Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 130 of 226
Found at i:40353253 original size:95 final size:95
Alignment explanation
Indices: 40353119--40353353 Score: 332
Period size: 95 Copynumber: 2.4 Consensus size: 95
40353109 TTCAATTATC
* *
40353119 TTTTTTTTCCATTTAAATTTAATTTTTTTCTCATTTCATTTATATTGTCTTTCT-TCCCATATAA
1 TTTTTTTTCCATTTAAATTTAATTTTTTTCTCATTTCATTTAAATTATCTTT-TATCCCATATAA
40353183 ATTTAATTTTTTTTCTCATTTCATTTAAATTA
65 ATTTAA-TTTTTTTCTCATTTCATTTAAATTA
* * *
40353215 TTTTTTTTCTATTTAAATATT-A-TTTTTTCTCATTTCATTTAAATTATCTTTTATTCCATTTAA
1 TTTTTTTTCCATTTAAAT-TTAATTTTTTTCTCATTTCATTTAAATTATCTTTTATCCCATATAA
40353278 ATTTAATTTTTTTCTCATTTCATTTAAATTA
65 ATTTAATTTTTTTCTCATTTCATTTAAATTA
* *
40353309 TCTTTCTTTCCATTTTAATTTTAATTTTTTTTCTCATTTCATTTA
1 T-TTTTTTTCCA-TTTAAATTTAA-TTTTTTTCTCATTTCATTTA
40353354 GATTTAATTT
Statistics
Matches: 124, Mismatches: 8, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
94 27 0.22
95 51 0.41
96 25 0.20
97 2 0.02
98 19 0.15
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (95 bp):
TTTTTTTTCCATTTAAATTTAATTTTTTTCTCATTTCATTTAAATTATCTTTTATCCCATATAAA
TTTAATTTTTTTCTCATTTCATTTAAATTA
Found at i:40353416 original size:78 final size:77
Alignment explanation
Indices: 40353128--40353407 Score: 309
Period size: 78 Copynumber: 3.8 Consensus size: 77
40353118 CTTTTTTTTC
* * * *
40353128 CATTTAAATTTAATTTTTTTCTCATTTCATTTATATTG-TCTTTCTTCCCA-TATAAATTTAATT
1 CATTTAAATTTAATTTTTTTCTCATTTCATTTA-AATGATCTTTCTTTCCATTTTAATTTTAATT
40353191 TTTTTTCTCATTT
65 TTTTTTCTCATTT
* * *
40353204 CATTTAAA-TT-ATTTTTTT-TC---T-ATTTAAAT-AT-TATTTTTTCTCA-TTTCATTTAAAT
1 CATTTAAATTTAATTTTTTTCTCATTTCATTTAAATGATCT-TTCTTTC-CATTTTAATTTTAAT
* * *
40353259 TATCTTT-T-ATTC
64 TTTTTTTCTCATTT
*
40353271 CATTTAAATTTAATTTTTTTCTCATTTCATTTAAATTATCTTTCTTTCCATTTTAATTTTAATTT
1 CATTTAAATTTAATTTTTTTCTCATTTCATTTAAATGATCTTTCTTTCCATTTTAATTTTAATTT
40353336 TTTTTCTCATTT
66 TTTTTCTCATTT
* *
40353348 CATTTAGATTTAATTTTTCTTCTCTTTTCATTTAAATGATCTTTCTTTCCATTTTAATTT
1 CATTTAAATTTAATTTTT-TTCTCATTTCATTTAAATGATCTTTCTTTCCATTTTAATTT
40353408 ACGTTTTTTA
Statistics
Matches: 169, Mismatches: 19, Indels: 30
0.78 0.09 0.14
Matches are distributed among these distances:
67 12 0.07
68 11 0.07
69 28 0.17
70 3 0.02
73 3 0.02
74 18 0.11
75 25 0.15
76 10 0.06
77 20 0.12
78 39 0.23
ACGTcount: A:0.24, C:0.13, G:0.01, T:0.62
Consensus pattern (77 bp):
CATTTAAATTTAATTTTTTTCTCATTTCATTTAAATGATCTTTCTTTCCATTTTAATTTTAATTT
TTTTTCTCATTT
Found at i:40356921 original size:113 final size:110
Alignment explanation
Indices: 40356751--40356960 Score: 269
Period size: 113 Copynumber: 1.9 Consensus size: 110
40356741 ACATGGCCCA
* * * *
40356751 CACCCAAATTTTTTTTATATACACTGGTGCCGGCCATCAGTGTTCCAAAATATAAAAAA-GATAC
1 CACCCAAATTTTTTTTAAATACACTGGTACCGGCCATCAGTGTCCCAAAATAAAAAAAATG-TAC
* * *
40356815 ATTGGGAGCCGAAAATTGTACTTGGTGCTGGCCATAACATGACCAG
65 ATTGGGAACCGAAAATTGTACCTGGTGCCGGCCATAACATGACCAG
* *
40356861 CACCCAAAATTTTTTTTTAAAATACACTGGTACCGGCCATCAGTGTCCCACAGTAAAAAAAATGT
1 CACCC-AAA-TTTTTTTT-AAATACACTGGTACCGGCCATCAGTGTCCCAAAATAAAAAAAATGT
* * *
40356926 GCCTTGGGAACTGAAAATTGTACCTGGTGCCGGCC
63 ACATTGGGAACCGAAAATTGTACCTGGTGCCGGCC
40356961 GTCTACTGGC
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
110 5 0.06
111 3 0.04
112 8 0.10
113 67 0.80
114 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (110 bp):
CACCCAAATTTTTTTTAAATACACTGGTACCGGCCATCAGTGTCCCAAAATAAAAAAAATGTACA
TTGGGAACCGAAAATTGTACCTGGTGCCGGCCATAACATGACCAG
Found at i:40358761 original size:41 final size:41
Alignment explanation
Indices: 40358692--40358966 Score: 394
Period size: 41 Copynumber: 6.7 Consensus size: 41
40358682 ATTTTTAGGG
40358692 CTTTAGCGGCGTTTTTCGAA-AAGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTT-GAAGAAGCGCCGCTAATGCTCGGGT
* *
40358733 CTTTAGCGGCGTTTTTGAAGAAGTGCCGCTAATGCTAGGGT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGT
40358774 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGT
* * *
40358815 CTTTAGCGGTGTTTTTGGAGAAGCGCTCGCTAATGCTCAGGT
1 CTTTAGCGGCGTTTTTGAAGAAGCGC-CGCTAATGCTCGGGT
* *
40358857 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAGTGCTCTGGT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGT
**
40358898 CTTTAGCGGCGTTTTTGATA-AAGCGCCGCTAATGCTC-TAT
1 CTTTAGCGGCGTTTTTGA-AGAAGCGCCGCTAATGCTCGGGT
* * *
40358938 TTTTAGCGGCGTTTTTTAAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGC
40358967 AAAAAATATT
Statistics
Matches: 214, Mismatches: 16, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
39 1 0.00
40 29 0.14
41 145 0.68
42 39 0.18
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGT
Found at i:40358885 original size:83 final size:82
Alignment explanation
Indices: 40358692--40358966 Score: 389
Period size: 83 Copynumber: 3.4 Consensus size: 82
40358682 ATTTTTAGGG
*
40358692 CTTTAGCGGCGTTTTTCGAA-AAGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTGAAGAAG
1 CTTTAGCGGCGTTTTT-GAAGAAGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTGGAGAAG
*
40358756 TGCCGCTAATGCT-AGGGT
65 CGCCGCTAATGCTCA-GGT
*
40358774 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGTCTTTAGCGGTGTTTTTGGAGAAGC
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTGGAGAAGC
40358839 GCTCGCTAATGCTCAGGT
66 GC-CGCTAATGCTCAGGT
* * *
40358857 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAGTGCTCTGGTCTTTAGCGGCGTTTTT-GATAAAG
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTGGA-GAAG
40358921 CGCCGCTAATGCTCTA--T
65 CGCCGCTAATGCTC-AGGT
* * *
40358938 TTTTAGCGGCGTTTTTTAAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGC
40358967 AAAAAATATT
Statistics
Matches: 178, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
81 30 0.17
82 73 0.41
83 74 0.42
84 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTGGAGAAGC
GCCGCTAATGCTCAGGT
Found at i:40358911 original size:124 final size:123
Alignment explanation
Indices: 40358692--40358966 Score: 401
Period size: 124 Copynumber: 2.2 Consensus size: 123
40358682 ATTTTTAGGG
* *
40358692 CTTTAGCGGCGTTTTTCGAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTGAAGAAGT
1 CTTTAGCGGCGTTTTTCGAAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGAAGAAGC
40358757 GCCGCTAATGCTAGGGTCTTTAGCGGCGTTTTTGA-AGAAGCGCCGCTAATGCTCGGGT
66 GCCGCTAATGCTAGGGTCTTTAGCGGCGTTTTTGATA-AAGCGCCGCTAATGCTCGGGT
* * *
40358815 CTTTAGCGGTGTTTTTGGAGAAGCGCTCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGAAGAAG
1 CTTTAGCGGCGTTTTTCGAAAAGCGC-CGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGAAGAAG
* ** **
40358880 CGCCGCTAGTGCTCTGGTCTTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTC-TAT
65 CGCCGCTAATGCTAGGGTCTTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTCGGGT
* **
40358938 TTTTAGCGGCGTTTTTTAAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTCGAAAAGCGCCGC
40358967 AAAAAATATT
Statistics
Matches: 135, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
122 3 0.02
123 45 0.33
124 86 0.64
125 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (123 bp):
CTTTAGCGGCGTTTTTCGAAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGAAGAAGC
GCCGCTAATGCTAGGGTCTTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTCGGGT
Found at i:40360859 original size:22 final size:22
Alignment explanation
Indices: 40360816--40360859 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
40360806 CCCATTTTAG
*
40360816 CCCTAAATTTCCCCCGTGAAAC
1 CCCTAAATTTCCCCCGTAAAAC
*
40360838 CCCTAATTTTCCCTCC-TAAAAC
1 CCCTAAATTTCCC-CCGTAAAAC
40360860 TCTTTTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.27, C:0.41, G:0.05, T:0.27
Consensus pattern (22 bp):
CCCTAAATTTCCCCCGTAAAAC
Found at i:40361070 original size:9 final size:9
Alignment explanation
Indices: 40361056--40361081 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40361046 TTTCACAAAC
40361056 AGGTTACAG
1 AGGTTACAG
40361065 AGGTTACAG
1 AGGTTACAG
40361074 AGGTTACA
1 AGGTTACA
40361082 ACCATTGCTG
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:0.35, C:0.12, G:0.31, T:0.23
Consensus pattern (9 bp):
AGGTTACAG
Found at i:40361210 original size:20 final size:19
Alignment explanation
Indices: 40361169--40361214 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40361159 CACACTTATC
*
40361169 TTTTTTTTATAGTAATTGA
1 TTTTTTTTATAGTAATTAA
**
40361188 TTTTTTTTATAGATTTTTAA
1 TTTTTTTTATAG-TAATTAA
40361208 TTTTTTT
1 TTTTTTT
40361215 AAATAGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTTTTTTATAGTAATTAA
Found at i:40363561 original size:43 final size:43
Alignment explanation
Indices: 40363505--40363667 Score: 229
Period size: 43 Copynumber: 3.8 Consensus size: 43
40363495 AAGATATATT
* * * * *
40363505 TTTAGTGGCGTTTGT-TTGAAAAGCGCCGTTAAAAGCCATGGTC
1 TTTAGCGGCGTTTGTGGT-AAAAGCGCCGCTAAAGGTCATGGTC
*
40363548 TTTAGCGGTGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGTC
* *
40363591 TTTAGCGGCGTTTGTGGTAAAAACGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGTC
*
40363634 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAG
40363668 TTAGCGACGC
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 107 0.99
44 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:40368167 original size:26 final size:26
Alignment explanation
Indices: 40368138--40368201 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
40368128 CGACTTATAA
40368138 CTCGTGTGAGCAGACCCATTTCACAG
1 CTCGTGTGAGCAGACCCATTTCACAG
*
40368164 CTCGTGTGAGCAGGCCCATTTCACAG
1 CTCGTGTGAGCAGACCCATTTCACAG
40368190 CTCGTGTGAGCA
1 CTCGTGTGAGCA
40368202 TTGATGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (26 bp):
CTCGTGTGAGCAGACCCATTTCACAG
Found at i:40371243 original size:14 final size:14
Alignment explanation
Indices: 40371224--40371252 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40371214 TTAGCCCAAT
40371224 ATTATCTTTAAAAA
1 ATTATCTTTAAAAA
40371238 ATTATCTTTAAAAA
1 ATTATCTTTAAAAA
40371252 A
1 A
40371253 CCCTATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTATCTTTAAAAA
Found at i:40378377 original size:11 final size:11
Alignment explanation
Indices: 40378361--40378385 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40378351 CCAAGCCCCG
40378361 TTTTTTATGTT
1 TTTTTTATGTT
40378372 TTTTTTATGTT
