Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 14 of 97
Found at i:6818790 original size:45 final size:49
Alignment explanation
Indices: 6818655--6818814 Score: 136
Period size: 47 Copynumber: 3.4 Consensus size: 49
6818645 CTAGTTTTTT
* * * * **
6818655 ATAAGGCATTGCGTGACTAGTTTCTGATAAAGTATTGTGTGACTAACTT-
1 ATAAGGCATTGCGTGACTTGTTTCAGATAAGGCATTGCATGACTAA-TTC
* * * * * *
6818704 -T-GGGCATTGCGTGACTAGTTTCTGATAAGGGATTGCATGACTAGTTG
1 ATAAGGCATTGCGTGACTTGTTTCAGATAAGGCATTGCATGACTAATTC
*
6818751 AT-AGGCATTGCGTGACTTG-TT-AG-TAAGGCATTGCGTGACTAATTC
1 ATAAGGCATTGCGTGACTTGTTTCAGATAAGGCATTGCATGACTAATTC
*
6818796 ATAAGGCATTGTGTGACTT
1 ATAAGGCATTGCGTGACTT
6818815 AGGCATTGCT
Statistics
Matches: 94, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
45 20 0.21
46 18 0.19
47 39 0.41
48 17 0.18
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (49 bp):
ATAAGGCATTGCGTGACTTGTTTCAGATAAGGCATTGCATGACTAATTC
Found at i:6818881 original size:21 final size:22
Alignment explanation
Indices: 6818847--6818903 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
6818837 ATGCAATGTA
* * *
6818847 TAAAAACTAGTCACGTAATGCC
1 TAAAACCTAATCACGTAATGAC
6818869 TAAAACC-AATCACGTAATGAC
1 TAAAACCTAATCACGTAATGAC
6818890 TAAAACCTAATCAC
1 TAAAACCTAATCAC
6818904 ACGATGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.46, C:0.25, G:0.09, T:0.21
Consensus pattern (22 bp):
TAAAACCTAATCACGTAATGAC
Found at i:6818910 original size:22 final size:21
Alignment explanation
Indices: 6818863--6818910 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
6818853 CTAGTCACGT
* **
6818863 AATGCCTAAAACCAATCACGT
1 AATGACTAAAACCAATCACAC
6818884 AATGACTAAAACCTAATCACAC
1 AATGACTAAAACC-AATCACAC
*
6818906 GATGA
1 AATGA
6818911 TTAAGTCATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.46, C:0.25, G:0.10, T:0.19
Consensus pattern (21 bp):
AATGACTAAAACCAATCACAC
Found at i:6821168 original size:112 final size:110
Alignment explanation
Indices: 6820930--6821143 Score: 326
Period size: 112 Copynumber: 1.9 Consensus size: 110
6820920 TAAAAATACT
* * *
6820930 AAATATGTTGATTTATTTATAACTTTTACAATTTAAAAATACACATTCTTTTGAAATTAATTATT
1 AAATATGTTGATTTAGTTATAACTTTCACAATTTAAAAATACACATTCTTTT--AATCAATTATT
6820995 CAACTCTTACCTAATTAACTTTTTATTTAAATTTACTCAAATTAGCA
64 CAACTCTTACCTAATTAACTTTTTATTTAAATTTACTCAAATTAGCA
*
6821042 AAATATGTTGATTTAGTTATAACTTTCACAATTTACAAATACACATTCTTTT-A-CAATTATTCA
1 AAATATGTTGATTTAGTTATAACTTTCACAATTTAAAAATACACATTCTTTTAATCAATTATTCA
* *
6821105 ACTCTTACTTAATTTA-TCTTTTATTTAAATTTACTCAAA
66 ACTCTTACCTAATTAACT-TTTTATTTAAATTTACTCAAA
6821144 ATTTCTTATA
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
107 1 0.01
108 44 0.46
109 1 0.01
112 49 0.52
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (110 bp):
AAATATGTTGATTTAGTTATAACTTTCACAATTTAAAAATACACATTCTTTTAATCAATTATTCA
ACTCTTACCTAATTAACTTTTTATTTAAATTTACTCAAATTAGCA
Found at i:6821965 original size:31 final size:31
Alignment explanation
Indices: 6821893--6821969 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
6821883 TTTTTTAAAT
*
6821893 ATTTTTTTCAATTTAGTTTATTAATATATCA
1 ATTTTTTTCAATTTAGTTTATTAATATATAA
*
6821924 ATTTTATTCAATTTAGTCCTTA-T-AT-TATAA
1 ATTTTTTTCAATTTAGT--TTATTAATATATAA
6821954 ATTTTTGTTCAATTTA
1 ATTTTT-TTCAATTTA
6821970 ATTTTTATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 9 0.22
31 27 0.68
32 1 0.03
33 3 0.08
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (31 bp):
ATTTTTTTCAATTTAGTTTATTAATATATAA
Found at i:6824961 original size:65 final size:66
Alignment explanation
Indices: 6824855--6824987 Score: 196
Period size: 65 Copynumber: 2.0 Consensus size: 66
6824845 GGTGACGGGT
* *
6824855 TGGATGAAACTGTCACTGAGCTCTCATCTCGTGCTGCTAGATATTTACTTTCTGGTT-TTGTCAG
1 TGGATGAAACTGTCACTGAGCTCTCATCTCATGCTGATAGATATTTACTTTCTGGTTATTGTCAG
6824919 A
66 A
*** * *
6824920 TGGATGAAACTGTTGTTGAGCTCTCATCTCATGCTGATAGATTTTTGCTTTCTGGTTATTGTCAG
1 TGGATGAAACTGTCACTGAGCTCTCATCTCATGCTGATAGATATTTACTTTCTGGTTATTGTCAG
6824985 A
66 A
6824986 TG
1 TG
6824988 TGTGCTCACT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
65 50 0.83
66 10 0.17
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.41
Consensus pattern (66 bp):
TGGATGAAACTGTCACTGAGCTCTCATCTCATGCTGATAGATATTTACTTTCTGGTTATTGTCAG
A
Found at i:6825350 original size:47 final size:47
Alignment explanation
Indices: 6825278--6825372 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
6825268 GTGTTAACCC
* *
6825278 TTGAGTCTTACATCTTGCATGGTTGAATGTCTGCAATTGCAGGACAG
1 TTGAGTCTTACATCTTGCATAGTTGAATGTCTACAATTGCAGGACAG
*
6825325 TTGAGTCTTACATCTTGCATAGTTGAATGTCTACCATTGCAGGACAG
1 TTGAGTCTTACATCTTGCATAGTTGAATGTCTACAATTGCAGGACAG
6825372 T
1 T
6825373 ACAAATTTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (47 bp):
TTGAGTCTTACATCTTGCATAGTTGAATGTCTACAATTGCAGGACAG
Found at i:6826707 original size:104 final size:104
Alignment explanation
Indices: 6826522--6826725 Score: 300
Period size: 104 Copynumber: 2.0 Consensus size: 104
6826512 TGTTGCAATG
* *
6826522 AGTGAATCGAAATGCGCTAGAGACAGTAGAGAGGAAGACTGGAGCAGTCCTTGAAGCGTAAGTGC
1 AGTGAATCGAAATGCGCTAGAGACAGCAGAGAGGAAGACTGGAGCAGTCCATGAAGCGTAAGTGC
*
6826587 TTTGGATGATAAGTGGTGAGGGATAAGAAAAGGTGAAAA
66 TTTGGATGACAAGTGGTGAGGGATAAGAAAAGGTGAAAA
** * * *
6826626 AGTGAATCGGGATGCGCTAGAGGCAGCAGAGAGGAAGACTGGAGCTGTCCATGAAGCGTAAGTGT
1 AGTGAATCGAAATGCGCTAGAGACAGCAGAGAGGAAGACTGGAGCAGTCCATGAAGCGTAAGTGC
* * * *
6826691 TTTGGGTGGCAGGTGGTGAGGGATGAGAAAAGGTG
66 TTTGGATGACAAGTGGTGAGGGATAAGAAAAGGTG
6826726 GAAGAGGTGA
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
104 88 1.00
ACGTcount: A:0.32, C:0.10, G:0.39, T:0.19
Consensus pattern (104 bp):
AGTGAATCGAAATGCGCTAGAGACAGCAGAGAGGAAGACTGGAGCAGTCCATGAAGCGTAAGTGC
TTTGGATGACAAGTGGTGAGGGATAAGAAAAGGTGAAAA
Found at i:6827913 original size:145 final size:143
Alignment explanation
Indices: 6827729--6828015 Score: 547
Period size: 145 Copynumber: 2.0 Consensus size: 143
6827719 ACACATATTA
6827729 GATAAATGCAATTTTTTTTTTTTTTTTCTTTGCTTTTACACTTGATAAGAAGCATAGGAACTTTA
1 GATAAATGCAATTTTTTTTTTTTTTTTCTTTGCTTTTACACTTGATAAGAAGCATAGGAACTTTA
6827794 CTTCCTATGGTGGATTGTTGTCTCAATTTCTAATATATATTAATAGGTTATAGATTAACACAATT
66 CTTCCTATGGTGGATTGTTGTCTCAATTTCTAATATATATTAATAGGTTATAGATTAACACAATT
6827859 ATTTACCAAGCANG
131 ATTTACCAAGCA-G
*
6827873 GATAAATGCCAATTTTTTTTTTTTTTTTTTTTGCTTTTACACTTGATAAGAAGCATAGGAACTTT
1 GATAAATG-CAATTTTTTTTTTTTTTTTCTTTGCTTTTACACTTGATAAGAAGCATAGGAACTTT
6827938 ACTTCCTATGGTGGATTGTTGTCTCAATTTCTAATATATATTAATAGGTTATAGATTAACACAAT
65 ACTTCCTATGGTGGATTGTTGTCTCAATTTCTAATATATATTAATAGGTTATAGATTAACACAAT
6828003 TATTTACCAAGCA
130 TATTTACCAAGCA
6828016 CACTGAATAT
Statistics
Matches: 141, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
144 8 0.06
145 133 0.94
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (143 bp):
GATAAATGCAATTTTTTTTTTTTTTTTCTTTGCTTTTACACTTGATAAGAAGCATAGGAACTTTA
CTTCCTATGGTGGATTGTTGTCTCAATTTCTAATATATATTAATAGGTTATAGATTAACACAATT
ATTTACCAAGCAG
Found at i:6828070 original size:2 final size:2
Alignment explanation
Indices: 6828022--6828062 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
6828012 AGCACACTGA
6828022 AT AT AT AT AT AT -T AT AT A- AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6828061 AT
1 AT
6828063 GTTATATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6831373 original size:2 final size:2
Alignment explanation
Indices: 6831368--6831411 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
6831358 TGTAAAAAAA
* * *
6831368 AT AT AT AC AT AT AT AT AT AT GT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6831410 AT
1 AT
6831412 CCAATGTGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6831394 original size:20 final size:20
Alignment explanation
Indices: 6831369--6831407 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
6831359 GTAAAAAAAA
6831369 TATATACATATATATATATG
1 TATATACATATATATATATG
6831389 TATATACATATATATATAT
1 TATATACATATATATATAT
6831408 ATATCCAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATACATATATATATATG
Found at i:6831765 original size:2 final size:2
Alignment explanation
Indices: 6831760--6831793 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6831750 TGTAAAAAAC
6831760 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6831794 ATAAGAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6831859 original size:2 final size:2
Alignment explanation
Indices: 6831854--6831910 Score: 71
Period size: 2 Copynumber: 28.5 Consensus size: 2
6831844 AAAAAAGAGA
* **
6831854 AT AT AT AT AT AT AT A- AT AT AT ANN NN AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
6831896 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
6831911 ATAAGAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6831887 original size:116 final size:111
Alignment explanation
Indices: 6831762--6831991 Score: 379
