Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 119 of 182
Found at i:38493757 original size:14 final size:14
Alignment explanation
Indices: 38493720--38493758 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
38493710 AATTTACCAT
38493720 TAATGAATAAATAAA
1 TAAT-AATAAATAAA
38493735 T-ATAGATAAATAAA
1 TAATA-ATAAATAAA
38493749 TAATAATAAA
1 TAATAATAAA
38493759 GATTTAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 17 0.77
15 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (14 bp):
TAATAATAAATAAA
Found at i:38494991 original size:29 final size:30
Alignment explanation
Indices: 38494936--38494997 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
38494926 ATATCAAAAT
* *
38494936 TATACATGAATTTTGATTTAATGTGCAATTA
1 TATACATGAACTTTAATTTAA-GTGCAATTA
*
38494967 TATACATGAACTTTAATTTGA-TGCAATTA
1 TATACATGAACTTTAATTTAAGTGCAATTA
38494996 TA
1 TA
38494998 CACGTAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.36
31 18 0.64
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (30 bp):
TATACATGAACTTTAATTTAAGTGCAATTA
Found at i:38495232 original size:29 final size:30
Alignment explanation
Indices: 38495197--38495268 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
38495187 TCAAATAAAA
38495197 AATTCATGTATAAAATTACACA-AAATCA-
1 AATTCATGTATAAAATTACACATAAATCAT
* * *
38495225 AAGTTCATGAATACAATTGCACATTAAATCAT
1 AA-TTCATGTATAAAATTACACA-TAAATCAT
38495257 AATTCATGTATA
1 AATTCATGTATA
38495269 GTTTTGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.06
29 17 0.47
31 15 0.42
32 2 0.06
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (30 bp):
AATTCATGTATAAAATTACACATAAATCAT
Found at i:38495930 original size:24 final size:24
Alignment explanation
Indices: 38495893--38495955 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
38495883 TAAACTAATA
* *
38495893 AGAGTTTTACTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
38495917 AGAGTTTAATTGAATCAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
38495941 AGAGTCTAATTGAAA
1 AGAGTTTAATTGAAA
38495956 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:38507227 original size:30 final size:30
Alignment explanation
Indices: 38507193--38507262 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
38507183 AAAACTCAAA
*
38507193 TTTGACCCTTGAACT-TCCTAAAAAATTGAT
1 TTTGACCCTCGAACTGTCC-AAAAAATTGAT
*
38507223 TTTGACCCTCGAACTGTCCAAAAATTTGAT
1 TTTGACCCTCGAACTGTCCAAAAAATTGAT
38507253 TTTGACCCTC
1 TTTGACCCTC
38507263 AAATTTTCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 34 0.92
31 3 0.08
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (30 bp):
TTTGACCCTCGAACTGTCCAAAAAATTGAT
Found at i:38507276 original size:30 final size:30
Alignment explanation
Indices: 38507210--38507349 Score: 113
Period size: 30 Copynumber: 4.7 Consensus size: 30
38507200 CTTGAACTTC
* * *
38507210 CTAAAAAATTGATTTTGACCCTCGAACTGT
1 CTAAAAAATTGATTTTGACCCTCAAAATTT
* * *
38507240 CCAAAAATTTGATTTTGACCCTCAAATTTT
1 CTAAAAAATTGATTTTGACCCTCAAAATTT
* * *
38507270 CT-AAAAATTGCATTTTAACCTTGAAAATTT
1 CTAAAAAATTG-ATTTTGACCCTCAAAATTT
* ** *
38507300 ATAAAAAATACATTTTGACCCCCAAAATTT
1 CTAAAAAATTGATTTTGACCCTCAAAATTT
* **
38507330 CCAAAATTTTGA-TTTGACCC
1 CTAAAAAATTGATTTTGACCC
38507350 CTTTTTCCTT
Statistics
Matches: 84, Mismatches: 24, Indels: 5
0.74 0.21 0.04
Matches are distributed among these distances:
29 15 0.18
30 63 0.75
31 6 0.07
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (30 bp):
CTAAAAAATTGATTTTGACCCTCAAAATTT
Found at i:38508014 original size:109 final size:104
Alignment explanation
Indices: 38507796--38508022 Score: 247
Period size: 109 Copynumber: 2.1 Consensus size: 104
38507786 CTCAAACGTA
* * * *
38507796 CTGGGTACGATTTTTCTTCGAACCTAACTAATTGAATATCCTATTCAAAAATCGAGGCAATATTC
1 CTGGGTATGATTTTTCTTCGAACATAAATAATTGAATATCCTATTCAAAAATCAAGGCAATATTC
* * ** * *
38507861 TTTTATTTTAGGAAAGTCGAGGAATTATGCCCTAACGTG
66 TGTTATTTTAGGAAACTCGAAAAATTATGCCCGAACATG
* * * *
38507900 CTGGGTATGATTTTTGTTTGAACATAAATAATTGAATATCCTATTCGAAACCAATTAATGCTCAA
1 CTGGGTATGATTTTTCTTCGAACATAAATAATTGAATATCCTATTC-AAA--AATCAA-G-GCAA
** *
38507965 TATTCTGTTATTTTAGGGGACTCGAAAAATTGTGCCCGAACATG
61 TATTCTGTTATTTTAGGAAACTCGAAAAATTATGCCCGAACATG
*
38508009 TTGGGTATGATTTT
1 CTGGGTATGATTTT
38508023 GCCTTGAACC
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
104 41 0.41
105 3 0.03
107 4 0.04
108 1 0.01
109 51 0.51
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (104 bp):
CTGGGTATGATTTTTCTTCGAACATAAATAATTGAATATCCTATTCAAAAATCAAGGCAATATTC
TGTTATTTTAGGAAACTCGAAAAATTATGCCCGAACATG
Found at i:38512523 original size:1 final size:1
Alignment explanation
Indices: 38512517--38512591 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
38512507 AATTTCACCC
* ** * * * * * * *
38512517 AAAAAAAATAAAAAAGGAAAAAAAGAAAGAAAAAGAAAAAAAAAAAGAAAGAAAAAAGAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
38512582 AAAAGAAAAA
1 AAAAAAAAAA
38512592 GGAGAGTCGA
Statistics
Matches: 54, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.85, C:0.01, G:0.12, T:0.01
Consensus pattern (1 bp):
A
Found at i:38512549 original size:19 final size:19
Alignment explanation
Indices: 38512527--38512594 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 19
38512517 AAAAAAAATA
38512527 AAAAAGGAAAAAAAGAAAG
1 AAAAAGGAAAAAAAGAAAG
*
38512546 AAAAAGAAAAAAAAAAAGAAAG
1 AAAAAG---GAAAAAAAGAAAG
*
38512568 AAAAAAGAAAACAAA-AAAG
1 AAAAAGGAAAA-AAAGAAAG
38512587 AAAAAGGA
1 AAAAAGGA
38512595 GAGTCGAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 21 0.51
20 3 0.07
22 17 0.41
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAGGAAAAAAAGAAAG
Found at i:38512562 original size:22 final size:23
Alignment explanation
Indices: 38512534--38512589 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
38512524 ATAAAAAAGG
38512534 AAAAAAAGAAAG-AAAAAGAAAA
1 AAAAAAAGAAAGAAAAAAGAAAA
38512556 AAAAAAAGAAAGAAAAAAGAAAA
1 AAAAAAAGAAAGAAAAAAGAAAA
*
38512579 CAAAAAAGAAA
1 AAAAAAAGAAA
38512590 AAGGAGAGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (23 bp):
AAAAAAAGAAAGAAAAAAGAAAA
Found at i:38512590 original size:12 final size:12
Alignment explanation
Indices: 38512517--38512591 Score: 73
Period size: 12 Copynumber: 6.2 Consensus size: 12
38512507 AATTTCACCC
*
38512517 AAAAAAAATAAA
1 AAAAAAAAGAAA
38512529 AAAGGAAAAA-AAGA
1 AAA--AAAAAGAA-A
*
38512543 AAGAAAAAGAAA
1 AAAAAAAAGAAA
38512555 AAAAAAAAG-AA
1 AAAAAAAAGAAA
*
38512566 AGAAAAAAGAAA
1 AAAAAAAAGAAA
*
38512578 ACAAAAAAGAAA
1 AAAAAAAAGAAA
38512590 AA
1 AA
38512592 GGAGAGTCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
11 10 0.19
12 31 0.58
13 4 0.08
14 8 0.15
ACGTcount: A:0.85, C:0.01, G:0.12, T:0.01
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:38513809 original size:148 final size:149
Alignment explanation
Indices: 38513617--38514092 Score: 471
Period size: 148 Copynumber: 3.2 Consensus size: 149
38513607 CCTGCAACGA
* *
38513617 TGAACCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCTT
1 TGAACCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCTT
* * *
38513682 AGAAGATGTGATGGGAAGGATTGA-GCTCACAACGACGAATCCGGTACTATGAAGATATGAAGGG
66 AAAAGATGTGATGGGAAGGATTGAGGC-CACAACGACGAATCCGGTACCATGAAGACATGAAGGG
38513746 AAAGGTTAAGGCCACATTGG
130 AAAGGTTAAGGCCACATTGG
38513766 TGAACCCGGTA-C-TACGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCT
1 TGAACCCGGTACCTTA-GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCT
* ** *
38513829 TAAAAGATGTGATGGGAAGGATTGAGGCCGCAACGGTGAATCCGGTACCATGAAGACATGAATGG
65 TAAAAGATGTGATGGGAAGGATTGAGGCCACAACGACGAATCCGGTACCATGAAGACATGAAGGG
* * ***
38513894 AAAGGTTGAGGCCGCAACAG
130 AAAGGTTAAGGCCACATTGG
** * * * ** ** ** *
38513914 CAAACCCAGTACCTTAGAAGATGTGATGGG-AAGGATTGAGGCTGCAATGGTAAATTCGGTACCA
1 TGAACCCGGTACCTTAGAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGCGAACCCAATACCT
* * * * * ** * ** *
38513978 T-GAAGATATGAAGGGAAAGTTTGAGGCCACAACGGTGAA-CTCGGTACCACGAAGATGTGATGG