1 TTTTTTATGTT
40378383 TTT
1 TTT
40378386 GGAGTCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTTTATGTT
Found at i:40379268 original size:50 final size:50
Alignment explanation
Indices: 40379138--40379283 Score: 184
Period size: 50 Copynumber: 2.9 Consensus size: 50
40379128 TTATTGAGGT
* * * *
40379138 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCGTTGGCACTGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGCATTGGCACCGA
* * *
40379188 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGCATTGGCACCGA
** * * *
40379238 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGCATTGGCA
40379284 GTACAGGAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 81 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACCATGTCTGGGATATGGCATTGGCACCGA
Found at i:40379559 original size:20 final size:20
Alignment explanation
Indices: 40379534--40379583 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
40379524 TGAGTTATTT
40379534 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
40379554 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
*
40379574 AAGAAAGCAA
1 AAGTAAGCAA
40379584 AGACTATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.58, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:40397857 original size:9 final size:9
Alignment explanation
Indices: 40397843--40397889 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
40397833 TTTATAAATG
40397843 TTAATATTT
1 TTAATATTT
40397852 TTAATAATTT
1 TTAAT-ATTT
40397862 TTAATATTT
1 TTAATATTT
*
40397871 TT-CTATTT
1 TTAATATTT
*
40397879 TAAATATTT
1 TTAATATTT
40397888 TT
1 TT
40397890 TTATAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.19
9 17 0.53
10 9 0.28
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
TTAATATTT
Found at i:40397858 original size:19 final size:18
Alignment explanation
Indices: 40397831--40397872 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
40397821 TTTCTATATG
40397831 TTTTTATAAATGTTAATA
1 TTTTTATAAATGTTAATA
* *
40397849 TTTTTAATAATTTTTAATA
1 TTTTT-ATAAATGTTAATA
40397868 TTTTT
1 TTTTT
40397873 CTATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATAAATGTTAATA
Found at i:40397863 original size:10 final size:10
Alignment explanation
Indices: 40397843--40397931 Score: 62
Period size: 10 Copynumber: 9.1 Consensus size: 10
40397833 TTTATAAATG
40397843 TTAAT-ATTT
1 TTAATAATTT
40397852 TTAATAATTT
1 TTAATAATTT
40397862 TTAAT-ATTT
1 TTAATAATTT
*
40397871 TT-CT-ATTT
1 TTAATAATTT
* *
40397879 TAAATATTTT
1 TTAATAATTT
*
40397889 TTTATAATTT
1 TTAATAATTT
40397899 TTCCAAATAATTT
1 TT---AATAATTT
* *
40397912 TTTATAA-GT
1 TTAATAATTT
40397921 TTAATAATTT
1 TTAATAATTT
40397931 T
1 T
40397932 ATTGATATTT
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
8 6 0.10
9 19 0.31
10 27 0.44
13 9 0.15
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
TTAATAATTT
Found at i:40397877 original size:27 final size:28
Alignment explanation
Indices: 40397847--40397901 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
40397837 TAAATGTTAA
*
40397847 TATTTTTAATAATTTTTAAT-ATTTTTC
1 TATTTTAAATAATTTTTAATAATTTTTC
* *
40397874 TATTTTAAATATTTTTTTATAATTTTTC
1 TATTTTAAATAATTTTTAATAATTTTTC
40397902 CAAATAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (28 bp):
TATTTTAAATAATTTTTAATAATTTTTC
Found at i:40408395 original size:21 final size:21
Alignment explanation
Indices: 40408349--40408401 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
40408339 GTGTGGTAAT
*
40408349 TATAAATACATGTGTAATAAA
1 TATATATACATGTGTAATAAA
* *
40408370 TATATATACATTTGTAATTAA
1 TATATATACATGTGTAATAAA
*
40408391 TATATGTACAT
1 TATATATACAT
40408402 ACTCATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (21 bp):
TATATATACATGTGTAATAAA
Found at i:40413269 original size:47 final size:47
Alignment explanation
Indices: 40413177--40413775 Score: 973
Period size: 47 Copynumber: 12.6 Consensus size: 47
40413167 TATTTGAATA
*
40413177 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGTCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40413226 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40413273 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
40413322 AATGTGAAATTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40413369 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40413418 AATGTGAAATTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40413465 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
40413512 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40413559 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
40413608 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40413655 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
40413702 AATGTGAAAGTGTATATATGCGACAGGGCCGAGTGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40413749 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
40413776 TCCCGAAGGG
Statistics
Matches: 516, Mismatches: 28, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
47 370 0.72
49 146 0.28
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40413289 original size:96 final size:96
Alignment explanation
Indices: 40413177--40413775 Score: 1012
Period size: 96 Copynumber: 6.3 Consensus size: 96
40413167 TATTTGAATA
*
40413177 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGTCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
40413242 TATGTGATAAGGCCGAATGGCCAATGTGATG
66 TATGTGATAAGGCCGAATGGCCAATGTGATG
*
40413273 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAATTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
40413338 TATGTGATAAGGCCGAATGGCCAATGTGATG
66 TATGTGATAAGGCCGAATGGCCAATGTGATG
*
40413369 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAATTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* * *
40413434 TATGTGATAAGGCCTAATAGCCGATGTGATG
66 TATGTGATAAGGCCGAATGGCCAATGTGATG
40413465 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* * *
40413528 TATGTGATAAGGCCTAATAGCCGATGTGATG
66 TATGTGATAAGGCCGAATGGCCAATGTGATG
40413559 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* *
40413624 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCGAATGGCCAATGTGATG
40413655 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* * * *
40413718 TATGCGACAGGGCCGAGTGGCCAATGTGATG
66 TATGTGATAAGGCCGAATGGCCAATGTGATG
*
40413749 GATGTGAAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
40413776 TCCCGAAGGG
Statistics
Matches: 485, Mismatches: 14, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
94 190 0.39
95 1 0.00
96 294 0.61
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (96 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
TATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:40413365 original size:143 final size:143
Alignment explanation
Indices: 40413177--40413775 Score: 981
Period size: 143 Copynumber: 4.2 Consensus size: 143
40413167 TATTTGAATA
*
40413177 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGTCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* *
40413242 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
64 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
40413307 ATGGCCGATGTGATG
129 ATGGCCGATGTGATG
* * *
40413322 AATGTGAAATTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
*
40413387 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA-T-TGTATATATGTGATAAGGCCTA
64 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
*
40413450 ATAGCCGATGTGATG
129 ATGGCCGATGTGATG
40413465 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
40413530 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
66 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
40413595 GGCCGATGTGATG
131 GGCCGATGTGATG
40413608 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * *
40413673 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGCGACAGGGCCGAGT
66 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
*
40413736 GGCCAATGTGATG
131 GGCCGATGTGATG
* *
40413749 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
40413776 TCCCGAAGGG
Statistics
Matches: 427, Mismatches: 23, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
141 97 0.23
142 1 0.00
143 275 0.64
144 1 0.00
145 53 0.12
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (143 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
GGCCGATGTGATG
Found at i:40413995 original size:37 final size:37
Alignment explanation
Indices: 40413894--40413995 Score: 168
Period size: 37 Copynumber: 2.8 Consensus size: 37
40413884 CCGAGCTCTA
*
40413894 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
40413931 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
* * *
40413968 AAGACCCGATAACTTCATGTGGAGATTT
1 AAGACCCGATGACTACGTGTGGAGATTT
40413996 CGTCTGAGCT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
Found at i:40418885 original size:13 final size:13
Alignment explanation
Indices: 40418869--40418895 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40418859 CGATCTCTTC
40418869 TGGGTATTCTATA
1 TGGGTATTCTATA
40418882 TGGGTATTCTATA
1 TGGGTATTCTATA
40418895 T
1 T
40418896 ATTCTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:40422735 original size:15 final size:15
Alignment explanation
Indices: 40422715--40422744 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40422705 TAGTTATATC
40422715 ACCAATTGGATTTTA
1 ACCAATTGGATTTTA
40422730 ACCAATTGGATTTTA
1 ACCAATTGGATTTTA
40422745 GTTAAGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
ACCAATTGGATTTTA
Found at i:40425822 original size:22 final size:21
Alignment explanation
Indices: 40425797--40425837 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40425787 TTAAAGGTTA
*
40425797 ATAAATAAATAGTTAATAAATG
1 ATAAATAAA-AGGTAATAAATG
*
40425819 ATAAATTAAAGGTAATAAA
1 ATAAATAAAAGGTAATAAA
40425838 ATAAAACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (21 bp):
ATAAATAAAAGGTAATAAATG
Found at i:40426594 original size:25 final size:24
Alignment explanation
Indices: 40426556--40426608 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
40426546 GTCATTAGGG
*
40426556 TTACCAATTTCAGCTCGTATGAGC
1 TTACCAATTTCAGCTCGCATGAGC
*
40426580 TTACCGATTCTCAGCTCGCATGAGC
1 TTACCAATT-TCAGCTCGCATGAGC
