Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 73 of 230
Found at i:20078111 original size:87 final size:86
Alignment explanation
Indices: 20077859--20078119 Score: 204
Period size: 87 Copynumber: 3.0 Consensus size: 86
20077849 TCGTTATATT
** * * * * * * * * *
20077859 CAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTATCTTCGATCTGCTTCGCTGTCAGTAC
1 CAACCTGCTCTACTACAACCGAGGGAGACAAGGCTGGTATCTTCAACCTGCTCCAC-GTCA-TGC
* * *
20077924 AGGAAGGCAAGGTTTGCTATCT-
64 AGGAAGGCAAGATCTGCCATCTC
* * ** * * *
20077946 TAAGTCTGCTCCGCTACAACCGAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCACGTCGATGC
1 CAA-CCTGCTCTACTACAACCGAGGGAGACAAGGCTGGTATCTTCAACCTGCTCCACGTC-ATGC
*
20078011 AGGAAGGCAAGATCTGCTATCTC
64 AGGAAGGCAAGATCTGCCATCTC
* *
20078034 CAACCTGCTCTACTACAACCGAGGGAGGCAAGGCTGGTATCTTTAACCTGCTCCAC-T-ACTGCT
1 CAACCTGCTCTACTACAACCGAGGGAGACAAGGCTGGTATCTTCAACCTGCTCCACGTCA-TGC-
* *
20078097 TAGGGAGGCCAGATCTGCCATCT
64 -AGGAAGGCAAGATCTGCCATCT
20078120 TCACTGATCT
Statistics
Matches: 146, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
84 1 0.01
85 3 0.02
86 1 0.01
87 91 0.62
88 50 0.34
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (86 bp):
CAACCTGCTCTACTACAACCGAGGGAGACAAGGCTGGTATCTTCAACCTGCTCCACGTCATGCAG
GAAGGCAAGATCTGCCATCTC
Found at i:20079410 original size:20 final size:20
Alignment explanation
Indices: 20079373--20079409 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
20079363 TTTTTACTTT
*
20079373 TTTTCATTATTTATTTTTCA
1 TTTTCATTATTCATTTTTCA
20079393 TTTTCATT-TTCATTTTT
1 TTTTCATTATTCATTTTT
20079410 TTTGACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTCATTATTCATTTTTCA
Found at i:20085505 original size:29 final size:28
Alignment explanation
Indices: 20085455--20085514 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
20085445 TTTAAAGCAC
*
20085455 AAAAGTATATATAAACATAAATATTTTAA
1 AAAAGTATATATAAACATAAAT-TATTAA
20085484 AAAAGTATCATA-AAA-ATAAAATTATTAA
1 AAAAGTAT-ATATAAACAT-AAATTATTAA
20085512 AAA
1 AAA
20085515 TATATAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 10 0.36
29 15 0.54
30 3 0.11
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (28 bp):
AAAAGTATATATAAACATAAATTATTAA
Found at i:20085525 original size:29 final size:29
Alignment explanation
Indices: 20085455--20085514 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
20085445 TTTAAAGCAC
* *
20085455 AAAAGTATATATAAACATAAATATTTTAA
1 AAAAGTATACATAAAAATAAATATTTTAA
20085484 AAAAGTAT-CATAAAAATAAA-ATTATTAA
1 AAAAGTATACATAAAAATAAATATT-TTAA
20085512 AAA
1 AAA
20085515 TATATAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 3 0.11
28 17 0.61
29 8 0.29
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAGTATACATAAAAATAAATATTTTAA
Found at i:20087852 original size:12 final size:13
Alignment explanation
Indices: 20087835--20087864 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
20087825 TATTACATTC
20087835 AATTTGATA-TTT
1 AATTTGATATTTT
20087847 AATTTGATATTTT
1 AATTTGATATTTT
20087860 AATTT
1 AATTT
20087865 ATCATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (13 bp):
AATTTGATATTTT
Found at i:20093268 original size:23 final size:23
Alignment explanation
Indices: 20093238--20093340 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 23
20093228 AGTGTTATTG
*
20093238 ATCAGTGGTAGCTACGACTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* * ** *
20093261 ATCGGTGGTATCTTTGGCTATAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
20093284 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTACGGCTACAT
**
20093307 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
20093330 ATCAGT-GTAGC
1 ATCAGTGGTAGC
20093341 ACTTATGTGC
Statistics
Matches: 63, Mismatches: 17, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
22 5 0.08
23 58 0.92
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:20093315 original size:46 final size:46
Alignment explanation
Indices: 20093238--20093340 Score: 145
Period size: 46 Copynumber: 2.3 Consensus size: 46
20093228 AGTGTTATTG
* * *
20093238 ATCAGTGGTAGCTACGACTACATATCGGTGGTATCTTTGGCTATAT
1 ATCAGTGGTAGCTACGACTACATATCAGTGGTAGCTTTGGCTACAT
* * *
20093284 TTCAGTGGTAGCTACGGCTACGTATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTACGACTACATATCAGTGGTAGCTTTGGCTACAT
20093330 ATCAGT-GTAGC
1 ATCAGTGGTAGC
20093341 ACTTATGTGC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 5 0.10
46 45 0.90
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTACGACTACATATCAGTGGTAGCTTTGGCTACAT
Found at i:20094581 original size:49 final size:49
Alignment explanation
Indices: 20094517--20094705 Score: 297
Period size: 49 Copynumber: 3.9 Consensus size: 49
20094507 CAATAAGTGA
*
20094517 TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGT
* * *
20094566 TATGTGATTATGTGTAAGACCATAGCTGGGCTATGGCATCGGTATACGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGT
* * *
20094615 TATGTGATTAGGTGTAAGACCATAGTTGGGCTATGGCATCGGTATATGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGT
* *
20094664 TATGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCGA
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGA
20094706 GAAAATAAGT
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 130 1.00
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (49 bp):
TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGT
Found at i:20102323 original size:25 final size:25
Alignment explanation
Indices: 20102279--20102328 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
20102269 AAACTAAAAT
20102279 TTTAAAATAAATTCACAAATTTAAA
1 TTTAAAATAAATTCACAAATTTAAA
20102304 TTTAAAA-AATATT-ACAAAATTTAAA
1 TTTAAAATAA-ATTCAC-AAATTTAAA
20102329 ATATTCTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (25 bp):
TTTAAAATAAATTCACAAATTTAAA
Found at i:20106919 original size:3 final size:3
Alignment explanation
Indices: 20106911--20106939 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20106901 TATGAGTAAT
20106911 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20106940 CCAATTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20109761 original size:24 final size:25
Alignment explanation
Indices: 20109708--20109763 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
20109698 AGAAATGGTG
*
20109708 AGTTTTAGTATTAAGTAATACGATG
1 AGTTTTAGTATTAAGTAATACGATA
* *
20109733 CGTTTTA-TATTAAGCTAA-ACGGTA
1 AGTTTTAGTATTAAG-TAATACGATA
20109757 AGTTTTA
1 AGTTTTA
20109764 ACAGGCTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (25 bp):
AGTTTTAGTATTAAGTAATACGATA
Found at i:20110033 original size:20 final size:21
Alignment explanation
Indices: 20109991--20110033 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20109981 GATTATTTTA
*
20109991 AAAACTCAATTGACTTAATCC
1 AAAACTCAATTGACTTAACCC
20110012 AAAA-TCAACTTGACTT-ACCC
1 AAAACTCAA-TTGACTTAACCC
20110032 AA
1 AA
20110034 TTGATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAACTCAATTGACTTAACCC
Found at i:20114756 original size:25 final size:27
Alignment explanation
Indices: 20114728--20114784 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 27
20114718 CGTACAGAAT
20114728 ATTTTAAATTTGT-AATATT-TTTT-AA
1 ATTTTAAATTTGTGAAT-TTATTTTAAA
20114753 A-TTTAAATTTGTGAATTTATTTTAAA
1 ATTTTAAATTTGTGAATTTATTTTAAA
20114779 ATTTTA
1 ATTTTA
20114785 GTTTTGCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 13 0.46
25 8 0.29
26 3 0.11
27 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (27 bp):
ATTTTAAATTTGTGAATTTATTTTAAA
Found at i:20120228 original size:25 final size:25
Alignment explanation
Indices: 20120184--20120233 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
20120174 AAACTAAAAT
20120184 TTTAAAATAAATTCACAAATTTAAA
1 TTTAAAATAAATTCACAAATTTAAA
20120209 TTTAAAA-AATATT-ACAAAATTTAAA
1 TTTAAAATAA-ATTCAC-AAATTTAAA
20120234 ATATTCTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (25 bp):
TTTAAAATAAATTCACAAATTTAAA
Found at i:20124803 original size:3 final size:3
Alignment explanation
Indices: 20124795--20124823 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20124785 TATGAGTAAT
20124795 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20124824 CCAATTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20127647 original size:24 final size:25
Alignment explanation
Indices: 20127594--20127649 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
20127584 AGAAATGGTG
*
20127594 AGTTTTAGTATTAAGTAATACGATG
1 AGTTTTAGTATTAAGTAATACGATA
* *
20127619 CGTTTTA-TATTAAGCTAA-ACGGTA
1 AGTTTTAGTATTAAG-TAATACGATA
20127643 AGTTTTA
1 AGTTTTA
20127650 ACAGGCTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (25 bp):
AGTTTTAGTATTAAGTAATACGATA
Found at i:20127921 original size:20 final size:21
Alignment explanation
Indices: 20127879--20127921 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20127869 GATTATTTTA
*
20127879 AAAACTCAATTGACTTAATCC
1 AAAACTCAATTGACTTAACCC
20127900 AAAA-TCAACTTGACTT-ACCC
1 AAAACTCAA-TTGACTTAACCC
20127920 AA
1 AA
20127922 TTGATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAACTCAATTGACTTAACCC
Found at i:20132663 original size:25 final size:25
Alignment explanation
Indices: 20132635--20132684 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
20132625 TACAGAATAT
20132635 TTTAAATTT-TGTAATATT-TTTTAAA
1 TTTAAATTTGTG-AAT-TTATTTTAAA
20132660 TTTAAATTTGTGAATTTATTTTAAA
1 TTTAAATTTGTGAATTTATTTTAAA
