCAC-TTTTAAATTTTA
42677476 AAATTTAGGTCCA
1 AAATTTA-GTCCA
42677489 ACTATTAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 13 0.39
29 3 0.09
30 13 0.39
31 4 0.12
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (29 bp):
AAATTTAGTCCATGCACTTTTAAATTTTA
Found at i:42684849 original size:18 final size:18
Alignment explanation
Indices: 42684822--42684914 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
42684812 TACGACCGTT
42684822 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
42684840 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
42684858 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
42684876 TACGGCACTATTTACGTA
1 TACGGTACTATTCACGTA
*
42684894 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
42684912 TAC
1 TAC
42684915 AGTAGTTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:42696029 original size:28 final size:28
Alignment explanation
Indices: 42695998--42696051 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
42695988 TTAAAATTTG
42695998 ATATATAAT-T-TTTAAAAATTAAAATAAA
1 ATATATAATATATTT-AAAA-TAAAATAAA
*
42696026 ATATTTAATATATTTAAAATAAAATA
1 ATATATAATATATTTAAAATAAAATA
42696052 CTTACCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 15 0.65
29 5 0.22
30 3 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATATATAATATATTTAAAATAAAATAAA
Found at i:42696032 original size:21 final size:21
Alignment explanation
Indices: 42695985--42696051 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
42695975 AAAGCTTTTT
* * *
42695985 TATTTAAAATTTGATATATAA
1 TATTTAAAATTTAAAATAAAA
* *
42696006 TTTTTAAAAATTAAAATAAAA
1 TATTTAAAATTTAAAATAAAA
42696027 TATTTAATATATTTAAAATAAAA
1 TATTTAA-A-ATTTAAAATAAAA
42696050 TA
1 TA
42696052 CTTACCAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
21 22 0.59
22 1 0.03
23 14 0.38
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
TATTTAAAATTTAAAATAAAA
Found at i:42740224 original size:80 final size:79
Alignment explanation
Indices: 42740087--42740311 Score: 247
Period size: 80 Copynumber: 2.8 Consensus size: 79
42740077 TTGAATGCTG
* * * * * *
42740087 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAGGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGAT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT
42740151 TGTGCGAGATA-CAAA
64 TGTGCGAGATATCAAA
* *
42740166 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATT
* * *
42740231 CGTGCGAGTTATTAAA
64 TGTGCGAGATATCAAA
* * * * * *
42740247 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
42740312 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
79 39 0.32
80 69 0.57
81 14 0.11
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:42740291 original size:39 final size:39
Alignment explanation
Indices: 42740087--42740309 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
42740077 TTGAATGCTG
* * * * * *
42740087 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAGGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGAT-ACTAAA
**
42740127 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
42740166 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
42740207 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
42740247 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
42740286 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
42740310 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 14 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:42740329 original size:79 final size:80
Alignment explanation
Indices: 42740167--42740344 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
42740157 AGATACAAAT
* * * *
42740167 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
42740232 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
42740247 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
42740311 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