Period size: 116 Copynumber: 2.0 Consensus size: 111
6831752 TAAAAAACAT
* *
6831762 ATATATATATATATATATATAATATATATATAATAAGAAATATGACTAATAACGATACTATGCTC
1 ATATATATATATATATATAT-ATATATATATAATAAGAAAAAT-AATAATAACGATACTATGCTC
6831827 AATAATTACCAACTAAAAAAAAAGAGAATATATATATATATAATATATA
64 AATAATTACCAACTAAAAAAAAAGAGAATATATATATATAT-ATATATA
6831876 NNNNATATATATATATATATATATATATATATATAATAAGAAAAATAATAATAACGATACTATGC
1 ----ATATATATATATATATATATATATATATATAATAAGAAAAATAATAATAACGATACTATGC
6831941 TCAATAATTACCAACTAAAAAAAAAGAGAATATATATATATATATATATA
62 TCAATAATTACCAACTAAAAAAAAAGAGAATATATATATATATATATATA
6831991 A
1 A
6831992 GCATTGTCTT
Statistics
Matches: 110, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
111 1 0.01
115 7 0.06
116 61 0.55
117 21 0.19
118 20 0.18
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.33
Consensus pattern (111 bp):
ATATATATATATATATATATATATATATATAATAAGAAAAATAATAATAACGATACTATGCTCAA
TAATTACCAACTAAAAAAAAAGAGAATATATATATATATATATATA
Found at i:6832303 original size:27 final size:27
Alignment explanation
Indices: 6832243--6832304 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
6832233 CAAGCGTGGC
*
6832243 AGCGCCCAGGGGCATTCCAAGAGCAGA
1 AGCGCCCAGGGACATTCCAAGAGCAGA
* * *
6832270 GGCGCCCAGGGACGTTCCAAGCGCAGA
1 AGCGCCCAGGGACATTCCAAGAGCAGA
*
6832297 AGTGCCCA
1 AGCGCCCA
6832305 AAAAACGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.32, G:0.34, T:0.08
Consensus pattern (27 bp):
AGCGCCCAGGGACATTCCAAGAGCAGA
Found at i:6833060 original size:104 final size:104
Alignment explanation
Indices: 6832859--6833069 Score: 269
Period size: 104 Copynumber: 2.0 Consensus size: 104
6832849 TATCCGTCAC
* *
6832859 CTCTTCCACCTTTTCTCATCCCTCATCACCTACCACCCAAAGCACTTATGCTTCAAAGACTGCTC
1 CTCTTCCACCTTTTCTCATCCCTCACCACCTACCACCCAAAGCACTTACGCTTCAAAGACTGCTC
* * * * *
6832924 CAATCTTCCTCTCTGCCGCCTTTGGCGTATCCCAATTCA
66 CAATCTTCCTCTCTACCACCTCTAGCGCATCCCAATTCA
* * * * *
6832963 CTCTTTCACCTTTTCTCATCCCTCACCACCTGCCACCTAAAGCACTTACGGTTCAAAGATTGCTC
1 CTCTTCCACCTTTTCTCATCCCTCACCACCTACCACCCAAAGCACTTACGCTTCAAAGACTGCTC
* * * * *
6833028 TAGTTTTCCTCTCTACCACCTCTAGTGCATCCCGATTCA
66 CAATCTTCCTCTCTACCACCTCTAGCGCATCCCAATTCA
6833067 CTC
1 CTC
6833070 ATTGCAACAC
Statistics
Matches: 90, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
104 90 1.00
ACGTcount: A:0.20, C:0.39, G:0.09, T:0.32
Consensus pattern (104 bp):
CTCTTCCACCTTTTCTCATCCCTCACCACCTACCACCCAAAGCACTTACGCTTCAAAGACTGCTC
CAATCTTCCTCTCTACCACCTCTAGCGCATCCCAATTCA
Found at i:6844108 original size:22 final size:24
Alignment explanation
Indices: 6844062--6844116 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
6844052 TAATAATATA
* *
6844062 ATAATATTAAAAAATTATTTTTTAT
1 ATAAT-TTTAAAAATTATTTATTAT
6844087 -TAATTTTAAAAATTA-TTATTAT
1 ATAATTTTAAAAATTATTTATTAT
6844109 ATAATTTT
1 ATAATTTT
6844117 TTTATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 6 0.22
23 17 0.63
24 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATAATTTTAAAAATTATTTATTAT
Found at i:6845528 original size:30 final size:32
Alignment explanation
Indices: 6845477--6845540 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 32
6845467 TATGACGTAT
6845477 AATAACAATATTTTTTCAATATGGTGTGTAAC
1 AATAACAATATTTTTTCAATATGGTGTGTAAC
*
6845509 AATAAC-AT-TTTTTTTAATATGGTGTGTAAC
1 AATAACAATATTTTTTCAATATGGTGTGTAAC
6845539 AA
1 AA
6845541 CTTAACCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 23 0.74
31 2 0.06
32 6 0.19
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (32 bp):
AATAACAATATTTTTTCAATATGGTGTGTAAC
Found at i:6845680 original size:44 final size:44
Alignment explanation
Indices: 6845586--6845707 Score: 138
Period size: 45 Copynumber: 2.7 Consensus size: 44
6845576 CATGTAATAA
* ** **
6845586 CGTGTCACATGTTTT-TATACATAGCGTGTAACAACCTAATTATGG
1 CGTGTCACATGTTTTGTAT--ATGGCGTGTAACAACCTAACCATAC
* *
6845631 TGTGTCACATGTTTTGTATATGGCGTGTAACAATCTAACCATAC
1 CGTGTCACATGTTTTGTATATGGCGTGTAACAACCTAACCATAC
*
6845675 CGTGTCACATGTTTTTGTATACGGCGTGTAACA
1 CGTGTCACATG-TTTTGTATATGGCGTGTAACA
6845708 TGTTTTTGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 29 0.44
45 34 0.52
46 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (44 bp):
CGTGTCACATGTTTTGTATATGGCGTGTAACAACCTAACCATAC
Found at i:6845706 original size:45 final size:45
Alignment explanation
Indices: 6845586--6845707 Score: 147
Period size: 44 Copynumber: 2.7 Consensus size: 45
6845576 CATGTAATAA
* * * ** **
6845586 CGTGTCACATGTTTTTATACATAGCGTGTAACAACCTAATTATGG
1 CGTGTCACATGTTTTTGTATATGGCGTGTAACAACCTAACCATAC
* *
6845631 TGTGTCACATG-TTTTGTATATGGCGTGTAACAATCTAACCATAC
1 CGTGTCACATGTTTTTGTATATGGCGTGTAACAACCTAACCATAC
*
6845675 CGTGTCACATGTTTTTGTATACGGCGTGTAACA
1 CGTGTCACATGTTTTTGTATATGGCGTGTAACA
6845708 TGTTTTTGTA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 35 0.54
45 30 0.46
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (45 bp):
CGTGTCACATGTTTTTGTATATGGCGTGTAACAACCTAACCATAC
Found at i:6845755 original size:45 final size:45
Alignment explanation
Indices: 6845700--6845786 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
6845690 TGTATACGGC
* *
6845700 GTGTAACATGTTTTTGTACATGACATGTGATAACCTAACCATAGT
1 GTGTAACATGTTTTTGTACATGACATGTAACAACCTAACCATAGT
* *
6845745 GTGTCACATGTTTTTGTACATGACGTGTAACAACCTAACCAT
1 GTGTAACATGTTTTTGTACATGACATGTAACAACCTAACCAT
6845787 GACATGTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (45 bp):
GTGTAACATGTTTTTGTACATGACATGTAACAACCTAACCATAGT
Found at i:6845804 original size:45 final size:45
Alignment explanation
Indices: 6845701--6845804 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
6845691 GTATACGGCG
* * **
6845701 TGTAACATGTTTTTGTACATGACATGTGATAACCTAACCATAGTG
1 TGTAACATGTTTTTGTACATGACATGTAACAACCTAACCATAGCA
* *
6845746 TGTCACATGTTTTTGTACATGACGTGTAACAACCTAACCAT-GACA
1 TGTAACATGTTTTTGTACATGACATGTAACAACCTAACCATAG-CA
*
6845791 TGTAACATATTTTT
1 TGTAACATGTTTTT
6845805 TTATATGGGG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
44 1 0.02
45 49 0.98
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (45 bp):
TGTAACATGTTTTTGTACATGACATGTAACAACCTAACCATAGCA
Found at i:6849241 original size:3 final size:3
Alignment explanation
Indices: 6849233--6849257 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6849223 TTCTCAGCAA
6849233 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
6849258 CCAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6853195 original size:6 final size:6
Alignment explanation
Indices: 6853186--6853212 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6853176 GACAGTGACA
6853186 GTGATT GTGATT GTGATT GTGATT GTG
1 GTGATT GTGATT GTGATT GTGATT GTG
6853213 GCAAAGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (6 bp):
GTGATT
Found at i:6855053 original size:83 final size:83
Alignment explanation
Indices: 6854963--6855145 Score: 255
Period size: 84 Copynumber: 2.2 Consensus size: 83
6854953 CATTTTTCTG
* *
6854963 TGTTAAATGTAACTAATGTAAAA-G-GTATATATAAAGATAGGGTTTTTAGAGAGATT-GAGTTA
1 TGTTAAATGTAACTAATGTAAAATGTGT-TATATAAAGATAGGGTTTTGAAAGAGATTGGA-TTA
6855025 CTATATATTCTATTTTTCAAA
64 CTATATATTCTATTTTT-AAA
* *
6855046 TGTTAAATGTAACTAAGGTAAAATGTGTTATCTAAAGATAGGGTTTTGAAAGAGATTGGATTACT
1 TGTTAAATGTAACTAATGTAAAATGTGTTATATAAAGATAGGGTTTTGAAAGAGATTGGATTACT
* *
6855111 ATATATTCTATTTTTGAG
66 ATATATTCTATTTTTAAA
*
6855129 TGTTAAATGTAATTAAT
1 TGTTAAATGTAACTAAT
6855146 AAAAAATTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
83 38 0.43
84 47 0.53
85 4 0.04
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.40
Consensus pattern (83 bp):
TGTTAAATGTAACTAATGTAAAATGTGTTATATAAAGATAGGGTTTTGAAAGAGATTGGATTACT
ATATATTCTATTTTTAAA
Found at i:6855157 original size:30 final size:30
Alignment explanation
Indices: 6855122--6855180 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
6855112 TATATTCTAT
*
6855122 TTTTGAGTGTTAAATGTAATTAATAAAAAA
1 TTTTGAGTATTAAATGTAATTAATAAAAAA
*
6855152 TTTTGAGTATTAAATGTAATTAATGAAAA
1 TTTTGAGTATTAAATGTAATTAATAAAAA
6855181 GTGATGCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (30 bp):
TTTTGAGTATTAAATGTAATTAATAAAAAA
Found at i:6855388 original size:30 final size:31
Alignment explanation
Indices: 6855344--6855404 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
6855334 TATACATTCT
* *
6855344 ATTTTTGAGTGTTAAATATAATTAATGAAAA
1 ATTTTTGAATGTTAAATATAATTAACGAAAA
*
6855375 ATTTTT-AATGTTAAATGTAATTAACGAAAA
1 ATTTTTGAATGTTAAATATAATTAACGAAAA
6855405 GTGATGCAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (31 bp):
ATTTTTGAATGTTAAATATAATTAACGAAAA
Found at i:6855406 original size:224 final size:226
Alignment explanation
Indices: 6854997--6855452 Score: 659
Period size: 224 Copynumber: 2.0 Consensus size: 226
6854987 GTATATATAA
* *
6854997 AGATAGGGTTTTTAGAGAGATTGAGTTACTATATATTCTATTTTTCAAATGTTAAATGTAACTAA
