Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 60 of 126
Found at i:17484227 original size:29 final size:27
Alignment explanation
Indices: 17484169--17484240 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 27
17484159 TTAACTTAAA
*
17484169 AACCCTAAACCCTTGACTTAAAAACCTT
1 AACCCTAAA-CCTTAACTTAAAAACCTT
*
17484197 AAACCCTTAA-CTTAACTTAAAAACCTTTT
1 -AACCCTAAACCTTAACTTAAAAACC--TT
17484226 AACCCTAAACCTTAA
1 AACCCTAAACCTTAA
17484241 ACCCTAACCC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 14 0.38
28 8 0.22
29 15 0.41
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.28
Consensus pattern (27 bp):
AACCCTAAACCTTAACTTAAAAACCTT
Found at i:17484271 original size:13 final size:13
Alignment explanation
Indices: 17484224--17484270 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
17484214 TAAAAACCTT
*
17484224 TTAACCCTAAACC
1 TTAACCCTAACCC
17484237 TTAAACCCTAACCC
1 TT-AACCCTAACCC
*
17484251 TTAACCTTAACCC
1 TTAACCCTAACCC
17484264 -TAACCCT
1 TTAACCCT
17484271 TGACTGGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 6 0.20
13 12 0.40
14 12 0.40
ACGTcount: A:0.34, C:0.40, G:0.00, T:0.26
Consensus pattern (13 bp):
TTAACCCTAACCC
Found at i:17487896 original size:252 final size:252
Alignment explanation
Indices: 17487382--17487952 Score: 853
Period size: 252 Copynumber: 2.3 Consensus size: 252
17487372 CCCAAACATG
* **
17487382 CTACTGTAGCAAAAGCGCGTCCACGTGGGCATGATTTCACAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGACCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
*
17487447 TTGAAGCGTTTTTATACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTTTTCCAGGACCTACT
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTCTTCCAGGACCTACT
*
17487512 GTAGCAAAAACGCGTCCACAAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAA
131 GTAGCAAAAACACGTCCACAAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAA
* *
17487577 GCGTTTTTTTAAACTATTTGCTCAGAAACATCAAGTCGAAATTATTTTTTCCAGGAC
196 GCGTTTTTTTAAACTATTTACTCAGAAACATCAACTCGAAATTATTTTTTCCAGGAC
* * *
17487634 CTACTGTAGCAAAAGCACGACCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGACCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
* *
17487699 TTGAAGCGTTTTTTTTAATTATTTGCTCAGAAATGTCAAGTCGAAATTATTTCTTCCAGGACCTA
66 TTGAAGCG-TTTTTAT-ACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTCTTCCAGGACCTA
* * * *
17487764 CTGTAGCAAAAGCACGTCCACGAA-GGCGTGATTTCAGAAATTCTTCTCATAAAGCATTCTGCTT
129 CTGTAGCAAAAACACGTCCAC-AAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
* * *
17487828 GACGCG-TTTTTTAAACTATTTACTCAGAAACGTCAACTCGAAATTA-TTTTTGCAGGAC
193 GAAGCGTTTTTTTAAACTATTTACTCAGAAACATCAACTCGAAATTATTTTTTCCAGGAC
* * * * * *
17487886 CTACTGTAGCAAAAGTGCGTA-CACGTTGGCGCAACTTCAGAAATTCTTCTGATAAAGCATCATG
1 CTACTGTAGCAAAAGCGCG-ACCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTG
17487950 CTT
65 CTT
17487953 TGATTTTATA
Statistics
Matches: 287, Mismatches: 28, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
252 134 0.47
253 44 0.15
254 107 0.37
255 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (252 bp):
CTACTGTAGCAAAAGCGCGACCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGTTTTTATACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTCTTCCAGGACCTACT
GTAGCAAAAACACGTCCACAAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAA
GCGTTTTTTTAAACTATTTACTCAGAAACATCAACTCGAAATTATTTTTTCCAGGAC
Found at i:17487928 original size:125 final size:127
Alignment explanation
Indices: 17487382--17487952 Score: 817
Period size: 127 Copynumber: 4.5 Consensus size: 127
17487372 CCCAAACATG
* ** *
17487382 CTACTGTAGCAAAAGCGCGTCCACGTGGGCATGATTTCACAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
17487447 TTGAAGCG--TTTTTATACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTTTTCCAGGAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
* *
17487507 CTACTGTAGCAAAAACGCGTCCACAAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
17487572 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACATCAAGTCGAAATTATTTTTTCCAGGAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
* *
17487634 CTACTGTAGCAAAAGCACGACCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * *
17487699 TTGAAGCGTTTTTTTTAATTATTTGCTCAGAAATGTCAAGTCGAAATTATTTCTTCCAGGAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
* * * * *
17487761 CTACTGTAGCAAAAGCACGTCCACGAAGGCGTGATTTCAGAAATTCTTCTCATAAAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * *
17487826 TTGACGCG-TTTTTTAAACTATTTACTCAGAAACGTCAACTCGAAATTA-TTTTTGCAGGAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
* * ** * * * * *
17487886 CTACTGTAGCAAAAGTGCGTACACGTTGGCGCAACTTCAGAAATTCTTCTGATAAAGCATCATGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
17487951 TT
66 TT
17487953 TGATTTTATA
Statistics
Matches: 402, Mismatches: 42, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
125 133 0.33
126 35 0.09
127 234 0.58
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (127 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
Found at i:17504248 original size:28 final size:33
Alignment explanation
Indices: 17504190--17504254 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 33
17504180 GCATGAGAAT
* *
17504190 TTTTCCTTTTTTTATCTCTCTTGTTCTTTT-CC
1 TTTTCCTTTCTTTATCTCTCCTGTTCTTTTCCC
17504222 TTTT-CTTTCTTT-TCTCTCCT-TTC-TTTCCC
1 TTTTCCTTTCTTTATCTCTCCTGTTCTTTTCCC
17504251 TTTT
1 TTTT
17504255 ATTTTTGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.10
29 9 0.30
30 7 0.23
31 7 0.23
32 4 0.13
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.69
Consensus pattern (33 bp):
TTTTCCTTTCTTTATCTCTCCTGTTCTTTTCCC
Found at i:17509936 original size:21 final size:22
Alignment explanation
Indices: 17509912--17509962 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
17509902 CGTATGGCAC
*
17509912 AATAATTTATTTTTC-TATTTA
1 AATAATTTATTTTTCATAATTA
*
17509933 AAT-ATGTATTTTTCATAATTA
1 AATAATTTATTTTTCATAATTA
*
17509954 ATTAATTTA
1 AATAATTTA
17509963 ATGAATTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 10 0.42
21 10 0.42
22 4 0.17
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
AATAATTTATTTTTCATAATTA
Found at i:17510424 original size:44 final size:44
Alignment explanation
Indices: 17510365--17510455 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
17510355 GTTGAAGCAA
* * *
17510365 AATAAAAGTTGTGATAATTATACATTTAAAAACAATTATATTTT
1 AATAAAAGTTATGATAATTACACATTTAAAAACAATTATAATTT
* * *
17510409 AATAGAAGTTATGATAATTACATATTTAAAAATAATTATAATTT
1 AATAAAAGTTATGATAATTACACATTTAAAAACAATTATAATTT
17510453 AAT
1 AAT
17510456 TTACAATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (44 bp):
AATAAAAGTTATGATAATTACACATTTAAAAACAATTATAATTT
Found at i:17510467 original size:256 final size:254
Alignment explanation
Indices: 17510065--17510534 Score: 619
Period size: 256 Copynumber: 1.8 Consensus size: 254
17510055 TATTTTTTTT
*
17510065 ATATTACTAAATTCACATTTAAAAAAAAATTAACGTAAAATAAAAGCTGCGATAATTATACATTT
1 ATATTACTAAATTCACATTTAAAAAAAAATTAACGCAAAATAAAAGCTGCGATAATTATACATTT
* *
17510130 AAAATAATCATAATTTATTAAAAGTTAAAATTGAGACTAATTACACATTTAAAAATAATTATAAT
66 AAAACAATCATAATTTAATAAAAGTT--AATT-AGACTAATTACACATTTAAAAATAATTATAAT
* * * * *
17510195 TTAATTTACAATTATTAATTAAAAAATGTTGTGCTAA-TTCTAAAATAAATTTATTACTTAAATA
128 TTAATTTACAATTATTAACTAAAAAA-ATTCTGCTAACTT-TAAAATAAAGTTATTACTTAAACA
*
17510259 AAAATCTAAGCTTAAAATATAGGGAAAACGTTAAATATAATTATAATTATAATTATTTTCAATC
191 AAAATCTAAGCATAAAATATAGGGAAAACGTTAAATATAATTATAATTATAATTATTTTCAATC
* *
17510323 ATATTACTAAATTCACATTTAAAAATTAAATAGTTGAA-GCAAAATAAAAGTTGTGATAATTATA
1 ATATTACTAAATTCACATTTAAAAA--AAA-A-TT-AACGCAAAATAAAAGCTGCGATAATTATA
* * * *
17510387 CATTTAAAAACAATTATATTTTAATAGAAGTT-A-T-GA-TAATTACATATTTAAAAATAATTAT
61 CATTT-AAAACAATCATAATTTAATAAAAGTTAATTAGACTAATTACACATTTAAAAATAATTAT
* *
17510448 AATTTAATTTACAATTATTAGCTAAAAAAATTCTGCTAACTTTAAAATAGAGTTATTACTTAAAC
125 AATTTAATTTACAATTATTAACTAAAAAAATTCTGCTAACTTTAAAATAAAGTTATTACTTAAAC
* * *
17510513 AGAACTCTAAGCATAGAATATA
190 AAAAATCTAAGCATAAAATATA
17510535 AGAAAAAGTT
Statistics
Matches: 185, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
255 46 0.25
256 53 0.29
257 2 0.01
258 25 0.14
259 1 0.01
260 4 0.02
261 1 0.01
262 30 0.16
263 23 0.12
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.37
Consensus pattern (254 bp):
ATATTACTAAATTCACATTTAAAAAAAAATTAACGCAAAATAAAAGCTGCGATAATTATACATTT
AAAACAATCATAATTTAATAAAAGTTAATTAGACTAATTACACATTTAAAAATAATTATAATTTA
ATTTACAATTATTAACTAAAAAAATTCTGCTAACTTTAAAATAAAGTTATTACTTAAACAAAAAT
CTAAGCATAAAATATAGGGAAAACGTTAAATATAATTATAATTATAATTATTTTCAATC
Found at i:17529592 original size:31 final size:30
Alignment explanation
Indices: 17529523--17529592 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
17529513 AGGTTTCATT
* *
17529523 TCAGTCACTCAACTTTAGAAAAATAACAAA
1 TCAGTCACTCAACATTACAAAAATAACAAA
* * *
17529553 ACAATCACT-AACATTATCAAAAAGTGACAAA
1 TCAGTCACTCAACATTA-CAAAAA-TAACAAA
17529584 TCAGTCACT
1 TCAGTCACT
17529593 TATTAACATT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 6 0.19
30 12 0.39
31 13 0.42
ACGTcount: A:0.49, C:0.21, G:0.07, T:0.23
Consensus pattern (30 bp):
TCAGTCACTCAACATTACAAAAATAACAAA
Found at i:17529654 original size:21 final size:21
Alignment explanation
Indices: 17529628--17529667 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17529618 AATGGGACCA
17529628 CTGATGTGGCAAGTTAACTAG
1 CTGATGTGGCAAGTTAACTAG
*
17529649 CTGATGTGGCTAGTTAACT
1 CTGATGTGGCAAGTTAACT
17529668 TGCCACGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
CTGATGTGGCAAGTTAACTAG
Found at i:17532251 original size:143 final size:145
Alignment explanation
Indices: 17532052--17532345 Score: 468
Period size: 143 Copynumber: 2.0 Consensus size: 145
17532042 TTACGATGGT
* * *
17532052 AAAAATACAATTTCATCATTTTAATAGTCTCCATCTTTATAATTTTTAAAGGATTAAATTAAAAT
1 AAAATTACAATTTCATCATTTTAATAGCCTCCATCTTTATAATTTTTAAAGGATTAAATCAAAAT
*
17532117 TTTATCATTTTT-AGGGGGTCAAAGTGCAATTGTACCTTTACTAATTTAAAATTTTAAAAATTTC
66 TTTATCATTTTTAAGGGGGCCAAAGTGCAATTGTACCTTTACTAATTTAAAATTTTAAAAATTTC
*
17532181 AAAGGGCCTAAAT-G
131 AAAGGGCATAAATAG
*
17532195 AAAATTACAATTTCA-CAATTTTAATAGCCTCTATCTTTATAATTTTTAAAGGATTAAATCAAAA
1 AAAATTACAATTTCATC-ATTTTAATAGCCTCCATCTTTATAATTTTTAAAGGATTAAATCAAAA
* * * *
17532259 TTTTATCATTTTTAAGGGGGCCAAAGTGTAATTTTATCTTTATTAATTTAAAATTTTAAAAATTT
65 TTTTATCATTTTTAAGGGGGCCAAAGTGCAATTGTACCTTTACTAATTTAAAATTTTAAAAATTT
17532324 CAAAGGGCATAAATAG
130 CAAAGGGCATAAATAG
17532340 AAAATT
1 AAAATT
17532346 TTCCATTTTA
Statistics
Matches: 138, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
142 1 0.01
143 71 0.51
144 59 0.43
145 7 0.05
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (145 bp):
AAAATTACAATTTCATCATTTTAATAGCCTCCATCTTTATAATTTTTAAAGGATTAAATCAAAAT
TTTATCATTTTTAAGGGGGCCAAAGTGCAATTGTACCTTTACTAATTTAAAATTTTAAAAATTTC
AAAGGGCATAAATAG
Found at i:17532992 original size:3 final size:3
Alignment explanation
Indices: 17532984--17533008 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17532974 ATTTTATTTG