42740326 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
42740345 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:42744960 original size:33 final size:33
Alignment explanation
Indices: 42744896--42745132 Score: 153
Period size: 33 Copynumber: 6.8 Consensus size: 33
42744886 ATGTGAAGGG
*
42744896 GGTTGCTAAGTGCTGATT-CCC---TCA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
42744923 GGTTGCTAAGTACTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
42744956 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
42744998 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
42745031 GGTTGCTAAGTGCTGATTCCACGGTATCATTGAATGT
1 GGTTGCTAAGTGCTGATTCCCCGAT-TCATTG---GT
* *
42745068 GAAAGGAGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 -----G-GTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
42745107 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
42745133 AACGGATAAC
Statistics
Matches: 165, Mismatches: 19, Indels: 45
0.72 0.08 0.20
Matches are distributed among these distances:
27 17 0.10
28 3 0.02
31 3 0.02
32 2 0.01
33 59 0.36
34 14 0.08
35 1 0.01
36 2 0.01
37 6 0.04
38 4 0.02
39 4 0.02
40 1 0.01
41 3 0.02
42 25 0.15
43 21 0.13
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:42744970 original size:102 final size:102
Alignment explanation
Indices: 42744789--42745019 Score: 372
Period size: 102 Copynumber: 2.3 Consensus size: 102
42744779 ATTGAATATA
* * ***
42744789 AAGGTGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCTGTGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTACTGATTCCCCGATTCATTGGT
* *
42744854 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
*
42744891 AAGGGGGTTGCTAAGTGCTGATTCCCTCAAGGGGTTGCTAAGTACTGATTCCCCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTACTGATTCCCCGATTCATTGGT
42744956 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
* *
42744993 AAAGGGGTTGCTAAGTGTTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
42745020 GATTCATTGG
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 118 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTACTGATTCCCCGATTCATTGGT
GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTG
Found at i:42745111 original size:76 final size:75
Alignment explanation
Indices: 42744919--42745130 Score: 334
Period size: 76 Copynumber: 2.8 Consensus size: 75
42744909 TGATTCCCTC
* *
42744919 AAGGGGTTGCTAAGTACTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
42744984 TTAAATGTGA
66 TTAAATGTGA
* *
42744994 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACGGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
42745059 ATTGAATGTGA
66 -TTAAATGTGA
* * * *
42745070 AAGGAGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
42745131 ATAACGGATA
Statistics
Matches: 125, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
75 61 0.49
76 64 0.51
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:42751154 original size:19 final size:19
Alignment explanation
Indices: 42751132--42751169 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42751122 TCAATTATCC
42751132 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
42751151 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
42751170 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:42756086 original size:17 final size:17
Alignment explanation
Indices: 42756064--42756102 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
42756054 TTTGTTAGTT
42756064 TTGATTAAAGGATTA-AA
1 TTGATTAAAGG-TTAGAA
*
42756081 TTGATTAAATGTTAGAA
1 TTGATTAAAGGTTAGAA
42756098 TTGAT
1 TTGAT
42756103 AGGGAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
TTGATTAAAGGTTAGAA
Found at i:42756721 original size:20 final size:20
Alignment explanation
Indices: 42756696--42756751 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
42756686 TGTATGGGAC
42756696 TTGCACTTCGGTGCCTCTAT
