Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 49 of 135
Found at i:17466395 original size:31 final size:31
Alignment explanation
Indices: 17466357--17466416 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
17466347 AATGATCACA
*
17466357 AAATTATTTGAAAATTTTAATTTAAGTCATT
1 AAATTATTCGAAAATTTTAATTTAAGTCATT
* *
17466388 AAATTATTCGAAAGTTTTTATTTAAGTCA
1 AAATTATTCGAAAATTTTAATTTAAGTCA
17466417 CTGAGTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (31 bp):
AAATTATTCGAAAATTTTAATTTAAGTCATT
Found at i:17469513 original size:32 final size:32
Alignment explanation
Indices: 17469453--17469513 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
17469443 TGGGATGATT
* *
17469453 TTATTGTTTAATTTATAGAATAATTTTTTACC
1 TTATTGTTTAATTCATAGAATAAGTTTTTACC
*
17469485 TTATTGTTTAATTCAT-GAAATTAGTTTTT
1 TTATTGTTTAATTCATAG-AATAAGTTTTT
17469514 TACTTGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.04
32 24 0.96
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (32 bp):
TTATTGTTTAATTCATAGAATAAGTTTTTACC
Found at i:17471773 original size:6 final size:7
Alignment explanation
Indices: 17471756--17471781 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17471746 TGAAATATAA
17471756 AAAAATT
1 AAAAATT
17471763 AAAAATT
1 AAAAATT
17471770 AAAAATT
1 AAAAATT
17471777 AAAAA
1 AAAAA
17471782 AGATAGACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:17472029 original size:35 final size:36
Alignment explanation
Indices: 17471978--17472045 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
17471968 ATTTTATAAA
* *
17471978 AAAATCATAATATATGTT-AAAATTATTTAAAAGAT
1 AAAAGCATAATATATGTTAAAAACTATTTAAAAGAT
17472013 AAAAGCATAATATATGTTAAAAACTATTTAAAA
1 AAAAGCATAATATATGTTAAAAACTATTTAAAA
17472046 TATTTGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (36 bp):
AAAAGCATAATATATGTTAAAAACTATTTAAAAGAT
Found at i:17472236 original size:17 final size:18
Alignment explanation
Indices: 17472206--17472259 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
17472196 TTAAATATTT
*
17472206 TTTTTATAATTTTTAAAC
1 TTTTTATAAGTTTTAAAC
*
17472224 TTTTTAT-AGTTTTGAAC
1 TTTTTATAAGTTTTAAAC
*
17472241 TTTTTTTATAATTTTTAAA
1 --TTTTTATAAGTTTTAAA
17472260 AAAATTGCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 8 0.28
18 7 0.24
19 7 0.24
20 7 0.24
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTTTATAAGTTTTAAAC
Found at i:17473013 original size:13 final size:13
Alignment explanation
Indices: 17472995--17473028 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
17472985 TTCGATTAAA
17472995 ATCGAATTAATCG
1 ATCGAATTAATCG
17473008 ATCGAATTAATCG
1 ATCGAATTAATCG
17473021 ATCGAATT
1 ATCGAATT
17473029 GATTTAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (13 bp):
ATCGAATTAATCG
Found at i:17498976 original size:17 final size:18
Alignment explanation
Indices: 17498933--17498979 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
17498923 TGTTAAAATT
17498933 TATAAATATTTTATAAAAA
1 TATAAATA-TTTATAAAAA
* *
17498952 TATGAATATTT-TAATAA
1 TATAAATATTTATAAAAA
17498969 TATAAATATTT
1 TATAAATATTT
17498980 CTATTTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.60
18 3 0.12
19 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TATAAATATTTATAAAAA
Found at i:17504287 original size:12 final size:12
Alignment explanation
Indices: 17504266--17504299 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17504256 TTGGAAATAT
*
17504266 ATATAAATGTAC
1 ATATATATGTAC
*
17504278 ATATATATGTAT
1 ATATATATGTAC
17504290 ATATATATGT
1 ATATATATGT
17504300 GTGTGTGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (12 bp):
ATATATATGTAC
Found at i:17507308 original size:59 final size:58
Alignment explanation
Indices: 17507177--17507574 Score: 392
Period size: 59 Copynumber: 6.7 Consensus size: 58
17507167 CTCAAGAGGT
* * *
17507177 CCCCAAACTTTTGCAAAATCATATTTTAA-CCCTCAAACTTTTCCAAAATCACATTTTAA
1 CCCCAAACTTTTCCAAAATTACATTTTAACCCCT-AAACTTTT-CAAAATCACATTTTAA
*** * *
17507236 TCCTTGAACTTTTCCAACATTACATTTTAACCCCTAAACTTTTCAAAATCATATTTTAA
1 -CCCCAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCAAAATCACATTTTAA
* * * * ** *
17507295 CCCTCGAACTTTTCCAAAATTACATTTTGACTCCC-AAAATTTCCCAAAATTTCATTTTGA
1 CCC-CAAACTTTTCCAAAATTACATTTTAAC-CCCTAAACTTT-TCAAAATCACATTTTAA
* * * *
17507355 CCCTTAAAC-TTTCCTAAAATTTCATTTTAACCTCC-AAACTTTTCTAAAATTACATTTTGA
1 CCC-CAAACTTTTCC-AAAATTACATTTTAACC-CCTAAACTTTTC-AAAATCACATTTTAA
*
17507415 CCCCTAAACTTTTCCAAAATTATATTTTAACCCC-AAACTTTTCCAAAATCACATTTTAA
1 CCCC-AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTT-CAAAATCACATTTTAA
* * * *
17507474 CCCCTAAACTTTTCCAAAAATACATTTTAACCCCTAAACATTTCAAAATCATATTTTGAC
1 CCCC-AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCAAAATCACATTTT-AA
* * *
17507534 CCCCACACTTTTCCAAAATTACATTTTGACTCCTAAACTTT
1 CCCCAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTT
17507575 CCCAAAATTA
Statistics
Matches: 286, Mismatches: 40, Indels: 25
0.81 0.11 0.07
Matches are distributed among these distances:
58 2 0.01
59 152 0.53
60 123 0.43
61 9 0.03
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (58 bp):
CCCCAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCAAAATCACATTTTAA
Found at i:17507351 original size:89 final size:88
Alignment explanation
Indices: 17507177--17507592 Score: 400
Period size: 89 Copynumber: 4.7 Consensus size: 88
17507167 CTCAAGAGGT
* * * * * *
17507177 CCCCAAACTTTTGCAAAATCATATTTTAACCCTCAAACTTTTCCAAAATCACATTTTAATCCTTG
1 CCCCAAACTTTTCCAAAATCATATTTTAACCCTCAAACTTTTCCAAAATTACATTTTGACCCCTA
* * *
17507242 AACTTTTCCAACATTACATTTTAA
66 AAATTTTCCAAAATT-TATTTTAA
*
17507266 CCCCTAAACTTTT-CAAAATCATATTTTAACCCTCGAACTTTTCCAAAATTACATTTTGACTCCC
1 CCCC-AAACTTTTCCAAAATCATATTTTAACCCTCAAACTTTTCCAAAATTACATTTTGAC-CCC
* *
17507330 -AAAATTTCCCAAAATTTCATTTTGA
64 TAAAATTTTCCAAAATTT-ATTTTAA
* * *
17507355 CCCTTAAAC-TTTCCTAAAAT-TTCATTTTAA-CCTCCAAACTTTTCTAAAATTACATTTTGACC
1 CCC-CAAACTTTTCC-AAAATCAT-ATTTTAACCCT-CAAACTTTTCCAAAATTACATTTTGACC
*
17507417 CCTAAACTTTTCCAAAATTATATTTTAA
62 CCTAAAATTTTCCAAAATT-TATTTTAA
* * *
17507445 CCCCAAACTTTTCCAAAATCACATTTTAACCC-CTAAACTTTTCCAAAAATACATTTTAACCCCT
1 CCCCAAACTTTTCCAAAATCATATTTTAACCCTC-AAACTTTTCCAAAATTACATTTTGACCCCT
* *
17507509 AAACA-TTT-CAAAATCATATTTTGAC
65 AAA-ATTTTCCAAAAT-TTATTTT-AA
* * * * * *
17507534 CCCCACACTTTTCCAAAATTACATTTTGACTCCT-AAACTTTCCCAAAATTACACTTTGA
1 CCCCAAACTTTTCCAAAATCATATTTTAAC-CCTCAAACTTTTCCAAAATTACATTTTGA
17507593 AACCTCATTT
Statistics
Matches: 274, Mismatches: 34, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
88 16 0.06
89 178 0.65
90 79 0.29
91 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (88 bp):
CCCCAAACTTTTCCAAAATCATATTTTAACCCTCAAACTTTTCCAAAATTACATTTTGACCCCTA
AAATTTTCCAAAATTTATTTTAA
Found at i:17507583 original size:30 final size:30
Alignment explanation
Indices: 17507177--17507586 Score: 424
Period size: 30 Copynumber: 13.8 Consensus size: 30
17507167 CTCAAGAGGT
* * *
17507177 CCCC-AAACTTTTGCAAAATCATATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
*
17507206 -CCCTCAAACTTTTCCAAAATCACATTTTAA
1 CCCCT-AAACTTTTCCAAAATTACATTTTAA
* * * *
17507236 TCCTTGAACTTTTCCAACATTACATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* *
17507266 CCCCTAAACTTTT-CAAAATCATATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* *
17507295 -CCCTCGAACTTTTCCAAAATTACATTTTGA
1 CCCCT-AAACTTTTCCAAAATTACATTTTAA
* * * *
17507325 CTCCC-AAAATTTCCCAAAATTTCATTTTGA
1 C-CCCTAAACTTTTCCAAAATTACATTTTAA
* *
17507355 CCCTTAAAC-TTTCCTAAAATTTCATTTTAA
1 CCCCTAAACTTTTCC-AAAATTACATTTTAA
* *
17507385 CCTCC-AAACTTTTCTAAAATTACATTTTGA
1 CC-CCTAAACTTTTCCAAAATTACATTTTAA
*
17507415 CCCCTAAACTTTTCCAAAATTATATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
*
17507445 CCCC-AAACTTTTCCAAAATCACATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
*
17507474 CCCCTAAACTTTTCCAAAAATACATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* * * *
17507504 CCCCTAAACATTT-CAAAATCATATTTTGA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* * *
17507533 CCCCCACACTTTTCCAAAATTACATTTTGA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* *
17507563 CTCCTAAACTTTCCCAAAATTACA
1 CCCCTAAACTTTTCCAAAATTACA
17507587 CTTTGAAACC
Statistics
Matches: 318, Mismatches: 49, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
28 7 0.02
29 77 0.24
30 223 0.70
31 8 0.03
32 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (30 bp):
CCCCTAAACTTTTCCAAAATTACATTTTAA
Found at i:17511812 original size:18 final size:18
Alignment explanation
Indices: 17511789--17511828 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17511779 GGCATCTTTT
17511789 AAAAAAGAAAAAAAAAAG
1 AAAAAAGAAAAAAAAAAG
* *
17511807 AAAAAAGAAAAGAAGAAG
1 AAAAAAGAAAAAAAAAAG
17511825 AAAA
1 AAAA
17511829 CAAAAGGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAAAG
Found at i:17511817 original size:23 final size:25
Alignment explanation
Indices: 17511790--17511847 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
17511780 GCATCTTTTA
*
17511790 AAAAAGAAAAAAAAAAGAAAA-AAG
1 AAAAAGAAAAAAAAAACAAAAGAAG
* *
17511814 -AAAAGAAGAAGAAAACAAAAGGAAG
1 AAAAAGAAAAAAAAAACAAAA-GAAG
17511839 AAAAAGAAA
1 AAAAAGAAA
17511848 GTCAAGATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 17 0.63
25 3 0.11
26 7 0.26
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (25 bp):
AAAAAGAAAAAAAAAACAAAAGAAG
Found at i:17511825 original size:11 final size:11
Alignment explanation
Indices: 17511791--17511847 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
17511781 CATCTTTTAA
*
17511791 AAAAGAAAAAA
1 AAAAGAAAAAG
17511802 AAAAGAAAAAAG
1 AAAAG-AAAAAG
*
17511814 AAAAGAAGAAG
1 AAAAGAAAAAG
*
17511825 AAAA-CAAAAG
1 AAAAGAAAAAG
*
17511835 -GAAGAAAAAG
1 AAAAGAAAAAG
17511845 AAA
1 AAA
17511848 GTCAAGATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
9 2 0.06
10 9 0.25
11 15 0.42
12 10 0.28
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:17511845 original size:6 final size:6
Alignment explanation
Indices: 17511790--17511847 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
17511780 GCATCTTTTA
*
17511790 AAAAAG AAAAA- AAAAAG AAAAA- AGAAAAG AAGAAG AAAACA- AAAGGAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAA-AG AAA--AAG
17511839 AAAAAG AAA
1 AAAAAG AAA
17511848 GTCAAGATGA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
5 6 0.14
6 30 0.70
7 3 0.07
8 4 0.09
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:17512716 original size:9 final size:10
Alignment explanation
Indices: 17512702--17512752 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
17512692 TATTTCATCC
17512702 AAAAAGGAAA
1 AAAAAGGAAA
17512712 AAAAGAGGAAA
1 AAAA-AGGAAA
17512723 AAAAAGAAGAAGA
1 AAAAAG--GAA-A
17512736 AAAAA-GAAA
1 AAAAAGGAAA
17512745 AAAAAGGA
1 AAAAAGGA
17512753 GAGGTCGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 6 0.17
10 11 0.31
11 10 0.28
12 3 0.08
13 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAAAGGAAA
Found at i:17512727 original size:13 final size:12
Alignment explanation
Indices: 17512709--17512749 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
17512699 TCCAAAAAGG
*
17512709 AAAAAAAGAGGA
1 AAAAAAAGAAGA
17512721 AAAAAAAGAAGA
1 AAAAAAAGAAGA