20132685 ATTTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 2 0.09
25 19 0.83
26 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (25 bp):
TTTAAATTTGTGAATTTATTTTAAA
Found at i:20138917 original size:25 final size:24
Alignment explanation
Indices: 20138861--20138917 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
20138851 TGTTTCATAT
*
20138861 AACTCACCGTTTAGCTTAATATAA
1 AACTCACCATTTAGCTTAATATAA
*
20138885 AACGCACCATATTA-CTTAATACTAA
1 AACTCACCAT-TTAGCTTAATA-TAA
20138910 AACTCACC
1 AACTCACC
20138918 GTTTGGAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.28
Consensus pattern (24 bp):
AACTCACCATTTAGCTTAATATAA
Found at i:20144229 original size:209 final size:211
Alignment explanation
Indices: 20143823--20144248 Score: 757
Period size: 209 Copynumber: 2.0 Consensus size: 211
20143813 CCAAACTAAA
* * * * *
20143823 CAGCAATTTCACACCAAAATTTGGACAGCATATATACAACAATTTAGGCAGCATATATACAACAT
1 CAGCATTTTCACACCAAAAATTGGACAGCATATATACAACAAATTAGGCAGCAAATATACAACAA
20143888 ATTGAGCAGCATTTTTGCACCAAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACAC
66 ATTGAGCAGCATTTTTGCACCAAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACAC
*
20143953 AACAAATTGAGTAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAA
131 AACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAA
20144018 TATACAACAAATTGAG
196 TATACAACAAATTGAG
* *
20144034 CAGCATTTTTACACCAAAAATT-GACAGCTTATATACAACAAATT-GGCAGCAAATATACAACAA
1 CAGCATTTTCACACCAAAAATTGGACAGCATATATACAACAAATTAGGCAGCAAATATACAACAA
20144097 ATTGAGCAGCATTTTTGCACCAAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACAC
66 ATTGAGCAGCATTTTTGCACCAAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACAC
*
20144162 AACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAA
131 AACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAA
20144227 TATACAACAAATTGAG
196 TATACAACAAATTGAG
20144243 CAGCAT
1 CAGCAT
20144249 ATATATACAA
Statistics
Matches: 206, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
209 167 0.81
210 20 0.10
211 19 0.09
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (211 bp):
CAGCATTTTCACACCAAAAATTGGACAGCATATATACAACAAATTAGGCAGCAAATATACAACAA
ATTGAGCAGCATTTTTGCACCAAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACAC
AACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAA
TATACAACAAATTGAG
Found at i:20144245 original size:23 final size:22
Alignment explanation
Indices: 20143843--20144273 Score: 290
Period size: 23 Copynumber: 18.5 Consensus size: 22
20143833 ACACCAAAAT
*
20143843 TTGGACAGCATATATACAACAAT
1 TTGG-CAGCATATATACAACAAA
*
20143866 TTAGGCAGCATATATACAACATA
1 TT-GGCAGCATATATACAACAAA
* * * *
20143889 TTGAGCAGCATTTTTGCACCAAAA
1 TTG-GCAGCATATATACAAC-AAA
* *
20143913 TTGGACAGCTTATACACAACAAA
1 TTGG-CAGCATATATACAACAAA
*
20143936 TTGGACAGCA-ATTACACAACAAA
1 TTGG-CAGCATA-TATACAACAAA
* * * *
20143959 TTGAGTAGCATTTTTACACCAAAAA
1 TTG-GCAGCATATATACA--ACAAA
* *
20143984 TTGGACAGCTTATATAAAACAAA
1 TTGG-CAGCATATATACAACAAA
*
20144007 TTGGCAGCAAATATACAACAAA
1 TTGGCAGCATATATACAACAAA
* * *
20144029 TTGAGCAGCATTTTTACACCAAAAA
1 TTG-GCAGCATATATACA--ACAAA
* *
20144054 TTGACAGCTTATATACAACAAA
1 TTGGCAGCATATATACAACAAA
*
20144076 TTGGCAGCAAATATACAACAAA
1 TTGGCAGCATATATACAACAAA
* * * *
20144098 TTGAGCAGCATTTTTGCACCAAAA
1 TTG-GCAGCATATATACAAC-AAA
* *
20144122 TTGGACAGCTTATACACAACAAA
1 TTGG-CAGCATATATACAACAAA
*
20144145 TTGGACAGCA-ATTACACAACAAA
1 TTGG-CAGCATA-TATACAACAAA
* * *
20144168 TTGAGCAGCATTTTTACACCAAAAA
1 TTG-GCAGCATATATACA--ACAAA
*
20144193 TTGGACAGCTTATATACAACAAA
1 TTGG-CAGCATATATACAACAAA
*
20144216 TTGGCAGCAAATATACAACAAA
1 TTGGCAGCATATATACAACAAA
*
20144238 TTGAGCAGCATATATATACAAGAAA
1 TTG-GCAGC--ATATATACAACAAA
20144263 TTGTGCAGCAT
1 TTG-GCAGCAT
20144274 TTAAGCATAA
Statistics
Matches: 318, Mismatches: 65, Indels: 50
0.73 0.15 0.12
Matches are distributed among these distances:
22 66 0.21
23 148 0.47
24 45 0.14
25 59 0.19
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.25
Consensus pattern (22 bp):
TTGGCAGCATATATACAACAAA
Found at i:20144265 original size:70 final size:70
Alignment explanation
Indices: 20143823--20144248 Score: 651
Period size: 70 Copynumber: 6.1 Consensus size: 70
20143813 CCAAACTAAA
* * * * * * *
20143823 CAGCAATTTCACACCAAAATTTGGACAGCATATATACAACAATTTAGGCAGCATATATACAACAT
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATT-GGCAGCAAATATACAACAA
20143888 ATTGAG
65 ATTGAG
* * * *
20143894 CAGCATTTTTGCACC-AAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACACAACAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGG-CAGCAAATATACAACAA
20143958 ATTGAG
65 ATTGAG
* *
20143964 TAGCATTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAATATACAACAAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
20144029 TTGAG
66 TTGAG
20144034 CAGCATTTTTACACCAAAAATT-GACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
20144098 TTGAG
66 TTGAG
* * * *
20144103 CAGCATTTTTGCACC-AAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACACAACAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGG-CAGCAAATATACAACAA
20144167 ATTGAG
65 ATTGAG
20144173 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
20144238 TTGAG
66 TTGAG
20144243 CAGCAT
1 CAGCAT
20144249 ATATATACAA
Statistics
Matches: 323, Mismatches: 27, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
68 6 0.02
69 85 0.26
70 161 0.50
71 71 0.22
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (70 bp):
CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
TTGAG
Found at i:20145033 original size:28 final size:28
Alignment explanation
Indices: 20145001--20145098 Score: 160
Period size: 28 Copynumber: 3.5 Consensus size: 28
20144991 TTTAATAAGT
** * *
20145001 TCGCACACTTAGTGCTCAATAATCAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
20145029 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
20145057 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
20145085 TCGCACACTTAGTG
1 TCGCACACTTAGTG
20145099 TCGAAAGTCA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.30
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:20145906 original size:15 final size:14
Alignment explanation
Indices: 20145886--20145941 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 14
20145876 ATGTTTTGTT
20145886 TTATTATAACATATA
1 TTATTATAA-ATATA
*
20145901 TTATTAT-ATTATTA
1 TTATTATAAATA-TA
*
20145915 TTATTTTAAAT-T-
1 TTATTATAAATATA
20145927 TTATTATAAATATA
1 TTATTATAAATATA
20145941 T
1 T
20145942 ATATATCACA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
12 10 0.30
13 4 0.12
14 10 0.30
15 9 0.27
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTATAAATATA
Found at i:20147868 original size:29 final size:29
Alignment explanation
Indices: 20147822--20147884 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
20147812 TGGTGCCTTT
*
20147822 GAACCAATAACTCAGATA-TCACTTGGTTC
1 GAACCAACAACTCAGATACT-ACTTGGTTC
* *
20147851 GAACCAACAGCTCGGATACTACTTGGTTC
1 GAACCAACAACTCAGATACTACTTGGTTC
*
20147880 CAACC
1 GAACC
20147885 TTGGCTCGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (29 bp):
GAACCAACAACTCAGATACTACTTGGTTC
Found at i:20156157 original size:23 final size:23
Alignment explanation
Indices: 20156131--20156179 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
20156121 TAATGACATA
20156131 AAAATGAAAATTTAAATTATTCC
1 AAAATGAAAATTTAAATTATTCC
20156154 AAAATGAAAATTTAAATTATTCC
1 AAAATGAAAATTTAAATTATTCC
20156177 AAA
1 AAA
20156180 TTAAAACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAATGAAAATTTAAATTATTCC
Found at i:20161718 original size:2 final size:2
Alignment explanation
Indices: 20161678--20161705 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20161668 TTAGAATGGC
20161678 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
20161706 TTTTCATTCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20162752 original size:59 final size:60
Alignment explanation
Indices: 20162681--20162867 Score: 218
Period size: 59 Copynumber: 3.0 Consensus size: 60
20162671 TTATAAAATT
20162681 AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTACTTCATTTAA
1 AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTACTTCATTTAA
*
20162741 AA-AAATTGTTTATAATTAAAAAATTATGCCACCTATATTT-AAAATTTACTTCATTTTTCAAAA
1 AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTACTTCA---TT-----
20162804 AAATAA
58 ---TAA
* *
20162810 AATAAATTGTTTATAATTAAAAAATCATGCCACCTATATTTAAACAATTAAC-TCATTT
1 AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATT-ACTTCATTT
20162868 CTATACTCAG
Statistics
Matches: 109, Mismatches: 4, Indels: 28
0.77 0.03 0.20
Matches are distributed among these distances:
58 12 0.11
59 38 0.35
60 3 0.03
61 2 0.02
68 2 0.02
69 5 0.05
70 37 0.34
71 8 0.07
72 2 0.02
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (60 bp):
AATAAATTGTTTATAATTAAAAAATTATGCCACCTATATTTAAAAAATTACTTCATTTAA
Found at i:20163584 original size:19 final size:20
Alignment explanation
Indices: 20163562--20163601 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
20163552 GAAGATAAAA
*
20163562 TAAAATATAAAAG-AAATGG
1 TAAAAAATAAAAGAAAATGG
20163581 TAAAAAATAAAAGAAAATGG
1 TAAAAAATAAAAGAAAATGG
20163601 T
1 T
20163602 TTTTTTGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
TAAAAAATAAAAGAAAATGG
Found at i:20167618 original size:40 final size:40
