Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 129 of 161
Found at i:40545038 original size:14 final size:14
Alignment explanation
Indices: 40545019--40545046 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40545009 TATTGTTTTC
40545019 CACTTTATCAAGGA
1 CACTTTATCAAGGA
40545033 CACTTTATCAAGGA
1 CACTTTATCAAGGA
40545047 ATCCGTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
CACTTTATCAAGGA
Found at i:40545835 original size:145 final size:145
Alignment explanation
Indices: 40545666--40545939 Score: 494
Period size: 145 Copynumber: 1.9 Consensus size: 145
40545656 GTCGCCAAGC
*
40545666 TGTCGAAACCATTTTTTTTGAAATTTTCAAAAATGGGGATCGAATTTGAAAATGGAAATCGGAGT
1 TGTCGAAACCATTTTTTTTGAAATTTTCAAAAATGGGGATCGAATTTGAAAATGAAAATCGGAGT
40545731 CGCCACCGATCTTTTATTTTGGTGTGATCGAATCACCATTAAAAATGATTTTAGGTCTACGAATA
66 CGCCACCGATCTTTTATTTTGGTGTGATCGAATCACCATTAAAAATGATTTTAGGTCTACGAATA
40545796 GTTATATACTATATT
131 GTTATATACTATATT
* * * *
40545811 TGTCGAAACCATTTTTTTTTAAATTTTGAAAAATGGGGATCGACTTTGAAAATGAAAATTGGAGT
1 TGTCGAAACCATTTTTTTTGAAATTTTCAAAAATGGGGATCGAATTTGAAAATGAAAATCGGAGT
*
40545876 CGCCACCGATCTTTTATTTTGGTGTGATCGGATCACCATTAAAAATGATTTTAGGTCTACGAAT
66 CGCCACCGATCTTTTATTTTGGTGTGATCGAATCACCATTAAAAATGATTTTAGGTCTACGAAT
40545940 TTTGAGAAAA
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 123 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (145 bp):
TGTCGAAACCATTTTTTTTGAAATTTTCAAAAATGGGGATCGAATTTGAAAATGAAAATCGGAGT
CGCCACCGATCTTTTATTTTGGTGTGATCGAATCACCATTAAAAATGATTTTAGGTCTACGAATA
GTTATATACTATATT
Found at i:40546820 original size:49 final size:43
Alignment explanation
Indices: 40546713--40546913 Score: 154
Period size: 43 Copynumber: 4.5 Consensus size: 43
40546703 TGTTTCTAAA
*
40546713 ATGACCTTTAGCGGCGCTTTTACCACAAACGCCGTTAAAGACC
1 ATGACCTTTAGCGGCGCTTATACCACAAACGCCGTTAAAGACC
* *
40546756 ATGACTTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGGTAAAGACC
1 ATGACCTTTAGCGGCGCTTATACCACAAACGCCG-T-----TAAAGACC
* * * * *
40546805 ATGACCTTTAGCGGCGCATT-T-CTAAAAAACACCGCTAAAGGCC
1 ATGACCTTTAGCGGCGC-TTATAC-CACAAACGCCGTTAAAGACC
* * * * * * *
40546848 ACGATCTTTAGCGACGCTTATCCCAAAAACGCCATTAAAAACC
1 ATGACCTTTAGCGGCGCTTATACCACAAACGCCGTTAAAGACC
* * *
40546891 ACGACCTTTAGCGACCCTTATAC
1 ATGACCTTTAGCGGCGCTTATAC
40546914 GCCACAATAA
Statistics
Matches: 127, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
42 2 0.02
43 87 0.69
44 2 0.02
48 1 0.01
49 33 0.26
50 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (43 bp):
ATGACCTTTAGCGGCGCTTATACCACAAACGCCGTTAAAGACC
Found at i:40546870 original size:92 final size:91
Alignment explanation
Indices: 40546713--40546880 Score: 223
Period size: 92 Copynumber: 1.8 Consensus size: 91
40546703 TGTTTCTAAA
* * * * *
40546713 ATGACCTTTAGCGGCGCTTTTACCACAAACGCCGTTAAAGACCATGACTTTTAGCGGCGCTTATC
1 ATGACCTTTAGCGGCGCTTTTA-CAAAAACACCGCTAAAGACCACGACTTTTAGCGACGCTTATC
*
40546778 CCACAAACGCCGCTAAAGGTAAAGACC
65 CCAAAAACGCCGCTAAAGGTAAAGACC
*
40546805 ATGACCTTTAGCGGCGCATTTCTA-AAAAACACCGCTAAAGGCCACGA-TCTTTAGCGACGCTTA
1 ATGACCTTTAGCGGCGC-TTT-TACAAAAACACCGCTAAAGACCACGACT-TTTAGCGACGCTTA
40546868 TCCCAAAAACGCC
63 TCCCAAAAACGCC
40546881 ATTAAAAACC
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
91 1 0.02
92 60 0.91
93 3 0.05
94 2 0.03
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.21
Consensus pattern (91 bp):
ATGACCTTTAGCGGCGCTTTTACAAAAACACCGCTAAAGACCACGACTTTTAGCGACGCTTATCC
CAAAAACGCCGCTAAAGGTAAAGACC
Found at i:40551573 original size:23 final size:23
Alignment explanation
Indices: 40551529--40551574 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40551519 AATGTTCGTA
* *
40551529 TTTTTTATTAATTTTTTATTTTG
1 TTTTTTATAAATTATTTATTTTG
40551552 TTTTTTATAAATTGATTT-TTTTG
1 TTTTTTATAAATT-ATTTATTTTG
40551575 CGGCGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.74
Consensus pattern (23 bp):
TTTTTTATAAATTATTTATTTTG
Found at i:40552264 original size:7 final size:7
Alignment explanation
Indices: 40552254--40552278 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40552244 ACTAACTCTT
40552254 AACCCCA
1 AACCCCA
40552261 AACCCCA
1 AACCCCA
40552268 AACCCCA
1 AACCCCA
40552275 AACC
1 AACC
40552279 ACTAACCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (7 bp):
AACCCCA
Found at i:40552358 original size:82 final size:82
Alignment explanation
Indices: 40552269--40552430 Score: 254
Period size: 82 Copynumber: 2.0 Consensus size: 82
40552259 CAAACCCCAA
* *
40552269 ACCCCAAA-CCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAA
1 ACCCCAAATCC-CTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAA
40552333 ATCATAAACCCTAACCCG
65 ATCATAAACCCTAACCCG
* * *
40552351 ACCCCAAATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACATTAATTAATCTAAA
1 ACCCCAAATCCCTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAA
*
40552416 TCCTAAACCCTAACC
66 TCATAAACCCTAACC
40552431 TAACACTAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
82 71 0.97
83 2 0.03
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (82 bp):
ACCCCAAATCCCTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAA
TCATAAACCCTAACCCG
Found at i:40552453 original size:82 final size:82
Alignment explanation
Indices: 40552272--40552455 Score: 228
Period size: 82 Copynumber: 2.2 Consensus size: 82
40552262 ACCCCAAACC
* *
40552272 CCAAACCACT-AACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATC
1 CCAAATCACTAAACC-CTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATC
* *
40552336 ATAAACCCTAACCCGACC
65 ATAAACCCTAACCCAACA
* * * * * *
40552354 CCAAATCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACATTAATTAATCTAAATCC
1 CCAAATCACTAAACCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATCA
*
40552419 TAAACCCTAACCTAACA
66 TAAACCCTAACCCAACA
*
40552436 CTAAATCTAC-AAACCCTAAA
1 CCAAATC-ACTAAACCCTAAA
40552456 TCCCTACCTC
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
82 82 0.95
83 4 0.05
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.26
Consensus pattern (82 bp):
CCAAATCACTAAACCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAATCA
TAAACCCTAACCCAACA
Found at i:40552534 original size:14 final size:15
Alignment explanation
Indices: 40552517--40552548 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
40552507 CTTAAATCAG
40552517 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
40552531 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
40552546 AAT
1 AAT
40552549 TTATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:40552964 original size:41 final size:41
Alignment explanation
Indices: 40552904--40553304 Score: 461
Period size: 41 Copynumber: 10.2 Consensus size: 41
40552894 AATGTTCAAT
40552904 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40552945 TAGAGATCTAAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* * * *
40552986 TAAAGATCTAAGCATTAGCGGCGCTTTTTTAAAAATGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40553027 TAAAGATCTGAGTATTAGCGGCGCTTTCTCAAAAATGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
40553068 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40553109 TAAAGATCTGAGCATTAGCGGCACTTTTTTC-AAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGC-TTTCTCAAAAACGCCGC
*
40553150 T--A-A----AG-A-TAGCGGCGCTTT-TTAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40553181 TAAAGATCTGAGCATTAGCGGCACTTTTTTC-AAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGC-TTTCTCAAAAACGCCGC
*
40553222 T--A-A----AG-A-TAGCGGCGCTTT-TTAAAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
* *
40553253 TAAAGATCTGAGCATTAGCGGCACTTTTTTTC-AAAACGCCGC
1 TAAAGATCTGAGCATTAGCGGCGC--TTTCTCAAAAACGCCGC
40553295 TAAAGATCTG
1 TAAAGATCTG
40553305 TAAGGTACAA
Statistics
Matches: 312, Mismatches: 22, Indels: 51
0.81 0.06 0.13
Matches are distributed among these distances:
30 2 0.01
31 28 0.09
32 16 0.05
33 4 0.01
34 6 0.02
38 6 0.02
39 4 0.01
40 16 0.05
41 200 0.64
42 29 0.09
43 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
TAAAGATCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
Found at i:40553175 original size:31 final size:32
Alignment explanation
Indices: 40553124--40553259 Score: 141
Period size: 31 Copynumber: 4.0 Consensus size: 32
40553114 ATCTGAGCAT
*
40553124 TAGCGGCACTTTTTTCAAAACGCCGCTAAAGA
1 TAGCGGCACTTTTTTAAAAACGCCGCTAAAGA
*
40553156 TAGCGGCGC-TTTTTAAAAACGCCGCTAAAGATCTGAGCA
1 TAGCGGCACTTTTTTAAAAACGCCGCT--A-A----AG-A
*
40553195 TTAGCGGCACTTTTTTCAAAACGCCGCTAAAGA
1 -TAGCGGCACTTTTTTAAAAACGCCGCTAAAGA
*
40553228 TAGCGGCGC-TTTTTAAAAACGCCGCTAAAGA
1 TAGCGGCACTTTTTTAAAAACGCCGCTAAAGA
40553259 T
1 T
40553260 CTGAGCATTA
Statistics
Matches: 88, Mismatches: 6, Indels: 21
0.77 0.05 0.18
Matches are distributed among these distances:
31 38 0.43
32 16 0.18
33 2 0.02
34 3 0.03
38 3 0.03
39 2 0.02
40 8 0.09
41 16 0.18
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (32 bp):
TAGCGGCACTTTTTTAAAAACGCCGCTAAAGA
Found at i:40553201 original size:72 final size:72
Alignment explanation
Indices: 40553083--40553301 Score: 411
Period size: 72 Copynumber: 3.0 Consensus size: 72
40553073 ATCTGAGCAT
*
40553083 TAGCGGCGCTTTCTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCACTTTTTTCAAAACGCC
1 TAGCGGCGCTTT-TTAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCACTTTTTTCAAAACGCC
40553148 GCTAAAGA
65 GCTAAAGA
40553156 TAGCGGCGCTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCACTTTTTTCAAAACGCCG
1 TAGCGGCGCTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCACTTTTTTCAAAACGCCG
40553221 CTAAAGA
66 CTAAAGA
40553228 TAGCGGCGCTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCACTTTTTTTCAAAACGCC
1 TAGCGGCGCTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCAC-TTTTTTCAAAACGCC
40553293 GCTAAAGA
65 GCTAAAGA
40553301 T
1 T
40553302 CTGTAAGGTA
Statistics
Matches: 144, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
72 108 0.75
73 36 0.25
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (72 bp):
TAGCGGCGCTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCACTTTTTTCAAAACGCCG
CTAAAGA
Found at i:40560998 original size:43 final size:43
Alignment explanation
Indices: 40560962--40561044 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
40560952 TCTTACATGT
*
40560962 AATC-CAATATCGATGCCAATGTCCCAGACAGGGTCTTACACAA
1 AATCTCAA-ATCGATGCCAATGTCCCAAACAGGGTCTTACACAA
*
40561005 AATCTCAAATCGATGCCAATGTCCCAAACATGGTCTTACA
1 AATCTCAAATCGATGCCAATGTCCCAAACAGGGTCTTACA
40561045 GAATATCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 34 0.92
44 3 0.08
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (43 bp):
AATCTCAAATCGATGCCAATGTCCCAAACAGGGTCTTACACAA
Found at i:40569290 original size:22 final size:22
Alignment explanation
Indices: 40569265--40569325 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
40569255 GAATTAGTGT
40569265 GCATCGAAGTGCAAATCAATAG
1 GCATCGAAGTGCAAATCAATAG
* * * *
40569287 GCATCGTAGTGCGAACCAGTAG
1 GCATCGAAGTGCAAATCAATAG
*
40569309 GCA-CCATAGTGCAAATC
1 GCATCGA-AGTGCAAATC
40569326 CCGTACAAGC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (22 bp):
GCATCGAAGTGCAAATCAATAG
Found at i:40576641 original size:82 final size:80