17512733 AGAAAAAAGAA-A
1 A-AAAAAAGAAGA
17512745 AAAAA
1 AAAAA
17512750 GGAGAGGTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 4 0.15
12 14 0.52
13 9 0.33
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAGA
Found at i:17513793 original size:49 final size:49
Alignment explanation
Indices: 17513675--17514242 Score: 399
Period size: 49 Copynumber: 11.6 Consensus size: 49
17513665 TTACCACGAG
* ** **
17513675 AACATGAAGGGAAAGATTTAAGCCGCAACAACGAATCC-AGTACAAC-GA
1 AACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCTCAGA
** * * * *
17513723 AGATTTGAA-GGAAAGGTTTAAGTTGCAACAGCGAACCTTGTACCTCAGA
1 A-ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGA
* * *
17513772 AACATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTA-C-CATGA
1 AACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCA-GA
* * * *
17513820 AGATATGGAGGGAAATG-TTTAAGTCACAACGGCGAACCTTGTACCTCAGA
1 A-ACATGAAGGGAAA-GATTTAAGTCGCAACGGCGAACCTAGTACCTCAGA
* * * *
17513870 AACATGAAGGGAAAGATTTAAGTCACAACGGTGAATCTAGTACCAC-GA
1 AACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGA
* * * *
17513918 AGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCCA-A
1 A-ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCT-CAGA
* * *
17513968 AACATAAAGGGAAAGATTTAAG-CAGCAACGACGAATCC-AGTACCAC-GA
1 AACATGAAGGGAAAGATTTAAGTC-GCAACGGCGAA-CCTAGTACCTCAGA
* * * ** * * *
17514016 AGATATGGAGGGAAAGGTTTAAGTCATAATGGCGAACCTTGTACCTCATA
1 A-ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGA
* * *
17514066 AACATGAAGGGAAATATTTAAGCCGCAACGGCGAATCC-AGTACCAC-GA
1 AACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCTCAGA
* * * * *
17514114 AGATATAAAGGGAAAGGTTTAAGTCGCATCGGCAAACCTTA-TACCTCAGA
1 A-ACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACC-TAGTACCTCAGA
* * * * * * * * *
17514164 AACATAAAGGGAAAGGTTGAGGCCGCCACGACGAACCCAGTACCTTAGA
1 AACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGA
* * * *
17514213 AGCATGACGGGAAAGATTGAAGCCGCAACG
1 AACATGAAGGGAAAGATTTAAGTCGCAACG
17514243 ATAAATCTTA
Statistics
Matches: 402, Mismatches: 92, Indels: 51
0.74 0.17 0.09
Matches are distributed among these distances:
47 4 0.01
48 52 0.13
49 325 0.81
50 19 0.05
51 2 0.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (49 bp):
AACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGA
Found at i:17514227 original size:98 final size:98
Alignment explanation
Indices: 17513675--17514207 Score: 719
Period size: 98 Copynumber: 5.4 Consensus size: 98
17513665 TTACCACGAG
** * * *
17513675 AACATGAAGGGAAAGATTTAAGCCGCAACAACGAATCCAGTACAACGAAGAT-TTGAAGGAAAGG
1 AACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGG
* *
17513739 TTTAAGTTGCAACAGCGAACCTTGTACCTCAGA
66 TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * * *
17513772 AACATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCATGAAGATATGGAGGGAAATG
1 AACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGG
*
17513837 TTTAAGTCACAACGGCGAACCTTGTACCTCAGA
66 TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * * *
17513870 AACATGAAGGGAAAGATTTAAGTCACAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGG
1 AACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGG
17513935 TTTAAGTCGCAACGGCGAACCTTGTACCTCCA-A
66 TTTAAGTCGCAACGGCGAACCTTGTACCT-CAGA
* * *
17513968 AACATAAAGGGAAAGATTTAAGCAGCAACGACGAATCCAGTACCACGAAGATATGGAGGGAAAGG
1 AACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGG
** * *
17514033 TTTAAGTCATAATGGCGAACCTTGTACCTCATA
66 TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* **
17514066 AACATGAAGGGAAATATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATAAAGGGAAAGG
1 AACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGG
* * *
17514131 TTTAAGTCGCATCGGCAAACCTTATACCTCAGA
66 TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
* * * * * * *
17514164 AACATAAAGGGAAAGGTTGAGGCCGCCACGACGAACCCAGTACC
1 AACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACC
17514208 TTAGAAGCAT
Statistics
Matches: 385, Mismatches: 48, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
97 48 0.12
98 335 0.87
99 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.18
Consensus pattern (98 bp):
AACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGG
TTTAAGTCGCAACGGCGAACCTTGTACCTCAGA
Found at i:17516671 original size:30 final size:30
Alignment explanation
Indices: 17516604--17517070 Score: 432
Period size: 30 Copynumber: 15.8 Consensus size: 30
17516594 AAAGATCCCT
* *
17516604 AAACTTTTCCAAAATCATATTTTGACCCCCC
1 AAACTTTTCCAAAATTACATTTTGA-CCCCC
* * * **
17516635 AAACTTTTCTAAAATCACATTTTAACCCTT
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* *
17516665 AAACTTTTCCAAAATTACATTTTGACCTCT
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* * *
17516695 AAACTTTT-CAAAATCATATTTTGACCCTC
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* *
17516724 GAACTTTTCC-AAATTACATTTTGACTCCC
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* * **
17516753 AAACTTTCCCAAAATTTCATTTTGACCCTT
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* * *
17516783 AAA-GTTTCCTAAAATTACATTTTAACCCCT
1 AAACTTTTCC-AAAATTACATTTTGACCCCC
* * *
17516813 AAACTTTTCTAAAATTACATTTTAACCCTC
1 AAACTTTTCCAAAATTACATTTTGACCCCC
*
17516843 AAACTTTTCCAAAA-T-CATATTGACCCCC
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* * * * *
17516871 AAAATTTTCCAAAATCACACTTTAACCCCT
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* * * *
17516901 AAACTTTTCCAAAATTATATTTT-AACACT
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* * * *
17516930 AAACTTTT-TAAAATCATATTTTGACCCCT
1 AAACTTTTCCAAAATTACATTTTGACCCCC
*
17516959 AAACTTTTCCAAAATTACATTTTGACTCCC
1 AAACTTTTCCAAAATTACATTTTGACCCCC
*
17516989 AAAC-TTCCCAAAATTACATTTTGACCCCC
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* * *
17517018 AAAC-TTTCCTAAAATTATATTTT-AACCTC
1 AAACTTTTCC-AAAATTACATTTTGACCCCC
* *
17517047 AAGCTTTTCCAAAATCACATTTTG
1 AAACTTTTCCAAAATTACATTTTG
17517071 GCCCTCGAAC
Statistics
Matches: 356, Mismatches: 69, Indels: 23
0.79 0.15 0.05
Matches are distributed among these distances:
28 35 0.10
29 124 0.35
30 171 0.48
31 26 0.07
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTGACCCCC
Found at i:17516765 original size:88 final size:87
Alignment explanation
Indices: 17516600--17517070 Score: 434
Period size: 88 Copynumber: 5.3 Consensus size: 87
17516590 CTCAAAAGAT
* * * *
17516600 CCCTAAACTTTTCCAAAATCATATTTTGACCCCCCAAACTTTTCTAAAATCACATTTTAACCCTT
1 CCCTAAACTTTTCCAAAATCACATTTTGA--CCCCAAACTTTTC-CAAATTACATTTTAACCC-C
*
17516665 AAACTTTTCCAAAATTACATTTTGAC
62 AAACTTTCCCAAAATTACATTTTGAC
* * * *
17516691 CTCTAAACTTTT-CAAAATCATATTTTGACCCTCGAACTTTTCCAAATTACATTTTGACTCCCAA
1 CCCTAAACTTTTCCAAAATCACATTTTGACCC-CAAACTTTTCCAAATTACATTTTAAC-CCCAA
*
17516755 ACTTTCCCAAAATTTCATTTTGAC
64 ACTTTCCCAAAATTACATTTTGAC
* * * * *
17516779 CCTTAAA-GTTTCCTAAAATTACATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAACCCTC
1 CCCTAAACTTTTCC-AAAATCACATTTTGACCCC-AAACTTTTC-CAAATTACATTTTAACCC-C
* *
17516843 AAACTTTTCCAAAA-T-CATATTGAC
62 AAACTTTCCCAAAATTACATTTTGAC
* * * * * * *
17516867 CCCCAAAATTTTCCAAAATCACACTTTAACCCCTAAACTTTTCCAAAATTATATTTTAACACTAA
1 CCCTAAACTTTTCCAAAATCACATTTTGACCCC-AAACTTTTCC-AAATTACATTTTAACCCCAA
** * *
17516932 ACTTT-TTAAAATCATATTTTGAC
64 ACTTTCCCAAAATTACATTTTGAC
* * *
17516955 CCCTAAACTTTTCCAAAATTACATTTTGACTCCCAAAC-TTCCCAAAATTACATTTTGACCCCCA
1 CCCTAAACTTTTCCAAAATCACATTTTGAC-CCCAAACTTTTCC-AAATTACATTTT-AACCCCA
* * *
17517019 AACTTTCCTAAAATTATATTTTAAC
63 AACTTTCCCAAAATTACATTTTGAC
* *
17517044 CTC-AAGCTTTTCCAAAATCACATTTTG
1 CCCTAAACTTTTCCAAAATCACATTTTG
17517071 GCCCTCGAAC
Statistics
Matches: 317, Mismatches: 49, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
86 4 0.01
87 26 0.08
88 170 0.54
89 62 0.20
90 44 0.14
91 11 0.03
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (87 bp):
CCCTAAACTTTTCCAAAATCACATTTTGACCCCAAACTTTTCCAAATTACATTTTAACCCCAAAC
TTTCCCAAAATTACATTTTGAC
Found at i:17518447 original size:17 final size:17
Alignment explanation
Indices: 17518416--17518449 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17518406 ATTACAAAAT
*
17518416 CAAATCTTATCAGATTA
1 CAAATCTTATAAGATTA
*
17518433 CAAATCTTCTAAGATTA
1 CAAATCTTATAAGATTA
17518450 ATTTCCATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:17527030 original size:20 final size:21
Alignment explanation
Indices: 17526992--17527031 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17526982 TTTTACTCTA
*
17526992 AAATTTTGTTTACTGTTTTTT
1 AAATTTTATTTACTGTTTTTT
17527013 AAATTTTATTTA-TGTTTTT
1 AAATTTTATTTACTGTTTTT
17527032 CACTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.68
Consensus pattern (21 bp):
AAATTTTATTTACTGTTTTTT
Found at i:17528169 original size:22 final size:22
Alignment explanation
Indices: 17528144--17528201 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
17528134 TGTTTAATCA
17528144 TGTTTAATCGATGTTGA-TATTT
1 TGTTTAATCGATGTT-ACTATTT
*
17528166 TGTTTAATCGATATTACTATTT
1 TGTTTAATCGATGTTACTATTT
17528188 TGTTTAATCG-TGTT
1 TGTTTAATCGATGTT
17528202 TAATCGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.22, C:0.07, G:0.16, T:0.55
Consensus pattern (22 bp):
TGTTTAATCGATGTTACTATTT
Found at i:17528202 original size:32 final size:32
Alignment explanation
Indices: 17528166--17528229 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
17528156 GTTGATATTT
17528166 TGTTTAATCGATATTACTATTTTGTTTAATCG
1 TGTTTAATCGATATTACTATTTTGTTTAATCG
*
17528198 TGTTTAATCGATATTGCTATTTTGTTTAATCG
1 TGTTTAATCGATATTACTATTTTGTTTAATCG
17528230 ATTACTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.53
Consensus pattern (32 bp):
TGTTTAATCGATATTACTATTTTGTTTAATCG
Found at i:17532301 original size:21 final size:21
Alignment explanation
Indices: 17532232--17532307 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
17532222 CTACCAGCTT
*
17532232 CCTCACCACCATCTCCCTCAC
1 CCTCACCACCATCTCCATCAC
* * * * *
17532253 CCTTACCACCTTTGTTGCCAACAT
1 CCTCACCACC-AT-CT-CCATCAC
*
17532277 CCTCACCACCATCTCCTTCAC
1 CCTCACCACCATCTCCATCAC
17532298 CCTCACCACC
1 CCTCACCACC
17532308 CTTGCTACCA
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
21 23 0.57
22 2 0.05
23 2 0.05
24 13 0.32
ACGTcount: A:0.20, C:0.54, G:0.03, T:0.24
Consensus pattern (21 bp):
CCTCACCACCATCTCCATCAC
Found at i:17532380 original size:48 final size:48
Alignment explanation
Indices: 17532283--17532383 Score: 121
Period size: 48 Copynumber: 2.1 Consensus size: 48
17532273 ACATCCTCAC
* * * *
17532283 CACCATCTCCTTCACCCTCACCACCCTTGCTACCAGCTTCCAAACCCT
1 CACCACCTCCATCACCCTCACCACCCTTACTACCAGCATCCAAACCCT
* * * * *
17532331 CACCACCTCCATCACCCTCACCACCCTTATTGCTAGCATCTAAATCCT
1 CACCACCTCCATCACCCTCACCACCCTTACTACCAGCATCCAAACCCT
17532379 CACCA
1 CACCA
17532384 TCTTTACTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.24, C:0.50, G:0.04, T:0.23
Consensus pattern (48 bp):
CACCACCTCCATCACCCTCACCACCCTTACTACCAGCATCCAAACCCT
Found at i:17533243 original size:21 final size:21
Alignment explanation
Indices: 17533169--17533244 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 21
17533159 TTATGAAACA
* *
17533169 TACATTTACACATACATTTGC
1 TACATTTACACATATAATTGC
17533190 TACATTTACACAT-TAATTATGAAAC
1 TACATTTACACATATAA-T-TG---C