Alignment explanation
Indices: 20167566--20167680 Score: 144
Period size: 40 Copynumber: 2.9 Consensus size: 40
20167556 TGGCGTTTGG
*
20167566 ACAAAAAACGCCGCTAAAAATCGAGCATTAGTGGCGCTTT
1 ACAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
* * * *
20167606 ACACAAAACGCCGCTAAAGATCGAGCTTTAGCGGCGCTAT
1 ACAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
* *
20167646 -CAGGAAACCGCCGCTAAAAAT-GAGCATTAGCGGCG
1 ACA-AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG
20167681 TTTTTTGTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 15 0.23
40 50 0.77
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (40 bp):
ACAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
Found at i:20167857 original size:41 final size:41
Alignment explanation
Indices: 20167737--20168058 Score: 504
Period size: 41 Copynumber: 7.9 Consensus size: 41
20167727 TTCAGACCTT
* * *
20167737 TCAGGGCTTTAGTGGCG-TTTTAAAAAAGCGCCACTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* *
20167777 TCAGGGCTTTAGCGGCGTTTTTTGGAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAATGC
* * *
20167819 TCAGGGCTTTAGCGGTGTTTTTGGAAAAGCGCCACTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
20167860 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
20167901 TCAGGGCTTTAACGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
20167942 TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
20167983 TCAAGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
20168024 TCAGGGCTTTAGCGGTGTTTTGTG-AAAAGCGCCGC
1 TCAGGGCTTTAGCGGCGTTTT-TGAAAAAGCGCCGC
20168059 AAAAACATTT
Statistics
Matches: 263, Mismatches: 16, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
40 16 0.06
41 210 0.80
42 37 0.14
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (41 bp):
TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:20168402 original size:14 final size:14
Alignment explanation
Indices: 20168385--20168421 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
20168375 GGGTTTAATA
20168385 TATATGATTTAGGG
1 TATATGATTTAGGG
* *
20168399 TATATGGTTTGGGG
1 TATATGATTTAGGG
20168413 TATATGATT
1 TATATGATT
20168422 AATTTAGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TATATGATTTAGGG
Found at i:20168633 original size:73 final size:69
Alignment explanation
Indices: 20168571--20168702 Score: 184
Period size: 68 Copynumber: 2.0 Consensus size: 69
20168561 TGGATTCGGT
*
20168571 GTTA-GGTTAAGG-TTTATGGTTTAAATTAATTA-CTGTATTTTAA-TT-TATATTAAATAAGGT
1 GTTAGGGTTAAGGATTTAGGGTTTAAATTAATTAGCT-T-TTTTAATTTATATATTAAATAAGGT
20168631 TTATAG
64 TTATAG
* *
20168637 GTTAGGGTTTAGGATTTAGGGTTTAGATTAATTAGCTTTTTTAATTTATATATTAAATAAGGTTT
1 GTTAGGGTTAAGGATTTAGGGTTTAAATTAATTAGCTTTTTTAATTTATATATTAAATAAGGTTT
20168702 A
66 A
20168703 GCGTTTTTAG
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
66 4 0.07
67 13 0.22
68 21 0.36
69 20 0.34
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (69 bp):
GTTAGGGTTAAGGATTTAGGGTTTAAATTAATTAGCTTTTTTAATTTATATATTAAATAAGGTTT
ATAG
Found at i:20174294 original size:43 final size:43
Alignment explanation
Indices: 20174240--20174536 Score: 195
Period size: 43 Copynumber: 6.7 Consensus size: 43
20174230 GTCAATGTTA
* * **
20174240 TAGCGGTGTTTTTAGTAGAAGCACCGCTAAAGGTCA-TGAG-CTT
1 TAGCGGCGTTTTTAGTAAAAGCGTCGCTAAAGGT-ATTG-GTCTT
**
20174283 TAGCGGCGTTTTGGGTAAAAGCGTCGCTAAAGGTATTGGTCTT
1 TAGCGGCGTTTTTAGTAAAAGCGTCGCTAAAGGTATTGGTCTT
* * *
20174326 TAGCGGTGATTTTAGAAAAAGCGTCGCTAAAGGTATTGGTCTT
1 TAGCGGCGTTTTTAGTAAAAGCGTCGCTAAAGGTATTGGTCTT
* * * * * **
20174369 TAGCGGCGATTCT-GCGAAAAGCATCGCTAAAGCTAAAGGTCCAAGTCTT
1 TAGCGGCGTTTTTAG-TAAAAGCGTCGCTAAAGGT--A--T--TGGTCTT
* * * * *
20174418 TAGCGGCGTTTTTGGGAAAAGCGCCACTAAAGGTCTTGGTCTT
1 TAGCGGCGTTTTTAGTAAAAGCGTCGCTAAAGGTATTGGTCTT
* * * * * * * *
20174461 TAGCGGCGTTTGTGGGACAAGTGCCGCTAAAGGTCTTGGTATT
1 TAGCGGCGTTTTTAGTAAAAGCGTCGCTAAAGGTATTGGTCTT
** *
20174504 TAGCGGCGTTTTTTTCTAAAAGCGCCGCTAAAG
1 TAGCGGCG-TTTTTAGTAAAAGCGTCGCTAAAG
20174537 TTAGCGACGC
Statistics
Matches: 205, Mismatches: 38, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
42 3 0.01
43 149 0.73
44 18 0.09
45 2 0.01
47 1 0.00
49 31 0.15
50 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
TAGCGGCGTTTTTAGTAAAAGCGTCGCTAAAGGTATTGGTCTT
Found at i:20174307 original size:85 final size:86
Alignment explanation
Indices: 20174212--20174399 Score: 197
Period size: 86 Copynumber: 2.2 Consensus size: 86
20174202 TGACGTTTGT
* * *
20174212 GAAAATGCGTCGCTAAAAGTCAAT-GT-TATAGCGGTGTTTTTAGTAGAAGCACCGCTAAAGGTC
1 GAAAA-GCGTCGCTAAAAGT-AATGGTCTATAGCGGTGATTTTAGAAAAAGCACCGCTAAAGGT-
* *
20174275 A-TGAG-CTTTAGCGGCG-TTTTGG
63 ATTG-GTCTTTAGCGGCGATTCTGC
* * * **
20174297 GTAAAAGCGTCGCTAAAGGTATTGGTCTTTAGCGGTGATTTTAGAAAAAGCGTCGCTAAAGGTAT
1 G-AAAAGCGTCGCTAAAAGTAATGGTCTATAGCGGTGATTTTAGAAAAAGCACCGCTAAAGGTAT
20174362 TGGTCTTTAGCGGCGATTCTGC
65 TGGTCTTTAGCGGCGATTCTGC
*
20174384 GAAAAGCATCGCTAAA
1 GAAAAGCGTCGCTAAA
20174400 GCTAAAGGTC
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
84 2 0.02
85 18 0.21
86 61 0.71
87 5 0.06
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (86 bp):
GAAAAGCGTCGCTAAAAGTAATGGTCTATAGCGGTGATTTTAGAAAAAGCACCGCTAAAGGTATT
GGTCTTTAGCGGCGATTCTGC
Found at i:20177137 original size:16 final size:16
Alignment explanation
Indices: 20177112--20177252 Score: 99
Period size: 16 Copynumber: 8.3 Consensus size: 16
20177102 CGAGAAATTT
*
20177112 TTTTTAAAACACGATAA
1 TTTTTGAAACACGA-AA
20177129 -TTTTGAAACAC-AATA
1 TTTTTGAAACACGAA-A
20177144 TTTTTTGAAGACACGGAAA
1 -TTTTTGAA-ACAC-GAAA
*
20177163 TTTTTTAAACA-GAGGAA
1 TTTTTGAAACACGA--AA
20177180 TTTTTTGAAACACGAAA
1 -TTTTTGAAACACGAAA
* *
20177197 CTTTTGAAACATGAAAAA
1 TTTTTGAAACACG--AAA
*
20177215 TTTTTGAAAACATGAAA
1 TTTTTG-AAACACGAAA
* *
20177232 ATTTTGAAACACGAGA
1 TTTTTGAAACACGAAA
20177248 TTTTT
1 TTTTT
20177253 TAAAAGGACG
Statistics
Matches: 101, Mismatches: 10, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
14 1 0.01
15 4 0.04
16 33 0.33
17 22 0.22
18 29 0.29
19 10 0.10
20 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (16 bp):
TTTTTGAAACACGAAA
Found at i:20177166 original size:18 final size:17
Alignment explanation
Indices: 20177112--20177244 Score: 80
Period size: 18 Copynumber: 7.8 Consensus size: 17
20177102 CGAGAAATTT
*
20177112 TTTTTAAAACAC-GATAA
1 TTTTTGAAACACGGA-AA
20177129 -TTTTGAAACAC--AATA
1 TTTTTGAAACACGGAA-A
20177144 TTTTTTGAAGACACGGAAA
1 -TTTTTGAA-ACACGGAAA
* * *
20177163 TTTTTTAAACAGAGGAAT
1 TTTTTGAAACA-CGGAAA
20177181 TTTTTGAAACAC-GAAA
1 TTTTTGAAACACGGAAA
* * *
20177197 CTTTTGAAACATGAAAAA
1 TTTTTGAAACACG-GAAA
*
20177215 TTTTTGAAA-ACATGAAA
1 TTTTTGAAACAC-GGAAA
*
20177232 ATTTTGAAACACG
1 TTTTTGAAACACG
20177245 AGATTTTTTA
Statistics
Matches: 89, Mismatches: 16, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
14 1 0.01
15 2 0.02
16 23 0.26
17 22 0.25
18 38 0.43
19 1 0.01
20 2 0.02
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGGAAA
Found at i:20177167 original size:19 final size:18
Alignment explanation
Indices: 20177129--20177253 Score: 79
Period size: 17 Copynumber: 7.2 Consensus size: 18
20177119 AACACGATAA
20177129 TTTTGAAACAC--AATATT
1 TTTTGAAACACGGAA-ATT
20177146 TTTTGAAGACACGGAAATT
1 TTTTGAA-ACACGGAAATT
*
20177165 TTTT-AAACA-GAGGAATT
1 TTTTGAAACACG-GAAATT
*
20177182 TTTTGAAACAC-GAAA-C
1 TTTTGAAACACGGAAATT
* * *
20177198 TTTTGAAACATGAAAAAT
1 TTTTGAAACACGGAAATT
* *
20177216 TTTTGAAA-ACATGAAA-A
1 TTTTGAAACAC-GGAAATT
*
20177233 TTTTGAAACAC-GAGATT
1 TTTTGAAACACGGAAATT
20177250 TTTT
1 TTTT
20177254 AAAAGGACGT
Statistics
Matches: 85, Mismatches: 12, Indels: 22
0.71 0.10 0.18
Matches are distributed among these distances:
16 14 0.16
17 38 0.45
18 24 0.28
19 7 0.08
20 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (18 bp):
TTTTGAAACACGGAAATT
Found at i:20177217 original size:35 final size:33
Alignment explanation
Indices: 20177111--20177242 Score: 115
Period size: 35 Copynumber: 3.8 Consensus size: 33
20177101 ACGAGAAATT
* * *
20177111 TTTTTTAAAACACGATAATTTTGAAACA-CAATA
1 TTTTTTGAAACACGA-AATTTTGAAACAGAAAAA
* **
20177144 TTTTTTGAAGACACGGAAATTTTTTAAACAGAGGAA
1 TTTTTTGAA-ACAC-GAAA-TTTTGAAACAGAAAAA
20177180 TTTTTTGAAACACGAAACTTTTGAAACATGAAAAA
1 TTTTTTGAAACACGAAA-TTTTGAAACA-GAAAAA
*
20177215 -TTTTTGAAAACATGAAAATTTTGAAACA
1 TTTTTTG-AAACACG-AAATTTTGAAACA
20177243 CGAGATTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
33 8 0.10
34 25 0.31
35 35 0.43
36 13 0.16
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (33 bp):
TTTTTTGAAACACGAAATTTTGAAACAGAAAAA
Found at i:20177735 original size:10 final size:9
Alignment explanation
Indices: 20177716--20177741 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
20177706 GGTTTTTTCC
20177716 TTTTTCTTT
1 TTTTTCTTT
20177725 TTTTTCTTT
1 TTTTTCTTT
20177734 TTTTTCTT
1 TTTTTCTT
20177742 CCTCTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:20177806 original size:14 final size:14
Alignment explanation
Indices: 20177787--20177813 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20177777 GGCACTCATG
20177787 GGCCTACTGCTGGT
1 GGCCTACTGCTGGT
20177801 GGCCTACTGCTGG
1 GGCCTACTGCTGG
20177814 CACTGGGATG
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:0.07, C:0.30, G:0.37, T:0.26
Consensus pattern (14 bp):
GGCCTACTGCTGGT
Found at i:20178037 original size:4 final size:4
Alignment explanation