17532984 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
17533009 TATCTCAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17537497 original size:13 final size:13
Alignment explanation
Indices: 17537479--17537508 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17537469 GCACTAAAAG
*
17537479 ACAACAGAAGCAA
1 ACAACAGAAACAA
17537492 ACAACAGAAACAA
1 ACAACAGAAACAA
17537505 ACAA
1 ACAA
17537509 AAACAATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.23, G:0.10, T:0.00
Consensus pattern (13 bp):
ACAACAGAAACAA
Found at i:17538462 original size:12 final size:12
Alignment explanation
Indices: 17538442--17538474 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17538432 ATAAAAAAAC
17538442 ATTTTATTTAAT
1 ATTTTATTTAAT
*
17538454 ATTTCATTTAAT
1 ATTTTATTTAAT
17538466 -TTTTATTTA
1 ATTTTATTTA
17538475 TTTACTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTTATTTAAT
Found at i:17539125 original size:40 final size:39
Alignment explanation
Indices: 17539081--17539190 Score: 109
Period size: 41 Copynumber: 2.7 Consensus size: 39
17539071 CGTCGTTTTT
17539081 AGCGGCG-TTTGGATAAAAACGCCGCTAAAGATCGAGCATG
1 AGCGGCGTTTTGG--AAAAACGCCGCTAAAGATCGAGCATG
* *
17539121 AGCGGCGCTTTTTGGCAAAACGCCGCTAAAGATCGAG-ATTT
1 AGCGGCG--TTTTGGAAAAACGCCGCTAAAGATCGAGCA-TG
*
17539162 AGAGGCGCTTTATGG-AAAACGCCGCTAAA
1 AGCGGCG-TTT-TGGAAAAACGCCGCTAAA
17539191 ATAAGCATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
40 25 0.41
41 31 0.51
43 5 0.08
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (39 bp):
AGCGGCGTTTTGGAAAAACGCCGCTAAAGATCGAGCATG
Found at i:17539143 original size:41 final size:40
Alignment explanation
Indices: 17539096--17539190 Score: 138
Period size: 41 Copynumber: 2.4 Consensus size: 40
17539086 CGTTTGGATA
* *
17539096 AAAACGCCGCTAAAGATCGAGCA-TGAGCGGCGCTTTTTGG
1 AAAACGCCGCTAAAGATCGAG-ATTGAGAGGCGCTTTATGG
*
17539136 CAAAACGCCGCTAAAGATCGAGATTTAGAGGCGCTTTATGG
1 -AAAACGCCGCTAAAGATCGAGATTGAGAGGCGCTTTATGG
17539177 AAAACGCCGCTAAA
1 AAAACGCCGCTAAA
17539191 ATAAGCATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
40 15 0.30
41 35 0.70
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGATTGAGAGGCGCTTTATGG
Found at i:17539437 original size:83 final size:81
Alignment explanation
Indices: 17539269--17539450 Score: 258
Period size: 83 Copynumber: 2.2 Consensus size: 81
17539259 CTTTCGGAGA
*
17539269 TTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCGTTTTTTGGAAAGCG
1 TTTAGCGGCGTTTTT-GGAAAGCGCCGCTAATGCCCAGGCCTTTAGCGGCGTTTTTTGGAAAGCG
*
17539334 CCGCTAATGCCCAGGCC
65 CCGCCAATGCCCAGGCC
* *
17539351 TTTAGCGGCGTTTTTGTGAAAGTGCCGCTAATGCCCCAGGCCTTTAGCGGTG-TTTTTGTGAAAG
1 TTTAGCGGCGTTTTTG-GAAAGCGCCGCTAATG-CCCAGGCCTTTAGCGGCGTTTTTTG-GAAAG
* *
17539415 CGCCGCCAATGCCTAGGGC
63 CGCCGCCAATGCCCAGGCC
*
17539434 TTTAGCAGCGTTTTTGG
1 TTTAGCGGCGTTTTTGG
17539451 GAGGGAAAGC
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
81 1 0.01
82 37 0.41
83 52 0.58
ACGTcount: A:0.17, C:0.24, G:0.30, T:0.29
Consensus pattern (81 bp):
TTTAGCGGCGTTTTTGGAAAGCGCCGCTAATGCCCAGGCCTTTAGCGGCGTTTTTTGGAAAGCGC
CGCCAATGCCCAGGCC
Found at i:17539449 original size:41 final size:41
Alignment explanation
Indices: 17539269--17539449 Score: 258
Period size: 41 Copynumber: 4.4 Consensus size: 41
17539259 CTTTCGGAGA
*
17539269 TTTAGCGGCGTTTTTAG-GAAAGCGCCGCTAATGCCCAGGGC
1 TTTAGCGGCGTTTTT-GTGAAAGCGCCGCTAATGCCCAGGCC
17539310 TTTAGCGGCGTTTTT-TGGAAAGCGCCGCTAATGCCCAGGCC
1 TTTAGCGGCGTTTTTGT-GAAAGCGCCGCTAATGCCCAGGCC
*
17539351 TTTAGCGGCGTTTTTGTGAAAGTGCCGCTAATGCCCCAGGCC
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATG-CCCAGGCC
* * * *
17539393 TTTAGCGGTGTTTTTGTGAAAGCGCCGCCAATGCCTAGGGC
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGCC
*
17539434 TTTAGCAGCGTTTTTG
1 TTTAGCGGCGTTTTTG
17539450 GGAGGGAAAG
Statistics
Matches: 127, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
41 88 0.69
42 39 0.31
ACGTcount: A:0.17, C:0.24, G:0.30, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGCC
Found at i:17539660 original size:66 final size:66
Alignment explanation
Indices: 17539589--17539788 Score: 391
Period size: 66 Copynumber: 3.0 Consensus size: 66
17539579 ATTTATATAT
17539589 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTGAAAATATTGAATTAATTATCA
1 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTGAAAATATTGAATTAATTATCA
17539654 C
66 C
17539655 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTGAAAATATTGAATTAATTATCA
1 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTGAAAATATTGAATTAATTATCA
17539720 C
66 C
*
17539721 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAAAATATTGAATTAATTATCA
1 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTGAAAATATTGAATTAATTATCA
17539786 C
66 C
17539787 TA
1 TA
17539789 TAGTTTAGGG
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 133 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (66 bp):
TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTGAAAATATTGAATTAATTATCA
C
Found at i:17539948 original size:15 final size:15
Alignment explanation
Indices: 17539928--17539976 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
17539918 GCCATTTTAA
17539928 GGTTTATGGATTATG
1 GGTTTATGGATTATG
17539943 GGTTTA-GAGATTATG
1 GGTTTATG-GATTATG
*
17539958 GG-TTATGGTTTAT-
1 GGTTTATGGATTATG
17539971 GGTTTA
1 GGTTTA
17539977 AAGGTTGGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 2 0.07
14 12 0.40
15 16 0.53
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:17539982 original size:21 final size:21
Alignment explanation
Indices: 17539958--17540005 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
17539948 AGAGATTATG
*
17539958 GGTTATGGTTTATGGTTTAAA
1 GGTTATGGTTTAAGGTTTAAA
** *
17539979 GGTTGGGGTTTAAGGTTTAGA
1 GGTTATGGTTTAAGGTTTAAA
17540000 GGTTAT
1 GGTTAT
17540006 ATGTTAAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (21 bp):
GGTTATGGTTTAAGGTTTAAA
Found at i:17543731 original size:35 final size:35
Alignment explanation
Indices: 17543665--17543731 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
17543655 TAATTGTATT
*
17543665 ATTAATTTATTATTTTAAATTCTAAATTTAAATTC
1 ATTAATTTATTATTTTAAATTCTAAAGTTAAATTC
* * *
17543700 ATTAATTTTTTATATTT-AGTTTTAAAGTTAAA
1 ATTAATTTATTAT-TTTAAATTCTAAAGTTAAA
17543732 ATTTTTGTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 24 0.89
36 3 0.11
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (35 bp):
ATTAATTTATTATTTTAAATTCTAAAGTTAAATTC
Found at i:17543911 original size:42 final size:42
Alignment explanation
Indices: 17543850--17544198 Score: 479
Period size: 42 Copynumber: 8.3 Consensus size: 42
17543840 GATATATTTT
* *
17543850 TAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTA
* *
17543892 TAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGTCTGCTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTA
* *
17543934 TAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTA
*
17543976 TAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TGATCTA
* * * *
17544019 TAGTGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCTTGAGCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TGATCTA
17544062 TAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-CTGATCTA
* **
17544104 TAGCGGCGTTTGTGGG-GAAGCATCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-CTGATCTA
* * *
17544146 TAGCGGCGTTT-TTGGAAAAGCGCCGTTAAAGGTCATGACCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TGATCTA
17544188 TAGCGGCGTTT
1 TAGCGGCGTTT
17544199 ATTTCTATAA
Statistics
Matches: 279, Mismatches: 24, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
41 4 0.01
42 213 0.76
43 62 0.22
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (42 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTA
Found at i:17545140 original size:42 final size:42
Alignment explanation
Indices: 17545040--17545150 Score: 199
Period size: 41 Copynumber: 2.7 Consensus size: 42
17545030 TGGCGTAAAA
*
17545040 CCTGCTAGGCTCA-AGCCTGATAAAAACTCACCGGCACTAGG
1 CCTGCTAGGCTTATAGCCTGATAAAAACTCACCGGCACTAGG
17545081 -CTGCTAGGCTTATAGCCTGATAAAAACTCACCGGCACTAGG
1 CCTGCTAGGCTTATAGCCTGATAAAAACTCACCGGCACTAGG
17545122 CCTGCTAGGCTTATAGCCTGATAAAAACT
1 CCTGCTAGGCTTATAGCCTGATAAAAACT
17545151 GATACATAGT
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
40 11 0.16
41 28 0.42
42 28 0.42
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.22
Consensus pattern (42 bp):
CCTGCTAGGCTTATAGCCTGATAAAAACTCACCGGCACTAGG
Found at i:17550601 original size:42 final size:43
Alignment explanation
Indices: 17550554--17550676 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 43
17550544 TAGAATTTCG
* *
17550554 ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCGT-T
1 ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCATCA
* * *
17550596 GTATATGATTTCGTGTAAGA-CACTGTCTGGGACAGTGGCATCA
1 ATATATGATTACGTGTAAGACCA-TGTCTGGGACATTGGCATCA
* * *
17550639 ATATTTGATTACATGTAAGACCATGTCTGGGACGTTGG
1 ATATATGATTACGTGTAAGACCATGTCTGGGACATTGG
17550677 AATTGTACGA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.03
42 34 0.51
43 29 0.43
44 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.33
Consensus pattern (43 bp):
ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCATCA
Found at i:17555940 original size:18 final size:18
Alignment explanation
Indices: 17555911--17555962 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
17555901 AGCAAGAAAC
17555911 TTGAGTTGAGCTCGCATCCT
1 TTGA-TTGAGCTCGCA-CCT
*
17555931 TTGA-TGAGCTCGCACTT
1 TTGATTGAGCTCGCACCT
17555948 TTGATTGAGCTCGCA
1 TTGATTGAGCTCGCA
17555963 AATATAGAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 6 0.20
18 20 0.67
20 4 0.13
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (18 bp):
TTGATTGAGCTCGCACCT
Found at i:17562747 original size:39 final size:40
Alignment explanation
Indices: 17562632--17562755 Score: 124
Period size: 40 Copynumber: 3.1 Consensus size: 40
17562622 CGCTTGGACA
* * *
17562632 AAAAACGTCGGTAAAAATCGAGCATTAGCGGTGCTTTATG
1 AAAAACGCCGGTAAAAATCGAGCATTAGCGGTGTTTTTTG
* * ** * * * *
17562672 GAAATCGCCACTAAAGATCAAGCATTAGAGGCGTTTTTTG
1 AAAAACGCCGGTAAAAATCGAGCATTAGCGGTGTTTTTTG
* *
17562712 AAAAACGCCGGTAAAAAT-GGGCATTAGCGGTGTTTTTCG
1 AAAAACGCCGGTAAAAATCGAGCATTAGCGGTGTTTTTTG
17562751 AAAAA
1 AAAAA
17562756 ATGCTACAAA
Statistics
Matches: 63, Mismatches: 21, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
39 21 0.33
40 42 0.67
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (40 bp):
AAAAACGCCGGTAAAAATCGAGCATTAGCGGTGTTTTTTG
Found at i:17563243 original size:15 final size:14
Alignment explanation
Indices: 17563223--17563271 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
17563213 ACTATTTTAA
*
17563223 GGTTTAGGGAGTAT
1 GGTTTAGGGATTAT
17563237 GGGTTTAGGGATTAT
1 -GGTTTAGGGATTAT
*
17563252 GGATTAGGGATTAT
1 GGTTTAGGGATTAT
17563266 GGTTTA
1 GGTTTA
17563272 AAGGTTGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:17563310 original size:15 final size:15
Alignment explanation