*
17533215 AGACATTTACACATATAATTGC
1 -TACATTTACACATATAATTGC
17533237 TACATTTA
1 TACATTTA
17533245 ATGTACTGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
20 1 0.02
21 21 0.48
22 3 0.07
25 3 0.07
26 13 0.30
27 3 0.07
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (21 bp):
TACATTTACACATATAATTGC
Found at i:17533411 original size:26 final size:26
Alignment explanation
Indices: 17533345--17533419 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
17533335 TTAAAATCAT
17533345 ATTAATTATGAAACATACATTTACAC
1 ATTAATTATGAAACATACATTTACAC
*
17533371 A-TACATT-T---TC-TACATTTACAC
1 ATTA-ATTATGAAACATACATTTACAC
17533392 ATTAATTATGAAACATACATTTACAC
1 ATTAATTATGAAACATACATTTACAC
17533418 AT
1 AT
17533420 GCTAACTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
21 15 0.38
22 4 0.10
25 4 0.10
26 17 0.43
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (26 bp):
ATTAATTATGAAACATACATTTACAC
Found at i:17535368 original size:31 final size:29
Alignment explanation
Indices: 17535333--17535395 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
17535323 AAAACAGAGT
* *
17535333 TTTAAGTTTTTTAAGAGTTAGAGAAAAAAAA
1 TTTAAGTCTTTTAAAAGTT-G-GAAAAAAAA
*
17535364 TTTAAGTCTTTTAAAAGTTGGTAAAAAAA
1 TTTAAGTCTTTTAAAAGTTGGAAAAAAAA
17535393 TTT
1 TTT
17535396 TGAATTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.38
30 1 0.03
31 17 0.59
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (29 bp):
TTTAAGTCTTTTAAAAGTTGGAAAAAAAA
Found at i:17537498 original size:39 final size:40
Alignment explanation
Indices: 17537435--17537551 Score: 107
Period size: 39 Copynumber: 3.0 Consensus size: 40
17537425 TTAGTATCAT
* *
17537435 GTTAAAAATATTT-GCATCACATTAGAAATATTGGTA-TGGA
1 GTTAAAAA-ATTTGGTATCA-ATTAGAAATATTGGTATTGCA
* *
17537475 GTTAAAAAATTTGGTATCAATTAGAAATAGTGATATTGCA
1 GTTAAAAAATTTGGTATCAATTAGAAATATTGGTATTGCA
* * * * *
17537515 -TTAAAAATTTTGGTACCCA-TAGGAATATTGGTCTTGC
1 GTTAAAAAATTTGGTATCAATTAGAAATATTGGTATTGC
17537552 CATTAGAAAG
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
38 14 0.22
39 34 0.53
40 16 0.25
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (40 bp):
GTTAAAAAATTTGGTATCAATTAGAAATATTGGTATTGCA
Found at i:17544111 original size:18 final size:18
Alignment explanation
Indices: 17544088--17544124 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17544078 TGCTTTTCAG
17544088 AAGCACTTTTGAGACAAA
1 AAGCACTTTTGAGACAAA
*
17544106 AAGCACTTTTGAGATAAA
1 AAGCACTTTTGAGACAAA
17544124 A
1 A
17544125 GTATTGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (18 bp):
AAGCACTTTTGAGACAAA
Found at i:17560281 original size:70 final size:67
Alignment explanation
Indices: 17560155--17560287 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
17560145 ATAAACAATA
* * * **
17560155 TAATTGTTTTGCCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACAACATAATTTTACCTTTTAA
17560220 CT
66 CT
* *
17560222 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAACAACGTAGTTTTACCTTT
1 TAATGGTTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAACAACATAATTTTACCTTT
17560287 T
63 T
17560288 TTTATTTGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 18 0.32
68 2 0.04
70 36 0.64
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACAACATAATTTTACCTTTTAA
CT
Found at i:17563814 original size:6 final size:6
Alignment explanation
Indices: 17563803--17563838 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
17563793 AGCATGGAGC
17563803 ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG
1 ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG
17563839 GATCACTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
ATGGTG
Found at i:17565935 original size:2 final size:2
Alignment explanation
Indices: 17565928--17565969 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
17565918 TGGTATATGG
17565928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17565970 GGCTGTAGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17574941 original size:31 final size:34
Alignment explanation
Indices: 17574905--17574989 Score: 88
Period size: 35 Copynumber: 2.4 Consensus size: 34
17574895 AAGTTATTCG
17574905 AATTCGAAAATTCAACTCGATTCG-AACTCG-A-
1 AATTCGAAAATTCAACTCGATTCGTAACTCGAAT
17574936 AATTCGAAAAAAAATTCAACTCGATTCGTTTAACTCGAAT
1 AATTCG----AAAATTCAACTCGATTCG--TAACTCGAAT
17574976 AATTCG-AAATTCAA
1 AATTCGAAAATTCAA
17574990 AAAATTTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
31 6 0.13
35 26 0.58
38 6 0.13
39 1 0.02
40 6 0.13
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (34 bp):
AATTCGAAAATTCAACTCGATTCGTAACTCGAAT
Found at i:17598413 original size:13 final size:13
Alignment explanation
Indices: 17598392--17598444 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
17598382 ACCGTTGACC
17598392 GACCGTTGACTTT
1 GACCGTTGACTTT
* *
17598405 GACCATTGATCGTT
1 GACCGTTGA-CTTT
**
17598419 GATTGTTGACTTT
1 GACCGTTGACTTT
17598432 GACCGTTGACTTT
1 GACCGTTGACTTT
17598445 TTTTCGAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
13 22 0.71
14 9 0.29
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.42
Consensus pattern (13 bp):
GACCGTTGACTTT
Found at i:17604122 original size:31 final size:28
Alignment explanation
Indices: 17604087--17604147 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 28
17604077 CACAACGAAC
* *
17604087 AAATAATTATACGAATTAATAAATAATACGA
1 AAATAAGTATAAGAA-TAAT-AA-AATACGA
17604118 AAATAAGTATAAGAATAATAAAATACGA
1 AAATAAGTATAAGAATAATAAAATACGA
17604146 AA
1 AA
17604148 TACAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 2 0.07
30 4 0.14
31 13 0.46
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (28 bp):
AAATAAGTATAAGAATAATAAAATACGA
Found at i:17604309 original size:30 final size:30
Alignment explanation
Indices: 17604275--17604591 Score: 342
Period size: 30 Copynumber: 10.7 Consensus size: 30
17604265 GAAGAGTTTG
*
17604275 GGGTTAAAATGTAATTTTTGAGAAGTTTAA
1 GGGTTAAAATGTGATTTTTGAGAAGTTTAA
* *
17604305 GGGTTAAAATGTGA-TTTTGAAAAAATTTAA
1 GGGTTAAAATGTGATTTTTG-AGAAGTTTAA
* **
17604335 AGGTTAAAATGTGATTTTTGAGAAGTTCGA
1 GGGTTAAAATGTGATTTTTGAGAAGTTTAA
*
17604365 GGGTTAAAATGTGATTTTTAAGAAGTTTAA
1 GGGTTAAAATGTGATTTTTGAGAAGTTTAA
*
17604395 GGGTTAAAATGTGATTTTT-AGAATGTTT-G
1 GGGTTAAAATGTGATTTTTGAGAA-GTTTAA
* *
17604424 GGGTTAAAATGTGATTTTTAAGAAGTTTAG
1 GGGTTAAAATGTGATTTTTGAGAAGTTTAA
* * *
17604454 GGGTTAAAATGGGATTTTTGAAAAGTTTGA
1 GGGTTAAAATGTGATTTTTGAGAAGTTTAA
* * * *
17604484 GCGTCAAAATATGATTTTTGAGAAGTTT-G
1 GGGTTAAAATGTGATTTTTGAGAAGTTTAA
* *
17604513 GGAGTTAAAATGGGATTTTTG-GAAAGTTT-G
1 GG-GTTAAAATGTGATTTTTGAG-AAGTTTAA
**
17604543 GGGTTAAAATGTGATTTTT-AGAAGTTTTG
1 GGGTTAAAATGTGATTTTTGAGAAGTTTAA
* *
17604572 GGGTCAAAATGTAATTTTTG
1 GGGTTAAAATGTGATTTTTG
17604592 TAAAGTTCAG
Statistics
Matches: 246, Mismatches: 31, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.02
29 69 0.28
30 166 0.67
31 5 0.02
ACGTcount: A:0.33, C:0.01, G:0.26, T:0.39
Consensus pattern (30 bp):
GGGTTAAAATGTGATTTTTGAGAAGTTTAA
Found at i:17604343 original size:90 final size:90
Alignment explanation
Indices: 17604246--17604412 Score: 230
Period size: 90 Copynumber: 1.9 Consensus size: 90
17604236 AAAAAATAGG
* *
17604246 GGTTAAAAAATAAAGTTTCGA-AGAGTTTG-GGGTTAAAATGTAATTTTTGAGAAGTTTAAGGGT
1 GGTTAAAAAAT-AAGTTTCGAGA-AGTTCGAGGGTTAAAATGTAATTTTTAAGAAGTTTAAGGGT
17604309 TAAAATGTGATTTTGAAAAAATTTAAA
64 TAAAATGTGATTTTGAAAAAATTTAAA
** * * * *
17604336 GGTTAAAATGTGATTTTTGAGAAGTTCGAGGGTTAAAATGTGATTTTTAAGAAGTTTAAGGGTTA
1 GGTTAAAAAATAAGTTTCGAGAAGTTCGAGGGTTAAAATGTAATTTTTAAGAAGTTTAAGGGTTA
17604401 AAATGTGATTTT
66 AAATGTGATTTT
17604413 TAGAATGTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
89 11 0.16
90 56 0.84
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.38
Consensus pattern (90 bp):
GGTTAAAAAATAAGTTTCGAGAAGTTCGAGGGTTAAAATGTAATTTTTAAGAAGTTTAAGGGTTA
AAATGTGATTTTGAAAAAATTTAAA
Found at i:17604459 original size:119 final size:116
Alignment explanation
Indices: 17604269--17604603 Score: 395
Period size: 119 Copynumber: 2.8 Consensus size: 116
17604259 AGTTTCGAAG
* * * * * *
17604269 AGTTTGGGGTTAAAATGTAATTTTTGAGAAGTTTAAGGGTTAAAATGTGATTTTGAAAAAATTTA
1 AGTTTAGGGTTAAAATGTGATTTTT-AGAAGTTT-GGGGTTAAAATGTGATTTTTAAGAAGTTTA
** * *
17604334 AAGGTTAAAATGTGATTTTTGAGAAGTTCGAGGGTTAAAATGTGATTTTTAAGA
64 GGGGTTAAAATGTGATTTTTGA-AAGTTCGAGGGTCAAAATATGATTTTTAAGA
17604388 AGTTTAAGGGTTAAAATGTGATTTTTAGAATGTTTGGGGTTAAAATGTGATTTTTAAGAAGTTTA
1 AGTTT-AGGGTTAAAATGTGATTTTTAGAA-GTTTGGGGTTAAAATGTGATTTTTAAGAAGTTTA
* * * *
17604453 GGGGTTAAAATGGGATTTTTGAAAAGTTTGAGCGTCAAAATATGATTTTTGAGA
64 GGGGTTAAAATGTGATTTTTG-AAAGTTCGAGGGTCAAAATATGATTTTTAAGA
* * * *
17604507 AGTTTGGGAGTTAAAATGGGATTTTTGGAAAGTTTGGGGTTAAAATGTGATTTTT-AGAAGTTTT
1 AGTTTAGG-GTTAAAATGTGATTTTTAG-AAGTTTGGGGTTAAAATGTGATTTTTAAGAAGTTTA
* *
17604571 GGGGTCAAAATGTAATTTTTGTAAAGTTC-AGGG
64 GGGGTTAAAATGTGATTTTTG-AAAGTTCGAGGG
17604604 ACCTCCTAAG
Statistics
Matches: 187, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
117 3 0.02
118 34 0.18
119 125 0.67
120 25 0.13
ACGTcount: A:0.33, C:0.01, G:0.27, T:0.39
Consensus pattern (116 bp):
AGTTTAGGGTTAAAATGTGATTTTTAGAAGTTTGGGGTTAAAATGTGATTTTTAAGAAGTTTAGG
GGTTAAAATGTGATTTTTGAAAGTTCGAGGGTCAAAATATGATTTTTAAGA
Found at i:17606932 original size:48 final size:48
Alignment explanation
Indices: 17606876--17607113 Score: 174
Period size: 48 Copynumber: 5.4 Consensus size: 48
17606866 GGTCTACTTA
* * *
17606876 TCTGTATCTCATTAGGAATATGATCGCCTCATTGATTTAATCCATTTC
1 TCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTC
* ** * *
17606924 TCTGTATCTCATCAGG-A-A-GA-CG---GA-T--TTTGGTCTACTTC
1 TCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTC
* *
17606962 TTTGTATCTCATCAGAAAGATGACCGCCTCATTGATTTAATCCATTTC
1 TCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTC
* ** * *
17607010 TCTGTATCTCATCAGGAAAATG---G----ATT-A--TGGTCTACTTC
1 TCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTC
* *
17607048 TTTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATTCATTTC
1 TCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTC
*
17607096 TCTGTATCTCATTAGGAA
1 TCTGTATCTCATCAGGAA
17607114 AATAGGGTTT
Statistics
Matches: 141, Mismatches: 29, Indels: 40
0.67 0.14 0.19
Matches are distributed among these distances:
38 50 0.35
39 1 0.01
40 3 0.02
41 7 0.05
42 2 0.01
44 2 0.01
45 7 0.05
46 3 0.02
47 1 0.01
48 65 0.46
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (48 bp):
TCTGTATCTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTC
Found at i:17606968 original size:38 final size:38
Alignment explanation
Indices: 17606921--17607067 Score: 105
Period size: 38 Copynumber: 3.6 Consensus size: 38
17606911 TTTAATCCAT
17606921 TTCTCTGTATCTCATCAGGAAGACGGATTTTGGTCTAC
1 TTCTCTGTATCTCATCAGGAAGACGGATTTTGGTCTAC
* * * ** * *
17606959 TTCTTTGTATCTCATCAGAAAGATGACCGCCTCATTGATTTAATCCAT
1 TTCTCTGTATCTCATCAG---GAAGA-CG---GA-T--TTTGGTCTAC
* * *
17607007 TTCTCTGTATCTCATCAGGAAAATGGATTATGGTCTAC
1 TTCTCTGTATCTCATCAGGAAGACGGATTTTGGTCTAC
*
17607045 TTCTTTGTATCTCATCAGGAAGA
1 TTCTCTGTATCTCATCAGGAAGA
17607068 TGACCGCCTC
Statistics
Matches: 80, Mismatches: 19, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
38 43 0.54
40 1 0.01
41 5 0.06
42 2 0.03
44 1 0.01