Indices: 20178030--20178106 Score: 72
Period size: 4 Copynumber: 19.0 Consensus size: 4
20178020 TTTTTATTTT
*
20178030 TTTC TTTCC CTTTC -TTC TTCC TTGTC CTTTC -TTC TTTC TTTC TTTC
1 TTTC TTT-C -TTTC TTTC TTTC TT-TC -TTTC TTTC TTTC TTTC TTTC
20178076 TTTC -TTC TCTT- TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC
20178107 ACGATCAGCG
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
3 11 0.18
4 39 0.63
5 7 0.11
6 5 0.08
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:20178080 original size:19 final size:19
Alignment explanation
Indices: 20178056--20178106 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 19
20178046 CTTCCTTGTC
20178056 CTTTCTTCTTTCTTTCTTT
1 CTTTCTTCTTTCTTTCTTT
20178075 CTTTCTTCTCTT-TTTCTTT
1 CTTTCTTCT-TTCTTTCTTT
20178094 CTTTCTTTCTTTC
1 CTTTC-TTCTTTC
20178107 ACGATCAGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
CTTTCTTCTTTCTTTCTTT
Found at i:20178098 original size:27 final size:28
Alignment explanation
Indices: 20178028--20178106 Score: 99
Period size: 27 Copynumber: 2.8 Consensus size: 28
20178018 TTTTTTTATT
* *
20178028 TTTTTCTTTCCCTTTC-TTCTTCCTTGTCC
1 TTTTTCTTT--CTTTCTTTCTTTCTTCTCC
20178057 TTTCTTCTTTCTTTCTTTCTTTCTTCT-C
1 TTT-TTCTTTCTTTCTTTCTTTCTTCTCC
20178085 TTTTTCTTTCTTTCTTTCTTTC
1 TTTTTCTTTCTTTCTTTCTTTC
20178107 ACGATCAGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 19 0.41
28 9 0.20
29 12 0.26
30 6 0.13
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (28 bp):
TTTTTCTTTCTTTCTTTCTTTCTTCTCC
Found at i:20178634 original size:29 final size:29
Alignment explanation
Indices: 20178590--20178733 Score: 135
Period size: 30 Copynumber: 4.9 Consensus size: 29
20178580 AATATCGTAA
* * **
20178590 AAATTTTAGGGCTAAAGTGTAATTTTGGG
1 AAATTTTAGGGTTAAAATGTAATTTTAAG
*
20178619 AAATTTTAGGGTTAAAATGTAATTCTAAG
1 AAATTTTAGGGTTAAAATGTAATTTTAAG
* *
20178648 AAAGTTTAAGGGTTAAAATGCAATTTTAAG
1 AAA-TTTTAGGGTTAAAATGTAATTTTAAG
* * * *
20178678 AAAGTTTAGAGGTTGAAATGTAATTTCAAA
1 AAATTTTAG-GGTTAAAATGTAATTTTAAG
* * * *
20178708 AAAGTTAAAGGTCAAAATGTAATTTT
1 AAATTTTAGGGTTAAAATGTAATTTT
20178734 TTTTAAAAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
29 45 0.48
30 49 0.52
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.35
Consensus pattern (29 bp):
AAATTTTAGGGTTAAAATGTAATTTTAAG
Found at i:20178712 original size:60 final size:58
Alignment explanation
Indices: 20178618--20178733 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 58
20178608 GTAATTTTGG
* * * *
20178618 GAAATTTTAGGGTTAAAATGTAATTCTAAGAAAGTTTAAGGGTTAAAATGCAATTTTAA
1 GAAAGTTTAGGGTTAAAATGTAATTCTAAAAAAG-TTAAAGGTCAAAATGCAATTTTAA
* *
20178677 GAAAGTTTAGAGGTTGAAATGTAATT-TCAAAAAAGTTAAAGGTCAAAATGTAATTTT
1 GAAAGTTTAG-GGTTAAAATGTAATTCT-AAAAAAGTTAAAGGTCAAAATGCAATTTT
20178734 TTTTAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 29 0.59
60 20 0.41
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.34
Consensus pattern (58 bp):
GAAAGTTTAGGGTTAAAATGTAATTCTAAAAAAGTTAAAGGTCAAAATGCAATTTTAA
Found at i:20181258 original size:27 final size:27
Alignment explanation
Indices: 20181228--20181306 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
20181218 TTGCCAATTA
* * * *
20181228 GTTTGGCAAGCTGGAGTTCACTAGTTG
1 GTTTGGCGAGCTGGGGTTCACCAGTAG
* *
20181255 GTTTGGCGAGTTGGGGTTCGCCAGTAG
1 GTTTGGCGAGCTGGGGTTCACCAGTAG
*
20181282 GTTTTGCGAGCTGGGGTTCACCAGT
1 GTTTGGCGAGCTGGGGTTCACCAGT
20181307 CTAAGTCAAG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.14, C:0.16, G:0.38, T:0.32
Consensus pattern (27 bp):
GTTTGGCGAGCTGGGGTTCACCAGTAG
Found at i:20181897 original size:14 final size:16
Alignment explanation
Indices: 20181880--20181911 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20181870 TCAAGTTGTG
20181880 TTTTT-AAGTTAT-TT
1 TTTTTAAAGTTATGTT
20181894 TTTTTAAAGTTATGTT
1 TTTTTAAAGTTATGTT
20181910 TT
1 TT
20181912 ATGCGTGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 7 0.44
16 4 0.25
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (16 bp):
TTTTTAAAGTTATGTT
Found at i:20184943 original size:25 final size:25
Alignment explanation
Indices: 20184895--20184943 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
20184885 CATAATTGAA
* * *
20184895 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
20184920 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
20184944 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:20185408 original size:43 final size:43
Alignment explanation
Indices: 20185339--20185420 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
20185329 TATGTGATTG
* *
20185339 ATATTGAAATGAAAAAGATTAGAAATGAATATGAGATGAAAAA
1 ATATTGAAATGAAAAAGATGAAAAATGAATATGAGATGAAAAA
* * *
20185382 ATATTGAAATGACAAATATGAAAAATGATTATGAGATGA
1 ATATTGAAATGAAAAAGATGAAAAATGAATATGAGATGA
20185421 GAAATGAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.55, C:0.01, G:0.18, T:0.26
Consensus pattern (43 bp):
ATATTGAAATGAAAAAGATGAAAAATGAATATGAGATGAAAAA
Found at i:20186344 original size:30 final size:30
Alignment explanation
Indices: 20186310--20186384 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
20186300 CACGGCTTGG
* *
20186310 ACACACGGGCGTGTGTCACACACGGGCAAC
1 ACACATGGGCGTGTGTCACACACAGGCAAC
*
20186340 ACACATGGGCATGTGTCACACACAGGCAAC
1 ACACATGGGCGTGTGTCACACACAGGCAAC
20186370 ACACATGGGCGTGTG
1 ACACATGGGCGTGTG
20186385 ACCCAAGTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.13
Consensus pattern (30 bp):
ACACATGGGCGTGTGTCACACACAGGCAAC
Found at i:20191678 original size:2 final size:2
Alignment explanation
Indices: 20191671--20191708 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20191661 CAAGGCTCAC
20191671 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
20191709 GATGATTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:20201036 original size:166 final size:166
Alignment explanation
Indices: 20200762--20201096 Score: 580
Period size: 166 Copynumber: 2.0 Consensus size: 166
20200752 AAGTTTTGAG
20200762 TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTT
1 TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTT
*
20200827 CAGGATCTTATGACTCTCTTGTGTTCTTCTTTTAGGAAATCTTTGAGCATTTTCATGTAATCATT
66 CAGGATCTTATGACTCTCTTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
20200892 GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
131 GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
* * **
20200928 TAAGGAACTGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTTATTTTTGATGACTTT
1 TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTT
* * *
20200993 GAGGATCTTATGACTCTGTTGTGTTCTTCTTTTAGGAAATCTTTCTGCATTTTCATGTAATCATT
66 CAGGATCTTATGACTCTCTTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
* *
20201058 GTGATTGTCTAGTTGTCTTCTCTAATTTCTTTTAAT
131 GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
20201094 TAA
1 TAA
20201097 TGTTAATTTT
Statistics
Matches: 159, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
166 159 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (166 bp):
TAAGGAAATGGTCATAACTTGATGTTTAATGGTGTGGGAATAAAATCTTCATTTCAGATGACTTT
CAGGATCTTATGACTCTCTTGTGTTCTTCTTTTAGGAAATCTTTCAGCATTTTCATGTAATCATT
GCGATTGTCTAGTTGTCTTCCCTAATTTCTTTTAAT
Found at i:20210985 original size:81 final size:81
Alignment explanation
Indices: 20210850--20211019 Score: 331
Period size: 81 Copynumber: 2.1 Consensus size: 81
20210840 ACTGAAAACG
20210850 AAGTGCATTACCAGATAAATCGAAATAGGGTAAACTAGCATGTAAGTGCATACTAGCGCATACAA
1 AAGTGCATTACCAGATAAATCGAAATAGGGTAAACTAGCATGTAAGTGCATACTAGCGCATACAA
20210915 CGCATCCTGGCGCACA
66 CGCATCCTGGCGCACA
*
20210931 AAGTGCATTACCAGATAAATCGAAATAGGGTAAACTGGCATGTAAGTGCATACTAGCGCATACAA
1 AAGTGCATTACCAGATAAATCGAAATAGGGTAAACTAGCATGTAAGTGCATACTAGCGCATACAA
20210996 CGCATCCTGGCGCACA
66 CGCATCCTGGCGCACA
20211012 AAGTGCAT
1 AAGTGCAT
20211020 ATTTGGCACA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 88 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (81 bp):
AAGTGCATTACCAGATAAATCGAAATAGGGTAAACTAGCATGTAAGTGCATACTAGCGCATACAA
CGCATCCTGGCGCACA
Found at i:20211280 original size:21 final size:21
Alignment explanation
Indices: 20211248--20211298 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
20211238 TATTCTCACT
20211248 CAATTCCATAACATATTTCAGA
1 CAATT-CATAACATATTTCAGA
20211270 CAATTCATAACATATTTCAGA
1 CAATTCATAACATATTTCAGA
20211291 CAATTCAT
1 CAATTCAT
20211299 GCTATTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (21 bp):
CAATTCATAACATATTTCAGA
Found at i:20214438 original size:68 final size:64
Alignment explanation
Indices: 20214287--20214444 Score: 192
Period size: 64 Copynumber: 2.4 Consensus size: 64
20214277 TATATATTTT
* * *
20214287 AAAGTTCTTGAGCTGAAATTAATGTACGAATTTTATATACATATGTGATTCAAATATAGGTTAT
1 AAAGTTCTTGAGCTGAATTTAATGTACGAATTTTACATACATATGTGATTCAAATATAGGTTAC
* * *
20214351 AAAGTTCTTGAGCTGAATTTAATTTATGAATTTTACATACATATGTGTATGGTTCGAATATAGGT
1 AAAGTTCTTGAGCTGAATTTAATGTACGAATTTTACATACATATGTG-A---TTCAAATATAGGT
20214416 TAC
62 TAC
*
20214419 AAA-TTCTTTGAACTGAATTTTAATGT
1 AAAGTTC-TTGAGCTGAA-TTTAATGT
20214445 TGTAAATTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
64 43 0.54
65 1 0.01
67 3 0.04
68 26 0.32
69 7 0.09
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAATGTACGAATTTTACATACATATGTGATTCAAATATAGGTTAC
Found at i:20214543 original size:41 final size:41
Alignment explanation