Indices: 17563282--17563323 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
17563272 AAGGTTGAGA
*
17563282 TTTAAGGTTTAGGGG
1 TTTAAGGGTTAGGGG
17563297 -TTAGAGGGTTAGGGG
1 TTTA-AGGGTTAGGGG
17563312 TTTAAGGGTTAG
1 TTTAAGGGTTAG
17563324 ACGTTATGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.12
15 18 0.75
16 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.43, T:0.36
Consensus pattern (15 bp):
TTTAAGGGTTAGGGG
Found at i:17563343 original size:21 final size:22
Alignment explanation
Indices: 17563304--17563344 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
17563294 GGGTTAGAGG
*
17563304 GTTAGGGGTTTAAGGGTTAGAC
1 GTTAGGGGTTTAAGAGTTAGAC
*
17563326 GTTATGGG-TTAAGAGTTAG
1 GTTAGGGGTTTAAGAGTTAG
17563345 GGATTTAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.02, G:0.39, T:0.34
Consensus pattern (22 bp):
GTTAGGGGTTTAAGAGTTAGAC
Found at i:17563571 original size:15 final size:15
Alignment explanation
Indices: 17563533--17563567 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
17563523 CATATTTTAA
17563533 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
17563548 GGTTTAGGGATTAT-
1 GGTTTAGGGAGTATG
17563562 GGTTTA
1 GGTTTA
17563568 AGGGTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:17563581 original size:14 final size:15
Alignment explanation
Indices: 17563562--17563618 Score: 73
Period size: 14 Copynumber: 3.9 Consensus size: 15
17563552 TAGGGATTAT
17563562 GGTTTAAGGGTT-GG
1 GGTTTAAGGGTTAGG
* *
17563576 GATTTAAGGTTTAGG
1 GGTTTAAGGGTTAGG
*
17563591 GGTTAAAGGGTTAGG
1 GGTTTAAGGGTTAGG
17563606 GGTTT-AGGGTTAG
1 GGTTTAAGGGTTAG
17563619 ACACATTAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
14 18 0.50
15 18 0.50
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:17563588 original size:21 final size:20
Alignment explanation
Indices: 17563554--17563594 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
17563544 TATGGGTTTA
*
17563554 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
17563574 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
17563595 AAAGGGTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:17563743 original size:284 final size:291
Alignment explanation
Indices: 17563331--17564045 Score: 920
Period size: 284 Copynumber: 2.5 Consensus size: 291
17563321 TAGACGTTAT
* * * ** *
17563331 GGGTTAAGAGTTAGGGATTTAGGGTTTAGGGATTCAGGGATCGAGTTAGGATTTTGGGCGTTTAG
1 GGGTTAACAATTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGATTTT-GG-GTTTAG
*
17563396 ATTAA--A--TTTTTAATATATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATA
64 ATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATA
* * *
17563457 AATTTGTTTAGGGTTTTTGGTTTAGGGTATATGATTTATTTAAGATTTAAGGCCGGTTTAGAAGT
129 AATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCAGTTTAGAAGT
*
17563522 TCATATTTTAAGGTTTAGGGAG-T-A-T-GGG-T-TTAGGGATTATGGTTTAAGGGTTGGGATTT
194 TCATATTTTAAGATTTAGGGAGATGATTAGGGTTGTTAGGGATTATGGTTTAA-GGTTGGGATTT
17563581 AAGGTTTAGGGGTTAAAGGG-TTAGGGG-T-TTA-
258 AAGGTTTAGGGGTT-AAGGGTTTAGGGGTTATTAG
* * *
17563612 GGGTTAGACACATTAGGGGTTAAAAG-TTAGGGATTTAGGGGTCGGGTTAGGATTTTGGGTTTAG
1 GGGTTA-ACA-ATTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGATTTTGGGTTTAG
* *
17563676 ATTAATTATTTTTTTAATTTATATTTTTAATATGTTCTTATGTAATTGTAAAAGAGATAATAATA
64 ATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATA
*
17563741 AATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCAGTTTAGGAGT
129 AATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCAGTTTAGAAGT
*
17563806 TCATATTTTAATATTTAGGGAGTATGGATTTAGGGATTTGGATTAGGGATTATGGTTTAAGGTTG
194 TCATATTTTAAGATTTAGGGAG-AT-GA-TTAGGG--TT-G-TTAGGGATTATGGTTTAAGGTTG
*
17563871 GGATTTAAGGTTTAGGGGTTAGGGGTTTAGGGGTTAGACGTTAG
252 GGATTTAAGGTTTAGGGGTTAAGGGTTTAGGGGTT--A--TTAG
* * * * * * * * *
17563915 GGGTTAAGAGTTAGGGATTTAAGGTTTATGGATTCAGGGGCCGAGTTAAGATTTTGAGTTAAGAT
1 GGGTTAACAATTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGATTTTGGGTTTAGAT
17563980 TAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAAA
66 TAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAAA
17564045 T
131 T
17564046 CAAATATATT
Statistics
Matches: 373, Mismatches: 33, Indels: 35
0.85 0.07 0.08
Matches are distributed among these distances:
280 11 0.03
281 8 0.02
282 30 0.08
283 10 0.03
284 133 0.36
286 1 0.00
288 1 0.00
290 1 0.00
291 3 0.01
294 1 0.00
295 4 0.01
296 32 0.09
297 19 0.05
301 11 0.03
302 102 0.27
303 6 0.02
ACGTcount: A:0.29, C:0.03, G:0.27, T:0.42
Consensus pattern (291 bp):
GGGTTAACAATTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGATTTTGGGTTTAGAT
TAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAATAAA
TTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCAGTTTAGAAGTTC
ATATTTTAAGATTTAGGGAGATGATTAGGGTTGTTAGGGATTATGGTTTAAGGTTGGGATTTAAG
GTTTAGGGGTTAAGGGTTTAGGGGTTATTAG
Found at i:17563853 original size:13 final size:14
Alignment explanation
Indices: 17563818--17563877 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 14
17563808 ATATTTTAAT
*
17563818 ATTTAGGGAGTATGG
1 ATTTAGGGA-TTTGG
17563833 ATTTAGGGATTTGG
1 ATTTAGGGATTTGG
17563847 A-TTAGGGATTATGG
1 ATTTAGGGATT-TGG
* *
17563861 -TTTAAGG-TTGGG
1 ATTTAGGGATTTGG
17563873 ATTTA
1 ATTTA
17563878 AGGTTTAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 2 0.05
13 15 0.38
14 13 0.33
15 9 0.23
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.40
Consensus pattern (14 bp):
ATTTAGGGATTTGG
Found at i:17563892 original size:7 final size:7
Alignment explanation
Indices: 17563882--17563930 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
17563872 GATTTAAGGT
17563882 TTAGGGG
1 TTAGGGG
17563889 TTAGGGG
1 TTAGGGG
17563896 TTTAGGGG
1 -TTAGGGG
**
17563904 TTAGACG
1 TTAGGGG
17563911 TTAGGGG
1 TTAGGGG
* *
17563918 TTAAGAG
1 TTAGGGG
17563925 TTAGGG
1 TTAGGG
17563931 ATTTAAGGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.20, C:0.02, G:0.47, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:17563899 original size:15 final size:15
Alignment explanation
Indices: 17563878--17563920 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
17563868 TTGGGATTTA
17563878 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
17563893 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
17563908 ACG-TTAGGGGTTA
1 AGGTTTAGGGGTTA
17563921 AGAGTTAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.19, C:0.02, G:0.47, T:0.33
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:17564597 original size:175 final size:176
Alignment explanation
Indices: 17564405--17564755 Score: 659
Period size: 175 Copynumber: 2.0 Consensus size: 176
17564395 ATTATTTAAT
17564405 TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
1 TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
* *
17564470 CAATATTTATTTTGAGAGTACTT-GGTTTTTTTATTTTGCAAACAATAAGTCAATTTATAAAAAA
66 CAATATTTATTTTGAGAGTACTTGGGTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAAA
17564534 CAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
131 CAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
* *
17564580 TTGGATAATTCTAACTTAATAATTAATTATAGCCATTTTATCATTTGTTTTCTTATTAAAATATA
1 TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
17564645 CAATATTTATTTTGAGAGTACTTGGGTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAAA
66 CAATATTTATTTTGAGAGTACTTGGGTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAAA
17564710 CAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
131 CAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
17564756 AAATGAAATA
Statistics
Matches: 171, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
175 86 0.50
176 85 0.50
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (176 bp):
TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
CAATATTTATTTTGAGAGTACTTGGGTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAAA
CAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
Found at i:17567611 original size:23 final size:23
Alignment explanation
Indices: 17567584--17567631 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
17567574 CTCCAACTAT
17567584 CAAAACAGATCACTCCACCATCC
1 CAAAACAGATCACTCCACCATCC
17567607 CAAAACAGATCACTCCACCATCC
1 CAAAACAGATCACTCCACCATCC
17567630 CA
1 CA
17567632 CGTCAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.44, G:0.04, T:0.12
Consensus pattern (23 bp):
CAAAACAGATCACTCCACCATCC
Found at i:17576470 original size:50 final size:51
Alignment explanation
Indices: 17576383--17576488 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 51
17576373 TGTATATATT
*
17576383 TTTAAAATATAAAAGAAATAATAAATTTTAAAATACA-TTTATCTAAAAAA
1 TTTAAAATATAAAAGAAATAATAAAATTTAAAATACACTTTATCTAAAAAA
* * * *
17576433 TTTAAAATATTACAA-AAATAA-AAAATTTAAATTTACATCTTTTTCTAAATAA
1 TTTAAAATA-TAAAAGAAATAATAAAATTTAAA-ATACA-CTTTATCTAAAAAA
17576485 TTTA
1 TTTA
17576489 CAAACAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
49 9 0.19
50 19 0.40
51 4 0.09
52 15 0.32
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.39
Consensus pattern (51 bp):
TTTAAAATATAAAAGAAATAATAAAATTTAAAATACACTTTATCTAAAAAA
Found at i:17576761 original size:16 final size:17
Alignment explanation
Indices: 17576735--17576766 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17576725 AATCACAAAT
17576735 TTACTGAGTTTTTGAGG
1 TTACTGAGTTTTTGAGG
17576752 TTAC-GAGTTTTTGAG
1 TTACTGAGTTTTTGAG
17576767 TTTATCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.19, C:0.06, G:0.28, T:0.47
Consensus pattern (17 bp):
TTACTGAGTTTTTGAGG
Found at i:17576844 original size:16 final size:17
Alignment explanation
Indices: 17576820--17576853 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17576810 ATTATATGTG
17576820 TTTAAATATAA-TTATA
1 TTTAAATATAATTTATA
*
17576836 TTTATATATAATTTATA
1 TTTAAATATAATTTATA
17576853 T
1 T
17576854 GTATTTTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAATATAATTTATA
Found at i:17584969 original size:12 final size:11
Alignment explanation
Indices: 17584952--17585008 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
17584942 AACAAATCAT
17584952 CTCTCATATTTC
1 CTCTCA-ATTTC
17584964 CTCTCAA-TTC
1 CTCTCAATTTC
17584974 CTCTCAATTTC
1 CTCTCAATTTC
*
17584985 CT-TCCAAAATT-
1 CTCT-C-AATTTC
17584996 CTCTCAATTTC
1 CTCTCAATTTC
17585007 CT
1 CT
17585009 TCCAAAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 15 0.39
11 12 0.32
12 11 0.29
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:17584999 original size:22 final size:22
Alignment explanation
Indices: 17584969--17585024 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
17584959 ATTTCCTCTC
17584969 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
17584992 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
17585014 AATTCTCTCAA
1 AATTCTCTCAA
17585025 ATCCATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:17585053 original size:51 final size:51
Alignment explanation
Indices: 17584996--17585099 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
17584986 TTCCAAAATT
*
17584996 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