1 AGATAGGGTTTTCAAAGAGATTGAGTTACTATATATTCTATTTTTCAAATGTTAAATGTAACTAA
*
6855062 GGTAAAATGTGTTATCTAAAGATAGGGTTTTGAAAGAGATTGGATTACTATATATTCTATTTTTG
66 GGTAAAATGTG---T-T--AGATAGGGTTTTGAAAGAGATTGGATTACTATACATTCTATTTTTG
* * *
6855127 AGTGTTAAATGTAATTAATAAAAAATTTTGAGTATTAAATGTAATTAATGAAAAGTGATGCAGAT
125 AGTGTTAAATATAATTAATAAAAAATTTTGAATATTAAATGTAATTAACGAAAAGTGATGCAGAT
*
6855192 CAACTAGTTAAAGATAAAATTTTAAAAGAGATTGAGT
190 CAACTACTTAAAGATAAAATTTTAAAAGAGATTGAGT
* * * *
6855229 AGATGGGGTTTTCAAAGAGATTGAGTTACTATATATATTCTATTTTTCAAGTGTTACATGTACCT
1 AGATAGGGTTTTCAAAGAGATTGAGTTAC--TATATATTCTATTTTTCAAATGTTAAATGTAACT
* * *
6855294 AAGGT-AAA-GTG-T-GTTAGGGTTTTGAGAGAGATTGGGTTACTATACATTCTATTTTTGAGTG
64 AAGGTAAAATGTGTTAGATAGGGTTTTGAAAGAGATTGGATTACTATACATTCTATTTTTGAGTG
* * *
6855355 TTAAATATAATTAATGAAAAATTTTTAATGTTAAATGTAATTAACGAAAAGTGATGCAGATCAAC
129 TTAAATATAATTAATAAAAAATTTTGAATATTAAATGTAATTAACGAAAAGTGATGCAGATCAAC
6855420 TACTTAAAGATAAAATTTTAAAAGAGATTGAGT
194 TACTTAAAGATAAAATTTTAAAAGAGATTGAGT
6855453 TACTACACAT
Statistics
Matches: 205, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
224 136 0.66
227 1 0.00
232 29 0.14
233 3 0.01
234 36 0.18
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (226 bp):
AGATAGGGTTTTCAAAGAGATTGAGTTACTATATATTCTATTTTTCAAATGTTAAATGTAACTAA
GGTAAAATGTGTTAGATAGGGTTTTGAAAGAGATTGGATTACTATACATTCTATTTTTGAGTGTT
AAATATAATTAATAAAAAATTTTGAATATTAAATGTAATTAACGAAAAGTGATGCAGATCAACTA
CTTAAAGATAAAATTTTAAAAGAGATTGAGT
Found at i:6855596 original size:15 final size:16
Alignment explanation
Indices: 6855577--6855617 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
6855567 CTATAATATC
6855577 AATAATTATATATTTTAT
1 AATAA-TATATA-TTTAT
6855595 AA-AATA-ATATTTAT
1 AATAATATATATTTAT
6855609 AATAATATA
1 AATAATATA
6855618 ATTACTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.33
15 7 0.33
16 3 0.14
17 2 0.10
18 2 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATAATATATATTTAT
Found at i:6856356 original size:3 final size:3
Alignment explanation
Indices: 6856348--6856374 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6856338 TAATCTTTAA
6856348 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
6856375 ATGCCTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6856845 original size:21 final size:22
Alignment explanation
Indices: 6856812--6856855 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
6856802 GTGTGCGATG
* *
6856812 TCAATTTATAAATAAATAGTTT
1 TCAAGTTATAAATAAATACTTT
*
6856834 TCAAGTTA-AAATATATACTTT
1 TCAAGTTATAAATAAATACTTT
6856855 T
1 T
6856856 TGAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (22 bp):
TCAAGTTATAAATAAATACTTT
Found at i:6871755 original size:78 final size:77
Alignment explanation
Indices: 6871630--6871910 Score: 332
Period size: 78 Copynumber: 3.6 Consensus size: 77
6871620 CATGGGCATG
* * *
6871630 TGACATTCCTATTATACATTAAGGTATAATGATGTCACTATATAAATATTATTAAAGTCCTTGTG
1 TGACATTCCTATTATACATTAAGGTATAATGATGCCAATATATAAATATCATTAAAGTCC-TGTG
*
6871695 ATAAGTGGACATG
65 ATAAGTGGACATA
* * * * * *
6871708 TGGCATTCCTATTATACATTAAGATATAATGATGCTAATATGTAAATACCATCAAAGTCACTGTG
1 TGACATTCCTATTATACATTAAGGTATAATGATGCCAATATATAAATATCATTAAAGTC-CTGTG
6871773 ATAAGTGGACATA
65 ATAAGTGGACATA
* *
6871786 TGGTC-TTCCTATTATACATTAAGGTATAATGATGCCAATATATAAATATCA-TCAAGATCCATG
1 T-GACATTCCTATTATACATTAAGGTATAATGATGCCAATATATAAATATCATTAAAG-TCC-TG
* * *
6871849 TCATAGGTGGGCATA
63 TGATAAGTGGACATA
* * * *
6871864 TGACATTCCTATTATACATGAAGGTATAATGGTACCAATATGTAAAT
1 TGACATTCCTATTATACATTAAGGTATAATGATGCCAATATATAAAT
6871911 TTAAGGTCTT
Statistics
Matches: 173, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
77 6 0.03
78 164 0.95
79 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (77 bp):
TGACATTCCTATTATACATTAAGGTATAATGATGCCAATATATAAATATCATTAAAGTCCTGTGA
TAAGTGGACATA
Found at i:6878377 original size:21 final size:21
Alignment explanation
Indices: 6878351--6878447 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
6878341 AAAATGGGTT
*
6878351 AATTTTAAGGTTTGGTGAATC
1 AATTTTAAGATTTGGTGAATC
* *
6878372 AATTTTAAGATTTTGTGAATT
1 AATTTTAAGATTTGGTGAATC
* *
6878393 AATTTTACAG-TTTGATGAATT
1 AATTTTA-AGATTTGGTGAATC
* * *
6878414 GATTTTAAGATTTTGTTAATC
1 AATTTTAAGATTTGGTGAATC
* *
6878435 GATTTTAAAATTT
1 AATTTTAAGATTT
6878448 AATAAATTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.49
Consensus pattern (21 bp):
AATTTTAAGATTTGGTGAATC
Found at i:6878396 original size:42 final size:42
Alignment explanation
Indices: 6878349--6878429 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
6878339 TTAAAATGGG
*
6878349 TTAATTTTA-AGGTTTGGTGAATCAATTTTAAGATTTTGTGAA
1 TTAATTTTACA-GTTTGATGAATCAATTTTAAGATTTTGTGAA
**
6878391 TTAATTTTACAGTTTGATGAATTGATTTTAAGATTTTGT
1 TTAATTTTACAGTTTGATGAATCAATTTTAAGATTTTGT
6878430 TAATCGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (42 bp):
TTAATTTTACAGTTTGATGAATCAATTTTAAGATTTTGTGAA
Found at i:6878440 original size:42 final size:42
Alignment explanation
Indices: 6878373--6878497 Score: 169
Period size: 42 Copynumber: 3.0 Consensus size: 42
6878363 TGGTGAATCA
** * * * *
6878373 ATTTTAAGATTTTGTGAATTAATTTTACAGTTTGATGAATTG
1 ATTTTAAGATTTTGTGAATCGATTTTAAAATTTAATAAATTG
*
6878415 ATTTTAAGATTTTGTTAATCGATTTTAAAATTTAATAAATTG
1 ATTTTAAGATTTTGTGAATCGATTTTAAAATTTAATAAATTG
* *
6878457 ATTTTAAAATTTTATGAATCGATTTTAAAATTTAATAAATT
1 ATTTTAAGATTTTGTGAATCGATTTTAAAATTTAATAAATT
6878498 CAAACTCTAG
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (42 bp):
ATTTTAAGATTTTGTGAATCGATTTTAAAATTTAATAAATTG
Found at i:6878442 original size:63 final size:63
Alignment explanation
Indices: 6878352--6878489 Score: 150
Period size: 63 Copynumber: 2.2 Consensus size: 63
6878342 AAATGGGTTA
* * ** * * * *
6878352 ATTTTAAGGTTTGGTGAATCAATTTTAAGATTTTGTGAATTAATTTTACAGTTTGATGAATTG
1 ATTTTAAGATTTGGTGAATCAATTTTAAAATTTAATAAATTAATTTTAAAATTTGATGAATCG
* * * * *
6878415 ATTTTAAGATTTTGTTAATCGATTTTAAAATTTAATAAATTGATTTTAAAATTTTATGAATCG
1 ATTTTAAGATTTGGTGAATCAATTTTAAAATTTAATAAATTAATTTTAAAATTTGATGAATCG
*
6878478 ATTTTAAAATTT
1 ATTTTAAGATTT
6878490 AATAAATTCA
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (63 bp):
ATTTTAAGATTTGGTGAATCAATTTTAAAATTTAATAAATTAATTTTAAAATTTGATGAATCG
Found at i:6878459 original size:21 final size:21
Alignment explanation
Indices: 6878410--6878497 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 21
6878400 CAGTTTGATG
* ** *
6878410 AATTGATTTTAAGATTTTGTT
1 AATTGATTTTAAAATTTAATA
*
6878431 AATCGATTTTAAAATTTAATA
1 AATTGATTTTAAAATTTAATA
* *
6878452 AATTGATTTTAAAATTTTATG
1 AATTGATTTTAAAATTTAATA
*
6878473 AATCGATTTTAAAATTTAATA
1 AATTGATTTTAAAATTTAATA
6878494 AATT
1 AATT
6878498 CAAACTCTAG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (21 bp):
AATTGATTTTAAAATTTAATA
Found at i:6903314 original size:8 final size:9
Alignment explanation
Indices: 6903296--6903325 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
6903286 ATGAGTGAAG
6903296 AAAATTAAA
1 AAAATTAAA
6903305 AAAATTAAAA
1 AAAATT-AAA
6903315 AAAATTAAA
1 AAAATTAAA
6903324 AA
1 AA
6903326 TTTGAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATTAAA
Found at i:6903315 original size:10 final size:10
Alignment explanation
Indices: 6903296--6903325 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6903286 ATGAGTGAAG
6903296 AAAATT-AAA
1 AAAATTAAAA
6903305 AAAATTAAAA
1 AAAATTAAAA
6903315 AAAATTAAAA
1 AAAATTAAAA
6903325 A
1 A
6903326 TTTGAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:6911144 original size:2 final size:2
Alignment explanation
Indices: 6911131--6911169 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
6911121 NNNNNNNNNN
* *
6911131 TA TA TA TT TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6911170 TCTCTTCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6929818 original size:2 final size:2
Alignment explanation
Indices: 6929796--6929841 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
6929786 TTGGACAGAC
* *
6929796 AG AG GG AG AG GG AG A- AG AG AG AG AG AG AG AG AG AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6929836 AG AG AG
1 AG AG AG
6929842 CGGATTGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6940332 original size:14 final size:14
Alignment explanation
Indices: 6940315--6940350 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
6940305 AAAAGGCGAA
6940315 AATAAAAGACAAAT
1 AATAAAAGACAAAT
*
6940329 AATAAAAAACAAAT
1 AATAAAAGACAAAT
*
6940343 AGTAAAAG
1 AATAAAAG
6940351 TATCAACTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (14 bp):
AATAAAAGACAAAT
Found at i:6942004 original size:25 final size:24
Alignment explanation
Indices: 6941962--6942009 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
6941952 TTCTATTATT
*
6941962 TTAATAAAAAAATTTAAAAAAATA
1 TTAATAAAAAAATATAAAAAAATA
*
6941986 TTAATCAAAAAAATATAAATAAAT
1 TTAAT-AAAAAAATATAAAAAAAT