45 4 0.05
46 1 0.01
48 23 0.29
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (38 bp):
TTCTCTGTATCTCATCAGGAAGACGGATTTTGGTCTAC
Found at i:17607116 original size:86 final size:86
Alignment explanation
Indices: 17606797--17607115 Score: 476
Period size: 86 Copynumber: 3.7 Consensus size: 86
17606787 CTCTCTATAC
* * ** * * *
17606797 CTCATCAAGAGGATGATTGCCTTATTGATTTAATCCACTTCTCTATATCTCATCAGGAAAACGGA
1 CTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTCTCTGTATCTCATCAGGAAAACGGA
* *
17606862 TTTTGGTCTACTTATCTGTAT
66 TTTTGGTCTACTTCTTTGTAT
* * * *
17606883 CTCATTAGGAATATGATCGCCTCATTGATTTAATCCATTTCTCTGTATCTCATCAGGAAGACGGA
1 CTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTCTCTGTATCTCATCAGGAAAACGGA
17606948 TTTTGGTCTACTTCTTTGTAT
66 TTTTGGTCTACTTCTTTGTAT
* *
17606969 CTCATCAGAAAGATGACCGCCTCATTGATTTAATCCATTTCTCTGTATCTCATCAGGAAAATGGA
1 CTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTCTCTGTATCTCATCAGGAAAACGGA
*
17607034 TTATGGTCTACTTCTTTGTAT
66 TTTTGGTCTACTTCTTTGTAT
* *
17607055 CTCATCAGGAAGATGACCGCCTCATTGATTTAATTCATTTCTCTGTATCTCATTAGGAAAA
1 CTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTCTCTGTATCTCATCAGGAAAA
17607116 TAGGGTTTTG
Statistics
Matches: 212, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 212 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.38
Consensus pattern (86 bp):
CTCATCAGGAAGATGACCGCCTCATTGATTTAATCCATTTCTCTGTATCTCATCAGGAAAACGGA
TTTTGGTCTACTTCTTTGTAT
Found at i:17618917 original size:30 final size:30
Alignment explanation
Indices: 17618859--17619142 Score: 267
Period size: 30 Copynumber: 9.5 Consensus size: 30
17618849 TAAAAATACA
* *
17618859 ATTTTTGAGAAGTTCGAGGGT--TAATGTG
1 ATTTTTGAAAAGTTCGAGGGTCAAAATGTG
*
17618887 ATTTTGGAAAAGTTCGAGGGTCAAAATGTG
1 ATTTTTGAAAAGTTCGAGGGTCAAAATGTG
* *
17618917 ATTTTTGAGAAGTTTGAGAGGTCAAAATGTG
1 ATTTTTGAAAAGTTCGAG-GGTCAAAATGTG
* *
17618948 ATTTTT-ATGAAGTTCGAGGGTCAAAATGTA
1 ATTTTTGA-AAAGTTCGAGGGTCAAAATGTG
* *
17618978 ATTTTTGGAAAGTTCGAGGGTTAAAATGTG
1 ATTTTTGAAAAGTTCGAGGGTCAAAATGTG
* *
17619008 ATTTTTGAGAAGTTTCGA-GGTTAAAATGTG
1 ATTTTTGAAAAG-TTCGAGGGTCAAAATGTG
* * * * *
17619038 ATTTTGGAAAAGTCCCAAGGTTAAAATGTG
1 ATTTTTGAAAAGTTCGAGGGTCAAAATGTG
* *
17619068 ATTTTT-AGAAAGTTTGA-GGTCAAAATATG
1 ATTTTTGA-AAAGTTCGAGGGTCAAAATGTG
* * * *
17619097 ATTTTAGAAAAGTT-TAGTGGTTAAAATGTT
1 ATTTTTGAAAAGTTCGAG-GGTCAAAATGTG
*
17619127 ATTTTTGAGAAGTTCG
1 ATTTTTGAAAAGTTCG
17619143 TGGACCTCTT
Statistics
Matches: 212, Mismatches: 32, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
28 20 0.09
29 25 0.12
30 135 0.64
31 32 0.15
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (30 bp):
ATTTTTGAAAAGTTCGAGGGTCAAAATGTG
Found at i:17619089 original size:119 final size:122
Alignment explanation
Indices: 17618851--17619140 Score: 337
Period size: 119 Copynumber: 2.4 Consensus size: 122
17618841 GGATTAATTA
* * *
17618851 AAAATACAATTTTT-GAGAAGTTCGAGGGTT--AATGTGATTTTGGAAAAG-TTCGAGGGTCAAA
1 AAAATATAATTTTTGGA-AAGTTCGAGGGTTAAAATGTGATTTTTGAGAAGTTTCGAGGGTCAAA
* * ***
17618912 ATGTGATTTTTGAGAAGTTTGAGAGGTCAAAATGTGATTTTTATGAAGTTCGAGGGTC
65 ATGTGATTTTGGAAAAGTCCCAGAGGTCAAAATGTGATTTTTATGAAGTTCGAGGGTC
* *
17618970 AAAATGTAATTTTTGGAAAGTTCGAGGGTTAAAATGTGATTTTTGAGAAGTTTCGA-GGTTAAAA
1 AAAATATAATTTTTGGAAAGTTCGAGGGTTAAAATGTGATTTTTGAGAAGTTTCGAGGGTCAAAA
* *
17619034 TGTGATTTTGGAAAAGTCCCA-AGGTTAAAATGTGATTTTTA-GAAAGTTTGA-GGTC
66 TGTGATTTTGGAAAAGTCCCAGAGGTCAAAATGTGATTTTTATG-AAGTTCGAGGGTC
* * * * *
17619089 AAAATATGATTTTAGAAAAGTT-TAGTGGTTAAAATGTTATTTTTGAGAAGTT
1 AAAATATAATTTTTGGAAAGTTCGAG-GGTTAAAATGTGATTTTTGAGAAGTT
17619141 CGTGGACCTC
Statistics
Matches: 147, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
118 2 0.01
119 73 0.50
120 28 0.19
121 39 0.27
122 5 0.03
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (122 bp):
AAAATATAATTTTTGGAAAGTTCGAGGGTTAAAATGTGATTTTTGAGAAGTTTCGAGGGTCAAAA
TGTGATTTTGGAAAAGTCCCAGAGGTCAAAATGTGATTTTTATGAAGTTCGAGGGTC
Found at i:17620742 original size:18 final size:17
Alignment explanation
Indices: 17620686--17620750 Score: 87
Period size: 17 Copynumber: 3.8 Consensus size: 17
17620676 GACATTTTTT
*
17620686 TTTAAA-TTTAAATAAA
1 TTTAAACTTAAAATAAA
* *
17620702 TTTAAATTTAGAATAAA
1 TTTAAACTTAAAATAAA
17620719 TTTAAACTTAAAATAAA
1 TTTAAACTTAAAATAAA
17620736 TTTTAAACTTAAAAT
1 -TTTAAACTTAAAAT
17620751 TGGGTTCGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.14
17 23 0.53
18 14 0.33
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:17624546 original size:25 final size:25
Alignment explanation
Indices: 17624500--17624553 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
17624490 AATTAAATTT
* *
17624500 TAATTTTTAATAATTTATATTTTTA
1 TAATTTTTAATAAGTTAAATTTTTA
*
17624525 TAATTTTTAA-AAGGTTAAATTTTTT
1 TAATTTTTAATAA-GTTAAATTTTTA
17624550 TAAT
1 TAAT
17624554 CATTTTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TAATTTTTAATAAGTTAAATTTTTA
Found at i:17626071 original size:59 final size:58
Alignment explanation
Indices: 17625920--17626110 Score: 156
Period size: 59 Copynumber: 3.2 Consensus size: 58
17625910 TTTTAGGGGT
* * * * *
17625920 AAAATGGTAATTTTTGTGAAATCGGGGCTAAAAATGGAA-TTTGGAAAGTTTGGGGAAT
1 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGAAATTTTGGAAAGTTCGGGG-AC
* * ** *
17625978 AAAATGGTAAATTTTGG-CAATAACAAGGTCAAAAATGAAATTTTGGAAAGTTCGGAGG-C
1 AAAATGGT-AATTTTGGTGAA-ATCGGGGTTAAAAATGAAATTTTGGAAAGTTCGG-GGAC
* * * * *
17626037 AAAACGGTAAGTTTTGGTGAAATCGGGGTTAAAAATGAGATTTAGGGAAGTTTGAGGGTA-
1 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGAAATTTTGGAAAGTTCG-GGG-AC
17626097 AAAATGGTAATTTT
1 AAAATGGTAATTTT
17626111 TGAAAGTTTT
Statistics
Matches: 103, Mismatches: 21, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
58 12 0.12
59 64 0.62
60 25 0.24
61 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.29
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGAAATTTTGGAAAGTTCGGGGAC
Found at i:17626147 original size:30 final size:30
Alignment explanation
Indices: 17626087--17626379 Score: 333
Period size: 30 Copynumber: 9.7 Consensus size: 30
17626077 TTTAGGGAAG
* *
17626087 TTTGAGGGTAAAAATGGTAATTTTTG-AAAGT
1 TTTG-GGGTCAAAAT-GTAATTTTAGAAAAGT
* * *
17626118 TTTGGGGTCAAAGTATAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTAGAAAAGT
* * *
17626148 TTTGGAGTCAAAATGTAATTTTGGAAAGGT
1 TTTGGGGTCAAAATGTAATTTTAGAAAAGT
17626178 TTTGGGGTCAAAATGTAATCTTTAG-AAAGT
1 TTTGGGGTCAAAATGTAAT-TTTAGAAAAGT
* * * *
17626208 TTTAGGGTTAAAATATAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTAGAAAAGT
*
17626238 TTAGGGGTCAAAATGTAATTTTCA-AAAAGT
1 TTTGGGGTCAAAATGTAATTTT-AGAAAAGT
* *
17626268 TTTTGGGTCAAAATATAATTTTCA-AAAAGT
1 TTTGGGGTCAAAATGTAATTTT-AGAAAAGT
* *
17626298 TTTAGGGTCGAAATGTAATTTTAGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTAGAAAAGT
* *
17626328 TTTAGGGTCGAAATGTAATTTTAGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTAGAAAAGT
*
17626358 TTTGGGGTCAAAATATAATTTT
1 TTTGGGGTCAAAATGTAATTTT
17626380 TGGACAATTT
Statistics
Matches: 228, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
29 13 0.06
30 207 0.91
31 8 0.04
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (30 bp):
TTTGGGGTCAAAATGTAATTTTAGAAAAGT
Found at i:17627434 original size:6 final size:6
Alignment explanation
Indices: 17627423--17627458 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
17627413 CCCTTTTATT
*
17627423 TATTAA TATTAA TATTAA TATTAA TGATTAT TATTA
1 TATTAA TATTAA TATTAA TATTAA T-ATTAA TATTA
17627459 TTTAAAACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TATTAA
Found at i:17628312 original size:6 final size:6
Alignment explanation
Indices: 17628303--17628406 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
17628293 TAATATTATT
* *
17628303 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -GTAAA TTTAAA TAAATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* * *
17628350 TTTAAA TTTAAGA --TAAA TTTAAA TCTAAA -TAAAA TTTAAA ATT-AA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
17628395 TTTAAA CTTAAA
1 TTTAAA TTTAAA
17628407 AATCAAAATC
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
4 3 0.04
5 18 0.23
6 50 0.65
7 1 0.01
8 5 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:17628337 original size:17 final size:16
Alignment explanation
Indices: 17628303--17628394 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 16
17628293 TAATATTATT
*
17628303 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
17628319 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAA-TAAA
17628336 TTTAAA--TAAATAAA
1 TTTAAATTTAAATAAA
17628350 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
*
17628367 TTTAAATCTAAATAAAA
1 TTTAAATTTAAAT-AAA
*
17628384 TTTAAAATTAA
1 TTTAAATTTAA
17628395 TTTAAACTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.15
15 4 0.06
16 16 0.24
17 37 0.55
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:17628406 original size:28 final size:28
Alignment explanation
Indices: 17628305--17628400 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 28
17628295 ATATTATTTT
* *
17628305 TAAATTT-AAT-TAAATTTAAATTTAAAG
1 TAAATTTAAATCTAAA-TAAAATTTAAAA
* * *
17628332 TAAATTTAAATAAATAAATTTAAATTTAAGA
1 TAAATTTAAAT--CTAAA-TAAAATTTAAAA
17628363 TAAATTTAAATCTAAATAAAATTTAAAA
1 TAAATTTAAATCTAAATAAAATTTAAAA
*
17628391 TTAATTTAAA
1 TAAATTTAAA
17628401 CTTAAAAATC
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
27 7 0.12
28 22 0.37
29 4 0.07
31 26 0.44
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (28 bp):
TAAATTTAAATCTAAATAAAATTTAAAA
Found at i:17632696 original size:206 final size:206
Alignment explanation
Indices: 17632342--17632748 Score: 805
Period size: 206 Copynumber: 2.0 Consensus size: 206
17632332 TTATCCAATT
*
17632342 ACAAGCCCCATAACCCTGGCCCAAACAAGCCCAATTACAAACCCTAATGTCCCAAACCAAATCAC
1 ACAAGCCCAATAACCCTGGCCCAAACAAGCCCAATTACAAACCCTAATGTCCCAAACCAAATCAC
17632407 ACAAAAATATCAAAAAACTTAGCAACTTGCTGTTGCCACCCATCCCTAGCCACTCTTTTGTCGCG
66 ACAAAAATATCAAAAAACTTAGCAACTTGCTGTTGCCACCCATCCCTAGCCACTCTTTTGTCGCG
17632472 CCCTGCCTTGCCCACTCGGATGATGCCACGTTAGCATCACCCCCAACGATTTATCCATTTGATCC
131 CCCTGCCTTGCCCACTCGGATGATGCCACGTTAGCATCACCCCCAACGATTTATCCATTTGATCC
17632537 TTCAATTACAA
196 TTCAATTACAA
17632548 ACAAGCCCAATAACCCTGGCCCAAACAAGCCCAATTACAAACCCTAATGTCCCAAACCAAATCAC
1 ACAAGCCCAATAACCCTGGCCCAAACAAGCCCAATTACAAACCCTAATGTCCCAAACCAAATCAC
17632613 ACAAAAATATCAAAAAACTTAGCAACTTGCTGTTGCCACCCATCCCTAGCCACTCTTTTGTCGCG
66 ACAAAAATATCAAAAAACTTAGCAACTTGCTGTTGCCACCCATCCCTAGCCACTCTTTTGTCGCG
17632678 CCCTGCCTTGCCCACTCGGATGATGCCACGTTAGCATCACCCCCAACGATTTATCCATTTGATCC
131 CCCTGCCTTGCCCACTCGGATGATGCCACGTTAGCATCACCCCCAACGATTTATCCATTTGATCC
17632743 TTCAAT
196 TTCAAT
17632749 ATTTTTTGAT
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
206 200 1.00
ACGTcount: A:0.31, C:0.35, G:0.11, T:0.22
Consensus pattern (206 bp):
ACAAGCCCAATAACCCTGGCCCAAACAAGCCCAATTACAAACCCTAATGTCCCAAACCAAATCAC
ACAAAAATATCAAAAAACTTAGCAACTTGCTGTTGCCACCCATCCCTAGCCACTCTTTTGTCGCG
CCCTGCCTTGCCCACTCGGATGATGCCACGTTAGCATCACCCCCAACGATTTATCCATTTGATCC
TTCAATTACAA
Found at i:17633148 original size:31 final size:31
Alignment explanation
Indices: 17633079--17633225 Score: 171
Period size: 30 Copynumber: 4.9 Consensus size: 31