17585047 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
17585098 CT
1 CT
17585100 TTTTTAAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:17586254 original size:7 final size:7
Alignment explanation
Indices: 17586244--17586268 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17586234 ATTCGATTGA
17586244 TATTTAG
1 TATTTAG
17586251 TATTTAG
1 TATTTAG
17586258 TATTTAG
1 TATTTAG
17586265 TATT
1 TATT
17586269 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:17586943 original size:18 final size:18
Alignment explanation
Indices: 17586917--17586953 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17586907 AGGTACGTTT
* *
17586917 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATATAC
17586935 CCTAACCCTTATATATAC
1 CCTAACCCTTATATATAC
17586953 C
1 C
17586954 ATTTTCCGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.35, G:0.05, T:0.32
Consensus pattern (18 bp):
CCTAACCCTTATATATAC
Found at i:17587198 original size:9 final size:9
Alignment explanation
Indices: 17587182--17587229 Score: 87
Period size: 9 Copynumber: 5.3 Consensus size: 9
17587172 GTCCTAAGTT
17587182 CGGAAGAAC
1 CGGAAGAAC
*
17587191 CAGAAGAAC
1 CGGAAGAAC
17587200 CGGAAGAAC
1 CGGAAGAAC
17587209 CGGAAGAAC
1 CGGAAGAAC
17587218 CGGAAGAAC
1 CGGAAGAAC
17587227 CGG
1 CGG
17587230 GTTTCATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.44, C:0.23, G:0.33, T:0.00
Consensus pattern (9 bp):
CGGAAGAAC
Found at i:17587510 original size:23 final size:23
Alignment explanation
Indices: 17587481--17588320 Score: 770
Period size: 23 Copynumber: 34.5 Consensus size: 23
17587471 TTTGATGTAA
*
17587481 TAAAAACCCTAACCTAATTTAAC
1 TAAAAACCCTAACCTAATTTAAT
*** *
17587504 CCTAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
17587527 TAAAAACCCTAACGTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
17587550 TAAAAACTCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
17587573 TAAAAACCCTAAACCCTTAA-TTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
*
17587597 -AAACCCTAACCTTAACCTAATTTAAT
1 TAAA----AACCCTAACCTAATTTAAT
*
17587623 TAAAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCTAATTTAAT
17587646 TAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAA--C---CC-TAACCTAATTTAAT
17587675 TAAAAACCCTAAAACCTTAA-TTAA-
1 TAAAAACCCT--AACC-TAATTTAAT
*
17587699 -AAACCCTAACCTTAACCTAATTTAAT
1 TAAA----AACCCTAACCTAATTTAAT
*
17587725 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
17587748 TATAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
17587771 TAAAAACCCTAAACTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
17587794 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* * *
17587817 TAAAAATCATAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* * *
17587840 TAAAAATCCTAAACT--CTTAAT
1 TAAAAACCCTAACCTAATTTAAT
17587861 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
17587884 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
17587907 TAAAAACCCTAACCTTAACCAAATTTAAT
1 TAAAAACCCTAACC-T-----AATTTAAT
* * *
17587936 TAATAACTCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
17587959 TAAAAACCCTAAACC---CTTAAT
1 TAAAAACCCT-AACCTAATTTAAT
17587980 TAAAAACCCTAATCTTAACATAATTTAAT
1 TAAAAACCCTAA-C----C-TAATTTAAT
*
17588009 TAAAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCTAATTTAAT
17588032 TAAAAACCCTAACATTAGCCTAATTTAAT
1 TAAAAACCCT---A--A-CCTAATTTAAT
17588061 TAAAAACCCTAACCTAACCTAATTTAAT
1 TAAAAA--C---CCTAACCTAATTTAAT
*
17588089 TAAAAACCCTAATCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
17588112 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
17588135 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
17588158 TAAAAACCCTAAACCCTTAA-TTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
* *
17588182 AAACTCAAACCTTAACCTAATTTAAT
1 TAA---AAACCCTAACCTAATTTAAT
17588208 TAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAA--C---CC-TAACCTAATTTAAT
17588237 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
17588260 TAAAAACCCTAACCTAATTTAAAC
1 TAAAAACCCTAACCTAATTT-AAT
***
17588284 CCTAAACCCTAAACCCTAATTTAAT
1 TAAAAACCCT-AA-CCTAATTTAAT
17588309 TAAAAACCCTAA
1 TAAAAACCCTAA
17588321 TCTTAACATA
Statistics
Matches: 684, Mismatches: 61, Indels: 143
0.77 0.07 0.16
Matches are distributed among these distances:
20 2 0.00
21 34 0.05
23 391 0.57
24 34 0.05
25 54 0.08
26 25 0.04
27 24 0.04
28 23 0.03
29 92 0.13
31 2 0.00
34 3 0.00
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.30
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:17587622 original size:29 final size:29
Alignment explanation
Indices: 17587589--17587686 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
17587579 CCCTAAACCC
17587589 TTAATTAAAAACCCTAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCTTAACCTAAT
17587618 TTAATTAAAAACCCTAACC-T-A---AA-
1 TTAATTAAAAACCCTAACCTTAACCTAAT
17587641 TTAATTAAAAACCCTAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCTTAACCTAAT
17587670 TTAATTAAAAACCCTAA
1 TTAATTAAAAACCCTAA
17587687 AACCTTAATT
Statistics
Matches: 63, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
23 19 0.30
24 3 0.05
25 1 0.02
27 1 0.02
28 3 0.05
29 36 0.57
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (29 bp):
TTAATTAAAAACCCTAACCTTAACCTAAT
Found at i:17588277 original size:125 final size:124
Alignment explanation
Indices: 17587604--17588332 Score: 633
Period size: 125 Copynumber: 5.9 Consensus size: 124
17587594 TAAAAACCCT
* * **
17587604 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAAATTAATTAAAAACCCTAACCTTAACCTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC-TAATTTAA
**** * *
17587669 TTTAATTAAAAACCCTAA---AACCTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
65 --TAAACCCAAACCTTAACCTAA-TTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
* * *
17587729 AACCCTAGCCTAATTTAATTATAAACCCTAACCTAATTTAATTAAAAACCCTAAACTAATTTAAT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAT
* * * *
17587794 TAA---AAACCCTAACCTAATTTAATTAAAAA---T---CATAGCCTAATTTAATTAAA
66 AAACCCAAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
* * *
17587844 AATCCTAAACT--CTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAA-
* * * *
17587907 TAAAAACCCTAACCTTAACCAAATTTAATTAATAA--CT---C-TAGCCTAATTTAATTAAA
65 T--AAACCCAAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
*
17587963 AACCCTAAACC---CTTAATTAAAAACCCTAATCTTAACATAATTTAATTAAAAACCCTAACCTA
1 AACCCT-AACCTAATTTAATTAAAAACCCTAA-C----C-TAATTTAATTAAAAACCCTAACCTA
* * * *
17588025 AATTAATTAAAAACCCTAACATTAGCCTAATTTAATTAAAAACCCTAACC-TAACCTAATTTAAT
59 ATTTAA-T--AAACCCAAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
17588089 TAAA
121 TAAA
* *
17588093 AACCCTAATCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAAT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAA-
* * * * *
17588158 TAAA---AACCCTAAACC---CTTAATTAAAAACTCAAACCTTAACCTAATTTAATTAAA
65 TAAACCCAAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
17588212 AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
1 AA--C---CC-TAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
* * *
17588277 -TT--TAAACCCTAAACCCTAAACCCTAATTTAATTAAAAACCCTAATCTTAACATAAT
60 TTTAATAAACCC-AAA-CCTTAA-CCTAATTTAATTAAAAACCCTAACCTTAACCTAAT
17588333 GTTAGATTTG
Statistics
Matches: 512, Mismatches: 51, Indels: 77
0.80 0.08 0.12
Matches are distributed among these distances:
113 48 0.09
114 1 0.00
115 26 0.05
116 2 0.00
118 18 0.04
119 92 0.18
120 6 0.01
121 22 0.04
122 4 0.01
124 14 0.03
125 167 0.33
126 37 0.07
127 5 0.01
129 3 0.01
130 49 0.10
131 1 0.00
132 17 0.03
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.30
Consensus pattern (124 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAAT
AAACCCAAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
Found at i:17588461 original size:116 final size:116
Alignment explanation
Indices: 17588326--17588546 Score: 381
Period size: 116 Copynumber: 1.9 Consensus size: 116
17588316 CCTAATCTTA
* *
17588326 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAA-TAATAATTTTACATAATTT
1 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAA-AAATTAATAATTGTACATAATTT
*
17588390 GATAATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTC
65 GATAATTTTACTAACCATTAATACAATTTTTTGACGTAATAATTTTACATTC
*
17588442 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAAAAATTAATAATTGTATATAATTTG
1 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAAAAATTAATAATTGTACATAATTTG
*
17588507 ATAATTTTCCTAACCATTAATACAATTTTTTGACGTAATA
66 ATAATTTTACTAACCATTAATACAATTTTTTGACGTAATA
17588547 CAATTTATCA
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
115 3 0.03
116 96 0.97
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (116 bp):
ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAAAAATTAATAATTGTACATAATTTG
ATAATTTTACTAACCATTAATACAATTTTTTGACGTAATAATTTTACATTC
Found at i:17591873 original size:126 final size:125
Alignment explanation
Indices: 17591578--17591955 Score: 537
Period size: 126 Copynumber: 3.0 Consensus size: 125
17591568 CCCAAACATG
* * *
17591578 CTACTGTAGCAAAAGCGCGTCCACGAGGGCCCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
* * * *
17591643 TAGAAGCAATTTTATATTATTTGCTTAGAAACGTC-AAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
* * *
17591702 CTACTGTAGCAAAAGA-GCG-CTGACGAGGCCGCGATTTCACAAATTCTTATCAAATAACATCCT
1 CTACTGTAGCAAAA-ACGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCT
17591765 GCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCATGAC
64 GCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTCCATGAC
* *
17591828 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
** **** *
17591893 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
17591953 CTA
1 CTA
17591956 AAAACCTTTA
Statistics
Matches: 226, Mismatches: 22, Indels: 11
0.87 0.08 0.04
Matches are distributed among these distances:
123 1 0.00
124 88 0.39
125 27 0.12
126 109 0.48
127 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
Found at i:17607449 original size:21 final size:22
Alignment explanation
Indices: 17607420--17607466 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
17607410 CAGAAGGAGT
*
17607420 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
17607442 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
17607463 GAGT
1 GAGT
17607467 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:17611753 original size:25 final size:26
Alignment explanation
Indices: 17611716--17611765 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
17611706 GTTGTAAATT
17611716 GGAAAAATATCTTCAG-AAATTTTCC
1 GGAAAAATATCTTCAGAAAATTTTCC
* * *
17611741 GGAACAATCTCTTTAGAAAATTTTC
1 GGAAAAATATCTTCAGAAAATTTTC
17611766 TCTCTATAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (26 bp):
GGAAAAATATCTTCAGAAAATTTTCC
Found at i:17613736 original size:22 final size:22
Alignment explanation
Indices: 17613711--17613757 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
17613701 TTCCATTTCA
17613711 CCTATTACCTTATTAACACACC