6942010 TAAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
TTAATAAAAAAATATAAAAAAATA
Found at i:6950194 original size:14 final size:14
Alignment explanation
Indices: 6950177--6950203 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6950167 CAAAACAAGC
6950177 AAAAAAAAATATTG
1 AAAAAAAAATATTG
6950191 AAAAAAAAATATT
1 AAAAAAAAATATT
6950204 TCTTTATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAAAAAAAATATTG
Found at i:6959211 original size:15 final size:16
Alignment explanation
Indices: 6959167--6959214 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
6959157 TCAAGAAAAA
*
6959167 TAAATATAAATAATATT
1 TAAAAATAAA-AATATT
*
6959184 TAAAAATACAAATATT
1 TAAAAATAAAAATATT
*
6959200 T-GAAATAAAAATATT
1 TAAAAATAAAAATATT
6959215 GTAGATATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 12 0.44
16 7 0.26
17 8 0.30
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAAAATAAAAATATT
Found at i:6967399 original size:29 final size:29
Alignment explanation
Indices: 6967324--6967384 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
6967314 CGTCTTCACA
6967324 ATAATATATCTGATTACACTTAGAAATAT
1 ATAATATATCTGATTACACTTAGAAATAT
6967353 ATAATATATCTGATTACACTTAGAAATAT
1 ATAATATATCTGATTACACTTAGAAATAT
6967382 ATA
1 ATA
6967385 TATTCACTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.38
Consensus pattern (29 bp):
ATAATATATCTGATTACACTTAGAAATAT
Found at i:6976697 original size:10 final size:10
Alignment explanation
Indices: 6976684--6976756 Score: 59
Period size: 10 Copynumber: 7.9 Consensus size: 10
6976674 CATGTTTACG
6976684 TAATCGTGTT
1 TAATCGTGTT
6976694 TAATCGTG-T
1 TAATCGTGTT
6976703 T-ATCGTGTT
1 TAATCGTGTT
*
6976712 TAATCATG-T
1 TAATCGTGTT
*
6976721 T-ATCTTGTT
1 TAATCGTGTT
* *
6976730 TAATCAT-AT
1 TAATCGTGTT
6976739 T-ATCGTGTT
1 TAATCGTGTT
*
6976748 TAAACGTGT
1 TAATCGTGT
6976757 ATACCAGACA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
8 15 0.30
9 12 0.24
10 23 0.46
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.49
Consensus pattern (10 bp):
TAATCGTGTT
Found at i:6976709 original size:18 final size:18
Alignment explanation
Indices: 6976686--6976750 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
6976676 TGTTTACGTA
*
6976686 ATCGTGTTTAATCGTGTT
1 ATCGTGTTTAATCATGTT
6976704 ATCGTGTTTAATCATGTT
1 ATCGTGTTTAATCATGTT
* *
6976722 ATCTTGTTTAATCATATT
1 ATCGTGTTTAATCATGTT
6976740 ATCGTGTTTAA
1 ATCGTGTTTAA
6976751 ACGTGTATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (18 bp):
ATCGTGTTTAATCATGTT
Found at i:6977020 original size:20 final size:20
Alignment explanation
Indices: 6976933--6977022 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 20
6976923 ATGTTATTAT
* * *
6976933 TATTTTTGTTTTATTATAAT
1 TATTTTTATTTAATTATAAA
*
6976953 TATTTTTA--TAATTATAGA
1 TATTTTTATTTAATTATAAA
** *
6976971 T-TTTAAATTTAAATAATAAA
1 TATTTTTATTT-AATTATAAA
*
6976991 -A-TTATATTTAATTATAAA
1 TATTTTTATTTAATTATAAA
6977009 TATTTTTATTTAAT
1 TATTTTTATTTAAT
6977023 CGTGTTAAAC
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
17 4 0.08
18 16 0.30
19 9 0.17
20 24 0.45
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTTTTATTTAATTATAAA
Found at i:6977035 original size:9 final size:9
Alignment explanation
Indices: 6977018--6977056 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
6977008 ATATTTTTAT
*
6977018 TTAATCGTG
1 TTAAACGTG
6977027 TTAAACGTG
1 TTAAACGTG
*
6977036 TTAATCGTG
1 TTAAACGTG
*
6977045 TAAAACGTG
1 TTAAACGTG
6977054 TTA
1 TTA
6977057 TTAATCGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (9 bp):
TTAAACGTG
Found at i:6977041 original size:18 final size:18
Alignment explanation
Indices: 6977018--6977056 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
6977008 ATATTTTTAT
*
6977018 TTAATCGTGTTAAACGTG
1 TTAATCGTGTAAAACGTG
6977036 TTAATCGTGTAAAACGTG
1 TTAATCGTGTAAAACGTG
6977054 TTA
1 TTA
6977057 TTAATCGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (18 bp):
TTAATCGTGTAAAACGTG
Found at i:6977772 original size:16 final size:16
Alignment explanation
Indices: 6977747--6977779 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6977737 AACATAATTA
6977747 ATAATTTTATAA-GTT
1 ATAATTTTATAATGTT
6977762 ATAAGTTTTATAATGTT
1 ATAA-TTTTATAATGTT
6977779 A
1 A
6977780 ACACAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (16 bp):
ATAATTTTATAATGTT
Found at i:6978168 original size:21 final size:21
Alignment explanation
Indices: 6978130--6978192 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
6978120 CACACAATAG
* * * *
6978130 AAAGTAAATATGTTTATATTT
1 AAAGTATATATATATATATTA
*
6978151 AAAGTATATATATATATACTA
1 AAAGTATATATATATATATTA
*
6978172 AAAGTATTTTAATATATATAT
1 AAAGTA-TAT-ATATATATAT
6978193 ATATAATAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 22 0.67
22 2 0.06
23 9 0.27
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (21 bp):
AAAGTATATATATATATATTA
Found at i:6979400 original size:22 final size:22
Alignment explanation
Indices: 6979337--6979424 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
6979327 ATTTTTTGTC
* *
6979337 ATTTTTTATTATTTAATTATTAT
1 ATTTTTTATT-TTTTATTATCAT
* **
6979360 TTTCGTTTTATTTCATATTATCAT
1 ATT--TTTTATTTTTTATTATCAT
* *
6979384 ATTTTTTATTTTTTATTCTCCT
1 ATTTTTTATTTTTTATTATCAT
* *
6979406 ATATTTTATTTTTTTTTAT
1 ATTTTTTATTTTTTATTAT
6979425 ATTCTAAGTT
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
22 31 0.62
23 2 0.04
24 10 0.20
25 7 0.14
ACGTcount: A:0.22, C:0.07, G:0.01, T:0.70
Consensus pattern (22 bp):
ATTTTTTATTTTTTATTATCAT
Found at i:6980405 original size:2 final size:2
Alignment explanation
Indices: 6980398--6980425 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6980388 TTACATAATC
6980398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6980426 TCTTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6981518 original size:10 final size:10
Alignment explanation
Indices: 6981503--6981535 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
6981493 CTCTCTCTCC
6981503 TTTTTCTTTT
1 TTTTTCTTTT
6981513 TTTTTCTTTT
1 TTTTTCTTTT
6981523 TTATTT-TTTT
1 TT-TTTCTTTT
6981533 TTT
1 TTT
6981536 CATTCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.05
10 18 0.82
11 3 0.14
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:6981801 original size:38 final size:37
Alignment explanation
Indices: 6981716--6982344 Score: 665
Period size: 38 Copynumber: 16.6 Consensus size: 37
6981706 TAAATGAGGT
* * * *
6981716 TCCTTAAAGCTGAGGTAACAAAATTTTAAAAATGAAC
1 TCCTCAAAGCTGAGGCAACGAAACTTTAAAAATGAAC
** *
6981753 TCCTCAAAATTGAGGCTACGAAACTTTAAAAATGAAAC
1 TCCTCAAAGCTGAGGCAACGAAACTTTAAAAATG-AAC
* **
6981791 TCCTTAAAATTGAGGCAACGAAACTTTAAAAATGAAAC
1 TCCTCAAAGCTGAGGCAACGAAACTTTAAAAATG-AAC
* *
6981829 TCCCCAAAGCTGAGGCGAC-ATAACTTTAAAAATGAAAC
1 TCCTCAAAGCTGAGGCAACGA-AACTTTAAAAATG-AAC
* * * *
6981867 TCCTCAAAACTGAGGCAACGAGACTTTTAAAATGTGAC
1 TCCTCAAAGCTGAGGCAACGAAACTTTAAAAATG-AAC
** *
6981905 TCCTCAAAATTGAGGTAACGAAACTTCTAAAAATGAAC
1 TCCTCAAAGCTGAGGCAACGAAACTT-TAAAAATGAAC
* * * * *
6981943 TCCTCAATGCTGAGGCAACGAGACTTTTAAAATGTGAT
1 TCCTCAAAGCTGAGGCAACGAAACTTTAAAAATG-AAC
* * * *
6981981 TCCTCAAAACTGAGGCAACGAGACTTTTAAAATGTGAC
1 TCCTCAAAGCTGAGGCAACGAAACTTTAAAAATG-AAC
*
6982019 TCCTCAAAGCTGAGGCAACGAAACTTCTAAAAATAAAC
1 TCCTCAAAGCTGAGGCAACGAAACTT-TAAAAATGAAC
6982057 TCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAAC
1 TCCTCAAAGCTGAGGCAACGAAAC-TTTAAAAATGAAC
*
6982095 TCCTCAAAGTTGAGGCAACGAAACTTTTTTAAAAAATGAAC
1 TCCTCAAAGCTGAGGCAACGAAAC---TTT-AAAAATGAAC
*
6982136 TCCTCAAA----NGGCAACGAAACTTTTAAAAATGAAC
1 TCCTCAAAGCTGAGGCAACGAAAC-TTTAAAAATGAAC
* * *
6982170 TCCTCGAAGTTGAGGCAACGAGACTTTTAAAAATGAAC
1 TCCTCAAAGCTGAGGCAACGAAAC-TTTAAAAATGAAC
* * * *
6982208 TCCTCAAAGCTGAGACAATGAGACTTTTGAAAATGAAC
1 TCCTCAAAGCTGAGGCAACGAAAC-TTTAAAAATGAAC
* *
6982246 TCCTCAAAGCTGAGGCAATGAAACTTTTAAAATGAAC
1 TCCTCAAAGCTGAGGCAACGAAACTTTAAAAATGAAC
*
6982283 TCTTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAAC
1 TCCTCAAAGCTGAGGCAACGAAAC-TTTAAAAATGAAC
* * *
6982321 TCCTCAAAACTGAGGTAACAAAAC
1 TCCTCAAAGCTGAGGCAACGAAAC
6982345 CTTTTTTCTT
Statistics
Matches: 514, Mismatches: 63, Indels: 29
0.85 0.10 0.05
Matches are distributed among these distances:
34 17 0.03
35 4 0.01
37 80 0.16
38 375 0.73
39 16 0.03
40 4 0.01
41 18 0.04
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23
Consensus pattern (37 bp):
TCCTCAAAGCTGAGGCAACGAAACTTTAAAAATGAAC
Found at i:6981907 original size:114 final size:113
Alignment explanation
Indices: 6981716--6982335 Score: 736
Period size: 114 Copynumber: 5.5 Consensus size: 113
6981706 TAAATGAGGT
* * * * * *
6981716 TCCTTAAAGCTGAGGTAAC-AAAATTTTAAAAATGAACTCCTCAAAATTGAGGCTACGAAACTTT
1 TCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGACTTT
* ** * *
6981780 AAAAATGAAACTCCTTAAAATTGAGGCAACGAAACTTTAAAAATGAAAC