65 TAAAAGATGTGATGGGAAGGATTGAGGCCACAACGACGAATC-CGGTACCATGAAGACATGAAGG
* * **
38514041 GAAAGGTTGAGGCCGCAACGG
129 GAAAGGTTAAGGCCACATTGG
* * *
38514062 TGAA-CCGATAACTTAGAAGATGTGATAGGAA
1 TGAACCCGGTACCTTAGAAGATGTGATGGGAA
38514093 GGATTTAGGT
Statistics
Matches: 276, Mismatches: 44, Indels: 15
0.82 0.13 0.04
Matches are distributed among these distances:
147 24 0.09
148 201 0.73
149 49 0.18
150 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (149 bp):
TGAACCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCTT
AAAAGATGTGATGGGAAGGATTGAGGCCACAACGACGAATCCGGTACCATGAAGACATGAAGGGA
AAGGTTAAGGCCACATTGG
Found at i:38513836 original size:99 final size:98
Alignment explanation
Indices: 38513533--38514269 Score: 588
Period size: 99 Copynumber: 7.5 Consensus size: 98
38513523 AAGGAAACAT
* * *
38513533 GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATGGGA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTA-C-TAGAAGATGTGATGGGA
** *
38513598 AAGGTTGA-GCCTGCAACGATGAACCCGGTACCTTA
64 AAGGTTGAGGCC-GCAACGGCGAACCCAGTACCTTA
*
38513633 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCTTAGAAGATGTGATGGG-
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTA-C-TAGAAGATGTGATGGGA
* * * *
38513697 AAGGATTGA-GCTCACAACGACGAATCCGGTA-C-TA
64 AAGG-TTGAGGC-CGCAACGGCGAACCCAGTACCTTA
* * * * **
38513731 TGAAGATATGAAGGGAAAGGTTAAGGCCACATTGGTGAACCCGGTACTACGAAGATGTGATGGGA
1 -GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACTA-GAAGATGTGATGGGA
*
38513796 AAGGTTGAGGCCGCAACGGCGAACCCAATACCTTA
64 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTA
* * * **
38513831 AAAGATGTGATGGG-AAGGATTGAGGCCGCAACGGTGAATCCGGTACCATGAAGACATGAAT-GG
1 GAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACTA-GAAGATGTG-ATGGG
* *
38513894 AAAGGTTGAGGCCGCAACAGCAAACCCAGTACCTTA
63 AAAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTA
* * * ** * * *
38513930 GAAGATGTGATGGG-AAGGATTGAGGCTGCAATGGTAAATTCGGTACCATGAAGATATGAAGGGA
1 GAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACTA-GAAGATGTGATGGGA
* * * * *
38513994 AAGTTTGAGGCCACAACGGTGAACTCGGTACC--A
64 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTA
* *
38514027 CGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAA-CCGATAACTTAGAAGATGTGATAGG
1 -GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGT-AC-TAGAAGATGTGATGGG
* ** * * ** *
38514091 -AAGGATTTAGGTTGCAACGACGAATCTGGTACCAT-
63 AAAGG-TTGAGGCCGCAACGGCGAACCCAGTACCTTA
** * * ** ** *
38514126 GAAGACATGAAGGGAAAGGTTGAGGCCGCAATGGAAAACCCAATACCTTAGAGGATGTGATGGG-
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTA-C-TAGAAGATGTGATGGGA
** * *
38514190 AAGGATTGAGGCCGCAACGGCGAATTCGGTACCAT-
64 AAGG-TTGAGGCCGCAACGGCGAACCCAGTACCTTA
* * * *
38514225 GAAGATGTAATGGGAAAGG-TGAAGCCTCAAAGGTGAACCCGGTAC
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
38514270 CTTAGGAACA
Statistics
Matches: 524, Mismatches: 93, Indels: 43
0.79 0.14 0.07
Matches are distributed among these distances:
97 10 0.02
98 153 0.29
99 275 0.52
100 85 0.16
101 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (98 bp):
GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACTAGAAGATGTGATGGGAAA
GGTTGAGGCCGCAACGGCGAACCCAGTACCTTA
Found at i:38514060 original size:49 final size:48
Alignment explanation
Indices: 38513533--38514270 Score: 569
Period size: 49 Copynumber: 15.0 Consensus size: 48
38513523 AAGGAAACAT
* * *
38513533 GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGTGAACCCGGTACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACC--A
*
38513583 GAAGATGTGATGGGAAAGGTTGA-GCCTGCAACGATGAACCCGGTACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCC-GCAACGGTGAACCCGGTACC--A
*
38513633 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCAGTACCTTA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACC--A
* ** * *
38513683 GAAGATGTGATGGG-AAGGATTGA-GCTCACAACGACGAATCCGGTACTA
1 GAAGATGTGATGGGAAAGG-TTGAGGC-CGCAACGGTGAACCCGGTACCA
* * * * ** *
38513731 TGAAGATATGAAGGGAAAGGTTAAGGCCACATTGGTGAACCCGGTACTA
1 -GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCA
* **
38513780 CGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAATACCTTA
1 -GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACC--A
* *
38513831 AAAGATGTGATGGG-AAGGATTGAGGCCGCAACGGTGAATCCGGTACCA
1 GAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCA
** * ** *
38513879 TGAAGACATGAAT-GGAAAGGTTGAGGCCGCAACAGCAAACCCAGTACCTTA
1 -GAAGATGTG-ATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACC--A
* * * **
38513930 GAAGATGTGATGGG-AAGGATTGAGGCTGCAATGGTAAATTCGGTACCA
1 GAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCA
* * * * *
38513978 TGAAGATATGAAGGGAAAGTTTGAGGCCACAACGGTGAACTCGGTACCA
1 -GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCA
* *
38514027 CGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAA-CCGATAACTTA
1 -GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGT-AC-CA
* * ** ** * *
38514077 GAAGATGTGATAGG-AAGGATTTAGGTTGCAACGACGAATCTGGTACCA
1 GAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCA
** * * ** **
38514125 TGAAGACATGAAGGGAAAGGTTGAGGCCGCAATGGAAAACCCAATACCTTA
1 -GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACC--A
* * **
38514176 GAGGATGTGATGGG-AAGGATTGAGGCCGCAACGGCGAATTCGGTACCA
1 GAAGATGTGATGGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCA
* * * *
38514224 TGAAGATGTAATGGGAAAGG-TGAAGCCTCAAAGGTGAACCCGGTACC
1 -GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACC
38514271 TTAGGAACAT
Statistics
Matches: 546, Mismatches: 112, Indels: 62
0.76 0.16 0.09
Matches are distributed among these distances:
48 33 0.06
49 263 0.48
50 244 0.45
51 6 0.01
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (48 bp):
GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCA
Found at i:38514520 original size:78 final size:76
Alignment explanation
Indices: 38514388--38515260 Score: 771
Period size: 78 Copynumber: 11.2 Consensus size: 76
38514378 GTTACATCAC
** * *
38514388 CATCCAATCTCTTACCCCAATCATGGGGCAGATTGCAGTCATCCAATCTCTTACCCCGATCATGG
1 CATCCAATCTCTTACCCTGATCAT-GGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGG
*
38514453 GGCAGATTGTAAC
65 GGCAGATTG-AAG
* * *
38514466 CATCCAATCTCTTACCCTGATCATGGGACAAATT-ATAGCCATCCAATCTGTTACCTCGATCATG
1 CATCCAATCTCTTACCCTGATCATGGG-CAGATTGA-AGCCATCCAATCTCTTACCCCGATCATG
*
38514530 GGGCAGATTGCAATCAT
64 GGGCAGATTG--A--AG
* * * * *
38514547 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGTATCCATCCGATCTCTTACCTCGATCATGG
1 CATCCAATCTCTTACCCTGATCAT-GGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGG
*
38514612 GGCAAATTGAAG
65 GGCAGATTGAAG
* * * * *
38514624 AATCCAATCTCTTACCCTAAT-AAGACGGTAGATTGAAGACAATCCAATCTCTTACCCCGATCAT
1 CATCCAATCTCTTACCCTGATCATG--GGCAGATTGAAG-CCATCCAATCTCTTACCCCGATCAT
38514688 GGGGCAGATTGAAG
63 GGGGCAGATTGAAG
* * *
38514702 -AACTCAATCTCTTATCCT-AGTCAGAGGGCAGATTGAAGACACA-CCAATCTCTTACCCCGATC
1 CATC-CAATCTCTTACCCTGA-TCA-TGGGCAGATTGAAG-C-CATCCAATCTCTTACCCCGATC
* * *
38514764 ATAGGGCATATTAAAG
61 ATGGGGCAGATTGAAG
* * * * *
38514780 CATCCAATCTTTTTCCCT-AGTCAGAGGGCAGAATGAAGACACA-CCAATCTCTTACCCCGATTA
1 CATCCAATCTCTTACCCTGA-TCA-TGGGCAGATTGAAG-C-CATCCAATCTCTTACCCCGATCA
*
38514843 TGAGGCAGATTGAAG
62 TGGGGCAGATTGAAG
* * * * * ** * **
38514858 CATCTAATCTCTTACCCCGATCATGGGGTAGATTGAAG-AATCCAATCTTTTACCCTTATTAAAG
1 CATCCAATCTCTTACCCTGATCAT-GGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGG
*
38514922 GGCAAATTGAAG
65 GGCAGATTGAAG
* * *
38514934 ACAATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG-CATCCAATTTCTTACCCTGATCAT
1 -C-ATCCAATCTCTTACCCTGATCATG-GGCAGATTGAAGCCATCCAATCTCTTACCCCGATCAT
*
38514998 GGGGTAGATTGAAG
63 GGGGCAGATTGAAG
* * * * * * *
38515012 AATTCAATCTCTTACCCTAATCA-GAAGGCAAATTAAAGACAATCTAATCTCTTACCCCGATCAT
1 CATCCAATCTCTTACCCTGATCATG--GGCAGATTGAAG-CCATCCAATCTCTTACCCCGATCAT
*
38515076 GAGGCAGATTGAAG
63 GGGGCAGATTGAAG
* * * * * * *