Alignment explanation
Indices: 40576543--40576797 Score: 347
Period size: 82 Copynumber: 3.2 Consensus size: 80
40576533 TTGAATAAAA
* * *
40576543 TCTATTTTGGGATTTATTCTCGCCGTTTAATAGATTTTATTCCATTTTGATTTTATTTCCAAATG
1 TCTATTTTGGGATTTATTCTCGCCGTTTAACAGATTTTATT--ATTTTGATTTTGTTTCCAAATA
* * *
40576608 AGAATTATTTGAATAAT
64 AGATTTAATTAAATAAT
* *
40576625 TCTATTTCGGGATTTATTCTCGTCGTTTAACAGA--TT-TTA-TTTGATTTTGTTTCCAAATAAG
1 TCTATTTTGGGATTTATTCTCGCCGTTTAACAGATTTTATTATTTTGATTTTGTTTCCAAATAAG
40576686 ATTTAATTAAATAAT
66 ATTTAATTAAATAAT
* *
40576701 TCTATTTTGGGATTTATTCTCGCCGTTTAACAAATTTTATTTGATTTTGATTTTGTTTCCAAACA
1 TCTATTTTGGGATTTATTCTCGCCGTTTAACAGATTTTA-TT-ATTTTGATTTTGTTTCCAAATA
40576766 AGATTTAATTAAATAAT
64 AGATTTAATTAAATAAT
*
40576783 TTTATTTTGGGATTT
1 TCTATTTTGGGATTT
40576798 CATCCTATCG
Statistics
Matches: 154, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
76 63 0.41
77 1 0.01
78 2 0.01
79 2 0.01
80 4 0.03
81 1 0.01
82 81 0.53
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.50
Consensus pattern (80 bp):
TCTATTTTGGGATTTATTCTCGCCGTTTAACAGATTTTATTATTTTGATTTTGTTTCCAAATAAG
ATTTAATTAAATAAT
Found at i:40576730 original size:158 final size:159
Alignment explanation
Indices: 40576543--40576841 Score: 413
Period size: 158 Copynumber: 1.9 Consensus size: 159
40576533 TTGAATAAAA
* * **
40576543 TCTATTTTGGGATTTATTCTCGCCGTTTAATAGATTTTATTCCATTTTGATTTTATTTCCAAATG
1 TCTATTTTGGGATTTATTCTCGCCGTTTAACAAATTTTATTCCATTTTGATTTTATTTCCAAACA
* * * * * * *
40576608 AGAATTATTTGAATAATTCTATTTCGGGATTT-ATTCTCGTCGTTTAACAGATTTTA-TTTGATT
66 AGAATTAATTAAATAATTCTATTTCGGGATTTCATCCT-ATCGTTCAACAGAATTGATTTTGATT
*
40576671 TTGTTTCCAAATAAGATTTAATTAAATAAT
130 TTGTTTCAAAATAAGATTTAATTAAATAAT
** *
40576701 TCTATTTTGGGATTTATTCTCGCCGTTTAACAAATTTTATTTGATTTTGATTTTGTTTCCAAACA
1 TCTATTTTGGGATTTATTCTCGCCGTTTAACAAATTTTATTCCATTTTGATTTTATTTCCAAACA
* * *
40576766 AGATTTAATTAAATAATTTTATTTTGGGATTTCATCCTATCGTTCAACAGAATTGATTTTGATTT
66 AGAATTAATTAAATAATTCTATTTCGGGATTTCATCCTATCGTTCAACAGAATTGATTTTGATTT
40576831 TGTTTCAAAAT
131 TGTTTCAAAAT
40576842 TTTAATTCTG
Statistics
Matches: 121, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
158 99 0.82
159 22 0.18
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (159 bp):
TCTATTTTGGGATTTATTCTCGCCGTTTAACAAATTTTATTCCATTTTGATTTTATTTCCAAACA
AGAATTAATTAAATAATTCTATTTCGGGATTTCATCCTATCGTTCAACAGAATTGATTTTGATTT
TGTTTCAAAATAAGATTTAATTAAATAAT
Found at i:40580269 original size:25 final size:25
Alignment explanation
Indices: 40580213--40580285 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
40580203 CAACTCGTAT
* *
40580213 GAGCTTACCGGTTTATAGCTCATGA
1 GAGCATACCGATTTATAGCTCATGA
* *
40580238 GATCATACCGATTTATAGCTCGTGA
1 GAGCATACCGATTTATAGCTCATGA
* *
40580263 -AGGCATACCGATTCACAGCTCAT
1 GA-GCATACCGATTTATAGCTCAT
40580286 ATAAGCATAC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 1 0.03
25 38 0.97
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (25 bp):
GAGCATACCGATTTATAGCTCATGA
Found at i:40580477 original size:31 final size:30
Alignment explanation
Indices: 40580442--40580500 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
40580432 TTTACATGAA
*
40580442 ATACATGGAAATG-ATTTTACATGATATATAG
1 ATACAT-GAAATGAATGTTACATG-TATATAG
*
40580473 ATACATGATATGAATGTTACATGTATAT
1 ATACATGAAATGAATGTTACATGTATAT
40580501 GGAAACTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (30 bp):
ATACATGAAATGAATGTTACATGTATATAG
Found at i:40584746 original size:41 final size:41
Alignment explanation
Indices: 40584539--40584735 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
40584529 TTTATCGTTA
* * * *
40584539 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
40584580 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
40584621 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
40584662 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
40584703 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
40584736 AAGAGCCGGT
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 143 0.97
42 2 0.01
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:40585030 original size:33 final size:33
Alignment explanation
Indices: 40584966--40585030 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
40584956 ATATATATTT
* * ** *
40584966 CATTCGGCATAGGTGGATATATTTATGTGTATG
1 CATTCGGCATAGGTGAAAATAAGTATATGTATG
*
40584999 CATTCGGCATAGGTGAAAATAAGTGTATGTAT
1 CATTCGGCATAGGTGAAAATAAGTATATGTAT
40585031 CTATGCATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.35
Consensus pattern (33 bp):
CATTCGGCATAGGTGAAAATAAGTATATGTATG
Found at i:40592506 original size:41 final size:41
Alignment explanation
Indices: 40592217--40592495 Score: 481
Period size: 41 Copynumber: 6.8 Consensus size: 41
40592207 TTTATCGTTA
* * * *
40592217 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
40592258 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
40592299 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
40592340 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
40592381 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
40592422 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
40592463 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
40592496 AAGAGCCGGT
Statistics
Matches: 230, Mismatches: 4, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 225 0.98
42 2 0.01
43 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:40592768 original size:33 final size:32
Alignment explanation
Indices: 40592712--40592775 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
40592702 AGATATGTAT
40592712 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
40592744 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
40592776 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:40592792 original size:33 final size:33
Alignment explanation
Indices: 40592719--40592792 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
40592709 TATATATATA
* * **
40592719 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
40592751 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
40592784 TGTATGTAT
1 TATATGTAT
40592793 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:40595288 original size:25 final size:25
Alignment explanation
Indices: 40595260--40595365 Score: 92
Period size: 25 Copynumber: 4.3 Consensus size: 25
40595250 AGCGCTCTCT
40595260 CGAGCCATATAACGGGAAGCTCATG
1 CGAGCCATATAACGGGAAGCTCATG
* *
40595285 CGAGCCATGA-AACGGAAAGCTTAT-
1 CGAGCCAT-ATAACGGGAAGCTCATG
* ** *
40595309 CTGGGCTTTATAACGGGAAGCTCATA
1 C-GAGCCATATAACGGGAAGCTCATG
* * *
40595335 AGAGCCATAT-TCAGGAAGCTCATG
1 CGAGCCATATAACGGGAAGCTCATG
40595359 CGAGCCA
1 CGAGCCA
40595366 ATATCGAGTA
Statistics
Matches: 62, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
24 19 0.31
25 42 0.68
26 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (25 bp):
CGAGCCATATAACGGGAAGCTCATG
Found at i:40595460 original size:24 final size:25
Alignment explanation
Indices: 40595433--40595489 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
40595423 AAGTTCAAGT
* *
40595433 GAGCC-TTATCGAGTAGCTCACAAA
1 GAGCCATTAACGAGAAGCTCACAAA
*
40595457 GAGCCAATTAACGGGAAGCTCACAAA
1 GAGCC-ATTAACGAGAAGCTCACAAA
40595483 GAGCCAT
1 GAGCCAT
40595490 AATCAGGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 5 0.18
25 2 0.07
26 21 0.75
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.16
Consensus pattern (25 bp):
GAGCCATTAACGAGAAGCTCACAAA
Found at i:40600931 original size:18 final size:18
Alignment explanation
Indices: 40600905--40600940 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40600895 TATTATAGTT
*
40600905 CAAACCATCAAAATATAC
1 CAAAACATCAAAATATAC
*
40600923 CAAAACATCAACATATAC
1 CAAAACATCAAAATATAC
40600941 ATTAAACCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.17
Consensus pattern (18 bp):
CAAAACATCAAAATATAC
Found at i:40601444 original size:29 final size:30
Alignment explanation
Indices: 40601389--40601456 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
40601379 AATTTTTTTA
*
40601389 ATTTTAAAAAATTCAAAAATTATAAAAA-ACT
1 ATTTTTAAAAATT-AAAAATTATAAAAATA-T
40601420 ATTTTTAAAAATT-AAAATTATAAAAATAT
1 ATTTTTAAAAATTAAAAATTATAAAAATAT
40601449 ATTTTTAA
1 ATTTTTAA
40601457 TTTTTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
29 22 0.63
30 1 0.03
31 12 0.34
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (30 bp):
ATTTTTAAAAATTAAAAATTATAAAAATAT
Found at i:40602906 original size:33 final size:33
Alignment explanation
Indices: 40602860--40603198 Score: 162
Period size: 33 Copynumber: 9.7 Consensus size: 33
40602850 TTATCCGTTA
*
40602860 TCGGTGGATTCAGCACTTAGCAACCACCAATGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
* **
40602894 TCGGGAAATCAGCACTTAGCAACCTCTTTTCACATTCAAAAAT
1 TCGGGGAATCAGCACTTAGCAA---C----CAC---CAATGAT
* *
40602937 ACGGTGGAATCAGCACTTAGCAACCACCAATGAA
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
40602971 TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGAT
1 TCGGGGAATCAGCACTTAGCAACCAC---CA-A--T--GAT
* *
40603012 ACGGTGGGATCAGCACTTAGCAACCACCAATGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
* *
40603046 TCGGGGAATCATCACTTAGCAACC-CC-TTGA-
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
* * *
40603076 ---GGGAATCAACACTTAGCAACCCCCTTCACATTTAAAAT
1 TCGGGGAATCAGCACTTAGCAA-CCAC--CA-A--T--GAT
* *
40603114 ACGGTGGAATCAGCACTTAGCAACCACCAATGAA
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
40603148 TCTGGGAATCAGCACTTAGCAACC-CC-----T
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
*
40603175 TGGGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
40603199 CCCTTTATAT
Statistics
Matches: 239, Mismatches: 31, Indels: 77
0.69 0.09 0.22
Matches are distributed among these distances:
27 40 0.17
28 2 0.01
29 1 0.00
31 4 0.02
32 4 0.02
33 75 0.31
34 20 0.08
35 1 0.00
36 5 0.02
37 5 0.02
38 2 0.01
39 5 0.02
40 3 0.01
41 10 0.04
42 37 0.15
43 8 0.03
44 17 0.07
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:40602988 original size:77 final size:75
Alignment explanation
Indices: 40602861--40603073 Score: 336
Period size: 75 Copynumber: 2.8 Consensus size: 75
40602851 TATCCGTTAT
* * *
40602861 CGGTGGATTCAGCACTTAGCAACCACCAATGATTCGGGAAATCAGCACTTAGCAACCTCTTTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACC-CCTTTCA
40602926 CATTCAAAAATA
65 CATT-AAAAATA
*
40602938 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
* *
40603003 ATTTAAGATA
66 ATTAAAAATA
* *
40603013 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCATCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
40603074 GAGGGAATCA
Statistics
Matches: 127, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
75 63 0.50
76 10 0.08
77 54 0.43
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTAAAAATA
Found at i:40603126 original size:102 final size:102
Alignment explanation
Indices: 40602942--40603203 Score: 389
Period size: 102 Copynumber: 2.5 Consensus size: 102
40602932 AAAATACGGT
* *
40602942 GGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCACATTT
1 GGAATCAGCACTTAGCAACC-CC-TTG-A---GGGAATCAGCACTTAGCAACCCCCTTCACATTT
* * *
40603007 AAGATACGGTGGGATCAGCACTTAGCAACCACCAATGATTCGG
60 AAAATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
40603050 GGAATCATCACTTAGCAACCCCTTGAGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATA
1 GGAATCAGCACTTAGCAACCCCTTGAGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATA
*
40603115 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCTG
66 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGG
*
40603152 GGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTT
1 GGAATCAGCACTTAGCAACCCCTTGAGGGAATCAGCACTTAGCAACCCCCTT
40603204 TATATTCAAT
Statistics
Matches: 143, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
102 119 0.83
105 1 0.01
106 2 0.01
107 2 0.01
108 19 0.13
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.21
Consensus pattern (102 bp):
GGAATCAGCACTTAGCAACCCCTTGAGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATA
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:40609097 original size:11 final size:11
Alignment explanation
Indices: 40609078--40609108 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40609068 AAAAGCAGTT
*
40609078 AACACGTTGAC
1 AACATGTTGAC
40609089 AACATGTTGAC
1 AACATGTTGAC
40609100 AACATGTTG
1 AACATGTTG
40609109 TCAGCTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (11 bp):
AACATGTTGAC
Found at i:40613550 original size:21 final size:21
Alignment explanation
Indices: 40613511--40613550 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40613501 GGAAGTGTGA
*
40613511 TTCTAGTAGTATTATTGCATC
1 TTCTAGTAGTAGTATTGCATC
40613532 TTCTAGTAGT-GTATCTGCA
1 TTCTAGTAGTAGTAT-TGCA
40613551 ATATCTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (21 bp):
TTCTAGTAGTAGTATTGCATC
Found at i:40613821 original size:12 final size:12
Alignment explanation
Indices: 40613788--40613822 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
40613778 TATTTGTGTC
40613788 TGCATTTGTATA
1 TGCATTTGTATA
* *
40613800 TGAATCTGTATA
1 TGCATTTGTATA
40613812 TGCATTTGTAT
1 TGCATTTGTAT
40613823 TTGATTATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (12 bp):
TGCATTTGTATA
Found at i:40614791 original size:15 final size:15
Alignment explanation
Indices: 40614773--40614803 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40614763 TTGAAAAATA
40614773 TTCAAAATAAATATT
1 TTCAAAATAAATATT
*
40614788 TTCATAATAAATATT
1 TTCAAAATAAATATT
40614803 T
1 T
40614804 ATTACAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
TTCAAAATAAATATT
Found at i:40615232 original size:9 final size:9
Alignment explanation
Indices: 40615218--40615294 Score: 84
Period size: 9 Copynumber: 8.4 Consensus size: 9
40615208 TTTGGTTAAA
40615218 AATTACCCG
1 AATTACCCG
40615227 AATTACCCG
1 AATTACCCG
*
40615236 AATTAACCG
1 AATTACCCG
* *
40615245 AATTAACCA
1 AATTACCCG
*
40615254 AATTAACCG
1 AATTACCCG
40615263 AATTA-CCG
1 AATTACCCG
*
40615271 AAAAATACCCG
1 --AATTACCCG
40615282 AATTACCCG
1 AATTACCCG
40615291 AATT
1 AATT
40615295 TTTTTATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
8 3 0.05
9 50 0.83
10 4 0.07
11 3 0.05
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:40617263 original size:86 final size:86
Alignment explanation
Indices: 40617158--40617328 Score: 333
Period size: 86 Copynumber: 2.0 Consensus size: 86
40617148 AGATGGAGCA
*
40617158 GGAGCTTTGACTGCCGCACTTGCGATGGATCTTGCATTCAAGGTGAACAAAGTGGCAGGAGTGGG
1 GGAGCTTTGACTGCCGCACTTGCGATGGATCTTGCATTCAAGGTGAACAAAGTGGCAGGAGGGGG
40617223 TGGTAGAGACCCAAAAAGGGT
66 TGGTAGAGACCCAAAAAGGGT
40617244 GGAGCTTTGACTGCCGCACTTGCGATGGATCTTGCATTCAAGGTGAACAAAGTGGCAGGAGGGGG
1 GGAGCTTTGACTGCCGCACTTGCGATGGATCTTGCATTCAAGGTGAACAAAGTGGCAGGAGGGGG
40617309 TGGTAGAGACCCAAAAAGGG
66 TGGTAGAGACCCAAAAAGGG
40617329 GGATTTCTTC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.20
Consensus pattern (86 bp):
GGAGCTTTGACTGCCGCACTTGCGATGGATCTTGCATTCAAGGTGAACAAAGTGGCAGGAGGGGG
TGGTAGAGACCCAAAAAGGGT
Found at i:40620485 original size:14 final size:14
Alignment explanation
Indices: 40620466--40620493 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40620456 GAACAAACTT
40620466 TGTAATATAAATTA
1 TGTAATATAAATTA
40620480 TGTAATATAAATTA
1 TGTAATATAAATTA
40620494 AATACATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TGTAATATAAATTA
Found at i:40620508 original size:21 final size:21
Alignment explanation
Indices: 40620483--40620556 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
40620473 TAAATTATGT
40620483 AATATAAATTAAATACATTAC
1 AATATAAATTAAATACATTAC
* * **
40620504 AATATTAAAACTTGGAACAAACTTTGT
1 AATA-T-AAA-TT--AA-ATACATTAC
40620531 AATATAAATTAAATACATTAC
1 AATATAAATTAAATACATTAC
40620552 AATAT
1 AATAT
40620557 TAAAAATTGG
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
21 14 0.36
22 3 0.08
23 3 0.08
24 4 0.10
25 3 0.08
26 3 0.08
27 9 0.23
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (21 bp):
AATATAAATTAAATACATTAC
Found at i:40620535 original size:48 final size:48
Alignment explanation
Indices: 40620480--40620588 Score: 209
Period size: 48 Copynumber: 2.3 Consensus size: 48
40620470 ATATAAATTA
*
40620480 TGTAATATAAATTAAATACATTACAATATTAAAACTTGGAACAAACTT
1 TGTAATATAAATTAAATACATTACAATATTAAAAATTGGAACAAACTT
40620528 TGTAATATAAATTAAATACATTACAATATTAAAAATTGGAACAAACTT
1 TGTAATATAAATTAAATACATTACAATATTAAAAATTGGAACAAACTT
40620576 TGTAATATAAATT
1 TGTAATATAAATT
40620589 TTGTTATATA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (48 bp):
TGTAATATAAATTAAATACATTACAATATTAAAAATTGGAACAAACTT
Found at i:40620564 original size:24 final size:24
Alignment explanation
Indices: 40620488--40620564 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
40620478 TATGTAATAT
40620488 AAATTAAATACATTACAATATTAA
1 AAATTAAATACATTACAATATTAA
* * * **
40620512 AACTTGGAACAAACTTTGTAATA-T--
1 AAATT--AA-ATACATTACAATATTAA
40620536 AAATTAAATACATTACAATATTAA
1 AAATTAAATACATTACAATATTAA
40620560 AAATT
1 AAATT
40620565 GGAACAAACT
Statistics
Matches: 37, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
21 9 0.24
22 3 0.08
24 13 0.35
26 3 0.08
27 9 0.24
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
AAATTAAATACATTACAATATTAA
Found at i:40620575 original size:110 final size:109
Alignment explanation
Indices: 40620427--40620651 Score: 351
Period size: 110 Copynumber: 2.1 Consensus size: 109
40620417 TAGTGCATTA
* *
40620427 AAATTACAACATTACAACACTAAAACTTGGAACAAACTTTGTAATATAAATTATGTAATATAAAT
1 AAATTAAAACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTATGTAATATAAAT
* *
40620492 TAAATACATTACAATATTAAAACTTGGAACAAACTTTGTAATAT
66 TAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
* * * *
40620536 AAATTAAATACATTACAATATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAA
1 AAATTAAA-ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTATGTAATATAAA
* *
40620601 TTAAATATATTACAACATTAAAAATTGGAACCAACTTTGTAATAT
65 TTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
40620646 AAATTA
1 AAATTA
40620652 GGCACATTGG
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
109 7 0.07
110 98 0.93
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (109 bp):
AAATTAAAACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTATGTAATATAAAT
TAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
Found at i:40620583 original size:27 final size:27
Alignment explanation
Indices: 40620504--40620583 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 27
40620494 AATACATTAC
*
40620504 AATATTAAAACTTGGAACAAACTTTGT
1 AATATTAAAAATTGGAACAAACTTTGT
* * **
40620531 AATA-T--AAATT--AA-ATACATTAC
1 AATATTAAAAATTGGAACAAACTTTGT
40620552 AATATTAAAAATTGGAACAAACTTTGT
1 AATATTAAAAATTGGAACAAACTTTGT
40620579 AATAT
1 AATAT
40620584 AAATTTTGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 12
0.64 0.15 0.20
Matches are distributed among these distances:
21 9 0.24
22 3 0.08
24 9 0.24
26 3 0.08
27 14 0.37
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (27 bp):
AATATTAAAAATTGGAACAAACTTTGT
Found at i:40620587 original size:24 final size:24
Alignment explanation
Indices: 40620515--40620588 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
40620505 ATATTAAAAC
40620515 TTGGAACAAACTTTGTAATATAAA
1 TTGGAACAAACTTTGTAATATAAA
* * **
40620539 TT--AA-ATACATTACAATATTAAAAA
1 TTGGAACAAACTTTGTAATA-T--AAA
40620563 TTGGAACAAACTTTGTAATATAAA
1 TTGGAACAAACTTTGTAATATAAA
40620587 TT
1 TT
40620589 TTGTTATATA
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
21 9 0.25
22 3 0.08
24 12 0.33
26 3 0.08
27 9 0.25
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (24 bp):
TTGGAACAAACTTTGTAATATAAA
Found at i:40620592 original size:62 final size:62
Alignment explanation
Indices: 40620526--40620650 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
40620516 TGGAACAAAC
*
40620526 TTTGTAATATAAATTAAATACATTACAATATTAAAAATTGGAACAAACTTTGTAATATAAAT
1 TTTGTAATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
* * *
40620588 TTTGTTATATAAATTAAATATATTACAACATTAAAAATTGGAACCAACTTTGTAATATAAAT
1 TTTGTAATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
40620650 T
1 T
40620651 AGGCACATTG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.38
Consensus pattern (62 bp):
TTTGTAATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
Found at i:40623734 original size:14 final size:14
Alignment explanation
Indices: 40623715--40623764 Score: 66
Period size: 14 Copynumber: 3.4 Consensus size: 14
40623705 TAATAATACA
40623715 TTTTCTTTCTTCTC
1 TTTTCTTTCTTCTC
40623729 TTTTCTTTCTT-TC
1 TTTTCTTTCTTCTC
40623742 TTTTCTTCTCTCTCTC
1 TTTTCTT-TCT-TCTC
40623758 TTGTTCT
1 TT-TTCT
40623765 GCTATTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.28
14 14 0.44
15 1 0.03
16 4 0.12
17 4 0.12
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTTCTTTCTTCTC
Found at i:40623868 original size:27 final size:27
Alignment explanation
Indices: 40623830--40623908 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
40623820 AATGCTATTG
*
40623830 GTGCTGCCTATCAGATAGGCACCATTA
1 GTGCCGCCTATCAGATAGGCACCATTA
*** * *
40623857 GTGCCGCCTATCAGATAGGGGTCACTG
1 GTGCCGCCTATCAGATAGGCACCATTA
* *
40623884 GTGCCACCTATCTGATAGGCACCAT
1 GTGCCGCCTATCAGATAGGCACCAT
40623909 ACCCTGATCC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (27 bp):
GTGCCGCCTATCAGATAGGCACCATTA
Found at i:40624012 original size:31 final size:31
Alignment explanation
Indices: 40623954--40624013 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
40623944 TATACCAGAA
* *
40623954 TGGACTAAGTGGTGCCGCCTATTACTTTGAG
1 TGGACAAAGTGGTGCCGCCTATCACTTTGAG
** *
40623985 TGGACAAAGTGGTGTTGCTTATCACTTTG
1 TGGACAAAGTGGTGCCGCCTATCACTTTG
40624014 GCACCACTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (31 bp):
TGGACAAAGTGGTGCCGCCTATCACTTTGAG
Found at i:40624389 original size:21 final size:21
Alignment explanation
Indices: 40624364--40624441 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
40624354 AAAATATATT
40624364 AAATATATATTTTTATGTTTA
1 AAATATATATTTTTATGTTTA
* * *
40624385 AAATATACTA-GTTTAAGTTTT
1 AAATATA-TATTTTTATGTTTA
* * *
40624406 TAGTTTA-AGTTTTTTATGTTTA
1 AAATATATA--TTTTTATGTTTA
40624428 AAATATATATTTTT
