Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 106 of 172
Found at i:35477161 original size:25 final size:25
Alignment explanation
Indices: 35477133--35477185 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
35477123 GAGAACTAAT
35477133 GTGGTAATAATT-AGAGAGTACGAAC
1 GTGGTAAT-ATTCAGAGAGTACGAAC
* *
35477158 GTGGTAATATTCAGAGGGTACTAAC
1 GTGGTAATATTCAGAGAGTACGAAC
35477183 GTG
1 GTG
35477186 CTAAGGCCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.26
Consensus pattern (25 bp):
GTGGTAATATTCAGAGAGTACGAAC
Found at i:35477436 original size:4 final size:4
Alignment explanation
Indices: 35477427--35477452 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
35477417 TATATATCAC
35477427 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
35477453 TTTTTTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:35478293 original size:20 final size:22
Alignment explanation
Indices: 35478258--35478297 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
35478248 AATAATTATC
35478258 ATTTCTATGTATTTCAAGTTTT
1 ATTTCTATGTATTTCAAGTTTT
35478280 ATTTCT-TG-ATTTCAAGTT
1 ATTTCTATGTATTTCAAGTT
35478298 CTTACCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (22 bp):
ATTTCTATGTATTTCAAGTTTT
Found at i:35482830 original size:48 final size:48
Alignment explanation
Indices: 35482759--35482933 Score: 212
Period size: 48 Copynumber: 3.7 Consensus size: 48
35482749 TACCACTGTT
* *
35482759 ATACGTGTAATGTGGTGCTAAGTGGATATACCACGATTACACATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
* *
35482807 ATACGTGTAACGTGCTGCTAAGTGGATATACCACGATTACAC--ATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
* * * * * * *
35482853 ATACATGTAATGTGATGCTAAGTGGATATGCCATGGTTACATATATCG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
* *
35482901 ATTCAT-TAACATGGTGCTAAGTGGATATACCAC
1 ATACATGTAACGTGGTGCTAAGTGGATATACCAC
35482934 TGTTAAACAT
Statistics
Matches: 109, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
46 39 0.36
47 22 0.20
48 48 0.44
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (48 bp):
ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
Found at i:35482964 original size:38 final size:38
Alignment explanation
Indices: 35482907--35482983 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
35482897 ATCGATTCAT
*
35482907 TAACATGGTGCTAAGTGGATATACCACT-GTTAAACATG
1 TAACATGGTGCCAAGTGGATATACCA-TGGTTAAACATG
* * * *
35482945 TAACGTGGTGCCAATTGGATATGCCATGGTTATACATG
1 TAACATGGTGCCAAGTGGATATACCATGGTTAAACATG
35482983 T
1 T
35482984 TAATTTGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (38 bp):
TAACATGGTGCCAAGTGGATATACCATGGTTAAACATG
Found at i:35485908 original size:15 final size:15
Alignment explanation
Indices: 35485885--35485939 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
35485875 GTATCGTATT
35485885 TTGGATTTCTTTAT-
1 TTGGATTTCTTTATC
* *
35485899 TCTGGGTTTCTCTATC
1 T-TGGATTTCTTTATC
35485915 TTGGATTTCTTTA-C
1 TTGGATTTCTTTATC
*
35485929 TTGGTTTTCTT
1 TTGGATTTCTT
35485940 GTTATCTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 12 0.35
15 21 0.62
16 1 0.03
ACGTcount: A:0.09, C:0.15, G:0.16, T:0.60
Consensus pattern (15 bp):
TTGGATTTCTTTATC
Found at i:35488610 original size:48 final size:48
Alignment explanation
Indices: 35488525--35488701 Score: 257
Period size: 48 Copynumber: 3.7 Consensus size: 48
35488515 TACCACGGTT
* *
35488525 ATACGTGTAACGTGGTGCTAAGTGGATATGCCACGATTACACATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
* * *
35488573 ATACATGAAACATAGTGCTAAGTGGATATACCACGATTACACATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
* * * *
35488621 ATACATGTAACGTGGTGCTAAGTGGATTTGCCACGGTTACATATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
*
35488669 ATTCAT-TAACGTGGTGCTAAGTGGATATACCAC
1 ATACATGTAACGTGGTGCTAAGTGGATATACCAC
35488702 AGTTAAACAT
Statistics
Matches: 114, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
47 25 0.22
48 89 0.78
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (48 bp):
ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
Found at i:35488726 original size:38 final size:38
Alignment explanation
Indices: 35488675--35488751 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
35488665 ATTGATTCAT
35488675 TAACGTGGTGCTAAGTGGATATACCACAGTTAAACATG
1 TAACGTGGTGCTAAGTGGATATACCACAGTTAAACATG
* * *
35488713 TAACGTGGTGCTAAGTGGATATGCCACGGTTATACATG
1 TAACGTGGTGCTAAGTGGATATACCACAGTTAAACATG
35488751 T
1 T
35488752 TAATTTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTGGATATACCACAGTTAAACATG
Found at i:35489847 original size:13 final size:13
Alignment explanation
Indices: 35489829--35489861 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
35489819 ACTATCAGAA
35489829 CGTTGATGTGAAG
1 CGTTGATGTGAAG
35489842 CGTTGATGTGAAG
1 CGTTGATGTGAAG
35489855 CGTTGAT
1 CGTTGAT
35489862 AAACTTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.36, T:0.33
Consensus pattern (13 bp):
CGTTGATGTGAAG
Found at i:35491677 original size:44 final size:43
Alignment explanation
Indices: 35491545--35491688 Score: 157
Period size: 44 Copynumber: 3.3 Consensus size: 43
35491535 CCAACATCCT
* * * *
35491545 AGACGTGGTCTTACATGT-AATCAAATATCGATGCCACTATCCC
1 AGACATGGTCTTACACGTAAATCAAA-ATCGATGCCAATGTCCC
* * * * *
35491588 AGACAGGGTCTTACACG-AAATCAAATTCGACGTCGATGTCCC
1 AGACATGGTCTTACACGTAAATCAAAATCGATGCCAATGTCCC
*
35491630 AGACATGGTCTTACACGTAAATCATAAGTCGATGCCAATGTCCC
1 AGACATGGTCTTACACGTAAATCA-AAATCGATGCCAATGTCCC
*
35491674 AGACATGGTCCTACA
1 AGACATGGTCTTACA
35491689 AGAAAACACA
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
42 27 0.33
43 27 0.33
44 29 0.35
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (43 bp):
AGACATGGTCTTACACGTAAATCAAAATCGATGCCAATGTCCC
Found at i:35498280 original size:29 final size:29
Alignment explanation
Indices: 35498238--35498338 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
35498228 CATGAAATTG
35498238 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
35498267 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
35498296 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
35498324 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
35498339 ACTTACTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 19 0.29
29 46 0.71
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:35504550 original size:45 final size:45
Alignment explanation
Indices: 35504494--35504706 Score: 417
Period size: 45 Copynumber: 4.7 Consensus size: 45
35504484 GGTTGAGCAT
*
35504494 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGC
35504539 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGC
35504584 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGC
35504629 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGC
35504674 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
35504707 GGGGCGGGTT
Statistics
Matches: 167, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 167 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.27
Consensus pattern (45 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGC
Found at i:35511295 original size:46 final size:46
Alignment explanation
Indices: 35511245--35511420 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
35511235 TGGTTGAGCA
35511245 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
35511291 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
35511336 CATCCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
35511384 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
35511421 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 62 0.58
47 28 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:35511401 original size:93 final size:93
Alignment explanation
Indices: 35511242--35511412 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
35511232 GGATGGTTGA
* * * *
35511242 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
35511307 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
35511335 GCATCCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
35511400 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
35511413 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:35514856 original size:12 final size:12
Alignment explanation
Indices: 35514839--35514864 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35514829 CATTCGGAAG
35514839 TATATATATACA
1 TATATATATACA
35514851 TATATATATACA
1 TATATATATACA
35514863 TA
1 TA
35514865 AGTATGCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:35515354 original size:29 final size:29
Alignment explanation
Indices: 35515312--35515412 Score: 159
Period size: 29 Copynumber: 3.5 Consensus size: 29
35515302 CATGAAATTG
35515312 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
35515341 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* *
35515370 GCACTAAGTGTGCGAGTTC-AATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
35515398 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
35515413 ACTTACTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
28 20 0.30
29 46 0.70
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:35527584 original size:57 final size:57
Alignment explanation
Indices: 35527515--35527628 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 57
35527505 GCACCTTCAC
* * * * *
35527515 GGATGTATCGCACACTAAGTGTCATCCTCGATAATTCACTCACTATGAGCCATTTCT
1 GGATGTATCGCACACTAAGTGCCATCCTCAATAACTCACACACTAAGAGCCATTTCT
* * *
35527572 GGATGTTTCGCACACTAAGTGCCATCCTCAATAACTCGCACACTAAGTGCCATTTCT
1 GGATGTATCGCACACTAAGTGCCATCCTCAATAACTCACACACTAAGAGCCATTTCT
35527629 CAAAATTGAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (57 bp):
GGATGTATCGCACACTAAGTGCCATCCTCAATAACTCACACACTAAGAGCCATTTCT
Found at i:35530982 original size:28 final size:28
Alignment explanation
Indices: 35530946--35531082 Score: 116
Period size: 28 Copynumber: 4.9 Consensus size: 28
35530936 ATTCTTCTCA
* * * *
35530946 ATGTTTCACACATTTAGTGCCTTCAC-GG
1 ATGTATCACACACTAAGTGCCATC-CTGG
35530974 ATGTATCACACACTAAGTGCCATCCTGG
1 ATGTATCACACACTAAGTGCCATCCTGG
* *
35531002 ATGTCTCACACACTAAGTGCCATCCTCG
1 ATGTATCACACACTAAGTGCCATCCTGG
* * * * *
35531030 AT-AATTCACTCATTAAGAGCCATTTCTGG
1 ATGTA-TCACACACTAAGTGCCA-TCCTGG
* *
35531059 ATGTTTCGCACACTAAGTGCCATC
1 ATGTATCACACACTAAGTGCCATC
35531083 TCAGTAACTC
Statistics
Matches: 85, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
27 1 0.01
28 65 0.76
29 19 0.22
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (28 bp):
ATGTATCACACACTAAGTGCCATCCTGG
Found at i:35534211 original size:22 final size:22
Alignment explanation
Indices: 35534141--35534199 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