17633069 GAACTTTCTT
*
17633079 AAAATTATATTTTGA-CCTCTAAACTTTTTCC
1 AAAATTACATTTTGACCCT-TAAACTTTTTCC
*
17633110 -AAATTACATTTTAACCCTTAAACTTTTTCC
1 AAAATTACATTTTGACCCTTAAACTTTTTCC
* *
17633140 AAAATTACATTTTAACCCTAAAAC-TTTTCC
1 AAAATTACATTTTGACCCTTAAACTTTTTCC
* *
17633170 AAAATTATA-TTTGACCCTCAAACTTTTT--
1 AAAATTACATTTTGACCCTTAAACTTTTTCC
* *
17633198 AAAATTGCATTTTGACCCCTAAACTTTT
1 AAAATTACATTTTGACCCTTAAACTTTT
17633226 CTAAAATCAT
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.07
29 28 0.27
30 42 0.41
31 25 0.25
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (31 bp):
AAAATTACATTTTGACCCTTAAACTTTTTCC
Found at i:17634773 original size:2 final size:2
Alignment explanation
Indices: 17634766--17634791 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17634756 TTTGTCATGC
17634766 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17634792 GTATGCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17635347 original size:17 final size:17
Alignment explanation
Indices: 17635316--17635388 Score: 101
Period size: 17 Copynumber: 4.2 Consensus size: 17
17635306 TGGATCGAAT
* *
17635316 TTTAATTTAAGTTTAAA
1 TTTATTTTAAATTTAAA
*
17635333 TTTCTTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
*
17635350 TTTAAATTTAAATTTAAA
1 TTT-ATTTTAAATTTAAA
17635368 TTTATTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
17635385 TTTA
1 TTTA
17635389 ACTAAATTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
17 34 0.69
18 15 0.31
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:17635352 original size:35 final size:35
Alignment explanation
Indices: 17635313--17635389 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
17635303 GTTTGGATCG
* * *
17635313 AATTTTAATTTAAGTTTAAATTTCTTTTAAATTTA
1 AATTTAAATTTAAATTTAAATTTATTTTAAATTTA
17635348 AATTTAAATTTAAATTTAAATTTATTTTAAATTTA
1 AATTTAAATTTAAATTTAAATTTATTTTAAATTTA
17635383 AATTTAA
1 AATTTAA
17635390 CTAAATTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (35 bp):
AATTTAAATTTAAATTTAAATTTATTTTAAATTTA
Found at i:17635359 original size:29 final size:29
Alignment explanation
Indices: 17635313--17635389 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
17635303 GTTTGGATCG
* * **
17635313 AATTTTAATTTAAGTTTAAATTTCTTTTA
1 AATTTAAATTTAAATTTAAATTTAATTTA
17635342 AATTTAAATTTAAATTTAAATTTAAATTT-
1 AATTTAAATTTAAATTTAAATTT-AATTTA
*
17635371 ATTTTAAATTTAAATTTAA
1 AATTTAAATTTAAATTTAA
17635390 CTAAATTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 39 0.93
30 3 0.07
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (29 bp):
AATTTAAATTTAAATTTAAATTTAATTTA
Found at i:17635382 original size:23 final size:24
Alignment explanation
Indices: 17635313--17635389 Score: 95
Period size: 23 Copynumber: 3.3 Consensus size: 24
17635303 GTTTGGATCG
* *
17635313 AATTTTAATTTAAGTTTAAATTT-
1 AATTTAAATTTAAATTTAAATTTA
**
17635336 CTTTTAAATTTAAATTTAAATTTA
1 AATTTAAATTTAAATTTAAATTTA
*
17635360 AATTTAAATTT-ATTTTAAATTTA
1 AATTTAAATTTAAATTTAAATTTA
17635383 AATTTAA
1 AATTTAA
17635390 CTAAATTTGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
23 37 0.80
24 9 0.20
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (24 bp):
AATTTAAATTTAAATTTAAATTTA
Found at i:17635397 original size:23 final size:23
Alignment explanation
Indices: 17635346--17635428 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
17635336 CTTTTAAATT
*
17635346 TAAA-TTTAAATTTAAATTTAAA
1 TAAATTTTAAATTTAAATTTAAC
**
17635368 TTTATTTTAAATTTAAATTTAAC
1 TAAATTTTAAATTTAAATTTAAC
* *
17635391 TAAATTTGAAA--TAAATATAAAC
1 TAAATTTTAAATTTAAAT-TTAAC
* *
17635413 TTAATGTTAAATTTAA
1 TAAATTTTAAATTTAA
17635429 GAGTCTAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
21 5 0.11
22 14 0.30
23 25 0.53
24 3 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAATTTTAAATTTAAATTTAAC
Found at i:17635428 original size:6 final size:6
Alignment explanation
Indices: 17635313--17635389 Score: 95
Period size: 6 Copynumber: 13.2 Consensus size: 6
17635303 GTTTGGATCG
* * **
17635313 AATTTT AATTTA AGTTTA AATTT- CTTTTA AATTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
17635360 AATTTA AATTT- ATTTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA AATTTA A
17635390 CTAAATTTGA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
5 7 0.12
6 53 0.88
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (6 bp):
AATTTA
Found at i:17637386 original size:29 final size:29
Alignment explanation
Indices: 17637304--17637555 Score: 188
Period size: 29 Copynumber: 8.5 Consensus size: 29
17637294 GGAAGTCCTT
* * *
17637304 AAACTATCCAGAAATTAAATTTTGACCTCC
1 AAACT-TCCAAAAATTACATTTTGACCTCG
* *
17637334 AAACTTCTCCAAAATT-CTAGTTTTAACCTCG
1 AAACTTC-CAAAAATTAC-A-TTTTGACCTCG
* * *
17637365 AAACTTTCAAAAATTACATTTTTACCCCTG
1 AAACTTCCAAAAATTACATTTTGACCTC-G
*
17637395 -AACTTCCAAAAATTACATTTTTGACC-CC
1 AAACTTCCAAAAATTACA-TTTTGACCTCG
* * *
17637423 AAAATGTCTAAAAATTACATTTTTGCCCTC-
1 AAACT-TCCAAAAATTACA-TTTTGACCTCG
* * * *
17637453 AAAATTCCAAAAATTCCAATTTTGACTTTG
1 AAACTTCCAAAAATTAC-ATTTTGACCTCG
* * * *
17637483 AAACTTCCAAAAAGTACATTTTTACCCCC
1 AAACTTCCAAAAATTACATTTTGACCTCG
* *
17637512 AAACTTCCAAAAAATACATTTTGCCCTCG
1 AAACTTCCAAAAATTACATTTTGACCTCG
*
17637541 AAACTTCTAAAAATT
1 AAACTTCCAAAAATT
17637556 CTAATTTTTC
Statistics
Matches: 176, Mismatches: 35, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
29 91 0.52
30 68 0.39
31 17 0.10
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTGACCTCG
Found at i:17637440 original size:59 final size:56
Alignment explanation
Indices: 17637373--17637597 Score: 179
Period size: 59 Copynumber: 3.9 Consensus size: 56
17637363 CGAAACTTTC
**
17637373 AAAAATTACATTTTTACCCCTGAACTTCCAAAAATTACATTTTTGACCCCAAAATGTCT
1 AAAAATTACATTTTT-CCCCCAAACTTCCAAAAATTACA-TTTTGACCCCAAAAT-TCT
* * * *** * *
17637432 AAAAATTACATTTTTGCCCTCAAAATTCCAAAAATTCCAATTTTGACTTTGAAACTTCC
1 AAAAATTACATTTTT-CCCCCAAACTTCCAAAAATTAC-ATTTTGAC-CCCAAAATTCT
* * *
17637491 AAAAAGTACATTTTTACCCCCAAACTTCCAAAAAATACATTTTG-CCCTCGAAACTTCT
1 AAAAATTACATTTTT-CCCCCAAACTTCCAAAAATTACATTTTGACCC-C-AAAATTCT
*
17637549 AAAAATT-CTAATTTTTCCCCCGACACTTCC-AAAATTACCATTTT-ACCCC
1 AAAAATTAC--ATTTTTCCCCC-AAACTTCCAAAAATTA-CATTTTGACCCC
17637598 CGAATGTCTG
Statistics
Matches: 133, Mismatches: 24, Indels: 19
0.76 0.14 0.11
Matches are distributed among these distances:
57 2 0.02
58 31 0.23
59 95 0.71
60 5 0.04
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.33
Consensus pattern (56 bp):
AAAAATTACATTTTTCCCCCAAACTTCCAAAAATTACATTTTGACCCCAAAATTCT
Found at i:17637591 original size:29 final size:29
Alignment explanation
Indices: 17637363--17637601 Score: 175
Period size: 29 Copynumber: 8.1 Consensus size: 29
17637353 GTTTTAACCT
*
17637363 CGAAACTTTCAAAAATTACATTTTTACCCC
1 CGAAACTTCCAAAAATTACATTTTT-CCCC
* *
17637393 TG-AACTTCCAAAAATTACATTTTTGACCC
1 CGAAACTTCCAAAAATTACATTTTT-CCCC
* * *
17637422 C-AAAATGTCTAAAAATTACATTTTTGCCCT
1 CGAAACT-TCCAAAAATTACATTTTT-CCCC
* * ** **
17637452 C-AAAATTCCAAAAATTCCAATTTTGACTT
1 CGAAACTTCCAAAAATTAC-ATTTTTCCCC
* *
17637481 TGAAACTTCCAAAAAGTACATTTTTACCCC
1 CGAAACTTCCAAAAATTACATTTTT-CCCC
* * *
17637511 C-AAACTTCCAAAAAATACATTTTGCCCT
1 CGAAACTTCCAAAAATTACATTTTTCCCC
*
17637539 CGAAACTTCTAAAAATT-CTAATTTTTCCCC
1 CGAAACTTCCAAAAATTAC--ATTTTTCCCC
* *
17637569 CGACACTTCC-AAAATTACCATTTTACCCC
1 CGAAACTTCCAAAAATTA-CATTTTTCCCC
17637598 CGAA
1 CGAA
17637602 TGTCTGAAAA
Statistics
Matches: 165, Mismatches: 34, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
28 5 0.03
29 96 0.58
30 63 0.38
31 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.32
Consensus pattern (29 bp):
CGAAACTTCCAAAAATTACATTTTTCCCC
Found at i:17637642 original size:59 final size:58
Alignment explanation
Indices: 17637574--17637715 Score: 144
Period size: 59 Copynumber: 2.4 Consensus size: 58
17637564 TCCCCCGACA
** * * *
17637574 CTTCCAAAATTACCATTTTACCCCCGAATGTCTGAAAATTTTATTTTTGATCC-T-AATT
1 CTTCCAAAATTACCATTTTACCCCCGAACATCT-AAAATGTCATTTTT-AACCTTAAATT
* * * *
17637632 CTTCCGAAAATTATCGTTTTGCCCTCGAACATCTAAAATGTCATTTTTAACCTTAAATT
1 CTTCC-AAAATTACCATTTTACCCCCGAACATCTAAAATGTCATTTTTAACCTTAAATT
*
17637691 TTTCCAAAATTACCACTTTTACCCC
1 CTTCCAAAATTACCA-TTTTACCCC
17637716 GAGAGTCCAA
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
57 3 0.05
58 26 0.39
59 37 0.56
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.39
Consensus pattern (58 bp):
CTTCCAAAATTACCATTTTACCCCCGAACATCTAAAATGTCATTTTTAACCTTAAATT
Found at i:17649335 original size:205 final size:205
Alignment explanation
Indices: 17649006--17650415 Score: 2191
Period size: 205 Copynumber: 6.9 Consensus size: 205
17648996 CTCAAATACA
* *
17649006 AGCAAATCTTCGAA-CCCTAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGG
1 AGCAAATCTTCGAATCCC-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT-AAATGG
* * * *
17649070 TTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCTTGAGGAGATCCAGAGAAGC
64 TTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGC
* *
17649135 GAATTAAAACAAGTGATACAGTCATCTTCCTGATGAGACACTAAGTAA-AAGACCAAATCAAACC
129 GAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAG-AAGAAGACCAAATCAAACC
17649199 CAGGCTCAATGCG
193 CAGGCTCAATGCG
17649212 AGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAATGGTT
1 AGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAATGGTT
* * * * *
17649277 ACCTTCCTGAAGAGACACTGAGAAATGAACCAAATTCGTCTTCCTAAGGAGATCCAGAGAAGCGA
66 AGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
* * *
17649342 ATTAAAACAAGTGATGCGGCCATCTTCCTGATGAGACATTGAGAAGAAGACCAAATCAAACCCAG
131 ATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCCAG
17649407 GCTCAATGCG
196 GCTCAATGCG
* *
17649417 AGCAAATCTTCGAATCCCAGCTTCTTGAAGAGATACTGAGAAGCAGGTCGAAGCAATAAATGGTT
1 AGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAATGGTT
*
17649482 AGCTTCCTGATGAGACATTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
66 AGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
* *
17649547 ATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACTCAG
131 ATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCCAG
17649612 GCTCAATGCG
196 GCTCAATGCG
*
17649622 AGCAAATCTTCGAATCCCAGCTTTCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAATGGTT
1 AGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAATGGTT
* * * *
17649687 AGCTTCCTAATGAGACACTGAGAAGTGAACCAAATTCGTCTTCCTAAGGAGATCCAAAGAAGCGA
66 AGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
* * *
17649752 ATTAAAACAAGTGATGCGATCATCTTCCTAATGAGACACTAAGAAGAAGACCAAATCAAACTCAG
131 ATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCCAG
17649817 GCTCAATGCG
196 GCTCAATGCG
* * * *
17649827 AGCAAATCTTCGAATCCCAGCTTCTTGATGAGATACTGAGAAGTAGGTAGAAGTAATAAATGGTT
1 AGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAATGGTT
* *
17649892 AGCTTCTTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGAGA
66 AGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
*
17649957 ATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAG
131 ATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCCAG
*
17650022 GCTCAATGTG
196 GCTCAATGCG
* *
17650032 AGCAAATCTTTGAATCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAATGGTT
1 AGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAATGGTT
* *
17650097 AGCTTCCTGATGAGACACTGAGAAGTGGACGAAATTCGTCTTCCTAAGGAGATCCAGAGAAGCGA
66 AGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
* * *
17650162 ATTAAAATAAGTGATGCGATCATCTTTCTGATGAGACACTAAGAAGAAGACCAAATCAAACCCAG
131 ATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCCAG
* *
17650227 GATCAATACG
196 GCTCAATGCG
* *
17650237 AGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAT-GT
1 AGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT-AAATGGT
* * * * *
17650301 TAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGACTTCCTGATGAGA-CATAGAGAAGC
65 TAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATC-CAGAGAAGC
* * * * * * *
17650365 GAATTGAAACAAGCGACGCAGTCATCTTCTTGA-GTAGATACTAAGAGGAAG
129 GAATTAAAACAAGTGATGCGGTCATCTTCCTGATG-AGACACTAAGAAGAAG
17650416 GTCAAGTTAA
Statistics
Matches: 1109, Mismatches: 90, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
204 4 0.00
205 1047 0.94
206 55 0.05
207 3 0.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (205 bp):
AGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAATGGTT
AGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
ATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCCAG
GCTCAATGCG
Found at i:17650786 original size:6 final size:6
Alignment explanation
Indices: 17650752--17650867 Score: 57
Period size: 6 Copynumber: 20.2 Consensus size: 6
17650742 GATTGGATCG
* * * * **
17650752 AATTTT AATTTA AGTTTA AA-TTG ATTTTA AATTTA TTTTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* ** *
17650799 AATTTA GATTT- GTTTTA AACTTA AA-TTA AA-TTA AATTTGA AA--TA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA
* *
17650843 AATGTA AACTT- AATGTTA AATTTA A
1 AATTTA AATTTA AAT-TTA AATTTA A
17650868 GAGTCCAAAT
Statistics
Matches: 83, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
4 3 0.04
5 20 0.24
6 54 0.65
7 6 0.07
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (6 bp):
AATTTA
Found at i:17650792 original size:23 final size:22
Alignment explanation
Indices: 17650753--17650796 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
17650743 ATTGGATCGA
17650753 ATTTTAATTTAAGTTTAAATTG
1 ATTTTAATTTAAGTTTAAATTG
**
17650775 ATTTTAAATTTATTTTTAAATT
1 ATTTT-AATTTAAGTTTAAATT
17650797 TAAATTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
ATTTTAATTTAAGTTTAAATTG
Found at i:17652878 original size:29 final size:29
Alignment explanation
Indices: 17652815--17653055 Score: 238
Period size: 30 Copynumber: 8.1 Consensus size: 29
17652805 AAAAATTATA
** *
17652815 TTTTGACCCCCAAACTTCTCCAAAATTCCAA
1 TTTTGACCCTAAAAC-T-TCCAAAATTCCAT
*
17652846 TTTTGACCCTAAAACTTCCACAAATTACAT
1 TTTTGACCCTAAAACTTCCA-AAATTCCAT
17652876 TTTTG-CCCT-AAACTTCCAAAAATTCCAT
1 TTTTGACCCTAAAACTTCC-AAAATTCCAT
*
17652904 TTTTAACCCTAAAACTTCCAAAAATTCCAT
1 TTTTGACCCTAAAACTTCC-AAAATTCCAT
***
17652934 TTTTG-CCCCCGAACTTCCAAGAATTCCAT
1 TTTTGACCCTAAAACTTCCAA-AATTCCAT
* * *
17652963 TTTTAACTCTAAAACTTCCAAAAGTTACA-
1 TTTTGACCCTAAAACTTCCAAAA-TTCCAT
* **
17652992 TTTTAACCCCGAAACTTCCAAAACTTCCAT
1 TTTTGACCCTAAAACTTCCAAAA-TTCCAT
*
17653022 TTTTGACCCTAACACTTCCAAAATTACCAT
1 TTTTGACCCTAAAACTTCCAAAATT-CCAT
17653052 TTTT
1 TTTT
17653056 CCCCCGGATG
Statistics
Matches: 176, Mismatches: 25, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
28 22 0.12
29 63 0.36
30 78 0.44
31 13 0.07
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTTGACCCTAAAACTTCCAAAATTCCAT
Found at i:17652977 original size:59 final size:58
Alignment explanation
Indices: 17652796--17653061 Score: 290
Period size: 59 Copynumber: 4.5 Consensus size: 58
17652786 TAAAAGTCCT
* * * *
17652796 AAACTATCCAAAAATTATA-TTTTGACCCCCAAACTTCTCCAAAATTCCAATTTTGACCCTA
1 AAACT-TCCAAAAATTACATTTTTG-CCCCCGAAC-T-TCCAAAATTCCATTTTTAACCCTA
* **
17652857 AAACTTCCACAAATTACATTTTTG-CCCTAAACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTACATTTTTGCCCCCGAACTTCC-AAAATTCCATTTTTAACCCTA
* *
17652915 AAACTTCCAAAAATTCCATTTTTGCCCCCGAACTTCCAAGAATTCCATTTTTAACTCTA
1 AAACTTCCAAAAATTACATTTTTGCCCCCGAACTTCCAA-AATTCCATTTTTAACCCTA
* ** *
17652974 AAACTTCCAAAAGTTACA-TTTTAACCCCGAAACTTCCAAAACTTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTACATTTTTGCCCCCG-AACTTCCAAAA-TTCCATTTTTAACCCTA
*
17653033 ACACTTCC-AAAATTACCATTTTT-CCCCCG
1 AAACTTCCAAAAATTA-CATTTTTGCCCCCG
17653062 GATGTCCAAA
Statistics
Matches: 178, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
57 3 0.02
58 61 0.34
59 89 0.50
60 15 0.08
61 10 0.06
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (58 bp):
AAACTTCCAAAAATTACATTTTTGCCCCCGAACTTCCAAAATTCCATTTTTAACCCTA
Found at i:17656011 original size:22 final size:22
Alignment explanation
Indices: 17655986--17656027 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
17655976 ATATATATGA
*
17655986 TATACTAGTGGTAGAAATTTTT
1 TATACTAGTGATAGAAATTTTT
*
17656008 TATACTAGTGATGGAAATTT
1 TATACTAGTGATAGAAATTT
17656028 GTAAGTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (22 bp):
TATACTAGTGATAGAAATTTTT
Found at i:17659544 original size:21 final size:22
Alignment explanation
Indices: 17659499--17659557 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
17659489 GATCTGAGGA
*
17659499 AAAATAAAAGAAAA-AAAATTG
1 AAAATAAAAGAAAATAGAATTG
17659520 AAAATAAAAGAAAATAGAATT-
1 AAAATAAAAGAAAATAGAATTG
*
17659541 AAAA-AAATAAAAAATAG
1 AAAATAAA-AGAAAATAG
17659558 GGAAGTCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 26 0.76
22 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.15
Consensus pattern (22 bp):
AAAATAAAAGAAAATAGAATTG
Found at i:17660385 original size:19 final size:19
Alignment explanation
Indices: 17660361--17660403 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17660351 AAACATAATT
17660361 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
17660380 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
17660399 TAAAT
1 TAAAT
17660404 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:17664728 original size:21 final size:22
Alignment explanation
Indices: 17664672--17664731 Score: 97
Period size: 21 Copynumber: 2.8 Consensus size: 22
17664662 CGATTTGAGG
17664672 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
17664693 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
17664715 AAAAA-AATAGAAAATAG
1 AAAAATAAAAGAAAATAG
17664732 TGAAGTCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:17665542 original size:19 final size:19
Alignment explanation
Indices: 17665518--17665560 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17665508 AAAAATAAAT
17665518 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
17665537 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
17665556 TAAAT
1 TAAAT
17665561 TCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:17666316 original size:105 final size:105
Alignment explanation
Indices: 17666141--17666335 Score: 238
Period size: 105 Copynumber: 1.9 Consensus size: 105
17666131 ATACATTGGA
* * **
17666141 CCTTTTGACGCGAAATGAAATGACACCCAAGCACTCCATCCCGGTTGCTCAACCTAACATGCTCT
1 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCATCCCGGTTACTCAACCTAACACACTCT
17666206 CAATTT-TATTATTT-TATTTCTTTTTGTAGAATGTGTTAGC
66 CAATTTAT-TTATTTCTATTT-TTTTTGTAGAATGTGTTAGC
* * **
17666246 CCTTTTGACG-TAAAGTGAAATGACAATCAAGCACTCCA-CCTCGGTTACTCAGTCTAACACACT
1 CCTTTTGACGCGAAA-TGAAATGACAACCAAGCACTCCATCC-CGGTTACTCAACCTAACACACT
17666309 C-CGAATTTATTTATTTCTATTTTTTTT
64 CTC-AATTTATTTATTTCTATTTTTTTT
17666336 CTTTTTTACC
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
104 6 0.08
105 65 0.84
106 6 0.08
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (105 bp):
CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCATCCCGGTTACTCAACCTAACACACTCT
CAATTTATTTATTTCTATTTTTTTTGTAGAATGTGTTAGC
Found at i:17667724 original size:21 final size:22
Alignment explanation
Indices: 17667691--17667752 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
17667681 TTAATTAGTC
* *
17667691 TTAGGATTTTTTTAAATTAGGGT
1 TTAGGA-TATTTTAAATTAGAGT
* *
17667714 TTTGG-TATTTTAAATAAGAGT
1 TTAGGATATTTTAAATTAGAGT
17667735 TTAGGATATTTTAAATTA
1 TTAGGATATTTTAAATTA
17667753 ATGGTTATAG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.53
22 11 0.34
23 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (22 bp):
TTAGGATATTTTAAATTAGAGT
Found at i:17667990 original size:28 final size:28
Alignment explanation
Indices: 17667937--17667990 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
17667927 GATCGAAAAT
* * *
17667937 ATTTAATTATTTTATTTTTATTTTTATA
1 ATTTAATTATTTTATTATAATATTTATA
17667965 ATTTAATTATTTT-TTAATAATATTTA
1 ATTTAATTATTTTATT-ATAATATTTA
17667991 ATTAATCTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 20 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
ATTTAATTATTTTATTATAATATTTATA
Found at i:17684288 original size:49 final size:50
Alignment explanation
Indices: 17684235--17684589 Score: 294
Period size: 49 Copynumber: 7.2 Consensus size: 50
17684225 TTTAAGTCAC
* *
17684235 AACGGCGAACCTTGTACCTCAGAAG-TATAAAGGGAAAGATTTAAGCCGT
1 AACGGCGAACCTAGTACCACAGAAGATATAAAGGGAAAGATTTAAGCCGT
* * * *
17684284 AACGGTGAATCTAGTACCACA-AAGATATAAATGGAAAGATTTAAGCCGC
1 AACGGCGAACCTAGTACCACAGAAGATATAAAGGGAAAGATTTAAGCCGT
* * *
17684333 AACGGCGAATCTAGTACCAC-GAAGATATAAAGGGAAAGGTTTAAGCCGC
1 AACGGCGAACCTAGTACCACAGAAGATATAAAGGGAAAGATTTAAGCCGT
* * * * * * * *
17684382 AACGACAAATCTAGTACCACA-AATATATGAAGGGAAAGGTTTAAGTCGC
1 AACGGCGAACCTAGTACCACAGAAGATATAAAGGGAAAGATTTAAGCCGT
* * ** * * *
17684431 AACGGCGAACCTTGCACCTTAGAAG-CATGAAGGGAAATATTTAAGCC-T
1 AACGGCGAACCTAGTACCACAGAAGATATAAAGGGAAAGATTTAAGCCGT
* * * *
17684479 CAACGGCGAATCTAGTACCAC-GAAGATATGAAGGGAAAGGTTTAAGTCGT
1 -AACGGCGAACCTAGTACCACAGAAGATATAAAGGGAAAGATTTAAGCCGT
* * * * * * ** **
17684529 GATGGCGAACCTTGTACCTCAAAAGCT-CGAAGGGAAAGATTTAAATCGT
1 AACGGCGAACCTAGTACCACAGAAGATATAAAGGGAAAGATTTAAGCCGT
*
17684578 GACGGCGAACCT
1 AACGGCGAACCT
17684590 TGTATCTTAG
Statistics
Matches: 251, Mismatches: 47, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
48 7 0.03
49 237 0.94
50 7 0.03
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (50 bp):
AACGGCGAACCTAGTACCACAGAAGATATAAAGGGAAAGATTTAAGCCGT
Found at i:17684546 original size:147 final size:147
Alignment explanation
Indices: 17684316--17684601 Score: 376
Period size: 147 Copynumber: 1.9 Consensus size: 147
17684306 AGATATAAAT
17684316 GGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATAAAGGGAAAGGTTTAAGCCG
1 GGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATAAAGGGAAAGGTTTAAGCCG
* * * *
17684381 CAACGACAAATCTAGTACCACAAATATAT-GAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
66 CAACGACAAACCTAGTACCACAAA-AGATCGAAGGGAAAGATTTAAATCGCAACGGCGAACCTTG
17684445 CACCTTAGAAGCATGAAG
130 CACCTTAGAAGCATGAAG
* * * *
17684463 GGAAATATTTAAGCCTCAACGGCGAATCTAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCG
1 GGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATAAAGGGAAAGGTTTAAGCCG
** * * * * * * ** *
17684528 TGATGGCGAACCTTGTACCTCAAAAGCTCGAAGGGAAAGATTTAAATCGTGACGGCGAACCTTGT
66 CAACGACAAACCTAGTACCACAAAAGATCGAAGGGAAAGATTTAAATCGCAACGGCGAACCTTGC
*
17684593 ATCTTAGAA
131 ACCTTAGAA
17684602 ACATCGAACC
Statistics