1 AAATATATATTTTT
40624442 TTTTATGTTT
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
19 1 0.03
21 24 0.60
22 14 0.35
23 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (21 bp):
AAATATATATTTTTATGTTTA
Found at i:40624411 original size:13 final size:13
Alignment explanation
Indices: 40624393--40624419 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40624383 TAAAATATAC
40624393 TAGTTTAAGTTTT
1 TAGTTTAAGTTTT
40624406 TAGTTTAAGTTTT
1 TAGTTTAAGTTTT
40624419 T
1 T
40624420 TATGTTTAAA
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:0.00, G:0.15, T:0.63
Consensus pattern (13 bp):
TAGTTTAAGTTTT
Found at i:40624433 original size:43 final size:40
Alignment explanation
Indices: 40624373--40624459 Score: 122
Period size: 43 Copynumber: 2.1 Consensus size: 40
40624363 TAAATATATA
40624373 TTTTTATGTTTAAAATATACTAGTTTAAGTTTTTA-GTTTAAGT
1 TTTTTATGTTTAAAATATA-TA-TTT--GTTTTTATGTTTAAGT
*
40624416 TTTTTATGTTTAAAATATATATTTTTTTTTATGTTTAAGT
1 TTTTTATGTTTAAAATATATATTTGTTTTTATGTTTAAGT
40624456 TTTT
1 TTTT
40624460 ACTTTTTAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
39 6 0.14
40 12 0.29
41 3 0.07
42 2 0.05
43 19 0.45
ACGTcount: A:0.28, C:0.01, G:0.09, T:0.62
Consensus pattern (40 bp):
TTTTTATGTTTAAAATATATATTTGTTTTTATGTTTAAGT
Found at i:40625381 original size:14 final size:14
Alignment explanation
Indices: 40625359--40625391 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
40625349 GGACAGGTCT
*
40625359 AGTAAGAAGTAGGG
1 AGTAGGAAGTAGGG
40625373 AGTAGGAAGTAGGG
1 AGTAGGAAGTAGGG
40625387 AGTAG
1 AGTAG
40625392 TGAGGGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.45, T:0.15
Consensus pattern (14 bp):
AGTAGGAAGTAGGG
Found at i:40627697 original size:21 final size:19
Alignment explanation
Indices: 40627673--40627718 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
40627663 TTATGTGTCC
*
40627673 ATATTATATATTATAAAAATA
1 ATATTATAT-TCATAAAAA-A
40627694 ATA-TATATTCATAAAAAA
1 ATATTATATTCATAAAAAA
40627712 ATATTAT
1 ATATTAT
40627719 TGTAACACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 11 0.48
20 5 0.22
21 3 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATTATATTCATAAAAAA
Found at i:40627715 original size:16 final size:18
Alignment explanation
Indices: 40627677--40627719 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
40627667 GTGTCCATAT
40627677 TATATATTATAAAAATAA
1 TATATATTATAAAAATAA
40627695 TATATATTCATAAAAA-AA
1 TATATATT-ATAAAAATAA
40627713 TAT-TATT
1 TATATATT
40627720 GTAACACCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 13 0.54
19 7 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TATATATTATAAAAATAA
Found at i:40647936 original size:24 final size:24
Alignment explanation
Indices: 40647908--40647956 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40647898 TTAGTAGGTC
* *
40647908 AAATAAACTATGCTAATAAATACT
1 AAATAAACTATACTAAGAAATACT
* *
40647932 AAATATATTATACTAAGAAATACT
1 AAATAAACTATACTAAGAAATACT
40647956 A
1 A
40647957 TATCTTCTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (24 bp):
AAATAAACTATACTAAGAAATACT
Found at i:40649899 original size:24 final size:24
Alignment explanation
Indices: 40649871--40649922 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
40649861 TTAGTAGGTC
* *
40649871 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40649895 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40649919 AAAT
1 AAAT
40649923 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40650134 original size:14 final size:15
Alignment explanation
Indices: 40650103--40650135 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40650093 TCATTCTATG
40650103 TAACATTCAATCTCTA
1 TAACATTCAA-CTCTA
40650119 TAACATTCAA-TCTA
1 TAACATTCAACTCTA
40650133 TAA
1 TAA
40650136 GAACAGCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (15 bp):
TAACATTCAACTCTA
Found at i:40653975 original size:131 final size:131
Alignment explanation
Indices: 40653741--40654003 Score: 474
Period size: 131 Copynumber: 2.0 Consensus size: 131
40653731 TATGTATGAG
* *
40653741 GCCAAAACACTTCTATGGTCCATCATGATGCCCAAACTTTTCAACCTAAAGCTTTACCTGACGGT
1 GCCAAAACACTTCTATGGTCCATCATAATGCCCAAACTTTTCAACCTAAAGCTTTACCTGACAGT
*
40653806 CCTGACCTCATTTTTCAGCTTAAAACCTACTACAAATTATAACCATCTCTCCAACTTCAGCTGAT
66 CCAGACCTCATTTTTCAGCTTAAAACCTACTACAAATTATAACCATCTCTCCAACTTCAGCTGAT
40653871 T
131 T
*
40653872 GCCAAAACACTTCTATGGTCCATC-TCAATGCCCAAACTTTTCAGCCTAAAGCTTTACCTGACAG
1 GCCAAAACACTTCTATGGTCCATCAT-AATGCCCAAACTTTTCAACCTAAAGCTTTACCTGACAG
40653936 TCCAGACCTCATTTTTCAGCTTAAAACCTACTACAAATTATAACCATCTCTCCAACTTCAGCTGA
65 TCCAGACCTCATTTTTCAGCTTAAAACCTACTACAAATTATAACCATCTCTCCAACTTCAGCTGA
40654001 TT
130 TT
40654003 G
1 G
40654004 AAAAGTGCCT
Statistics
Matches: 127, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
130 1 0.01
131 126 0.99
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (131 bp):
GCCAAAACACTTCTATGGTCCATCATAATGCCCAAACTTTTCAACCTAAAGCTTTACCTGACAGT
CCAGACCTCATTTTTCAGCTTAAAACCTACTACAAATTATAACCATCTCTCCAACTTCAGCTGAT
T
Found at i:40658330 original size:26 final size:26
Alignment explanation
Indices: 40658322--40658376 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
40658312 CTTAATATTT
40658322 AAGTAAATATATATAATATAATAATA
1 AAGTAAATATATATAATATAATAATA
*
40658348 AAGTAAATATA-ATAAAATAAATAAGTA
1 AAGTAAATATATATAATAT-AATAA-TA
40658375 AA
1 AA
40658377 TGAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.23
26 16 0.62
27 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (26 bp):
AAGTAAATATATATAATATAATAATA
Found at i:40658360 original size:22 final size:22
Alignment explanation
Indices: 40658321--40658390 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
40658311 ACTTAATATT
*
40658321 TAAGTAAATATATATAATATAATAA
1 TAAGTAAATATA-ATAAAAT-A-AA
40658346 TAAAGTAAATATAATAAAATAAA
1 T-AAGTAAATATAATAAAATAAA
*
40658369 TAAGTAAATGA-AATAAATTAAA
1 TAAGTAAAT-ATAATAAAATAAA
40658391 AAACAAAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 18 0.44
23 4 0.10
24 1 0.02
25 7 0.17
26 11 0.27
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (22 bp):
TAAGTAAATATAATAAAATAAA
Found at i:40659425 original size:40 final size:39
Alignment explanation
Indices: 40659306--40659443 Score: 118
Period size: 40 Copynumber: 3.5 Consensus size: 39
40659296 CTTCGAGGCA
* * * *
40659306 ATGAGACACTGGGTGTCAATTTATTACTTTGGATATATTCG
1 ATGAGACACTAGGTGTCAAATTA-TACTTCGGAT-TATCCG
* * * *
40659347 ATGAGGCACTAGGTG-CCAATT-TACTTCGGTTTAGCCG
1 ATGAGACACTAGGTGTCAAATTATACTTCGGATTATCCG
* *
40659384 ATGAGACACTAGGTGTAAAATTAGTACTTCGAATTATCCG
1 ATGAGACACTAGGTGTCAAATTA-TACTTCGGATTATCCG
* * *
40659424 ATGAGGCACTGGGTGCCAAA
1 ATGAGACACTAGGTGTCAAA
40659444 CTGGTGTGTT
Statistics
Matches: 76, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 18 0.24
38 12 0.16
40 33 0.43
41 13 0.17
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (39 bp):
ATGAGACACTAGGTGTCAAATTATACTTCGGATTATCCG
Found at i:40659946 original size:2 final size:2
Alignment explanation
Indices: 40659941--40659971 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40659931 GTTATATATA
40659941 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
40659972 TTATGTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:40661122 original size:15 final size:15
Alignment explanation
Indices: 40661099--40661142 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
40661089 TGTCACATGT
*
40661099 CCATTTGTCACACAC
1 CCATGTGTCACACAC
*
40661114 GC-TCGTGTCACACAC
1 CCAT-GTGTCACACAC
40661129 CCATGTGTCACACA
1 CCATGTGTCACACA
40661143 TTAAAACCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.23
Consensus pattern (15 bp):
CCATGTGTCACACAC
Found at i:40663250 original size:137 final size:138
Alignment explanation
Indices: 40662985--40663258 Score: 331
Period size: 137 Copynumber: 2.0 Consensus size: 138
40662975 CTGTAAAATG
* * *
40662985 GGTCTGCTCACAGAAGCTAACAGTCGGAATGTAAGCTACACAATGCTACTCACACAAGCTGATGA
1 GGTCTGCTCACACAAGCTAACAGTCGGAATGTAAGCTACACAATGCCACTCACACAAGCTGACGA
* * **
40663050 GTATCCATAAAGTAATGTCAGACCTCAGCCATCAGTGGGACATTCAAGACCAGCACCTGAAACAT
66 GTATCCACAAAG-AATGTCAGACCTCAGCCATCAGTAGGACATTCAAGACCAGCACCCAAAACAT
40663115 GGTAACCTA
130 GGTAACCTA
*** * ** *
40663124 GGTCTGCTCACACAAGCTATTGGTCGGAATGTAA-CTATATGATGCCGCTCACACAAGCTGACGA
1 GGTCTGCTCACACAAGCTAACAGTCGGAATGTAAGCTACACAATGCCACTCACACAAGCTGACGA
* * *
40663188 GTATCCACAACA-AATG-CTGGAACC-CAGCCATCGGTATGACATTCAAGACCAGCACCCAAAAC
66 GTATCCACAA-AGAATGTC-AG-ACCTCAGCCATCAGTAGGACATTCAAGACCAGCACCCAAAAC
40663250 ATGGTAACC
128 ATGGTAACC
40663259 CGAATGGCAT
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
136 1 0.01
137 47 0.41
138 36 0.31
139 31 0.27
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (138 bp):
GGTCTGCTCACACAAGCTAACAGTCGGAATGTAAGCTACACAATGCCACTCACACAAGCTGACGA
GTATCCACAAAGAATGTCAGACCTCAGCCATCAGTAGGACATTCAAGACCAGCACCCAAAACATG
GTAACCTA
Found at i:40665778 original size:15 final size:15
Alignment explanation
Indices: 40665758--40665790 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40665748 TTATGTGTCC
*
40665758 TATGTAATTATTATT
1 TATGTAAATATTATT
40665773 TATGTAAATATTATT
1 TATGTAAATATTATT
40665788 TAT
1 TAT
40665791 CCATAGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TATGTAAATATTATT
Found at i:40668128 original size:28 final size:31
Alignment explanation
Indices: 40668096--40668156 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 31
40668086 AATAATGTAG
40668096 TTTAATTTGA-AATCCTAAA-ATTTAA-TTA
1 TTTAATTTGATAATCCTAAATATTTAAGTTA
**
40668124 TTTAATTTGATAATTTTAAATATTTAAGTTA
1 TTTAATTTGATAATCCTAAATATTTAAGTTA
40668155 TT
1 TT
40668157 ATATAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 10 0.36
29 7 0.25
30 6 0.21
31 5 0.18
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTAATTTGATAATCCTAAATATTTAAGTTA
Found at i:40670589 original size:24 final size:24
Alignment explanation
Indices: 40670557--40670605 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
40670547 TAATCGAACG
40670557 TAAGATTAGCGTCAAATAGTAATA
1 TAAGATTAGCGTCAAATAGTAATA
40670581 TAAGATTAGCGTCAAATAGTAATA
1 TAAGATTAGCGTCAAATAGTAATA
40670605 T
1 T
40670606 TATGAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (24 bp):
TAAGATTAGCGTCAAATAGTAATA
Found at i:40678896 original size:26 final size:26
Alignment explanation
Indices: 40678849--40678903 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
40678839 TTGATTAGAG
* *
40678849 ATGTTGAAGGTAGAAAGGTGTTCAAC
1 ATGTTGAAGGCAGAAAGATGTTCAAC
*
40678875 ATGTTGAAGGCAGAGAGATGTTCAAC
1 ATGTTGAAGGCAGAAAGATGTTCAAC
40678901 ATG
1 ATG
40678904 AAAATGAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.09, G:0.31, T:0.25
Consensus pattern (26 bp):
ATGTTGAAGGCAGAAAGATGTTCAAC
Found at i:40681784 original size:15 final size:15
Alignment explanation
Indices: 40681764--40681792 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40681754 TATTTGAAAT
40681764 TAAATGTTGTGAGAA
1 TAAATGTTGTGAGAA
40681779 TAAATGTTGTGAGA
1 TAAATGTTGTGAGA
40681793 GTCTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (15 bp):
TAAATGTTGTGAGAA