1 CCTATTACCTTATTAACACACC
17613733 CCTATTACCTTATTAACACACC
1 CCTATTACCTTATTAACACACC
17613755 CCT
1 CCT
17613758 TCTTTAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.32
Consensus pattern (22 bp):
CCTATTACCTTATTAACACACC
Found at i:17614591 original size:21 final size:21
Alignment explanation
Indices: 17614545--17614598 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
17614535 ATGTCAATTA
*
17614545 TATTTTTATTTATGAAAAGTG
1 TATTTTTATTTATAAAAAGTG
* *
17614566 AATTTTTTTTTATAAAAGAGT-
1 TATTTTTATTTATAAAA-AGTG
*
17614587 TATTTTGATTTA
1 TATTTTTATTTA
17614599 ACAATCAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (21 bp):
TATTTTTATTTATAAAAAGTG
Found at i:17616401 original size:29 final size:30
Alignment explanation
Indices: 17616358--17616416 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
17616348 GTTTTTACAC
*
17616358 TTTCACAATCATTTTATTTCCTCTTAATCG
1 TTTCACAATCATTTTATTACCTCTTAATCG
* * *
17616388 TTTCACCA-CATTTTCTTACTTCTTAATCG
1 TTTCACAATCATTTTATTACCTCTTAATCG
17616417 GCTCCCTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTCACAATCATTTTATTACCTCTTAATCG
Found at i:17623935 original size:19 final size:19
Alignment explanation
Indices: 17623908--17623946 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
17623898 TGATTTATTT
*
17623908 TAAGCTTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
17623927 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
17623946 T
1 T
17623947 GACTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:17626359 original size:27 final size:27
Alignment explanation
Indices: 17626308--17626365 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
17626298 GTAATTAATC
** * *
17626308 AAGAGTTATATCTTTTGGTTATTGATA
1 AAGAGTTATATCACTTGATTATTGACA
*
17626335 AAGAGTTATATCACTTGATTTTTGACA
1 AAGAGTTATATCACTTGATTATTGACA
17626362 AAGA
1 AAGA
17626366 ACTATAACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (27 bp):
AAGAGTTATATCACTTGATTATTGACA
Found at i:17628720 original size:11 final size:11
Alignment explanation
Indices: 17628697--17628743 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
17628687 AACAAATCCT
17628697 CTCTCATATTTC
1 CTCTCA-ATTTC
17628709 CTCTCAATTTC
1 CTCTCAATTTC
* *
17628720 CTTTCAATTTT
1 CTCTCAATTTC
17628731 CTCTCAATTTC
1 CTCTCAATTTC
17628742 CT
1 CT
17628744 TCCAAAATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:17628754 original size:22 final size:22
Alignment explanation
Indices: 17628709--17628755 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
17628699 CTCATATTTC
* **
17628709 CTCTCAATTTCCTTTCAATTTT
1 CTCTCAATTTCCTTCCAAAATT
17628731 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
17628753 CTC
1 CTC
17628756 ATAAATCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.47
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:17628778 original size:51 final size:51
Alignment explanation
Indices: 17628721--17628846 Score: 182
Period size: 51 Copynumber: 2.5 Consensus size: 51
17628711 CTCAATTTCC
* * *
17628721 TTTCAATTTTCTCTCAATTTCCTTCCAAAATTCTCAT-AAATCCATATTTAA
1 TTTCAATTTCCTCTCAATTTCCTTCCAAAAATCTC-TCAAACCCATATTTAA
* *
17628772 TTTCAATTTCCTCTCAAATTCATTCCAAAAATCTCTCAAACCCATATTTAA
1 TTTCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAA
*
17628823 TTTCAATTTGCTCTCAATTTCCTT
1 TTTCAATTTCCTCTCAATTTCCTT
17628847 TTTTTAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
50 1 0.02
51 65 0.98
ACGTcount: A:0.30, C:0.25, G:0.01, T:0.44
Consensus pattern (51 bp):
TTTCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAA
Found at i:17631166 original size:25 final size:25
Alignment explanation
Indices: 17631133--17631246 Score: 98
Period size: 25 Copynumber: 4.7 Consensus size: 25
17631123 TTTAAATTTA
*
17631133 TTATTTGATGTATTAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
**
17631158 TTATTTGATGTAATACGCATAGAAAGT
1 TTATTTGATGTAATA-AAATAG-AAGT
** *
17631185 TT-TTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
17631203 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
17631229 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
17631247 ACCCTAATCT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 5 0.07
21 4 0.06
23 2 0.03
24 3 0.04
25 35 0.51
26 10 0.14
27 6 0.09
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:17631288 original size:29 final size:29
Alignment explanation
Indices: 17631246--17631865 Score: 571
Period size: 29 Copynumber: 20.4 Consensus size: 29
17631236 ATGTAATAAA
17631246 AACCCTAATC-TAACCTAATTAAAAACCCT
1 AACCCTAA-CATAACCTAATTAAAAACCCT
*
17631275 AACCCTAACATAACCTAATTAAAGACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* * *****
17631304 AACCCTAACCCTAACCTTAACCTAACCTAATTAAA
1 AACCCTAA-CATAACC-TAA-TTAA---AAACCCT
* *
17631339 AACCATAACCCTAACAAACCTAATTAAAAACCCT
1 AACCCTAA--C--A-TAACCTAATTAAAAACCCT
* *
17631373 AACCCTAACCTAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
17631402 AACCCTAACATAACTTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
17631431 AACCCTAACCTAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
17631460 AACCCTAACATAACTTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
17631489 AACCCTAACCTAA-CAAACCTTAACATAA-CCT
1 AACCCTAACATAACCTAA--TTAA-A-AACCCT
**** * * *
17631520 AATTAAAAACCCTAACCCTAACCTAACCTAATTAAAAACCC
1 AA-CCCTAA-CATAA-CCTAA--T----T-A--AAAACCCT
* * ** * *
17631561 AAACCCATAACATAACCTAATTAAAAACCCA
1 AACCCTAACAT--AACCTAATTAAAAACCCT
*
17631592 AACCCTAACATAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
17631621 AACCCTAACATAACTTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
17631650 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
17631679 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
17631708 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
17631737 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
17631766 AACCTTAACATAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
17631795 AACCCTAACATAACATAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
17631824 ACCCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
17631853 AGCCCTAACATAA
1 AACCCTAACATAA
17631866 TAATTTTACA
Statistics
Matches: 492, Mismatches: 70, Indels: 58
0.79 0.11 0.09
Matches are distributed among these distances:
28 3 0.01
29 389 0.79
30 10 0.02
31 21 0.04
32 8 0.02
33 6 0.01
34 10 0.02
35 14 0.03
36 2 0.00
37 3 0.01
38 4 0.01
39 5 0.01
40 9 0.02
41 7 0.01
42 1 0.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (29 bp):
AACCCTAACATAACCTAATTAAAAACCCT
Found at i:17631315 original size:41 final size:41
Alignment explanation
Indices: 17631269--17631353 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 41
17631259 CCTAATTAAA
* *
17631269 AACCCTAACCCTAACATAACCTAATTAAAGACCCTAACCCT
1 AACCCTAACCCTAACATAACCTAATTAAAAACCATAACCCT
* *
17631310 AACCCTAACCTTAACCTAACCTAATTAAAAACCATAACCCT
1 AACCCTAACCCTAACATAACCTAATTAAAAACCATAACCCT
17631351 AAC
1 AAC
17631354 AAACCTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.44, C:0.35, G:0.01, T:0.20
Consensus pattern (41 bp):
AACCCTAACCCTAACATAACCTAATTAAAAACCATAACCCT
Found at i:17631329 original size:11 final size:12
Alignment explanation
Indices: 17631299--17631331 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17631289 CTAATTAAAG
*
17631299 ACCCTAACCCTA
1 ACCCTAACCTTA
17631311 ACCCTAACCTTA
1 ACCCTAACCTTA
17631323 A-CCTAACCT
1 ACCCTAACCT
17631332 AATTAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.21
Consensus pattern (12 bp):
ACCCTAACCTTA
Found at i:17631448 original size:58 final size:58
Alignment explanation
Indices: 17631310--17631861 Score: 732
Period size: 58 Copynumber: 9.3 Consensus size: 58
17631300 CCCTAACCCT
*
17631310 AACCCTAACCTTAACCTAACCTAATTAAAAA-CCATAACCCTAACA-AACCTAATTAAA
1 AACCCTAACCCTAACCTAACCTAATTAAAAACCCA-AACCCTAACATAACCTAATTAAA
*
17631367 AACCCTAACCCTAACCTAACCTAATTAAAAACCCAAACCCTAACATAACTTAATTAAA
1 AACCCTAACCCTAACCTAACCTAATTAAAAACCCAAACCCTAACATAACCTAATTAAA
*
17631425 AACCCTAACCCTAACCTAACCTAATTAAAAACCCAAACCCTAACATAACTTAATTAAA
1 AACCCTAACCCTAACCTAACCTAATTAAAAACCCAAACCCTAACATAACCTAATTAAA
* * *
17631483 AACCCTAACCCTAACCTAA-CAAACCTTAACATAACCTAATTAAAAACCCTAACCCTAACCTAAC
1 AACCCTAACCCTAACCTAACCTAA--TTAA-A-AACC------CAAACCCTAA-CATAA-----C
17631547 CTAATTAAA
50 CTAATTAAA
* *
17631556 AACCCAAACCCATAACATAACCTAATTAAAAACCCAAACCCTAACATAACCTAATTAAA
1 AACCCTAACCC-TAACCTAACCTAATTAAAAACCCAAACCCTAACATAACCTAATTAAA
* * * *
17631615 AACCCAAACCCTAACATAACTTAATTAAAAACCCAAACCCTAACCTAACCTAATTAAA
1 AACCCTAACCCTAACCTAACCTAATTAAAAACCCAAACCCTAACATAACCTAATTAAA
*
17631673 AACCCTAACCCTAACCTAACCTAATTAAAAACCCTAACCCTAACATAACCTAATTAAA
1 AACCCTAACCCTAACCTAACCTAATTAAAAACCCAAACCCTAACATAACCTAATTAAA
* *
17631731 AACCCTAACCCTAACCTAACCTAATTAAAAACCCTAACCTTAACATAACCTAATTAAA
1 AACCCTAACCCTAACCTAACCTAATTAAAAACCCAAACCCTAACATAACCTAATTAAA
* * * * *
17631789 AACCCAAACCCTAACATAACATAATTAAAAACCCTACCCCTAACATAACCTAATTAAA
1 AACCCTAACCCTAACCTAACCTAATTAAAAACCCAAACCCTAACATAACCTAATTAAA
*
17631847 AACCCTAGCCCTAAC
1 AACCCTAACCCTAAC
17631862 ATAATAATTT
Statistics
Matches: 449, Mismatches: 26, Indels: 39
0.87 0.05 0.08
Matches are distributed among these distances:
57 43 0.10
58 312 0.69
59 25 0.06
60 1 0.00
61 4 0.01
64 4 0.01
65 9 0.02
67 9 0.02
68 4 0.01
71 4 0.01
72 1 0.00
73 23 0.05
74 7 0.02
75 3 0.01
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (58 bp):
AACCCTAACCCTAACCTAACCTAATTAAAAACCCAAACCCTAACATAACCTAATTAAA
Found at i:17631479 original size:87 final size:87
Alignment explanation
Indices: 17631310--17631865 Score: 711
Period size: 87 Copynumber: 6.2 Consensus size: 87
17631300 CCCTAACCCT
* * * *
17631310 AACCCTAACCTTAACCTAACCTAATTAAAAACCATAACCCTAACA-AACCTAATTAAAAACCCTA
1 AACCCTAACCCTAACATAACCTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCAA
*
17631374 ACCCTAACCTAACCTAATTAAA
66 ACCCTAACATAACCTAATTAAA
* * *
17631396 AACCCAAACCCTAACATAACTTAATTAAAAACCCTAACCCTAACCTAACCTAATTAAAAACCCAA
1 AACCCTAACCCTAACATAACCTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCAA
*
17631461 ACCCTAACATAACTTAATTAAA
66 ACCCTAACATAACCTAATTAAA
* * * *
17631483 AACCCTAACCCTAACCTAA-CAAACCTTAACATAACCTAATTAAAAACCCTAACCCTAACCTAAC
1 AACCCTAACCCTAACATAACCTAA--TTAA-A-AACC---CT---AACCCTAA-CAT-A----AC
17631547 CTAATTAAAAACCCAAACCCATAACATAACCTAATTAAA
50 CTAATTAAAAACCCAAACCC-TAACATAACCTAATTAAA
* * *
17631586 AACCCAAACCCTAACATAACCTAATTAAAAACCCAAACCCTAACATAACTTAATTAAAAACCCAA
1 AACCCTAACCCTAACATAACCTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCAA
*
17631651 ACCCTAACCTAACCTAATTAAA
66 ACCCTAACATAACCTAATTAAA
* *
17631673 AACCCTAACCCTAACCTAACCTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCTA
1 AACCCTAACCCTAACATAACCTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCAA
*
17631738 ACCCTAACCTAACCTAATTAAA
66 ACCCTAACATAACCTAATTAAA
* * * *
17631760 AACCCTAACCTTAACATAACCTAATTAAAAACCCAAACCCTAACATAACATAATTAAAAACCCTA
1 AACCCTAACCCTAACATAACCTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCAA
*
17631825 CCCCTAACATAACCTAATTAAA
66 ACCCTAACATAACCTAATTAAA
*
17631847 AACCCTAGCCCTAACATAA