35534131 TACGAGCTGA
* *
35534141 TGAACAATAAGCTCTATTGAGC
1 TGAACAGTAAGCTCTATCGAGC
*
35534163 T-AAAATGGTAAGCTCTATCGAGC
1 TGAACA--GTAAGCTCTATCGAGC
35534186 TGAACAGTAAGCTC
1 TGAACAGTAAGCTC
35534200 ATACTAGCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 3 0.10
22 9 0.30
23 15 0.50
24 3 0.10
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (22 bp):
TGAACAGTAAGCTCTATCGAGC
Found at i:35545749 original size:17 final size:19
Alignment explanation
Indices: 35545714--35545750 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
35545704 TTTAATTAGG
35545714 ATTATGAGATAAAATTATT
1 ATTATGAGATAAAATTATT
*
35545733 ATTATTAGA-AAAA-TATT
1 ATTATGAGATAAAATTATT
35545750 A
1 A
35545751 CTGTATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
ATTATGAGATAAAATTATT
Found at i:35549776 original size:25 final size:24
Alignment explanation
Indices: 35549733--35549796 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 24
35549723 TCAAAAATTT
*
35549733 AATTAAAATTATTAATAATTCAATG-
1 AATTAAAA--ATTAATAATTCAAAGA
*
35549758 AATTGAAAAATTAACTAATTGAAAGA
1 AATT-AAAAATTAA-TAATTCAAAGA
35549784 AATTAAAAATTAA
1 AATTAAAAATTAA
35549797 GAGGAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 5 0.15
25 21 0.62
26 8 0.24
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (24 bp):
AATTAAAAATTAATAATTCAAAGA
Found at i:35575966 original size:46 final size:46
Alignment explanation
Indices: 35575913--35576031 Score: 211
Period size: 46 Copynumber: 2.6 Consensus size: 46
35575903 ACATCTCTCA
* *
35575913 CATTAGCCATTTGGCTTTACCACATATCCATCTCATACACGTTTCG
1 CATTAGCCATTCGGCTTTACCACATATCCATCTCATACACATTTCG
*
35575959 CATTAGCCATTCGGCTTTACCTCATATCCATCTCATACACATTTCG
1 CATTAGCCATTCGGCTTTACCACATATCCATCTCATACACATTTCG
35576005 CATTAGCCATTCGGCTTTACCACATAT
1 CATTAGCCATTCGGCTTTACCACATAT
35576032 ATACACTTCC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.34
Consensus pattern (46 bp):
CATTAGCCATTCGGCTTTACCACATATCCATCTCATACACATTTCG
Found at i:35576374 original size:31 final size:31
Alignment explanation
Indices: 35576336--35576394 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
35576326 AAGTGTCACA
35576336 CATGTTCACATTCATCACATTGGCCATTATG
1 CATGTTCACATTCATCACATTGGCCATTATG
35576367 CATGTTCACATTCATCACATTGGCCATT
1 CATGTTCACATTCATCACATTGGCCATT
35576395 CGGCCTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (31 bp):
CATGTTCACATTCATCACATTGGCCATTATG
Found at i:35581128 original size:31 final size:31
Alignment explanation
Indices: 35581090--35581150 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
35581080 TTTCATATTG
35581090 CATATTTCATAACACTAGGCCGAAGCCTTTT
1 CATATTTCATAACACTAGGCCGAAGCCTTTT
** *
35581121 CATATTTCATATTACTAGGCTGAAGCCTTT
1 CATATTTCATAACACTAGGCCGAAGCCTTT
35581151 ACTGAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (31 bp):
CATATTTCATAACACTAGGCCGAAGCCTTTT
Found at i:35581417 original size:23 final size:23
Alignment explanation
Indices: 35581363--35581481 Score: 202
Period size: 23 Copynumber: 5.1 Consensus size: 23
35581353 CCTAGCCTCT
* *
35581363 TTTAATAACTGGGGCAAAAGTCCT
1 TTTAATAACTGGGGCATAAG-CCC
35581387 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
35581410 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
35581433 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
35581456 TTTAATAACTGGGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
35581479 TTT
1 TTT
35581482 TTCACTTCCT
Statistics
Matches: 92, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
23 73 0.79
24 19 0.21
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:35581557 original size:20 final size:20
Alignment explanation
Indices: 35581532--35581578 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
35581522 TTATGATTAC
35581532 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
35581552 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
35581572 ACCATGT
1 ATCATGT
35581579 TTATCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:35585240 original size:39 final size:40
Alignment explanation
Indices: 35585083--35585254 Score: 249
Period size: 40 Copynumber: 4.3 Consensus size: 40
35585073 GCTACTCGTT
* * *
35585083 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
35585123 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
35585163 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
35585203 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
35585242 CAAATGCCTTCGG
1 CAAATGCCTTCGG
35585255 ATCTTAGTCT
Statistics
Matches: 121, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
39 34 0.28
40 85 0.70
41 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:35585267 original size:119 final size:120
Alignment explanation
Indices: 35585085--35585300 Score: 287
Period size: 119 Copynumber: 1.8 Consensus size: 120
35585075 TACTCGTTCA
* *
35585085 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGTACAAATGCCTTCGGGACTTAACCTGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCTGGAT
* *
35585150 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
35585205 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCTGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCTGG
* *
35585267 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
35585301 GCTCGGACAT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.05
119 59 0.71
120 20 0.24
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCTGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:35585291 original size:79 final size:79
Alignment explanation
Indices: 35585083--35585307 Score: 238
Period size: 79 Copynumber: 2.8 Consensus size: 79
35585073 GCTACTCGTT
* * * * * * *
35585083 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGTACAAATGCCTTCGGGACTTAACCTGG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCGG
*
35585148 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * *
35585163 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCGG
*
35585227 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
** * * * *
35585242 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCTCG
1 CAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCCG
35585306 GA
64 GA
35585308 CATCATTCGA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
78 3 0.02
79 58 0.48
80 58 0.48
81 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:35586526 original size:56 final size:56
Alignment explanation
Indices: 35586440--35586559 Score: 213
Period size: 56 Copynumber: 2.1 Consensus size: 56
35586430 TATTAGTTTA
35586440 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
* *
35586496 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATTACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
35586552 TTTCCCAT
1 TTGCCCAT
35586560 CATCCCTTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:35596371 original size:21 final size:21
Alignment explanation
Indices: 35596345--35596386 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
35596335 CTGATATCCA
35596345 TAGCTCCGTACAGAATGCCAC
1 TAGCTCCGTACAGAATGCCAC
35596366 TAGCTCCGTACAGAATGCCAC
1 TAGCTCCGTACAGAATGCCAC
35596387 CTACCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (21 bp):
TAGCTCCGTACAGAATGCCAC
Found at i:35602261 original size:47 final size:47
Alignment explanation
Indices: 35602188--35602457 Score: 209
Period size: 47 Copynumber: 5.8 Consensus size: 47
35602178 ATTTGTTTGT
* * * *
35602188 GAGCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCACATTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACGACA-TATGA
* * * * *
35602234 GAGCCAGTGTAAGACCATGTCTGGGACAAT-GCATTGGC-ATTGAGACGA
1 GAGCCAGTGTAAGACCATGTCTGGGAC-ATGGCATCGACGA--CATATGA
* * *
35602282 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACTACGAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACGAC-ATATGA
* * * * * *
35602328 TAGTCAATGTAAGACCATGTCTGGTACATGGCATCAACTTGAGATAT--
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC--GACATATGA
*
35602375 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATAT--
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC--GACATATGA
*
35602422 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCG
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
35602458 GTACCTTACC
Statistics
Matches: 188, Mismatches: 26, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
46 36 0.19
47 115 0.61
48 32 0.17
49 4 0.02
50 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACGACATATGA
Found at i:35602349 original size:94 final size:94
Alignment explanation
Indices: 35602187--35602456 Score: 302
Period size: 94 Copynumber: 2.9 Consensus size: 94
35602177 CATTTGTTTG
* * * * *
35602187 TGAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCAC-ATTATGAGAGCCAGTGTAAGACCA
1 TGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACTACGA-GATGATAGCCAGTGTAAGACCA
***
35602251 TGTCTGGGACAAT-GCATTGGCATTGAGACGA
65 TGTCTGGGACAATGGCATCAAC-TTGAGA-GA
* *
35602282 -GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACTACGAGATGATAGTCAATGTAAGACCAT
1 TGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACTACGAGATGATAGCCAGTGTAAGACCAT
* *
35602346 GTCTGGTAC-ATGGCATCAACTTGAGATA
66 GTCTGGGACAATGGCATCAACTTGAGAGA
* *
35602374 TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACT-TGAGAT-ATGAGCCAGTGTAAGAC
1 TGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACTACGAGATGAT-AGCCAGTGTAAGAC
*
35602437 CATGTCTAGGAC-ATGGCATC
63 CATGTCTGGGACAATGGCATC
35602457 GGTACCTTAC
Statistics
Matches: 151, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
92 1 0.01
93 23 0.15
94 117 0.77
95 10 0.07
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (94 bp):
TGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACTACGAGATGATAGCCAGTGTAAGACCAT
GTCTGGGACAATGGCATCAACTTGAGAGA
Found at i:35602577 original size:63 final size:63
Alignment explanation
Indices: 35602507--35602633 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
35602497 GTGTTCCAAA
*
35602507 TGGTTCAACGGTGAATGTTATGTTCTTAAGCTAATGAAGAAAGTATAACCGTGTGGTGAATGG
1 TGGTTCAACGGTGAATGTTATGTTCTTAAGCTAATGAAGAAAGTATAACCCTGTGGTGAATGG
* *
35602570 TGGTTCAATGGTGATTGTTATGTTCTTAAGCTAATGAAGAAAGTATAACCCTGTGGTGAATGG
1 TGGTTCAACGGTGAATGTTATGTTCTTAAGCTAATGAAGAAAGTATAACCCTGTGGTGAATGG
35602633 T
1 T
35602634 ACAGGTACCT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.34
Consensus pattern (63 bp):
TGGTTCAACGGTGAATGTTATGTTCTTAAGCTAATGAAGAAAGTATAACCCTGTGGTGAATGG
Found at i:35610035 original size:47 final size:44
Alignment explanation
Indices: 35609923--35610146 Score: 130
Period size: 47 Copynumber: 4.8 Consensus size: 44
35609913 ATTTGTTTGT
* *