Found at i:40683298 original size:37 final size:38
Alignment explanation
Indices: 40683257--40683328 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
40683247 CCTACTGTTA
* *
40683257 CTGTT-GAATGAATACATATTAAGCATGTCTACTGCCT
1 CTGTTGGAATAAATACATATTAAGCATGACTACTGCCT
* *
40683294 CTGTTGGACTAAATACATTTTAAGCATGACTACTG
1 CTGTTGGAATAAATACATATTAAGCATGACTACTG
40683329 TTTATGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 5 0.17
38 25 0.83
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (38 bp):
CTGTTGGAATAAATACATATTAAGCATGACTACTGCCT
Found at i:40696401 original size:21 final size:21
Alignment explanation
Indices: 40696362--40696402 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40696352 CAAACCCTAA
*
40696362 TAAGTATCGATACTTTTTGAT
1 TAAGTATCAATACTTTTTGAT
40696383 TAAGTATCAATA-TTATTTGA
1 TAAGTATCAATACTT-TTTGA
40696403 AATATTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (21 bp):
TAAGTATCAATACTTTTTGAT
Found at i:40697530 original size:44 final size:44
Alignment explanation
Indices: 40697480--40697570 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
40697470 AACTATGTTC
*
40697480 TTAGTTTCTCACTTAAACT-TTGATTAGTGTAGATTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTT-ATTAGTGTAGATTATTTTAATA
*
40697524 TTAGTTTCCCACTTAAACTCTTATTAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTTATTAGTGTAGATTATTTTAATA
40697568 TTA
1 TTA
40697571 TTTGACCTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 42 0.95
45 2 0.05
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTTATTAGTGTAGATTATTTTAATA
Found at i:40703192 original size:2 final size:2
Alignment explanation
Indices: 40703178--40703213 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
40703168 ATCATTTGAG
*
40703178 TA TA TA TG T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40703214 GTATCTATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:40707719 original size:30 final size:30
Alignment explanation
Indices: 40707683--40707745 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
40707673 ACTTATTTTA
40707683 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
40707713 TTGTTAATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
40707743 TTG
1 TTG
40707746 CTTGTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:40709543 original size:16 final size:16
Alignment explanation
Indices: 40709522--40709552 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40709512 TTATTTTATG
40709522 TTTAAATTTAGTATAT
1 TTTAAATTTAGTATAT
*
40709538 TTTAAATTTATTATA
1 TTTAAATTTAGTATA
40709553 ATACTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTAAATTTAGTATAT
Found at i:40711625 original size:25 final size:25
Alignment explanation
Indices: 40711603--40711650 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40711593 AATTAATAAT
*
40711603 AAAATTATTAATAAAATTAAATACA
1 AAAATTAATAATAAAATTAAATACA
* *
40711628 ATAATTAATAATAAATTTAAATA
1 AAAATTAATAATAAAATTAAATA
40711651 TGTTTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAATTAATAATAAAATTAAATACA
Found at i:40711647 original size:12 final size:12
Alignment explanation
Indices: 40711593--40711647 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
40711583 TGAACATTTT
40711593 AATTAATAATAA
1 AATTAATAATAA
*
40711605 AATTATTAATAA
1 AATTAATAATAA
*
40711617 AATTAAATACA-AT
1 AATT-AATA-ATAA
40711630 AATTAATAATAA
1 AATTAATAATAA
*
40711642 ATTTAA
1 AATTAA
40711648 ATATGTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 1 0.03
12 25 0.71
13 8 0.23
14 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
AATTAATAATAA
Found at i:40713114 original size:21 final size:19
Alignment explanation
Indices: 40713090--40713134 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
40713080 TTGGTCCTCA
40713090 ATTTTAAGGTAATTTTAAGT
1 ATTTTAAGGTAATTTT-AGT
**
40713110 CATTTTATTGTAATTTTAGT
1 -ATTTTAAGGTAATTTTAGT
40713130 ATTTT
1 ATTTT
40713135 TGAGGTCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 3 0.14
21 14 0.64
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58
Consensus pattern (19 bp):
ATTTTAAGGTAATTTTAGT
Found at i:40714217 original size:22 final size:23
Alignment explanation
Indices: 40714192--40714237 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
40714182 GTACTACTCG
40714192 AACTTT-T-AACCCAATACTTTAT
1 AACTTTATCAACCCAATA-TTTAT
40714214 AACTTTATCCAACCCAATATTTAT
1 AACTTTAT-CAACCCAATATTTAT
40714238 TTTTCTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.29
23 1 0.05
24 5 0.24
25 9 0.43
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (23 bp):
AACTTTATCAACCCAATATTTAT
Found at i:40714538 original size:57 final size:58
Alignment explanation
Indices: 40714471--40714589 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 58
40714461 TTCATTTTTT
* * **
40714471 ATTTTTATTTTTATTTTGGAGAAAACCACATTCATTTGCAAATGATTT-C-ATTTCTCC
1 ATTTTCATTTTCATTTTGGAGAAAACCACAACCATTTGCAAATG-TTTCCTATTTCTCC
** *
40714528 ATTTTCATTTTCATTTTGGAGAAAACCTTAACCATTTTCAAATGTTTCCTATTTCTCC
1 ATTTTCATTTTCATTTTGGAGAAAACCACAACCATTTGCAAATGTTTCCTATTTCTCC
40714586 ATTT
1 ATTT
40714590 CACCAATTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 3 0.06
57 38 0.72
58 12 0.23
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.48
Consensus pattern (58 bp):
ATTTTCATTTTCATTTTGGAGAAAACCACAACCATTTGCAAATGTTTCCTATTTCTCC
Found at i:40714977 original size:71 final size:71
Alignment explanation
Indices: 40714829--40714970 Score: 257
Period size: 71 Copynumber: 2.0 Consensus size: 71
40714819 ACTAGTGCTA
40714829 GTCCAATGACCTTGTTATAAATGAGTGACTCTCATAGGATATGCTTAATCTCTTTGGGATAATAT
1 GTCCAATGACCTTGTTATAAATGAGTGACTCTCATAGGATATGCTTAATCTCTTTGGGATAATAT
40714894 TCATTC
66 TCATTC
* * *
40714900 GTCCAATGACCTTGTTATAAATGAGTTACTCTCATAGGGTATGCTTAGTCTCTTTGGGATAATAT
1 GTCCAATGACCTTGTTATAAATGAGTGACTCTCATAGGATATGCTTAATCTCTTTGGGATAATAT
40714965 TCATTC
66 TCATTC
40714971 TCCCAATATG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (71 bp):
GTCCAATGACCTTGTTATAAATGAGTGACTCTCATAGGATATGCTTAATCTCTTTGGGATAATAT
TCATTC
Found at i:40717734 original size:29 final size:29
Alignment explanation
Indices: 40717702--40717769 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
40717692 ACCAAAAAAA
40717702 GCCGTTTTTTTCAAAATTTACCGAAATGG
1 GCCGTTTTTTTCAAAATTTACCGAAATGG
* * ** *
40717731 GCCGATTTTTTGATTATTTACCGGAATGG
1 GCCGTTTTTTTCAAAATTTACCGAAATGG
*
40717760 GCCATTTTTT
1 GCCGTTTTTT
40717770 GGGAAATCGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (29 bp):
GCCGTTTTTTTCAAAATTTACCGAAATGG
Found at i:40718129 original size:51 final size:51
Alignment explanation
Indices: 40718053--40718167 Score: 194
Period size: 51 Copynumber: 2.3 Consensus size: 51
40718043 TCCTCTCTAA
*
40718053 TCCTCTTAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
* *
40718104 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTTAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
40718155 TCCCCTCAATTTC
1 TCCTCTCAATTTC
40718168 ATTTTTTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.28, C:0.29, G:0.00, T:0.43
Consensus pattern (51 bp):
TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
Found at i:40718202 original size:30 final size:31
Alignment explanation
Indices: 40718168--40718233 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
40718158 CCTCAATTTC
40718168 ATTTTTT-AAAATAAATTTAAAATTTTTTAT
1 ATTTTTTAAAAATAAATTTAAAATTTTTTAT
* **
40718198 ATTTTTTAAAAATAATTTTAATTTTTTTTAT
1 ATTTTTTAAAAATAAATTTAAAATTTTTTAT
40718229 ATTTT
1 ATTTT
40718234 CATCAATGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTTTTTAAAAATAAATTTAAAATTTTTTAT
Found at i:40719129 original size:30 final size:30
Alignment explanation
Indices: 40719088--40719180 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 30
40719078 TAAACCATGT
*
40719088 ACTTTTC-AAAATTTACATTTTGGCCCTAA
1 ACTTTTCTAAAATTTACATTTTGACCCTAA
* *
40719117 ACTTTTCTAAAATTTACATTTAGACCCTTAT
1 ACTTTTCTAAAATTTACATTTTGACCC-TAA
*
40719148 AC-TTTCTTAAAATTT-CACTTTGACCCCTAA
1 ACTTTTC-TAAAATTTACATTTTGA-CCCTAA
40719178 ACT
1 ACT
40719181 CTTAAGAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 7 0.13
30 31 0.58
31 15 0.28
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (30 bp):
ACTTTTCTAAAATTTACATTTTGACCCTAA
Found at i:40720657 original size:16 final size:16
Alignment explanation
Indices: 40720636--40720667 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40720626 CGTGTTCTCA
40720636 AAAAATTCTCATGTTT
1 AAAAATTCTCATGTTT
*
40720652 AAAAATTGTCATGTTT
1 AAAAATTCTCATGTTT
40720668 CGCAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (16 bp):
AAAAATTCTCATGTTT
Found at i:40720743 original size:17 final size:17
Alignment explanation
Indices: 40720701--40720743 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
40720691 TTTTTCAGGT
*
40720701 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
*
40720718 TTTCCAAAATTCTCGTG
1 TTTCAAAAATTCTCGTG
40720735 TTTCAAAAA
1 TTTCAAAAA
40720744 AAAATTCCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTG
Found at i:40720747 original size:21 final size:21
Alignment explanation
Indices: 40720723--40720765 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
40720713 TCGTGTTTCC
40720723 AAAATTCTCGT-GTTTCAAAAA
1 AAAATTC-CGTAGTTTCAAAAA
*
40720744 AAAATTCCGTATTTTCAAAAA
1 AAAATTCCGTAGTTTCAAAAA
40720765 A
1 A
40720766 TATTGTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAATTCCGTAGTTTCAAAAA
Found at i:40720780 original size:16 final size:17
Alignment explanation
Indices: 40720755--40720797 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
40720745 AAATTCCGTA
40720755 TTTTCAAAAAATATTGTG
1 TTTTC-AAAAATATTGTG
* *
40720773 -TTTCAAAATTCTTGTG
1 TTTTCAAAAATATTGTG
40720789 TTTTCAAAA
1 TTTTCAAAA
40720798 CAAGAGATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (17 bp):
TTTTCAAAAATATTGTG
Found at i:40726508 original size:12 final size:13
Alignment explanation
Indices: 40726477--40726529 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 13
40726467 ACAAAAAAAT
40726477 AAAAAAA-AG-CA
1 AAAAAAATAGACA
40726488 GAAAAAAATAGA-A
1 -AAAAAAATAGACA
40726501 AAAAAAATAGACA
1 AAAAAAATAGACA
40726514 AAACAAAA-A-ACA
1 AAA-AAAATAGACA
40726526 AAAA
1 AAAA
40726530 GGGGAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 1 0.03
12 24 0.65
13 8 0.22
14 4 0.11
ACGTcount: A:0.81, C:0.08, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAAAATAGACA
Found at i:40726562 original size:17 final size:16
Alignment explanation
Indices: 40726518--40726561 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
40726508 TAGACAAAAC
40726518 AAAAAACAAAAAGGGG
1 AAAAAACAAAAAGGGG
40726534 AAAAAACAAAAAGGGG
1 AAAAAACAAAAAGGGG
40726550 AAAAAACAAAAA
1 AAAAAACAAAAA
40726562 AAGAAGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAAAGGGG
Found at i:40727433 original size:30 final size:30
Alignment explanation
Indices: 40727399--40727457 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
40727389 ACTTGAGGTT
* *
40727399 TTTTTGAAACCCTGTTTCTTTCAAGAAATA
1 TTTTTAAAACCCTGTTTCTTTCAAAAAATA
** *
40727429 TTTTTAAAATTCTGTTTTTTTCAAAAAAT
1 TTTTTAAAACCCTGTTTCTTTCAAAAAAT