1 AACCCTAACCCTAACATAA
17631866 TAATTTTACA
Statistics
Matches: 415, Mismatches: 36, Indels: 37
0.85 0.07 0.08
Matches are distributed among these distances:
86 41 0.10
87 252 0.61
88 25 0.06
89 1 0.00
90 4 0.01
92 1 0.00
93 3 0.01
94 8 0.02
96 8 0.02
97 3 0.01
98 1 0.00
100 4 0.01
101 1 0.00
102 26 0.06
103 34 0.08
104 3 0.01
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.20
Consensus pattern (87 bp):
AACCCTAACCCTAACATAACCTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAAACCCAA
ACCCTAACATAACCTAATTAAA
Found at i:17631513 original size:44 final size:44
Alignment explanation
Indices: 17631458--17631546 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
17631448 ATTAAAAACC
*
17631458 CAAACCCTAACATAACTTAATTAAAAACCCTAACCCTAACCTAA
1 CAAACCCTAACATAACCTAATTAAAAACCCTAACCCTAACCTAA
*
17631502 CAAACCTTAACATAACCTAATTAAAAACCCTAACCCTAACCTAA
1 CAAACCCTAACATAACCTAATTAAAAACCCTAACCCTAACCTAA
17631546 C
1 C
17631547 CTAATTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (44 bp):
CAAACCCTAACATAACCTAATTAAAAACCCTAACCCTAACCTAA
Found at i:17631923 original size:55 final size:55
Alignment explanation
Indices: 17631863--17632019 Score: 296
Period size: 55 Copynumber: 2.9 Consensus size: 55
17631853 AGCCCTAACA
17631863 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
*
17631918 TAATAATTTTACATAGTTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
*
17631973 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAATACAATT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATT
17632020 ATCAATTAAT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 99 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (55 bp):
TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
Found at i:17632414 original size:15 final size:16
Alignment explanation
Indices: 17632389--17632423 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
17632379 TAACATGAGC
17632389 GCATGGATAACGAAGT
1 GCATGGATAACGAAGT
17632405 GCAT-GATAACGAAGT
1 GCATGGATAACGAAGT
17632420 GCAT
1 GCAT
17632424 CAAACTTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (16 bp):
GCATGGATAACGAAGT
Found at i:17635285 original size:126 final size:127
Alignment explanation
Indices: 17635060--17635537 Score: 772
Period size: 126 Copynumber: 3.8 Consensus size: 127
17635050 CCCAAACTTG
* *
17635060 CTACTGTAGCAAAATCA-CGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTG
1 CTACTATAGCAAAAT-ATCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTG
17635124 GTAGAAGCGATTTTATACT-TTTGCTCAGAAACATCAAAAAAAAAAAATATTTCTTACATGAC
65 GTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAAAAATATTTCTTACATGAC
*
17635186 CTACTATAGCAAAATATCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGG
1 CTACTATAGCAAAATATCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
17635251 TAGAAGCGATTTTATACT-TTTGCTCAGAAACATCAAAAAAAAAAAATATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAAAAATATTTCTTACATGAC
17635312 CTACTATAGCAAAATATCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTATAGCAAAATATCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* * *
17635377 TAGAAGTGATTTTATACTATTTGCTCAGAAACTTC---AAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAAAAATATTTCTTACATGAC
* ** * *
17635436 CTACTGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTATAGCAAAATATCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
17635501 TAGATGCGATTTTATACTATTTGAC-CAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACATCAA
17635538 CTCGAAATAA
Statistics
Matches: 334, Mismatches: 13, Indels: 10
0.94 0.04 0.03
Matches are distributed among these distances:
124 113 0.34
125 2 0.01
126 204 0.61
127 15 0.04
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (127 bp):
CTACTATAGCAAAATATCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAAAAATATTTCTTACATGAC
Found at i:17635512 original size:250 final size:251
Alignment explanation
Indices: 17635060--17635537 Score: 766
Period size: 250 Copynumber: 1.9 Consensus size: 251
17635050 CCCAAACTTG
* *
17635060 CTACTGTAGCAAAATCACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGG
1 CTACTATAGCAAAATCACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
17635125 TAGAAGCGATTTTATACTTTTGCTCAGAAACATCAAAAAAAAAAAATATTTCTTACATGACCTAC
66 TAGAAGCGATTTTATACTTTTGCTCAGAAACATC--AAAAAAAAAATATTTCTTACATGACCTAC
* * * *
17635190 TATAGCAAAATATCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGGTAGA
129 TATAGCAAAATAGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGA
17635255 AGCGATTTTATACT-TTTG-CTCAGAAACATCAAAAAAAAAAAATATTTCTTACATGAC
194 AGCGATTTTATACTATTTGAC-CAGAAACATCAAAAAAAAAAAATATTTCTTACATGAC
17635312 CTACTATAGCAAAAT-ATCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTG
1 CTACTATAGCAAAATCA-CGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTG
* * *
17635376 GTAGAAGTGATTTTATACTATTTGCTCAGAAACTTC-AAAAAAAATTATTTCTTACATGACCTAC
65 GTAGAAGCGATTTTATACT-TTTGCTCAGAAACATCAAAAAAAAAATATTTCTTACATGACCTAC
* *
17635440 TGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGA
129 TATAGCAAAATAGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGA
* *
17635505 TGCGATTTTATACTATTTGACCAGAAACGTCAA
194 AGCGATTTTATACTATTTGACCAGAAACATCAA
17635538 CTCGAAATAA
Statistics
Matches: 209, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
250 99 0.47
251 16 0.08
252 79 0.38
253 15 0.07
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (251 bp):
CTACTATAGCAAAATCACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTTTTGCTCAGAAACATCAAAAAAAAAATATTTCTTACATGACCTACTA
TAGCAAAATAGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGAAG
CGATTTTATACTATTTGACCAGAAACATCAAAAAAAAAAAATATTTCTTACATGAC
Found at i:17645763 original size:42 final size:42
Alignment explanation
Indices: 17645717--17645847 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
17645707 GCCTGAAGGC
* * *
17645717 TGAACAGAAGCTCATGAGAGCTAAACGGAAACCTATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
** * *
17645759 TGAACAGAAGCTTGTAAGAGCTGAACGAAAACCCATAAGAGT
1 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
* * * * * *
17645801 TTAACTGAAGCTCAAAAGAGTTGAATGGAAACCCATTAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
17645843 TGAAC
1 TGAAC
17645848 GAAAACTCAT
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.19
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
Found at i:17645783 original size:21 final size:21
Alignment explanation
Indices: 17645702--17645784 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 21
17645692 ACATCATTTT
*
17645702 CAGAAGCCT-GAAG-GCTGAA
1 CAGAAGCCTATAAGAGCTGAA
* *
17645721 CAGAAG-CTCATGAGAGCTAAA
1 CAGAAGCCT-ATAAGAGCTGAA
* * * *
17645742 CGGAAACCTATAAGGGTTGAA
1 CAGAAGCCTATAAGAGCTGAA
* *
17645763 CAGAAGCTTGTAAGAGCTGAA
1 CAGAAGCCTATAAGAGCTGAA
17645784 C
1 C
17645785 GAAAACCCAT
Statistics
Matches: 45, Mismatches: 15, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
18 2 0.04
19 6 0.13
20 2 0.04
21 33 0.73
22 2 0.04
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.16
Consensus pattern (21 bp):
CAGAAGCCTATAAGAGCTGAA
Found at i:17649842 original size:13 final size:13
Alignment explanation
Indices: 17649824--17649849 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17649814 TGATTTATAT
17649824 GTGTGAAAATTTC
1 GTGTGAAAATTTC
17649837 GTGTGAAAATTTC
1 GTGTGAAAATTTC
17649850 ATCGTTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:17658038 original size:42 final size:43
Alignment explanation
Indices: 17657921--17658090 Score: 143
Period size: 43 Copynumber: 3.9 Consensus size: 43
17657911 CAGGATTCTA
* *
17657921 ATATGAGTTATCGTGTAAGACCACGTCTGGGAC-GTTGGCGTCGAT
1 ATATGA-TT-TCGTGTAAGACCATGTCTGGGACAG-TGGCATCGAT
* *
17657966 TTGA-GATTTACGTGTAAGATCATGTCTGGGACA-TCGGCATCG-T
1 AT-ATGATTT-CGTGTAAGACCATGTCTGGGACAGT-GGCATCGAT
* * *
17658009 ATATGATTTCGTGTAAGACCCTGTTTGGGACAGTGGCATTGAT
1 ATATGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
* * * *
17658052 ATTTGATTACATGTAAGACCACGTCTGGGAC-GTTGGCAT
1 ATATGATTTCGTGTAAGACCATGTCTGGGACAG-TGGCAT
17658091 TGTAAGAGCT
Statistics
Matches: 102, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 28 0.27
43 42 0.41
44 28 0.27
45 3 0.03
46 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
ATATGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
Found at i:17659909 original size:57 final size:57
Alignment explanation
Indices: 17659821--17660652 Score: 1664
Period size: 57 Copynumber: 14.6 Consensus size: 57
17659811 GACTTAGTAA
17659821 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17659878 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17659935 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17659992 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660049 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660106 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660163 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660220 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660277 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660334 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660391 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660448 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660505 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660562 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
17660619 AATTATACTTGGTTATAAGTTAAGTATTCGATTG
1 AATTATACTTGGTTATAAGTTAAGTATTCGATTG
17660653 CCATGATTCA
Statistics
Matches: 775, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 775 1.00
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (57 bp):
AATTATACTTGGTTATAAGTTAAGTATTCGATTGGTATATGATTGGTATATGAAATG
Found at i:17662040 original size:7 final size:7
Alignment explanation
Indices: 17662025--17662055 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
17662015 TCGAGCTTGA
*
17662025 AAAAGAG
1 AAAATAG
17662032 AAAATAG
1 AAAATAG
17662039 AAAATAG
1 AAAATAG
17662046 AAAATAG
1 AAAATAG
17662053 AAA
1 AAA
17662056 TAAAGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (7 bp):
AAAATAG
Found at i:17663504 original size:24 final size:24
Alignment explanation
Indices: 17663471--17663517 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
17663461 AAGGGGTAAC
* *
17663471 AAGAAGATGAAATGTTAAAGGTTA
1 AAGAAGATGAAAGGTGAAAGGTTA
*
17663495 AAGAATATGAAAGGTGAAAGGTT
1 AAGAAGATGAAAGGTGAAAGGTT
17663518 GAACATCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (24 bp):
AAGAAGATGAAAGGTGAAAGGTTA
Found at i:17671555 original size:93 final size:93
Alignment explanation
Indices: 17671139--17671515 Score: 754
Period size: 93 Copynumber: 4.1 Consensus size: 93
17671129 CATTCGGCCA
17671139 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
1 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
17671204 CGTTGCTTTGAATACTTCAAAACCCATG
66 CGTTGCTTTGAATACTTCAAAACCCATG
17671232 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
1 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
17671297 CGTTGCTTTGAATACTTCAAAACCCATG