35609923 GAGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATAA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTAGAA
* * *
35609969 GAGCCATTGTAAGACCATGTCTGGGACAATGCATTGG-CATTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGAC-ATGCATCGGCCATT-AGA--A
* * * * **
35610017 GAGCTAGTGTAAGACATGTTTGGGACGTGCATCGACTACGAGATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTAGA--A
* * * * *
35610063 TAGTTAATGTAAGACCATGTCTGGTACATGGCATC-GAC-TTGAGATA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCATT-AGA-A
*
35610109 TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG
1 -GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG
35610147 TACCTTACCC
Statistics
Matches: 135, Mismatches: 32, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
45 4 0.03
46 37 0.27
47 67 0.50
48 27 0.20
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (44 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTAGAA
Found at i:35612994 original size:40 final size:40
Alignment explanation
Indices: 35612900--35613044 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
35612890 TACTCGAATG
*
35612900 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
35612941 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * * *
35612981 ATATCCGGGCTAAGTCCCGAAGGAATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
35613021 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
35613045 CTTGTGCAAG
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 60 0.67
41 28 0.31
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:35616599 original size:46 final size:46
Alignment explanation
Indices: 35616537--35616918 Score: 387
Period size: 46 Copynumber: 8.3 Consensus size: 46
35616527 TTATCGCTGT
* * * *
35616537 AATTGAGGTGTATAAATGTTGTTAATTG-AGATGTTAAAGTGCAGCA
1 AATTGAAGTGTTTAAATGTTGTAAATTGAAG-TGTTAAAGTGCTGCA
* *
35616583 AATTGAAGTGCTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTACA
1 AATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTGCA
* * * ** *
35616629 AAGTGAAGTGTTTGAATGTTGTAAGTTGAAGTGTTTAAA-TATTGTA
1 AATTGAAGTGTTTAAATGTTGTAAATTGAAGTG-TTAAAGTGCTGCA
* * ** ** * *
35616675 AAATGAAGTGTTTAAGTACTACAAATTGAAGTGTT-TAGTTGCTGGA
1 AATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAG-TGCTGCA
* * *
35616721 AATTG-AGAAGTATAAATGTTGTTAATTG-AGATGTTAAAGTGCTGCA
1 AATTGAAG-TGTTTAAATGTTGTAAATTGAAG-TGTTAAAGTGCTGCA
* *
35616767 AATTGAAGTGTTTAAATGCTATAAATTGAAGTGTTAAAGTGCTGCA
1 AATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTGCA
* * *
35616813 AATTGAAGTGTTTAAATGCTATAAATTGAGGTGTTAAAGTGCTGCA
1 AATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTGCA
* * * * *
35616859 AATTGAAGTTTTTAAATGTTGTAAATTGAAGTTTTTAAGTACAGCA
1 AATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTGCA
35616905 AATTGAAGTGTTTA
1 AATTGAAGTGTTTA
35616919 GGTGCTGAAA
Statistics
Matches: 275, Mismatches: 52, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
44 1 0.00
45 6 0.02
46 255 0.93
47 13 0.05
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.37
Consensus pattern (46 bp):
AATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTGCA
Found at i:35616608 original size:23 final size:23
Alignment explanation
Indices: 35616495--35616918 Score: 276
Period size: 23 Copynumber: 18.5 Consensus size: 23
35616485 TCATCACTAA
** *
35616495 TGAAGTGTTTAGTTGCTGGAAAT
1 TGAAGTGTTTAAATGCTGTAAAT
*
35616518 T-AAGATGTTT-TATCGCTGT-AAT
1 TGAAG-TGTTTAAAT-GCTGTAAAT
* * * *
35616540 TGAGGTGTATAAATGTTGTTAAT
1 TGAAGTGTTTAAATGCTGTAAAT
* *
35616563 TG-AGATG-TTAAAGTGCAGCAAAT
1 TGAAG-TGTTTAAA-TGCTGTAAAT
* *
35616586 TGAAGTGCTTAAATGTTGTAAAT
1 TGAAGTGTTTAAATGCTGTAAAT
** *
35616609 TGAAGTG-TTAAAGTGCTACAAAG
1 TGAAGTGTTTAAA-TGCTGTAAAT
* * *
35616632 TGAAGTGTTTGAATGTTGTAAGT
1 TGAAGTGTTTAAATGCTGTAAAT
** *
35616655 TGAAGTGTTTAAATATTGTAAAA
1 TGAAGTGTTTAAATGCTGTAAAT
* * **
35616678 TGAAGTGTTTAAGTACTACAAAT
1 TGAAGTGTTTAAATGCTGTAAAT
** *
35616701 TGAAGTGTTTAGTTGCTGGAAAT
1 TGAAGTGTTTAAATGCTGTAAAT
* * * *
35616724 TG-AGAAGTATAAATGTTGTTAAT
1 TGAAG-TGTTTAAATGCTGTAAAT
*
35616747 TG-AGATG-TTAAAGTGCTGCAAAT
1 TGAAG-TGTTTAAA-TGCTGTAAAT
*
35616770 TGAAGTGTTTAAATGCTATAAAT
1 TGAAGTGTTTAAATGCTGTAAAT
*
35616793 TGAAGTG-TTAAAGTGCTGCAAAT
1 TGAAGTGTTTAAA-TGCTGTAAAT
*
35616816 TGAAGTGTTTAAATGCTATAAAT
1 TGAAGTGTTTAAATGCTGTAAAT
* *
35616839 TGAGGTG-TTAAAGTGCTGCAAAT
1 TGAAGTGTTTAAA-TGCTGTAAAT
* *
35616862 TGAAGTTTTTAAATGTTGTAAAT
1 TGAAGTGTTTAAATGCTGTAAAT
* * * * *
35616885 TGAAGTTTTTAAGTACAGCAAAT
1 TGAAGTGTTTAAATGCTGTAAAT
35616908 TGAAGTGTTTA
1 TGAAGTGTTTA
35616919 GGTGCTGAAA
Statistics
Matches: 311, Mismatches: 71, Indels: 38
0.74 0.17 0.09
Matches are distributed among these distances:
22 42 0.14
23 241 0.77
24 28 0.09
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.37
Consensus pattern (23 bp):
TGAAGTGTTTAAATGCTGTAAAT
Found at i:35616667 original size:69 final size:69
Alignment explanation
Indices: 35616582--35616918 Score: 344
Period size: 69 Copynumber: 4.9 Consensus size: 69
35616572 AAAGTGCAGC
* * *
35616582 AAATTGAAGTGCTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTACAAAGTGAAGTGTTTGAATG
1 AAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATG
*
35616647 TTGT
66 CTGT
* * * * * **
35616651 AAGTTGAAGTGTTTAAATATTGTAAAATGAAGTGTTTAAGTACTACAAATTGAAGTGTTTAGTTG
1 AAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATG
*
35616716 CTGG
66 CTGT
* * * *
35616720 AAATTG-AGAAGTATAAATGTTGTTAATTG-AGATGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
1 AAATTGAAG-TGTTTAAATGTTGTAAATTGAAG-TGTTAAAGTGCTACAAATTGAAGTGTTTAAA
*
35616783 TGCTAT
64 TGCTGT
* * * *
35616789 AAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAA-TGCTATAAATTGAGGTG-TTAAA
1 AAATTGAAGTGTTTAAA-TGTTGTAAATTGAAGTG-TTAAAGTGCTACAAATTGAAGTGTTTAAA
*
35616851 GTGCTGC
64 -TGCTGT
* * * *
35616858 AAATTGAAGTTTTTAAATGTTGTAAATTGAAGTTTTTAAGTAC-AGCAAATTGAAGTGTTTA
1 AAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTA-CAAATTGAAGTGTTTA
35616919 GGTGCTGAAA
Statistics
Matches: 214, Mismatches: 43, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
68 18 0.08
69 179 0.84
70 17 0.08
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.37
Consensus pattern (69 bp):
AAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATG
CTGT
Found at i:35617717 original size:82 final size:84
Alignment explanation
Indices: 35617623--35617826 Score: 227
Period size: 86 Copynumber: 2.4 Consensus size: 84
35617613 AAAGGCGTTG
* * * * **
35617623 CTAAAAGTCAAGTTCTTTAGCAGCGTTTGTGGAGAGAGCA-CT-AAGAGTCATGTTCTTTAGTGG
1 CTAAAGGTCAAGTTCTTTAGCGGCGTTTATGGAGAAAGCACCTAAAG-GTCATGTTCTTTAGCAG
* * *
35617686 CATTTTTGGGAAAA-TGCCA
65 AAATTTTAGGAAAAGTGCCA
* *
35617705 CTAAAGGTCAAGTTATTTAGCGGCGTTTATGGAGAAAGCACCGCTAAAGGTTATGTTCTTTAGCA
1 CTAAAGGTCAAGTTCTTTAGCGGCGTTTATGGAGAAAGCA-C-CTAAAGGTCATGTTCTTTAGCA
* *
35617770 GAAATTTTAGGAAAAGTGTCG
64 GAAATTTTAGGAAAAGTGCCA
*
35617791 CTAAAGGTCATGTTCTTTAGCGGCGTTTATGG-GAAA
1 CTAAAGGTCAAGTTCTTTAGCGGCGTTTATGGAGAAA
35617827 AGTGTTGCTA
Statistics
Matches: 102, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
82 35 0.34
85 31 0.30
86 36 0.35
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (84 bp):
CTAAAGGTCAAGTTCTTTAGCGGCGTTTATGGAGAAAGCACCTAAAGGTCATGTTCTTTAGCAGA
AATTTTAGGAAAAGTGCCA
Found at i:35617753 original size:43 final size:43
Alignment explanation
Indices: 35617622--35617863 Score: 185
Period size: 43 Copynumber: 5.7 Consensus size: 43
35617612 GAAAGGCGTT
* * * * *
35617622 GCTAAAAGTCAAGTTCTTTAGCAGCGTTTGTGGAG--AGAG-C
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTATGGAGAAAGTGTC
* * * * * *
35617662 ACT-AAGAGTCATGTTCTTTAGTGGCATTTTTGG-GAAAATGCC
1 GCTAAAG-GTCATGTTCTTTAGCGGCGTTTATGGAGAAAGTGTC
* * * ***
35617704 ACTAAAGGTCAAGTTATTTAGCGGCGTTTATGGAGAAAGCACC
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTATGGAGAAAGTGTC
* ***
35617747 GCTAAAGGTTATGTTCTTTAGCAGAAATTT-TAGGA-AAAGTGTC
1 GCTAAAGGTCATGTTCTTTAGC-GGCGTTTAT-GGAGAAAGTGTC
*
35617790 GCTAAAGGTCATGTTCTTTAGCGGCGTTTATGG-GAAAAGTGTT
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTATGGAG-AAAGTGTC
*
35617833 GCTAAAAGTCATGTTCTTTAGCGGCGTTTAT
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTAT
35617864 TTAGCGGCAC
Statistics
Matches: 158, Mismatches: 33, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
39 3 0.02
40 23 0.15
41 2 0.01
42 31 0.20
43 92 0.58
44 7 0.04
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.33
Consensus pattern (43 bp):
GCTAAAGGTCATGTTCTTTAGCGGCGTTTATGGAGAAAGTGTC
Found at i:35617810 original size:86 final size:82
Alignment explanation
Indices: 35617622--35617826 Score: 225
Period size: 82 Copynumber: 2.5 Consensus size: 82
35617612 GAAAGGCGTT
* * * * ** *
35617622 GCTAAAAGTCAAGTTCTTTAGCAGCGTTTGTGGAGAGAGCACTAAGAGTCATGTTCTTTAGTGGC
1 GCTAAAGGTCAAGTTCTTTAGCGGCGTTTATGGAGAAAGCACTAAGAGTCATGTTCTTTAGCAGA
* *
35617687 ATTTTTGGGAAAATGCC
66 AATTTTAGGAAAATGCC
* * *
35617704 ACTAAAGGTCAAGTTATTTAGCGGCGTTTATGGAGAAAGCACCGCTAA-AGGTTATGTTCTTTAG
1 GCTAAAGGTCAAGTTCTTTAGCGGCGTTTATGGAGAAAGCA---CTAAGA-GTCATGTTCTTTAG
*
35617768 CAGAAATTTTAGGAAAAGTGTC
62 CAGAAATTTTAGGAAAA-TGCC
*
35617790 GCTAAAGGTCATGTTCTTTAGCGGCGTTTATGG-GAAA
1 GCTAAAGGTCAAGTTCTTTAGCGGCGTTTATGGAGAAA
35617827 AGTGTTGCTA
Statistics
Matches: 102, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
82 35 0.34
84 1 0.01
85 33 0.32
86 33 0.32
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (82 bp):
GCTAAAGGTCAAGTTCTTTAGCGGCGTTTATGGAGAAAGCACTAAGAGTCATGTTCTTTAGCAGA
AATTTTAGGAAAATGCC
Found at i:35621804 original size:29 final size:28
Alignment explanation
Indices: 35621772--35621861 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
35621762 AGCTTCGGCT
*
35621772 ATCGATTATAAAAATGGATGGTGACGACC
1 ATCGAATATAAAAA-GGATGGTGACGACC
* * *
35621801 ATCGACTATGAAAAGGGATGGTGACAACC
1 ATCGAATAT-AAAAAGGATGGTGACGACC
**
35621830 ATCGAATATGAAAAAGGATGGTTTCGACC
1 ATCGAATAT-AAAAAGGATGGTGACGACC
35621859 ATC
1 ATC
35621862 AAACATGAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 48 0.92
30 4 0.08
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (28 bp):
ATCGAATATAAAAAGGATGGTGACGACC
Found at i:35621869 original size:29 final size:28
Alignment explanation
Indices: 35621781--35621872 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
35621771 TATCGATTAT
*
35621781 AAAAATGGATGGTGACGACCATCGACTATG
1 AAAAA-GGATGGTGACGACCATCAAC-ATG
* * *
35621811 AAAAGGGATGGTGACAACCATCGAATATG
1 AAAAAGGATGGTGACGACCATC-AACATG
**
35621840 AAAAAGGATGGTTTCGACCATCAAACATG
1 AAAAAGGATGGTGACGACCATC-AACATG
35621869 AAAA
1 AAAA
35621873 GGGACAGTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.18