Indices: 20214485--20214579 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
20214475 TTGAAATTTT
*
20214485 CAGGC-TTGATGCCGGTG-AAT-TAATTCAGACTTTATGTCTAG
1 CAGGCTTTG-TGCCGGTGAAATGT-A-TCAGACTTTATGCCTAG
* * *
20214526 GAGGCTTTGTGCCGGTGAAATGTATCAGGCTTTGTGCCTAG
1 CAGGCTTTGTGCCGGTGAAATGTATCAGACTTTATGCCTAG
20214567 CAGGCTTTGTGCC
1 CAGGCTTTGTGCC
20214580 TAGCAGGCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
41 38 0.83
42 7 0.15
43 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (41 bp):
CAGGCTTTGTGCCGGTGAAATGTATCAGACTTTATGCCTAG
Found at i:20214572 original size:16 final size:16
Alignment explanation
Indices: 20214551--20214590 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
20214541 TGAAATGTAT
20214551 CAGGCTTTGTGCCTAG
1 CAGGCTTTGTGCCTAG
20214567 CAGGCTTTGTGCCTAG
1 CAGGCTTTGTGCCTAG
20214583 CAGGCTTT
1 CAGGCTTT
20214591 ACGCCGGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.12, C:0.25, G:0.30, T:0.33
Consensus pattern (16 bp):
CAGGCTTTGTGCCTAG
Found at i:20222219 original size:68 final size:64
Alignment explanation
Indices: 20222068--20222225 Score: 192
Period size: 64 Copynumber: 2.4 Consensus size: 64
20222058 TATATATTTT
* * *
20222068 AAAGTTCTTGAGCTGAAATTAATGTACGAATTTTATATACATATGTGATTCAAATATAGGTTAT
1 AAAGTTCTTGAGCTGAATTTAATGTACGAATTTTACATACATATGTGATTCAAATATAGGTTAC
* * *
20222132 AAAGTTCTTGAGCTGAATTTAATTTATGAATTTTACATACATATGTGTATGGTTCGAATATAGGT
1 AAAGTTCTTGAGCTGAATTTAATGTACGAATTTTACATACATATGTG-A---TTCAAATATAGGT
20222197 TAC
62 TAC
*
20222200 AAA-TTCTTTGAACTGAATTTTAATGT
1 AAAGTTC-TTGAGCTGAA-TTTAATGT
20222226 TGTAAATTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
64 43 0.54
65 1 0.01
67 3 0.04
68 26 0.32
69 7 0.09
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAATGTACGAATTTTACATACATATGTGATTCAAATATAGGTTAC
Found at i:20222354 original size:16 final size:16
Alignment explanation
Indices: 20222332--20222371 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
20222322 TGAAATGTAT
20222332 CAGGCTTTGTGCCTAG
1 CAGGCTTTGTGCCTAG
*
20222348 TAGGCTTTGTGCCTAG
1 CAGGCTTTGTGCCTAG
20222364 CAGGCTTT
1 CAGGCTTT
20222372 ACGCCGGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.23, G:0.30, T:0.35
Consensus pattern (16 bp):
CAGGCTTTGTGCCTAG
Found at i:20225804 original size:21 final size:20
Alignment explanation
Indices: 20225779--20225817 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
20225769 TAGAAATAAG
20225779 TATATAAATTAAATGCTAACA
1 TATATAAATTAAAT-CTAACA
* *
20225800 TATATCAATTGAATCTAA
1 TATATAAATTAAATCTAA
20225818 TCATGGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (20 bp):
TATATAAATTAAATCTAACA
Found at i:20226980 original size:20 final size:20
Alignment explanation
Indices: 20226955--20227092 Score: 77
Period size: 20 Copynumber: 6.9 Consensus size: 20
20226945 ATAGATGCGT
20226955 AACAGAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
*
20226975 AACAGAGGCA-C-AATTTTGCA
1 AACAGAGGCACCGAA--GTGCA
* * *
20226995 ATCAAAGGCA-CGATTGTGCA
1 AACAGAGGCACCGA-AGTGCA
** * **
20227015 ATGAGAGGCACTGCTGTGCA
1 AACAGAGGCACCGAAGTGCA
** *
20227035 AACAGAAACACCGAAGTGTA
1 AACAGAGGCACCGAAGTGCA
* *
20227055 AATAGAGGCACTGAAGTGCGA
1 AACAGAGGCACCGAAGTGC-A
*
20227076 AA-AGAGGCACTGAAGTG
1 AACAGAGGCACCGAAGTG
20227093 TAATCCCGTA
Statistics
Matches: 90, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 82 0.91
21 5 0.06
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.14
Consensus pattern (20 bp):
AACAGAGGCACCGAAGTGCA
Found at i:20228865 original size:42 final size:42
Alignment explanation
Indices: 20228818--20228898 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
20228808 TTTCGAACAG
20228818 ATTGGTTATTAAAACAATTCATTAATTACATTAATATACATT
1 ATTGGTTATTAAAACAATTCATTAATTACATTAATATACATT
20228860 ATTGGTTATTAAAACAATTCATTAATTACATTAATATAC
1 ATTGGTTATTAAAACAATTCATTAATTACATTAATATAC
20228899 TTTGTATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (42 bp):
ATTGGTTATTAAAACAATTCATTAATTACATTAATATACATT
Found at i:20235243 original size:38 final size:38
Alignment explanation
Indices: 20235189--20235287 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
20235179 ACCAGTAGGC
* ** *
20235189 CGAAGG-CCAGTAGATAACTGTTCGTACGGTGTTGCCT
1 CGAAGGACCAGTAGATAACCGTTCACACAGTGTTGCCT
*
20235226 CGAAGGACCAGTGGATAACCGTTCACACAGTGTTGCCT
1 CGAAGGACCAGTAGATAACCGTTCACACAGTGTTGCCT
* *
20235264 CGAAGGACGAGTAGATAGCCGTTC
1 CGAAGGACCAGTAGATAACCGTTC
20235288 CATGATTTCC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 6 0.11
38 47 0.89
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.22
Consensus pattern (38 bp):
CGAAGGACCAGTAGATAACCGTTCACACAGTGTTGCCT
Found at i:20241261 original size:7 final size:7
Alignment explanation
Indices: 20241258--20241300 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
20241248 AATAAAAAAG
20241258 AAAAGAA
1 AAAAGAA
20241265 AAAAGAA
1 AAAAGAA
20241272 AAAAGAA
1 AAAAGAA
20241279 AAAA-AA
1 AAAAGAA
20241285 AAGAA-AA
1 AA-AAGAA
20241292 AAAAGAA
1 AAAAGAA
20241299 AA
1 AA
20241301 TTAAATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:20241273 original size:18 final size:19
Alignment explanation
Indices: 20241251--20241293 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
20241241 AAATAACAAT
20241251 AAAAAAGAAAAGAAAAAAG
1 AAAAAAGAAAAGAAAAAAG
20241270 AAAAAAGAAAA-AAAAAAG
1 AAAAAAGAAAAGAAAAAAG
20241288 AAAAAA
1 AAAAAA
20241294 AAGAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAGAAAAAAG
Found at i:20241294 original size:19 final size:20
Alignment explanation
Indices: 20241251--20241300 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 20
20241241 AAATAACAAT
20241251 AAAAAAGAAAAGAAAAAAG-
1 AAAAAAGAAAAGAAAAAAGA
20241270 AAAAAAGAAAA-AAAAAAGAA
1 AAAAAAGAAAAGAAAAAAG-A
20241290 AAAAAAGAAAA
1 AAAAAAGAAAA
20241301 TTAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.24
19 11 0.38
20 11 0.38
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAGAAAAAAGA
Found at i:20241310 original size:19 final size:18
Alignment explanation
Indices: 20241227--20241300 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
20241217 ATAAATCCAG
* *
20241227 AAAAGAAGAAAAACAAATA
1 AAAAGAA-AAAAAAAAAAA
* * *
20241246 ACAATAAAAAAGAAAAGAA
1 AAAAGAAAAAA-AAAAAAA
*
20241265 AAAAGAAAAAAGAAAAAA
1 AAAAGAAAAAAAAAAAAA
20241283 AAAAGAAAAAAAAGAAAA
1 AAAAGAAAAAAAA-AAAA
20241301 TTAAATAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 21 0.49
19 22 0.51
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAAAA
Found at i:20243166 original size:9 final size:9
Alignment explanation
Indices: 20243152--20243178 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
20243142 ATATTTATAA
20243152 CTCATAAAC
1 CTCATAAAC
20243161 CTCATAAAC
1 CTCATAAAC
20243170 CTCATAAAC
1 CTCATAAAC
20243179 AAAAGCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (9 bp):
CTCATAAAC
Found at i:20247045 original size:20 final size:20
Alignment explanation
Indices: 20247020--20247059 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20247010 AACATTCAAA
20247020 ATACCATAATCACAA-CCAAG
1 ATACCATAA-CACAAGCCAAG
20247040 ATACCATAACACAAGCCAAG
1 ATACCATAACACAAGCCAAG
20247060 CCATATGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.50, C:0.30, G:0.07, T:0.12
Consensus pattern (20 bp):
ATACCATAACACAAGCCAAG
Found at i:20248186 original size:25 final size:25
Alignment explanation
Indices: 20248158--20248254 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 25
20248148 GTATGCGCAT
* * *
20248158 ACGAGTTATGAATCGGTATGCTCTC
1 ACGAGCTATAAATCGGTAAGCTCTC
20248183 ACGAGCTATAAATCGGTAAGCTCAT-
1 ACGAGCTATAAATCGGTAAGCTC-TC
* * *
20248208 ACGAGCTGA-GAATCGATAAGCTCTA
1 ACGAGCT-ATAAATCGGTAAGCTCTC
**
20248233 ACGAGCT-GCAATCGGTAAGCTC
1 ACGAGCTATAAATCGGTAAGCTC
20248255 ATATGAACCG
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
24 13 0.21
25 46 0.75
26 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (25 bp):
ACGAGCTATAAATCGGTAAGCTCTC
Found at i:20254414 original size:9 final size:9
Alignment explanation
Indices: 20254400--20254448 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
20254390 GTAGTGATTC
20254400 AATTCGGTT
1 AATTCGGTT
*
20254409 AATTCGGGT
1 AATTCGGTT
20254418 AATTCGGTT
1 AATTCGGTT
* *
20254427 AATTTGTTT
1 AATTCGGTT
20254436 AATTCGGTT
1 AATTCGGTT
20254445 AATT
1 AATT
20254449 TTAAACCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.47
Consensus pattern (9 bp):
AATTCGGTT
Found at i:20254802 original size:18 final size:19
Alignment explanation
Indices: 20254771--20254806 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
20254761 TTAATTAATT
20254771 TGATTTTGATTTTTGTTCC
1 TGATTTTGATTTTTGTTCC
20254790 TGATTTT-ATTTTTGTTC
1 TGATTTTGATTTTTGTTC
20254807 AAATTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.11, C:0.08, G:0.14, T:0.67
Consensus pattern (19 bp):
TGATTTTGATTTTTGTTCC
Found at i:20256635 original size:7 final size:7
Alignment explanation
Indices: 20256625--20256649 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20256615 TATAATGATA
20256625 ATTATTT
1 ATTATTT
20256632 ATTATTT
1 ATTATTT
20256639 ATTATTT
1 ATTATTT
20256646 ATTA
1 ATTA
20256650 ATATTTTAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
ATTATTT
Found at i:20263388 original size:27 final size:27
Alignment explanation
Indices: 20263348--20263401 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