66 TAAAATGTGACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATG-AAC
* *
6981829 TCCCCAAAGCTGAGGCGAC-ATAAC-TTTAAAAATGAAACTCCTCAAAACTGAGGCAACGAGACT
1 TCCTCAAAGCTGAGGCAACGA-AACTTTTAAAAATG-AACTCCTCAAAACTGAGGCAACGAGACT
* *
6981892 TTTAAAATGTGACTCCTCAAAATTGAGGTAACGAAACTTCTAAAAATGAAC
64 TTTAAAATGTGACTCCTCAAAACTGAGGCAACGAAACTT-TAAAAATGAAC
* * * *
6981943 TCCTCAATGCTGAGGCAACGAGACTTTT-AAAATGTGATTCCTCAAAACTGAGGCAACGAGACTT
1 TCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATG-AACTCCTCAAAACTGAGGCAACGAGACTT
* *
6982007 TTAAAATGTGACTCCTCAAAGCTGAGGCAACGAAACTTCTAAAAATAAAC
65 TTAAAATGTGACTCCTCAAAACTGAGGCAACGAAACTT-TAAAAATGAAC
** *
6982057 TCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAGTTGAGGCAACGAAACTTT
1 TCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAC--T
** *
6982122 TTTAAAAAATGAACTCCTC-AAA---NGGCAACGAAACTTTTAAAAATGAAC
64 TTTAAAATGTG-ACTCCTCAAAACTGAGGCAACGAAAC-TTTAAAAATGAAC
* * * * * *
6982170 TCCTCGAAGTTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAGCTGAGACAATGAGACTTT
1 TCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGACTTT
* * * *
6982235 TGAAAATG-AACTCCTCAAAGCTGAGGCAATGAAACTTTTAAAATGAAC
66 T-AAAATGTGACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAAC
*
6982283 TCTTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAACTGAGG
1 TCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAACTGAGG
6982336 TAACAAAACC
Statistics
Matches: 436, Mismatches: 56, Indels: 30
0.84 0.11 0.06
Matches are distributed among these distances:
110 7 0.02
111 6 0.01
112 4 0.01
113 161 0.37
114 221 0.51
115 18 0.04
116 12 0.03
117 7 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23
Consensus pattern (113 bp):
TCCTCAAAGCTGAGGCAACGAAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGACTTT
TAAAATGTGACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAAC
Found at i:6997869 original size:2 final size:2
Alignment explanation
Indices: 6997862--6997889 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6997852 TGCTGAGACG
6997862 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6997890 NATGTCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6997957 original size:2 final size:2
Alignment explanation
Indices: 6997950--6997994 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
6997940 TGTGCGTGCT
*
6997950 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA CA GA GA -A
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6997991 GA GA
1 GA GA
6997995 CTCAAATGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.02, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6997960 original size:94 final size:93
Alignment explanation
Indices: 6997796--6997983 Score: 351
Period size: 94 Copynumber: 2.0 Consensus size: 93
6997786 AGAATAAAAA
6997796 AATGTCAAAAAAGCGCGCTTCGTAGTAGGCACAGTGAGTTGGGGCTTGAATGTGCGTGCTGAGAC
1 AATGTCAAAAAAGCGCGCTTCGTAGTAGGCACAGTGAGTTGGGGCTTGAATGTGCGTGCTGAGAC
6997861 GGAGAGAGAGAGAGAGAGAGAGAGAGAG
66 GGAGAGAGAGAGAGAGAGAGAGAGAGAG
6997889 ANATGTCAAAAAAGCGCGCTTCGTAGTAGGCACAGTGAGTTGGGGCTTGAATGTGCGTGCTGAGA
1 A-ATGTCAAAAAAGCGCGCTTCGTAGTAGGCACAGTGAGTTGGGGCTTGAATGTGCGTGCTGAGA
6997954 -GAGAGAGAGAGAGAGAGAGAGAGAGAGAG
65 CG-GAGAGAGAGAGAGAGAGAGAGAGAGAG
6997983 A
1 A
6997984 CAGAGAAGAG
Statistics
Matches: 93, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
93 2 0.02
94 91 0.98
ACGTcount: A:0.33, C:0.11, G:0.39, T:0.16
Consensus pattern (93 bp):
AATGTCAAAAAAGCGCGCTTCGTAGTAGGCACAGTGAGTTGGGGCTTGAATGTGCGTGCTGAGAC
GGAGAGAGAGAGAGAGAGAGAGAGAGAG
Found at i:6999520 original size:21 final size:21
Alignment explanation
Indices: 6999494--6999543 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
6999484 AAGATCTAGC
6999494 CTTCACACAAGGCTCAAAAGT
1 CTTCACACAAGGCTCAAAAGT
*
6999515 CTTCACACAAGGTTCAAAAGT
1 CTTCACACAAGGCTCAAAAGT
6999536 -TGTCACAC
1 CT-TCACAC
6999544 TTGGAGCTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (21 bp):
CTTCACACAAGGCTCAAAAGT
Found at i:7005072 original size:4 final size:4
Alignment explanation
Indices: 7005065--7005102 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
7005055 TATTGTTAGT
7005065 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
7005103 TATATGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:7007892 original size:24 final size:23
Alignment explanation
Indices: 7007850--7007902 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
7007840 TAATTTTAAA
*
7007850 AATATTTATTTTGAAATATTTTT
1 AATATTTATTTTGAAATATTTAT
*
7007873 GAATATTTATCTTT-ACATATTTAT
1 -AATATTTAT-TTTGAAATATTTAT
7007897 AATATT
1 AATATT
7007903 GCACTATGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 6 0.23
24 17 0.65
25 3 0.12
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
AATATTTATTTTGAAATATTTAT
Found at i:7013103 original size:2 final size:2
Alignment explanation
Indices: 7013096--7013127 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7013086 TTATAAACAG
7013096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7013128 TAGATGAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7024205 original size:2 final size:2
Alignment explanation
Indices: 7024198--7024228 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7024188 TGATATGAGC
7024198 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7024229 GTTTCCTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7028052 original size:32 final size:35
Alignment explanation
Indices: 7027976--7028057 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 35
7027966 GTTGTATAAT
*
7027976 TTAAATATTAATATTTTAAATTAATTTTTTTAAAG
1 TTAAATATTAATATTTTAAATTAATTATTTTAAAG
* **
7028011 TTAATTATTAATATTTT-TTTTAA-TATTTT-AAG
1 TTAAATATTAATATTTTAAATTAATTATTTTAAAG
7028043 TTAAATATTAATATT
1 TTAAATATTAATATT
7028058 GATTAAACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 17 0.40
33 5 0.12
34 4 0.10
35 16 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (35 bp):
TTAAATATTAATATTTTAAATTAATTATTTTAAAG
Found at i:7035602 original size:24 final size:24
Alignment explanation
Indices: 7035551--7035603 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
7035541 AACATGAGCC
*
7035551 ATAAAATTTAATTGTATTATATTT
1 ATAAAATTTAATTGTATTATATTA
7035575 ATAAAATTTAATATG-ATTCAT-TTA
1 ATAAAATTTAAT-TGTATT-ATATTA
7035599 ATAAA
1 ATAAA
7035604 TGTGTCAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
ATAAAATTTAATTGTATTATATTA
Found at i:7036058 original size:30 final size:30
Alignment explanation
Indices: 7036006--7036080 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
7035996 TTGTATGCTT
* * * *
7036006 TTAACGAGGAACCATGAGGATATTACACTC
1 TTAACGAGGAGCCATAAAGATATAACACTC
7036036 TTAACG-GAGAGCCATAAAGATATAACACTC
1 TTAACGAG-GAGCCATAAAGATATAACACTC
7036066 TTAACGAGGAGCCAT
1 TTAACGAGGAGCCAT
7036081 GAATCTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 1 0.03
30 37 0.95
31 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (30 bp):
TTAACGAGGAGCCATAAAGATATAACACTC
Found at i:7040629 original size:262 final size:262
Alignment explanation
Indices: 7040169--7040660 Score: 689
Period size: 262 Copynumber: 1.9 Consensus size: 262
7040159 ATGGAATATC
* * * * *
7040169 AATTTTTAGCATTAGCAGTTACTGGAAAGGAACTAGAATGATTGAGAAATTTGTTATTAGATATA
1 AATTTTTAGCATTAGCAGCTACTGGAAAGGAACAAAAATGACTAAGAAATTTGTTATTAGATATA
* ** **
7040234 AAGTTGTGGTTATAATCGAAACCAGCCATTTTTATATATTGTGATAGTGATGCTACAATATGTGT
66 AAGTTATGGCCATAATCGAAACCAGCCATTTCCATATATTGTGATAGTGATGCTACAATATGTGT
* * * * *
7040299 TGCCCACAATAAGATTTATTATAAAAAGTCTAGATATATAAGTTTGTGACATGCCTACATAGGAA
131 TGCCCACAATAAGATTTATAATAAAAAGTCTAGATACATAAGTTTGTAACATACCTACATAAGAA
* * * *
7040364 AATTAATTTTGAATGATGTTGTAACAATAGTTTATGTCTTGCATTACGCATTCCACAATGGCATC
196 AATTAATCTCGAATGATGTTGTAAAAATAGGTTATGTCTTGCATTACGCATTCCACAATGGCATC
7040429 TG
261 TG
** * * *
7040431 AATTTTTAGCATTAGCAGCTGTTGGAAAGGAAGAAAAATGACTAAGCAATTTGTTATTAGTTATA
1 AATTTTTAGCATTAGCAGCTACTGGAAAGGAACAAAAATGACTAAGAAATTTGTTATTAGATATA
* *
7040496 AAGTTATGGCCATAATCGAAACCAGCCATTTCCGTATGTTGTGATAGTGA-GACTACAATATGTG
66 AAGTTATGGCCATAATCGAAACCAGCCATTTCCATATATTGTGATAGTGATG-CTACAATATGTG
** **
7040560 TTGCCCACAATAAGATTTATAATGGAAAGTCTAGATACATAAGTTTGTAACATATTTACATAAGA
130 TTGCCCACAATAAGATTTATAATAAAAAGTCTAGATACATAAGTTTGTAACATACCTACATAAGA
*
7040625 AAATTAATCTCGAATGGTGTTGTAAAAATAGGTTAT
195 AAATTAATCTCGAATGATGTTGTAAAAATAGGTTAT
7040661 CTTAAGTCTT
Statistics
Matches: 198, Mismatches: 31, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
261 1 0.01
262 197 0.99
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (262 bp):
AATTTTTAGCATTAGCAGCTACTGGAAAGGAACAAAAATGACTAAGAAATTTGTTATTAGATATA
AAGTTATGGCCATAATCGAAACCAGCCATTTCCATATATTGTGATAGTGATGCTACAATATGTGT
TGCCCACAATAAGATTTATAATAAAAAGTCTAGATACATAAGTTTGTAACATACCTACATAAGAA
AATTAATCTCGAATGATGTTGTAAAAATAGGTTATGTCTTGCATTACGCATTCCACAATGGCATC
TG
Found at i:7041971 original size:10 final size:10