38515090 CACCCAATCTCGTACCCTAATCATAGGGCATATTGACA-TCATTCAATCTCTTACCTCGATCATG
1 CATCCAATCTCTTACCCTGATCAT-GGGCAGATTGA-AGCCATCCAATCTCTTACCCCGATCATG
38515154 GGGCAGATTGAAG
64 GGGCAGATTGAAG
* **
38515167 CATCCAATCTCTTACCATGATCATCGGGCAGATTGAA-ATATCCAATCTCTTACCCCGATCATGG
1 CATCCAATCTCTTACCCTGATCAT-GGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGG
38515231 GGCAGATTGAAG
65 GGCAGATTGAAG
* *
38515243 TTATCCAATCTTTTACCC
1 -CATCCAATCTCTTACCC
38515261 CTAAAATCAA
Statistics
Matches: 658, Mismatches: 108, Indels: 59
0.80 0.13 0.07
Matches are distributed among these distances:
75 3 0.00
76 95 0.14
77 113 0.17
78 370 0.56
79 8 0.01
80 3 0.00
81 63 0.10
82 3 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (76 bp):
CATCCAATCTCTTACCCTGATCATGGGCAGATTGAAGCCATCCAATCTCTTACCCCGATCATGGG
GCAGATTGAAG
Found at i:38514638 original size:38 final size:38
Alignment explanation
Indices: 38514389--38515261 Score: 729
Period size: 38 Copynumber: 22.4 Consensus size: 38
38514379 TTACATCACC
* * *
38514389 ATCCAATCTCTTACCCCAATCATGGGGCAGATTGCAGTC
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-A
**
38514428 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGTAACC
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTG-AAGA
* * * *
38514467 ATCCAATCTCTTACCCTGATCATGGGACAAATT-ATAGCC
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGA-AG-A
* * *
38514506 ATCCAATCTGTTACCTCGATCATGGGGCAGATTGCAATCA
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTG-AA-GA
***
38514546 TCATCCAATCTCTTACCCCGATCATGGGGCAGATTGTATCC
1 --ATCCAATCTCTTACCCCGATCATGGGGCAGATTG-AAGA
* * *
38514587 ATCCGATCTCTTACCTCGATCATGGGGCAAATTGAAGA
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
** * * *
38514625 ATCCAATCTCTTACCCTAAT-AAGACGGTAGATTGAAGACA
1 ATCCAATCTCTTACCCCGATCATG-GGGCAGATTGAAG--A
38514665 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
* *
38514703 A-CTCAATCTCTTA-TCCTAGTCA-GAGGGCAGATTGAAGA
1 ATC-CAATCTCTTACCCCGA-TCATG-GGGCAGATTGAAGA
* * * * *
38514741 CACACCAATCTCTTACCCCGATCATAGGGCATATTAAAGC
1 -A-TCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
** * *
38514781 ATCCAATCT-TTTTCCCTAGTCA-GAGGGCAGAATGAAGA
1 ATCCAATCTCTTACCCCGA-TCATG-GGGCAGATTGAAGA
* * * *
38514819 CACACCAATCTCTTACCCCGATTATGAGGCAGATTGAAGC
1 -A-TCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
* *
38514859 ATCTAATCTCTTACCCCGATCATGGGGTAGATTGAAGA
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
* ** * ** *
38514897 ATCCAATCTTTTACCCTTATTAAAGGGCAAATTGAAGACA
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG--A
* *
38514937 ATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAGC
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
* * *
38514975 ATCCAATTTCTTACCCTGATCATGGGGTAGATTGAAGA
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
* ** * * *
38515013 ATTCAATCTCTTACCCTAATCA-GAAGGCAAATTAAAGACA
1 ATCCAATCTCTTACCCCGATCATG-GGGCAGATTGAAG--A
* * *
38515053 ATCTAATCTCTTACCCCGATCATGAGGCAGATTGAAGC
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
* * ** * * **
38515091 ACCCAATCTCGTACCCTAATCATAGGGCATATTGACATC
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGA-AGA
* * *
38515130 ATTCAATCTCTTACCTCGATCATGGGGCAGATTGAAGC
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
** *
38515168 ATCCAATCTCTTACCATGATCATCGGGCAGATTGAA-A
1 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
*
38515205 TATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGTT
1 -ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-A
*
38515245 ATCCAATCTTTTACCCC
1 ATCCAATCTCTTACCCC
38515262 TAAAATCAAG
Statistics
Matches: 664, Mismatches: 134, Indels: 72
0.76 0.15 0.08
Matches are distributed among these distances:
37 15 0.02
38 291 0.44
39 173 0.26
40 136 0.20
41 16 0.02
42 33 0.05
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (38 bp):
ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA
Found at i:38514809 original size:116 final size:115
Alignment explanation
Indices: 38514388--38515260 Score: 670
Period size: 116 Copynumber: 7.5 Consensus size: 115
38514378 GTTACATCAC
* * * * *
38514388 CATCCAATCTCTTACCCCAATCATGGGGCAGATTGCAGTCATCCAATCTCTTACCC-CGATCATG
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-AATCCAATCTTTTACCCTAG-TCA-G
* * * *
38514452 -GGGCAGATTGTA-ACCATCCAATCTCTTACCCTGATCATG-GGACAAATT-ATAG
63 AGGGCAGATTGAAGACAAT-CAATCTCTTACCCCGATCATGAGG-CAGATTGA-AG
* * * * *
38514504 CCATCCAATCTGTTACCTCGATCATGGGGCAGATTGCAATCATCATCCAATCTCTTACCC-CGAT
1 -CATCCAATCTCTTACCCCGATCATGGGGCAGATTG-AA-GA--ATCCAATCTTTTACCCTAG-T
* * * * * * *
38514568 CATG-GGGCAGATTGTA-TCCATCCGATCTCTTACCTCGATCATGGGGCAAATTGAAG
60 CA-GAGGGCAGATTGAAGACAAT-CAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* ** * * * * *
38514624 AATCCAATCTCTTACCCTAAT-AAGACGGTAGATTGAAGACAATCCAATCTCTTACCC-CGATCA
1 CATCCAATCTCTTACCCCGATCATG-GGGCAGATTGAAG--AATCCAATCTTTTACCCTAG-TCA
* * *
38514687 TG-GGGCAGATTGAAGA-ACTCAATCTCTTA-TCCTAGTCA-GAGGGCAGATTGAAG
62 -GAGGGCAGATTGAAGACAATCAATCTCTTACCCCGA-TCATGA-GGCAGATTGAAG
* * * * * *
38514740 ACACACCAATCTCTTACCCCGATCATAGGGCATATTAAAGCATCCAATCTTTTTCCCTAGTCAGA
1 -CA-TCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTTTTACCCTAGTCAGA
* * *
38514805 GGGCAGAATGAAGACACACCAATCTCTTACCCCGATTATGAGGCAGATTGAAG
64 GGGCAGATTGAAGACA-ATCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * * *
38514858 CATCTAATCTCTTACCCCGATCATGGGGTAGATTGAAGAATCCAATCTTTTACCCTTA-TTAAAG
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTTTTACCC-TAGTCAGAG
*
38514922 GGCAAATTGAAGACAATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
65 GGCAGATTGAAGACAAT-CAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * * * * * *
38514974 CATCCAATTTCTTACCCTGATCATGGGGTAGATTGAAGAATTCAATCTCTTACCCTAATCAGAAG
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTTTTACCCTAGTCAGAGG
* *
38515039 GCAAATTAAAGACAATCTAATCTCTTACCCCGATCATGAGGCAGATTGAAG
66 GCAGATTGAAGACAATC-AATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * ** * * ** * * *
38515090 CACCCAATCTCGTACCCTAATCATAGGGCATATTGACATCATTCAATCTCTTA-CCTCGATCATG
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGA-AGAATCCAATCTTTTACCCTAG-TCA-G
** *
38515154 -GGGCAGATTGAAG-C-ATCCAATCTCTTACCATGATCATCG-GGCAGATTGAAA
63 AGGGCAGATTGAAGACAAT-CAATCTCTTACCCCGATCAT-GAGGCAGATTGAAG
* *
38515205 TATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGTTATCCAATCTTTTACCC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-AATCCAATCTTTTACCC
38515261 CTAAAATCAA
Statistics
Matches: 624, Mismatches: 100, Indels: 65
0.79 0.13 0.08
Matches are distributed among these distances:
114 1 0.00
115 78 0.12
116 287 0.46
117 102 0.16
118 55 0.09
119 31 0.05
120 67 0.11
121 3 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (115 bp):
CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTTTTACCCTAGTCAGAGG
GCAGATTGAAGACAATCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
Found at i:38516102 original size:22 final size:22
Alignment explanation
Indices: 38516077--38516119 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
38516067 AACCCATGAA
38516077 AATA-CAAAAAAAAGGAGCATTG
1 AATAGCAAAAAAAAGG-GCATTG
**
38516099 AATAGCAATCAAAAGGGCATT
1 AATAGCAAAAAAAAGGGCATT
38516120 TGAAAGGTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.53, C:0.12, G:0.19, T:0.16
Consensus pattern (22 bp):
AATAGCAAAAAAAAGGGCATTG
Found at i:38517033 original size:60 final size:59
Alignment explanation
Indices: 38516936--38517103 Score: 174
Period size: 60 Copynumber: 2.8 Consensus size: 59
38516926 GCCCCTATTT
* * * * ** *
38516936 TATCCAAAAACTCAAATTTGACCCCTAAACTTCCTAAAAATTTGATTTTGGCCCTCGAAC
1 TATCAAAAAACTC-ATTTTAACCCCTAAACTTTCTAAAAATTTGATTTTAACCCTCAAAC
* * **
38516996 TATCAAAAAACTCGATTTTAACCCTTAAATTTTCTAAAAATTACATTTTAACCCTCAAAC
1 TATCAAAAAACTC-ATTTTAACCCCTAAACTTTCTAAAAATTTGATTTTAACCCTCAAAC
* * * *
38517056 TTTCTAAAAATTACATTTTAACCCCTAAACTTTCTAAAATTTTGATTT
1 TATCAAAAAACT-CATTTTAACCCCTAAACTTTCTAAAAATTTGATTT
38517104 GTCCTTTTTT