20263338 ATAAAAATCC
*
20263348 TTGTCTAAATCCCATCCAAGTCGGGTT
1 TTGTCTAAACCCCATCCAAGTCGGGTT
*
20263375 TTGTCTAAACCCCATTCAAGTCGGGTT
1 TTGTCTAAACCCCATCCAAGTCGGGTT
20263402 GGGCGGGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (27 bp):
TTGTCTAAACCCCATCCAAGTCGGGTT
Found at i:20264378 original size:21 final size:19
Alignment explanation
Indices: 20264354--20264396 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
20264344 AAAATAAAAT
20264354 AATTAAGATAAAAATATTACA
1 AATTAA-ATAAAAATATTA-A
* *
20264375 AATTAATTTAAAATATTAA
1 AATTAAATAAAAATATTAA
20264394 AAT
1 AAT
20264397 ATTGTACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AATTAAATAAAAATATTAA
Found at i:20264800 original size:18 final size:18
Alignment explanation
Indices: 20264754--20264816 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 18
20264744 TCGAGATAAT
20264754 GAAAAAT-ATTAAATTTAAA
1 GAAAAATAATT-AA-TTAAA
20264773 -AATAAA-AATTAATTAAA
1 GAA-AAATAATTAATTAAA
20264790 GAAAAATAATTTAA-TAAA
1 GAAAAATAA-TTAATTAAA
*
20264808 TAAAAATAA
1 GAAAAATAA
20264817 ACTAGAAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 8 0.21
18 20 0.53
19 10 0.26
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
GAAAAATAATTAATTAAA
Found at i:20264803 original size:19 final size:18
Alignment explanation
Indices: 20264781--20264816 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20264771 AAAATAAAAA
20264781 TTAATTAAAGAAAAATAAT
1 TTAA-TAAAGAAAAATAAT
*
20264800 TTAATAAATAAAAATAA
1 TTAATAAAGAAAAATAA
20264817 ACTAGAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
TTAATAAAGAAAAATAAT
Found at i:20267526 original size:13 final size:13
Alignment explanation
Indices: 20267508--20267532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20267498 TAATTTATAT
20267508 GTGTGAAAATTTC
1 GTGTGAAAATTTC
20267521 GTGTGAAAATTT
1 GTGTGAAAATTT
20267533 GATAGTTTGA
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:20268988 original size:41 final size:41
Alignment explanation
Indices: 20268928--20269040 Score: 181
Period size: 41 Copynumber: 2.8 Consensus size: 41
20268918 TATAATTGGT
* * *
20268928 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
20268969 TTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
* *
20269010 CTTCAGACTTTATGTCTAGCAGGCTTCATGC
1 TTTCAGACTTTATGTCTAGCAGGCTTGATGC
20269041 TAGTGTACTT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (41 bp):
TTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
Found at i:20269062 original size:41 final size:39
Alignment explanation
Indices: 20268929--20269053 Score: 126
Period size: 41 Copynumber: 3.1 Consensus size: 39
20268919 ATAATTGGTT
* * * * * *
20268929 TTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTAT
1 TTCAGACTTTATGTCTAGCAGGCTTCATGCCAGTG-A-TAC
* *
20268970 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGGCTTCATGCCAGTG-A-TAC
*
20269011 TTCAGACTTTATGTCTAGCAGGCTTCATGCTAGTG-TAC
1 TTCAGACTTTATGTCTAGCAGGCTTCATGCCAGTGATAC
20269049 TTCAG
1 TTCAG
20269054 TAAGCTTTAG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
38 8 0.10
41 69 0.90
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (39 bp):
TTCAGACTTTATGTCTAGCAGGCTTCATGCCAGTGATAC
Found at i:20271435 original size:6 final size:6
Alignment explanation
Indices: 20271421--20271467 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
20271411 AGAACAAATT
* * *
20271421 AGATAC AGATGC AGATGC AGATGC AGA-GT AGAT-C AGATAC AGATGC
1 AGATGC AGATGC AGATGC AGATGC AGATGC AGATGC AGATGC AGATGC
20271467 A
1 A
20271468 AAACAAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 8 0.23
6 27 0.77
ACGTcount: A:0.40, C:0.15, G:0.28, T:0.17
Consensus pattern (6 bp):
AGATGC
Found at i:20272260 original size:62 final size:63
Alignment explanation
Indices: 20272122--20272291 Score: 193
Period size: 62 Copynumber: 2.7 Consensus size: 63
20272112 TCCTTCACAT
* * * * *
20272122 GGCCTAGACACACGCCCGTGTCACTGTCCCGTGTGACCTTAAATCCAAAACAGTAAGTTACAC
1 GGCCTGGACACACGCCCGTGTCCCTGACCCGTGTGACCTTAAATCAAAAACAATAAGTTACAC
* * * * * *
20272185 AGCCTGGACACACGCCTGTGTCCCTGACCTGTGTGACC-T-AATGTAAAAACAATGAGTTATAC
1 GGCCTGGACACACGCCCGTGTCCCTGACCCGTGTGACCTTAAAT-CAAAAACAATAAGTTACAC
*
20272247 GGCCTGGACACACGCCCGTGTCCCTCG-CTCGTGTGACCTTAAATC
1 GGCCTGGACACACGCCCGTGTCCCT-GACCCGTGTGACCTTAAATC
20272292 CATAAACAGT
Statistics
Matches: 87, Mismatches: 16, Indels: 8
0.78 0.14 0.07
Matches are distributed among these distances:
61 3 0.03
62 47 0.54
63 34 0.39
64 3 0.03
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.22
Consensus pattern (63 bp):
GGCCTGGACACACGCCCGTGTCCCTGACCCGTGTGACCTTAAATCAAAAACAATAAGTTACAC
Found at i:20273557 original size:18 final size:19
Alignment explanation
Indices: 20273531--20273567 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20273521 TTAAAAAGTC
*
20273531 AAAATAATAT-ATAAAAAT
1 AAAAAAATATCATAAAAAT
20273549 AAAAAAATATCATAAAAAT
1 AAAAAAATATCATAAAAAT
20273568 TTGAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAAATATCATAAAAAT
Found at i:20273651 original size:15 final size:15
Alignment explanation
Indices: 20273631--20273661 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20273621 ACTTTTTAGA
20273631 ATTTTAGAATTATAT
1 ATTTTAGAATTATAT
*
20273646 ATTTTAGAATTTTAT
1 ATTTTAGAATTATAT
20273661 A
1 A
20273662 AAAAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTAGAATTATAT
Found at i:20273673 original size:23 final size:22
Alignment explanation
Indices: 20273617--20273674 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
20273607 CTTGAAATTT
*
20273617 AAATACTTTTTAGAATTTTAGAA
1 AAATA-TTTTTAGAATTTTAAAA
**
20273640 TTATATATTTTAGAATTTTATAAA
1 AAATAT-TTTTAGAATTTTA-AAA
20273664 AAATATTTTTA
1 AAATATTTTTA
20273675 AACCTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 1 0.04
23 21 0.75
24 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
AAATATTTTTAGAATTTTAAAA
Found at i:20273700 original size:18 final size:18
Alignment explanation
Indices: 20273679--20273730 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
20273669 TTTTTAAACC
* *
20273679 TTTTTTTTATTTTTTACA
1 TTTTTTTCAATTTTTACA
20273697 TTTTTTTCAATTTTTACA
1 TTTTTTTCAATTTTTACA
* * *
20273715 ATATTTTAAATTTTTA
1 TTTTTTTCAATTTTTA
20273731 ATAACATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTTTCAATTTTTACA
Found at i:20273716 original size:9 final size:9
Alignment explanation
Indices: 20273689--20273730 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
20273679 TTTTTTTTAT
*
20273689 TTTTTACAT
1 TTTTTACAA
*
20273698 TTTTTTCAA
1 TTTTTACAA
20273707 TTTTTACAA
1 TTTTTACAA
20273716 TATTTTA-AA
1 T-TTTTACAA
20273725 TTTTTA
1 TTTTTA
20273731 ATAACATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
8 5 0.17
9 19 0.66
10 5 0.17
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTTACAA
Found at i:20274226 original size:30 final size:30
Alignment explanation
Indices: 20274192--20274254 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
20274182 ACTTATTTTA
20274192 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* *
20274222 TTGTTAATTTTGTTATTATTTTAGAGTCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
20274252 TTG
1 TTG
20274255 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:20274402 original size:12 final size:11
Alignment explanation
Indices: 20274369--20274408 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
20274359 GATATATTAT
*
20274369 ATAATTTAAAA
1 ATAATATAAAA
*
20274380 ATTATATAAAA
1 ATAATATAAAA
20274391 ATAATATAAAA
1 ATAATATAAAA
20274402 ATTAATA
1 A-TAATA
20274409 CGGGCGTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 20 0.80
12 5 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:20275324 original size:19 final size:21
Alignment explanation
Indices: 20275288--20275343 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
20275278 AAAAAAAGAA
20275288 TCAAAATAATTTTCAAAAA-T
1 TCAAAATAATTTTCAAAAATT
20275308 TCAAAAT-ATTTAT-AAAAATT
1 TCAAAATAATTT-TCAAAAATT
*
20275328 TCAAAA-AAATTTCAAA
1 TCAAAATAATTTTCAAA
20275344 TTTTATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (21 bp):
TCAAAATAATTTTCAAAAATT
Found at i:20275718 original size:13 final size:13
Alignment explanation
Indices: 20275700--20275728 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
20275690 AAAATAAGAC
20275700 TAATCAAGTCTAT
1 TAATCAAGTCTAT
20275713 TAATCAAGTCTAT
1 TAATCAAGTCTAT
20275726 TAA
1 TAA
20275729 CTTGAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (13 bp):
TAATCAAGTCTAT
Found at i:20279538 original size:40 final size:39
Alignment explanation
Indices: 20279457--20279560 Score: 190
Period size: 39 Copynumber: 2.6 Consensus size: 39
20279447 TATATATATA
20279457 TTTTTATTTTTTTAATTTTAAAATATTTTTAAAATACTT
1 TTTTTATTTTTTTAATTTTAAAATATTTTTAAAATACTT
20279496 TTTTTATTTTTTTAATTTTAAAATATTTTTAAAATACTT
1 TTTTTATTTTTTTAATTTTAAAATATTTTTAAAATACTT
*
20279535 TTTTTAATTTTTTTATTTTTAAAATA
1 TTTTT-ATTTTTTTAATTTTAAAATA
20279561 AATTTTTGGT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
39 44 0.70
40 19 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (39 bp):
TTTTTATTTTTTTAATTTTAAAATATTTTTAAAATACTT
Found at i:20283816 original size:25 final size:26
Alignment explanation
Indices: 20283780--20283898 Score: 93
Period size: 25 Copynumber: 4.7 Consensus size: 26
20283770 GTTTTGACCC