1 TTGCACTTCGGTGCCTCTAT
** * *
42756716 TTGCACTTTAGTGCCCCTTT
1 TTGCACTTCGGTGCCTCTAT
*
42756736 TTGCACTTCGATGCCT
1 TTGCACTTCGGTGCCT
42756752 TTGATCGCAC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.11, C:0.30, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTAT
Found at i:42758328 original size:14 final size:14
Alignment explanation
Indices: 42758287--42758334 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
42758277 GTTTTAACTT
**
42758287 TAATTAATCAAAAT
1 TAATTAATCAAACC
*
42758301 TAATTTAATTAAACC
1 TAA-TTAATCAAACC
42758316 TAATTAATCAAACC
1 TAATTAATCAAACC
42758330 ATAAT
1 -TAAT
42758335 CACAATTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATTAATCAAACC
Found at i:42763534 original size:50 final size:49
Alignment explanation
Indices: 42763469--42763644 Score: 147
Period size: 50 Copynumber: 3.5 Consensus size: 49
42763459 TTCGGAAAGT
* *
42763469 AAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGTAATGTCTGGGAAGC
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTCAACTG-AATGTCTGGGAAGC
* * ** * * * *
42763519 ATGATTCGCTGTTGTGGCTTTAAT-TTGTTCCGCTGCATCGCCTGGGAGGT
1 AAGATTCGCCGTTGTGGCTTTAATCTT-TTCAACTGAAT-GTCTGGGAAGC
* * * * *
42763569 AAGATTCGCTGTTGTAGCTTTGATCTTTTGAACTGCAATGTCAGGGAAGC
1 AAGATTCGCCGTTGTGGCTTTAATCTTTTCAACTG-AATGTCTGGGAAGC
* * *
42763619 AAGATTCACCGATGTGGTTTTAATCT
1 AAGATTCGCCGTTGTGGCTTTAATCT
42763645 ATTCCACGGC
Statistics
Matches: 95, Mismatches: 27, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
49 4 0.04
50 87 0.92
51 4 0.04
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (49 bp):
AAGATTCGCCGTTGTGGCTTTAATCTTTTCAACTGAATGTCTGGGAAGC
Found at i:42763689 original size:100 final size:100
Alignment explanation
Indices: 42763465--42763736 Score: 265
Period size: 100 Copynumber: 2.8 Consensus size: 100
42763455 AACTTTCGGA
* * * * * * *
42763465 AAGTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGTAATGTCTGGGAAGCATGATTCGCTG
1 AAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTGAACTGCAATGTCAGGGAAGCAAGATTCACCG
* * * * * **
42763530 TTGTGGCTTTAATTTGTTCCGCTGCATCGCCTGGG
66 ATGTGGCTTTAATCTATTCCACGGCATCGCCAAGG
* * * *
42763565 AGGTAAGATTCGCTGTTGTAGCTTTGATCTTTTGAACTGCAATGTCAGGGAAGCAAGATTCACCG
1 AAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTGAACTGCAATGTCAGGGAAGCAAGATTCACCG
*
42763630 ATGTGGTTTTAATCTATTCCACGGCATCGCCAAGG
66 ATGTGGCTTTAATCTATTCCACGGCATCGCCAAGG
* * * *
42763665 AAGTAGGATTCGCCGCTGTGGCTTT-A---GTT----TGCAATGTC-GAGGAAGCAAGATTCACT
1 AAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTGAACTGCAATGTCAG-GGAAGCAAGATTCACC
42763721 GATGTGGCTTTAATCT
65 GATGTGGCTTTAATCT
42763737 GTTCTACTAC
Statistics
Matches: 144, Mismatches: 27, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
91 1 0.01
92 39 0.27
96 2 0.01
99 1 0.01
100 101 0.70
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (100 bp):
AAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTGAACTGCAATGTCAGGGAAGCAAGATTCACCG
ATGTGGCTTTAATCTATTCCACGGCATCGCCAAGG
Found at i:42763891 original size:44 final size:44
Alignment explanation
Indices: 42763788--42764175 Score: 141
Period size: 44 Copynumber: 8.5 Consensus size: 44
42763778 GGTCTATTCC
* * * *
42763788 ACTGTAATCTCAGGGAGATAAGA-CC-TGA-TGTGATCTACTCT
1 ACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCTGCTCT
** *
42763829 ACTGTAA-CTTCAAAGAGATAAGATCCTTTATTTTAATCTGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCTGCTCT
* * * *
42763873 ACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCT
1 ACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTTAATCTGCTCT
* * * ** *
42763917 GCTGTAACCTCAGGGAGAT-AGATTTCTGGCTTCAATCTGATGCGATCTACTCT
1 ACTGTAATCTCAGGGAGATAAGA--TC---CTT-TAT-T--T-TAATCTGCTCT
* * * *
42763970 ATTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCTGCTCT
* * * * *
42764014 ATTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCT
1 ACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTTAATCTGCTCT
* * * * *
42764058 GCTGAAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATACGATCTACTCT
1 ACTGTAATCTCAGGGAGATAAGA--TC---CTT-TAT-T-TTA--ATCTGCTCT
* * * *
42764112 ACTGTAA-CTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCTGCTCT
42764156 ACTGTAATCTCAGGGAGATA
1 ACTGTAATCTCAGGGAGATA
42764176 GGATTACTAG
Statistics
Matches: 251, Mismatches: 58, Indels: 73
0.66 0.15 0.19
Matches are distributed among these distances:
40 1 0.00
41 19 0.08
42 4 0.02
43 8 0.03
44 134 0.53
45 5 0.02
46 3 0.01
47 2 0.01
48 4 0.02
49 5 0.02
50 3 0.01
51 3 0.01
52 7 0.03
53 24 0.10
54 29 0.12
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
ACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCTGCTCT
Found at i:42764070 original size:141 final size:142
Alignment explanation
Indices: 42763812--42764239 Score: 718
Period size: 142 Copynumber: 3.0 Consensus size: 142
42763802 GAGATAAGAC
* * *
42763812 CTGATGTGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTTTATTTTAATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
42763877 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAACCTCAGGGAGAT-AGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGAAATCTCAGGGAGATAAGATT
42763941 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* *
42763953 CTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCATTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
42764018 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGAAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGAAATCTCAGGGAGATAAGATT
42764083 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* *
42764095 CTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
42764160 TAATCTCAGGGAGATAGGATTACTAGCTTCAATTTGCTCTACT-ATAATCTCTA-GGAGATAAGA
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGA-AATCTC-AGGGAGATAAGA
42764223 TTTCTGGCTTCAAT
129 TTTCTGGCTTCAAT
42764237 CTG
1 CTG
42764240 CTCCACTGTA
Statistics
Matches: 271, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
141 118 0.44
142 152 0.56
143 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGAAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:42764209 original size:44 final size:44
Alignment explanation
Indices: 42764146--42764268 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 44
42764136 CTTTTATTTT
* *
42764146 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * *
42764190 AATTTGCTCTACTATAATCTCTA-GGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTC-AGGGAGATAAGATTACTAGCTTC
*
42764234 AATCTGCTCCACTGTAA-CACCAGGGAGATAAGATT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATT
42764269 CATCATTTCC
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
43 2 0.03
44 62 0.95
45 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:42764544 original size:130 final size:130
Alignment explanation
Indices: 42764357--42764590 Score: 360
Period size: 130 Copynumber: 1.8 Consensus size: 130
42764347 CCTTACACTT
* * *
42764357 GAAGATAAGATTTACCCTCGTCGATCTGTTCCACTACTACTTAGGAAGATAAGATCTGCAATTTC
1 GAAGATAAGATTCACCCTCGTCGATCTGCTCCACTACTACTTAGGAAGACAAGATCTGCAATTTC
42764422 CAACCCATTCCACTGCTGGTCAGGGACATAGGACGTGTGGCTTAATTTGTTTCCCTACTCTAGGG
66 CAACCCATTCCACTGCTGGTCAGGGACATAGGACGTGTGGCTTAATTTGTTTCCCTACTCTAGGG
* * * * * * *
42764487 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGCAATTTC
1 GAAGATAAGATTCACCCTCGTCGATCTGCTCCACTACTACTTAGGAAGACAAGATCTGCAATTTC
* *
42764552 CAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTG
66 CAACCCATTCCACTGCTGGTCAGGGACATAGGACGTGTG
42764591 ATTTCACCGA
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
130 92 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (130 bp):
GAAGATAAGATTCACCCTCGTCGATCTGCTCCACTACTACTTAGGAAGACAAGATCTGCAATTTC
CAACCCATTCCACTGCTGGTCAGGGACATAGGACGTGTGGCTTAATTTGTTTCCCTACTCTAGGG