40426605 TTAC
1 TTAC
40426609 TGTTATTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (24 bp):
TTACCAATTTCAGCTCGCATGAGC
Found at i:40434873 original size:22 final size:21
Alignment explanation
Indices: 40434845--40434909 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
40434835 ATTATTTTGC
40434845 AAAAAATAAAAATAAATAAAAT
1 AAAAAATAAAAA-AAATAAAAT
* *
40434867 AAAAAATAACACAAAATTAAAT
1 AAAAAATAA-AAAAAATAAAAT
40434889 AAAAAA-ATAAAAAAATAAAAT
1 AAAAAATA-AAAAAAATAAAAT
40434910 TACAGAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 11 0.30
22 24 0.65
23 2 0.05
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAAAATAAAAAAAATAAAAT
Found at i:40442945 original size:70 final size:69
Alignment explanation
Indices: 40442868--40443001 Score: 200
Period size: 70 Copynumber: 1.9 Consensus size: 69
40442858 AAACAAGTCG
*
40442868 ATGCTCATAAGAGCTAGTCCAACCGAAACACGCCGATGCT-AATAAGAGTTA-TTCCAACCGAAA
1 ATGCTCATAAGAGCTAGTCCAACCGAAACACGCC-ATGCTCAA-AAGAGCTAGTT-CAACCGAAA
40442931 CACGCTA
63 CACGCTA
* *
40442938 ATGCTCATAAGAGCTAGTCCAACTGAAACACGTCATGCTCAAAAGAGCTAGTTCAACCGAAACA
1 ATGCTCATAAGAGCTAGTCCAACCGAAACACGCCATGCTCAAAAGAGCTAGTTCAACCGAAACA
40443002 TGCCAAACAG
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
69 23 0.39
70 36 0.61
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (69 bp):
ATGCTCATAAGAGCTAGTCCAACCGAAACACGCCATGCTCAAAAGAGCTAGTTCAACCGAAACAC
GCTA
Found at i:40442966 original size:35 final size:35
Alignment explanation
Indices: 40442833--40443001 Score: 180
Period size: 35 Copynumber: 4.9 Consensus size: 35
40442823 AACACACCAG
* * * * * *
40442833 ATGCTCGTAAGAGCCAATCCAACCAAAACAAG-TCG
1 ATGCTCATAAGAGCTAGTCCAACCGAAACACGCT-A
**
40442868 ATGCTCATAAGAGCTAGTCCAACCGAAACACGCCG
1 ATGCTCATAAGAGCTAGTCCAACCGAAACACGCTA
* * *
40442903 ATGCTAATAAGAGTTATTCCAACCGAAACACGCTA
1 ATGCTCATAAGAGCTAGTCCAACCGAAACACGCTA
* *
40442938 ATGCTCATAAGAGCTAGTCCAACTGAAACACG-TC
1 ATGCTCATAAGAGCTAGTCCAACCGAAACACGCTA
* *
40442972 ATGCTCAAAAGAGCTAGTTCAACCGAAACA
1 ATGCTCATAAGAGCTAGTCCAACCGAAACA
40443002 TGCCAAACAG
Statistics
Matches: 114, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
34 28 0.25
35 86 0.75
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (35 bp):
ATGCTCATAAGAGCTAGTCCAACCGAAACACGCTA
Found at i:40446606 original size:22 final size:22
Alignment explanation
Indices: 40446581--40446623 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40446571 TTGTCTGCAC
* *
40446581 GACTTATATTTTATGTAATTAA
1 GACTTATATCTTATCTAATTAA
*
40446603 GACTTGTATCTTATCTAATTA
1 GACTTATATCTTATCTAATTA
40446624 GGGCTACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (22 bp):
GACTTATATCTTATCTAATTAA
Found at i:40452691 original size:71 final size:71
Alignment explanation
Indices: 40452608--40452750 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
40452598 TCAAAACCCA
40452608 AGTTAGTGTGTCTGTACATGGTTCAACTGAATTCATCCATAACAAGGATTTTGCACATGTATTCA
1 AGTTAGTGTGTCTGTACATGGTTCAACTGAATTCATCCATAACAAGGATTTTGCACATGTATTCA
40452673 TATCAT
66 TATCAT
40452679 AGTTAGTGTGTCTGTACATGGTTCAACTGAATTCATCCATAACAAGGATTTTGCACATGTATTCA
1 AGTTAGTGTGTCTGTACATGGTTCAACTGAATTCATCCATAACAAGGATTTTGCACATGTATTCA
40452744 TATCAT
66 TATCAT
40452750 A
1 A
40452751 TAGATCAACA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (71 bp):
AGTTAGTGTGTCTGTACATGGTTCAACTGAATTCATCCATAACAAGGATTTTGCACATGTATTCA
TATCAT
Found at i:40456592 original size:19 final size:20
Alignment explanation
Indices: 40456568--40456613 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
40456558 ATTCTTGTCG
40456568 AAAAATAATTAAA-TAT-TAT
1 AAAAATAATTAAATTATGT-T
40456587 AAAAATAATTAAATTATGTT
1 AAAAATAATTAAATTATGTT
40456607 AAAAATA
1 AAAAATA
40456614 TGAACATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.52
20 11 0.44
21 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAATAATTAAATTATGTT
Found at i:40459177 original size:50 final size:49
Alignment explanation
Indices: 40459123--40459260 Score: 118
Period size: 50 Copynumber: 2.8 Consensus size: 49
40459113 TCATTGAGAT
* *
40459123 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 TATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGA
* * * * * *
40459173 TATGAGA-ACTCCTATGTAATACCATATCTCGGATATGACATTGGCA-GTA
1 TATGAGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACG-A
* * * * *
40459222 CAAGAAACATCCCATGTAAGACCATGTTTGGGACATGGC
1 TATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGC
40459261 TTTTGCATGT
Statistics
Matches: 67, Mismatches: 18, Indels: 7
0.73 0.20 0.08
Matches are distributed among these distances:
48 1 0.01
49 28 0.42
50 38 0.57
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (49 bp):
TATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGA
Found at i:40462079 original size:36 final size:36
Alignment explanation
Indices: 40462039--40462110 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
40462029 GGGTAACCAA
40462039 CCAAAA-TCGAGGGACGCAAGGACTACAATCCAACTT
1 CCAAAACT-GAGGGACGCAAGGACTACAATCCAACTT
40462075 CCAAAACTGAGGGACGCAAGGACTACAATCCAACTT
1 CCAAAACTGAGGGACGCAAGGACTACAATCCAACTT
40462111 TTATAACTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.39, C:0.28, G:0.19, T:0.14
Consensus pattern (36 bp):
CCAAAACTGAGGGACGCAAGGACTACAATCCAACTT
Found at i:40463925 original size:13 final size:14
Alignment explanation
Indices: 40463907--40463947 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
40463897 TTTTCAAAGA
40463907 TATGGTTTAGGA-T
1 TATGGTTTAGGACT
*
40463920 TATGGTTTATGACT
1 TATGGTTTAGGACT
*
40463934 TACGGTTTA-GACT
1 TATGGTTTAGGACT
40463947 T
1 T
40463948 TAGGGGTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (14 bp):
TATGGTTTAGGACT
Found at i:40464038 original size:25 final size:26
Alignment explanation
Indices: 40464004--40464055 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
40463994 TTGTTTGTGG
**
40464004 TTTACGGGTTTAATTTTTATGGTTAA
1 TTTACGGGTTTAAGATTTATGGTTAA
40464030 TTTA-GGGTTTAAGATTTATGGTTAA
1 TTTACGGGTTTAAGATTTATGGTTAA
40464055 T
1 T
40464056 GTGTACGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.25, C:0.02, G:0.21, T:0.52
Consensus pattern (26 bp):
TTTACGGGTTTAAGATTTATGGTTAA
Found at i:40466238 original size:25 final size:24
Alignment explanation
Indices: 40466210--40466257 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40466200 TGCAGGCTTC
40466210 TAATACTGTTTGTTCATAAATTTGG
1 TAATACT-TTTGTTCATAAATTTGG
* *
40466235 TAATAGTTTTGTTCATAACTTTG
1 TAATACTTTTGTTCATAAATTTG
40466258 AAACTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (24 bp):
TAATACTTTTGTTCATAAATTTGG
Found at i:40467338 original size:16 final size:16
Alignment explanation
Indices: 40467317--40467349 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40467307 TATTATACAT
40467317 AACTTACATAACTTAC
1 AACTTACATAACTTAC
40467333 AACTTACATAACTTAC
1 AACTTACATAACTTAC
40467349 A
1 A
40467350 TTAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:40467485 original size:103 final size:103
Alignment explanation
Indices: 40467336--40467611 Score: 543
Period size: 103 Copynumber: 2.7 Consensus size: 103
40467326 AACTTACAAC
40467336 TTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAC
1 TTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAC
40467401 TTACAACTTACATAACTTACATTAATATTACACATAAA
66 TTACAACTTACATAACTTACATTAATATTACACATAAA
*
40467439 TTACATAACTTACATTAAAATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAC
1 TTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAC
40467504 TTACAACTTACATAACTTACATTAATATTACACATAAA
66 TTACAACTTACATAACTTACATTAATATTACACATAAA
40467542 TTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAC
1 TTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAC
40467607 TTACA
66 TTACA
40467612 TTAATATTAC
Statistics
Matches: 171, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 171 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (103 bp):
TTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAC
TTACAACTTACATAACTTACATTAATATTACACATAAA
Found at i:40467539 original size:22 final size:22
Alignment explanation
Indices: 40467513--40467634 Score: 78
Period size: 22 Copynumber: 5.6 Consensus size: 22
40467503 CTTACAACTT
40467513 ACATAACTTACATTAATATTAC
1 ACATAACTTACATTAATATTAC
* *
40467535 ACATAAATTACA-TAA-CTTAC
1 ACATAACTTACATTAATATTAC
* *
40467555 A-TTAATATTATACA-TAA-ATT--
1 ACAT-A-ACT-TACATTAATATTAC
* *
40467575 ACATAACTTAATTAATTAATATTAT
1 ACATAACTT-A--CATTAATATTAC
40467600 ACATAACTTACATTAATATTAC
1 ACATAACTTACATTAATATTAC
*
40467622 ACATAAATTACAT
1 ACATAACTTACAT
40467635 AACTTACATT
Statistics
Matches: 78, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
18 1 0.01
19 4 0.05
20 8 0.10
21 7 0.09
22 45 0.58
23 3 0.04
24 1 0.01
25 9 0.12
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (22 bp):
ACATAACTTACATTAATATTAC
Found at i:40467637 original size:190 final size:190
Alignment explanation
Indices: 40467409--40467992 Score: 1075
Period size: 190 Copynumber: 3.1 Consensus size: 190
40467399 ACTTACAACT
*
40467409 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAA-A-ATTATACATAAATT
1 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACA-TA-ACTTAAATT
40467472 ACATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAACTTACATTAATATTACAC
64 ACATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAACTTACATTAATATTACAC
40467537 ATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
129 ATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
40467599 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
1 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
*
40467664 ATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAATTTACATTAATATTACACAT
66 ATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAACTTACATTAATATTACACAT
* *
40467729 AAATTACATAACTTACATTAATA-CATAACTTAAATTACATAACTTAATTAATTAATATTA
131 AAATTACATAACTTACATTAATATTAT-ACATAAATTACATAACTTAATTAATTAATATTA
40467789 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
1 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
40467854 ATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAACTTACATTAATATTACACAT
66 ATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAACTTACATTAATATTACACAT
*
40467919 AAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTCATATTA
131 AAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
40467979 TACATAACTTACAT
1 TACATAACTTACAT
40467993 AACTTACAAC
Statistics
Matches: 382, Mismatches: 8, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
189 2 0.01
190 374 0.98
191 5 0.01
192 1 0.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (190 bp):
TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
ATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAACTTACATTAATATTACACAT
AAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
Found at i:40467675 original size:293 final size:292
Alignment explanation
Indices: 40467302--40468045 Score: 1019
Period size: 293 Copynumber: 2.6 Consensus size: 292
40467292 TAGAAGCCAC
* *
40467302 ATTAATATTATACATAACTTACA-TAA-CTT--AC--AACTTACATAACTTACATTAATATTATA
1 ATTAATATTATACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATATTATA
40467361 CATAAATTACATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAACTTACATTAA
66 CATAAATTACATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAACTTACATTAA
40467426 TATTACACATAAATTACATAACTTACATTAA-A-ATTATACATAAATTACATAACTTAATTAATT
131 TATTACACATAAATTACATAACTTACATTAATACA-TA-ACATAAATTACATAACTTAATTAATT
* *
40467489 AATATTATACATAACTTACAACTT-ACA-TA-ACTTACATTA-ATATTAC-ACATAAATTACATA
194 AATATTATACATAACTTAC-A-TTAACATTACACATAAATTACATA--ACTACATAAA-TACATA
* * *
40467549 ACTTACATTA-AT-ATTATACATAAATTACATAACTTA-A-TTA
254 ACTTAAATTACATAACT-TA-ATAAATTA-AT-A-TTATACATA
*
40467589 ATTAATATTATACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATA-CATA
1 ATTAATATTATACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATATTAT-
* *
40467653 ACTTAAATTACATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAATTTACATTA
65 ACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAACTTACATTA
*
40467718 ATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTACATAACTTAATTAATTA
130 ATATTACACATAAATTACATAACTTACATTAATACATAACATAAATTACATAACTTAATTAATTA
* *
40467783 ATATTATACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTA
195 ATATTATACATAACTTACATTAACATTACACATAAATTACATAAC-TACATAAATACATAACTTA
*
40467848 AATTACATAACTTAATTAATTAATATTATACATA
259 AATTACATAACTTAATAAATTAATATTATACATA
*
40467882 ACTTACA-ACT-TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATATTA
1 A-TTA-ATATTATACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATATTA
*
40467945 TACATAAATTACATAACTTAATTAATTCATATTATACATAACTTACATAACTTAC--AACTTACA
64 TACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC--AACTTACATAACTTACA
*
40468008 TTAATATTATACATAAATTACATAACTTACATTAATAC
127 TTAATATTACACATAAATTACATAACTTACATTAATAC
40468046 GACATAACTT
Statistics
Matches: 413, Mismatches: 20, Indels: 42
0.87 0.04 0.09
Matches are distributed among these distances:
287 23 0.06
288 3 0.01
289 2 0.00
291 7 0.02
292 7 0.02
293 307 0.74
294 40 0.10
295 22 0.05
296 2 0.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.38
Consensus pattern (292 bp):
ATTAATATTATACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATATTATA
CATAAATTACATAACTTAATTAATTAATATTATACATAACTTACAACTTACATAACTTACATTAA
TATTACACATAAATTACATAACTTACATTAATACATAACATAAATTACATAACTTAATTAATTAA
TATTATACATAACTTACATTAACATTACACATAAATTACATAACTACATAAATACATAACTTAAA
TTACATAACTTAATAAATTAATATTATACATA
Found at i:40467706 original size:103 final size:103
Alignment explanation
Indices: 40467599--40468045 Score: 689
Period size: 103 Copynumber: 4.5 Consensus size: 103
40467589 ATTAATATTA
40467599 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
1 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
40467664 ATAACTTAATTAATTAATATTATACATAACTTACAACT
66 ATAACTTAATTAATTAATATTATACATAACTTACAACT
*
40467702 TACATAATTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
1 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
40467767 ATAACTTAATTAATTAATATTATACATAACTTAC-A-T
66 ATAACTTAATTAATTAATATTATACATAACTTACAACT
40467803 TA-AT-A-TTAC---------AC--ATAAATTACATAACTTACATTAATACATAACTTAAATTAC
1 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
40467854 ATAACTTAATTAATTAATATTATACATAACTTACAACT
66 ATAACTTAATTAATTAATATTATACATAACTTACAACT
* *
40467892 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATA-TTATACATAAATTA
1 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATA-ACTTAAATTA
*
40467956 CATAACTTAATTAATTCATATTATACATAACTTACATAACT
65 CATAACTTAATTAATTAATATTATACATAACTTAC--AACT
*
40467997 TAC--AACTTACATTAATATTATACATAAATTACATAACTTACATTAATAC
1 TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATAC
40468046 GACATAACTT
Statistics
Matches: 319, Mismatches: 5, Indels: 39
0.88 0.01 0.11
Matches are distributed among these distances:
87 74 0.23
88 1 0.00
89 5 0.02
90 2 0.01
91 1 0.00
92 4 0.01
98 4 0.01
99 1 0.00
100 2 0.01
101 5 0.02
102 3 0.01
103 210 0.66
105 7 0.02
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (103 bp):
TACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTAC
ATAACTTAATTAATTAATATTATACATAACTTACAACT
Found at i:40473642 original size:21 final size:21
Alignment explanation
Indices: 40473616--40473661 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
40473606 CTACAACTTA
* * *
40473616 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAACGAGAG
40473637 AAGCAGAGGCAGCAACGAGAG
1 AAGCAGAGGCAGCAACGAGAG
40473658 AAGC
1 AAGC
40473662 TAAGGTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.39, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCAGCAACGAGAG
Found at i:40473668 original size:87 final size:87
Alignment explanation
Indices: 40473567--40473733 Score: 266
Period size: 87 Copynumber: 1.9 Consensus size: 87
40473557 GGCAACATCA
* *
40473567 AGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTTAAAGCAGATGCGGCA
1 AGAGAAGCTAAGGTTCAACAAAAG-TATGAAGAACTCCAAC-AGCAACTTAAAGCAGATGCGGCA
*
40473630 GCGAGAGAAGCAGAGGCAGCAACG
64 GCGAGAAAAGCAGAGGCAGCAACG
*
40473654 AGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCAACAGCAGCTTAAAGCAGATGCGGCAGC
1 AGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCAACAGCAACTTAAAGCAGATGCGGCAGC
40473719 GAGAAAAGCAGAGGC
66 GAGAAAAGCAGAGGC
40473734 TAAAGCGAGG
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
86 1 0.01
87 68 0.92
88 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.28, T:0.11
Consensus pattern (87 bp):
AGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCAACAGCAACTTAAAGCAGATGCGGCAGC
GAGAAAAGCAGAGGCAGCAACG
Found at i:40473754 original size:21 final size:21
Alignment explanation
Indices: 40473730--40473770 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40473720 AGAAAAGCAG
40473730 AGGCT-AAAGCGAGGGAAGTAC
1 AGGCTGAAA-CGAGGGAAGTAC
*
40473751 AGGCTGCAACGAGGGAAGTA
1 AGGCTGAAACGAGGGAAGTA
40473771 GAACAGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.37, C:0.15, G:0.39, T:0.10
Consensus pattern (21 bp):
AGGCTGAAACGAGGGAAGTAC
Found at i:40474138 original size:43 final size:42
Alignment explanation
Indices: 40474077--40474371 Score: 371
Period size: 43 Copynumber: 7.0 Consensus size: 42
40474067 CAAAATTAGC
* *
40474077 GGCATTTTTTGCATAAGCGCCACTAAAGACCATGGTCTATAGT
1 GGCATTTTTTG-TTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
40474120 GGCATTTTTCGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCATTTTTTG-TTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
40474163 GGCGTTTTTTGGTTAAGCGCCGCTAAAGACCATGGTCTGTAGT
1 GGCATTTTTT-GTTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
40474206 GGCGTTTTTTGGTTAAGCGCCGCTAAAGACCATTGTCTATAGT
1 GGCATTTTTT-GTTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * * *
40474249 GGCATTTTTTGGTAAGCGTCGCTAAACA-CACGGTTTATAGT
1 GGCATTTTTTGTTAAGCGCCGCTAAAGACCATGGTCTATAGT
** *
40474290 GGCGGTTTTT-TTAAGCGCGGCTAAAGACCATGGTCTATAGT
1 GGCATTTTTTGTTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
40474331 GGCATTTTTAT-TTAAGCGCCGCTACAGACCATGGTCTATAG
1 GGCATTTTT-TGTTAAGCGCCGCTAAAGACCATGGTCTATAG
40474372 CGGCGTTGTA
Statistics
Matches: 221, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
40 13 0.06
41 36 0.16
42 44 0.20
43 127 0.57
44 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (42 bp):
GGCATTTTTTGTTAAGCGCCGCTAAAGACCATGGTCTATAGT
Found at i:40479615 original size:13 final size:12
Alignment explanation
Indices: 40479597--40479638 Score: 54
Period size: 10 Copynumber: 3.7 Consensus size: 12
40479587 TGTGAGCGAG
40479597 AAAAGAACATTGA
1 AAAAGAA-ATTGA
40479610 AAAAGAAATTG-
1 AAAAGAAATTGA
40479621 -AAAGAAA-TGA
1 AAAAGAAATTGA
40479631 AAAAGAAA
1 AAAAGAAA
40479639 AAGATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 7 0.26
11 7 0.26
12 4 0.15
13 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.17, T:0.12
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:40479698 original size:12 final size:12
Alignment explanation
Indices: 40479681--40479759 Score: 56
Period size: 12 Copynumber: 6.6 Consensus size: 12
40479671 AGTGAAAAGC
40479681 AAAAAGAGATTG
1 AAAAAGAGATTG
*
40479693 AAAAAGAAATTG
1 AAAAAGAGATTG
*
40479705 --AAAGAGA-AG
1 AAAAAGAGATTG
*
40479714 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
40479729 AAAAAGAAATTG
1 AAAAAGAGATTG
*
40479741 AAAAAGAGTTTG
1 AAAAAGAGATTG
*
40479753 CAAAAGA
1 AAAAAGA
40479760 AACGAGTGAA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 29 0.56
13 5 0.10
15 7 0.13
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:40479722 original size:15 final size:15
Alignment explanation
Indices: 40479704--40479737 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40479694 AAAAGAAATT
40479704 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
40479719 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
40479734 GAAA
1 GAAA
40479738 TTGAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:40479743 original size:21 final size:20
Alignment explanation
Indices: 40479691--40479743 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 20
40479681 AAAAAGAGAT
40479691 TGAAAAAGAAATTGAAAGA-
1 TGAAAAAGAAATTGAAAGAG
*
40479710 -GAAGAA-AAA--GAAAGAG
1 TGAAAAAGAAATTGAAAGAG
40479726 TGGAAAAAGAAATTGAAA
1 T-GAAAAAGAAATTGAAA
40479744 AAGAGTTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
15 6 0.23