Statistics
Matches: 87, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
60 86 0.99
61 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (59 bp):
TATCAAAAAACTCATTTTAACCCCTAAACTTTCTAAAAATTTGATTTTAACCCTCAAAC
Found at i:38517035 original size:30 final size:30
Alignment explanation
Indices: 38517010--38517094 Score: 143
Period size: 30 Copynumber: 2.8 Consensus size: 30
38517000 AAAAAACTCG
*
38517010 ATTTTAACCCTTAAATTTTCTAAAAATTAC
1 ATTTTAACCCTTAAACTTTCTAAAAATTAC
*
38517040 ATTTTAACCCTCAAACTTTCTAAAAATTAC
1 ATTTTAACCCTTAAACTTTCTAAAAATTAC
*
38517070 ATTTTAACCCCTAAACTTTCTAAAA
1 ATTTTAACCCTTAAACTTTCTAAAA
38517095 TTTTGATTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.39
Consensus pattern (30 bp):
ATTTTAACCCTTAAACTTTCTAAAAATTAC
Found at i:38517219 original size:30 final size:31
Alignment explanation
Indices: 38517138--38517220 Score: 75
Period size: 30 Copynumber: 2.7 Consensus size: 31
38517128 TTTTACCTCA
*
38517138 AAACTTTCATTTTGTTT-TAAATTAATCCTTT
1 AAACTTT-ATTTTGTTTCAAAATTAATCCTTT
*** *
38517169 ATTTTTTA-TTT-CTTCTAAAATTAA-CCTTT
1 AAACTTTATTTTGTTTC-AAAATTAATCCTTT
38517198 AAACTTTATTTTGTTTCAAAATT
1 AAACTTTATTTTGTTTCAAAATT
38517221 GGCCCTTCCT
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
28 2 0.05
29 13 0.33
30 17 0.44
31 7 0.18
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.55
Consensus pattern (31 bp):
AAACTTTATTTTGTTTCAAAATTAATCCTTT
Found at i:38517702 original size:104 final size:106
Alignment explanation
Indices: 38517594--38517844 Score: 267
Period size: 109 Copynumber: 2.3 Consensus size: 106
38517584 TCAAACATAC
* * *
38517594 TGGGTACGATTTTTCTTCGAACCTAAGTAACTGAATATCCTATT-TAA-AAATCGA-G-GCAATA
1 TGGGTATGATTTTTCTT-GAACCTAAGTAA-TGAATATCCTATTCGAATAAATCAATGCGCAATA
* * **
38517655 TTCTTTTATTTTAAGGAAGTCGAGGAATTATACCCTAACGTGT
64 TTCTGTTATTTTAAGGAACTCGAAAAATTATACCCTAACGTGT
* * * * *
38517698 TGGGTATGATTTTTGTTTGAACCTAAATAATTGAATATCCTATTCGGAATCAATTAATGCTCAAT
1 TGGGTATGATTTTT-CTTGAACCTAAGTAA-TGAATATCCTATTC-GAATAAATCAATGCGCAAT
* * * *
38517763 ATTCTGTTATTTTAGGGGACTCGAAAAATTGTACCCTAATGTGT
63 ATTCTGTTATTTTAAGGAACTCGAAAAATTATACCCTAACGTGT
38517807 TGGGTATGATTTTTCCTTGAACCTAAGTAATCGAATAT
1 TGGGTATGATTTTT-CTTGAACCTAAGTAAT-GAATAT
38517845 TTCGTTTAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
104 37 0.31
105 2 0.02
106 2 0.02
107 4 0.03
108 2 0.02
109 73 0.61
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (106 bp):
TGGGTATGATTTTTCTTGAACCTAAGTAATGAATATCCTATTCGAATAAATCAATGCGCAATATT
CTGTTATTTTAAGGAACTCGAAAAATTATACCCTAACGTGT
Found at i:38524090 original size:24 final size:24
Alignment explanation
Indices: 38524062--38524118 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
38524052 TAAGCTAATA
* * *
38524062 AGAGTTTGAGTGAAACAAATAAAT
1 AGAGTTTAAGTAAAACAAATAAAC
*
38524086 AGAGTTTAATTAAAACAAATAAAC
1 AGAGTTTAAGTAAAACAAATAAAC
38524110 AGAGTTTAA
1 AGAGTTTAA
38524119 TTGGAAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (24 bp):
AGAGTTTAAGTAAAACAAATAAAC
Found at i:38524119 original size:24 final size:24
Alignment explanation
Indices: 38524074--38524120 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
38524064 AGTTTGAGTG
*
38524074 AAACAAATAAATAGAGTTTAATTA
1 AAACAAATAAACAGAGTTTAATTA
38524098 AAACAAATAAACAGAGTTTAATT
1 AAACAAATAAACAGAGTTTAATT
38524121 GGAAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTA
Found at i:38532004 original size:24 final size:24
Alignment explanation
Indices: 38531911--38531996 Score: 136
Period size: 24 Copynumber: 3.6 Consensus size: 24
38531901 CGTTATTCTG
38531911 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
38531935 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
* * * *
38531959 GTTCTGGACTCATAGGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
38531983 ATTCTGGGCTCGTA
1 ATTCTGGGCTCGTA
38531997 TGGGCTAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:38537259 original size:1 final size:1
Alignment explanation
Indices: 38537255--38537299 Score: 81
Period size: 1 Copynumber: 45.0 Consensus size: 1
38537245 TATTTTTAAA
*
38537255 CCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
38537300 AAAAAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.02, C:0.98, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:38537957 original size:13 final size:13
Alignment explanation
Indices: 38537939--38537963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38537929 GACAAATACT
38537939 TATTTCACGCGAG
1 TATTTCACGCGAG
38537952 TATTTCACGCGA
1 TATTTCACGCGA
38537964 TTTTCAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (13 bp):
TATTTCACGCGAG
Found at i:38538456 original size:30 final size:30
Alignment explanation
Indices: 38538416--38538483 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
38538406 AACACAAACA
*
38538416 GGGT-AAAAAATGGAGCTGTGGAGAATTT-G
1 GGGTCAAAAAAT-GAGCTGTGGAAAATTTAG
** *
38538445 GGGTCAAAAAATGATTTTTGGAAAATTTAG
1 GGGTCAAAAAATGAGCTGTGGAAAATTTAG
38538475 GGGTCAAAA
1 GGGTCAAAA
38538484 TGTGATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.38, C:0.04, G:0.31, T:0.26
Consensus pattern (30 bp):
GGGTCAAAAAATGAGCTGTGGAAAATTTAG
Found at i:38538466 original size:29 final size:30
Alignment explanation
Indices: 38538434--38538552 Score: 111
Period size: 30 Copynumber: 4.0 Consensus size: 30
38538424 AATGGAGCTG
**
38538434 TGGAGAATTT-GGGGTCAAAAAATGATTTT
1 TGGAGAATTTAGGGGTCAAAATGTGATTTT
*
38538463 TGGAAAATTTAGGGGTCAAAATGTGATTTT
1 TGGAGAATTTAGGGGTCAAAATGTGATTTT
* * *
38538493 T-GAGGAGTTTGGGGGCCAAAATGTGATTTT
1 TGGA-GAATTTAGGGGTCAAAATGTGATTTT
* * *
38538523 TGTGA-AA-TTCGGTGTCAAAATGTAATTTT
1 TG-GAGAATTTAGGGGTCAAAATGTGATTTT
38538552 T
1 T
38538553 ACGAAGTTCG
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
29 30 0.41
30 42 0.57
32 2 0.03
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.37
Consensus pattern (30 bp):
TGGAGAATTTAGGGGTCAAAATGTGATTTT
Found at i:38538551 original size:59 final size:59
Alignment explanation
Indices: 38538475--38538699 Score: 174
Period size: 59 Copynumber: 3.8 Consensus size: 59
38538465 GAAAATTTAG
* * * * *
38538475 GGGTCAAAATGTGATTTTTGA-GGAGTTTGGGGGCCAAAATGTGATTTTTGTGAAATTCG-
1 GGGTCAAAATGTAATTTTT-ACGAAGTTCGAGGGCCAAAATGT-AATTTTGTGAAATTCGA
* ** *
38538534 GTGTCAAAATGTAATTTTTACGAAGTTCGAGGGTTAAAATGTAATTTTGTGAAGTTCGA
1 GGGTCAAAATGTAATTTTTACGAAGTTCGAGGGCCAAAATGTAATTTTGTGAAATTCGA
* * ** *
38538593 GGGTCAAAATGTAATTTTGT--GAAGTTCGAGGGTCAAAATATAAATTTTACGAAGTTC-A
1 GGGTCAAAATGTAATTTT-TACGAAGTTCGAGGGCCAAAATGT-AATTTTGTGAAATTCGA
* * ** * *
38538651 GAGGTTAAAATATAATTTTTGA-GAAGTTTAAGGGTCAAAATGTACTTTT
1 G-GGTCAAAATGTAATTTTT-ACGAAGTTCGAGGGCCAAAATGTAATTTT
38538700 TGAGAAGTTT
Statistics
Matches: 139, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
58 37 0.27
59 83 0.60
60 19 0.14
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (59 bp):
GGGTCAAAATGTAATTTTTACGAAGTTCGAGGGCCAAAATGTAATTTTGTGAAATTCGA
Found at i:38538575 original size:30 final size:29
Alignment explanation
Indices: 38538475--38538708 Score: 206
Period size: 30 Copynumber: 7.9 Consensus size: 29
38538465 GAAAATTTAG
* * * *
38538475 GGGTCAAAATGTGATTTTTGAGGAGTTTGG
1 GGGTCAAAATGTAATTTTT-AGAAGTTCGA
* * * *
38538505 GGGCCAAAATGTGATTTTTGTGAAATTCG-
1 GGGTCAAAATGTAATTTTT-AGAAGTTCGA
*
38538534 GTGTCAAAATGTAATTTTTACGAAGTTCGA
1 GGGTCAAAATGTAATTTTTA-GAAGTTCGA
*
38538564 GGGTTAAAATGTAATTTTGT-GAAGTTCGA
1 GGGTCAAAATGTAATTTT-TAGAAGTTCGA
38538593 GGGTCAAAATGTAATTTTGT-GAAGTTCGA
1 GGGTCAAAATGTAATTTT-TAGAAGTTCGA
* *
38538622 GGGTCAAAATATAAATTTTACGAAGTTC-A
1 GGGTCAAAATGTAATTTTTA-GAAGTTCGA
* * **
38538651 GAGGTTAAAATATAATTTTTGAGAAGTTTAA
1 G-GGTCAAAATGTAATTTTT-AGAAGTTCGA
*
38538682 GGGTCAAAATGTACTTTTTGAGAAGTT
1 GGGTCAAAATGTAATTTTT-AGAAGTT
38538709 TGGGGACCTT
Statistics
Matches: 175, Mismatches: 21, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
28 1 0.01
29 78 0.45
30 92 0.53
31 4 0.02
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTTAGAAGTTCGA
Found at i:38544849 original size:17 final size:17
Alignment explanation
Indices: 38544822--38544857 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
38544812 AAAATTAAAC
38544822 GAAAGAGAGAAAGGAAAT
1 GAAAGAGAGAAA-GAAAT
38544840 GAAA-AGAGAAAGAAAT
1 GAAAGAGAGAAAGAAAT
38544856 GA
1 GA
38544858 GGAAATTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.06
Consensus pattern (17 bp):
GAAAGAGAGAAAGAAAT
Found at i:38545703 original size:20 final size:18
Alignment explanation
Indices: 38545647--38545703 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
38545637 TTTTAAAATT
* *
38545647 TATTAAAATGTTATAAAA
1 TATTAAAATATAATAAAA
* *
38545665 TATTAAAATATCATTAAA
1 TATTAAAATATAATAAAA
38545683 TATTATAAATTATAATAAAA
1 TATTA-AAA-TATAATAAAA
38545703 T
1 T
38545704 TGTTACAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 20 0.62
19 3 0.09
20 9 0.28
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
TATTAAAATATAATAAAA
Found at i:38548372 original size:30 final size:30
Alignment explanation
Indices: 38548337--38548398 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
38548327 AAATTTTTTA
*
38548337 TTTTTTCCCAAAACTTTTACTCCGCTCCCAC
1 TTTTTTCCCAAAAC-TTTACTCCCCTCCCAC
***
38548368 TTTTTTTTTAAAACTTTACTCCCCTCCCAC
1 TTTTTTCCCAAAACTTTACTCCCCTCCCAC
38548398 T
1 T
38548399 CCCATCACCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.19, C:0.35, G:0.02, T:0.44
Consensus pattern (30 bp):
TTTTTTCCCAAAACTTTACTCCCCTCCCAC
Found at i:38550962 original size:21 final size:21
Alignment explanation
Indices: 38550915--38550990 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
38550905 AATAGTGCAG
* *
38550915 ACTTTTACCGATATAAGTGAC
1 ACTTCTACCGATATAAGTCAC
*
38550936 AGTTCTACCGATATAAGTCAC
1 ACTTCTACCGATATAAGTCAC
* * * * **
38550957 TCTTCTATCGAAACAAGTCTT
1 ACTTCTACCGATATAAGTCAC
*
38550978 ACTTTTACCGATA
1 ACTTCTACCGATA
38550991 CTAAAAACTC
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (21 bp):
ACTTCTACCGATATAAGTCAC
Found at i:38555663 original size:24 final size:24
Alignment explanation
Indices: 38555636--38555765 Score: 206
Period size: 24 Copynumber: 5.4 Consensus size: 24
38555626 ATTTAGCCCA
*
38555636 TACGAGCCCAGAATGGTTAGCTCC
1 TACGAGCCCAGAATGGTTAGCTCT
* * *
38555660 TACGAGCCTAGAACGGCTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
38555684 TACGAGCCCAGAACGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
38555708 TACGAGCCCAGAATGGTTAACTCT
1 TACGAGCCCAGAATGGTTAGCTCT
38555732 TACGAGCCCAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
38555756 TACGAGCCCA
1 TACGAGCCCA
38555766 AAATCAGAAT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 97 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (24 bp):
TACGAGCCCAGAATGGTTAGCTCT
Found at i:38559879 original size:24 final size:24
Alignment explanation
Indices: 38559847--38559976 Score: 199
Period size: 24 Copynumber: 5.4 Consensus size: 24
38559837 ATTTAGCCCA
*
38559847 TACGAGCCCAGAATGGTTAACT-T
1 TACGAGCCCAGAATGGTTAGCTCT
38559870 CTACGAGCCCAGAATGGTTAGCTCT
1 -TACGAGCCCAGAATGGTTAGCTCT
38559895 TACGAGCCCAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
* * *
38559919 TACGAGCACAAAATAGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
38559943 TATGAGCCCAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
38559967 TACGAGCCCA
1 TACGAGCCCA
38559977 AAATCAGAAT
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
24 95 0.99
25 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (24 bp):
TACGAGCCCAGAATGGTTAGCTCT
Found at i:38559899 original size:48 final size:48
Alignment explanation
Indices: 38559820--38559980 Score: 207
Period size: 48 Copynumber: 3.3 Consensus size: 48
38559810 CTTTAATTCA
* * * * *
38559820 TTACGAGCACAGACAATATTTAGCCCATACGAGCCCAGAATGGTTAACT-
1 TTACGAGCCCA-A-AATAGTTAGCTCTTACGAGCCCAGAATGGTTAGCTC
* *
38559869 TCTACGAGCCCAGAATGGTTAGCTCTTACGAGCCCAGAATGGTTAGCTC
1 T-TACGAGCCCAAAATAGTTAGCTCTTACGAGCCCAGAATGGTTAGCTC
* *
38559918 TTACGAGCACAAAATAGTTAGCTCTTATGAGCCCAGAATGGTTAGCTC
1 TTACGAGCCCAAAATAGTTAGCTCTTACGAGCCCAGAATGGTTAGCTC
38559966 TTACGAGCCCAAAAT
1 TTACGAGCCCAAAAT
38559981 CAGAATAACG
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
48 87 0.89
49 2 0.02
50 9 0.09
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (48 bp):
TTACGAGCCCAAAATAGTTAGCTCTTACGAGCCCAGAATGGTTAGCTC
Found at i:38559995 original size:28 final size:27
Alignment explanation
Indices: 38559962--38560022 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
38559952 AGAATGGTTA
38559962 GCTCTTACGAGCCCAAAATCAGAATAAC
1 GCTCTTACGAG-CCAAAATCAGAATAAC
** *
38559990 GCTCTTTTGAGCCAGAATCAGAATAAC
1 GCTCTTACGAGCCAAAATCAGAATAAC
38560017 GCTCTT
1 GCTCTT
38560023 TTAAGCCAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (27 bp):
GCTCTTACGAGCCAAAATCAGAATAAC
Found at i:38560015 original size:27 final size:27
Alignment explanation
Indices: 38559978--38560038 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
38559968 ACGAGCCCAA
*
38559978 AATCAGAATAACGCTCTTTTGAGCCAG
1 AATCAGAATAACGCTCTTTTAAGCCAG
38560005 AATCAGAATAACGCTCTTTTAAGCCAG
1 AATCAGAATAACGCTCTTTTAAGCCAG
38560032 AATCAGA
1 AATCAGA
38560039 TTACTCCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (27 bp):
AATCAGAATAACGCTCTTTTAAGCCAG
Found at i:38561794 original size:51 final size:51
Alignment explanation
Indices: 38561715--38561856 Score: 230
Period size: 51 Copynumber: 2.8 Consensus size: 51
38561705 CCGTATAAGA
* * *
38561715 ATTCATATACTCACGATGACACTGAGTCATCGGACCTTTAATTCGTCATGG
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATTCGTCATGG
* *
38561766 ATTCATTTACTCATAATGACACTTAGTCATTGGACCTTTAATTCGTCATGG
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATTCGTCATGG
38561817 ATTCATTTACTCATGATGACACTTAGTCATCGGACACTTT
1 ATTCATTTACTCATGATGACACTTAGTCATCGGAC-CTTT
38561857 CGTTTATAGC
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
51 79 0.95
52 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (51 bp):
ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATTCGTCATGG
Found at i:38565431 original size:30 final size:30
Alignment explanation
Indices: 38565397--38565575 Score: 129
Period size: 30 Copynumber: 6.0 Consensus size: 30
38565387 TTTAGTCTCT
38565397 AAACTTTTTAGAAATTCGATTTTAACCCTC
1 AAACTTTTTAGAAATTCGATTTTAACCCTC
* * *
38565427 AAACTTTTCAAAAATTTGATTTTAACCC-C
1 AAACTTTTTAGAAATTCGATTTTAACCCTC
* *
38565456 TAAACTTTTCCA-AAATTAC-ATTTTAACCCCTA
1 -AAACTTTT-TAGAAATT-CGATTTTAA-CCCTC
*
38565488 AAACTTTTTCA-AAATTAC-ATTTTAA-CCTT
1 AAACTTTTT-AGAAATT-CGATTTTAACCCTC
* * *
38565517 AAACTTTCTAGAAATTTGATTTTGAGCCCT-
1 AAACTTTTTAGAAATTCGATTTT-AACCCTC
* * * *
38565547 ACAGTTTTTAGAAATTTGATTTTGACCCT
1 AAACTTTTTAGAAATTCGATTTTAACCCT
38565576 AAAATTCTCA
Statistics
Matches: 124, Mismatches: 15, Indels: 21
0.77 0.09 0.13
Matches are distributed among these distances:
28 1 0.01
29 26 0.21
30 66 0.53
31 31 0.25
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (30 bp):
AAACTTTTTAGAAATTCGATTTTAACCCTC
Found at i:38565449 original size:60 final size:61
Alignment explanation
Indices: 38565374--38565539 Score: 171
Period size: 60 Copynumber: 2.8 Consensus size: 61
38565364 CTCGAATTTC
* * ** *
38565374 TTCAAGATTATATTTTAGTCTCTAAACTTTTTAGAAATTCGATTTTAA-CCCTCAAAC-TT
1 TTCAAAATTACATTTTAACCTCTAAACTTTTTAGAAATTCGATTTTAACCCCTAAAACTTT
** * *
38565433 TTCAAAAATTTGATTTTAACCCCTAAACTTTTCCA-AAATTAC-ATTTTAACCCCTAAAACTTT
1 TTC-AAAATTACATTTTAACCTCTAAACTTTT-TAGAAATT-CGATTTTAACCCCTAAAACTTT
* *
38565495 TTCAAAATTACATTTTAACCT-TAAACTTTCTAGAAATTTGATTTT
1 TTCAAAATTACATTTTAACCTCTAAACTTTTTAGAAATTCGATTTT
38565540 GAGCCCTACA
Statistics
Matches: 86, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
59 4 0.05
60 52 0.60
61 25 0.29
62 5 0.06
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (61 bp):
TTCAAAATTACATTTTAACCTCTAAACTTTTTAGAAATTCGATTTTAACCCCTAAAACTTT
Found at i:38565492 original size:31 final size:30