Found at i:42766636 original size:6 final size:6
Alignment explanation
Indices: 42766625--42766669 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
42766615 CTTCTTATCA
* * *
42766625 ATTTTT ATTTTT ATTTTG ATTTTG ATTTTG AGTTTG ATTTTG ATT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATT
42766670 GATTTTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (6 bp):
ATTTTG
Found at i:42774511 original size:27 final size:27
Alignment explanation
Indices: 42774474--42774817 Score: 360
Period size: 27 Copynumber: 12.8 Consensus size: 27
42774464 TGCGATACGT
* *
42774474 GGGTAAAATTATCGAAATACCCTCGAT
1 GGGTAAAATTATCGAAATACCCTCAAA
* *
42774501 GGGTAAAATTATCAAAATACCCTCAAT
1 GGGTAAAATTATCGAAATACCCTCAAA
*
42774528 GGGTAAAATTACCGAAATACCCTCGAAA
1 GGGTAAAATTATCGAAATACCCTC-AAA
42774556 -GGTAAAATTATCGAAATACCCT-AAA
1 GGGTAAAATTATCGAAATACCCTCAAA
* * *
42774581 GGGTAAAATTATCAAAATACTCTCGAA
1 GGGTAAAATTATCGAAATACCCTCAAA
* * *
42774608 GAGTAAAATTATTGAAATACCCTCAAT
1 GGGTAAAATTATCGAAATACCCTCAAA
42774635 GGGTAAAATTATCGAAATACCCTCGAAA
1 GGGTAAAATTATCGAAATACCCTC-AAA
* * * *
42774663 -GATTAAATTA-CTAAAGTACTCTCAAA
1 GGGTAAAATTATCGAAA-TACCCTCAAA
* *
42774689 GGGTAAAATTATTGAAATACTCTCAATA
1 GGGTAAAATTATCGAAATACCCTCAA-A
*
42774717 -GGTATAATTATCGAAATACCCTCAAA
1 GGGTAAAATTATCGAAATACCCTCAAA
** **
42774743 GGAAAAAATTATCGAAATACCCTTGAA
1 GGGTAAAATTATCGAAATACCCTCAAA
* *
42774770 GGGTAAAATTA-CTGTAAT-CCCCCAAA
1 GGGTAAAATTATC-GAAATACCCTCAAA
* *
42774796 GGGTAAAATTTTTGAAATACCC
1 GGGTAAAATTATCGAAATACCC
42774818 CTGAGGGGTA
Statistics
Matches: 262, Mismatches: 43, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
25 3 0.01
26 48 0.18
27 203 0.77
28 8 0.03
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (27 bp):
GGGTAAAATTATCGAAATACCCTCAAA
Found at i:42775073 original size:26 final size:26
Alignment explanation
Indices: 42775042--42775109 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
42775032 TTATTGGCAA
*
42775042 CTTTGCTGCGATATTGATACTGATAG
1 CTTTGCTGCGATATTGATACTGACAG
* * * *
42775068 CTTTGCTGTGTTACTGATACTGGCAG
1 CTTTGCTGCGATATTGATACTGACAG
42775094 CTTTGCTGCGATATTG
1 CTTTGCTGCGATATTG
42775110 GTGTGTTGGC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.40
Consensus pattern (26 bp):
CTTTGCTGCGATATTGATACTGACAG
Found at i:42775255 original size:28 final size:29
Alignment explanation
Indices: 42775223--42775298 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
42775213 GATAACTATT
*
42775223 TTGGGCTAAGACCCACAC-TGTTACTGTA
1 TTGGGCTAAGACCCACACTTATTACTGTA
*
42775251 TTGGGCTAAGGCCCACACTTTATTACTGTA
1 TTGGGCTAAGACCCACAC-TTATTACTGTA
* *
42775281 TTGGGCTATGCCCCACAC
1 TTGGGCTAAGACCCACAC
42775299 ACTGCTATTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 17 0.40
30 25 0.60
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (29 bp):
TTGGGCTAAGACCCACACTTATTACTGTA
Found at i:42775311 original size:30 final size:30
Alignment explanation
Indices: 42775223--42775311 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
42775213 GATAACTATT
*
42775223 TTGGGCTAAG-ACC-CACACTGTTACTGTA
1 TTGGGCTAAGCCCCACACACTGTTACTGTA
* ** *
42775251 TTGGGCTAAGGCCCACACTTTATTACTGTA
1 TTGGGCTAAGCCCCACACACTGTTACTGTA
* * *
42775281 TTGGGCTATGCCCCACACACTGCTATTGTA
1 TTGGGCTAAGCCCCACACACTGTTACTGTA
42775311 T
1 T
42775312 AAGGCTCAGG
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 10 0.21
29 2 0.04
30 36 0.75
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31
Consensus pattern (30 bp):
TTGGGCTAAGCCCCACACACTGTTACTGTA
Found at i:42780971 original size:27 final size:27
Alignment explanation
Indices: 42780934--42781278 Score: 301
Period size: 27 Copynumber: 12.8 Consensus size: 27
42780924 TGTGGTTCGT
* *
42780934 GGGTAAAATTATCGAAATACCCTCGAT
1 GGGTAAAATTATCGAAATACCCTCAAA
*
42780961 GGGTAAAATTA-CTGAAATACCCTCAAT
1 GGGTAAAATTATC-GAAATACCCTCAAA
* *