* *
20283780 ACAGCTCATGTGAGCATACT-GATTT
1 ACAGCTCGTGTGAGCATACTAGATCT
* *
20283805 ATAGCTCGTGTGAGCATA-TCGATCT
1 ACAGCTCGTGTGAGCATACTAGATCT
* * *
20283830 ACAGATCGTGTGAGCATA-TAGGTTT
1 ACAGCTCGTGTGAGCATACTAGATCT
* * * *
20283855 ATAGCTTGTGAGAGCATAC-CGATCT
1 ACAGCTCGTGTGAGCATACTAGATCT
* *
20283880 ACAGCTCGAGTGAACATAC
1 ACAGCTCGTGTGAGCATAC
20283899 CGTTTCACAG
Statistics
Matches: 72, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
24 1 0.01
25 71 0.99
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (26 bp):
ACAGCTCGTGTGAGCATACTAGATCT
Found at i:20283846 original size:50 final size:51
Alignment explanation
Indices: 20283788--20283898 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 51
20283778 CCACAGCTCA
* *
20283788 TGTGAGCATACT-GATTTATAGCTCGTGTGAGCATATCGATCTACAGATCG
1 TGTGAGCATACTAGATTTATAGCTCGTGAGAGCATACCGATCTACAGATCG
* * *
20283838 TGTGAGCATA-TAGGTTTATAGCTTGTGAGAGCATACCGATCTACAGCTCG
1 TGTGAGCATACTAGATTTATAGCTCGTGAGAGCATACCGATCTACAGATCG
* *
20283888 AGTGAACATAC
1 TGTGAGCATAC
20283899 CGTTTCACAG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.02
50 51 0.98
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (51 bp):
TGTGAGCATACTAGATTTATAGCTCGTGAGAGCATACCGATCTACAGATCG
Found at i:20284603 original size:20 final size:20
Alignment explanation
Indices: 20284561--20284607 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
20284551 TATTTAAGCT
*
20284561 AAAGATAATAAATGCAAGGG
1 AAAGATAATAAATGCAAAGG
*
20284581 AAAG-TAATGAAATGCAAATG
1 AAAGATAAT-AAATGCAAAGG
20284601 AAA-ATAA
1 AAAGATAA
20284608 GAAAATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.60, C:0.04, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAGATAATAAATGCAAAGG
Found at i:20286834 original size:41 final size:41
Alignment explanation
Indices: 20286777--20286860 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
20286767 CCAAGGTATA
20286777 AAGGCTAAAAGTGTAAATAAACCTAAGCTACATTGATAACT
1 AAGGCTAAAAGTGTAAATAAACCTAAGCTACATTGATAACT
20286818 AAGGCTAAAAGTGTAAATAAACCTAAGCTACATTGATAACT
1 AAGGCTAAAAGTGTAAATAAACCTAAGCTACATTGATAACT
20286859 AA
1 AA
20286861 CTTAAGTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (41 bp):
AAGGCTAAAAGTGTAAATAAACCTAAGCTACATTGATAACT
Found at i:20286847 original size:23 final size:23
Alignment explanation
Indices: 20286780--20286847 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
20286770 AGGTATAAAG
20286780 GCTAAAAGTGTAAATAAACCTAA
1 GCTAAAAGTGTAAATAAACCTAA
* *
20286803 GCT-ACA-T-T-GAT-AA-CTAA
1 GCTAAAAGTGTAAATAAACCTAA
20286820 GGCTAAAAGTGTAAATAAACCTAA
1 -GCTAAAAGTGTAAATAAACCTAA
20286844 GCTA
1 GCTA
20286848 CATTGATAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
17 4 0.12
18 5 0.15
19 4 0.12
20 2 0.06
21 2 0.06
22 4 0.12
23 9 0.26
24 4 0.12
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (23 bp):
GCTAAAAGTGTAAATAAACCTAA
Found at i:20291200 original size:37 final size:37
Alignment explanation
Indices: 20291075--20291210 Score: 121
Period size: 37 Copynumber: 3.7 Consensus size: 37
20291065 AGGTCTTCGA
* * * * * * *
20291075 AGCATTTGTCATGTTATTGGCTGGACTAGCTCTACGG
1 AGCATTTGGCGTGTTATCGGTTGGATTACCTCTATGG
* *
20291112 AGCATTTGGCGTGTTATCGGTTGGATTAGCTCTTTGG
1 AGCATTTGGCGTGTTATCGGTTGGATTACCTCTATGG
* * * *
20291149 AACATATGGTGTGTTATCAGTTGGATTACCTCTCAT-G
1 AGCATTTGGCGTGTTATCGGTTGGATTACCTCT-ATGG
* *
20291186 AGCATTTGACGTGTTTTCGGTTGGA
1 AGCATTTGGCGTGTTATCGGTTGGA
20291211 CTATTGTGCT
Statistics
Matches: 79, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
37 78 0.99
38 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.38
Consensus pattern (37 bp):
AGCATTTGGCGTGTTATCGGTTGGATTACCTCTATGG
Found at i:20297649 original size:40 final size:40
Alignment explanation
Indices: 20297573--20297656 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
20297563 TGTATAAGCC
*
20297573 TTCAGGAGTACCGAAGTACAAACAGAGACATATATGTGCA
1 TTCAGGAGTACCGAAGTACAAACAGAGACACATATGTGCA
* * * *
20297613 TTCAGGGGTACTGAAGTACAAACATG-GGCACGTATGTGCA
1 TTCAGGAGTACCGAAGTACAAACA-GAGACACATATGTGCA
20297653 TTCA
1 TTCA
20297657 TAGAACAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
40 37 0.97
41 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (40 bp):
TTCAGGAGTACCGAAGTACAAACAGAGACACATATGTGCA
Found at i:20299657 original size:14 final size:14
Alignment explanation
Indices: 20299638--20299665 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20299628 GATAATGTTT
20299638 TTGAATTTGATAAA
1 TTGAATTTGATAAA
20299652 TTGAATTTGATAAA
1 TTGAATTTGATAAA
20299666 CGAAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
TTGAATTTGATAAA
Found at i:20306276 original size:50 final size:49
Alignment explanation
Indices: 20306200--20306535 Score: 255
Period size: 50 Copynumber: 6.7 Consensus size: 49
20306190 GTGATGTCAG
* * * *
20306200 GGAAGCAAGATTCGCCGCTGTGGCTTTAATCTGTTCCACTGCACTATTTA
1 GGAAGCAAGATTCGCCGATGTAGCTTTAATCTGTT-CACTGCACTGTCTA
* * * * * * * *
20306250 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTCTTAACTACAATGTCGA
1 GGAAGCAAGATTCGCCGATGTAGCTTTAATC-TGTTCACTGCACTGTCTA
* *
20306300 GGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTTCACTGCACTGTCT-
1 GGAAGCAAGATTCGCCGATGTAGCTTTAATCTG-TTCACTGCACTGTCTA
* * * * *
20306349 GGAAGGTAAGATTCGCTGATGTAGCTTTAATCTTTTGAACTGCAATGTC-A
1 GGAA-GCAAGATTCGCCGATGTAGCTTTAATCTGTT-CACTGCACTGTCTA
* * * * * *
20306399 GGGAAGCAAGATTCACCGATATGGCTTTAATTTGTTCCACTGCA-TCGCCTG
1 -GGAAGCAAGATTCGCCGATGTAGCTTTAATCTGTT-CACTGCACT-GTCTA
* * ** * * * *
20306450 GGAGGTAAGATTCGCTAATGTAGCTTTAATCTTTTGAACTGCAATGTCAA
1 GGAAGCAAGATTCGCCGATGTAGCTTTAATCTGTT-CACTGCACTGTCTA
* *
20306500 GGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTC
1 GGAAGCAAGATTCGCCGATGTAGCTTTAATCTGTTC
20306536 CACTACATCG
Statistics
Matches: 216, Mismatches: 61, Indels: 19
0.73 0.21 0.06
Matches are distributed among these distances:
49 8 0.04
50 200 0.93
51 8 0.04
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (49 bp):
GGAAGCAAGATTCGCCGATGTAGCTTTAATCTGTTCACTGCACTGTCTA
Found at i:20306358 original size:100 final size:99
Alignment explanation
Indices: 20306193--20306539 Score: 495
Period size: 100 Copynumber: 3.5 Consensus size: 99
20306183 CATAACTGTG
* * * *
20306193 ATGTCAGGGAAGCAAGATTCGCCGCTGTGGCTTTAATCTGTTCCACTGCACTATTTAGGAA-GTA
1 ATGTCA-GGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACTGTCT-GGAAGGTA
* *
20306257 AGATTCGCTGTTGTAGCTTTAATCTTCTT-AACTACA
64 AGATTCGCTGATGTAGCTTTAATCTT-TTGAACTGCA
20306293 ATGTCGAGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTT-CACTGCACTGTCTGGAAGGTA
1 ATGTC-AGGAAGCAAGATTCACCGATGTGGCTTTAATCTG-TTCCACTGCACTGTCTGGAAGGTA
20306357 AGATTCGCTGATGTAGCTTTAATCTTTTGAACTGCA
64 AGATTCGCTGATGTAGCTTTAATCTTTTGAACTGCA
* * * *
20306393 ATGTCAGGGAAGCAAGATTCACCGATATGGCTTTAATTTGTTCCACTGCA-TCGCCTGGGAGGTA
1 ATGTCA-GGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACT-GTCTGGAAGGTA
*
20306457 AGATTCGCTAATGTAGCTTTAATCTTTTGAACTGCA
64 AGATTCGCTGATGTAGCTTTAATCTTTTGAACTGCA
20306493 ATGTCAAGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACT
1 ATGTC-AGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACT
20306540 ACATCGCTTG
Statistics
Matches: 226, Mismatches: 13, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
99 10 0.04
100 212 0.94
101 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (99 bp):
ATGTCAGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACTGTCTGGAAGGTAAG
ATTCGCTGATGTAGCTTTAATCTTTTGAACTGCA
Found at i:20308145 original size:7 final size:8
Alignment explanation
Indices: 20308110--20308144 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
20308100 TCATTTTCCA
20308110 TTTTCATT
1 TTTTCATT
*
20308118 TTTTTATT
1 TTTTCATT
20308126 TTTTCATT
1 TTTTCATT
20308134 TTTTCATT
1 TTTTCATT
20308142 TTT
1 TTT
20308145 CGTCTCTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTCATT
Found at i:20311032 original size:20 final size:21
Alignment explanation
Indices: 20310990--20311033 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
20310980 ATCTTTTGCA
20310990 TTTGCTCCAGTTTCTCTAATC
1 TTTGCTCCAGTTTCTCTAATC
* * *
20311011 TTTGGTCCA-TTTCTTTAGTC
1 TTTGCTCCAGTTTCTCTAATC
20311031 TTT
1 TTT
20311034 CGACGAGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.11, C:0.23, G:0.11, T:0.55
Consensus pattern (21 bp):
TTTGCTCCAGTTTCTCTAATC
Found at i:20321446 original size:28 final size:29
Alignment explanation
Indices: 20321410--20321470 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
20321400 ATCAAAAAAA
*
20321410 TTTTCTTCTCTCAATTTCT-CCAACATCT
1 TTTTCTTCTCTCAATTTCTCCCAACATAT
* *
20321438 TTTTCTTCTCTTATTTTCTCCCAACATAT
1 TTTTCTTCTCTCAATTTCTCCCAACATAT
20321467 TTTT
1 TTTT
20321471 TTCCACTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTCTTCTCTCAATTTCTCCCAACATAT
Found at i:20324346 original size:16 final size:16
Alignment explanation
Indices: 20324322--20324360 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20324312 AAGAAATAAC
* *
20324322 TAAAGTAAATAAACAA
1 TAAAATAAACAAACAA
20324338 TAAAATAAACAAACAA
1 TAAAATAAACAAACAA
*
20324354 TTAAATA
1 TAAAATA
20324361 GGTTAAACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.21
Consensus pattern (16 bp):
TAAAATAAACAAACAA
Found at i:20331094 original size:25 final size:25
Alignment explanation
Indices: 20331065--20331225 Score: 76
Period size: 25 Copynumber: 6.4 Consensus size: 25