40727458 CAACTCATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (30 bp):
TTTTTAAAACCCTGTTTCTTTCAAAAAATA
Found at i:40727668 original size:76 final size:76
Alignment explanation
Indices: 40727429--40728798 Score: 1670
Period size: 77 Copynumber: 17.8 Consensus size: 76
40727419 TCAAGAAATA
* * * *
40727429 TTTTTAAAATTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAAGTGAGTTGAGCCTCGGGTC
1 TTTTTTAATTTCTGCTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
40727494 ACGCTGAGGTATTT
65 ACGCTGAGGTA--T
* *
40727508 TTTCAATTTAATTTCTG-ATTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGG
1 TTT---TTTAATTTCTGCTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
*
40727572 GTCACACTGAGGTAT
62 GTCACGCTGAGGTAT
*
40727587 TTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGTC
1 TTTTTTAATTTCTGCTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
*
40727652 ACACTGAGGTAT
65 ACGCTGAGGTAT
40727664 TTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTTAATTTCTGCTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
40727729 ACGCTGAGGTAT
65 ACGCTGAGGTAT
*
40727741 TTTTTTAATTTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTTAATTTCTGCTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
40727806 ACGCTGAGGTAT
65 ACGCTGAGGTAT
* *
40727818 TTTTTTAAATTTCTACTTTTTTTCAAAAAATTAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
1 TTTTTT-AATTTCTGC-TTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
40727883 TCACGCTGAGGTA-
63 TCACGCTGAGGTAT
* * *
40727896 -TTTTTAATTTATGTCTTTTTT-TAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTC
1 TTTTTTAATTTCTG-CTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
*
40727959 ACACTGAGGTATT
65 ACGCTGAGGTA-T
40727972 TTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTTAATTTCTGCTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
40728037 ACGCTGAGGTA-
65 ACGCTGAGGTAT
* * *
40728048 -TTTTTAATTTATGTCTTTTTT-TAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCAGGTC
1 TTTTTTAATTTCTG-CTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
40728111 ACGCTGAGGTATT
65 ACGCTGAGGTA-T
** *
40728124 TTTTTTAATTTCTATTTTTTTTCAAAAAATCAACTCATAATACAGAGATGAGTTGAGCCTCGGGT
1 TTTTTTAATTTCT-GCTTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
40728189 CACGCTGAGGTATT
64 CACGCTGAGGTA-T
* *
40728203 TTTTTTAAATTTCTGCTTTTTTAAAAAAATCAACTCATAATATAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTT-AATTTCTGCTTTTTT-CAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
* * *
40728268 CATGCCGAGGTGT
64 CACGCTGAGGTAT
* **
40728281 TTCTTTTAAATTTC--CGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGTTTCGGGT
1 TT-TTTT-AATTTCTGCTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
* *
40728344 CATGCCGAGGTAT
64 CACGCTGAGGTAT
* **
40728357 TTCTTTTAAATTTC--CGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGTTTCGGGT
1 TT-TTTT-AATTTCTGCTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
* *
40728420 CATGCCGAGGTAT
64 CACGCTGAGGTAT
* **
40728433 TTCTTTTAAATTTC--CGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGTTTCGGGT
1 TT-TTTT-AATTTCTGCTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
* *
40728496 CATGCCGAGGTAT
64 CACGCTGAGGTAT
*
40728509 TTCTTTTAAATTTC--CGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TT-TTTT-AATTTCTGCTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
*
40728572 CATGCTGAGGTACT
64 CACGCTGAGGTA-T
* * * * * * **
40728586 TCTTTTAAATTTCTG--TTTTTCAAAAATCAGCTCATATTGCGATAGGTGAGTTGAGCCTTGGAC
1 T-TTTTTAATTTCTGCTTTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT
* *
40728649 CATGCCGAGGTAT
64 CACGCTGAGGTAT
* * *
40728662 TTCTTTTAAATTTCT--ATTTTTCAAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCTCGGG
1 TT-TTTT-AATTTCTGCTTTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG
* *
40728725 TCACGCCGAGTTA-
63 TCACGCTGAGGTAT
* * *
40728738 TTTTTCAATTTATG--TTTTTCAAAAATCAACTCAT-ATTCTGAGAGGTGAGTTGAGCCTCGGG
1 TTTTTTAATTTCTGCTTTTTTCAAAAATCAACTCATAATAC--AGAGGTGAGTTGAGCCTCGGG
40728799 GCACATGTCG
Statistics
Matches: 1187, Mismatches: 72, Indels: 69
0.89 0.05 0.05
Matches are distributed among these distances:
73 3 0.00
74 147 0.12
75 16 0.01
76 346 0.29
77 351 0.30
78 61 0.05
79 190 0.16
80 7 0.01
81 57 0.05
82 9 0.01
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (76 bp):
TTTTTTAATTTCTGCTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCA
CGCTGAGGTAT
Found at i:40728057 original size:152 final size:154
Alignment explanation
Indices: 40727427--40728798 Score: 1620
Period size: 152 Copynumber: 8.9 Consensus size: 154
40727417 TTTCAAGAAA
* * * *
40727427 TATTTTTAAAATTCTGT-TTTTTTCAAAAAATCAACTCATAATACAGAAGTGAGTTGAGCCTCGG
1 TATTTTTTAATTTATGTCTTTTTT-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
* *
40727491 GTCACGCTGAGGTATTTTTTCAATTTAATTTCTG-ATTTTTCAAAAAATCAACTCATAATACAGA
65 GTCACGCTGAGGTA-TTTTT---TTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGA
* *
40727555 GGTGAGTTGAGTCTCGGGTCACACTGAGG
126 GGTGAGTTGAGCCTCGGGTCACGCTGAGG
* *
40727584 TATTTTTTTAATTTCTG-CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCG
1 TA-TTTTTTAATTTATGTCTTTTTT-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
*
40727648 GGTCACACTGAGGTATTTTTTT-AATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGT
64 GGTCACGCTGAGGTATTTTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGT
40727712 GAGTTGAGCCTCGGGTCACGCTGAGG
129 GAGTTGAGCCTCGGGTCACGCTGAGG
*
40727738 TATTTTTTTAATTTCTGT-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
1 TA-TTTTTTAATTTATGTCTTTTTT-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
* *
40727802 GGTCACGCTGAGGTATTTTTTTAAATTTCTACTTTTTTTCAAAAAATTAACTCATAATACAGAGG
64 GGTCACGCTGAGGTATTTTTTTAAATTTCTGC-TTTTTTCAAAAAATCAACTCATAATACAGAGG
40727867 TGAGTTGAGCCTCGGGTCACGCTGAGG
128 TGAGTTGAGCCTCGGGTCACGCTGAGG
* *
40727894 TA-TTTTTAATTTATGTCTTTTTT-TAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGG
1 TATTTTTTAATTTATGTCTTTTTTAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
* *
40727957 TCACACTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGA
66 TCACGCTGAGGTATTTTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGA
40728022 GTTGAGCCTCGGGTCACGCTGAGG
131 GTTGAGCCTCGGGTCACGCTGAGG
* *
40728046 TA-TTTTTAATTTATGTCTTTTTT-TAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCAGG
1 TATTTTTTAATTTATGTCTTTTTTAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
* ** *
40728109 TCACGCTGAGGTATTTTTTTTAATTTCTATTTTTTTTCAAAAAATCAACTCATAATACAGAGATG
66 TCACGCTGAGGTATTTTTTTAAATTTCT-GCTTTTTTCAAAAAATCAACTCATAATACAGAGGTG
40728174 AGTTGAGCCTCGGGTCACGCTGAGG
130 AGTTGAGCCTCGGGTCACGCTGAGG
* *
40728199 TATTTTTTTTAAATTTCTG-CTTTTTTAAAAAAATCAACTCATAATATAGAGGTGAGTTGAGCCT
1 TA--TTTTTT-AATTTATGTCTTTTTT-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCT
* * * *
40728263 CGGGTCATGCCGAGGTGTTTCTTTTAAATTTC--CGTTTTTC-AAAAATCAACTCATAATACAGA
62 CGGGTCACGCTGAGGTATTT-TTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGA
** * *
40728325 GGTGAGTTGAGTTTCGGGTCATGCCGAGG
126 GGTGAGTTGAGCCTCGGGTCACGCTGAGG
* * * * **
40728354 TATTTCTTTTAAATT-T-CCGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGTTTCG
1 TA-TT-TTTTAATTTATGTCTTTTTTAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
* * *
40728417 GGTCATGCCGAGGTATTTCTTTTAAATTTC--CGTTTTTC-AAAAATCAACTCATAATACAGAGG
64 GGTCACGCTGAGGTATTT-TTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGG
** * *
40728479 TGAGTTGAGTTTCGGGTCATGCCGAGG
128 TGAGTTGAGCCTCGGGTCACGCTGAGG
* * * *
40728506 TATTTCTTTTAAATT-T-CCGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
1 TA-TT-TTTTAATTTATGTCTTTTTTAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
* * * * * *
40728569 GGTCATGCTGAGGTACTTCTTTTAAATTTCTG--TTTTTC-AAAAATCAGCTCATATTGCGATAG
64 GGTCACGCTGAGGTA-TTTTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATAC-AGAG
* ** * *
40728631 GTGAGTTGAGCCTTGGACCATGCCGAGG
127 GTGAGTTGAGCCTCGGGTCACGCTGAGG
* * * *
40728659 TATTTCTTTTAA---ATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCT
1 TA-TT-TTTTAATTTATGTCT-TTTTTAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCT
* * * * *
40728721 CGGGTCACGCCGA-GT-TATTTTTCAATTTATG--TTTTTC-AAAAATCAACTCAT-ATTCTGAG
62 CGGGTCACGCTGAGGTATTTTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATAC--AG
40728780 AGGTGAGTTGAGCCTCGGG
125 AGGTGAGTTGAGCCTCGGG
40728799 GCACATGTCG
Statistics
Matches: 1113, Mismatches: 76, Indels: 58
0.89 0.06 0.05
Matches are distributed among these distances:
150 2 0.00
151 51 0.05
152 378 0.34
153 206 0.19
154 188 0.17
155 66 0.06
156 78 0.07
157 14 0.01
158 120 0.11
159 10 0.01
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (154 bp):
TATTTTTTAATTTATGTCTTTTTTAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
TCACGCTGAGGTATTTTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGA
GTTGAGCCTCGGGTCACGCTGAGG
Found at i:40728862 original size:75 final size:74
Alignment explanation
Indices: 40727445--40728872 Score: 734
Period size: 76 Copynumber: 18.6 Consensus size: 74
40727435 AAATTCTGTT
* * * * * *
40727445 TTTTTCAAAAAATCAACTCATAATAC-AGAAGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
1 TTTTTC-AAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGTTA-TTT
40727509 TTCAATTTAATTTCTG
64 TTCAATTT-A----TG
* * * * * * *
40727525 ATTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGTCTCGGGTCACACTGAGGTATTT
1 -TTTTTC-AAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGTTA-TT
* *
40727589 TTTTAATTTCTG
63 TTTCAATTTATG
* * * * * * *
40727601 CTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGTCTCGGGTCACACTGAGGTATT
1 --TTTTTC-AAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGTTA-T
* *
40727665 TTTTTAATTTCTG
62 TTTTCAATTTATG
* * * * *
40727678 CTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 --TTTTTC-AAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGTTA-T
* *
40727742 TTTTTAATTTCTG
62 TTTTCAATTTATG
* * * * *
40727755 TTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 --TTTTTC-AAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGA-GT-TA
* *
40727819 TTTTTAAATTTCTACTT
61 TTTTTCAA-TT-TA-TG
* * * * *
40727836 TTTTTCAAAAAATTAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
1 TTTTTC-AAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGTTATTTT
40727900 T-AATTTATG
65 TCAATTTATG
** * * * * * * *
40727909 TCTTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTTGGGTCACACTGAGGTATTT
1 --TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGA-GT-TAT
* *
40727973 TTTTTAATTTCTG
62 TTTTCAATTTATG
* * * * *
40727986 CTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 --TTTTTC-AAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGTTATT
40728050 TTT-AATTTATG
63 TTTCAATTTATG
** * * * * * *
40728061 TCTTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTT
1 --TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGA-GT-TAT
* *
40728125 TTTTTAATTTCTATTT
62 TTTTCAA-TT-TA-TG
* * * * * *
40728141 TTTTTCAAAAAATCAACTCATAATAC-AGAGATGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
1 TTTTTC-AAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGA-G--TTAT