Alignment explanation
Indices: 38565332--38565523 Score: 153
Period size: 30 Copynumber: 6.4 Consensus size: 30
38565322 CATAAAAAAG
* *
38565332 CCCCTAAACTTTTCCAAAATTTCATTTTGA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
* * * * *
38565362 -CCCTCGAA-TTTCTTCAAGATTATATTTTAG
1 CCCCT-AAACTTT-TCCAAAATTACATTTTAA
* * *
38565392 TCTCTAAACTTTT-TAGAAATT-CGATTTTAA
1 CCCCTAAACTTTTCCA-AAATTAC-ATTTTAA
* **
38565422 -CCCTCAAACTTTTCAAAAATTTGATTTTAA
1 CCCCT-AAACTTTTCCAAAATTACATTTTAA
38565452 CCCCTAAACTTTTCCAAAATTACATTTTAA
1 CCCCTAAACTTTTCCAAAATTACATTTTAA
*
38565482 CCCCTAAAACTTTTTCAAAATTACATTTTAA
1 CCCCT-AAACTTTTCCAAAATTACATTTTAA
*
38565513 -CCTTAAACTTT
1 CCCCTAAACTTT
38565524 CTAGAAATTT
Statistics
Matches: 130, Mismatches: 21, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
29 18 0.14
30 77 0.59
31 35 0.27
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (30 bp):
CCCCTAAACTTTTCCAAAATTACATTTTAA
Found at i:38565547 original size:60 final size:59
Alignment explanation
Indices: 38565348--38565547 Score: 156
Period size: 60 Copynumber: 3.3 Consensus size: 59
38565338 AACTTTTCCA
** * * ** *
38565348 AAATTTCATTTTGACCCTCGAA-TTTCTTCAAGATTATATTTTAGTCTCTAAACTTTTTAG
1 AAATTTCATTTTGACCCTAAAACTTT-TTCAAAATTACATTTTAACCT-TAAACTTTCTAG
* * ** * *
38565408 AAA-TTCGATTTTAACCCTCAAAC-TTTTCAAAAATTTGATTTTAACCCCTAAACTTTTCCA-
1 AAATTTC-ATTTTGACCCTAAAACTTTTTC-AAAATTACATTTTAA-CCTTAAAC-TTTCTAG
* *
38565468 AAATTACATTTTAACCCCTAAAACTTTTTCAAAATTACATTTTAACCTTAAACTTTCTAG
1 AAATTTCATTTTGA-CCCTAAAACTTTTTCAAAATTACATTTTAACCTTAAACTTTCTAG
*
38565528 AAATTTGATTTTGAGCCCTA
1 AAATTTCATTTTGA-CCCTA
38565548 CAGTTTTTAG
Statistics
Matches: 111, Mismatches: 20, Indels: 18
0.74 0.13 0.12
Matches are distributed among these distances:
59 11 0.10
60 67 0.60
61 28 0.25
62 5 0.05
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.41
Consensus pattern (59 bp):
AAATTTCATTTTGACCCTAAAACTTTTTCAAAATTACATTTTAACCTTAAACTTTCTAG
Found at i:38567549 original size:12 final size:12
Alignment explanation
Indices: 38567534--38567572 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
38567524 CCAAAGAAAA
*
38567534 ATGCAAGAATAG
1 ATGCAAGAACAG
*
38567546 ATGCAAAAACAG
1 ATGCAAGAACAG
*
38567558 TTGCAAGAACAG
1 ATGCAAGAACAG
38567570 ATG
1 ATG
38567573 ACGAGAATGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.49, C:0.13, G:0.23, T:0.15
Consensus pattern (12 bp):
ATGCAAGAACAG
Found at i:38573708 original size:50 final size:50
Alignment explanation
Indices: 38573629--38574162 Score: 557
Period size: 50 Copynumber: 10.8 Consensus size: 50
38573619 TGATACCCTA
* * * *
38573629 AAGATATGAAGGG-AAGATTGAGGCAGCAACGGCGAACCTGGTACCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAG
* * * *
38573678 AAGATGTGATGGGAAAGGTTGAGGTCGCAACGGTGAACCTGATACCAT-G
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAG
* * *
38573727 AAAATATGAAT-GGAAAGGTTGAGGTCGCAACGGCGAATCC-GGTACCTTAG
1 AAGATGTG-ATGGGAAAGGTTGAGGCCGCAACGGCGAA-CCTGGTACCTTAG
* * ** *
38573777 AAGAAGTGATGGGAAAGGTTGAGGTCGCAACAACGAA-CTCGGTACCAT-G
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCT-GGTACCTTAG
* * *
38573826 AAGATATGA-AGGAAAGGTTGAAGCCGCAACGGCGAACCTGGTACCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAG
* * * *
38573875 AAGATGTGATGGGAAAGGTTGATGCCACAACGGTGAA-CTCGATACCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCT-GGTACCTTAG
* * * **
38573925 AAGATGTTATGGGAAAGGTTGAGGCCTCAACGACGAACCCAGTACCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAG
* * * ** **
38573975 AAGATGTGATGGAAAAGGTTGAGGTCACAACGATGAACCTGGTACCACA-
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAG
* * *
38574024 AAGATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAA-CTCGGTACCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCT-GGTACCTTAG
* * * * *
38574074 AAGATGTGATGGGAAAGGTTGAGACTGCAACAGTGAACCCGGTACCTTAG
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAG
*
38574124 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACC
1 AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACC
38574163 CCGTACCATG
Statistics
Matches: 399, Mismatches: 71, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
48 32 0.08
49 108 0.27
50 257 0.64
51 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.18
Consensus pattern (50 bp):
AAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTTAG
Found at i:38574176 original size:99 final size:100
Alignment explanation
Indices: 38573620--38574169 Score: 591
Period size: 99 Copynumber: 5.6 Consensus size: 100
38573610 CAATGAATTT
* * * * * *
38573620 GATACCCTA-AAGATATGAAGGG-AAGATTGAGGCAGCAACGGCGAACCTGGTACCTTAGAAGAT
1 GATACCATAGAAGATATGATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGAT
* * *
38573683 GTGATGGGAAAGGTTGAGGTCGCAACGGTGAACCT
66 GTGATGGGAAAGGTTGAGCTCGCAACAGTGAACCC
* * * *
38573718 GATACCAT-GAAAATATGAAT-GGAAAGGTTGAGGTCGCAACGGCGAATCCGGTACCTTAGAAGA
1 GATACCATAGAAGATATG-ATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGA
* * ** *
38573781 AGTGATGGGAAAGGTTGAGGTCGCAACAACGAACTC
65 TGTGATGGGAAAGGTTGAGCTCGCAACAGTGAACCC
* * * * *
38573817 GGTACCAT-GAAGATATGA-AGGAAAGGTTGAAGCCGCAACGGCGAACCTGGTACCTTAGAAGAT
1 GATACCATAGAAGATATGATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGAT
* * *
38573880 GTGATGGGAAAGGTTGATGC-CACAACGGTGAACTC
66 GTGATGGGAAAGGTTGA-GCTCGCAACAGTGAACCC
* * * * *
38573915 GATACCTTAGAAGATGTTATGGGAAAGGTTGAGGCCTCAACGACGAACCCAGTACCTTAGAAGAT
1 GATACCATAGAAGATATGATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGAT
* * * *
38573980 GTGATGGAAAAGGTTGAGGTCACAAC-GATGAACCT
66 GTGATGGGAAAGGTTGAGCTCGCAACAG-TGAACCC
* * * *
38574015 GGTACCACA-AAGATATGAAGGGAAAGGTTGAGGCCGCAAC-AGCGAACTCGGTACCTTAGAAGA
1 GATACCATAGAAGATATGATGGGAAAGGTTGAGGCCGCAACGA-CGAACCCGGTACCTTAGAAGA
38574078 TGTGATGGGAAAGGTTGAGACT-GCAACAGTGAACCC
65 TGTGATGGGAAAGGTTGAG-CTCGCAACAGTGAACCC
* * * *
38574114 GGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCCGTACC
1 GATACCATAGAAGATATGATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACC
38574170 ATGAAGAAAA
Statistics
Matches: 379, Mismatches: 59, Indels: 26
0.82 0.13 0.06
Matches are distributed among these distances:
98 91 0.24
99 173 0.46
100 114 0.30
101 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (100 bp):
GATACCATAGAAGATATGATGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCTTAGAAGAT
GTGATGGGAAAGGTTGAGCTCGCAACAGTGAACCC
Found at i:38574255 original size:40 final size:41
Alignment explanation
Indices: 38574201--38574416 Score: 193
Period size: 40 Copynumber: 5.4 Consensus size: 41
38574191 AGATTGAAGA
*
38574201 ATCCAATCTTTTACCCTAGTCAGAGGGTAGATTGAAGACAC
1 ATCCAATCTCTTACCCTAGTCAGAGGGTAGATTGAAGACAC
* *
38574242 AT-TAATCTCTTACCCT-GATCA-TGGGTAAGATTGAAG---C
1 ATCCAATCTCTTACCCTAG-TCAGAGGGT-AGATTGAAGACAC
* * * *
38574279 ATCCAATCTTTTACCCTAGTTAGAGGGCAGATTAAAGACAC
1 ATCCAATCTCTTACCCTAGTCAGAGGGTAGATTGAAGACAC
* *
38574320 A-CCAATCTCTTACCC-CGCTCATAGGGGTAGATTGAAG---C
1 ATCCAATCTCTTACCCTAG-TCAGA-GGGTAGATTGAAGACAC
* *
38574358 ATCCAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACATC
1 ATCCAATCTCTTACCCTAGTCAGAGGGTAGATTGAAGACA-C
*
38574400 ATCCTAATCTTTTACCC
1 ATCC-AATCTCTTACCC
38574417 CTAAAGATAA
Statistics
Matches: 138, Mismatches: 20, Indels: 32
0.73 0.11 0.17
Matches are distributed among these distances:
37 3 0.02
38 36 0.26
39 28 0.20
40 40 0.29
41 15 0.11
42 5 0.04
43 11 0.08
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (41 bp):
ATCCAATCTCTTACCCTAGTCAGAGGGTAGATTGAAGACAC
Found at i:38574319 original size:78 final size:79
Alignment explanation
Indices: 38574190--38574417 Score: 307
Period size: 78 Copynumber: 2.9 Consensus size: 79
38574180 CATGACAGGA
* *
38574190 AAGATTGAAGAATCCAATCTTTTACCCTAGTCAGAGGGTAGATTGAAGACACATTAATCTCTTAC
1 AAGATTGAAGCATCCAATCTTTTACCCTAGTCAGAGGGCAGATTGAAGACACATTAATCTCTTAC
*
38574255 CCTGATCAT-GGGT
66 CCCGATCATAGGGT
* * **
38574268 AAGATTGAAGCATCCAATCTTTTACCCTAGTTAGAGGGCAGATTAAAGACACACCAATCTCTTAC