42780988 GGGTAAAATTACCAAAATACCC-CTAAA
1 GGGTAAAATTATCGAAATACCCTC-AAA
**
42781015 GGGTAAAATTATCGAAATACCCTTGAA
1 GGGTAAAATTATCGAAATACCCTCAAA
* *
42781042 GGGTAAAATTA-CTGAAATACTCTCGAA
1 GGGTAAAATTATC-GAAATACCCTCAAA
* * *
42781069 GGGTAAACTTACCGAAATACCCTCAAT
1 GGGTAAAATTATCGAAATACCCTCAAA
* *
42781096 GGGTAAAATTATCGAAACACCCTTAAA
1 GGGTAAAATTATCGAAATACCCTCAAA
**
42781123 GGGTAAAATTA-CTGAAATACCCTCACC
1 GGGTAAAATTATC-GAAATACCCTCAAA
* * * *
42781150 GAGTAAAATTA-CTAAAATACCCACGAA
1 GGGTAAAATTATC-GAAATACCCTCAAA
* * * * *
42781177 TGATGAAATTACCAAAATACCCTCAAA
1 GGGTAAAATTATCGAAATACCCTCAAA
*
42781204 GGG-AAAATT-TACTGAAATACCCTCGAA
1 GGGTAAAATTAT-C-GAAATACCCTCAAA
* * *
42781231 GGGTAAAATTACCGTAATGCTCCT-AAA
1 GGGTAAAATTATCGAAATAC-CCTCAAA
42781258 GGGTAAAATTATCGAAATACC
1 GGGTAAAATTATCGAAATACC
42781279 TCCGAGAGGT
Statistics
Matches: 258, Mismatches: 47, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
26 11 0.04
27 234 0.91
28 13 0.05
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.23
Consensus pattern (27 bp):
GGGTAAAATTATCGAAATACCCTCAAA
Found at i:42781073 original size:81 final size:80
Alignment explanation
Indices: 42780934--42781278 Score: 399
Period size: 81 Copynumber: 4.3 Consensus size: 80
42780924 TGTGGTTCGT
* *
42780934 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACTGAAATACCCTCAATGGGTAAAATTA
1 GGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACTGAAATACCCTCAA-GGGTAAAATTA
42780999 CCAAAATACCCCTAAA
65 CCAAAATACCCCTAAA
** * *
42781015 GGGTAAAATTATCGAAATACCCTTGAAGGGTAAAATTACTGAAATACTCTCGAAGGGTAAACTTA
1 GGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACTGAAATACCCTC-AAGGGTAAAATTA
* *
42781080 CCGAAATA-CCCTCAAT
65 CCAAAATACCCCT-AAA
* * * *
42781096 GGGTAAAATTATCGAAACACCCTTAAAGGGTAAAATTACTGAAATACCCTCACCGAGTAAAATTA
1 GGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACTGAAATACCCTCA-AGGGTAAAATTA
* *
42781161 CTAAAATACCCAC-GAA
65 CCAAAATACCC-CTAAA
* * * * *
42781177 TGATGAAATTACCAAAATACCCTCAAAGGG-AAAATTTACTGAAATACCCTCGAAGGGTAAAATT
1 GGGTAAAATTATCGAAATACCCTCAAAGGGTAAAA-TTACTGAAATACCCTC-AAGGGTAAAATT
** * *
42781241 ACCGTAATGCTCCTAAA
64 ACCAAAATACCCCTAAA
42781258 GGGTAAAATTATCGAAATACC
1 GGGTAAAATTATCGAAATACC
42781279 TCCGAGAGGT
Statistics
Matches: 220, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
80 10 0.05
81 204 0.93
82 5 0.02
83 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.23
Consensus pattern (80 bp):
GGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACTGAAATACCCTCAAGGGTAAAATTAC
CAAAATACCCCTAAA
Found at i:42781293 original size:54 final size:54
Alignment explanation
Indices: 42780934--42781278 Score: 351
Period size: 54 Copynumber: 6.4 Consensus size: 54
42780924 TGTGGTTCGT
* * *
42780934 GGGTAAAATTATCGAAATACCCTCGATGGGTAAAATTACTGAAATACCCTCAAT
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCAAA
* * * * **
42780988 GGGTAAAATTACCAAAATACCC-CTAAAGGGTAAAATTATCGAAATACCCTTGAA
1 GGGTAAAATTATCGAAATACCCTC-GAAGGGTAAAATTACCGAAATACCCTCAAA
* * *
42781042 GGGTAAAATTA-CTGAAATACTCTCGAAGGGTAAACTTACCGAAATACCCTCAAT
1 GGGTAAAATTATC-GAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCAAA
* ** * **
42781096 GGGTAAAATTATCGAAACACCCTTAAAGGGTAAAATTACTGAAATACCCTCACC
1 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCAAA
* * * * * * *
42781150 GAGTAAAATTA-CTAAAATACCCACGAATGATGAAATTACCAAAATACCCTCAAA
1 GGGTAAAATTATC-GAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCAAA
* *
42781204 GGG-AAAATT-TACTGAAATACCCTCGAAGGGTAAAATTACCGTAATGCTCCT-AAA
1 GGGTAAAATTAT-C-GAAATACCCTCGAAGGGTAAAATTACCGAAATAC-CCTCAAA
42781258 GGGTAAAATTATCGAAATACC
1 GGGTAAAATTATCGAAATACC
42781279 TCCGAGAGGT
Statistics
Matches: 234, Mismatches: 47, Indels: 20
0.78 0.16 0.07
Matches are distributed among these distances:
53 9 0.04
54 212 0.91
55 12 0.05
56 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.23