Consensus pattern (28 bp):
AAAAAGGATGGTGACGACCATCAACATG
Found at i:35633557 original size:24 final size:24
Alignment explanation
Indices: 35633529--35633577 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
35633519 TATGGAAGTG
35633529 GGAAAGAGTAACAATGGACTTTGT
1 GGAAAGAGTAACAATGGACTTTGT
35633553 GGAAAGAGTAACAATGGACTTTGT
1 GGAAAGAGTAACAATGGACTTTGT
35633577 G
1 G
35633578 AGTGGGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.31, T:0.24
Consensus pattern (24 bp):
GGAAAGAGTAACAATGGACTTTGT
Found at i:35639386 original size:29 final size:29
Alignment explanation
Indices: 35639340--35639467 Score: 143
Period size: 29 Copynumber: 4.4 Consensus size: 29
35639330 TCAACGACCA
* *
35639340 ATGAAAAGGGATAACTTCGGCTATTGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
*
35639369 ATGAACAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
* * * *
35639398 ATGAAAAGGGAT-GGTGAC-GATCATCGAAT
1 ATGAAAAGGGATAGCT-TCGGCT-ATCGATT
* *
35639427 ATGAAAAGGGATAGCTTTGGCTATTGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
35639456 ATGAAAAGGGAT
1 ATGAAAAGGGAT
35639468 TGTGACGACC
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
28 4 0.05
29 73 0.90
30 4 0.05
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.27
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGATT
Found at i:35639431 original size:58 final size:58
Alignment explanation
Indices: 35639368--35639554 Score: 207
Period size: 58 Copynumber: 3.2 Consensus size: 58
35639358 GGCTATTGAT
* *
35639368 TATGAACAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGATCATCGAA
1 TATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAA
* * * *
35639426 TATGAAAAGGGATAGCTTTGGCTATTGATTATGAAAAGGGATTGTGACGACCATCAAA
1 TATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAA
* * * * * **
35639484 TATAAAAAAGGAT-GGTGACGGCCA-CGATTAATGAAAAGGGATGGTTTCGACCATCGAA
1 TATGAAAAGGGATAGCT-TCGGCTATCGATT-ATGAAAAGGGATGGTGACGACCATCGAA
* *
35639542 CATGAAAACGGAT
1 TATGAAAAGGGAT
35639555 GGTTACAACC
Statistics
Matches: 107, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
57 6 0.06
58 101 0.94
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (58 bp):
TATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCGAA
Found at i:35639497 original size:87 final size:87
Alignment explanation
Indices: 35639339--35639525 Score: 216
Period size: 87 Copynumber: 2.1 Consensus size: 87
35639329 ATCAACGACC
* * * * * * *
35639339 AATGAAAAGGGATAACTTCGGCTATTGATTATGAACAGGGATAGCTTCGGCTATCGATTATGAAA
1 AATGAAAAGGGATAACTTCGGCTATTGATTATGAAAAGGGATAGCTACGACCATCAAATATAAAA
* *
35639404 AGGGATGGTGACGATCATCGAAT
66 AAGGATGGTGACGACCA-CGAAT
* * *
35639427 -ATGAAAAGGGATAGCTTTGGCTATTGATTATGAAAAGGGATTG-TGACGACCATCAAATATAAA
1 AATGAAAAGGGATAACTTCGGCTATTGATTATGAAAAGGGATAGCT-ACGACCATCAAATATAAA
* *
35639490 AAAGGATGGTGACGGCCACGATT
65 AAAGGATGGTGACGACCACGAAT
35639513 AATGAAAAGGGAT
1 AATGAAAAGGGAT
35639526 GGTTTCGACC
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
86 5 0.06
87 78 0.94
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (87 bp):
AATGAAAAGGGATAACTTCGGCTATTGATTATGAAAAGGGATAGCTACGACCATCAAATATAAAA
AAGGATGGTGACGACCACGAAT
Found at i:35639546 original size:29 final size:29
Alignment explanation
Indices: 35639391--35639567 Score: 133
Period size: 29 Copynumber: 6.1 Consensus size: 29
35639381 AGCTTCGGCT
* *
35639391 ATCGATTATGAAAAGGGATGGTGACGATC
1 ATCGAATATGAAAAGGGATGGTGACGACC
* ** * *
35639420 ATCGAATATGAAAAGGGATAGCT-TTGGCT
1 ATCGAATATGAAAAGGGAT-GGTGACGACC
* * *
35639449 ATTGATTATGAAAAGGGATTGTGACGACC
1 ATCGAATATGAAAAGGGATGGTGACGACC
* * * *
35639478 ATCAAATATAAAAAAGGATGGTGACGGCC
1 ATCGAATATGAAAAGGGATGGTGACGACC
* **
35639507 A-CGATTAATGAAAAGGGATGGTTTCGACC
1 ATCGAAT-ATGAAAAGGGATGGTGACGACC
* * * *
35639536 ATCGAACATGAAAACGGATGGTTACAACC
1 ATCGAATATGAAAAGGGATGGTGACGACC
35639565 ATC
1 ATC
35639568 ATTTAGCATA
Statistics
Matches: 110, Mismatches: 34, Indels: 8
0.72 0.22 0.05
Matches are distributed among these distances:
28 4 0.04
29 101 0.92
30 5 0.05
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (29 bp):
ATCGAATATGAAAAGGGATGGTGACGACC
Found at i:35643471 original size:38 final size:38
Alignment explanation
Indices: 35643397--35643549 Score: 225
Period size: 38 Copynumber: 4.0 Consensus size: 38
35643387 GAATCCAGTC
* **
35643397 ACCAGCACAAAGCCTGCGGGACTTTAAGCTCGGATATGGT
1 ACCAGCACAAAGCCTGCGGGA-TTTAA-CCCGGATATATT
* * *
35643437 ACCAACACTAAGCCTGTGGGATTTAACCCGGATATATT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATATT
35643475 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATATT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATATT
*
35643513 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAT
35643550 NNNNNNNNNN
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
38 80 0.78
39 5 0.05
40 18 0.17
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (38 bp):
ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATATT
Found at i:35645443 original size:40 final size:40
Alignment explanation
Indices: 35645364--35645527 Score: 186
Period size: 40 Copynumber: 4.1 Consensus size: 40
35645354 CGAATGATAA
* * ** *
35645364 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTCGCTATAT
* * *
35645404 CCGGGCTATGACCCGAAGGCATTTATGCTAG-CGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTCG-CTATAT
* * *
35645444 CCGGCCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTCGCTATAT
* * *
35645484 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTCGCTATAT
35645524 CCGG
1 CCGG
35645528 TTAAATCCCG
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 104 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGTCGCTATAT
Found at i:35645522 original size:80 final size:80
Alignment explanation
Indices: 35645364--35645527 Score: 249
Period size: 80 Copynumber: 2.0 Consensus size: 80
35645354 CGAATGATAA
* *
35645364 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGACCCGAAGGCATTTA
1 CCGGACTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
*
35645429 TGCTAGCGATTATAT
66 TGCGAGCGATTATAT
* * *
35645444 CCGGCCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGACTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
*
35645509 TGCGAGTTG-TTATAT
66 TGCGAG-CGATTATAT
35645524 CCGG
1 CCGG
35645528 TTAAATCCCG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
80 75 0.99
81 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGACTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
TGCGAGCGATTATAT
Found at i:35653711 original size:40 final size:40
Alignment explanation
Indices: 35653632--35653795 Score: 159
Period size: 40 Copynumber: 4.1 Consensus size: 40
35653622 CGGATGATAA
* * * ** *
35653632 CCGGACTAAGATCCGAAGGTATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTCGCTATAT
* * *
35653672 CCGGGCTATGACCCGAAGGCATTTATGCTAG-CGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTCG-CTATAT
* * *
35653712 CCGGGATAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTCGCTATAT
* * * * *
35653752 CCAGGCTAAGACCCGAAGGCATTTGTGTGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTCGCTATAT
35653792 CCGG
1 CCGG
35653796 TTAAATCCCG
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 100 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGTCGCTATAT
Found at i:35658399 original size:24 final size:24
Alignment explanation
Indices: 35658372--35658420 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
35658362 ATCATAGAAA
*
35658372 GTGTACAT-TGGCACTATGTGTGCG
1 GTGTA-ATATGGCACTATGCGTGCG
*
35658396 GTGTAGTATGGCACTATGCGTGCG
1 GTGTAATATGGCACTATGCGTGCG
35658420 G
1 G
35658421 AGTTGAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.16, C:0.16, G:0.37, T:0.31
Consensus pattern (24 bp):
GTGTAATATGGCACTATGCGTGCG
Found at i:35658433 original size:24 final size:24
Alignment explanation
Indices: 35658382--35658452 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
35658372 GTGTACATTG
* * * *
35658382 GCACTATGTGTGCGGTGTAGTATG
1 GCACTATGTGTGCGGAGTTGAATA
*
35658406 GCACTATGCGTGCGGAGTTGAATA
1 GCACTATGTGTGCGGAGTTGAATA
* *
35658430 GCACTATGTGTGCTGATTTGAAT
1 GCACTATGTGTGCGGAGTTGAAT
35658453 GTCAACATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.21, C:0.14, G:0.32, T:0.32
Consensus pattern (24 bp):
GCACTATGTGTGCGGAGTTGAATA
Found at i:35665627 original size:55 final size:55
Alignment explanation
Indices: 35665561--35665672 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
35665551 TTATAAAAAA
* *
35665561 ATGGTTAATTGATATGTTGTAAATGTTAAGTGTTAAATGAAATGGAAATGATATT
1 ATGGTTAATTGATAAGTGGTAAATGTTAAGTGTTAAATGAAATGGAAATGATATT
35665616 ATGGTTAATTGATAAGTGGTAAATGTTAAGTGTTAAATGAAATGGAAATGATATT
1 ATGGTTAATTGATAAGTGGTAAATGTTAAGTGTTAAATGAAATGGAAATGATATT
35665671 AT
1 AT
35665673 ATTGGAATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.38
Consensus pattern (55 bp):
ATGGTTAATTGATAAGTGGTAAATGTTAAGTGTTAAATGAAATGGAAATGATATT
Found at i:35666413 original size:24 final size:24
Alignment explanation
Indices: 35666386--35666456 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
35666376 ATCATAGAAA
35666386 GTGTACAT-TGGCACTATGTGTGCG
1 GTGTA-ATATGGCACTATGTGTGCG
*
35666410 GTGTAGTATGGCACTATGTGTGCG
1 GTGTAATATGGCACTATGTGTGCG
*
35666434 GAGTTGAATA--GCACTATGTGTGC
1 GTG-T-AATATGGCACTATGTGTGC
35666457 TGATTTGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.02
24 36 0.88
25 1 0.02
26 3 0.07
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.32
Consensus pattern (24 bp):
GTGTAATATGGCACTATGTGTGCG
Found at i:35666477 original size:26 final size:24
Alignment explanation
Indices: 35666396--35666466 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
35666386 GTGTACATTG
* * * *
35666396 GCACTATGTGTGCGGTGTAGTATG
1 GCACTATGTGTGCGGAGTTGAATA
35666420 GCACTATGTGTGCGGAGTTGAATA
1 GCACTATGTGTGCGGAGTTGAATA
* *
35666444 GCACTATGTGTGCTGATTTGAAT
1 GCACTATGTGTGCGGAGTTGAAT
35666467 GTCAACATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGGAGTTGAATA
Found at i:35668366 original size:39 final size:40
Alignment explanation
Indices: 35668321--35668492 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
35668311 GCTCCTCGTT
* * *
35668321 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* *
35668361 C-AATGCCTTCGGGACATAACCCGGATTTAATAATTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
35668400 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
35668440 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
35668480 CAAATGCCTTCGG
1 CAAATGCCTTCGG
35668493 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.29
40 79 0.68