66 CGTTGCTTTGAATACTTCAAAACCCATG
17671325 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
1 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
17671390 CGTTGCTTTGAATACTTCAAAACCCATG
66 CGTTGCTTTGAATACTTCAAAACCCATG
17671418 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
1 TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
17671483 CGTTGCTTTGAATACTTCAAAACCCATG
66 CGTTGCTTTGAATACTTCAAAACCCATG
17671511 TCTTA
1 TCTTA
17671516 ATTTTGTGAA
Statistics
Matches: 284, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 284 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (93 bp):
TCTTAGGGATTTCAATTCAAGGTTAGTTTGATTTTAGTTTTTGATAATTTTTACGTTTTTGAGAT
CGTTGCTTTGAATACTTCAAAACCCATG
Found at i:17672649 original size:41 final size:41
Alignment explanation
Indices: 17672592--17672788 Score: 367
Period size: 41 Copynumber: 4.8 Consensus size: 41
17672582 TTTATCGTTA
* *
17672592 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
17672633 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
17672674 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
17672715 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
17672756 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
17672789 AAGAGCATGT
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 153 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:17681197 original size:7 final size:7
Alignment explanation
Indices: 17681185--17681220 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
17681175 TGGTTGTAAA
*
17681185 TGGACTT
1 TGGACAT
*
17681192 TGGACTT
1 TGGACAT
17681199 TGGACAT
1 TGGACAT
17681206 TGGACAT
1 TGGACAT
17681213 TGGACAT
1 TGGACAT
17681220 T
1 T
17681221 TATTTTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (7 bp):
TGGACAT
Found at i:17682770 original size:24 final size:24
Alignment explanation
Indices: 17682725--17682788 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
17682715 GAGTTACAAG
* *
17682725 AAGATGAAAGGTTAAAGGTTAAAA
1 AAGATGAAAGGTGAAAGCTTAAAA
* **
17682749 AAGATGAAAGGTGGAAGCTTAAGG
1 AAGATGAAAGGTGAAAGCTTAAAA
*
17682773 GAGATGAAAGGTGAAA
1 AAGATGAAAGGTGAAA
17682789 AGTTGATCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.33, T:0.17
Consensus pattern (24 bp):
AAGATGAAAGGTGAAAGCTTAAAA
Found at i:17682979 original size:29 final size:29
Alignment explanation
Indices: 17682913--17682979 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
17682903 TTATCAAAAC
17682913 TACACATGAACTTTGATTCAATATGCAATT
1 TACACATGAACTTTGATT-AATATGCAATT
* * *
17682943 TGATACATGAAGTTTGATT-TTATGCAATT
1 T-ACACATGAACTTTGATTAATATGCAATT
17682972 ATACACAT
1 -TACACAT
17682980 TAAACTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
29 14 0.45
30 2 0.06
31 15 0.48
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (29 bp):
TACACATGAACTTTGATTAATATGCAATT
Found at i:17687109 original size:51 final size:51
Alignment explanation
Indices: 17687033--17687135 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
17687023 TGAATTGCAT
*
17687033 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAGAAACAATCTA
1 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
*
17687084 CGAGTGTAGGCTTGAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
1 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
17687135 C
1 C
17687136 TTACTTTTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (51 bp):
CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
Found at i:17690176 original size:112 final size:114
Alignment explanation
Indices: 17690035--17690241 Score: 276
Period size: 112 Copynumber: 1.8 Consensus size: 114
17690025 TTGTTTTTCA
** * *
17690035 TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGATGCGAAGAAAGATGACAACCAAGCACCCCA
1 TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGACACAAAGAAAGATGACAACCAAACACCCCA
*
17690100 -CCCTGGTTACTCAGCCCAACATACTCCTAATTTATTATATTTATATATG
66 TCCC-GGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
* * * *
17690149 TTTTT-TTT-CTTAAGAATATATTGAACCTTTTGACATAAAGAGAGATGACAGCCAAACACCCCA
1 TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGACACAAAGAAAGATGACAACCAAACACCCCA
* * *
17690212 TCCCGGTTACTTAGCCTAACACATTCCTAA
66 TCCCGGTTACTCAGCCCAACACACTCCTAA
17690242 AAAATTTTTG
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
112 69 0.86
113 6 0.08
114 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (114 bp):
TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGACACAAAGAAAGATGACAACCAAACACCCCA
TCCCGGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
Found at i:17691398 original size:4 final size:4
Alignment explanation
Indices: 17691382--17691428 Score: 62
Period size: 4 Copynumber: 11.8 Consensus size: 4
17691372 TATCCAAACA
17691382 AAAT AAAGT -AAT AAAT -AAT AAAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAA-T AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA
17691429 AATAAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 4 0.10
4 31 0.79
5 4 0.10
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:17691399 original size:12 final size:11
Alignment explanation
Indices: 17691382--17691450 Score: 72
Period size: 12 Copynumber: 6.3 Consensus size: 11
17691372 TATCCAAACA
17691382 AAATAAAGTAAT
1 AAATAAA-TAAT
*
17691394 AAATAATAAAAT
1 AAATAA-ATAAT
17691406 AAATAAATAAAT
1 AAATAAAT-AAT
17691418 AAATAAATAA-
1 AAATAAATAAT
17691428 AAATAAA-AAT
1 AAATAAATAAT
*
17691438 AAAGAAA-AAT
1 AAATAAATAAT
17691448 AAA
1 AAA
17691451 AACTGGGTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
9 2 0.04
10 19 0.37
11 3 0.06
12 26 0.51
13 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:17691406 original size:20 final size:19
Alignment explanation
Indices: 17691381--17691440 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
17691371 ATATCCAAAC
17691381 AAAATAAAGTAATAAATAAT
1 AAAATAAA-TAATAAATAAT
17691401 AAAATAAATAAATAAATAA-
1 AAAATAAAT-AATAAATAAT
17691420 ATAAATAAA-AATAAA-AAT
1 A-AAATAAATAATAAATAAT
17691438 AAA
1 AAA
17691441 GAAAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.11
18 7 0.19
19 2 0.05
20 24 0.65
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAATAAATAATAAATAAT
Found at i:17691412 original size:16 final size:15
Alignment explanation
Indices: 17691381--17691451 Score: 74
Period size: 16 Copynumber: 4.6 Consensus size: 15
17691371 ATATCCAAAC
*
17691381 AAAATAAAGT-AATA
1 AAAATAAAATAAATA
17691395 AATAATAAAATAAATA
1 AA-AATAAAATAAATA
17691411 AATAA-ATAAATAAATA
1 AA-AATA-AAATAAATA
*
17691427 AAAATAAAAATAAAGA
1 AAAAT-AAAATAAATA
17691443 AAAATAAAA
1 AAAATAAAA
17691452 ACTGGGTTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.04
15 14 0.28
16 33 0.66
17 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
AAAATAAAATAAATA
Found at i:17695100 original size:14 final size:14
Alignment explanation
Indices: 17695083--17695127 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
17695073 TGACAGAATA
17695083 ATGACATGAGAAAG
1 ATGACATGAGAAAG
17695097 ATGACATGAGAATA-
1 ATGACATGAGAA-AG
17695111 ATGACATGAGAAAG
1 ATGACATGAGAAAG
17695125 ATG
1 ATG
17695128 TGCAAATAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (14 bp):
ATGACATGAGAAAG
Found at i:17695531 original size:27 final size:28
Alignment explanation
Indices: 17695476--17695546 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
17695466 CAATATTTTA
* * *
17695476 TAATTTAA-TCAAT-TATTTAATTGATT
1 TAATTTAACCCAATATATTTAATTAAAT
17695502 TAATTTAACCCAATATATTTAA-TAAAT
1 TAATTTAACCCAATATATTTAATTAAAT
17695529 TAATTTAACCCAATATAT
1 TAATTTAACCCAATATAT
17695547 AATTTAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 8 0.20
27 25 0.62
28 7 0.17
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.45
Consensus pattern (28 bp):
TAATTTAACCCAATATATTTAATTAAAT
Found at i:17700189 original size:23 final size:23
Alignment explanation
Indices: 17700146--17700190 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17700136 TATTTGTTTT
* *
17700146 ATATTTAAATATTATTTTTAATA
1 ATATTTAAATATTAATATTAATA
17700169 ATATTTAAATATTAATATTAAT
1 ATATTTAAATATTAATATTAAT
17700191 TTATACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTAAATATTAATATTAATA
Found at i:17705159 original size:3 final size:3
Alignment explanation
Indices: 17705151--17705176 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17705141 AATGGAGAGA
17705151 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
17705177 AATATATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:17706199 original size:25 final size:25
Alignment explanation
Indices: 17706165--17706212 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
17706155 CATAAACGCA
17706165 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTATGAGCGTCCTGATATAG
*
17706190 GCTCTTTATGAGCTTCCTGATAT
1 GCTCTTTATGAGCGTCCTGATAT
17706213 GACTCACTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (25 bp):
GCTCTTTATGAGCGTCCTGATATAG
Found at i:17716992 original size:30 final size:30
Alignment explanation
Indices: 17716953--17717010 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
17716943 TTTTATAAAT
17716953 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
17716983 AATTTATATTTCATATATTAAAATATTT
1 AATTAATATTTCATATATTAAAATATTT
17717011 TTTTATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 19 0.76
31 4 0.16
32 2 0.08
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:17725952 original size:27 final size:28
Alignment explanation
Indices: 17725904--17725971 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
17725894 AAAAATATTA
* **
17725904 AAAAATATTTTTTAATTTTTTTTACTTTT
1 AAAAATA-ATTTTAATGATTTTTACTTTT
* *
17725933 -GAAATAATTTTAATGATTTTTATTTTT
1 AAAAATAATTTTAATGATTTTTACTTTT
17725960 AAAAATAATTTT
1 AAAAATAATTTT
17725972 TATTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (28 bp):
AAAAATAATTTTAATGATTTTTACTTTT
Found at i:17725952 original size:28 final size:27
Alignment explanation
Indices: 17725934--17725984 Score: 61
Period size: 25 Copynumber: 1.9 Consensus size: 27
17725924 TTTACTTTTG
*
17725934 AAATAATTTTAATGATTTTTATTTTTAA
1 AAATAATTTTAAT-ATTTTTACTTTTAA
*
17725962 AAATAATTTT--TATTTTTATTTTT
1 AAATAATTTTAATATTTTTACTTTT
17725985 TATTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.52
26 1 0.04
28 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
AAATAATTTTAATATTTTTACTTTTAA
Found at i:17725982 original size:12 final size:12
Alignment explanation
Indices: 17725965--17726004 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
17725955 TTTTTAAAAA
17725965 TAATTTTTATTTT
1 TAATTTTTA-TTT
*
17725978 TATTTTTTATTT
1 TAATTTTTATTT
*
17725990 TAATTTTAATTT
1 TAATTTTTATTT
17726002 TAA
1 TAA
17726005 AAAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TAATTTTTATTT
Found at i:17725985 original size:27 final size:28
Alignment explanation
Indices: 17725904--17725985 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 28
17725894 AAAAATATTA
*
17725904 AAAAATATTTTTTAATTTTT-TTTACTTTT
1 AAAAATAATTTTTAATTTTTATTT--TTTT
* *
17725933 -GAAATAA-TTTTAATGATTTT-TATTTTT