Consensus pattern (54 bp):
GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTCAAA
Found at i:42781541 original size:26 final size:26
Alignment explanation
Indices: 42781488--42781542 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
42781478 TTTGCCACAA
* * *
42781488 ATACTGTTACTGGCAGCTTTGCTCTG
1 ATACTGATACTGGCAGCTCTACTCTG
*
42781514 ATACTGATACTGGCAGCTCTACTGTG
1 ATACTGATACTGGCAGCTCTACTCTG
42781540 ATA
1 ATA
42781543 TTATTATTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTCTACTCTG
Found at i:42781679 original size:28 final size:29
Alignment explanation
Indices: 42781637--42781720 Score: 98
Period size: 30 Copynumber: 2.9 Consensus size: 29
42781627 TTTGTACTAA
* * * *
42781637 TTACTATTTTAGGCTAAGGCCTATAC-TG
1 TTACTATATTGGGCTAAGGCCCACACTTG
42781665 TTACTATATTGGGCTAAGGCCCACACTTTG
1 TTACTATATTGGGCTAAGGCCCACAC-TTG
* *
42781695 TTACTGTATTGGGCTATGGCCCACAC
1 TTACTATATTGGGCTAAGGCCCACAC
42781721 ACTACTACTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
28 22 0.46
30 26 0.54
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (29 bp):
TTACTATATTGGGCTAAGGCCCACACTTG
Found at i:42781730 original size:30 final size:30
Alignment explanation
Indices: 42781666--42781744 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
42781656 CCTATACTGT
* ** **
42781666 TACTATATTGGGCTAAGGCCCACACTTTGT
1 TACTGTATTGGGCTAAGGCCCACACACTAC
*
42781696 TACTGTATTGGGCTATGGCCCACACACTAC
1 TACTGTATTGGGCTAAGGCCCACACACTAC
* *
42781726 TACTGTATAGGGCTTAGGC
1 TACTGTATTGGGCTAAGGC
42781745 TCAGACTGAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (30 bp):
TACTGTATTGGGCTAAGGCCCACACACTAC
Found at i:42785805 original size:19 final size:21
Alignment explanation
Indices: 42785783--42785822 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
42785773 ATAATTATAA
42785783 AAATAATTAA-A-TTTTAATT
1 AAATAATTAACATTTTTAATT
*
42785802 AAATTATTAACATTTTTAATT
1 AAATAATTAACATTTTTAATT
42785823 TTTTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATAATTAACATTTTTAATT
Found at i:42785834 original size:12 final size:12
Alignment explanation
Indices: 42785817--42785858 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
42785807 ATTAACATTT
42785817 TTAATTTTTTTA
1 TTAATTTTTTTA
* *
42785829 TTAATTTTATAA
1 TTAATTTTTTTA
42785841 TTAA--TTTTTA
1 TTAATTTTTTTA
42785851 TTAATTTT
1 TTAATTTT
42785859 AATTTATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.33
12 16 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTAATTTTTTTA
Found at i:42785836 original size:10 final size:10
Alignment explanation
Indices: 42785823--42785868 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
42785813 ATTTTTAATT
42785823 TTTTTATTAA
1 TTTTTATTAA
42785833 TTTTATAATTAA
1 TTTT-T-ATTAA
42785845 TTTTTATTAA
1 TTTTTATTAA
* *
42785855 TTTTAATTTA
1 TTTTTATTAA
42785865 TTTT
1 TTTT
42785869 CGACAGTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 21 0.66
11 2 0.06
12 9 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTATTAA
Found at i:42792080 original size:46 final size:46
Alignment explanation
Indices: 42792021--42792135 Score: 194
Period size: 46 Copynumber: 2.5 Consensus size: 46
42792011 GACACCGTAG
* **
42792021 ACAGAACGACTAAAAGCCATAAGTATCACAGCAACGCTGCCTGTTA
1 ACAGAACGGCTAAAAGCCATAAGTATCACAGCAACGCTGCCAATTA
*
42792067 ACAGAATGGCTAAAAGCCATAAGTATCACAGCAACGCTGCCAATTA
1 ACAGAACGGCTAAAAGCCATAAGTATCACAGCAACGCTGCCAATTA
42792113 ACAGAACGGCTAAAAGCCATAAG
1 ACAGAACGGCTAAAAGCCATAAG
42792136 CAAAAAGGCA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (46 bp):
ACAGAACGGCTAAAAGCCATAAGTATCACAGCAACGCTGCCAATTA
Found at i:42792416 original size:27 final size:27
Alignment explanation
Indices: 42792339--42792581 Score: 226
Period size: 27 Copynumber: 9.0 Consensus size: 27
42792329 TTAGATCATC
42792339 TTACCCTTCG-GGAGTATTTT-GATAATT
1 TTACCCTTCGAGG-GTATTTTAG-TAATT
* **
42792366 TTACCCTTCGA-AGTATTTCGGTAATT