41 4 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:35668421 original size:40 final size:39
Alignment explanation
Indices: 35668323--35668545 Score: 193
Period size: 40 Copynumber: 5.6 Consensus size: 39
35668313 TCCTCGTTCA
* * * * *
35668323 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAATTCGCAC
* *
35668362 AATGCCTTCGGGACATAACCCGGATTTAATAATTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAATTCGCAC
35668401 GAATGCCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAAT-TCGCAC
* *
35668441 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GT-ATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAAT-TCGCAC
** * * * *
35668481 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGT-AATTCGCAC
* *
35668522 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
35668546 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
39 41 0.26
40 102 0.65
41 12 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAATTCGCAC
Found at i:35668505 original size:80 final size:79
Alignment explanation
Indices: 35668321--35668545 Score: 233
Period size: 80 Copynumber: 2.8 Consensus size: 79
35668311 GCTCCTCGTT
* * * * *
35668321 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
35668385 ATTTAATAATTCGCA
65 ATTTAATAATTCGCA
* * *
35668400 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
*
35668465 AATTT-GT-ATCTCGCA
64 AATTTAATAAT-TCGCA
* * * * *
35668480 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
35668544 GA
63 GA
35668546 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
78 1 0.01
79 41 0.34
80 67 0.55
81 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAATTCGCA
Found at i:35668554 original size:41 final size:41
Alignment explanation
Indices: 35668477--35668554 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
35668467 TTTGTATCTC
* * *
35668477 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
35668518 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
35668555 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:35671637 original size:21 final size:21
Alignment explanation
Indices: 35671613--35671656 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
35671603 GTCATCTTGA
35671613 TGCTCGATTGGAAACTATTGT
1 TGCTCGATTGGAAACTATTGT
35671634 TGCTCGATTGGAAACTATTGT
1 TGCTCGATTGGAAACTATTGT
35671655 TG
1 TG
35671657 TAGGCGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.39
Consensus pattern (21 bp):
TGCTCGATTGGAAACTATTGT
Found at i:35676670 original size:38 final size:38
Alignment explanation
Indices: 35676589--35676814 Score: 283
Period size: 38 Copynumber: 5.9 Consensus size: 38
35676579 GAATCCAATC
* * *
35676589 ACCAGCACAAAGCCTGCGGGACTTTAAGCTCGGATATAGT
1 ACCAGCACGAAGCCTGCGGGA-TTTAA-CCCGGATATATT
* * * *
35676629 ACTAGCACTAAGCCCGCGAGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
*
35676667 ACTAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
* **
35676705 ACCAGCACGAAGCCTGCGGGATTTAAACCTTATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
* ** *
35676743 ACCAGCACGAAACCTGTAGGATTTAACCCTGATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
*
35676781 ACCAGCACGAAGCCTGCGGG-CTTAACCCGGATAT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATAT
35676815 GTATCGAGTG
Statistics
Matches: 163, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
37 12 0.07
38 129 0.79
39 5 0.03
40 17 0.10
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (38 bp):
ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
Found at i:35678683 original size:267 final size:267
Alignment explanation
Indices: 35678202--35678735 Score: 987
Period size: 267 Copynumber: 2.0 Consensus size: 267
35678192 CTCTTTTATT
* *
35678202 TTTTTTTCTCTTTAAGAAATCGGCAATAAAGAACAAAAGTAATTAACCTTGTTCTTTTCATCCAT
1 TTTTTCTCTCTTTAAGAAATCGGCAATAAAGAACAAAAGTAATTAACCTTGTTCTTTTCACCCAT
* *
35678267 TTACTAATTTTATTATAATATAAAATTTTTATTACATATTATAATACATTTATATATATAAATAC
66 TTACTAATTTTATTATAATATAAAATTGTTATTACATATTATAATACATTTATATATAAAAATAC
*
35678332 ATATAAAATTTATACTTTTTCAACTACTAAACCACATGGCCGGCCATTATAAAAAAAATGGCAAT
131 ATATAAAATTTATACTTTTTCAACTACTAAACCACATGGCCGGCCACTATAAAAAAAATGGCAAT
*
35678397 TTGACATGCACATCCTTATGATTTTTAAACCATATAGTAATAAGCCATCACATAAATACCTAGCA
196 TTGACATGCACATCCTTATGATTTTCAAACCATATAGTAATAAGCCATCACATAAATACCTAGCA
35678462 CATTTTC
261 CATTTTC
* *
35678469 TTTTTCTCTCTTTAAGCAATCGGCAATGAAGAACAAAAGTAATTAACCTTGTTCTTTTCACCCAT
1 TTTTTCTCTCTTTAAGAAATCGGCAATAAAGAACAAAAGTAATTAACCTTGTTCTTTTCACCCAT
35678534 TTACTAATTTTATTATAATATAAAATTGTTATTACATATTATAATACATTTATATATAAAAATAC
66 TTACTAATTTTATTATAATATAAAATTGTTATTACATATTATAATACATTTATATATAAAAATAC
*
35678599 ATATAAAATTTATACTTTTTCAACTACTAAACCACATGGCCGGCCACTATCAAAAAAATGGCAAT
131 ATATAAAATTTATACTTTTTCAACTACTAAACCACATGGCCGGCCACTATAAAAAAAATGGCAAT
35678664 TTGACATGCACATCCTTATGATTTTCAAACCATATAGTAATAAGCCATCACATAAATACCTAGCA
196 TTGACATGCACATCCTTATGATTTTCAAACCATATAGTAATAAGCCATCACATAAATACCTAGCA
35678729 CATTTTC
261 CATTTTC
35678736 AAAATTCTCA
Statistics
Matches: 258, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
267 258 1.00
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (267 bp):
TTTTTCTCTCTTTAAGAAATCGGCAATAAAGAACAAAAGTAATTAACCTTGTTCTTTTCACCCAT
TTACTAATTTTATTATAATATAAAATTGTTATTACATATTATAATACATTTATATATAAAAATAC
ATATAAAATTTATACTTTTTCAACTACTAAACCACATGGCCGGCCACTATAAAAAAAATGGCAAT
TTGACATGCACATCCTTATGATTTTCAAACCATATAGTAATAAGCCATCACATAAATACCTAGCA
CATTTTC
Found at i:35681296 original size:18 final size:17
Alignment explanation
Indices: 35681271--35681309 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
35681261 TTAATTTTAT
35681271 TTTAATTAGTAGTTCTA
1 TTTAATTAGTAGTTCTA
* *
35681288 TTTATATTATTATTTCTA
1 TTTA-ATTAGTAGTTCTA
35681306 TTTA
1 TTTA
35681310 CCCATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTAATTAGTAGTTCTA
Found at i:35681371 original size:6 final size:6
Alignment explanation
Indices: 35681356--35681420 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
35681346 AAATGTAATT
* * *
35681356 AAAATC AAAATA AAAATAA AAAGATA AAAA-A TAAAAGA AAAATA AACATA
1 AAAATA AAAATA AAAAT-A AAA-ATA AAAATA -AAAATA AAAATA AAAATA
* *
35681406 AAGATA AAGATA AAA
1 AAAATA AAAATA AAA
35681421 TTTATTTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
5 1 0.02
6 38 0.76
7 9 0.18
8 2 0.04
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:35681418 original size:18 final size:18
Alignment explanation
Indices: 35681374--35681420 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
35681364 AATAAAAATA
35681374 AAAAGATAAAAAATAAAAG
1 AAAAGAT-AAAAATAAAAG
*
35681393 AAAA-ATAAACAT-AAAG
1 AAAAGATAAAAATAAAAG
35681409 ATAAAGATAAAA
1 A-AAAGATAAAA
35681421 TTTATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 5 0.21
17 8 0.33
18 7 0.29
19 4 0.17
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (18 bp):
AAAAGATAAAAATAAAAG
Found at i:35688675 original size:44 final size:45
Alignment explanation
Indices: 35688593--35688688 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 45
35688583 GAATAAATAG
*
35688593 AAATAGAGAAATGGAAAACATTTAGAAATAATTATGG-TTTCTCCA
1 AAATGGAGAAATGGAAAACATTTAGAAATAATTATGGTTTTCT-CA
* * *
35688638 AAATGGAGAAAT-GAAATCATTT-GAAAATTATTGTGGTTTTCTCA
1 AAATGGAGAAATGGAAAACATTTAG-AAATAATTATGGTTTTCTCA
35688682 AAATGGA
1 AAATGGA
35688689 AATAGAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
43 1 0.02
44 28 0.62
45 16 0.36
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (45 bp):
AAATGGAGAAATGGAAAACATTTAGAAATAATTATGGTTTTCTCA
Found at i:35692308 original size:40 final size:41
Alignment explanation
Indices: 35692141--35692300 Score: 200
Period size: 41 Copynumber: 3.9 Consensus size: 41
35692131 AGTTCCAAAA
* * * *
35692141 CATAGCCGAAGCTAT-TATAATCTCGTACACTAAGTGTCTTT
1 CATAGCCGAAGCTATCT-CAGTCTCGCACACTAAGTGCCTTT
* *
35692182 CATAGCCAAAACTATCTCAGTCTCGCACACTAAGTGCCTTT
1 CATAGCCGAAGCTATCTCAGTCTCGCACACTAAGTGCCTTT
*
35692223 CATAGCCGAAGCTATCTCAGTCTCGCACACTAATTGCCTTT
1 CATAGCCGAAGCTATCTCAGTCTCGCACACTAAGTGCCTTT
**
35692264 CATAGCCGAAGCTAT-TTTGAT-TCGCACACTAAGTGCC
1 CATAGCCGAAGCTATCTCAG-TCTCGCACACTAAGTGCC
35692301 AAACATAGTA
Statistics
Matches: 105, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
40 17 0.16
41 87 0.83
42 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (41 bp):
CATAGCCGAAGCTATCTCAGTCTCGCACACTAAGTGCCTTT
Found at i:35699828 original size:19 final size:20
Alignment explanation
Indices: 35699789--35699844 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
35699779 GGTGAGAAGT
* *
35699789 AAAAGTTTTGGGGGAAAT-A
1 AAAAGTTTTGGGGGGATTAA
35699808 AAAAGTTTTGGGGGGATTAA
1 AAAAGTTTTGGGGGGATTAA
* *
35699828 AAAAATATTGGGGGGAT
1 AAAAGTTTTGGGGGGAT
35699845 GGGTTTGGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.39, C:0.00, G:0.34, T:0.27
Consensus pattern (20 bp):
AAAAGTTTTGGGGGGATTAA
Found at i:35700014 original size:56 final size:57
Alignment explanation
Indices: 35699948--35700069 Score: 228
Period size: 56 Copynumber: 2.2 Consensus size: 57
35699938 AGAATAAATG
*
35699948 GGGGTAAAATTTTGGGAGCGAAATATTCAAAACAAAATTGGGGGGGCGGGGGGATTT
1 GGGGTAAAATTTTGGGAGCGAAATATTCAAAACAAAATTGGGGGGGAGGGGGGATTT
35700005 -GGGTAAAATTTTGGGAGCGAAATATTCAAAACAAAATTGGGGGGGAGGGGGGATTT
1 GGGGTAAAATTTTGGGAGCGAAATATTCAAAACAAAATTGGGGGGGAGGGGGGATTT
35700061 GGGGTAAAA
1 GGGGTAAAA
35700070 CGGGGGCAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
56 55 0.87
57 8 0.13
ACGTcount: A:0.34, C:0.06, G:0.39, T:0.22
Consensus pattern (57 bp):
GGGGTAAAATTTTGGGAGCGAAATATTCAAAACAAAATTGGGGGGGAGGGGGGATTT
Found at i:35703272 original size:16 final size:18
Alignment explanation
Indices: 35703248--35703285 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
35703238 ACATACTTTA
*
35703248 ACAATTTACATA-T-AAC
1 ACAAATTACATACTCAAC
35703264 ACAAATTACATACTCAAC
1 ACAAATTACATACTCAAC
35703282 ACAA
1 ACAA
35703286 TGATATATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 1 0.05
18 7 0.37
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (18 bp):
ACAAATTACATACTCAAC
Found at i:35705177 original size:37 final size:37
Alignment explanation
Indices: 35705127--35705205 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
35705117 TTATTACGAA
* * *
35705127 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
35705164 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
35705201 GTCTT
1 GTCTT
35705206 TAGAGCTCGG
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:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:35705402 original size:47 final size:47
Alignment explanation
Indices: 35705324--35705734 Score: 750
Period size: 47 Copynumber: 8.7 Consensus size: 47
35705314 CCCTTCGGGA