Matches: 118, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
146 2 0.02
147 116 0.98
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (147 bp):
GGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATAAAGGGAAAGGTTTAAGCCG
CAACGACAAACCTAGTACCACAAAAGATCGAAGGGAAAGATTTAAATCGCAACGGCGAACCTTGC
ACCTTAGAAGCATGAAG
Found at i:17684561 original size:98 final size:99
Alignment explanation
Indices: 17684217--17684572 Score: 427
Period size: 98 Copynumber: 3.6 Consensus size: 99
17684207 ACAGGTTTGG
*
17684217 AGGG-AAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAG-TATAAAGGGAAAGATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCTATAAAGGGAAAGATTTAAG
* *
17684280 CCGT-AACGGTGAATCTAGTACCACAAAGATATAA
66 CC-TCAACGGCGAATCTAGTACCACAAAGATATGA
* * * * * * * *
17684314 ATGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAGATATAAAGGGAAAGGTTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCTATAAAGGGAAAGATTTAAG
* * * *
17684378 CCGCAACGACAAATCTAGTACCACAAATATATGA
66 CCTCAACGGCGAATCTAGTACCACAAAGATATGA
* * * *
17684412 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGCACCTTAGAAGC-ATGAAGGGAAATATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCTATAAAGGGAAAGATTTAAG
*
17684476 CCTCAACGGCGAATCTAGTACCACGAAGATATGA
66 CCTCAACGGCGAATCTAGTACCACAAAGATATGA
** * * **
17684510 AGGGAAAGGTTTAAGTCGTGATGGCGAACCTTGTACCTCAAAAGCT-CGAAGGGAAAGATTTAA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCTATAAAGGGAAAGATTTAA
17684573 ATCGTGACGG
Statistics
Matches: 215, Mismatches: 39, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
97 7 0.03
98 204 0.95
99 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.20
Consensus pattern (99 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCTATAAAGGGAAAGATTTAAG
CCTCAACGGCGAATCTAGTACCACAAAGATATGA
Found at i:17689459 original size:141 final size:140
Alignment explanation
Indices: 17689211--17689477 Score: 363
Period size: 141 Copynumber: 1.9 Consensus size: 140
17689201 TAGAAAAAAA
* * * * * * *
17689211 TTGAGAAGATGGTTATGAAAAAATAACTCGAGATTCTGAGAAATCTGATATATGATAATGGGGGT
1 TTGAGAAGATGGTTATGAAAAAATAACCCCAAATTCTAAAAAATCTGATATATGATAATGAGAGT
* * *
17689276 TGAAATTTGTAGGTAAAAAAGCTCCAAGTAGGATATTATGTCATCAAAAGTACAGTACATCGTAT
66 TGAAATTTGTAGGGAAAAAAGCTCCAAGCAGGATATTATGTCAGCAAAAGTACAGTACATCGTAT
17689341 TTTAAAAATT
131 TTTAAAAATT
* * * *
17689351 TTGAGAAGATGGTTCTTAAAAAATAACCCCAAATTCTCAAAAAATCTGATATCTGATAGTGAGAG
1 TTGAGAAGATGGTTATGAAAAAATAACCCCAAATTCT-AAAAAATCTGATATATGATAATGAGAG
* * * *
17689416 TTGAAATTTGTAGGGAAAAACGCTCCAAGCAGGATGTTGTGTCAGCAAAAGTACAGTGCATC
65 TTGAAATTTGTAGGGAAAAAAGCTCCAAGCAGGATATTATGTCAGCAAAAGTACAGTACATC
17689478 CTGCTTGGAG
Statistics
Matches: 108, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
140 32 0.30
141 76 0.70
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (140 bp):
TTGAGAAGATGGTTATGAAAAAATAACCCCAAATTCTAAAAAATCTGATATATGATAATGAGAGT
TGAAATTTGTAGGGAAAAAAGCTCCAAGCAGGATATTATGTCAGCAAAAGTACAGTACATCGTAT
TTTAAAAATT
Found at i:17689773 original size:28 final size:29
Alignment explanation
Indices: 17689696--17689786 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 29
17689686 TATCTCATCA
* *
17689696 AAATAATTTTTTCAGAACATAT-TACGTC
1 AAATTATTTTTTCAGAACACATCTACGTC
* * * *
17689724 AAATT-TATTTTCAAAACTCATCTTC-TC
1 AAATTATTTTTTCAGAACACATCTACGTC
*
17689751 AAATTATTTTTTCAGAACACATC-ACATC
1 AAATTATTTTTTCAGAACACATCTACGTC
17689779 -AATTATTT
1 AAATTATTT
17689787 AGATATATTG
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
27 28 0.56
28 22 0.44
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (29 bp):
AAATTATTTTTTCAGAACACATCTACGTC
Found at i:17689931 original size:30 final size:31
Alignment explanation
Indices: 17689896--17689954 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
17689886 AAATGCAAAT
*
17689896 TTTAGATATATT-GTTTTGAATTTTTAGAAA
1 TTTAGATATATTAGTTTTGAAATTTTAGAAA
*
17689926 TTTAGATATGTTAGTTTTGAAATTTTAGA
1 TTTAGATATATTAGTTTTGAAATTTTAGA
17689955 CTTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (31 bp):
TTTAGATATATTAGTTTTGAAATTTTAGAAA
Found at i:17702414 original size:23 final size:23
Alignment explanation
Indices: 17702384--17702510 Score: 105
Period size: 23 Copynumber: 5.6 Consensus size: 23
17702374 GAATGCTAGC
* *
17702384 GTGCTTACTGTTTTGCACTTTGT
1 GTGCCTACTGTTTTGCACTGTGT
* *
17702407 GTGCTTACTGTTTCGCACT-TCGT
1 GTGCCTACTGTTTTGCACTGT-GT
* * * * *
17702430 GAGCCTACTGATTTGCGCTATAT
1 GTGCCTACTGTTTTGCACTGTGT
* *
17702453 GCGCCTACTG-ATTGCACTGTGT
1 GTGCCTACTGTTTTGCACTGTGT
**
17702475 GTGCCTACTGGATTGCACTGTGT
1 GTGCCTACTGTTTTGCACTGTGT
*
17702498 GTGCTTACTGTTT
1 GTGCCTACTGTTT
17702511 CCCCAGCACT
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.21
23 66 0.78
24 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.41
Consensus pattern (23 bp):
GTGCCTACTGTTTTGCACTGTGT
Found at i:17702507 original size:45 final size:46
Alignment explanation
Indices: 17702389--17702507 Score: 118
Period size: 45 Copynumber: 2.6 Consensus size: 46
17702379 CTAGCGTGCT
* * *
17702389 TACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCACTTCGTGAGCC
1 TACTGATTTGCACTATGTGTGCTTACTGATTCGCACTTCGTGAGCC
* * * * *
17702435 TACTGATTTGCGCTATATGCGCCTACTGATT-GCACTGT-GTGTGCC
1 TACTGATTTGCACTATGTGTGCTTACTGATTCGCACT-TCGTGAGCC
*
17702480 TACTGGA-TTGCACTGTGTGTGCTTACTG
1 TACT-GATTTGCACTATGTGTGCTTACTG
17702508 TTTCCCCAGC
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
45 31 0.53
46 27 0.47
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.39
Consensus pattern (46 bp):
TACTGATTTGCACTATGTGTGCTTACTGATTCGCACTTCGTGAGCC
Found at i:17707109 original size:22 final size:24
Alignment explanation
Indices: 17707067--17707111 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
17707057 ATCGAGATCC
*
17707067 AAGATTTACATCGAAGTTTTGGGA
1 AAGATTTACATCGAAGCTTTGGGA
17707091 AAGA-TTACAT-GAAGCTTTGGG
1 AAGATTTACATCGAAGCTTTGGG
17707112 TACTGATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 6 0.30
24 4 0.20
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (24 bp):
AAGATTTACATCGAAGCTTTGGGA
Found at i:17709523 original size:23 final size:23
Alignment explanation
Indices: 17709493--17709546 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
17709483 ACGCTAGCGC
* *
17709493 GCTTACTGTTTCGCATTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
17709516 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
17709539 GCCTACTG
1 GCTTACTG
17709547 ATTTGCGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:17709587 original size:22 final size:21
Alignment explanation
Indices: 17709535--17709607 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
17709525 TTCGCACTTC
* *
17709535 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGA-TT-CACTGT
*
17709558 GTGCGCCTACTGATTACACTGT
1 GTGTGCCTACTGATT-CACTGT
*
17709580 GTGTGCCTACTGGATTGACTGT
1 GTGTGCCTACT-GATTCACTGT
17709602 GTGTGC
1 GTGTGC
17709608 TTGCTGTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
22 27 0.63
23 16 0.37
ACGTcount: A:0.14, C:0.22, G:0.29, T:0.36
Consensus pattern (21 bp):
GTGTGCCTACTGATTCACTGT
Found at i:17710783 original size:74 final size:74
Alignment explanation
Indices: 17710659--17711100 Score: 695
Period size: 74 Copynumber: 6.0 Consensus size: 74
17710649 TTAGCAAAGA
* * * **
17710659 AAGGACTTGAGGCTTCATCGATAATTTAGATACTAGAAGCTTTACAAGACAAGCTAACAGGTAGT
1 AAGGACTTGAGGCTTCGTCGATAATTTAGATACTAGAAGCTTTACGAGACAAGCTAAGAGACAGT
*
17710724 CTTGAATAG
66 CTTGAACAG
*
17710733 AAGGACTTGAGGCTTCGTCGATAATTTAGATACTAGAAGCTTTACGAGACAGGCTAAGAGACAGT
1 AAGGACTTGAGGCTTCGTCGATAATTTAGATACTAGAAGCTTTACGAGACAAGCTAAGAGACAGT
*
17710798 CTTGAACAT
66 CTTGAACAG
* *
17710807 AAGGACTTGAGGCTTCGTCGATAATTTAGATACTAGAAACTTTACGAGACAAGCTAAGAGACAAT
1 AAGGACTTGAGGCTTCGTCGATAATTTAGATACTAGAAGCTTTACGAGACAAGCTAAGAGACAGT
17710872 CTTGAACAG
66 CTTGAACAG
* * *
17710881 AAAGACTTGAGGCTTCGTCGATAATTTAGATACTAAAAGCTTTACGAGATAAGCTAAGAGACAGT
1 AAGGACTTGAGGCTTCGTCGATAATTTAGATACTAGAAGCTTTACGAGACAAGCTAAGAGACAGT
*
17710946 CTTGAACAT
66 CTTGAACAG
* * *
17710955 AAGAACTTGAGGCTTCGTCGATAATTTAGATACTAGAAACTTTACGAGACAAGCTAAGAGACAAT
1 AAGGACTTGAGGCTTCGTCGATAATTTAGATACTAGAAGCTTTACGAGACAAGCTAAGAGACAGT
17711020 CTTGAACAG
66 CTTGAACAG
* * * *
17711029 AAGGACTAGAGGCTTCGTCGATAATTTAGATACTAAAAGCTTTATGAGACAAGCTAAGAGACAAT
1 AAGGACTTGAGGCTTCGTCGATAATTTAGATACTAGAAGCTTTACGAGACAAGCTAAGAGACAGT
17711094 CTTGAAC
66 CTTGAAC
17711101 TGGATAGCAT
Statistics
Matches: 338, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 338 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (74 bp):
AAGGACTTGAGGCTTCGTCGATAATTTAGATACTAGAAGCTTTACGAGACAAGCTAAGAGACAGT
CTTGAACAG
Found at i:17711796 original size:19 final size:19
Alignment explanation
Indices: 17711756--17711797 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
17711746 ATTTTAAAAC
* *
17711756 AAAATTGAATTTAGTTTTA
1 AAAATTCAATTTAGTTTAA
17711775 AAAATTCAATTTTA-TTTAA
1 AAAATTCAA-TTTAGTTTAA
17711794 AAAA
1 AAAA
17711798 AATTTCTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (19 bp):
AAAATTCAATTTAGTTTAA
Found at i:17713022 original size:22 final size:22
Alignment explanation
Indices: 17712994--17713047 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 22
17712984 TAAAATAAGT
*
17712994 ATAATTCAATAAATTAAAAATA
1 ATAATTCAAAAAATTAAAAATA
17713016 ATAATTCACCAAAAAATTAAAAATA
1 ATAATT---CAAAAAATTAAAAATA
17713041 ATAATTC
1 ATAATTC
17713048 TCCATTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 7 0.25
25 21 0.75
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAATTCAAAAAATTAAAAATA
Found at i:17716971 original size:3 final size:3
Alignment explanation
Indices: 17716963--17716993 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
17716953 TGGATAAGTT
*
17716963 GAA GAA GAA GAA GAA GAA GAA GAC GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
17716994 CGATAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.03, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17718377 original size:22 final size:23
Alignment explanation
Indices: 17718361--17718403 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17718351 TAATATATCT
17718361 TAAAAA-TAAATTAAATATTCCA
1 TAAAAATTAAATTAAATATTCCA
*
17718383 TAAAAATTAAATTAAAGATTC
1 TAAAAATTAAATTAAATATTC
17718404 TATCTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAAATTAAATTAAATATTCCA
Found at i:17719687 original size:40 final size:41
Alignment explanation
Indices: 17719638--17719734 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 41
17719628 CTTTAACTAT
* * * *
17719638 TCATCCAAAATATGATGCTCTCACGTACGAGCTTAAATTGG
1 TCATCCAAAATATGATGCTCTCACGCACAAGCTTAAATCGA
* * * *
17719679 TCA-CCAAAATAAGGTGCTCTTAGGCACAAGCTTAAATCGA
1 TCATCCAAAATATGATGCTCTCACGCACAAGCTTAAATCGA
*
17719719 TCATCTAAAATATGAT
1 TCATCCAAAATATGAT
17719735 TCTCCTAAAC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
40 32 0.73
41 12 0.27
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (41 bp):
TCATCCAAAATATGATGCTCTCACGCACAAGCTTAAATCGA
Found at i:17721790 original size:8 final size:7
Alignment explanation
Indices: 17721763--17721789 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17721753 ACTAAAAGGA
17721763 AAAAAAG
1 AAAAAAG
17721770 AAAAAAG