17 3 0.12
18 10 0.38
19 3 0.12
21 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (20 bp):
TGAAAAAGAAATTGAAAGAG
Found at i:40485829 original size:22 final size:21
Alignment explanation
Indices: 40485804--40485847 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
40485794 TGATAAACTT
40485804 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
40485826 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
40485847 T
1 T
40485848 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:40493073 original size:27 final size:26
Alignment explanation
Indices: 40493032--40493093 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
40493022 AAAGGTTGTT
*
40493032 AAATGATCAAAATACCCTCAAAAGGTA
1 AAATGACCAAAATACCC-CAAAAGGTA
* * *
40493059 AAATGACCAACATACCCCTAGAGGTA
1 AAATGACCAAAATACCCCAAAAGGTA
*
40493085 AAATTACCA
1 AAATGACCA
40493094 TTTTACCCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.48, C:0.23, G:0.11, T:0.18
Consensus pattern (26 bp):
AAATGACCAAAATACCCCAAAAGGTA
Found at i:40497495 original size:48 final size:46
Alignment explanation
Indices: 40497442--40497547 Score: 140
Period size: 48 Copynumber: 2.3 Consensus size: 46
40497432 ACAATAATGT
**
40497442 AGATAAACTGCCACATAATCAAAATTGTGGACAAGCCACCAAAATCGC
1 AGATAAACTGCCACATAATC-AAATCATGGACAAGCCACC-AAATCGC
* * *
40497490 AGATAAACTACCACATAATCAAATCATGGACAAGCCACCACATTGC
1 AGATAAACTGCCACATAATCAAATCATGGACAAGCCACCAAATCGC
*
40497536 AAATAAACTGCC
1 AGATAAACTGCC
40497548 CCATTCTTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 15 0.29
47 17 0.33
48 19 0.37
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.17
Consensus pattern (46 bp):
AGATAAACTGCCACATAATCAAATCATGGACAAGCCACCAAATCGC
Found at i:40499182 original size:53 final size:53
Alignment explanation
Indices: 40499100--40499203 Score: 181
Period size: 53 Copynumber: 2.0 Consensus size: 53
40499090 CGAGGAAAGA
40499100 TGAAAACCATGAATTAGCTCGATCATACTTTTACGCTCTAGTTGTCAAGCTGG
1 TGAAAACCATGAATTAGCTCGATCATACTTTTACGCTCTAGTTGTCAAGCTGG
* **
40499153 TGAAAATCATGAATTAGCTCGATTGTACTTTTACGCTCTAGTTGTCAAGCT
1 TGAAAACCATGAATTAGCTCGATCATACTTTTACGCTCTAGTTGTCAAGCT
40499204 AAGTTCATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (53 bp):
TGAAAACCATGAATTAGCTCGATCATACTTTTACGCTCTAGTTGTCAAGCTGG
Found at i:40499315 original size:20 final size:19
Alignment explanation
Indices: 40499290--40499356 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
40499280 ACTGAATTAT
40499290 CCCCTGTTTGTACTTAGGTA
1 CCCCTGTTTGTACTTA-GTA
* * *
40499310 CCCCTGAATTGCACATACGTA
1 CCCCTG-TTTGTACTTA-GTA
* *
40499331 CCCTTATTTGTACTTTAGTA
1 CCCCTGTTTGTAC-TTAGTA
40499351 CCCCTG
1 CCCCTG
40499357 AATTACACAT
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.36
Consensus pattern (19 bp):
CCCCTGTTTGTACTTAGTA
Found at i:40499333 original size:21 final size:21
Alignment explanation
Indices: 40499307--40499370 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
40499297 TTGTACTTAG
40499307 GTACCCCTGAATTGCACATAC
1 GTACCCCTGAATTGCACATAC
* * * *
40499328 GTA-CCCTTATTTGTACTTTA-
1 GTACCCCTGAATTGCAC-ATAC
*
40499348 GTACCCCTGAATTACACATAC
1 GTACCCCTGAATTGCACATAC
40499369 GT
1 GT
40499371 GCCCATGTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (21 bp):
GTACCCCTGAATTGCACATAC
Found at i:40499353 original size:41 final size:41
Alignment explanation
Indices: 40499296--40499396 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 41
40499286 TTATCCCCTG
* *
40499296 TTTGTACTTAGGTACCCCTGAATTGCACATACGTACCCTTA
1 TTTGTACTTAGGTACCCCTGAATTACACATACGTACCCATA
* *
40499337 TTTGTACTTTA-GTACCCCTGAATTACACATACGTGCCCATG
1 TTTGTAC-TTAGGTACCCCTGAATTACACATACGTACCCATA
* *
40499378 TTTGTACATCGGTACCCCT
1 TTTGTACTTAGGTACCCCT
40499397 CATATGTGTC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 1 0.02
41 48 0.92
42 3 0.06
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.35
Consensus pattern (41 bp):
TTTGTACTTAGGTACCCCTGAATTACACATACGTACCCATA
Found at i:40499454 original size:41 final size:41
Alignment explanation
Indices: 40499397--40499489 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
40499387 CGGTACCCCT
* * *
40499397 CATATGTGTCCCTGTTTGTACTTC-AGTACCCCTAAATTGCA
1 CATATGTGCCCCTGTTTGCACTTCGA-TACCCCTAAATAGCA
* *
40499438 CATATGTGCCCCTGTTTGCACTTCGATACCCTTGAATAGCA
1 CATATGTGCCCCTGTTTGCACTTCGATACCCCTAAATAGCA
*
40499479 CATACGTGCCC
1 CATATGTGCCC
40499490 TATTTACACT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 44 0.98
42 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (41 bp):
CATATGTGCCCCTGTTTGCACTTCGATACCCCTAAATAGCA
Found at i:40506313 original size:41 final size:41
Alignment explanation
Indices: 40506249--40506367 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 41
40506239 GTGTAAACTG
*
40506249 AGGCATGTATATGCTATTCAAGGGTACCAAAGTACAAATAA
1 AGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAATAA
* * *
40506290 AGGCATGTATGTGCAATTTAAGGGTACCGAAGTACAAAT-A
1 AGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAATAA
* * * * *
40506330 GGGCACGTATATACAATTC-AGGCGTACCGAAGTGCAAA
1 AGGCATGTATATGCAATTCAAGG-GTACCAAAGTACAAA
40506368 CAGGGGATAA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 29 0.43
41 35 0.52
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (41 bp):
AGGCATGTATATGCAATTCAAGGGTACCAAAGTACAAATAA
Found at i:40506358 original size:40 final size:39
Alignment explanation
Indices: 40506250--40506372 Score: 129
Period size: 40 Copynumber: 3.1 Consensus size: 39
40506240 TGTAAACTGA
* * *
40506250 GGCATGTATATGCTATTCAAGGGTACCAAAGTACAAATAAA
1 GGCATGTATATGCAATTC-AGGGTACCGAAGTACAAAT-AG
* *
40506291 GGCATGTATGTGCAATTTAAGGGTACCGAAGTACAAATAG
1 GGCATGTATATGCAA-TTCAGGGTACCGAAGTACAAATAG
* * * *
40506331 GGCACGTATATACAATTCAGGCGTACCGAAGTGCAAACAG
1 GGCATGTATATGCAATTCAGG-GTACCGAAGTACAAATAG
40506371 GG
1 GG
40506373 GATAATTCAA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
39 5 0.07
40 31 0.45
41 31 0.45
42 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (39 bp):
GGCATGTATATGCAATTCAGGGTACCGAAGTACAAATAG
Found at i:40509969 original size:16 final size:16
Alignment explanation
Indices: 40509938--40509982 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
40509928 AAATATCTTA
40509938 AATTAATTT-T-AATT
1 AATTAATTTCTCAATT
40509952 AATTAATTTCTCAATT
1 AATTAATTTCTCAATT
*
40509968 AAATAATTTTCTCAA
1 AATTAA-TTTCTCAA
40509983 CCAAATTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 9 0.33
17 8 0.30
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTTCTCAATT
Found at i:40509980 original size:17 final size:16
Alignment explanation
Indices: 40509935--40509982 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
40509925 AATAAATATC
40509935 TTAAATTAATTT-T-AA
1 TTAAA-TAATTTCTCAA
*
40509950 TTAATTAATTTCTCAA
1 TTAAATAATTTCTCAA
40509966 TTAAATAATTTTCTCAA
1 TTAAATAA-TTTCTCAA
40509983 CCAAATTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.21
15 5 0.18
16 9 0.32
17 8 0.29
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATAATTTCTCAA
Found at i:40512844 original size:50 final size:50
Alignment explanation
Indices: 40512720--40513016 Score: 292
Period size: 50 Copynumber: 5.8 Consensus size: 50
40512710 GATAATAACA
* * * ** * * *
40512720 TGCCAAAGCCATATCCCATACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * **
40512769 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
40512819 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * *
40512869 TGCCAACGCCATGTCCTAGACATGGTCTTACATAGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
40512919 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
40512975 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40513017 TTACCCAAAT
Statistics
Matches: 210, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 129 0.61
53 2 0.01
56 39 0.19
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:40519039 original size:41 final size:41
Alignment explanation
Indices: 40518994--40519129 Score: 254
Period size: 41 Copynumber: 3.3 Consensus size: 41
40518984 TGCAATTAAT
40518994 CTCTAACTTGTTTTATTATTATTTTGGTACCTAAAAAGAGC
1 CTCTAACTTGTTTTATTATTATTTTGGTACCTAAAAAGAGC
*
40519035 CTCTAACTTGTTTTATTATTATTATGGTACCTAAAAAGAGC
1 CTCTAACTTGTTTTATTATTATTTTGGTACCTAAAAAGAGC
*
40519076 CTCTAACTTATTTTATTATTATTTTGGTACCTAAAAAGAGC
1 CTCTAACTTGTTTTATTATTATTTTGGTACCTAAAAAGAGC
40519117 CTCTAACTTGTTT
1 CTCTAACTTGTTT
40519130 CATATTTGTG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 91 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.44
Consensus pattern (41 bp):
CTCTAACTTGTTTTATTATTATTTTGGTACCTAAAAAGAGC
Found at i:40520016 original size:14 final size:15
Alignment explanation
Indices: 40519989--40520017 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40519979 GCTGCACCGT
40519989 TATAATCACAATGAA
1 TATAATCACAATGAA
40520004 TATAATC-CAATGAA
1 TATAATCACAATGAA
40520018 GAAGTGCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (15 bp):
TATAATCACAATGAA
Found at i:40529327 original size:48 final size:48
Alignment explanation
Indices: 40529275--40529366 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
40529265 AAGTACCCTA
* * *
40529275 CTTGCCAGGTACCCAACTC-ACCATGTAGCCAGCTCATTGGATAGCCAG
1 CTTGCCAAGTACCCAAC-CGACCAGGTAGCCAGCTCACTGGATAGCCAG
* *
40529323 CTTGCCAAGTACCCAACCGACTAGGTAGCCAGCTCCCTGGATAG
1 CTTGCCAAGTACCCAACCGACCAGGTAGCCAGCTCACTGGATAG
40529367 AGGTTCTCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
47 1 0.03
48 37 0.97
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.20
Consensus pattern (48 bp):
CTTGCCAAGTACCCAACCGACCAGGTAGCCAGCTCACTGGATAGCCAG
Found at i:40536918 original size:23 final size:22
Alignment explanation
Indices: 40536866--40536918 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40536856 TCCACGTCTT
*
40536866 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40536888 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40536911 TTTCTTTT
1 TTTCTTTT
40536919 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40543880 original size:24 final size:26
Alignment explanation
Indices: 40543835--40543896 Score: 92
Period size: 24 Copynumber: 2.4 Consensus size: 26
40543825 AAAAAAAATA
*
40543835 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATA-TATAACTATTTTTATTT