* * * * * *
35705324 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35705371 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35705418 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35705465 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35705512 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35705559 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35705606 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35705653 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35705700 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
35705735 AGAATCCTAA
Statistics
Matches: 354, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 354 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:35708941 original size:40 final size:40
Alignment explanation
Indices: 35708909--35709180 Score: 393
Period size: 40 Copynumber: 6.8 Consensus size: 40
35708899 CCAGCATGAT
* * * *
35708909 TGCTCTTCGAGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
35708949 TGCTCTTCAGGG-TTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTC-GGGACTTAGCCCGGATATATCACTAGCACGAA
* *
35708989 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGTACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
35709029 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
35709069 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
35709109 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
35709149 TACTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
35709181 CTCAATTCTC
Statistics
Matches: 208, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 3 0.01
40 203 0.98
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:35710632 original size:47 final size:47
Alignment explanation
Indices: 35710554--35710966 Score: 727
Period size: 47 Copynumber: 8.7 Consensus size: 47
35710544 CCCTTCGGGA
* * * * * *
35710554 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
35710601 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35710648 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35710695 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35710742 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35710789 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35710836 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35710883 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35710932 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
35710967 AGAATCCTAA
Statistics
Matches: 352, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 306 0.87
49 46 0.13
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:35712128 original size:18 final size:18
Alignment explanation
Indices: 35712105--35712146 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
35712095 CATATGCATT
35712105 TTTAATCACATCAAGCAA
1 TTTAATCACATCAAGCAA
35712123 TTTAATCACATCAAGCAA
1 TTTAATCACATCAAGCAA
35712141 TTTAAT
1 TTTAAT
35712147 ACAATTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (18 bp):
TTTAATCACATCAAGCAA
Found at i:35714269 original size:34 final size:35
Alignment explanation
Indices: 35714231--35714317 Score: 113
Period size: 34 Copynumber: 2.5 Consensus size: 35
35714221 CAGACACATA
* * **
35714231 TATTATACATATAACACCTATGCACGTAAATAT-T
1 TATTATATATATAACACCCATGCACACAAATATAT
*
35714265 TATTATATATATAACACCCATGCACACATATATAT
1 TATTATATATATAACACCCATGCACACAAATATAT
*
35714300 TATGATATATATAACACC
1 TATTATATATATAACACC
35714318 AAAACCCATA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 28 0.61
35 18 0.39
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (35 bp):
TATTATATATATAACACCCATGCACACAAATATAT
Found at i:35715606 original size:16 final size:16
Alignment explanation
Indices: 35715575--35715615 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
35715565 TATTAATACC
35715575 ATTATTATT-TTATTT
1 ATTATTATTATTATTT
35715590 AATTATTATTATT-TTT
1 -ATTATTATTATTATTT
*
35715606 ACTATTATTA
1 ATTATTATTA
35715616 ACTAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 9 0.39
16 12 0.52
17 2 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTATTATTATTATTT
Found at i:35719370 original size:151 final size:150
Alignment explanation
Indices: 35719097--35719396 Score: 528
Period size: 151 Copynumber: 2.0 Consensus size: 150
35719087 GCCATGTGTG
* *
35719097 ACACACGGTCATGTAGCGTTGACAGTGAACTTTTTCAGCTTTCGTCGATTACTATTTTTCGTATT
1 ACACACGGCCATGTAGCATTGACAGTGAACTTTTTCAGCTTTCGTCGATTACTATTTTTCGTATT
*
35719162 TTCGATACACACTTGAGTATTTTATGATGTTGTTTCAAACACGAGTAATCCCAAAACCTAAATTG
66 TTCGATACACACTTGAGTATTTTATGATGTTGATTCAAACACGAGTAATCCCAAAACCTAAATTG
35719227 AAAATTAACACAACCAATTC
131 AAAATTAACACAACCAATTC
* * *
35719247 ACACACGGCCATGTAGCATTGATAGTGAACTTTTTCAGCTTTTGTCGATTACTATTTTTTCGTGT
1 ACACACGGCCATGTAGCATTGACAGTGAACTTTTTCAGCTTTCGTCGATTACTA-TTTTTCGTAT
35719312 TTTCGATACACACTTGAGTATTTTATGATGTTGATTCAAACACGAGTAATCCCAAAACCTAAATT
65 TTTCGATACACACTTGAGTATTTTATGATGTTGATTCAAACACGAGTAATCCCAAAACCTAAATT
*
35719377 GACAATTAACACAACCAATT
130 GAAAATTAACACAACCAATT
35719397 TCAATAATGA
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
150 50 0.35
151 92 0.65
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (150 bp):
ACACACGGCCATGTAGCATTGACAGTGAACTTTTTCAGCTTTCGTCGATTACTATTTTTCGTATT
TTCGATACACACTTGAGTATTTTATGATGTTGATTCAAACACGAGTAATCCCAAAACCTAAATTG
AAAATTAACACAACCAATTC
Found at i:35719729 original size:21 final size:21
Alignment explanation
Indices: 35719704--35719743 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35719694 TTAACAGCAA
* *
35719704 CCCAAACCATTAAAGAAAATT
1 CCCAAAACAATAAAGAAAATT
35719725 CCCAAAACAATAAAGAAAA
1 CCCAAAACAATAAAGAAAA
35719744 GAACAGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.23, G:0.05, T:0.12
Consensus pattern (21 bp):
CCCAAAACAATAAAGAAAATT
Found at i:35723412 original size:38 final size:38
Alignment explanation
Indices: 35723367--35723540 Score: 215
Period size: 38 Copynumber: 4.5 Consensus size: 38
35723357 GGCTTAAAGA
* * *
35723367 CCCGCAGGCTAT-ATGCTGGAAATATATCCGGGTTAAAT
1 CCCGCAGGCT-TCGTGCTGGTATTATATCCGGGTTAAAT
*
35723405 CCCGCAGGCTTCGTACTGGTATTATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAAT
35723443 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAAT
* * * * *
35723481 CCCGCAAGCCTAGTGCTGGTATTATATCTGAGCTTAAAGT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCG-GGTTAAA-T
* *
35723521 CCCGCAGGTTTTGTGCTGGT
1 CCCGCAGGCTTCGTGCTGGT
35723541 GACTGGATTT
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
37 1 0.01
38 95 0.80
39 6 0.05
40 17 0.14
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.30
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAAT
Found at i:35732167 original size:86 final size:85
Alignment explanation
Indices: 35732042--35732248 Score: 281
Period size: 86 Copynumber: 2.4 Consensus size: 85
35732032 ATACTATCTC
* *** *
35732042 ATATCGATGCCATTGTCCCAGACAG-GGTCTTACACGAATCAAATACGATGTTGATGTCCCAGAC
1 ATATCGATGCCAATGT-CCAGAC-GTGGTCTTACACGAATCAAATACGATGCCAATATCCCAGAC
35732106 ATGGTCTTACACGTAACCACAT
64 ATGGTCTTACACGTAACCACAT
* *
35732128 ATATCGATGCCAACGTCTCAGACGTGGTCTTACATGAATCAAATACGATGCCAATATCCCAGACA
1 ATATCGATGCCAATGTC-CAGACGTGGTCTTACACGAATCAAATACGATGCCAATATCCCAGACA
* *
35732193 TGGTCTTACATGTAACCACGT
65 TGGTCTTACACGTAACCACAT
*
35732214 ATATTGATGCCAATGTCCTAGACGTGGTCTTACAC
1 ATATCGATGCCAATGTCC-AGACGTGGTCTTACAC
35732249 TAAAACACAT
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
85 3 0.03
86 103 0.97
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (85 bp):
ATATCGATGCCAATGTCCAGACGTGGTCTTACACGAATCAAATACGATGCCAATATCCCAGACAT
GGTCTTACACGTAACCACAT
Found at i:35732203 original size:41 final size:41
Alignment explanation
Indices: 35732046--35732248 Score: 181
Period size: 41 Copynumber: 4.8 Consensus size: 41
35732036 TATCTCATAT
* *
35732046 CGATGCCATTGTCCCAGACAGGGTCTTACACGAATCAAATA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGAATCAAATA
*** *
35732087 CGATGTTGATGTCCCAGACATGGTCTTACACGTAACCACATATA
1 CGATGCCAATGTCCCAGACATGGTCTTACACG-AATCA-A-ATA
* * * *
35732131 TCGATGCCAACGTCTCAGACGTGGTCTTACATGAATCAAATA
1 -CGATGCCAATGTCCCAGACATGGTCTTACACGAATCAAATA
* * * *
35732173 CGATGCCAATATCCCAGACATGGTCTTACATGTAACCACGTATA
1 CGATGCCAATGTCCCAGACATGGTCTTACACG-AATCA--AATA
* * *
35732217 TTGATGCCAATGTCCTAGACGTGGTCTTACAC
1 -CGATGCCAATGTCCCAGACATGGTCTTACAC
35732249 TAAAACACAT
Statistics
Matches: 129, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
41 55 0.43
42 11 0.09
43 2 0.02
44 10 0.08
45 51 0.40
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (41 bp):
CGATGCCAATGTCCCAGACATGGTCTTACACGAATCAAATA
Found at i:35733567 original size:28 final size:28
Alignment explanation
Indices: 35733535--35733590 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
35733525 TTTGGATAAC
*
35733535 ACTCTTTTATTG-TATCCTCTGGCTCCCA
1 ACTCTTTCATTGCT-TCCTCTGGCTCCCA
*
35733563 ACTCTTTCATTGCTTCCTTTGGCTCCCA
1 ACTCTTTCATTGCTTCCTCTGGCTCCCA
35733591 CATTGCTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.12, C:0.34, G:0.11, T:0.43
Consensus pattern (28 bp):
ACTCTTTCATTGCTTCCTCTGGCTCCCA
Found at i:35736835 original size:34 final size:34
Alignment explanation
Indices: 35736792--35736859 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
35736782 CCAACACTAG
35736792 CTACTGAGGTAGCTCTCGAGCTCATAGGTGGTCT
1 CTACTGAGGTAGCTCTCGAGCTCATAGGTGGTCT
35736826 CTACTGAGGTAGCTCTCGAGCTCATAGGTGGTCT
1 CTACTGAGGTAGCTCTCGAGCTCATAGGTGGTCT
35736860 ATCCCGATCC
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:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (34 bp):
CTACTGAGGTAGCTCTCGAGCTCATAGGTGGTCT
Found at i:35745242 original size:45 final size:42
Alignment explanation
Indices: 35745137--35745346 Score: 181
Period size: 41 Copynumber: 4.9 Consensus size: 42
35745127 ATGCTATCTC
* * * *
35745137 ATATTGATGCCACTGTCCCAGACAGGGTCTTACACGAATCAA
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAACCAA
* *
35745179 ATA-CGATGCCGATGTCCCAGACATGGTCTTACATGTAACCACA
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACG-AACCA-A
* * * * *
35745222 TATATCGATGCCAATATCCCAAACGTGGTCTTCCACGAATCAA
1 -ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAACCAA
* *
35745265 ATAT-GATGCCAATGTTCCAAACATGGTCTTACACGTAACCACA
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACG-AACCA-A
* * ** * *
35745308 TATATTGATTCCAACATCCCAGACGTGGTCTTAAACGAA
1 -ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAA
35745347 AACACATATT
Statistics
Matches: 135, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
41 54 0.40
42 15 0.11
43 3 0.02
44 13 0.10
45 50 0.37
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (42 bp):
ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAACCAA
Found at i:35745259 original size:86 final size:86
Alignment explanation
Indices: 35745162--35745346 Score: 271
Period size: 86 Copynumber: 2.2 Consensus size: 86
35745152 TCCCAGACAG
* * *
35745162 GGTCTTACACGAATCAAATACGATGCCGATGTCCCAGACATGGTCTTACATGTAACCACATATAT
1 GGTCTTACACGAATCAAATACGATGCCAATGTCCCAAACATGGTCTTACACGTAACCACATATAT
*
35745227 CGATGCCAATATCCCAAACGT
66 CGATGCCAACATCCCAAACGT
* * *
35745248 GGTCTTCCACGAATCAAATATGATGCCAATGTTCCAAACATGGTCTTACACGTAACCACATATAT
1 GGTCTTACACGAATCAAATACGATGCCAATGTCCCAAACATGGTCTTACACGTAACCACATATAT
* * *
35745313 TGATTCCAACATCCCAGACGT
66 CGATGCCAACATCCCAAACGT
*
35745334 GGTCTTAAACGAA
1 GGTCTTACACGAA
35745347 AACACATATT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (86 bp):
GGTCTTACACGAATCAAATACGATGCCAATGTCCCAAACATGGTCTTACACGTAACCACATATAT
CGATGCCAACATCCCAAACGT
Found at i:35745353 original size:45 final size:45
Alignment explanation
Indices: 35745137--35745355 Score: 175
Period size: 45 Copynumber: 5.0 Consensus size: 45
35745127 ATGCTATCTC
* * * * *
35745137 ATATTGATGCCACTGTCCCAGACAGGGTCTTACACG-AATCA-A-
1 ATATTGATGCCAATATCCCAAACATGGTCTTACACGTAACCACAT
* * * * *
35745179 ATA-CGATGCCGATGTCCCAGACATGGTCTTACATGTAACCACAT
1 ATATTGATGCCAATATCCCAAACATGGTCTTACACGTAACCACAT
* * * *
35745223 ATATCGATGCCAATATCCCAAACGTGGTCTTCCACG-AATCA-A-
1 ATATTGATGCCAATATCCCAAACATGGTCTTACACGTAACCACAT
* *
35745265 ATA-TGATGCCAATGTTCCAAACATGGTCTTACACGTAACCACAT
1 ATATTGATGCCAATATCCCAAACATGGTCTTACACGTAACCACAT
* * * * * * *
35745309 ATATTGATTCCAACATCCCAGACGTGGTCTTAAACGAAAACACAT
1 ATATTGATGCCAATATCCCAAACATGGTCTTACACGTAACCACAT
35745354 AT
1 AT
35745356 TGGAATCCTA
Statistics
Matches: 141, Mismatches: 28, Indels: 13
0.77 0.15 0.07
Matches are distributed among these distances:
41 54 0.38
42 14 0.10
43 3 0.02
44 10 0.07
45 60 0.43
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (45 bp):
ATATTGATGCCAATATCCCAAACATGGTCTTACACGTAACCACAT
Found at i:35749485 original size:45 final size:45
Alignment explanation
Indices: 35749434--35749524 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
35749424 AAAACATATT
35749434 TTATTTTAATCTAGGAACAAAAACGATTGAATTTTAAAATTTAAA
1 TTATTTTAATCTAGGAACAAAAACGATTGAATTTTAAAATTTAAA
*
35749479 TTATTTTAATCTAGGAACAAAAACGGTTGAATTTTAAAATTTAAA
1 TTATTTTAATCTAGGAACAAAAACGATTGAATTTTAAAATTTAAA
35749524 T
1 T
35749525 CCAAGACCCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (45 bp):
TTATTTTAATCTAGGAACAAAAACGATTGAATTTTAAAATTTAAA
Found at i:35751002 original size:55 final size:55
Alignment explanation
Indices: 35750939--35751042 Score: 181
Period size: 55 Copynumber: 1.9 Consensus size: 55
35750929 TTAATTGCAG
* * *
35750939 TGTCAGCAGCTACTAAAAAAACAGAATAATAGGAAATTACAAACAAACCATATTA
1 TGTCAGCAGCTACCAAAAAAAAAGAATAATAAGAAATTACAAACAAACCATATTA
35750994 TGTCAGCAGCTACCAAAAAAAAAGAATAATAAGAAATTACAAACAAACC
1 TGTCAGCAGCTACCAAAAAAAAAGAATAATAAGAAATTACAAACAAACC
35751043 CCATTATCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.17
Consensus pattern (55 bp):
TGTCAGCAGCTACCAAAAAAAAAGAATAATAAGAAATTACAAACAAACCATATTA
Found at i:35753151 original size:40 final size:40
Alignment explanation
Indices: 35753107--35753186 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
35753097 GTCTTTACCA
35753107 TTCATCATACCAAAGAAAAAGTCTTTACCATTCATTATTG
1 TTCATCATACCAAAGAAAAAGTCTTTACCATTCATTATTG
35753147 TTCATCATACCAAAGAAAAAGTCTTTACCATTCATTATTG
1 TTCATCATACCAAAGAAAAAGTCTTTACCATTCATTATTG
35753187 CTTGCTTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (40 bp):
TTCATCATACCAAAGAAAAAGTCTTTACCATTCATTATTG
Found at i:35753728 original size:113 final size:113
Alignment explanation
Indices: 35753537--35753991 Score: 910
Period size: 113 Copynumber: 4.0 Consensus size: 113
35753527 TTAAAATTTT
35753537 ATATTAATTTTTTTACAGTACATTTTATATTAGAGTTTGTACTATCCAAATTTGAGCCAACTCTA
1 ATATTAATTTTTTTACAGTACATTTTATATTAGAGTTTGTACTATCCAAATTTGAGCCAACTCTA
35753602 TCTTATTATAAAAAAATTAATAACCTAAATTCTAAAATGACTTTAACC
66 TCTTATTATAAAAAAATTAATAACCTAAATTCTAAAATGACTTTAACC
35753650 ATATTAATTTTTTTACAGTACATTTTATATTAGAGTTTGTACTATCCAAATTTGAGCCAACTCTA
1 ATATTAATTTTTTTACAGTACATTTTATATTAGAGTTTGTACTATCCAAATTTGAGCCAACTCTA
35753715 TCTTATTATAAAAAAATTAATAACCTAAATTCTAAAATGACTTTAACC
66 TCTTATTATAAAAAAATTAATAACCTAAATTCTAAAATGACTTTAACC
35753763 ATATTAATTTTTTTACAGTACATTTTATATTAGAGTTTGTACTATCCAAATTTGAGCCAACTCTA
1 ATATTAATTTTTTTACAGTACATTTTATATTAGAGTTTGTACTATCCAAATTTGAGCCAACTCTA
35753828 TCTTATTATAAAAAAATTAATAACCTAAATTCTAAAATGACTTTAACC
66 TCTTATTATAAAAAAATTAATAACCTAAATTCTAAAATGACTTTAACC
35753876 ATATTAATTTTTTTACAGTACATTTTATATTAGAGTTTGTACTATCCAAATTTGAGCCAACTCTA
1 ATATTAATTTTTTTACAGTACATTTTATATTAGAGTTTGTACTATCCAAATTTGAGCCAACTCTA
35753941 TCTTATTATAAAAAAATTAATAACCTAAATTCTAAAATGACTTTAACC
66 TCTTATTATAAAAAAATTAATAACCTAAATTCTAAAATGACTTTAACC
35753989 ATA
1 ATA
35753992 CATGATTCAA
Statistics
Matches: 342, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 342 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (113 bp):
ATATTAATTTTTTTACAGTACATTTTATATTAGAGTTTGTACTATCCAAATTTGAGCCAACTCTA
TCTTATTATAAAAAAATTAATAACCTAAATTCTAAAATGACTTTAACC
Found at i:35760017 original size:6 final size:6
Alignment explanation
Indices: 35760006--35760046 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
35759996 TGCTCAAAGA
* *
35760006 TCAATT TCAATT TCAATT TCAATT TCAATA TCAATA TCAAT
1 TCAATT TCAATT TCAATT TCAATT TCAATT TCAATT TCAAT
35760047 ATATGTTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (6 bp):
TCAATT
Found at i:35760475 original size:87 final size:87
Alignment explanation
Indices: 35760370--35760631 Score: 524
Period size: 87 Copynumber: 3.0 Consensus size: 87
35760360 TATTGGTCTC
35760370 TATCTGAAAGACAGTCCTCAAAATCCTACAATCGAAAGGTCTTAATGAACTGTCAAGTTCATGCT
1 TATCTGAAAGACAGTCCTCAAAATCCTACAATCGAAAGGTCTTAATGAACTGTCAAGTTCATGCT
35760435 TCTTATGCATAATTGCCAGATT
66 TCTTATGCATAATTGCCAGATT
35760457 TATCTGAAAGACAGTCCTCAAAATCCTACAATCGAAAGGTCTTAATGAACTGTCAAGTTCATGCT
1 TATCTGAAAGACAGTCCTCAAAATCCTACAATCGAAAGGTCTTAATGAACTGTCAAGTTCATGCT
35760522 TCTTATGCATAATTGCCAGATT
66 TCTTATGCATAATTGCCAGATT
35760544 TATCTGAAAGACAGTCCTCAAAATCCTACAATCGAAAGGTCTTAATGAACTGTCAAGTTCATGCT
1 TATCTGAAAGACAGTCCTCAAAATCCTACAATCGAAAGGTCTTAATGAACTGTCAAGTTCATGCT
35760609 TCTTATGCATAATTGCCAGATT
66 TCTTATGCATAATTGCCAGATT
35760631 T
1 T
35760632 TATTTTAAGA
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 175 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (87 bp):
TATCTGAAAGACAGTCCTCAAAATCCTACAATCGAAAGGTCTTAATGAACTGTCAAGTTCATGCT
TCTTATGCATAATTGCCAGATT
Found at i:35763141 original size:28 final size:28
Alignment explanation
Indices: 35763109--35763165 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
35763099 CACATTCTAT
*
35763109 TTTCCCTACCGTGAGTGTACAATTACAC
1 TTTCCCTACAGTGAGTGTACAATTACAC
35763137 TTTCCCTACAGTGAGTGTACAATTACAC
1 TTTCCCTACAGTGAGTGTACAATTACAC
35763165 T
1 T
35763166 CGATGACGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (28 bp):
TTTCCCTACAGTGAGTGTACAATTACAC
Found at i:35786836 original size:29 final size:29
Alignment explanation
Indices: 35786794--35786850 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
35786784 AGTGATGAAG
*
35786794 ATGTTTCAGCAGTCACAGAATCTGCCATT
1 ATGTTTCAGCAGTCACAGAATCCGCCATT
35786823 ATGTTTCAGCAGTCACAGAATCCGCCAT
1 ATGTTTCAGCAGTCACAGAATCCGCCAT
35786851 CTTAGACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (29 bp):
ATGTTTCAGCAGTCACAGAATCCGCCATT
Found at i:35787175 original size:33 final size:33
Alignment explanation
Indices: 35787128--35787207 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
35787118 TAGCGGCGTT
* *
35787128 TTTTTGCGGTGCTTATCAAAACGCCGTAAATTG
1 TTTTAGCGGTGCTTATCAAAACACCGTAAATTG
* *
35787161 TTTTAGCGGCGCTTATCAAAGCACCGTAAATTG
1 TTTTAGCGGTGCTTATCAAAACACCGTAAATTG
35787194 TTTTAGCGGTGCTT
1 TTTTAGCGGTGCTT
35787208 TTCTATAGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (33 bp):
TTTTAGCGGTGCTTATCAAAACACCGTAAATTG
Found at i:35787933 original size:25 final size:26
Alignment explanation
Indices: 35787896--35787945 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
35787886 ATTTTATTTT
35787896 TATTATTATTTTT-AAATTATTAAAA
1 TATTATTATTTTTGAAATTATTAAAA
*
35787921 TATTA-TATTTTTTGATATTATTAAA
1 TATTATTA-TTTTTGAAATTATTAAA
35787946 CATACATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 2 0.09
25 10 0.45
26 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TATTATTATTTTTGAAATTATTAAAA
Found at i:35788030 original size:16 final size:16
Alignment explanation
Indices: 35788008--35788044 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
35787998 ATATTTCATT
35788008 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
35788025 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
35788040 TAATA
1 TAATA
35788045 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:35797653 original size:14 final size:14
Alignment explanation
Indices: 35797617--35797655 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
35797607 GGCTGTAACA
*
35797617 AAGTTATTTTTTAG
1 AAGTTATTTTCTAG
*
35797631 AAATTATTTTCTAG
1 AAGTTATTTTCTAG
*
35797645 AAGTCATTTTC
1 AAGTTATTTTC
35797656 AATGAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (14 bp):
AAGTTATTTTCTAG
Found at i:35800501 original size:13 final size:15
Alignment explanation
Indices: 35800483--35800519 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
35800473 ATTCAAAGTA
35800483 ATAATTAA-T-TAAT
1 ATAATTAACTATAAT
35800496 ATAATTAACTATAAT
1 ATAATTAACTATAAT
35800511 ATTAATTAA
1 A-TAATTAA
35800520 GTGATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 1 0.05
15 5 0.24
16 7 0.33
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATTAACTATAAT
Found at i:35803330 original size:18 final size:17
Alignment explanation
Indices: 35803295--35803335 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
35803285 TTCAATTTAT
35803295 TTTATTTTATATAAATA
1 TTTATTTTATATAAATA
* *
35803312 TTTATTTATATTTATATA
1 TTTATTT-TATATAAATA
35803330 TTTATT
1 TTTATT
35803336 CGTTAACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATTTTATATAAATA
Found at i:35809092 original size:12 final size:13
Alignment explanation
Indices: 35809071--35809096 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35809061 CAAAATAACT
35809071 AAAACAAAAAAAA
1 AAAACAAAAAAAA
35809084 AAAACAAAAAAAA
1 AAAACAAAAAAAA
35809097 GGCAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAA
Found at i:35809710 original size:16 final size:16
Alignment explanation
Indices: 35809675--35809741 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 16