1 AAAAAAG
17721777 AAAAAAG
1 AAAAAAG
17721784 AAAAAA
1 AAAAAA
17721790 AAACCAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:17729357 original size:21 final size:21
Alignment explanation
Indices: 17729331--17729404 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
17729321 AAGACAAGCT
17729331 TAAAAT-ACAAAAAGTTTTAA
1 TAAAATAACAAAAAGTTTTAA
* *
17729351 TAGAAATAACAAAATA-ATCT--
1 TA-AAATAACAAAA-AGTTTTAA
17729371 TAAAAT-ACAAAAAGTTTTAA
1 TAAAATAACAAAAAGTTTTAA
17729391 TAAAAATAACAAAA
1 T-AAAATAACAAAA
17729405 TAATCTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
17 1 0.02
18 8 0.19
19 4 0.10
20 5 0.12
21 9 0.21
22 14 0.33
23 1 0.02
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.26
Consensus pattern (21 bp):
TAAAATAACAAAAAGTTTTAA
Found at i:17729373 original size:40 final size:40
Alignment explanation
Indices: 17729329--17729413 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
17729319 AAAAGACAAG
*
17729329 CTTAAAATACAAAAAGTTTTAATAGAAATAACAAAATAAT
1 CTTAAAATACAAAAAGTTTTAATAAAAATAACAAAATAAT
17729369 CTTAAAATACAAAAAGTTTTAATAAAAATAACAAAATAAT
1 CTTAAAATACAAAAAGTTTTAATAAAAATAACAAAATAAT
17729409 CTTAA
1 CTTAA
17729414 TTTTCTTATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (40 bp):
CTTAAAATACAAAAAGTTTTAATAAAAATAACAAAATAAT
Found at i:17729413 original size:23 final size:23
Alignment explanation
Indices: 17729347--17729414 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 23
17729337 ACAAAAAGTT
*
17729347 TTAATAGAAATAACAAAATAATC
1 TTAATAAAAATAACAAAATAATC
* *
17729370 -T--T-AAAAT-ACAAAA-AGTT
1 TTAATAAAAATAACAAAATAATC
17729387 TTAATAAAAATAACAAAATAATC
1 TTAATAAAAATAACAAAATAATC
17729410 TTAAT
1 TTAAT
17729415 TTTCTTATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
17 2 0.06
18 7 0.21
19 4 0.12
20 2 0.06
21 5 0.15
22 7 0.21
23 7 0.21
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.29
Consensus pattern (23 bp):
TTAATAAAAATAACAAAATAATC
Found at i:17732585 original size:14 final size:14
Alignment explanation
Indices: 17732566--17732604 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
17732556 TCAGAAAAGT
*
17732566 AAATCATTTTTCAA
1 AAATCATTTTCCAA
*
17732580 AAATCATTTTCCTA
1 AAATCATTTTCCAA
17732594 AAATCATTTTC
1 AAATCATTTTC
17732605 AGTCAAAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:17733285 original size:22 final size:22
Alignment explanation
Indices: 17733260--17733301 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17733250 TGAATTTTTT
17733260 TTTCAATTTTATTTTTCAAAAA
1 TTTCAATTTTATTTTTCAAAAA
*
17733282 TTTCAATTTTTTTTTTCAAA
1 TTTCAATTTTATTTTTCAAA
17733302 TACAAGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTCAATTTTATTTTTCAAAAA
Found at i:17735350 original size:3 final size:3
Alignment explanation
Indices: 17735344--17735370 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17735334 CTGCTGCTGC
17735344 TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT
17735371 GGTGGTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:17736718 original size:15 final size:16
Alignment explanation
Indices: 17736693--17736726 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
17736683 GTAATGTAAT
17736693 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
17736709 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
17736724 TTT
1 TTT
17736727 TTAAAGGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:17741430 original size:18 final size:18
Alignment explanation
Indices: 17741388--17741432 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
17741378 ATGAAATTGT
*
17741388 ATAAATATTATTAAAATG
1 ATAAATTTTATTAAAATG
**
17741406 A-AAATTTTATTTTAATG
1 ATAAATTTTATTAAAATG
17741423 ATAAATTTTA
1 ATAAATTTTA
17741433 AGTTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
ATAAATTTTATTAAAATG
Found at i:17742736 original size:92 final size:92
Alignment explanation
Indices: 17742578--17742763 Score: 268
Period size: 92 Copynumber: 2.0 Consensus size: 92
17742568 CACCAGCTAT
* * * *
17742578 CATAATAAAACACATATTGATAGTTCAGGTACCATACTTGACATTTTCAAAGTATAGGTATCACA
1 CATAAGAAAACACATATTGATAGTTCAGATACCACACTTGACATTTTCAAAGTACAGGTATCACA
* *
17742643 TTGGATATTTTATGAAAGTACAGGTAC
66 TTGAATATTTTATGAAAGTACAAGTAC
*
17742670 CATAAGAAAACACATATTGATAGTTCAGATACCACA-TTGGACATTTTCAAAGTACATGTA-CTA
1 CATAAGAAAACACATATTGATAGTTCAGATACCACACTT-GACATTTTCAAAGTACAGGTATC-A
*
17742733 CATTGAATATTTTATGGAAGTACAAGTAC
64 CATTGAATATTTTATGAAAGTACAAGTAC
17742762 CA
1 CA
17742764 AATGTGACAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
91 3 0.04
92 81 0.96
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (92 bp):
CATAAGAAAACACATATTGATAGTTCAGATACCACACTTGACATTTTCAAAGTACAGGTATCACA
TTGAATATTTTATGAAAGTACAAGTAC
Found at i:17744020 original size:17 final size:17
Alignment explanation
Indices: 17743994--17744034 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
17743984 GATATAAATA
*
17743994 TTACAAATAGGTTGGAT
1 TTACAAATAGGTTCGAT
*
17744011 TTACAGATAGGTTCGAT
1 TTACAAATAGGTTCGAT
17744028 TTACAAA
1 TTACAAA
17744035 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (17 bp):
TTACAAATAGGTTCGAT
Found at i:17751555 original size:16 final size:16
Alignment explanation
Indices: 17751534--17751564 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17751524 TAAAAAAACA
17751534 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
17751550 ATATAACATTTATAA
1 ATATAAAATTTATAA
17751565 AAAAAGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:17754185 original size:3 final size:3
Alignment explanation
Indices: 17754177--17754208 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17754167 ACTTCTCTTT
17754177 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
17754209 AAAGGAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:17754336 original size:3 final size:3
Alignment explanation
Indices: 17754321--17754359 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
17754311 TTCAGAACAT
* * *
17754321 TTC TTC TTG TTC TTC TGC TTC TTC TCC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
17754360 CAGCAGCAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.05, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:17754924 original size:29 final size:29
Alignment explanation
Indices: 17754822--17754925 Score: 117
Period size: 29 Copynumber: 3.6 Consensus size: 29
17754812 TGTTTTTAAT
17754822 AATTAATATTTACTTTTA-TGTC-AAAAAAA
1 AATTAATATTTAC--TTAGTGTCAAAAAAAA
17754851 AATTAATATTTACTT--TGTCAAAAAATAA
1 AATTAATATTTACTTAGTGTCAAAAAA-AA
* * *
17754879 TAATTAATATTTACTTAGTTTGATAAAAAA
1 -AATTAATATTTACTTAGTGTCAAAAAAAA
17754909 AATTAATATTTACTTAG
1 AATTAATATTTACTTAG
17754926 AAAATTCTTG
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
26 4 0.06
27 7 0.10
28 2 0.03
29 45 0.67
30 2 0.03
31 7 0.10
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (29 bp):
AATTAATATTTACTTAGTGTCAAAAAAAA
Found at i:17769800 original size:1 final size:1
Alignment explanation
Indices: 17769794--17769822 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
17769784 TCAAAGCTTC
17769794 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
17769823 TTATAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:17772193 original size:24 final size:24
Alignment explanation
Indices: 17772165--17772215 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
17772155 AATTTGACTC
17772165 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
17772189 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
17772213 AAA
1 AAA
17772216 GATTATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:17777627 original size:7 final size:7
Alignment explanation
Indices: 17777613--17777667 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
17777603 AAAAATTAAA
17777613 TCCAAAG
1 TCCAAAG
*
17777620 TTCAAAG
1 TCCAAAG
17777627 TCCAAA-
1 TCCAAAG
** *
17777633 AACGAAG
1 TCCAAAG
17777640 TCCAAAG
1 TCCAAAG
*
17777647 TCCAAAA
1 TCCAAAG
17777654 T-CAAAG
1 TCCAAAG
17777660 TCCAAAG
1 TCCAAAG
17777667 T
1 T
17777668 AATTAAACAC
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
6 8 0.22
7 28 0.78
ACGTcount: A:0.47, C:0.24, G:0.13, T:0.16
Consensus pattern (7 bp):
TCCAAAG
Found at i:17777645 original size:20 final size:20
Alignment explanation
Indices: 17777615--17777667 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
17777605 AAATTAAATC
*
17777615 CAAAGTTCAAAGTCCAAAAA
1 CAAAGTCCAAAGTCCAAAAA
* *
17777635 CGAAGTCCAAAGTCCAAAAT
1 CAAAGTCCAAAGTCCAAAAA
17777655 CAAAGTCCAAAGT
1 CAAAGTCCAAAGT
17777668 AATTAAACAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.49, C:0.23, G:0.13, T:0.15
Consensus pattern (20 bp):
CAAAGTCCAAAGTCCAAAAA
Found at i:17778405 original size:37 final size:37
Alignment explanation
Indices: 17778282--17778420 Score: 158
Period size: 37 Copynumber: 3.8 Consensus size: 37
17778272 TATCATAGTG
* *
17778282 GCATGCTTAACATGCGAATCA-AA-ATCAGAAATATG
1 GCATGCTTAACATGCGAATCAGAATATCAAAAATATA
*
17778317 GCATGCTTAACATGCGAATCGGAATATCAAAAATATA
1 GCATGCTTAACATGCGAATCAGAATATCAAAAATATA
*
17778354 GCATGCTTAACATGCGAGTCAGAATATC-AAAATAATA
1 GCATGCTTAACATGCGAATCAGAATATCAAAAAT-ATA
** * * * *
17778391 TTATGTTTATCATGCGAATCAAAACATCAA
1 GCATGCTTAACATGCGAATCAGAATATCAA
17778421 TAATTCAATA
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
35 20 0.23
36 7 0.08
37 60 0.68
38 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (37 bp):
GCATGCTTAACATGCGAATCAGAATATCAAAAATATA
Found at i:17788811 original size:11 final size:11
Alignment explanation
Indices: 17788791--17788865 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
17788781 AAGCCTCTCA
*
17788791 TCTTTCCTTTC
1 TCTTTTCTTTC
*
17788802 TCTTTTCTTTT
1 TCTTTTCTTTC
*
17788813 TCTCATTCATTTC
1 TCT-TTTC-TTTC
*
17788826 T-TATTTTTTTC
1 TCT-TTTCTTTC
17788837 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
17788849 TATTTTCTTCC
1 TCTTTTCTTTC
17788860 TCTTTT
1 TCTTTT
17788866 AATCACACTT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
11 28 0.57
12 17 0.35
13 4 0.08
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:17788849 original size:12 final size:12
Alignment explanation
Indices: 17788793--17788857 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 12
17788783 GCCTCTCATC
*
17788793 TTTCCTTTCTCT
1 TTTCTTTTCTCT
17788805 TTTCTTTT-TCT
1 TTTCTTTTCTCT
* *
17788816 CATTCATTTCT-T
1 -TTTCTTTTCTCT
17788828 ATTT-TTTTCTCT
1 -TTTCTTTTCTCT
*
17788840 TTTCTTTTCTAT
1 TTTCTTTTCTCT
17788852 TTTCTT
1 TTTCTT
17788858 CCTCTTTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 11 0.26
12 30 0.71
13 1 0.02
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCTTTTCTCT
Found at i:17788852 original size:22 final size:22
Alignment explanation
Indices: 17788791--17788865 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
17788781 AAGCCTCTCA
* *
17788791 TCTTTCCTTTCTCTTTTCTTTTTC
1 TCTTTTCTTT-TCTATT-TTTTTC
* *
17788815 TC-ATTCATTTCTTATTTTTTTC
1 TCTTTTCTTTTC-TATTTTTTTC
*
17788837 TCTTTTCTTTTCTATTTTCTTCC
1 TCTTTTCTTTTCTATTTT-TTTC
17788860 TCTTTT
1 TCTTTT
17788866 AATCACACTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
22 16 0.39
23 23 0.56
24 2 0.05
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (22 bp):
TCTTTTCTTTTCTATTTTTTTC
Done.