40543862 ACCAAAATATAT-A-TATTTTTATTT
1 ACCAAAATATATAACTATTTTTATTT
40543886 ACCAAAATATA
1 ACCAAAATATA
40543897 CCAAAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 21 0.62
25 1 0.03
26 3 0.09
27 9 0.26
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.45
Consensus pattern (26 bp):
ACCAAAATATATAACTATTTTTATTT
Found at i:40544036 original size:4 final size:4
Alignment explanation
Indices: 40544027--40544156 Score: 51
Period size: 4 Copynumber: 32.0 Consensus size: 4
40544017 GAAGGAGAGG
* * *
40544027 GAAA GAAA GAAA GAAA GGAAG GAGAG GAAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
* * *
40544075 GAAAA GGACAG GAGAA GAGAA -AAA -AAA GAAA G-AA GAAGA GGAG GAAA
1 G-AAA -GA-AA GA-AA GA-AA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA
*
40544122 GGAGAA GAAA -AAA GAAA G-AA -AAA GAAG GAAA GAAA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
40544157 AGGAAAGGAG
Statistics
Matches: 98, Mismatches: 13, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
3 19 0.19
4 49 0.50
5 26 0.27
6 4 0.04
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:40544056 original size:18 final size:18
Alignment explanation
Indices: 40544035--40544089 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
40544025 GGGAAAGAAA
40544035 GAAAGAAAGGAAGGAGAG
1 GAAAGAAAGGAAGGAGAG
**
40544053 GAAAGAAA-GAAAAAGAAG
1 GAAAGAAAGGAAGGAG-AG
40544071 GAAAGAAAAGGACAGGAGA
1 GAAAG-AAAGGA-AGGAGA
40544090 AGAGAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 5 0.17
18 15 0.52
19 3 0.10
20 3 0.10
21 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.36, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGGAAGGAGAG
Found at i:40544056 original size:22 final size:18
Alignment explanation
Indices: 40544031--40544156 Score: 74
Period size: 22 Copynumber: 6.4 Consensus size: 18
40544021 GAGAGGGAAA
40544031 GAAAGAAAGAAAGGAAGGAGAG
1 GAAAGAAAGAAA--AA-GA-AG
40544053 GAAAGAAAGAAAAAGAAG
1 GAAAGAAAGAAAAAGAAG
**
40544071 GAAAGAAAAGGACAGGAGAAG
1 GAAAG-AAA-GA-AAAAGAAG
*
40544092 AGAAAAAAAAGAAAGAAGAAG
1 -G-AAAGAAAGAAA-AAGAAG
* * * *
40544113 AGGAGGAAAGGAGAAGAA-
1 -GAAAGAAAGAAAAAGAAG
*
40544131 AAAAGAAAGAAAAAGAAG
1 GAAAGAAAGAAAAAGAAG
40544149 GAAAGAAA
1 GAAAGAAA
40544157 AGGAAAGGAG
Statistics
Matches: 81, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
17 12 0.15
18 14 0.17
19 10 0.12
20 11 0.14
21 15 0.19
22 16 0.20
23 3 0.04
ACGTcount: A:0.67, C:0.01, G:0.33, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGAAAAAGAAG
Found at i:40544068 original size:36 final size:37
Alignment explanation
Indices: 40544028--40544184 Score: 148
Period size: 37 Copynumber: 4.2 Consensus size: 37
40544018 AAGGAGAGGG
*
40544028 AAAGAAAGAAAG-AAAGGAAGGAGAGGAAAGAAAGAA
1 AAAGAAAGAAAGAAAAGGAAGGAGAAGAAAGAAAGAA
*
40544064 AAAGAAGGAAAGAAAAGGACAGGAGAAG--AGAAA-AA
1 AAAGAAAGAAAGAAAAGGA-AGGAGAAGAAAGAAAGAA
40544099 AAAGAAAG-AAGAAGAGGAGGAAAGGAGAAGAAAAAAGAAAGAA
1 AAAGAAAGAAAGAA-A--AGG-AAGGAGAAG---AAAGAAAGAA
*
40544142 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAA-AAA-AA
1 AAAGAAAGAAAGAAAAGG-AAGGAGAAGA-AAGAAAGAA
40544179 AAAGAA
1 AAAGAA
40544185 GACGAGGGAA
Statistics
Matches: 103, Mismatches: 4, Indels: 27
0.77 0.03 0.20
Matches are distributed among these distances:
34 5 0.05
35 10 0.10
36 16 0.16
37 25 0.24
38 12 0.12
39 2 0.02
41 13 0.13
42 5 0.05
43 10 0.10
44 5 0.05
ACGTcount: A:0.68, C:0.01, G:0.31, T:0.00
Consensus pattern (37 bp):
AAAGAAAGAAAGAAAAGGAAGGAGAAGAAAGAAAGAA
Found at i:40544071 original size:27 final size:27
Alignment explanation
Indices: 40544017--40544073 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
40544007 GGTGGGGGGA
*
40544017 GAAGGAGAGGGAAAGAAAGAAAGAAAG
1 GAAGGAGAGGGAAAGAAAGAAAAAAAG
40544044 GAAGGAGA-GGAAAGAAAGAAAAAGAAG
1 GAAGGAGAGGGAAAGAAAGAAAAA-AAG
40544071 GAA
1 GAA
40544074 AGAAAAGGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (27 bp):
GAAGGAGAGGGAAAGAAAGAAAAAAAG
Found at i:40544215 original size:36 final size:35
Alignment explanation
Indices: 40544028--40544217 Score: 99
Period size: 36 Copynumber: 5.3 Consensus size: 35
40544018 AAGGAGAGGG
* * * *
40544028 AAAGAAAGAAAGAA-AGGAAGGAGAGGAAAGAAAGAA
1 AAAGAAAAAAAGAAGA-G-AGGAAAGGAAGGAAAAAA
** * *
40544064 AAAGAAGGAAAGAA-A-AGGACAGGAGAAGAGAAAAA
1 AAAGAAAAAAAGAAGAGAGGAAAGGA-AGGA-AAAAA
* *
40544099 AAAG-AAAGAAGAAGAGGAGGAAAGGAGAAGAAAAAA
1 AAAGAAAAAAAGAAGA-GAGGAAAGGA-AGGAAAAAA
* *
40544135 GAAAGAAAAAGAAGGAA-AGA--AAAGGAAAGGAGAAGAG
1 -AAAGAAAAA-AA-GAAGAGAGGAAAGG-AAGGA-AAAAA
*
40544172 AAA-AAAAAAAGAAGACGAGGGAAGGAAGGAAAAAA
1 AAAGAAAAAAAGAAGA-GAGGAAAGGAAGGAAAAAA
40544207 AAAGAAAAAAA
1 AAAGAAAAAAA
40544218 TGTAATTTTT
Statistics
Matches: 124, Mismatches: 14, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
33 11 0.09
34 13 0.10
35 22 0.18
36 42 0.34
37 25 0.20
38 5 0.04
39 3 0.02
40 3 0.02
ACGTcount: A:0.68, C:0.01, G:0.31, T:0.00
Consensus pattern (35 bp):
AAAGAAAAAAAGAAGAGAGGAAAGGAAGGAAAAAA
Found at i:40544217 original size:73 final size:78
Alignment explanation
Indices: 40544054--40544217 Score: 250
Period size: 78 Copynumber: 2.2 Consensus size: 78
40544044 GAAGGAGAGG
*
40544054 AAAGAAAGAAAAAGAAGGAAAGAAAAGGACAGGAGAAGAGAAAAAAAAGAAAGAAGAAGAGGAGG
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAGAAAGAAGAAGAGGAGG
40544119 AAAGGAGAAGAAA
66 AAAGGAGAAGAAA
*
40544132 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAG-AAAAAAA-AAAGAAGACGAGGGAA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAGAAAGAAGAAGA-GG-A
40544195 GG-AAGGA-AA-AAA
64 GGAAAGGAGAAGAAA
40544207 AAAGAAA-AAAA
1 AAAGAAAGAAAA
40544218 TGTAATTTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
74 4 0.05
75 10 0.12
76 12 0.15
77 14 0.17
78 42 0.51
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.00
Consensus pattern (78 bp):
AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAGAAAGAAGAAGAGGAGG
AAAGGAGAAGAAA
Found at i:40544971 original size:27 final size:27
Alignment explanation
Indices: 40544941--40544996 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
40544931 AAAGAGGGTG
*
40544941 ATGGAGGGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAGGCGGCACCA
40544968 ATGGAGAGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAGGCGGCACCA
40544995 AT
1 AT
40544997 ATGTGGCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.34, T:0.09
Consensus pattern (27 bp):
ATGGAGAGGAATAAAAAGGCGGCACCA
Found at i:40548564 original size:18 final size:18
Alignment explanation
Indices: 40548541--40548577 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40548531 ATCCCAATGA
40548541 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
40548559 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
40548577 T
1 T
40548578 TACCACCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.46, G:0.08, T:0.35
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:40549081 original size:18 final size:18
Alignment explanation
Indices: 40549060--40549096 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40549050 TGAGTTTTCG
40549060 AATTCAAATAACTCGAAT
1 AATTCAAATAACTCGAAT
*
40549078 AATTCAAATAATTCGAAT
1 AATTCAAATAACTCGAAT
40549096 A
1 A
40549097 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTCAAATAACTCGAAT
Found at i:40550687 original size:3 final size:3
Alignment explanation
Indices: 40550679--40550722 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
40550669 TCTTAATACT
40550679 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
40550723 TAATAATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:40551552 original size:23 final size:23
Alignment explanation
Indices: 40551526--40551571 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
40551516 GCGTAACTGC
40551526 TGTATAGTAATAGGGTGCCCGAA
1 TGTATAGTAATAGGGTGCCCGAA
* *
40551549 TGTATAGTTATAGGGTGCGCGAA
1 TGTATAGTAATAGGGTGCCCGAA
40551572 GCCCACCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.33, T:0.28
Consensus pattern (23 bp):
TGTATAGTAATAGGGTGCCCGAA
Found at i:40551799 original size:26 final size:28
Alignment explanation
Indices: 40551767--40551830 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
40551757 TTTTTTTTGT
40551767 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
40551793 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
40551821 ATATTTTGGT
1 ATATTTTGGT
40551831 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 14 0.39
27 7 0.19
28 15 0.42
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:40552145 original size:21 final size:18
Alignment explanation
Indices: 40552114--40552158 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
40552104 AAAAAACCTT
*
40552114 AAAAATATTTAAAATTGCA
1 AAAAATATTTAAAATT-AA
40552133 AAAAATCATTTTAAAATTAA
1 AAAAAT-A-TTTAAAATTAA
40552153 AAAAAT
1 AAAAAT
40552159 TACAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 8 0.35
21 9 0.39
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAAATATTTAAAATTAA
Found at i:40552610 original size:8 final size:8
Alignment explanation
Indices: 40552600--40552666 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
40552590 ATATTTAAAT
*
40552600 ATTTTTTT
1 ATTTTTTA
*
40552608 ATTATTTA
1 ATTTTTTA
*
40552616 ATTTTATA
1 ATTTTTTA
40552624 ATTTTTT-
1 ATTTTTTA
*
40552631 ATTTTTAA
1 ATTTTTTA
*
40552639 ATAATTTTA
1 AT-TTTTTA
40552648 ATGATTTTTA
1 AT--TTTTTA
40552658 ATTTTTTA
1 ATTTTTTA
40552666 A
1 A
40552667 AATAATTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
7 6 0.13
8 27 0.57
9 6 0.13
10 8 0.17
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (8 bp):
ATTTTTTA
Found at i:40552643 original size:26 final size:29
Alignment explanation
Indices: 40552614--40552675 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
40552604 TTTTATTATT
*
40552614 TAATTTT-ATAATTTTTTA-TTTTT-AAA
1 TAATTTTAATAATTTTTAATTTTTTAAAA
*
40552640 TAATTTTAATGATTTTTAATTTTTTAAAA
1 TAATTTTAATAATTTTTAATTTTTTAAAA
40552669 TAATTTT
1 TAATTTT
40552676 TTGTATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.23
27 9 0.29
28 5 0.16
29 10 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (29 bp):
TAATTTTAATAATTTTTAATTTTTTAAAA
Found at i:40552676 original size:21 final size:21
Alignment explanation