Alignment explanation
Indices: 7041958--7041995 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
7041948 CCAAAAAGAC
7041958 AGGAAAAAAA
1 AGGAAAAAAA
7041968 AGGAAAAAAA
1 AGGAAAAAAA
*
7041978 AGGAAAAACA
1 AGGAAAAAAA
7041988 AGGCAAAA
1 AGG-AAAA
7041996 GCCAATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 22 0.85
11 4 0.15
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (10 bp):
AGGAAAAAAA
Found at i:7041974 original size:20 final size:21
Alignment explanation
Indices: 7041951--7041996 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
7041941 ATAAAATCCA
*
7041951 AAAAGACAGGAAAAAAAAGG-
1 AAAAGAAAGGAAAAAAAAGGC
* *
7041971 AAAAAAAAGGAAAAACAAGGC
1 AAAAGAAAGGAAAAAAAAGGC
7041992 AAAAG
1 AAAAG
7041997 CCAATTGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.72, C:0.07, G:0.22, T:0.00
Consensus pattern (21 bp):
AAAAGAAAGGAAAAAAAAGGC
Found at i:7044027 original size:26 final size:24
Alignment explanation
Indices: 7043972--7044028 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 24
7043962 TTGTCTTATT
*
7043972 AATTGATTAATTAAAAATTAAAAA
1 AATTTATTAATTAAAAATTAAAAA
7043996 ACATTTATTATATT-AAAATTAAAAGA
1 A-ATTTATTA-ATTAAAAATTAAAA-A
7044022 GAATTTA
1 -AATTTA
7044029 ATTTTTTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 1 0.04
25 17 0.61
26 9 0.32
27 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (24 bp):
AATTTATTAATTAAAAATTAAAAA
Found at i:7056436 original size:3 final size:3
Alignment explanation
Indices: 7056428--7056481 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
7056418 CCACTTCTAT
* *
7056428 TAA TAA TAA TAA CAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7056476 TAA TAA
1 TAA TAA
7056482 AAGCTTTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:7056598 original size:13 final size:13
Alignment explanation
Indices: 7056580--7056607 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7056570 GGCAAGTTAG
7056580 CATTGACCAATGA
1 CATTGACCAATGA
7056593 CATTGACCAATGA
1 CATTGACCAATGA
7056606 CA
1 CA
7056608 ACAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.21
Consensus pattern (13 bp):
CATTGACCAATGA
Found at i:7062521 original size:2 final size:2
Alignment explanation
Indices: 7062480--7062507 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7062470 GAATAAATAA
7062480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7062508 TATTGCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7071579 original size:35 final size:35
Alignment explanation
Indices: 7071540--7071633 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
7071530 CATACAGAAT
* ** * *
7071540 AATTAGAACAAGTGAAGCGTTACTTCACGCAAAAC
1 AATTAGAATAAGTGAAGCACTACTTAAAGCAAAAC
* *
7071575 AATTAGAATAAGTGGAGTACTACTTAAAGCAAAAC
1 AATTAGAATAAGTGAAGCACTACTTAAAGCAAAAC
*
7071610 AATTAGAATAAGTAAAGCACTACT
1 AATTAGAATAAGTGAAGCACTACT
7071634 CTATATGGAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (35 bp):
AATTAGAATAAGTGAAGCACTACTTAAAGCAAAAC
Found at i:7078029 original size:21 final size:21
Alignment explanation
Indices: 7077990--7078056 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
7077980 TCATCTCCTG
* **
7077990 CCCCTCAGCCTTCAACTCCAC
1 CCCCTCAACCTTCTTCTCCAC
**
7078011 CCCCTCAACCTTCTTCTCCTG
1 CCCCTCAACCTTCTTCTCCAC
*
7078032 CTCCTCAACCCTCTACTTCTCCAC
1 CCCCTCAA-CCT-T-CTTCTCCAC
7078056 C
1 C
7078057 AGCTTCTACC
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 23 0.66
22 3 0.09
23 1 0.03
24 8 0.23
ACGTcount: A:0.15, C:0.55, G:0.03, T:0.27
Consensus pattern (21 bp):
CCCCTCAACCTTCTTCTCCAC
Found at i:7078185 original size:21 final size:20
Alignment explanation
Indices: 7078161--7078227 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
7078151 TCCTCTTCCT
7078161 CACCCCCACCTTCAACGGCAA
1 CACCCCCACC-TCAACGGCAA
* * ** **
7078182 CACCACCATCCTCCACCACCT
1 CACCCCCA-CCTCAACGGCAA
7078203 CACCCCCACCATCAACGGCAA
1 CACCCCCACC-TCAACGGCAA
7078224 CACC
1 CACC
7078228 ACCATCCTCC
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.28, C:0.57, G:0.06, T:0.09
Consensus pattern (20 bp):
CACCCCCACCTCAACGGCAA
Found at i:7078205 original size:42 final size:42
Alignment explanation
Indices: 7078158--7078255 Score: 178
Period size: 42 Copynumber: 2.3 Consensus size: 42
7078148 CCATCCTCTT
7078158 CCTCACCCCCACCTTCAACGGCAACACCACCATCCTCCACCA
1 CCTCACCCCCACCTTCAACGGCAACACCACCATCCTCCACCA
*
7078200 CCTCACCCCCACCATCAACGGCAACACCACCATCCTCCACCA
1 CCTCACCCCCACCTTCAACGGCAACACCACCATCCTCCACCA
*
7078242 CCTCTCCCCCACCT
1 CCTCACCCCCACCT
7078256 CCCGCCGGAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.24, C:0.59, G:0.04, T:0.12
Consensus pattern (42 bp):
CCTCACCCCCACCTTCAACGGCAACACCACCATCCTCCACCA
Found at i:7078240 original size:39 final size:39
Alignment explanation
Indices: 7078145--7078240 Score: 138
Period size: 42 Copynumber: 2.4 Consensus size: 39
7078135 CCCGGCGACC
** *
7078145 CCACCATCCTCTTCCTCACCCCCACCTTCAACGGCAACA
1 CCACCATCCTCCACCTCACCCCCACCATCAACGGCAACA
7078184 CCACCATCCTCCACCACCTCACCCCCACCATCAACGGCAACA
1 CCACCATCCT---CCACCTCACCCCCACCATCAACGGCAACA
7078226 CCACCATCCTCCACC
1 CCACCATCCTCCACC
7078241 ACCTCTCCCC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
39 15 0.29
42 36 0.71
ACGTcount: A:0.25, C:0.57, G:0.04, T:0.14
Consensus pattern (39 bp):
CCACCATCCTCCACCTCACCCCCACCATCAACGGCAACA
Found at i:7080771 original size:15 final size:15
Alignment explanation
Indices: 7080753--7080784 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7080743 TAATGTTATA
7080753 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
7080768 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
7080783 AT
1 AT
7080785 AATATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:7080787 original size:33 final size:32
Alignment explanation
Indices: 7080749--7080859 Score: 102
Period size: 33 Copynumber: 3.3 Consensus size: 32
7080739 TTTGTAATGT
7080749 TATAATTAAAATAAAAAATATTAAAATAAAATA
1 TATAATTAAAATAAAAAA-ATTAAAATAAAATA
* *
7080782 TATAATATAAGAAT-TAAAAATTAAAATAAAATT
1 TATAAT-TAA-AATAAAAAAATTAAAATAAAATA
* *
7080815 TAT-A-TAATATAGGTTAAAAATTAAAATAAAATA
1 TATAATTAAAATA---AAAAAATTAAAATAAAATA
7080848 TATAATATAAAA
1 TATAAT-TAAAA
7080860 AATTATACTA
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
29 2 0.03
30 3 0.05
32 1 0.02
33 43 0.67
34 8 0.12
35 3 0.05
36 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (32 bp):
TATAATTAAAATAAAAAAATTAAAATAAAATA
Found at i:7080899 original size:34 final size:32
Alignment explanation
Indices: 7080838--7080924 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 32
7080828 TTAAAAATTA
* *
7080838 AAATAAAATATATAATATAAAAAATTATACTAAAG
1 AAATAAAATA-A-AATATATAAAATTATAAT-AAG
*
7080873 AAATGAAAATAAAATATATAAGATTATAATAAG
1 AAAT-AAAATAAAATATATAAAATTATAATAAG
7080906 AAATAAAAATAAAATATAT
1 AAAT-AAAATAAAATATAT
7080925 GACATTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
33 21 0.45
34 15 0.32
35 5 0.11
36 6 0.13
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.28
Consensus pattern (32 bp):
AAATAAAATAAAATATATAAAATTATAATAAG
Found at i:7081651 original size:13 final size:13
Alignment explanation
Indices: 7081633--7081657 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7081623 ATTTTGAAGG
7081633 ATTATATTTTAAT
1 ATTATATTTTAAT
7081646 ATTATATTTTAA
1 ATTATATTTTAA
7081658 AACTTGAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTATATTTTAAT
Found at i:7090081 original size:2 final size:2
Alignment explanation
Indices: 7090069--7090106 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
7090059 TTGCAATGGA
*
7090069 AG AG A- AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
7090107 TGGGGGACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:7090143 original size:11 final size:11
Alignment explanation
Indices: 7090127--7090162 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
7090117 GGCTTTTCTT
7090127 TTTTCTTTTTC
1 TTTTCTTTTTC
7090138 TTTTCTTTTT-
1 TTTTCTTTTTC
*
7090148 TTTTCTCTTTC
1 TTTTCTTTTTC
7090159 TTTT
1 TTTT
7090163 GGCTGGGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:7092003 original size:27 final size:29
Alignment explanation
Indices: 7091952--7092005 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
7091942 TTTGATTTAA
7091952 AATAAAAATATATAAATTTAATTAAATAT
1 AATAAAAATATATAAATTTAATTAAATAT
*
7091981 AATAAAAATA-A-AAATTTATTTAAAT
1 AATAAAAATATATAAATTTAATTAAAT
7092006 TTCTCCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.54
28 1 0.04
29 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AATAAAAATATATAAATTTAATTAAATAT
Found at i:7099092 original size:21 final size:22
Alignment explanation
Indices: 7099066--7099106 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
7099056 TTCTTCTTTT
7099066 CATTATATTAA-AATTAAAATG
1 CATTATATTAACAATTAAAATG
7099087 CATTATATTAACAATTAAAA
1 CATTATATTAACAATTAAAA