1 AAGATTGAAGCATCCAATCTTTTACCCTAGTCAGAGGGCAGATTGAAGACACATTAATCTCTTAC
*
38574333 CCCGCTCATAGGGGT
66 CCCGATCATA-GGGT
* * *
38574348 -AGATTGAAGCATCCAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACATCATCCTAATCTTT
1 AAGATTGAAGCATCCAATCTTTTACCCTAGTCAGAGGGCAGATTGAAGACA-CAT--TAATCTCT
38574412 TACCCC
63 TACCCC
38574418 TAAAGATAAG
Statistics
Matches: 130, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
78 66 0.51
79 46 0.35
80 6 0.05
82 12 0.09
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (79 bp):
AAGATTGAAGCATCCAATCTTTTACCCTAGTCAGAGGGCAGATTGAAGACACATTAATCTCTTAC
CCCGATCATAGGGT
Found at i:38576424 original size:30 final size:30
Alignment explanation
Indices: 38576368--38576581 Score: 162
Period size: 30 Copynumber: 7.3 Consensus size: 30
38576358 ATAAAAGAGC
* * *
38576368 CCCT-AAACTCTTCCATAATT-TCATTTTGA
1 CCCTCAAACTTTTCCAAAATTAT-ATTTTAA
*
38576397 CCCTCAAA-TTTCTCCAAAATTATATTTTAGT
1 CCCTCAAACTTT-TCCAAAATTATATTTTA-A
** *
38576428 CCC-CAAACTTTTTAAAAATT-TGATCTTAA
1 CCCTCAAACTTTTCCAAAATTAT-ATTTTAA
* *
38576457 CCCTTAAACTTTTCCAAAATCATATTTTAA
1 CCCTCAAACTTTTCCAAAATTATATTTTAA
** *
38576487 CCC-CAAACTTTTTTAAAATTACATTTTAA
1 CCCTCAAACTTTTCCAAAATTATATTTTAA
* *
38576516 CCCTCAAACTTTT-AAAAAGTT-GATTTTAA
1 CCCTCAAACTTTTCCAAAA-TTATATTTTAA
38576545 CCCTCAAAC-TTTCCAAAAATT-TGATTTTAA
1 CCCTCAAACTTTTCC-AAAATTAT-ATTTTAA
38576575 CCC-CAAA
1 CCCTCAAA
38576582 ATTCTCAGAA
Statistics
Matches: 150, Mismatches: 22, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
28 3 0.02
29 60 0.40
30 79 0.53
31 8 0.05
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
CCCTCAAACTTTTCCAAAATTATATTTTAA
Found at i:38576525 original size:59 final size:60
Alignment explanation
Indices: 38576384--38576581 Score: 203
Period size: 59 Copynumber: 3.4 Consensus size: 60
38576374 ACTCTTCCAT
* * *
38576384 AATTTCATTTTGACCCTCAAA-TTTCTCCAAAATTATATTTTAGTCCCCAAACTTTTTAAA
1 AATTTCATTTTAACCCTCAAACTTT-TCCAAAATCATATTTTAGACCCCAAACTTTTTAAA
* * * *
38576444 AATTTGATCTTAACCCTTAAACTTTTCCAAAATCATATTTTA-ACCCCAAACTTTTTTAA
1 AATTTCATTTTAACCCTCAAACTTTTCCAAAATCATATTTTAGACCCCAAACTTTTTAAA
* * **
38576503 AATTACATTTTAACCCTCAAACTTTT-AAAAAGT--TGATTTTA-ACCCTCAAACTTTCCAAA
1 AATTTCATTTTAACCCTCAAACTTTTCCAAAA-TCAT-ATTTTAGACCC-CAAACTTTTTAAA
*
38576562 AATTTGATTTTAACCC-CAAA
1 AATTTCATTTTAACCCTCAAA
38576582 ATTCTCAGAA
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.01
58 18 0.15
59 62 0.53
60 33 0.28
61 3 0.03
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (60 bp):
AATTTCATTTTAACCCTCAAACTTTTCCAAAATCATATTTTAGACCCCAAACTTTTTAAA
Found at i:38576601 original size:59 final size:58
Alignment explanation
Indices: 38576480--38576601 Score: 129
Period size: 59 Copynumber: 2.1 Consensus size: 58
38576470 CCAAAATCAT
*** * * * *
38576480 ATTTTAACCCCAAACTTTTTTAAAATTACATTTTAACCCTCAAACTTTTAAAAAGTTG
1 ATTTTAACCCCAAACTTTCCAAAAATTACATTTTAACCCTCAAAATTTCAAAAACTTC
** *
38576538 ATTTTAACCCTCAAACTTTCCAAAAATTTGATTTTAACCC-CAAAATTCTCAGAAACTTC
1 ATTTTAACCC-CAAACTTTCCAAAAATTACATTTTAACCCTCAAAATT-TCAAAAACTTC
38576597 ATTTT
1 ATTTT
38576602 TCGACCTCGT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
58 16 0.31
59 36 0.69
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (58 bp):
ATTTTAACCCCAAACTTTCCAAAAATTACATTTTAACCCTCAAAATTTCAAAAACTTC
Found at i:38577640 original size:38 final size:38
Alignment explanation
Indices: 38577560--38577652 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 38
38577550 GTACGTGTGT
* * * * *
38577560 TTATCGGGCTAAGTGCCTAGCAGGCTTTATGTTAGTGT
1 TTATCGGGCTTAGTGCCAAGCAGGCTTCATGCTAGTGG
* *
38577598 TTATCGGGCTTAGTGCCAAGCAGGCTTCGTGCTGGTGG
1 TTATCGGGCTTAGTGCCAAGCAGGCTTCATGCTAGTGG
* *
38577636 TTATCGAGCTTAATGCC
1 TTATCGGGCTTAGTGCC
38577653 TAACAAGCTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.33
Consensus pattern (38 bp):
TTATCGGGCTTAGTGCCAAGCAGGCTTCATGCTAGTGG
Found at i:38577663 original size:38 final size:38
Alignment explanation
Indices: 38577598--38577672 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
38577588 ATGTTAGTGT
* * * *
38577598 TTATCGGGCTTAGTGCCAAGCAGGCTTCGTGCTGGTGG
1 TTATCGAGCTTAATGCCAAGCAAGCTTCGTGCAGGTGG
*
38577636 TTATCGAGCTTAATGCCTAA-CAAGCTTCTTGCAGGTG
1 TTATCGAGCTTAATGCC-AAGCAAGCTTCGTGCAGGTG
38577673 TATTGAATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 29 0.94
39 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (38 bp):
TTATCGAGCTTAATGCCAAGCAAGCTTCGTGCAGGTGG
Found at i:38578382 original size:30 final size:30
Alignment explanation
Indices: 38578343--38578408 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
38578333 ATATGACTGG
38578343 TAAGC-TAAGTATCCTTTATACGAGCTTAC
1 TAAGCATAAGTATCCTTTATACGAGCTTAC
38578372 TAAGCATAAGTATCCTTTATACGAGCTTAC
1 TAAGCATAAGTATCCTTTATACGAGCTTAC
38578402 TAAGCAT
1 TAAGCAT
38578409 TAGTTGCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 5 0.14
30 31 0.86
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (30 bp):
TAAGCATAAGTATCCTTTATACGAGCTTAC
Found at i:38582914 original size:13 final size:12
Alignment explanation
Indices: 38582894--38582941 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
38582884 GTAAAAAACT
38582894 TAATAAATAATA
1 TAATAAATAATA
38582906 TAGATAAATAAATA
1 TA-ATAAAT-AATA
* *
38582920 TATAAAAATTATA
1 TA-ATAAATAATA
38582933 TAATAAATA
1 TAATAAATA
38582942 TACTTATCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 7 0.24
13 11 0.38
14 11 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
TAATAAATAATA
Found at i:38583067 original size:20 final size:21
Alignment explanation
Indices: 38583044--38583086 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
38583034 ATTTTTATAA
*
38583044 TTTTGTATTAATGTTTA-ATT
1 TTTTGTATAAATGTTTATATT
* *
38583064 TTTTTTATAAATTTTTATATT
1 TTTTGTATAAATGTTTATATT
38583085 TT
1 TT
38583087 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTGTATAAATGTTTATATT
Found at i:38583088 original size:17 final size:15
Alignment explanation
Indices: 38583066--38583100 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
38583056 GTTTAATTTT
38583066 TTTTATAAATTTTTATA
1 TTTTAT-AATTTTTA-A
38583083 TTTTATAATTTTTAA
1 TTTTATAATTTTTAA
38583098 TTT
1 TTT
38583101 CTTTTACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 8 0.44
17 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATAATTTTTAA
Found at i:38583105 original size:19 final size:19
Alignment explanation
Indices: 38583052--38583117 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
38583042 AATTTTGTAT
* *
38583052 TAATGTTTAATTTTTTTTA
1 TAATTTTTAATTTATTTTA
38583071 TAAATTTTT-A--TATTTTA
1 T-AATTTTTAATTTATTTTA
*
38583088 TAATTTTTAATTTCTTTTA
1 TAATTTTTAATTTATTTTA
*
38583107 CAATTTTTAAT
1 TAATTTTTAAT
38583118 CTTTTTTAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 7 0.18
17 8 0.21
19 18 0.46
20 6 0.15
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (19 bp):
TAATTTTTAATTTATTTTA
Found at i:38583939 original size:17 final size:17
Alignment explanation
Indices: 38583905--38583947 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
38583895 AAGAAGATGT
38583905 AAGGTTAAAGGTAAATGG
1 AAGGTT-AAGGTAAATGG
*
38583923 GAGGTTAAGG-AAGATGG
1 AAGGTTAAGGTAA-ATGG
38583940 AAGGTTAA
1 AAGGTTAA
38583948 AAGTCAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.21
Consensus pattern (17 bp):
AAGGTTAAGGTAAATGG
Found at i:38604157 original size:18 final size:18
Alignment explanation
Indices: 38604121--38604158 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
38604111 TAGATTTGAA
*
38604121 AAAAGTAAAAGCAAAAAG
1 AAAAGTAAAAGAAAAAAG
38604139 AAAAG-AAAAGAAAAGAAG
1 AAAAGTAAAAGAAAA-AAG
38604157 AA
1 AA
38604159 TTGGTGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (18 bp):
AAAAGTAAAAGAAAAAAG
Found at i:38607880 original size:70 final size:71
Alignment explanation
Indices: 38607804--38607956 Score: 254
Period size: 71 Copynumber: 2.2 Consensus size: 71
38607794 AGCCTCCCAA
*