35809665 TAAATTACTA
* **
35809675 ATTATAATTTTATTTT
1 ATTATAATTCTATTCC
*
35809691 ATTATAGTTCTATTCC
1 ATTATAATTCTATTCC
* *
35809707 ATTACAACTTC-ATTAC
1 ATTATAA-TTCTATTCC
*
35809723 ATTATAACTCTATTCC
1 ATTATAATTCTATTCC
35809739 ATT
1 ATT
35809742 TCAATAAACC
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
15 2 0.05
16 34 0.87
17 3 0.08
ACGTcount: A:0.31, C:0.16, G:0.01, T:0.51
Consensus pattern (16 bp):
ATTATAATTCTATTCC
Found at i:35812801 original size:29 final size:27
Alignment explanation
Indices: 35812756--35812813 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
35812746 ATAATTTTTA
35812756 ATTTTTTTCAAAAAAGTACTCTAGTTT
1 ATTTTTTTCAAAAAAGTACTCTAGTTT
* *
35812783 ATTTTTTCTGAAATAAAGTACTTTAGTTT
1 ATTTTTT-TCAAA-AAAGTACTCTAGTTT
35812812 AT
1 AT
35812814 ACCACCGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (27 bp):
ATTTTTTTCAAAAAAGTACTCTAGTTT
Found at i:35813575 original size:19 final size:19
Alignment explanation
Indices: 35813551--35813622 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 19
35813541 GTAAGGGTTA
35813551 ATTTTAATTTTTAAATATT
1 ATTTTAATTTTTAAATATT
*
35813570 ATTTTAATTTTTTAAT-TT
1 ATTTTAATTTTTAAATATT
*
35813588 A-TGTAATTTTTATTAATATTT
1 ATTTTAATTTTTA--AATA-TT
35813609 ATCTTATAATTTTT
1 AT-TT-TAATTTTT
35813623 TTAAAAGTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
17 9 0.21
18 3 0.07
19 18 0.43
21 3 0.07
23 1 0.02
24 8 0.19
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (19 bp):
ATTTTAATTTTTAAATATT
Found at i:35815681 original size:64 final size:62
Alignment explanation
Indices: 35815610--35815758 Score: 203
Period size: 64 Copynumber: 2.4 Consensus size: 62
35815600 TTTCATTTCG
35815610 TAAAATAGAAGTTGTTTTGAATATATTT-GTA-TAAAATTATTTTTACATTTTGTCCTATTTAAT
1 TAAAATAGAAGTTGTTTTGAATAT-TTTAGTAGT-AAATTATTTTTACATTTTGTCCTATTT-A-
35815673 A
62 A
* * *
35815674 TAAAATAGAAGTTGTTTTGAATGTTTTAGTAGTCAATTATTTTTATATTTTGTCCTATTTAA
1 TAAAATAGAAGTTGTTTTGAATATTTTAGTAGTAAATTATTTTTACATTTTGTCCTATTTAA
* *
35815736 TAAAATAAAAGTTCTTTTGAATA
1 TAAAATAGAAGTTGTTTTGAATA
35815759 AGGCAATAGA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
62 21 0.27
63 4 0.05
64 51 0.66
65 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.49
Consensus pattern (62 bp):
TAAAATAGAAGTTGTTTTGAATATTTTAGTAGTAAATTATTTTTACATTTTGTCCTATTTAA
Found at i:35820976 original size:127 final size:125
Alignment explanation
Indices: 35820816--35821120 Score: 395
Period size: 127 Copynumber: 2.4 Consensus size: 125
35820806 GGATGTACCA
* *
35820816 TAGAAAAAAAGCGTCTAGGTGG-GAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCCTACTTGA
1 TAGAAAAAGAGCGTCCAGG-GGAGAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCCTACTTGA
* * * **
35820880 AGCGTTTTTTATCCTATT-TTTTCAGAACCATCTTCTT-AAAATTATT-TGTTTCAGAAACTGCT
65 AGCGCTTTTGACCCT-TTATTTT-AGAACCATCTT-TTCAAAATTATTAT-TTT-AGAAACTAAT
35820942 G
125 G
* * * *
35820943 TAGAAAAAGAGCTTCCAGGGGAGAGTTTTTTTCAGTACTTTTGCTGACTGTGCATCCTACTTGAA
1 TAGAAAAAGAGCGTCCAGGGGAGAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCCTACTTGAA
35821008 GCGCTTTTGACCCTTTATTTTAGAACCATCTTTTCAAAATTATTATTTTAGAAACTAATG
66 GCGCTTTTGACCCTTTATTTTAGAACCATCTTTTCAAAATTATTATTTTAGAAACTAATG
** *
35821068 TAGAAAAAGAGCGTCCAGCTGAGAGCTTTGTT-AGTACTTTTGCTAACAGTGCA
1 TAGAAAAAGAGCGTCCAGGGGAGAGCTTTTTTCAGTACTTTTGCTAACAGTGCA
35821121 ACAAAGCATC
Statistics
Matches: 156, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
124 19 0.12
125 38 0.24
126 27 0.17
127 72 0.46
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (125 bp):
TAGAAAAAGAGCGTCCAGGGGAGAGCTTTTTTCAGTACTTTTGCTAACAGTGCATCCTACTTGAA
GCGCTTTTGACCCTTTATTTTAGAACCATCTTTTCAAAATTATTATTTTAGAAACTAATG
Found at i:35821352 original size:28 final size:28
Alignment explanation
Indices: 35821316--35821425 Score: 118
Period size: 28 Copynumber: 3.9 Consensus size: 28
35821306 CAAAAACACT
* *
35821316 AAAACCCCTAAACATGAATTTATTTTTA
1 AAAATCCCTAAACCTGAATTTATTTTTA
*
35821344 AAAATCCCTAAACC-GTAAGTTATTTTTTA
1 AAAATCCCTAAACCTG-AATTTA-TTTTTA
* * *
35821373 AAAA-CCATAAACCTTAATTTATTTTTT
1 AAAATCCCTAAACCTGAATTTATTTTTA
35821400 AAAATCCCTAAAACCT-AATTTATTTT
1 AAAATCCCT-AAACCTGAATTTATTTT
35821426 CTCTAAAATC
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
27 10 0.14
28 43 0.62
29 16 0.23
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAATCCCTAAACCTGAATTTATTTTTA
Found at i:35822197 original size:25 final size:24
Alignment explanation
Indices: 35822151--35822200 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
35822141 TTGATTTATG
** *
35822151 AATTTTTTTTTTATTTTTAAAAAT
1 AATTTTTTTTTTAAATTGAAAAAT
35822175 AATTTTTATTTTTAAATTGAAAAAT
1 AATTTTT-TTTTTAAATTGAAAAAT
35822200 A
1 A
35822201 TGTTAGACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
AATTTTTTTTTTAAATTGAAAAAT
Found at i:35822765 original size:30 final size:29
Alignment explanation
Indices: 35822729--35822820 Score: 87
Period size: 31 Copynumber: 3.1 Consensus size: 29
35822719 ATGGTTTATA
35822729 AAAATTAAATCAAATCAAAATTTTATGTAT
1 AAAATTAAATCAAATCAAAA-TTTATGTAT
* *
35822759 AAAATTACA-CAAAATCAAAGTTTATGTAT
1 AAAATTAAATC-AAATCAAAATTTATGTAT
* * * *
35822788 GATATTACACATTAAATCAAAATTCATGTAT
1 AAAATTA-A-ATCAAATCAAAATTTATGTAT
35822819 AA
1 AA
35822821 TTTTAATAGT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
29 15 0.31
30 16 0.33
31 18 0.37
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAATTAAATCAAATCAAAATTTATGTAT
Found at i:35822783 original size:29 final size:30
Alignment explanation
Indices: 35822740--35822820 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
35822730 AAATTAAATC
35822740 AAATCAAAATTTTATGTATAAAATTACACA-
1 AAATCAAAA-TTTATGTATAAAATTACACAT
* * *
35822770 AAATCAAAGTTTATGTATGATATTACACATT
1 AAATCAAAATTTATGTATAAAATTACACA-T
*
35822801 AAATCAAAATTCATGTATAA
1 AAATCAAAATTTATGTATAA
35822821 TTTTAATAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 18 0.42
30 8 0.19
31 17 0.40
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTTATGTATAAAATTACACAT
Found at i:35824218 original size:9 final size:8
Alignment explanation
Indices: 35824193--35824233 Score: 57
Period size: 9 Copynumber: 5.0 Consensus size: 8
35824183 GGTAGTTTCA
35824193 TTCCTTTT
1 TTCCTTTT
35824201 TT-CTTTT
1 TTCCTTTT
35824208 TTCCTTCTT
1 TTCCTT-TT
35824217 TTCCTTCTT
1 TTCCTT-TT
35824226 TTCCTTTT
1 TTCCTTTT
35824234 CGAAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.23
8 7 0.23
9 17 0.55
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (8 bp):
TTCCTTTT
Found at i:35824847 original size:3 final size:3
Alignment explanation
Indices: 35824833--35825125 Score: 252
Period size: 3 Copynumber: 97.3 Consensus size: 3
35824823 AATTAATAAA
* * * * *
35824833 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT GAA CA- CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
35824880 TAT TGT TAT TCT TAT TAT ATAT TAT CAT TAC TATT TAT TAT TAC CAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* * * * * *
35824927 TAT TAT TAC TAT TAT TTT TAT TTT TAT TAC TAT TAT CAT TAT TCT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * ** *
35824975 TAT TAA TAT TAT TAT TAT TAT TAT CAT GCT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * **
35825023 TA- AAT TAT TAT TAT TCTT TAT TAT TAT TAT TAT TCAT GCT TAT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
* * *
35825069 TAT TAC TAT TAT TAT TA- TAT TA- TAT TAT TCT TAT TCTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
35825113 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
35825126 TCTTATTTTG
Statistics
Matches: 228, Mismatches: 53, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
2 7 0.03
3 210 0.92
4 11 0.05
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:35825143 original size:17 final size:18
Alignment explanation
Indices: 35825121--35825162 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
35825111 ATTATTATTA
35825121 TTATTTCTTA-TTTT-GTT
1 TTATTT-TTACTTTTAGTT
*
35825138 TTATTTTTACTTTTATTT
1 TTATTTTTACTTTTAGTT
35825156 TTATTTT
1 TTATTTT
35825163 ATTTTACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 10 0.45
18 9 0.41
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (18 bp):
TTATTTTTACTTTTAGTT
Found at i:35825151 original size:6 final size:5
Alignment explanation
Indices: 35825077--35825168 Score: 51
Period size: 6 Copynumber: 16.6 Consensus size: 5
35825067 ATTATTACTA
* * *
35825077 TTATT ATTATA TTATA TTATT CTTATTCT TTATT ATTATT ATTATT ATT-TC
1 TTATT -TTATT TTATT TTATT -TTA-T-T TTATT -TTATT -TTATT -TTATT
*
35825128 TTATT TTGTT TTATTT TTACTT TTATTT TTATT TTATT TTA
1 TTATT TTATT TTA-TT TTA-TT TTA-TT TTATT TTATT TTA
35825169 CAATTAGCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
4 2 0.03
5 28 0.39
6 37 0.51
7 4 0.06
8 1 0.01
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (5 bp):
TTATT
Found at i:35825153 original size:12 final size:11
Alignment explanation
Indices: 35825105--35825167 Score: 58
Period size: 12 Copynumber: 5.7 Consensus size: 11
35825095 ATTCTTATTC
*
35825105 TTTATTATTAT
1 TTTATTTTTAT
*
35825116 TATTATTATT-T
1 T-TTATTTTTAT
* *
35825127 CTTA-TTTTGT
1 TTTATTTTTAT
35825137 TTTATTTTTACT
1 TTTATTTTTA-T
35825149 TTTATTTTTAT
1 TTTATTTTTAT
35825160 TTTATTTT
1 TTTATTTT
35825168 ACAATTAGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
9 3 0.07
10 7 0.16
11 15 0.34
12 19 0.43
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:35825167 original size:22 final size:24
Alignment explanation
Indices: 35824926--35825169 Score: 126
Period size: 24 Copynumber: 10.4 Consensus size: 24
35824916 ATTATTACCA
35824926 TTATTATTAC-TATTATTTTTA-T
1 TTATTATTACTTATTATTTTTATT
**
35824948 TT-TTATTAC-TATTATCATTATT
1 TTATTATTACTTATTATTTTTATT
* *
35824970 CTTATTATTA-ATATTATTATTATT
1 -TTATTATTACTTATTATTTTTATT
* * * *
35824994 ATTATCA-TGCTTATTATTATTACTA
1 -TTATTATTACTTATTATTTTTA-TT
35825019 TTATTAAATTA-TTATTATTCTTTA--
1 TTATT--ATTACTTATTATT-TTTATT
**
35825043 TTATTATTA-TTATTCATGCTTA--
1 TTATTATTACTTATT-ATTTTTATT
35825065 TTATTATTAC-TATTATTATTATATT
1 TTATTATTACTTATTATT-TT-TATT
* *
35825090 ATATTATT-CTTATTCTTTATTATT
1 TTATTATTACTTATTATTT-TTATT
* * *
35825114 ATTATTATTATTTCTTA-TTTTGTT
1 -TTATTATTACTTATTATTTTTATT
*
35825138 TTATTTTTACTT-TTATTTTTATT
1 TTATTATTACTTATTATTTTTATT
35825161 TTATT-TTAC
1 TTATTATTAC
35825170 AATTAGCTTG
Statistics
Matches: 176, Mismatches: 25, Indels: 42
0.72 0.10 0.17
Matches are distributed among these distances:
21 18 0.10
22 36 0.20
23 28 0.16
24 53 0.30
25 24 0.14
26 13 0.07
27 4 0.02
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (24 bp):
TTATTATTACTTATTATTTTTATT
Done.