* *
40728205 TTTTAAATTTCTG
62 TTTTCAATTTATG
* * ** * * *
40728218 CTTTTTTAAAAAAATCAACTCATAAT-ATAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTGTT
1 --TTTTT-CAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGA-GT-TA
* **
40728282 TCTTTTAAATTTCCG
61 T-TTTTCAATTTATG
* * ** * * *
40728297 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGTTTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGA-GT-TAT-T
* **
40728361 TTTAAATTTCCG
63 TTTCAATTTATG
* * ** * * *
40728373 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGTTTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGA-GT-TAT-T
* **
40728437 TTTAAATTTCCG
63 TTTCAATTTATG
* * ** * * *
40728449 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGTTTCGGGTCATGCCGAGGTATTTCT
1 TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGA-GT-TAT-T
* **
40728513 TTTAAATTTCCG
63 TTTCAATTTATG
* * * * * *
40728525 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCTGAGGTACTTCT
1 TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGTTA--T-T
* *
40728589 TTTAAATTTCTG
63 TTTCAATTTATG
* * * * * * ** * *
40728601 TTTTTCAAAAATCAGCTCATATTGCGATAGGTGAGTTGAGCCTTGGACCATGCCGAGGTATTTCT
1 TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGA-GT-TAT-T
* * *
40728666 TTTAAATTTCTA
63 TTTCAATTTATG
* * * *
40728678 TTTTTCAAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCTCGGGTCACGCCGAGTTATTTTT
1 TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGTTATTTTT
40728743 CAATTTATG
66 CAATTTATG
* * * *
40728752 TTTTTCAAAAATCAACTCATATTCTGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGA-TGTA-T
1 TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCAC--GCCGAGT-TATT
* *
40728815 TTTCGATTTTTG
63 TTTCAATTTATG
* * * *
40728827 TTTTTCGAAGATAAACTCATAATCCAAGAGGTGAGTTGAGTCTCGG
1 TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGG
40728873 TTCGCACGCC
Statistics
Matches: 1206, Mismatches: 105, Indels: 78
0.87 0.08 0.06
Matches are distributed among these distances:
73 1 0.00
74 151 0.13
75 75 0.06
76 335 0.28
77 322 0.27
78 67 0.06
79 174 0.14
80 11 0.01
81 70 0.06
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (74 bp):
TTTTTCAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGTTATTTTT
CAATTTATG
Found at i:40729104 original size:30 final size:31
Alignment explanation
Indices: 40729087--40729204 Score: 113
Period size: 30 Copynumber: 4.0 Consensus size: 31
40729077 ACCCCTGTAC
*
40729087 TTTTC-AAAATTTACATTTTGA-CCTTAAAA
1 TTTTCTAAAATTTACATTTTGACCCCTAAAA
40729116 TTTTCTAAAATTTACATTTTGACCCC-AAAA
1 TTTTCTAAAATTTACATTTTGACCCCTAAAA
* * * * *
40729146 ATTTCTAAAA-TTAAATTTCGA-CCCTTATA
1 TTTTCTAAAATTTACATTTTGACCCCTAAAA
* *
40729175 CTTTCTCAAAATTT-CACTTTGACCCCTAAA
1 TTTTCT-AAAATTTACATTTTGACCCCTAAA
40729205 CTCTTAAGAA
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
28 3 0.04
29 21 0.30
30 38 0.54
31 9 0.13
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (31 bp):
TTTTCTAAAATTTACATTTTGACCCCTAAAA
Found at i:40730085 original size:18 final size:18
Alignment explanation
Indices: 40730059--40730314 Score: 156
Period size: 18 Copynumber: 14.5 Consensus size: 18
40730049 TTAAAAAAAA
40730059 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* *
40730076 TCGTGTTTTCAAAAACTC
1 TCGTGTTTTCAAAAATTT
*
40730094 CCGTGTTTT-AAAAA-TT
1 TCGTGTTTTCAAAAATTT
*
40730110 TC-TGCTTTTTCAAAAA-CT
1 TCGTG--TTTTCAAAAATTT
*
40730128 CCTGTGTTTT-AAAAATTT
1 TC-GTGTTTTCAAAAATTT
* *
40730146 CCGTG-TTTCCAAAATTT
1 TCGTGTTTTCAAAAATTT
* *
40730163 CCCGTG-TTTCAAAAATCT
1 -TCGTGTTTTCAAAAATTT
* *
40730181 TCATGTTTTCAAAATTTT
1 TCGTGTTTTCAAAAATTT
* * ** *
40730199 TCTTGTTTACAAAGGTTC
1 TCGTGTTTTCAAAAATTT
*
40730217 TGGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* ***
40730234 TCATGTTTTCAAAAAAAA
1 TCGTGTTTTCAAAAATTT
**
40730252 TCACGTTTTCCAAAAATTT
1 TCGTGTTTT-CAAAAATTT
* *
40730271 TCATG-TTTCAAAAATTA
1 TCGTGTTTTCAAAAATTT
40730288 TCGTGTTTTCAAAAACTTT
1 TCGTGTTTTCAAAAA-TTT
40730307 T-GTGTTTT
1 TCGTGTTTT
40730315 GTAAATTTTC
Statistics
Matches: 186, Mismatches: 39, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
15 2 0.01
16 5 0.03
17 55 0.30
18 109 0.59
19 13 0.07
20 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:40730099 original size:35 final size:35
Alignment explanation
Indices: 40730060--40730194 Score: 157
Period size: 35 Copynumber: 3.9 Consensus size: 35
40730050 TAAAAAAAAT
40730060 CGTGTTTCAAAAATTTTCGTGTTTTCAAAAACTCC
1 CGTGTTTCAAAAATTTTCGTGTTTTCAAAAACTCC
*
40730095 CGTGTTTTAAAAA-TTTC-TGCTTTTTCAAAAACTCC
1 CGTGTTTCAAAAATTTTCGTG--TTTTCAAAAACTCC
* * * * **
40730130 TGTGTTTTAAAAATTTCCGTGTTTCCAAAATTTCC
1 CGTGTTTCAAAAATTTTCGTGTTTTCAAAAACTCC
* *
40730165 CGTGTTTCAAAAATCTTCATGTTTTCAAAA
1 CGTGTTTCAAAAATTTTCGTGTTTTCAAAA
40730195 TTTTTCTTGT
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
33 2 0.02
34 4 0.05
35 73 0.87
36 3 0.04
37 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (35 bp):
CGTGTTTCAAAAATTTTCGTGTTTTCAAAAACTCC
Found at i:40730125 original size:53 final size:54
Alignment explanation
Indices: 40730062--40730304 Score: 171
Period size: 53 Copynumber: 4.6 Consensus size: 54
40730052 AAAAAAATCG
*
40730062 TGTTTCAAAAATTTTCGTGTTTTCAAAAACTCCCGTGTTTTAAAAATTTCTGC-
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAACTCCCGTGTTTCAAAAATTTCTGCA
* * * * * * * *
40730115 TTTTTCAAAAA-CTCCTGTGTTTT-AAAAATTTCCGTGTTTCCAAAATTTC-CCG
1 TGTTTCAAAAATTTTC-GTGTTTTCAAAAACTCCCGTGTTTCAAAAATTTCTGCA
* * ** ** * ** *
40730167 TGTTTCAAAAATCTTCATGTTTTCAAAATTTTTCTTGTTT-ACAAAGGTTCTG-G
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAACTCCCGTGTTTCA-AAAATTTCTGCA
* * *
40730220 TGTTTCAAAAATTTTCATGTTTTCAAAAAAAATCACGT-TTTCCAAAAATTT-T-CA
1 TGTTTCAAAAATTTTCGTGTTTTC--AAAAACTCCCGTGTTT-CAAAAATTTCTGCA
*
40730274 TGTTTCAAAAATTATCGTGTTTTCAAAAACT
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAACT
40730305 TTTGTGTTTT
Statistics
Matches: 149, Mismatches: 30, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
51 1 0.01
52 46 0.31
53 63 0.42
54 26 0.17
55 12 0.08
56 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (54 bp):
TGTTTCAAAAATTTTCGTGTTTTCAAAAACTCCCGTGTTTCAAAAATTTCTGCA
Found at i:40730313 original size:35 final size:33
Alignment explanation
Indices: 40730061--40730313 Score: 125
Period size: 35 Copynumber: 7.2 Consensus size: 33
40730051 AAAAAAAATC
***
40730061 GTGTTTCAAAAATTTTCGTGTTTTCAAAAACTCCC
1 GTGTTTCAAAAA-TTTCGTGTTTTCAAAAA-TTTT
* **
40730096 GTGTTTTAAAAATTTC-TGCTTTTTCAAAAACTCCT
1 GTGTTTCAAAAATTTCGTG--TTTTCAAAAA-TTTT
* * *
40730131 GTGTTTTAAAAATTTCCGTG-TTTCCAAAATTTCCC
1 GTGTTTCAAAAATTT-CGTGTTTTCAAAAATTT--T
* *
40730166 GTGTTTCAAAAATCTTCATGTTTTCAAAATTTTT
1 GTGTTTCAAAAAT-TTCGTGTTTTCAAAAATTTT
* ** *
40730200 CTTGTTTACAAAGGTTCTGGTG-TTTCAAAAATTTT
1 -GTGTTT-CAAAAATT-TCGTGTTTTCAAAAATTTT
* ** **
40730235 CATGTTTTCAAAAAAAATCACGTTTTCCAAAAATTTT
1 -GTG-TTTC-AAAAATTTCGTGTTTT-CAAAAATTTT
*
40730272 CATGTTTCAAAAATTATCGTGTTTTCAAAAACTTTT
1 -GTGTTTCAAAAATT-TCGTGTTTTCAAAAA-TTTT
40730308 GTGTTT
1 GTGTTT
40730314 TGTAAATTTT
Statistics
Matches: 171, Mismatches: 30, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
33 3 0.02
34 12 0.07
35 95 0.56
36 45 0.26
37 16 0.09
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (33 bp):
GTGTTTCAAAAATTTCGTGTTTTCAAAAATTTT
Found at i:40730336 original size:17 final size:17
Alignment explanation
Indices: 40730311--40730367 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
40730301 AACTTTTGTG
*
40730311 TTTTGTAAATTTTCGTA
1 TTTTTTAAATTTTCGTA
* *
40730328 TTTTTTAAATTCTCATA
1 TTTTTTAAATTTTCGTA
** * *
40730345 TTTCATAAACTTTCGTG
1 TTTTTTAAATTTTCGTA
40730362 TTTTTT
1 TTTTTT
40730368 GAAAAAATCC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (17 bp):
TTTTTTAAATTTTCGTA
Found at i:40730441 original size:17 final size:17
Alignment explanation
Indices: 40730419--40730494 Score: 50
Period size: 17 Copynumber: 4.5 Consensus size: 17
40730409 TATTTTTTCA
40730419 AAAATTTCTGTATTTTT
1 AAAATTTCTGTATTTTT
*
40730436 AAAATTCTCGTGT-TTTGT
1 AAAATT-TC-TGTATTTTT
* * *
40730454 -AAATTTTTATGTTTTT
1 AAAATTTCTGTATTTTT
**
40730470 AAAA-TTCTCGTATTTCA
1 AAAATTTCT-GTATTTTT
40730487 AAAATTTC
1 AAAATTTC
40730495 CGTGCTTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
15 2 0.05
16 8 0.18
17 22 0.50
18 9 0.20
19 3 0.07
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (17 bp):
AAAATTTCTGTATTTTT
Found at i:40730504 original size:34 final size:34
Alignment explanation
Indices: 40730414--40730507 Score: 107
Period size: 34 Copynumber: 2.8 Consensus size: 34
40730404 AAATCTATTT
* *
40730414 TTTCAAAAATTTCTGTATTTTTAAAATTCTCGTG
1 TTTCAAAAATTTCTGTGTTTTTAAAATTCTCGTA
*** * *
40730448 TTTTGTAAATTTTTATGTTTTTAAAATTCTCGTA
1 TTTCAAAAATTTCTGTGTTTTTAAAATTCTCGTA
* *
40730482 TTTCAAAAATTTCCGTGCTTTTAAAA
1 TTTCAAAAATTTCTGTGTTTTTAAAA
40730508 ACTTTTCTTG
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (34 bp):
TTTCAAAAATTTCTGTGTTTTTAAAATTCTCGTA
Found at i:40730576 original size:16 final size:16
Alignment explanation
Indices: 40730555--40730586 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40730545 CGTGTTCTCA
40730555 AAAAATTCTCATGTTT
1 AAAAATTCTCATGTTT
*
40730571 AAAAATTGTCATGTTT
1 AAAAATTCTCATGTTT
40730587 CGCAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (16 bp):
AAAAATTCTCATGTTT
Found at i:40730662 original size:17 final size:17
Alignment explanation
Indices: 40730620--40730662 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
40730610 TTTTTCAGGT
*
40730620 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
*
40730637 TTTCCAAAATTCTCGTG
1 TTTCAAAAATTCTCGTG
40730654 TTTCAAAAA
1 TTTCAAAAA
40730663 AAAATTCCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTG
Found at i:40730666 original size:21 final size:21
Alignment explanation
Indices: 40730642--40730684 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
40730632 TCGTGTTTCC
40730642 AAAATTCTCGT-GTTTCAAAAA
1 AAAATTC-CGTAGTTTCAAAAA
*
40730663 AAAATTCCGTATTTTCAAAAA
1 AAAATTCCGTAGTTTCAAAAA
40730684 A
1 A
40730685 TATTGTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAATTCCGTAGTTTCAAAAA
Found at i:40730693 original size:55 final size:57
Alignment explanation
Indices: 40730619--40730726 Score: 152
Period size: 55 Copynumber: 1.9 Consensus size: 57
40730609 TTTTTTCAGG
*
40730619 TTTTCAAAAATTTTCGTGTTTCCAAAATTCTCGTG-TTTCAAAA-AAAA-ATTCCGTA
1 TTTTCAAAAATATTCGTGTTT-CAAAATTCTCGTGTTTTCAAAACAAAAGATTCCGTA
*
40730674 TTTTCAAAAAATATT-GTGTTTCAAAATTCTTGTGTTTTCAAAACAAAAGATTC
1 TTTTC-AAAAATATTCGTGTTTCAAAATTCTCGTGTTTTCAAAACAAAAGATTC
40730727 TCGTGTTTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
54 12 0.26
55 19 0.40
56 12 0.26
57 4 0.09
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (57 bp):
TTTTCAAAAATATTCGTGTTTCAAAATTCTCGTGTTTTCAAAACAAAAGATTCCGTA
Found at i:40730699 original size:16 final size:17
Alignment explanation
Indices: 40730674--40730716 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
40730664 AAATTCCGTA
40730674 TTTTCAAAAAATATTGTG
1 TTTTC-AAAAATATTGTG
* *
40730692 -TTTCAAAATTCTTGTG