1 AAAAATAATTTTTAAT--TTTTATTTTTTT
17725960 AAAAATAATTTTT-ATTTTTATTTTTT
1 AAAAATAATTTTTAATTTTTATTTTTT
17725986 ATTTTAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
26 4 0.09
27 16 0.37
28 13 0.30
29 10 0.23
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (28 bp):
AAAAATAATTTTTAATTTTTATTTTTTT
Found at i:17726807 original size:52 final size:53
Alignment explanation
Indices: 17726729--17726838 Score: 186
Period size: 52 Copynumber: 2.1 Consensus size: 53
17726719 AATGCTTGAA
* *
17726729 ATTTGTCGTCCGAAGGTTGAGTGCTAGTAATTAATTTGTTTTCAAACTT-ATC
1 ATTTGTCCTCCGAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
*
17726781 ATTTGTCCTCCTAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
1 ATTTGTCCTCCGAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
17726834 ATTTG
1 ATTTG
17726839 CTTGCTCGAC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 46 0.85
53 8 0.15
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (53 bp):
ATTTGTCCTCCGAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
Found at i:17728074 original size:81 final size:81
Alignment explanation
Indices: 17727981--17728145 Score: 312
Period size: 81 Copynumber: 2.0 Consensus size: 81
17727971 ATGAGGCAAA
17727981 CAAAAATGACTATTTTGATAGTTTACCCATTTTAAAAATAATAATTTTAAATAATATTCTTTACA
1 CAAAAATGACTATTTTGATAGTTTACCCATTTTAAAAATAATAATTTTAAATAATATTCTTTACA
17728046 TATTATTGAAAATATT
66 TATTATTGAAAATATT
* *
17728062 CAAAAATTACTATTTTGATAGTTTTCCCATTTTAAAAATAATAATTTTAAATAATATTCTTTACA
1 CAAAAATGACTATTTTGATAGTTTACCCATTTTAAAAATAATAATTTTAAATAATATTCTTTACA
17728127 TATTATTGAAAATATT
66 TATTATTGAAAATATT
17728143 CAA
1 CAA
17728146 TATTAATATT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (81 bp):
CAAAAATGACTATTTTGATAGTTTACCCATTTTAAAAATAATAATTTTAAATAATATTCTTTACA
TATTATTGAAAATATT
Found at i:17730246 original size:55 final size:55
Alignment explanation
Indices: 17730183--17730296 Score: 228
Period size: 55 Copynumber: 2.1 Consensus size: 55
17730173 GATTGTGGAA
17730183 TTAAACAAAAAAACTACCAATGTACAAAATATTAACCTTTAATTTAATAAAAAAT
1 TTAAACAAAAAAACTACCAATGTACAAAATATTAACCTTTAATTTAATAAAAAAT
17730238 TTAAACAAAAAAACTACCAATGTACAAAATATTAACCTTTAATTTAATAAAAAAT
1 TTAAACAAAAAAACTACCAATGTACAAAATATTAACCTTTAATTTAATAAAAAAT
17730293 TTAA
1 TTAA
17730297 TAGAATTATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (55 bp):
TTAAACAAAAAAACTACCAATGTACAAAATATTAACCTTTAATTTAATAAAAAAT
Found at i:17739074 original size:87 final size:87
Alignment explanation
Indices: 17738928--17739276 Score: 662
Period size: 87 Copynumber: 4.0 Consensus size: 87
17738918 AATTTAGTAT
17738928 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
1 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
17738993 GTTAATTATTAACTTAAAAATC
66 GTTAATTATTAACTTAAAAATC
17739015 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
1 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
17739080 GTTAATTATTAACTTAAAAATC
66 GTTAATTATTAACTTAAAAATC
17739102 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
1 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
17739167 GTTAATTATTAACTTAAAAATC
66 GTTAATTATTAACTTAAAAATC
17739189 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
1 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
* * * *
17739254 GTCACTAATTAACTTAAACATC
66 GTTAATTATTAACTTAAAAATC
17739276 T
1 T
17739277 TAACCACTTC
Statistics
Matches: 258, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 258 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (87 bp):
TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
GTTAATTATTAACTTAAAAATC
Found at i:17739444 original size:14 final size:15
Alignment explanation
Indices: 17739416--17739445 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17739406 ACAAGAGTTG
17739416 AAATAAAATAATAAA
1 AAATAAAATAATAAA
17739431 AAATAAAA-AATAAA
1 AAATAAAATAATAAA
17739445 A
1 A
17739446 GGTGAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAATAATAAA
Found at i:17739445 original size:6 final size:7
Alignment explanation
Indices: 17739416--17739445 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
17739406 ACAAGAGTTG
17739416 AAATAAA
1 AAATAAA
17739423 ATAATAAA
1 A-AATAAA
17739431 AAATAAA
1 AAATAAA
17739438 AAATAAA
1 AAATAAA
17739445 A
1 A
17739446 GGTGAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:17750710 original size:14 final size:14
Alignment explanation
Indices: 17750691--17750717 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17750681 CATAAATGAT
17750691 AAAATTTTCACACG
1 AAAATTTTCACACG
17750705 AAAATTTTCACAC
1 AAAATTTTCACAC
17750718 ATATCACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (14 bp):
AAAATTTTCACACG
Found at i:17754566 original size:9 final size:9
Alignment explanation
Indices: 17754552--17754586 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
17754542 ATTATTTTAG
17754552 AAAATTTTT
1 AAAATTTTT
*
17754561 AAAA-TTTA
1 AAAATTTTT
17754569 AAAATTTTT
1 AAAATTTTT
17754578 AAAATTTTT
1 AAAATTTTT
17754587 TTGAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
AAAATTTTT
Found at i:17754574 original size:17 final size:18
Alignment explanation
Indices: 17754547--17754584 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
17754537 AAATTATTAT
17754547 TTTAGAAAATTTTTAAAA
1 TTTAGAAAATTTTTAAAA
17754565 TTTA-AAAATTTTTAAAA
1 TTTAGAAAATTTTTAAAA
17754582 TTT
1 TTT
17754585 TTTTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTAGAAAATTTTTAAAA
Found at i:17754611 original size:28 final size:29
Alignment explanation
Indices: 17754555--17754618 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
17754545 ATTTTAGAAA
* *
17754555 ATTTTTAAAATTTAAAAATTTTTAAAATT
1 ATTTTTGAAATTAAAAAATTTTTAAAATT
*
17754584 -TTTTTGAAATTAAAAAATTATTT-TAATT
1 ATTTTTGAAATTAAAAAATT-TTTAAAATT
17754612 ATTTTTG
1 ATTTTTG
17754619 TATTTTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTTGAAATTAAAAAATTTTTAAAATT
Found at i:17757976 original size:25 final size:25
Alignment explanation
Indices: 17757947--17757994 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
17757937 ATTTATTACT
17757947 TACAAATTTCTTTACACATCCAGTG
1 TACAAATTTCTTTACACATCCAGTG
17757972 TACAAATTTCTTTACACATCCAG
1 TACAAATTTCTTTACACATCCAG
17757995 CATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.35
Consensus pattern (25 bp):
TACAAATTTCTTTACACATCCAGTG
Found at i:17758019 original size:42 final size:44
Alignment explanation
Indices: 17757972--17758066 Score: 140
Period size: 42 Copynumber: 2.2 Consensus size: 44
17757962 ACATCCAGTG
* *
17757972 TACAAATTTCTTTACACATCCAGCAT-A-TATAAATTTATTACT
1 TACAAATTTCTCTACACATCCAGCATAAGTAAAAATTTATTACT
**
17758014 TACAAATTTCTCTACACATCCAGTGTAAGTAAAAATTTATTACT
1 TACAAATTTCTCTACACATCCAGCATAAGTAAAAATTTATTACT
17758058 TACAAATTT
1 TACAAATTT
17758067 ATTACTTACA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 23 0.49
43 1 0.02
44 23 0.49
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (44 bp):
TACAAATTTCTCTACACATCCAGCATAAGTAAAAATTTATTACT
Found at i:17758066 original size:15 final size:15
Alignment explanation
Indices: 17758046--17758081 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
17758036 GTGTAAGTAA
17758046 AAATTTATTACTTAC
1 AAATTTATTACTTAC
17758061 AAATTTATTACTTAC
1 AAATTTATTACTTAC
17758076 AAATTT
1 AAATTT
17758082 CTTTACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTTATTACTTAC
Found at i:17758297 original size:17 final size:16
Alignment explanation
Indices: 17758270--17758410 Score: 112
Period size: 16 Copynumber: 8.5 Consensus size: 16
17758260 TTTTACTAAT
17758270 ATTATAA-TTTTCATC
1 ATTATAATTTTTCATC
17758285 ATTATAATTTTTTCATC
1 ATTATAA-TTTTTCATC
17758302 ATTATAATTTTTCATC
1 ATTATAATTTTTCATC
* *
17758318 ATTATAA--TATCAGGGC
1 ATTATAATTTTTCA--TC
** *
17758334 CGTAGGAAATTTTTTACTAAT-
1 ATTA--TAA-TTTTT-C--ATC
17758355 ATTATAA-TTTTCATC
1 ATTATAATTTTTCATC
17758370 ATTATAATTTTTTCATC
1 ATTATAA-TTTTTCATC
17758387 ATTATAATTTTTCATC
1 ATTATAATTTTTCATC
17758403 ATTATAAT
1 ATTATAAT
17758411 ATCAAGGCCC
Statistics
Matches: 101, Mismatches: 10, Indels: 29
0.72 0.07 0.21
Matches are distributed among these distances:
14 6 0.06
15 14 0.14
16 37 0.37
17 34 0.34
18 2 0.02
19 2 0.02
21 4 0.04
22 1 0.01
24 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (16 bp):
ATTATAATTTTTCATC
Found at i:17758332 original size:85 final size:85
Alignment explanation
Indices: 17758217--17758419 Score: 397
Period size: 85 Copynumber: 2.4 Consensus size: 85
17758207 CTCTTGCTAT
17758217 ATTATAATTTTTCATCATTATAATATCAGGGCCGTAGGAAATTTTTTACTAATATTATAATTTTC
1 ATTATAATTTTTCATCATTATAATATCAGGGCCGTAGGAAATTTTTTACTAATATTATAATTTTC
17758282 ATCATTATAATTTTTTCATC
66 ATCATTATAATTTTTTCATC
17758302 ATTATAATTTTTCATCATTATAATATCAGGGCCGTAGGAAATTTTTTACTAATATTATAATTTTC
1 ATTATAATTTTTCATCATTATAATATCAGGGCCGTAGGAAATTTTTTACTAATATTATAATTTTC
17758367 ATCATTATAATTTTTTCATC
66 ATCATTATAATTTTTTCATC
*
17758387 ATTATAATTTTTCATCATTATAATATCAAGGCC
1 ATTATAATTTTTCATCATTATAATATCAGGGCC
17758420 CTGATATTTA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 117 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (85 bp):
ATTATAATTTTTCATCATTATAATATCAGGGCCGTAGGAAATTTTTTACTAATATTATAATTTTC
ATCATTATAATTTTTTCATC
Found at i:17761224 original size:22 final size:22
Alignment explanation
Indices: 17761167--17761232 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
17761157 GTCAATTATG
17761167 TGTTAATTCAAGACTTATGTAA
1 TGTTAATTCAAGACTTATGTAA
** *
17761189 TGTT--TTTTA-A-TTATGTAG
1 TGTTAATTCAAGACTTATGTAA
17761207 TGTTAATTCAAGACTTATGTAA
1 TGTTAATTCAAGACTTATGTAA
17761229 TGTT
1 TGTT
17761233 TTCAATTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 11 0.32
19 1 0.03
20 6 0.18
21 1 0.03
22 15 0.44
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (22 bp):
TGTTAATTCAAGACTTATGTAA
Found at i:17761300 original size:20 final size:18
Alignment explanation
Indices: 17761273--17761327 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
17761263 TAATAGTTTT
17761273 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
* * *
17761291 AGATTTATGTAATGCTTT-T
1 A-A-TTATGTAGTGATTTAA
17761310 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
17761328 TTCGAGTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
17 12 0.43
18 2 0.07
19 2 0.07
20 12 0.43
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (18 bp):
AATTATGTAGTGATTTAA
Found at i:17761317 original size:17 final size:16
Alignment explanation
Indices: 17761258--17761329 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 16
17761248 ACTCAAAGAC
17761258 TTATGTAATAGTTTTAA
1 TTATGTAAT-GTTTTAA
* *
17761275 TTATGTAGTGATTTAAAGA
1 TTATGTAATG-TTT-TA-A
17761294 TTTATGTAATGCTTTTAA
1 -TTATGTAATG-TTTTAA
* *
17761312 TTATGTAGTGATTTAA
1 TTATGTAATGTTTTAA
17761328 TT
1 TT
17761330 CGAGTAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
16 8 0.18
17 20 0.45
18 2 0.05
19 2 0.05
20 12 0.27
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.51
Consensus pattern (16 bp):
TTATGTAATGTTTTAA
Done.