Indices: 40552651--40552696 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
40552641 AATTTTAATG
*
40552651 ATTTTTAAT-TTTTTAAAATA
1 ATTTTTTATATTTTTAAAATA
*
40552671 ATTTTTTGTATTTTTAAAATA
1 ATTTTTTATATTTTTAAAATA
40552692 ATTTT
1 ATTTT
40552697 CCATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTTTTATATTTTTAAAATA
Found at i:40566718 original size:25 final size:26
Alignment explanation
Indices: 40566668--40566718 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
40566658 AGTTGTAGAG
*
40566668 AGAAAATTCTCTCAAGAGATTATTTC
1 AGAAAATTCTCTAAAGAGATTATTTC
* *
40566694 AGAAAATT-TCTAAAGATATTTTTTC
1 AGAAAATTCTCTAAAGAGATTATTTC
40566719 TAATTTACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTTC
Found at i:40570631 original size:21 final size:21
Alignment explanation
Indices: 40570593--40570645 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
40570583 ACGACAATAG
40570593 AAGCTCG-AA-AGCTGAACAA
1 AAGCTCGTAAGAGCTGAACAA
* *
40570612 AAGCTCGTAAGAGCTTAACAG
1 AAGCTCGTAAGAGCTGAACAA
*
40570633 AAGCTCATAAGAG
1 AAGCTCGTAAGAG
40570646 TTGATCCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.24
20 2 0.07
21 20 0.69
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (21 bp):
AAGCTCGTAAGAGCTGAACAA
Found at i:40572378 original size:29 final size:29
Alignment explanation
Indices: 40572343--40572400 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
40572333 ATAATACATA
*
40572343 CATGATAATACATGTAAAACGTTGAAATG
1 CATGATAATACATGTAAAAAGTTGAAATG
40572372 CATGATAATACATGTAAAAAGTTGAAATG
1 CATGATAATACATGTAAAAAGTTGAAATG
40572401 GGTGAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.28
Consensus pattern (29 bp):
CATGATAATACATGTAAAAAGTTGAAATG
Found at i:40572509 original size:11 final size:11
Alignment explanation
Indices: 40572488--40572553 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 11
40572478 GATTAATAAT
*
40572488 ATATCATAAATG
1 ATAT-ATAAATA
40572500 ATATATAAATA
1 ATATATAAATA
40572511 ATAT-TAAAT-
1 ATATATAAATA
* *
40572520 TTACATAAA-A
1 ATATATAAATA
40572530 ATATATAGAATA
1 ATATATA-AATA
*
40572542 ATACAT-AATA
1 ATATATAAATA
40572552 AT
1 AT
40572554 TTGAAGAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 2 0.05
10 20 0.45
11 12 0.27
12 10 0.23
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.35
Consensus pattern (11 bp):
ATATATAAATA
Found at i:40572602 original size:22 final size:23
Alignment explanation
Indices: 40572577--40572626 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
40572567 CATGAAAACA
40572577 TAAAATAAT-TATATGATAAATT
1 TAAAATAATATATATGATAAATT
*
40572599 TAAAATAATAATATGTGATAAATT
1 TAAAATAAT-ATATATGATAAATT
40572623 TAAA
1 TAAA
40572627 CAACATTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.36
24 16 0.64
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (23 bp):
TAAAATAATATATATGATAAATT
Found at i:40574228 original size:50 final size:50
Alignment explanation
Indices: 40574133--40574809 Score: 415
Period size: 50 Copynumber: 13.5 Consensus size: 50
40574123 TAACTCGTAA
* ** * *
40574133 CTTTAATCTGTTTAACTGTGATGTC-GAGGAAGCAAGACTCGCTGTTGTAG
1 CTTTAATCTGTTTCACTGCAATGCCTG-GGAAGCAAGATTCGCTGTTGTAG
* * * * * *
40574183 CTTCAATCTGTTCCACTACACTGCCTGGGAAGTAAGATTCACTGTTGTAG
1 CTTTAATCTGTTTCACTGCAATGCCTGGGAAGCAAGATTCGCTGTTGTAG
* * * ** *
40574233 CTTTAATCTTTTTAACTGCAATG-TTGGGGAAGCAAGATTAACCGTTGT-G
1 CTTTAATCTGTTTCACTGCAATGCCT-GGGAAGCAAGATTCGCTGTTGTAG
** * * ** *
40574282 ACTTTAATCTGTTTCACTGCACCGCCAGAGAAATAAGATTCGCTATTGTAG
1 -CTTTAATCTGTTTCACTGCAATGCCTGGGAAGCAAGATTCGCTGTTGTAG
* * * ** * * *
40574333 CTTTAATCTTTTTAACTGCAATGTC-GGGAAAGCAAGATTTACCGATGTGG
1 CTTTAATCTGTTTCACTGCAATGCCTGGG-AAGCAAGATTCGCTGTTGTAG
* * ** * * *
40574383 CTTTAATCTATTCCACTGCACCGCTTGAGAAGTAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTTCACTGCAATGCCTGGGAAGCAAGATTCGCTGTTGTAG
* * * * * * *
40574433 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCTATTGTGG
1 CTTTAATCTGTTTCACTGCAATGCCTGGGAAGCAAGATTCGCTGTTGTAG
* * *
40574483 CTTTAATCTGTTCCACTGC-ATCCCCTAGGG-AGTAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTTCACTGCAAT-GCCT-GGGAAGCAAGATTCGCTGTTGTAG
* * * * * * * *
40574533 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGG
1 CTTTAATCTGTTTCACTGCAATGCCTGGGAAGCAAGATTCGCTGTTGTAG
* * ** * * *
40574583 CTTTAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCTGTTCTAG
1 CTTTAATCTGTTTCACTGCAATGCCTGGGAAGCAAGATTCGCTGTTGTAG
* * ** * * * *
40574633 CTTTAATCTTTTTAACTGCAATATC-GGGAAAGCAAGATTCACCGATGTGG
1 CTTTAATCTGTTTCACTGCAATGCCTGGG-AAGCAAGATTCGCTGTTGTAG
* * *
40574683 CTTTAATCTGTTTCACTGC-ATCGCTTGGGGAGTAAGATTCG-TCGTTGT-G
1 CTTTAATCTGTTTCACTGCAAT-GCCTGGGAAGCAAGATTCGCT-GTTGTAG
* * * * *
40574732 ACTTTAATCCT-TTTAACTGCAATGTC-GGGAAGGCAAGATTCACCGTTGTGG
1 -CTTTAAT-CTGTTTCACTGCAATGCCTGGGAA-GCAAGATTCGCTGTTGTAG
* * *
40574783 CTTTAATCTGCTCCACTGCACTGCCTG
1 CTTTAATCTGTTTCACTGCAATGCCTG
40574810 AGAGGGTGAA
Statistics
Matches: 458, Mismatches: 146, Indels: 45
0.71 0.22 0.07
Matches are distributed among these distances:
49 21 0.05
50 419 0.91
51 18 0.04
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (50 bp):
CTTTAATCTGTTTCACTGCAATGCCTGGGAAGCAAGATTCGCTGTTGTAG
Found at i:40574267 original size:100 final size:100
Alignment explanation
Indices: 40574133--40574809 Score: 853
Period size: 100 Copynumber: 6.8 Consensus size: 100
40574123 TAACTCGTAA
* ** * * * * * *
40574133 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGACTCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
* *
40574198 CTACACTGCCTGGGAAGTAAGATTCACTGTTGTAG
66 CTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTAG
* * * *
40574233 CTTTAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTAACCGTTGTGACTTTAATCTGTTTCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
* * * * *
40574298 CTGCACCGCCAGAGAAATAAGATTCGCTATTGTAG
66 CTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTAG
* * * *
40574333 CTTTAATCTTTTTAACTGCAATGTCGGGAAAGCAAGATTTACCGATGTGGCTTTAATCTATTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
* * *
40574398 CTGCACCGCTTGAGAAGTAAGATTCGCTGTTGTAG
66 CTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTAG
* * **
40574433 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCTATTGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
*
40574498 CTGCA-TCCCCTAGGG-AGTAAGATTCGCTGTTGTAG
66 CTGCACT-GCCT-GGGAAGTAAGATTCGCTGTTGTAG
*
40574533 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
* * * *
40574598 CTACACCGCCAGGGAAGTAAGATTCGCTGTTCTAG
66 CTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTAG
* * * *
40574633 CTTTAATCTTTTTAACTGCAATATCGGGAAAGCAAGATTCACCGATGTGGCTTTAATCTGTTTCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
* *
40574698 CTGCA-TCGCTTGGGGAGTAAGATTCG-TCGTTGT-G
66 CTGCACT-GCCTGGGAAGTAAGATTCGCT-GTTGTAG
* *
40574732 ACTTTAATCCTTTTAACTGCAATGTC-GGGAAGGCAAGATTCACCGTTGTGGCTTTAATCTGCTC
1 -CTTTAATCTTTTTAACTGCAATGTCGGGGAA-GCAAGATTCACCGTTGTGGCTTTAATCTGTTC
40574796 CACTGCACTGCCTG
64 CACTGCACTGCCTG
40574810 AGAGGGTGAA
Statistics
Matches: 499, Mismatches: 69, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
99 9 0.02
100 487 0.98
101 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
CTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTAG
Found at i:40576116 original size:13 final size:13
Alignment explanation
Indices: 40576100--40576129 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40576090 CATTTTTACT
*
40576100 TTTTCCTTTTTCA
1 TTTTCCATTTTCA
40576113 TTTTCCATTTTCA
1 TTTTCCATTTTCA
40576126 TTTT
1 TTTT
40576130 TCGCTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCCATTTTCA
Found at i:40578991 original size:15 final size:15
Alignment explanation
Indices: 40578971--40579000 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40578961 AATGGACTTT
*
40578971 AATGCATGTAATGAA
1 AATGCATGAAATGAA
40578986 AATGCATGAAATGAA
1 AATGCATGAAATGAA
40579001 TGCCTAGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (15 bp):
AATGCATGAAATGAA
Found at i:40581514 original size:22 final size:23
Alignment explanation
Indices: 40581481--40581539 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
40581471 AGAATGATAC
*
40581481 ATGA-AAACTTAAAATAAT-TAT
1 ATGATAAATTTAAAATAATATAT
40581502 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATAT
*
40581526 GTGATAAATTTAAA
1 ATGATAAATTTAAA
40581540 CAACATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
24 16 0.48
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATAT
Found at i:40587072 original size:5 final size:5
Alignment explanation
Indices: 40587062--40587087 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40587052 TGAGCATTCG
40587062 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
40587088 AATTTTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:40587881 original size:30 final size:31
Alignment explanation
Indices: 40587842--40587901 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
40587832 GGAGGTGGGA
*
40587842 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
40587873 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
40587902 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:40588129 original size:9 final size:9
Alignment explanation
Indices: 40588115--40588151 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40588105 TATAGTTTGA
40588115 TATTCGAAT
1 TATTCGAAT
40588124 TATTCGAAT
1 TATTCGAAT
*
40588133 TATTCGAGT
1 TATTCGAAT
40588142 TATTCGAAT
1 TATTCGAAT
40588151 T
1 T
40588152 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40588576 original size:17 final size:18
Alignment explanation
Indices: 40588542--40588577 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40588532 TGAATTTTTA
40588542 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
40588560 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
40588577 T
1 T
40588578 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:40589256 original size:28 final size:30
Alignment explanation
Indices: 40589219--40589280 Score: 101
Period size: 28 Copynumber: 2.1 Consensus size: 30
40589209 ATTATTTAAT
40589219 TAATAAATATCT-TTTACTTAAA-AATAAA
1 TAATAAATATCTATTTACTTAAATAATAAA
*
40589247 TAATAAATATCTATTTACTTAAATAATAAG