7099107 ATAACATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (22 bp):
CATTATATTAACAATTAAAATG
Found at i:7125221 original size:15 final size:17
Alignment explanation
Indices: 7125194--7125226 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
7125184 ATATTAATAT
7125194 TTTAAACT-AAAAATTA
1 TTTAAACTAAAAAATTA
7125210 TTTAAA-TAAAAAATTA
1 TTTAAACTAAAAAATTA
7125226 T
1 T
7125227 CCCAAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTAAACTAAAAAATTA
Found at i:7125760 original size:15 final size:16
Alignment explanation
Indices: 7125742--7125771 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7125732 TTAATAAGTC
7125742 AAATATTTA-AGTGTA
1 AAATATTTATAGTGTA
7125757 AAATATTTATAGTGT
1 AAATATTTATAGTGT
7125772 TAAGAAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (16 bp):
AAATATTTATAGTGTA
Found at i:7130767 original size:28 final size:28
Alignment explanation
Indices: 7130710--7130767 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
7130700 AGAATAATAT
** * *
7130710 TTATCTTTTAATATTAAATATTGTTTAA
1 TTATCTTTTAATACAAAATATTATTAAA
7130738 TTATCTTTTAATACAAAATATTATTAAA
1 TTATCTTTTAATACAAAATATTATTAAA
7130766 TT
1 TT
7130768 CTAATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (28 bp):
TTATCTTTTAATACAAAATATTATTAAA
Found at i:7130780 original size:22 final size:22
Alignment explanation
Indices: 7130746--7130820 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
7130736 AATTATCTTT
*
7130746 TAATACAAAATATTATTAAATTC
1 TAATA-AAAATATTATTAAATTA
* *
7130769 TAATAAAAATATGT-TTATATTT
1 TAATAAAAATAT-TATTAAATTA
** * *
7130791 TGGTGAAAATATTATTTAATTA
1 TAATAAAAATATTATTAAATTA
7130813 TAATAAAA
1 TAATAAAA
7130821 GTTATTTTGA
Statistics
Matches: 39, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.82
23 6 0.15
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (22 bp):
TAATAAAAATATTATTAAATTA
Found at i:7130931 original size:49 final size:49
Alignment explanation
Indices: 7130871--7130978 Score: 200
Period size: 49 Copynumber: 2.2 Consensus size: 49
7130861 ACAAAATAAA
7130871 TTTTTTAATTTTAATAAAGAGTATTTA-TTTTTTAAAATAGTTTTTTAG
1 TTTTTTAATTTTAATAAAGAGTATTTATTTTTTTAAAATAGTTTTTTAG
7130919 NTTTTTTAATTTTAATAAAGAGTATTTATTTTTTTAAAATAGTTTTTTAG
1 -TTTTTTAATTTTAATAAAGAGTATTTATTTTTTTAAAATAGTTTTTTAG
7130969 TTTTTTAATT
1 TTTTTTAATT
7130979 AAAAAATTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
49 37 0.64
50 21 0.36
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.60
Consensus pattern (49 bp):
TTTTTTAATTTTAATAAAGAGTATTTATTTTTTTAAAATAGTTTTTTAG
Found at i:7131011 original size:22 final size:22
Alignment explanation
Indices: 7130921--7131011 Score: 53
Period size: 21 Copynumber: 4.2 Consensus size: 22
7130911 TTTTTTAGNT
*
7130921 TTTTTAATTTTAATAAAGAGTA
1 TTTTAAATTTTAATAAAGAGTA
** * * *
7130943 -TTTATTTTTTTA-AAATAGTT
1 TTTTAAATTTTAATAAAGAGTA
** * *
7130963 TTTTAGTTTTTTAATTAAAAAAT-
1 TTTTA-AATTTTAA-TAAAGAGTA
7130986 TTTTAAATTTTAATAAAGAGTA
1 TTTTAAATTTTAATAAAGAGTA
7131008 TTTT
1 TTTT
7131012 TATCATTTAT
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
20 6 0.12
21 18 0.35
22 17 0.33
23 5 0.10
24 5 0.10
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
TTTTAAATTTTAATAAAGAGTA
Found at i:7135385 original size:27 final size:27
Alignment explanation
Indices: 7135344--7135416 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
7135334 CGCTCTTTAG
**
7135344 GAGCTTCTGTGCTTGGAACA-CTCTTGA
1 GAGCTTCTGCACTTGGAACACCTC-TGA
* * * *
7135371 GTGCTTTTGCACTTGGAACGCCTCTGG
1 GAGCTTCTGCACTTGGAACACCTCTGA
7135398 GAGCTTCTGCACTTGGAAC
1 GAGCTTCTGCACTTGGAAC
7135417 GCCCCTAGGC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 34 0.92
28 3 0.08
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (27 bp):
GAGCTTCTGCACTTGGAACACCTCTGA
Found at i:7135431 original size:27 final size:27
Alignment explanation
Indices: 7135373--7135425 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
7135363 ACTCTTGAGT
* * *
7135373 GCTTTTGCACTTGGAACGCCTCTGGGA
1 GCTTCTGCACTTGGAACGCCCCTAGGA
7135400 GCTTCTGCACTTGGAACGCCCCTAGG
1 GCTTCTGCACTTGGAACGCCCCTAGG
7135426 CTCTTCCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.26
Consensus pattern (27 bp):
GCTTCTGCACTTGGAACGCCCCTAGGA
Found at i:7139892 original size:2 final size:2
Alignment explanation
Indices: 7139885--7139909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7139875 GAACGACAAT
7139885 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
7139910 ACTGAATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:7145582 original size:9 final size:9
Alignment explanation
Indices: 7145568--7145678 Score: 98
Period size: 9 Copynumber: 12.3 Consensus size: 9
7145558 AGATGCACCT
7145568 AACATAACG
1 AACATAACG
7145577 AACATAACG
1 AACATAACG
*
7145586 AACACAACG
1 AACATAACG
7145595 AACATAACG
1 AACATAACG
* *
7145604 AACACAAGG
1 AACATAACG
* *
7145613 ACCATAATG
1 AACATAACG
* *
7145622 AATATAAGG
1 AACATAACG
* *
7145631 AACACAAGG
1 AACATAACG
* *
7145640 AATATAATG
1 AACATAACG
7145649 AACATAAC-
1 AACATAACG
*
7145657 AGACACAACG
1 A-ACATAACG
7145667 AACATAACG
1 AACATAACG
7145676 AAC
1 AAC
7145679 TTTTAAAAGA
Statistics
Matches: 81, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
8 1 0.01
9 79 0.98
10 1 0.01
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.11
Consensus pattern (9 bp):
AACATAACG
Found at i:7145598 original size:27 final size:27
Alignment explanation
Indices: 7145569--7145678 Score: 114
Period size: 27 Copynumber: 4.1 Consensus size: 27
7145559 GATGCACCTA
* *
7145569 ACATAACGAACATAACGAACACAACGA
1 ACATAACGAACACAACGAACATAACGA
* * *
7145596 ACATAACGAACACAAGGACCATAATGA
1 ACATAACGAACACAACGAACATAACGA
* * * * *
7145623 ATATAAGGAACACAAGGAATATAATGA
1 ACATAACGAACACAACGAACATAACGA
7145650 ACATAAC-AGACACAACGAACATAACGA
1 ACATAACGA-ACACAACGAACATAACGA
7145677 AC
1 AC
7145679 TTTTAAAAGA
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 1 0.01
27 67 0.99
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.11
Consensus pattern (27 bp):
ACATAACGAACACAACGAACATAACGA
Found at i:7149014 original size:7 final size:7
Alignment explanation
Indices: 7149004--7149028 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
7148994 GATATATATT
7149004 ATAATTA
1 ATAATTA
7149011 ATAATTA
1 ATAATTA
7149018 ATAATTA
1 ATAATTA
7149025 ATAA
1 ATAA
7149029 GTTTATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAATTA
Found at i:7150033 original size:5 final size:5
Alignment explanation
Indices: 7150019--7150057 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
7150009 ATGTCTCAAC
7150019 AAAT- AAATA AAATA AAGATA AAATA AAATA AAATA AAAT
1 AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA AAAT
7150058 TAGAATCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
6 5 0.15
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:7150042 original size:16 final size:15
Alignment explanation
Indices: 7150019--7150057 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
7150009 ATGTCTCAAC
7150019 AAAT-AAATAAAATA
1 AAATAAAATAAAATA
7150033 AAGATAAAATAAAATA
1 AA-ATAAAATAAAATA
7150049 AAATAAAAT
1 AAATAAAAT
7150058 TAGAATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 9 0.39
16 12 0.52
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAAAATAAAATA
Found at i:7156999 original size:17 final size:18
Alignment explanation
Indices: 7156945--7156997 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
7156935 TTAAAATATT
*
7156945 TAAATTATTTAAAATTAAA
1 TAAATT-TTTATAATTAAA
*
7156964 TAAAATTTT-TAATTAAA
1 TAAATTTTTATAATTAAA
7156981 TAAATTTTTATAATTAA
1 TAAATTTTTATAATTAA
7156998 TAGTTAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.50
18 10 0.33
19 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTTTTATAATTAAA
Found at i:7157290 original size:20 final size:19
Alignment explanation
Indices: 7157261--7157321 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
7157251 TTTAATTATG
*
7157261 TTAATTTATTGAATTTATAA
1 TTAATATATT-AATTTATAA
* *
7157281 TTAATATATTTAATGTATAT
1 TTAATATA-TTAATTTATAA
7157301 TTGAATAT-TTAATTTAATAA
1 TT-AATATATTAATTT-ATAA
7157321 T
1 T
7157322 AGATACATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 6 0.18
20 20 0.61
21 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAATATATTAATTTATAA
Found at i:7164759 original size:116 final size:114
Alignment explanation
Indices: 7164433--7164774 Score: 594
Period size: 116 Copynumber: 3.0 Consensus size: 114
7164423 TTTAAGAAAG
* *
7164433 AAGAGCCCTTTTGTCGTTTATCTAATAAATAAAAAAATCTTTTTTAAATTATTATTTTTGAAAAT
1 AAGAGCCCTTTTGTCGTTTATCTAATAAATAAAAAAACCCTTTTTAAATTATTATTTTTGAAAAT
7164498 ATTTGTGTGATAATTAATGTGTTTACTTAATATATGTATATACATAAAC
66 ATTTGTGTGATAATTAATGTGTTTACTTAATATATGTATATACATAAAC
*
7164547 AAGAGCCCTTTTGTCGTTTATCTAATAAATGAAAAAACCCCTTTTTAAATTATTATTTTTGAAAA