1 TTTTCAAAAATATTGTG
40730708 TTTTCAAAA
1 TTTTCAAAA
40730717 CAAAAGATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (17 bp):
TTTTCAAAAATATTGTG
Found at i:40731415 original size:7 final size:7
Alignment explanation
Indices: 40731403--40731427 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40731393 AGTCGATTGA
40731403 TATTTAG
1 TATTTAG
40731410 TATTTAG
1 TATTTAG
40731417 TATTTAG
1 TATTTAG
40731424 TATT
1 TATT
40731428 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:40732105 original size:18 final size:18
Alignment explanation
Indices: 40732079--40732113 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40732069 AAGTGTGTTT
* *
40732079 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
40732097 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
40732114 TCCTTTTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:40732542 original size:25 final size:25
Alignment explanation
Indices: 40732514--40732582 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
40732504 TTTAAATTTA
*
40732514 TTATCTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* *
40732539 TTATTTAATATAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
40732564 TCAATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
40732583 ACCCTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 23 0.62
26 14 0.38
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.38
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:40732601 original size:18 final size:18
Alignment explanation
Indices: 40732578--40732673 Score: 98
Period size: 18 Copynumber: 5.7 Consensus size: 18
40732568 TTTGATGTAA
* *
40732578 TAAAAACCCTAATTTATT
1 TAAAAACCCTAACTTAAT
40732596 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
**
40732614 TAAAAACCCTAAC---CC
1 TAAAAACCCTAACTTAAT
40732629 T---AA-CCTAACTTAAT
1 TAAAAACCCTAACTTAAT
40732643 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
40732661 TAAAAACTCTAAC
1 TAAAAACCCTAAC
40732674 CCTAACCTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
11 6 0.09
12 2 0.03
14 1 0.02
15 1 0.02
17 2 0.03
18 52 0.81
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAACCCTAACTTAAT
Found at i:40732636 original size:47 final size:47
Alignment explanation
Indices: 40732585--40732945 Score: 407
Period size: 47 Copynumber: 7.2 Consensus size: 47
40732575 TAATAAAAAC
*
40732585 CCTAATTTATTTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
* *
40732632 CCTAACTTAATTAAAAACCCTAACTTAATTAAAAACTCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
40732679 CCTAATTTAATTAAAAACTCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATT--AAA----AACCCTAA-C----TTAATTAAAAACCCTAACCCTAA
** * *
40732737 CCCTAACCTAATTAAAAACCCTAAGTTAATTAAAAACCCTTACCCTAA
1 -CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
** *
40732785 CCTAACCTAATTAAAAATCCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
*
40732832 CCTAACTTACTTAAAAATCCTAACCCTAACCCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAA--T--TT---AAT--TAA---AAACCCTAACTTAATTAAAAACCCTAACCCTAA
40732891 CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
40732938 CCTAATTT
1 CCTAATTT
40732946 TACATAATTT
Statistics
Matches: 273, Mismatches: 17, Indels: 48
0.81 0.05 0.14
Matches are distributed among these distances:
47 144 0.53
48 22 0.08
49 3 0.01
50 3 0.01
51 1 0.00
52 3 0.01
53 16 0.06
54 4 0.01
55 2 0.01
56 3 0.01
57 4 0.01
58 22 0.08
59 46 0.17
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (47 bp):
CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
Found at i:40732645 original size:29 final size:29
Alignment explanation
Indices: 40732603--40732760 Score: 149
Period size: 29 Copynumber: 5.8 Consensus size: 29
40732593 ATTTAAAAAC
40732603 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
40732632 CCTAACTTAATTAAAAACCCTAA-CTTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* * * **
40732660 -TTAA--AAACT-CTAACCCTAA-CCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
40732684 --T---TTAATTAAAAACTCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
40732708 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
40732737 CCCTAACCTAATTAAAAACCCTAA
1 -CCTAACTTAATTAAAAACCCTAA
40732761 GTTAATTAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
22 3 0.03
23 8 0.08
24 17 0.16
25 3 0.03
26 1 0.01
27 3 0.03
28 4 0.04
29 45 0.43
30 21 0.20
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.27
Consensus pattern (29 bp):
CCTAACTTAATTAAAAACCCTAACCCTAA
Found at i:40732708 original size:35 final size:29
Alignment explanation
Indices: 40732650--40732760 Score: 168
Period size: 29 Copynumber: 3.8 Consensus size: 29
40732640 AATTAAAAAC
*
40732650 CCTAACTTAATTAAAAACTCTAACCCTAA
1 CCTAATTTAATTAAAAACTCTAACCCTAA
40732679 CCTAATTTAATTAAAAACTCTAACCCTAA
1 CCTAATTTAATTAAAAACTCTAACCCTAA
*
40732708 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACTCTAACCCTAA
** *
40732737 CCCTAACCTAATTAAAAACCCTAA
1 -CCTAATTTAATTAAAAACTCTAA
40732761 GTTAATTAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 56 0.73
30 21 0.27
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACTCTAACCCTAA
Found at i:40732756 original size:18 final size:18
Alignment explanation
Indices: 40732735--40732827 Score: 83
Period size: 18 Copynumber: 5.6 Consensus size: 18
40732725 CCCTAACCCT
40732735 AACCCTAACCTAATTAAA
1 AACCCTAACCTAATTAAA
**
40732753 AACCCTAAGTTAATTAAA
1 AACCCTAACCTAATTAAA
* *
40732771 AACCCTTACC---CT---
1 AACCCTAACCTAATTAAA
40732783 AA-CCTAACCTAATTAAA
1 AACCCTAACCTAATTAAA
* *
40732800 AATCCTAACTTAATTAAA
1 AACCCTAACCTAATTAAA
40732818 AACCCTAACC
1 AACCCTAACC
40732828 CTAACCTAAC
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
11 6 0.11
12 2 0.04
14 1 0.02
15 1 0.02
17 2 0.04
18 45 0.79
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (18 bp):
AACCCTAACCTAATTAAA
Found at i:40732769 original size:106 final size:105
Alignment explanation
Indices: 40732603--40732914 Score: 331
Period size: 106 Copynumber: 3.0 Consensus size: 105
40732593 ATTTAAAAAC
*
40732603 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTAAAAACCCTAACTTAATTAAAAAC
* **
40732668 TCTAACCCTAACCTAATTTAATTAAAAACTCTAACCCTAA
66 CCTAACCCTAACCTAACCTAATTAAAAACTCTAACCCTAA
* *
40732708 CCTAATTTAATTAAAAACCCTAACCCTAACCCTAACCTAATTAAAAACCCTAAGTTAATTAAAAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA-CCTAACCTAATTAAAAACCCTAACTTAATTAAAAA
*
40732773 CCCTTACCCTAACCTAACCTAATT--AAA----AA---T--
65 CCCTAACCCTAACCTAACCTAATTAAAAACTCTAACCCTAA
*
40732803 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTACTTAAAAATCCTAACCCTAACCCTAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAAC---C-T---AAT--TAA---AAACCCTAAC
** *
40732868 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAC
54 TTAATTAAAAACCCTAACCCTAACCTAACCTAATTAAAAACTCTAAC
40732915 TTAATTAAAA
Statistics
Matches: 174, Mismatches: 13, Indels: 32
0.79 0.06 0.15
Matches are distributed among these distances:
94 6 0.03
95 28 0.16
97 2 0.01
98 1 0.01
100 2 0.01
101 3 0.02
103 3 0.02
104 3 0.02
105 28 0.16
106 93 0.53
108 3 0.02
112 2 0.01
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (105 bp):
CCTAACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTAAAAACCCTAACTTAATTAAAAAC
CCTAACCCTAACCTAACCTAATTAAAAACTCTAACCCTAA
Found at i:40732836 original size:29 final size:29
Alignment explanation
Indices: 40732803--40732914 Score: 188
Period size: 29 Copynumber: 3.8 Consensus size: 29
40732793 AATTAAAAAT
40732803 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* *
40732832 CCTAACTTACTTAAAAATCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
40732861 CCCTAACTTAATTAAAAACCCTAACCCTAA
1 -CCTAACTTAATTAAAAACCCTAACCCTAA
*
40732891 CCTAATTTAATTAAAAACCCTAAC
1 CCTAACTTAATTAAAAACCCTAAC
40732915 TTAATTAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
29 50 0.65
30 27 0.35
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (29 bp):
CCTAACTTAATTAAAAACCCTAACCCTAA
Found at i:40732855 original size:153 final size:153
Alignment explanation
Indices: 40732595--40732942 Score: 574
Period size: 153 Copynumber: 2.3 Consensus size: 153
40732585 CCTAATTTAT
*
40732595 TTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACTTAA
1 TTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTAAAAACCCTAACTTAA
* * *
40732660 TTAAAAACTCTAACCCTAACCTAATTTAATTAAAAACTCTAACCCTAA-CCTAATTTAATTAAAA
66 TTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACTCTAACCCTAACCCTAACTTAATTAAAA
40732724 ACCCTAACCCTAACCCTAACCTAA
131 ACCCTAACCCTAA-CCTAACCTAA
* * *
40732748 TTAAAAACCCTAAGTTAATTAAAAACCCTTACCCTAACCTAACCTAATTAAAAATCCTAACTTAA
1 TTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTAAAAACCCTAACTTAA
*
40732813 TTAAAAACCCTAACCCTAACCTAACTTACTTAAAAA-TCCTAACCCTAACCCTAACTTAATTAAA
66 TTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACT-CTAACCCTAACCCTAACTTAATTAAA
**
40732877 AACCCTAACCCTAACCTAATTTAA
130 AACCCTAACCCTAACCTAACCTAA
40732901 TTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAA
1 TTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAA
40732943 TTTTACATAA
Statistics
Matches: 181, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
152 1 0.01
153 152 0.84
154 28 0.15
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.26
Consensus pattern (153 bp):
TTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTAAAAACCCTAACTTAA
TTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACTCTAACCCTAACCCTAACTTAATTAAAA
ACCCTAACCCTAACCTAACCTAA
Found at i:40732913 original size:124 final size:121
Alignment explanation
Indices: 40732679--40732932 Score: 296
Period size: 124 Copynumber: 2.0 Consensus size: 121
40732669 CTAACCCTAA
* * *
40732679 CCTAATTTAATTAAAAACTCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCCTAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAAC
** * ** *
40732744 CTAATTAAAAACCCTAAGTTAATTAAAAACCCTTACCCTAACCTAACCTAATTAAAAAT
66 CTAATTAAAAACCCTAACCTAACTAAAAA--CTTA-CAAAACCTAACCTAATTAAAAAC
* *
40732803 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTACTTAAAAATCCTAACCCTAACCCTAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAAC
* * *
40732868 TTAATTAAAAACCCTAACCCTAACCTAATTTAA-TTA-AAAACCCTAACTTAATTAAAAAC
66 CTAATTAAAAACCCTAA-CCTAA-CTAA--AAACTTACAAAA-CCTAACCTAATTAAAAAC
40732927 CCTAAC
1 CCTAAC
40732933 CCTAACCTAA
Statistics
Matches: 111, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
123 2 0.02
124 98 0.88
125 6 0.05
126 3 0.03
128 2 0.02
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (121 bp):
CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAAC
CTAATTAAAAACCCTAACCTAACTAAAAACTTACAAAACCTAACCTAATTAAAAAC
Found at i:40732918 original size:18 final size:18
Alignment explanation
Indices: 40732891--40732932 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
40732881 CTAACCCTAA
*
40732891 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
40732909 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
40732927 CCTAAC
1 CCTAAC
40732933 CCTAACCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.29
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Done.