1 TAATAAATATCTATTTACTTAAATAATAAA
40589277 TAAT
1 TAAT
40589281 TTAAATCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 12 0.39
29 10 0.32
30 9 0.29
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (30 bp):
TAATAAATATCTATTTACTTAAATAATAAA
Found at i:40592863 original size:10 final size:10
Alignment explanation
Indices: 40592848--40592898 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
40592838 AAGTTAATTT
40592848 AATTTTTAAA
1 AATTTTTAAA
40592858 AATTTTTAAA
1 AATTTTTAAA
*
40592868 AA-TTTTACTA
1 AATTTTTA-AA
*
40592878 TATTTTT-AA
1 AATTTTTAAA
40592887 AATTTTTAAA
1 AATTTTTAAA
40592897 AA
1 AA
40592899 AATTATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 12 0.35
10 18 0.53
11 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:40592868 original size:9 final size:9
Alignment explanation
Indices: 40592848--40592897 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
40592838 AAGTTAATTT
40592848 AATTTTTAAA
1 AATTTTT-AA
40592858 AATTTTTAA
1 AATTTTTAA
*
40592867 AAATTTTACTA
1 AATTTTTA--A
*
40592878 TATTTTTAA
1 AATTTTTAA
40592887 AATTTTTAA
1 AATTTTTAA
40592896 AA
1 AA
40592898 AAATTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 20 0.59
10 7 0.21
11 7 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (9 bp):
AATTTTTAA
Found at i:40593245 original size:11 final size:11
Alignment explanation
Indices: 40593229--40593258 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40593219 ATTTTATTAA
40593229 TATAAATATTT
1 TATAAATATTT
40593240 TATAAATATTT
1 TATAAATATTT
*
40593251 TATTAATA
1 TATAAATA
40593259 AATAAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATAAATATTT
Found at i:40602133 original size:17 final size:16
Alignment explanation
Indices: 40602113--40602145 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
40602103 TTTTAATAAA
40602113 TAAAATAATATTAATAT
1 TAAAATAATA-TAATAT
40602130 TAAAATAATATAATAT
1 TAAAATAATATAATAT
40602146 AAATATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATAATATAATAT
Found at i:40602135 original size:22 final size:22
Alignment explanation
Indices: 40602110--40602152 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40602100 AAATTTTAAT
*
40602110 AAATAAAATAATATTAATATTA
1 AAATAAAATAATATAAATATTA
*
40602132 AAATAATATAATATAAATATT
1 AAATAAAATAATATAAATATT
40602153 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATAAAATAATATAAATATTA
Found at i:40604180 original size:33 final size:33
Alignment explanation
Indices: 40604086--40604181 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
40604076 AACAGAGCCA
* * *
40604086 GTGTTTATTGTCCCGATGGACTTTA-TTTGTTTT
1 GTGTTTACTGTCCCAATGGAC-TTACTTTGTTTC
**
40604119 GTGTTTACTGTCCCAGCGGACTTACTTTGTTTC
1 GTGTTTACTGTCCCAATGGACTTACTTTGTTTC
* *
40604152 GTGTTTACTATCCCAATGGACTTGCTTTGT
1 GTGTTTACTGTCCCAATGGACTTACTTTGT
40604182 GGATGCCATA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 3 0.06
33 50 0.94
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
GTGTTTACTGTCCCAATGGACTTACTTTGTTTC
Found at i:40608980 original size:36 final size:36
Alignment explanation
Indices: 40608932--40609044 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
40608922 GTCGGTTATC
*
40608932 CGACTAGCGTTGGGTGCAATAATTTGTCGACTCGTT
1 CGACTAGCGTTGGGTGCAATAATTTGTCGACTTGTT
* * * * *
40608968 CGACTAGTGTT-GG-GCAA-AACTATTTTCG-GTTATC
1 CGACTAGCGTTGGGTGCAATAA-T-TTGTCGACTTGTT
* *
40609002 CGACTAGCGTTGAGTGCAATAATTTGTTGACTTGTT
1 CGACTAGCGTTGGGTGCAATAATTTGTCGACTTGTT
40609038 CGACTAG
1 CGACTAG
40609045 TGCTAGGCAT
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
33 2 0.03
34 17 0.29
35 12 0.21
36 25 0.43
37 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (36 bp):
CGACTAGCGTTGGGTGCAATAATTTGTCGACTTGTT
Found at i:40609039 original size:70 final size:71
Alignment explanation
Indices: 40608918--40609078 Score: 229
Period size: 70 Copynumber: 2.3 Consensus size: 71
40608908 GATGAGTAAA
* * *
40608918 TATCG-TCGGTTATCCGACTAGCGTTGGGTGCAATAATTTGTCGACTCGTTCGACTAGTGTTGGG
1 TATCGTTCGGTTATCCGACTAGCGTTGAGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTAGG
40608982 CAAAAC
66 CAAAAC
* * *
40608988 TAT-TTTCGGTTATCCGACTAGCGTTGAGTGCAATAATTTGTTGACTTGTTCGACTAGTGCTAGG
1 TATCGTTCGGTTATCCGACTAGCGTTGAGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTAGG
*
40609052 CATAAC
66 CAAAAC
*
40609058 TATCGTT-GGTTATCTGACTAG
1 TATCGTTCGGTTATCCGACTAG
40609079 AGCTAGGTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
70 78 0.98
71 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (71 bp):
TATCGTTCGGTTATCCGACTAGCGTTGAGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTAGG
CAAAAC
Found at i:40626247 original size:36 final size:36
Alignment explanation
Indices: 40626207--40626278 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
40626197 ATGTAATTGC
* * * *
40626207 TAATTCAATTGCATGGAATTTTATGGATGTATATGT
1 TAATTCAATTGAATGGAAGTTTATCGAAGTATATGT
40626243 TAATTCAATTGAATGGAAGTTTATCGAAGTATATGT
1 TAATTCAATTGAATGGAAGTTTATCGAAGTATATGT
40626279 ATTTATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (36 bp):
TAATTCAATTGAATGGAAGTTTATCGAAGTATATGT
Found at i:40626395 original size:36 final size:35
Alignment explanation
Indices: 40626345--40626454 Score: 116
Period size: 34 Copynumber: 3.1 Consensus size: 35
40626335 AGTAACTATC
* *
40626345 GTCGATTATCTGACTAGCGCTGGGCGCAATAATTT
1 GTCGATTGTCTGACTAGCGCTGGGCACAATAATTT
* * * * *
40626380 GTCGTCTTGTTTGACTAGTGTTGGGCACAACT-A-TC
1 GTCG-ATTGTCTGACTAGCGCTGGGCACAA-TAATTT
*
40626415 GTCGATTGTCTGACTAGCACTGGGCACAATAATTT
1 GTCGATTGTCTGACTAGCGCTGGGCACAATAATTT
40626450 GTCGA
1 GTCGA
40626455 CTATTTCGGC
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
33 1 0.02
34 21 0.36
35 15 0.26
36 20 0.34
37 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (35 bp):
GTCGATTGTCTGACTAGCGCTGGGCACAATAATTT
Found at i:40626451 original size:70 final size:70
Alignment explanation
Indices: 40626338--40626616 Score: 255
Period size: 70 Copynumber: 4.0 Consensus size: 70
40626328 ACGGATGAGT
* *
40626338 AACTATCGTCGATTATCTGACTAGCGCTGGGCGCAATAATTTGTCGTCTTGTTTGACTAGTGTTG
1 AACTATCGTCGATTATCTGACTAGCGCTGGGCGCAATAATTTGTCGACTTGTTCGACTAGTGTTG
40626403 GGCAC
66 GGCAC
* * * * *
40626408 AACTATCGTCGATTGTCTGACTAGCACTGGGCACAATAATTTGTCGACTAT-TTCGGCTAATGTT
1 AACTATCGTCGATTATCTGACTAGCGCTGGGCGCAATAATTTGTCGACT-TGTTCGACTAGTGTT
*
40626472 GGGTAC
65 GGGCAC
* * * * * **
40626478 AAATATCGTCGGTTATC-CAGCTAGCGCTTGGCGCAATAATTTGTCGACTCGTTCGACTA--GCA
1 AACTATCGTCGATTATCTGA-CTAGCGCTGGGCGCAATAATTTGTCGACTTGTTCGACTAGTGTT
*
40626540 AGGCAC
65 GGGCAC
* * * ** * * * *
40626546 AACTATCG-CCAGTTAT-TCGACTAGTGTTGGGCATAATAATTTTTCGACTCGTTCAACTAGTTT
1 AACTATCGTCGA-TTATCT-GACTAGCGCTGGGCGCAATAATTTGTCGACTTGTTCGACTAGTGT
40626609 TGGGCAC
64 TGGGCAC
40626616 A
1 A
40626617 CAAATGATCT
Statistics
Matches: 165, Mismatches: 36, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
67 1 0.01
68 48 0.29
69 2 0.01
70 113 0.68
71 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (70 bp):
AACTATCGTCGATTATCTGACTAGCGCTGGGCGCAATAATTTGTCGACTTGTTCGACTAGTGTTG
GGCAC
Found at i:40632800 original size:79 final size:81
Alignment explanation
Indices: 40632664--40632848 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
40632654 TTGAATGATG
*
40632664 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
40632728 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
40632743 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
40632805 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
40632823 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40632849 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:40632862 original size:40 final size:40
Alignment explanation
Indices: 40632665--40632848 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
40632655 TGAATGATGT
* * * *
40632665 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
40632705 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
40632745 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40632783 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40632824 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40632849 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:40632870 original size:79 final size:79
Alignment explanation
Indices: 40632665--40632881 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 79
40632655 TGAATGATGT
** * * * **
40632665 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
40632728 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
40632745 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
40632810 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
40632824 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
40632882 TACGTGATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 71 0.61
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:40647144 original size:40 final size:40
Alignment explanation
Indices: 40647100--40647218 Score: 150
Period size: 40 Copynumber: 3.0 Consensus size: 40
40647090 AGCACTATGG
*
40647100 TGCTCCTAACAGTACTTTCGTACTTCTAATAGCACAACAA
1 TGCTCCTGACAGTACTTTCGTACTTCTAATAGCACAACAA
* * **
40647140 TGCTCCTGACCGTACTTTCGTAC-TCTTAGTAGCACAACGG
1 TGCTCCTGACAGTACTTTCGTACTTC-TAATAGCACAACAA
* * *
40647180 TGCTCCTGACAGTACTTTCATACTCCTGATAGCACAACA
1 TGCTCCTGACAGTACTTTCGTACTTCTAATAGCACAACA
40647219 GTAGATTCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.03
40 63 0.95
41 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.29
Consensus pattern (40 bp):
TGCTCCTGACAGTACTTTCGTACTTCTAATAGCACAACAA
Found at i:40652552 original size:6 final size:6
Alignment explanation
Indices: 40652536--40652576 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
40652526 TAGGTTTCTA
*
40652536 AAAATG GAAATG AAAATG AAAATG AAAATG AAAATG AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT
40652577 TTGCAATCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:40652805 original size:5 final size:5
Alignment explanation
Indices: 40652795--40652820 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40652785 TGAGCATTCG
40652795 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
40652821 AATTTTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Done.