1 AAGAGCCCTTTTGTCGTTTATCTAATAAAT-AAAAAAACCCTTTTTAAATTATTATTTTTGAAAA
7164612 TATTTGTGTGATAATTAATGTGTTTACTTAATATATGTATATACATAAAC
65 TATTTGTGTGATAATTAATGTGTTTACTTAATATATGTATATACATAAAC
* *
7164662 AAGAGCCCTTTTTGTCATTTATCTAATAAATAAAAAAAACCCTTTTCAAATTATTATTTTTGAAA
1 AAGAGCCC-TTTTGTCGTTTATCTAATAAAT-AAAAAAACCCTTTTTAAATTATTATTTTTGAAA
**
7164727 ATATTCATGTGATAATTAATGTGTTTACTTAATATATGTATATACATA
64 ATATTTGTGTGATAATTAATGTGTTTACTTAATATATGTATATACATA
7164775 TGCGTAAAGC
Statistics
Matches: 217, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
114 30 0.14
115 89 0.41
116 98 0.45
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (114 bp):
AAGAGCCCTTTTGTCGTTTATCTAATAAATAAAAAAACCCTTTTTAAATTATTATTTTTGAAAAT
ATTTGTGTGATAATTAATGTGTTTACTTAATATATGTATATACATAAAC
Found at i:7170190 original size:27 final size:27
Alignment explanation
Indices: 7170156--7170268 Score: 113
Period size: 27 Copynumber: 4.2 Consensus size: 27
7170146 TGCCCAAGGA
7170156 GTTCCAAGCGTGGAAGCCCCTAAGGG-T
1 GTTCCAAGCGTGGAAGCCCCT-AGGGAT
*
7170183 GTTCCAAGCGTGGAAGCGTCC-AGGGAT
1 GTTCCAAGCGTGGAAGC-CCCTAGGGAT
* * * *
7170210 GTTCCAAGTGTGAAAGCTCTTAGGGAT
1 GTTCCAAGCGTGGAAGCCCCTAGGGAT
* * * *
7170237 GTTCCAAGCGTAGAAACGCCTAGAGAT
1 GTTCCAAGCGTGGAAGCCCCTAGGGAT
7170264 GTTCC
1 GTTCC
7170269 CAGTGCAAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
26 6 0.08
27 64 0.89
28 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (27 bp):
GTTCCAAGCGTGGAAGCCCCTAGGGAT
Found at i:7170401 original size:27 final size:26
Alignment explanation
Indices: 7170371--7170636 Score: 191
Period size: 27 Copynumber: 9.8 Consensus size: 26
7170361 CTCAGGGGTA
7170371 TTCCAAGCTCGGAAGCGCCCCAAGGA-G
1 TTCCAAGCT-GGAAGCG-CCCAAGGATG
7170398 TTCCAAGCATGGAAGCGCCCAAGGATG
1 TTCCAAGC-TGGAAGCGCCCAAGGATG
* *
7170425 TTCCAAG-TAAGGAAGTGCCCATGGATG
1 TTCCAAGCT--GGAAGCGCCCAAGGATG
7170452 TTCCAAGCATGGAAGCGCCCAAGGGA-G
1 TTCCAAGC-TGGAAGCGCCCAA-GGATG
* * *
7170479 TTCCAAGCGAGGAAGCGCCCAGGGGTG
1 TTCCAAGC-TGGAAGCGCCCAAGGATG
** * *
7170506 TTCTTAGCGTGGAAGCGCCCAGGGGTG
1 TTCCAAGC-TGGAAGCGCCCAAGGATG
* *
7170533 TTCCAAGCGTGGAAGCGCCCAGGGGTG
1 TTCCAAGC-TGGAAGCGCCCAAGGATG
* * *
7170560 TTCCAAACGAGGAAGCGCCCAGGGGA-G
1 TTCCAAGC-TGGAAGCGCCCA-AGGATG
* * *
7170587 TTCCAAGCATAGAAGCG-CCTAGGAGAG
1 TTCCAAGC-TGGAAGCGCCCAAGGA-TG
* *
7170614 TTCCAAGCATGGAAACACCCAAG
1 TTCCAAGC-TGGAAGCGCCCAAG
7170637 AACAAACATA
Statistics
Matches: 201, Mismatches: 26, Indels: 23
0.80 0.10 0.09
Matches are distributed among these distances:
25 4 0.02
26 12 0.06
27 173 0.86
28 11 0.05
29 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.33, T:0.14
Consensus pattern (26 bp):
TTCCAAGCTGGAAGCGCCCAAGGATG
Found at i:7170455 original size:54 final size:53
Alignment explanation
Indices: 7170371--7170636 Score: 243
Period size: 54 Copynumber: 4.9 Consensus size: 53
7170361 CTCAGGGGTA
** *
7170371 TTCCAAGCTCGGAAGCGCCCCAAGGA-GTTCCAAGCATGGAAGCGCCCAAGGATG
1 TTCCAAGCAAGGAAGCG-CCCAGGGATGTTCCAAGCATGGAAGCGCCCAAGGA-G
* * *
7170425 TTCCAAGTAAGGAAGTGCCCATGGATGTTCCAAGCATGGAAGCGCCCAAGGGAG
1 TTCCAAGCAAGGAAGCGCCCAGGGATGTTCCAAGCATGGAAGCGCCCAA-GGAG
* * ** * * *
7170479 TTCCAAGCGAGGAAGCGCCCAGGGGTGTTCTTAGCGTGGAAGCGCCCAGGGGTG
1 TTCCAAGCAAGGAAGCGCCCAGGGATGTTCCAAGCATGGAAGCGCCCA-AGGAG
** * * *
7170533 TTCCAAGCGTGGAAGCGCCCAGGGGTGTTCCAAACGA-GGAAGCGCCCAGGGGAG
1 TTCCAAGCAAGGAAGCGCCCAGGGATGTTCCAAGC-ATGGAAGCGCCCA-AGGAG
* * *
7170587 TTCCAAGCATA-GAAGCGCCTAGGAGA-GTTCCAAGCATGGAAACACCCAAG
1 TTCCAAGCA-AGGAAGCGCCCAGG-GATGTTCCAAGCATGGAAGCGCCCAAG
7170637 AACAAACATA
Statistics
Matches: 176, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
53 9 0.05
54 163 0.93
55 4 0.02
ACGTcount: A:0.27, C:0.26, G:0.33, T:0.14
Consensus pattern (53 bp):
TTCCAAGCAAGGAAGCGCCCAGGGATGTTCCAAGCATGGAAGCGCCCAAGGAG
Found at i:7170508 original size:81 final size:80
Alignment explanation
Indices: 7170371--7170636 Score: 279
Period size: 81 Copynumber: 3.3 Consensus size: 80
7170361 CTCAGGGGTA
* * *
7170371 TTCCAAGC-TCGGAAGCGCCCCAA-GGAGTTCCAAGC-ATGGAAGCGCCCAAGGATGTTCCAAGT
1 TTCCAAGCAT-GGAAGCG-CCCAAGGGAGTTCCAAGCGA-GGAAGCGCCCAGGGGTGTTCCAAGC
*
7170433 AAGGAAGTGCCCATGGATG
63 AAGGAAGCGCCCA-GGATG
** **
7170452 TTCCAAGCATGGAAGCGCCCAAGGGAGTTCCAAGCGAGGAAGCGCCCAGGGGTGTTCTTAGCGTG
1 TTCCAAGCATGGAAGCGCCCAAGGGAGTTCCAAGCGAGGAAGCGCCCAGGGGTGTTCCAAGCAAG
*
7170517 GAAGCGCCCAGGGGTG
66 GAAGCGCCCA-GGATG
* * * * *
7170533 TTCCAAGCGTGGAAGCGCCCAGGGGTGTTCCAAACGAGGAAGCGCCCAGGGGAGTTCCAAGCATA
1 TTCCAAGCATGGAAGCGCCCAAGGGAGTTCCAAGCGAGGAAGCGCCCAGGGGTGTTCCAAGCA-A
* *
7170598 -GAAGCGCCTAGGAGAG
65 GGAAGCGCCCAGGA-TG
* *
7170614 TTCCAAGCATGGAAACACCCAAG
1 TTCCAAGCATGGAAGCGCCCAAG
7170637 AACAAACATA
Statistics
Matches: 154, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
80 7 0.05
81 145 0.94
82 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.33, T:0.14
Consensus pattern (80 bp):
TTCCAAGCATGGAAGCGCCCAAGGGAGTTCCAAGCGAGGAAGCGCCCAGGGGTGTTCCAAGCAAG
GAAGCGCCCAGGATG
Found at i:7171832 original size:46 final size:48
Alignment explanation
Indices: 7171746--7171837 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 48
7171736 CTTATTTTTT
*
7171746 AATCAAAGTATCATGCATCAACTAATTAATAACGGATCAAG-CCTTTA
1 AATCAAAGTATCATGCACCAACTAATTAATAACGGATCAAGTCCTTTA
* *
7171793 AATCAAGAG-ATCATGCACCAATTAATTATTAA-GGATCAAGTCCTT
1 AATCAA-AGTATCATGCACCAACTAATTAATAACGGATCAAGTCCTT
7171838 AACTTAGCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 8 0.20
47 30 0.75
48 2 0.05
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.28
Consensus pattern (48 bp):
AATCAAAGTATCATGCACCAACTAATTAATAACGGATCAAGTCCTTTA
Found at i:7177596 original size:5 final size:5
Alignment explanation
Indices: 7177586--7177612 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
7177576 TAAGACAAGC
7177586 AAAGA AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AA
7177613 GAATTTGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:7178167 original size:2 final size:2
Alignment explanation
Indices: 7178162--7178256 Score: 145
Period size: 2 Copynumber: 47.5 Consensus size: 2
7178152 CAAAAAATTC
* *
7178162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT NT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
7178204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
7178246 GT AT AT AT AT A
1 AT AT AT AT AT A
7178257 ACTGTGAGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7199339 original size:21 final size:19
Alignment explanation
Indices: 7199282--7199339 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
7199272 AAACCTTTTA
*
7199282 TACTTAAATATTTGTCTTAT
1 TACTTAAATATTT-TATTAT
*
7199302 TA-ATAAATATATTTATTATT
1 TACTTAAATAT-TTTATTA-T
7199322 TACTTAAATATTTATATT
1 TACTTAAATATTT-TATT
7199340 TTTCAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 11 0.35
20 9 0.29
21 11 0.35
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (19 bp):
TACTTAAATATTTTATTAT
Found at i:7200521 original size:20 final size:20
Alignment explanation
Indices: 7200466--7200509 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
7200456 AATATTTCAA
*
7200466 TAATAA-ATTATTATTAATT
1 TAATAACATTATTATTAAAT
7200485 TAATAACATTATTATTAAAT
1 TAATAACATTATTATTAAAT
7200505 TAATA
1 TAATA
7200510 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATAACATTATTATTAAAT
Found at i:7208404 original size:20 final size:21
Alignment explanation
Indices: 7208352--7208405 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
7208342 TGCGAATTTG
7208352 AGTTATTCTAAGGTACATTTTTCT
1 AGTTATTCT-AGG--CATTTTTCT
*
7208376 GGTTATTCTAGGCATTTTT-T
1 AGTTATTCTAGGCATTTTTCT
*
7208396 AGTTTTTCTA
1 AGTTATTCTA
7208406 AAGAATTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.33
21 7 0.26
23 3 0.11
24 8 0.30
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.54
Consensus pattern (21 bp):
AGTTATTCTAGGCATTTTTCT
Found at i:7224667 original size:12 final size:13
Alignment explanation
Indices: 7224644--7224675 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
7224634 GGTAGTAAAG
7224644 AAAGAGAGAAGAA
1 AAAGAGAGAAGAA
7224657 AAAGA-AGAAG-A
1 AAAGAGAGAAGAA
7224668 AAAGAGAG
1 AAAGAGAG
7224676 TTGAATTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 7 0.39
13 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAAGAGAGAAGAA
Found at i:7224911 original size:2 final size:2
Alignment explanation
Indices: 7224904--7224933 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7224894 CCCTCCCCTC
7224904 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
7224934 TTTCATTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:7226047 original size:2 final size:2
Alignment explanation
Indices: 7226040--7226076 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
7226030 ATATTGTTTA
7226040 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7226077 AACATTGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.