20331055 AAACCAAACC
*
20331065 AAGCCTTTGTGGTGAATTATATAG-A
1 AAGCCTTTGTGGTGAATCATAT-GTA
* * *
20331090 AAGCCTTCGTGGTGAGTCATCTGTA
1 AAGCCTTTGTGGTGAATCATATGTA
** * *
20331115 AAGCCTTTGTGGCAAATCATTTGGA
1 AAGCCTTTGTGGTGAATCATATGTA
*** * * * *
20331140 AATTTTTTGTGGCGAGTCATCTATA
1 AAGCCTTTGTGGTGAATCATATGTA
* * *
20331165 AAGCTTTTGTGGTGAAT--TGTTTAA
1 AAGCCTTTGTGGTGAATCATATGT-A
* * * *
20331189 TAAGCCTTTGTGGCGAGTCATTTCTA
1 -AAGCCTTTGTGGTGAATCATATGTA
20331215 AAGCCTTTGTG
1 AAGCCTTTGTG
20331226 TCGAATTTTC
Statistics
Matches: 102, Mismatches: 29, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
23 3 0.03
24 2 0.02
25 93 0.91
26 1 0.01
27 3 0.03
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (25 bp):
AAGCCTTTGTGGTGAATCATATGTA
Found at i:20331249 original size:100 final size:99
Alignment explanation
Indices: 20331065--20331451 Score: 303
Period size: 100 Copynumber: 3.9 Consensus size: 99
20331055 AAACCAAACC
* * *
20331065 AAGCCTTTGTGGTGAATTATATAGAAAGCCTTCGTGGTGAGTCATCTGTAAAGCCTTTGTGGCAA
1 AAGCCTTTGTGGTGAATTGTATA-AAAGCCTTTGTGGCGAGTCATCTGTAAAGCCTTTGTGGCAA
*** *
20331130 ATCATTTGGAAATTTTTTGTGGCGAGTCATCTATA
65 ATCATTTGGAAAGCCTTTGTGGCAAGTCATCTATA
* * * * * *
20331165 AAGCTTTTGTGGTGAATTGTTTAATAAGCCTTTGTGGCGAGTCATTTCTAAAGCCTTTGTGTCGA
1 AAGCCTTTGTGGTGAATTGTATAA-AAGCCTTTGTGGCGAGTCATCTGTAAAGCCTTTGTGGCAA
* *
20331230 AT-TTTCTGGGAAGCCTTTGTGGCAAGTCATCTATA
65 ATCATT-TGGAAAGCCTTTGTGGCAAGTCATCTATA
* * * * * *
20331265 AAGCCTTTGTGGCGAATTGTCTAGGAAGCCTTTGCGGCGAGTCATCTGTAAAGCCTTTTTAGCAA
1 AAGCCTTTGTGGTGAATTGTATA-AAAGCCTTTGTGGCGAGTCATCTGTAAAGCCTTTGTGGCAA
** * * * * *
20331330 ATTGTTCAGG-AAGCTTTTGTGGCAATTCATATGTA
65 ATCATT-TGGAAAGCCTTTGTGGCAAGTCATCTATA
* * * ** * * * * * * *
20331365 AATCCTTTGTGCCT-AATTGTTTGGGAAGCTTTTGCGACGAGTCATCTGTAAGGCATTTGGGGCG
1 AAGCCTTTGTG-GTGAATTGTAT-AAAAGCCTTTGTGGCGAGTCATCTGTAAAGCCTTTGTGGCA
** *
20331429 AATTGTTTGGGAAGCCTTTGTGG
64 AATCATTTGGAAAGCCTTTGTGG
20331452 TGAATATTTT
Statistics
Matches: 233, Mismatches: 47, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
99 5 0.02
100 223 0.96
101 5 0.02
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (99 bp):
AAGCCTTTGTGGTGAATTGTATAAAAGCCTTTGTGGCGAGTCATCTGTAAAGCCTTTGTGGCAAA
TCATTTGGAAAGCCTTTGTGGCAAGTCATCTATA
Found at i:20331268 original size:25 final size:25
Alignment explanation
Indices: 20331089--20331322 Score: 107
Period size: 25 Copynumber: 9.4 Consensus size: 25
20331079 AATTATATAG
* ** *
20331089 AAAGCCTTCGTGGTGAGTCATCTGT
1 AAAGCCTTTGTGGCAAGTCATCTAT
* * **
20331114 AAAGCCTTTGTGGCAAATCATTTGG
1 AAAGCCTTTGTGGCAAGTCATCTAT
*** *
20331139 AAATTTTTTGTGGCGAGTCATCTAT
1 AAAGCCTTTGTGGCAAGTCATCTAT
* * ** *
20331164 AAAGCTTTTGTGGTGAA-TTGTTTA-
1 AAAGCCTTTGTGG-CAAGTCATCTAT
* * *
20331188 ATAAGCCTTTGTGGCGAGTCATTTCT
1 A-AAGCCTTTGTGGCAAGTCATCTAT
* ** **
20331214 AAAGCCTTTGTGTCGAA-TTTTCTGG
1 AAAGCCTTTGTGGC-AAGTCATCTAT
*
20331239 GAAGCCTTTGTGGCAAGTCATCTAT
1 AAAGCCTTTGTGGCAAGTCATCTAT
** *
20331264 AAAGCCTTTGTGGCGAA-TTGTCTAG
1 AAAGCCTTTGTGGC-AAGTCATCTAT
* * * *
20331289 GAAGCCTTTGCGGCGAGTCATCTGT
1 AAAGCCTTTGTGGCAAGTCATCTAT
20331314 AAAGCCTTT
1 AAAGCCTTT
20331323 TTAGCAAATT
Statistics
Matches: 149, Mismatches: 52, Indels: 16
0.69 0.24 0.07
Matches are distributed among these distances:
24 5 0.03
25 139 0.93
26 5 0.03
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (25 bp):
AAAGCCTTTGTGGCAAGTCATCTAT
Found at i:20331333 original size:50 final size:49
Alignment explanation
Indices: 20331065--20331451 Score: 274
Period size: 50 Copynumber: 7.7 Consensus size: 49
20331055 AAACCAAACC
* * * * * *
20331065 AAGCCTTTGTGGTGAATTATATAGAAAGCCTTCGTGGTGAGTCATCTGTA
1 AAGCCTTTGT-GCGAATTGTCTAGGAAGCCTTTGTGGCGAGTCATCTGTA
* ** * *** *
20331115 AAGCCTTTGTGGCAAATCAT-TTGGAAATTTTTTGTGGCGAGTCATCTATA
1 AAGCCTTTGT-GCGAATTGTCTAGG-AAGCCTTTGTGGCGAGTCATCTGTA
* * * ** * *
20331165 AAGCTTTTGTGGTGAATTGTTTAATAAGCCTTTGTGGCGAGTCATTTCTA
1 AAGCCTTTGT-GCGAATTGTCTAGGAAGCCTTTGTGGCGAGTCATCTGTA
* * * *
20331215 AAGCCTTTGTGTCGAATTTTCTGGGAAGCCTTTGTGGCAAGTCATCTATA
1 AAGCCTTTGTG-CGAATTGTCTAGGAAGCCTTTGTGGCGAGTCATCTGTA
*
20331265 AAGCCTTTGTGGCGAATTGTCTAGGAAGCCTTTGCGGCGAGTCATCTGTA
1 AAGCCTTTGT-GCGAATTGTCTAGGAAGCCTTTGTGGCGAGTCATCTGTA
* * * * * *
20331315 AAGCCTTTTTAGCAAATTGT-TCAGGAAGCTTTTGTGGCAATTCATATGTA
1 AAGCCTTTGT-GCGAATTGTCT-AGGAAGCCTTTGTGGCGAGTCATCTGTA
* * * * * * *
20331365 AATCCTTTGTGCCTAATTGTTTGGGAAGCTTTTGCGACGAGTCATCTGTA
1 AAGCCTTTGTG-CGAATTGTCTAGGAAGCCTTTGTGGCGAGTCATCTGTA
* * * * *
20331415 AGGCATTTGGGGCGAATTGTTTGGGAAGCCTTTGTGG
1 AAGCCTTT-GTGCGAATTGTCTAGGAAGCCTTTGTGG
20331452 TGAATATTTT
Statistics
Matches: 265, Mismatches: 64, Indels: 16
0.77 0.19 0.05
Matches are distributed among these distances:
49 5 0.02
50 255 0.96
51 5 0.02
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (49 bp):
AAGCCTTTGTGCGAATTGTCTAGGAAGCCTTTGTGGCGAGTCATCTGTA
Found at i:20331495 original size:25 final size:25
Alignment explanation
Indices: 20331478--20331525 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
20331468 CCTTTGTGTC
20331478 GAGTCATCTATAAAGCCTTTATGAT
1 GAGTCATCTATAAAGCCTTTATGAT
*
20331503 GAGTCATCTGTAAAGCCTTTATG
1 GAGTCATCTATAAAGCCTTTATG
20331526 GTGAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (25 bp):
GAGTCATCTATAAAGCCTTTATGAT
Found at i:20332816 original size:27 final size:26
Alignment explanation
Indices: 20332783--20332840 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
20332773 TTTCATTCCT
*
20332783 AAAAGAAGGAAAATAATACAAACTAA
1 AAAAGAAAGAAAATAATACAAACTAA
**
20332809 ACAAAGAAATTAAATAATACAAACTAA
1 A-AAAGAAAGAAAATAATACAAACTAA
20332836 AAAAG
1 AAAAG
20332841 GCATTCAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.14
Consensus pattern (26 bp):
AAAAGAAAGAAAATAATACAAACTAA
Found at i:20336638 original size:18 final size:19
Alignment explanation
Indices: 20336595--20336630 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20336585 TTTATTTAAT
20336595 ATATAA-TAATAAAATATA
1 ATATAATTAATAAAATATA
*
20336613 ATATAATTAATATAATAT
1 ATATAATTAATAAAATAT
20336631 GTATAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAATTAATAAAATATA
Found at i:20337884 original size:15 final size:15
Alignment explanation
Indices: 20337864--20337894 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20337854 AAATCTACTG
20337864 AAATAGATGAATTAC
1 AAATAGATGAATTAC
20337879 AAATAGATGAATTAC
1 AAATAGATGAATTAC
20337894 A
1 A
20337895 TACAACATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (15 bp):
AAATAGATGAATTAC
Found at i:20338814 original size:21 final size:23
Alignment explanation
Indices: 20338772--20338814 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
20338762 TAATTAATTA
*
20338772 TAAACAGAAGCAAATCTCTTTTC
1 TAAACAGAAGCAAATATCTTTTC
*
20338795 TAAA-AGAAG-AAATATGTTTT
1 TAAACAGAAGCAAATATCTTTT
20338815 AAAACACGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (23 bp):
TAAACAGAAGCAAATATCTTTTC
Found at i:20341678 original size:69 final size:69
Alignment explanation
Indices: 20341592--20341729 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
20341582 GAAAAGATGT
*
20341592 GTGAACAGGAAAGATTCCTTGCAA-AGAATGATGCATGAATAGAAAAGT-TTCCCTGCAAGAAAA
1 GTGAACAGGAAAGATTCCTTGCAAGA-AATGATGCATGAACAGAAAA-TATTCCCTGCAAGAAAA
20341655 GACAAG
64 GACAAG
* **
20341661 GTGAACAGGAAATATTCCTTGCAAGAAATGATGTGTGAACAGAAAATATTCCCTGCAAGAAAAGA
1 GTGAACAGGAAAGATTCCTTGCAAGAAATGATGCATGAACAGAAAATATTCCCTGCAAGAAAAGA
20341726 CAAG
66 CAAG
20341730 AAAAAGAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
68 1 0.02
69 61 0.97
70 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.20
Consensus pattern (69 bp):
GTGAACAGGAAAGATTCCTTGCAAGAAATGATGCATGAACAGAAAATATTCCCTGCAAGAAAAGA
CAAG
Found at i:20341708 original size:34 final size:34
Alignment explanation
Indices: 20341579--20341725 Score: 138
Period size: 34 Copynumber: 4.3 Consensus size: 34
20341569 AGAAATGATA
* * *
20341579 CAAGAAAAGATGTGTGAACAGGAAAGATTCCTTG
1 CAAGAAAAGATGTGTGAACAGAAAATATTCCCTG
* ** *
20341613 CAA-AGAATGATGCATGAATAGAAAAGT-TTCCCTG
1 CAAGA-AAAGATGTGTGAACAGAAAA-TATTCCCTG
* * *
20341647 CAAGAAAAGACAAG-GTGAACAGGAAATATTCCTTG
1 CAAGAAAAG--ATGTGTGAACAGAAAATATTCCCTG
*
20341682 CAAGAAATGATGTGTGAACAGAAAATATTCCCTG
1 CAAGAAAAGATGTGTGAACAGAAAATATTCCCTG
20341716 CAAGAAAAGA
1 CAAGAAAAGA
20341726 CAAGAAAAAG
Statistics
Matches: 88, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
33 3 0.03
34 59 0.67
35 24 0.27
36 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (34 bp):
CAAGAAAAGATGTGTGAACAGAAAATATTCCCTG
Found at i:20341789 original size:19 final size:19
Alignment explanation
Indices: 20341765--20341805 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
20341755 CTGTAATTTG
*
20341765 TATTTTTGTAATTAGAGAA
1 TATTTTTGTAATGAGAGAA
20341784 TATTTTTGTAATGAGAGAA
1 TATTTTTGTAATGAGAGAA
20341803 TAT
1 TAT
20341806 ATTCTCTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (19 bp):
TATTTTTGTAATGAGAGAA
Found at i:20341964 original size:22 final size:22
Alignment explanation
Indices: 20341939--20341981 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20341929 CATTTGAGTT
*
20341939 GTTTCTCCAAATTTTC-CAAAAA
1 GTTTCT-CAAAGTTTCTCAAAAA
20341961 GTTTCTCAAAGTTTCTCAAAA
1 GTTTCTCAAAGTTTCTCAAAA
20341982 TTTTTAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (22 bp):
GTTTCTCAAAGTTTCTCAAAAA
Done.