1 TTACCCTTCGAGGGTATTTTAGTAATT
* *
42792392 TTACCCTTCAAAGGTATTTTAGTAATT
1 TTACCCTTCGAGGGTATTTTAGTAATT
* *
42792419 TTACCCTTTGAGGGTATTTCAGTAATT
1 TTACCCTTCGAGGGTATTTTAGTAATT
* *
42792446 TTACCCTTTGAGGGTA-TTTCGTTAATT
1 TTACCCTTCGAGGGTATTTTAG-TAATT
* * *
42792473 TTACACTTCGGGGGTATTTTGGTAATT
1 TTACCCTTCGAGGGTATTTTAGTAATT
* ** *
42792500 TTACCCTTCGAAGGTATTTCGGTATTT
1 TTACCCTTCGAGGGTATTTTAGTAATT
*
42792527 TTACCAC-TCGAGGGTATTTTAATAATT
1 TTACC-CTTCGAGGGTATTTTAGTAATT
** * *
42792554 TTACCCTTTAAGGGTATTTAAGTCATT
1 TTACCCTTCGAGGGTATTTTAGTAATT
42792581 T
1 T
42792582 AAAAACCTTT
Statistics
Matches: 178, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
26 25 0.14
27 148 0.83
28 5 0.03
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.44
Consensus pattern (27 bp):
TTACCCTTCGAGGGTATTTTAGTAATT
Found at i:42798170 original size:16 final size:15
Alignment explanation
Indices: 42798145--42798175 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
42798135 CTTTTAATAC
42798145 ACTAGCACAAAGCCT
1 ACTAGCACAAAGCCT
42798160 ACTAGGCACAAAGCCT
1 ACTA-GCACAAAGCCT
42798176 GAATAACACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.32, G:0.16, T:0.13
Consensus pattern (15 bp):
ACTAGCACAAAGCCT
Found at i:42798204 original size:38 final size:38
Alignment explanation
Indices: 42798143--42798235 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 38
42798133 AACTTTTAAT
*
42798143 ACACTAGCACAAAGCCTACTAGGCACAAAGCCTGAATA
1 ACACCAGCACAAAGCCTACTAGGCACAAAGCCTGAATA
* * * *
42798181 ACACCAGCATAAAGCTTGCTAGGCACAGAGCCTGAATA
1 ACACCAGCACAAAGCCTACTAGGCACAAAGCCTGAATA
42798219 ACACC-GACACAAAGCCT
1 ACACCAG-CACAAAGCCT
42798236 GAATAACACC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 1 0.02
38 46 0.98
ACGTcount: A:0.40, C:0.30, G:0.17, T:0.13
Consensus pattern (38 bp):
ACACCAGCACAAAGCCTACTAGGCACAAAGCCTGAATA
Found at i:42798234 original size:22 final size:22
Alignment explanation
Indices: 42798204--42798245 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
42798194 GCTTGCTAGG
*
42798204 CACAGAGCCTGAATAACACCGA
1 CACAAAGCCTGAATAACACCGA
42798226 CACAAAGCCTGAATAACACC
1 CACAAAGCCTGAATAACACC
42798246 AAGATAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.33, G:0.14, T:0.10
Consensus pattern (22 bp):
CACAAAGCCTGAATAACACCGA
Found at i:42798254 original size:22 final size:22
Alignment explanation
Indices: 42798204--42798257 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
42798194 GCTTGCTAGG
* *
42798204 CACAGAGCCTGAATAACACCGA
1 CACAAAGCCTGAATAACACCAA
42798226 CACAAAGCCTGAATAACACCAA
1 CACAAAGCCTGAATAACACCAA
* *
42798248 GATAAAGCCT
1 CACAAAGCCT
42798258 ACTAGGCAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.30, G:0.15, T:0.11
Consensus pattern (22 bp):
CACAAAGCCTGAATAACACCAA
Found at i:42798273 original size:60 final size:60
Alignment explanation
Indices: 42798166--42798278 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
42798156 GCCTACTAGG
* * * *
42798166 CACAAAGCCTGAATAACACCAGCATAAAGCTTGCTAGGCACAGAGCCTGAATAACACCGA
1 CACAAAGCCTGAATAACACCAGCATAAAGCCTACTAGGCACAAAGCCTAAATAACACCGA
*
42798226 CACAAAGCCTGAATAACACCAAG-ATAAAGCCTACTAGGCAGAAAGCCTAAATA
1 CACAAAGCCTGAATAACACC-AGCATAAAGCCTACTAGGCACAAAGCCTAAATA
42798279 GCATTATACT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 45 0.96
61 2 0.04
ACGTcount: A:0.43, C:0.27, G:0.17, T:0.13
Consensus pattern (60 bp):
CACAAAGCCTGAATAACACCAGCATAAAGCCTACTAGGCACAAAGCCTAAATAACACCGA
Found at i:42801549 original size:23 final size:23
Alignment explanation
Indices: 42801505--42801549 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
42801495 ATAATAAGTT
**
42801505 TAAAAATAATATTAAGCCAATAA
1 TAAAAATAATATTAAAACAATAA
* *
42801528 TAAAAATAATGTTAAAATAATA
1 TAAAAATAATATTAAAACAATA
42801550 TATGAACATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAAAATAATATTAAAACAATAA
Done.