38607804 GTATCGGTAGAAGTCCC-AGCCACAACTTCTTTACTCTCTAAAGTTTGTTCTACCGATAGAACTC
1 GTATCGGTAGAAGTCCCGAGCCACAACTTCTTTACTCTCTAAAGTTTGTTCTACCCATAGAACTC
38607868 TTGGTT
66 TTGGTT
* * * *
38607874 GTATCGGTAGAAGTCCCGGGCCACAACTTTTTTACTCTCTAGAGTTTGTTCTACCCATAGAAGTC
1 GTATCGGTAGAAGTCCCGAGCCACAACTTCTTTACTCTCTAAAGTTTGTTCTACCCATAGAACTC
38607939 TTGGTT
66 TTGGTT
38607945 GTATCGGTAGAA
1 GTATCGGTAGAA
38607957 CCAAGAGATG
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 17 0.22
71 60 0.78
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (71 bp):
GTATCGGTAGAAGTCCCGAGCCACAACTTCTTTACTCTCTAAAGTTTGTTCTACCCATAGAACTC
TTGGTT
Found at i:38620022 original size:20 final size:20
Alignment explanation
Indices: 38619977--38620015 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
38619967 AATTAAGTTA
*
38619977 GTTTAATTAATTTAATTATG
1 GTTTAATTAACTTAATTATG
38619997 GTTTAATTAACTTAATTAT
1 GTTTAATTAACTTAATTAT
38620016 TTCTTAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.54
Consensus pattern (20 bp):
GTTTAATTAACTTAATTATG
Found at i:38620850 original size:12 final size:13
Alignment explanation
Indices: 38620820--38620852 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38620810 AATTTAATAT
38620820 TTAATATTTAAACA
1 TTAAT-TTTAAACA
38620834 TTAATTTTAAACA
1 TTAATTTTAAACA
38620847 -TAATTT
1 TTAATTT
38620853 GTTTCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 8 0.42
14 5 0.26
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAATTTTAAACA
Found at i:38621872 original size:30 final size:31
Alignment explanation
Indices: 38621838--38621905 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
38621828 TTTTTGACCC
*
38621838 AATTTTATACTTAAACTTGACA-CTTTTCTT
1 AATTTGATACTTAAACTTGACATCTTTTCTT
* * * *
38621868 AATTTGCTACTTGAACTTGGCATTTTTTTCTT
1 AATTTGATACTTAAACTTGACA-TCTTTTCTT
38621900 AATTTG
1 AATTTG
38621906 GTACCTAAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 18 0.58
32 13 0.42
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.51
Consensus pattern (31 bp):
AATTTGATACTTAAACTTGACATCTTTTCTT
Found at i:38625409 original size:11 final size:12
Alignment explanation
Indices: 38625382--38625406 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38625372 ACAGAATCAT
38625382 AATCTCTAAAAA
1 AATCTCTAAAAA
38625394 AATCTCTAAAAA
1 AATCTCTAAAAA
38625406 A
1 A
38625407 TCTGAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AATCTCTAAAAA
Found at i:38626558 original size:20 final size:20
Alignment explanation
Indices: 38626533--38626596 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
38626523 ATAAAAACGC
*
38626533 ATAAAAATAACATCAAAACA
1 ATAAAAATAACACCAAAACA
38626553 ATAAAAATAACAACCAAAACA
1 ATAAAAATAAC-ACCAAAACA
*
38626574 GCA-ACAAAATAACAGCAAAACA
1 --ATA-AAAATAACACCAAAACA
38626596 A
1 A
38626597 CATCAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 12 0.32
21 8 0.21
22 9 0.24
23 9 0.24
ACGTcount: A:0.69, C:0.19, G:0.03, T:0.09
Consensus pattern (20 bp):
ATAAAAATAACACCAAAACA
Found at i:38626585 original size:23 final size:23
Alignment explanation
Indices: 38626536--38626675 Score: 87
Period size: 23 Copynumber: 6.3 Consensus size: 23
38626526 AAAACGCATA
* *
38626536 AAAATAACATC-AAAACAA-TA-
1 AAAATAACAACAAAAACAACAAC
* *
38626556 AAAATAACAACCAAAACAGCAAC
1 AAAATAACAACAAAAACAACAAC
* *
38626579 AAAATAACAGC-AAAACAACATC
1 AAAATAACAACAAAAACAACAAC
* **
38626601 -AAA-AACAACAAAAATAGTAAC
1 AAAATAACAACAAAAACAACAAC
* *
38626622 AAAAACAACAACAAAAATAACAAC
1 -AAAATAACAACAAAAACAACAAC
* *
38626646 AAAACTATC-ACGAAAACAACAATC
1 AAAA-TAACAACAAAAACAACAA-C
38626670 AAAATA
1 AAAATA
38626676 GTAAAAAAAC
Statistics
Matches: 94, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
20 15 0.16
21 16 0.17
22 10 0.11
23 30 0.32
24 23 0.24
ACGTcount: A:0.68, C:0.20, G:0.03, T:0.09
Consensus pattern (23 bp):
AAAATAACAACAAAAACAACAAC
Found at i:38626608 original size:43 final size:43
Alignment explanation
Indices: 38626536--38626625 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
38626526 AAAACGCATA
* * *
38626536 AAAATAACATCAAAACAATAAAAATAACAACCAAAACAGCAAC
1 AAAATAACAGCAAAACAACAAAAATAACAACAAAAACAGCAAC
* * *
38626579 AAAATAACAGCAAAACAACATCAAA-AACAACAAAAATAGTAAC
1 AAAATAACAGCAAAACAACA-AAAATAACAACAAAAACAGCAAC
38626622 AAAA
1 AAAA
38626626 ACAACAACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
43 37 0.93
44 3 0.08
ACGTcount: A:0.69, C:0.19, G:0.03, T:0.09
Consensus pattern (43 bp):
AAAATAACAGCAAAACAACAAAAATAACAACAAAAACAGCAAC
Found at i:38626614 original size:55 final size:55
Alignment explanation
Indices: 38626536--38626667 Score: 151
Period size: 55 Copynumber: 2.4 Consensus size: 55
38626526 AAAACGCATA
* * * * *
38626536 AAAATAACATCAAAACAATAAAAATAACAACCAAAACAGCAAC-AAAATAACAGC
1 AAAACAACATCAAAACAACAAAAATAACAACAAAAACAACAACAAAAATAACAAC
**
38626590 AAAACAACATCAAAAACAACAAAAATAGTAACAAAAACAACAACAAAAATAACAAC
1 AAAACAACATC-AAAACAACAAAAATAACAACAAAAACAACAACAAAAATAACAAC
*
38626646 AAAACTATCA-CGAAAACAACAA
1 AAAAC-AACATC-AAAACAACAA
38626668 TCAAAATAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
54 10 0.15
55 27 0.41
56 26 0.39
57 3 0.05
ACGTcount: A:0.68, C:0.20, G:0.03, T:0.08
Consensus pattern (55 bp):
AAAACAACATCAAAACAACAAAAATAACAACAAAAACAACAACAAAAATAACAAC
Found at i:38626631 original size:24 final size:24
Alignment explanation
Indices: 38626604--38626649 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
38626594 CAACATCAAA
**
38626604 AACAACAAAAATAGTAACAAAAAC
1 AACAACAAAAATAACAACAAAAAC
38626628 AACAACAAAAATAACAACAAAA
1 AACAACAAAAATAACAACAAAA
38626650 CTATCACGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.74, C:0.17, G:0.02, T:0.07
Consensus pattern (24 bp):
AACAACAAAAATAACAACAAAAAC
Found at i:38626642 original size:21 final size:21
Alignment explanation
Indices: 38626600--38626644 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
38626590 AAAACAACAT
*
38626600 CAAAAACAACAAAAATAGTAA
1 CAAAAACAACAAAAATAATAA
38626621 CAAAAACAACAACAAA-AATAA
1 CAAAAACAACAA-AAATAATAA
38626642 CAA
1 CAA
38626645 CAAAACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.73, C:0.18, G:0.02, T:0.07
Consensus pattern (21 bp):
CAAAAACAACAAAAATAATAA
Found at i:38626710 original size:17 final size:17
Alignment explanation
Indices: 38626677--38626710 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38626667 ATCAAAATAG
*
38626677 TAAAAAAACCAAAACAA
1 TAAAAAAAACAAAACAA
*
38626694 TAAAAAAAACAACACAA
1 TAAAAAAAACAAAACAA
38626711 AAACAGCAAT
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:0.76, C:0.18, G:0.00, T:0.06
Consensus pattern (17 bp):
TAAAAAAAACAAAACAA
Found at i:38634342 original size:12 final size:13
Alignment explanation
Indices: 38634324--38634353 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
38634314 TTTTCAATTA
38634324 ACTTTGCCTTTAC
1 ACTTTGCCTTTAC
38634337 -CTTTGCCTTTAC
1 ACTTTGCCTTTAC
38634349 ACTTT
1 ACTTT
38634354 AACTCTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.30, G:0.07, T:0.50
Consensus pattern (13 bp):
ACTTTGCCTTTAC
Found at i:38647888 original size:43 final size:42
Alignment explanation
Indices: 38647815--38648002 Score: 153
Period size: 43 Copynumber: 4.4 Consensus size: 42
38647805 CGAGTCATAG
**
38647815 GTCTTCCTTTTAAATGTAATTTCATGCTCATTCCAAGAAATGA
1 GTCTTCC-TTTAAACATAATTTCATGCTCATTCCAAGAAATGA
* * * * *
38647858 GTCTTCCTTTAAAACATAATCTCATTCTCATCCCGAGACATGA
1 GTCTTCCTTT-AAACATAATTTCATGCTCATTCCAAGAAATGA
* * ** *
38647901 GTCTTCCTTTAAACATATTTTCATGCTCATTCCGAGTCACGA
1 GTCTTCCTTTAAACATAATTTCATGCTCATTCCAAGAAATGA
* * ** * *
38647943 ATCTTCCATTTATACA-AATTCTCATGCTCAACCCGAGACATGA
1 GTCTTCC-TTTAAACATAATT-TCATGCTCATTCCAAGAAATGA
*
38647986 GTCTTCCATTTATACAT
1 GTCTTCC-TTTAAACAT
38648003 CAAGTGTTTC
Statistics
Matches: 120, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
42 38 0.32
43 82 0.68
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (42 bp):
GTCTTCCTTTAAACATAATTTCATGCTCATTCCAAGAAATGA
Found at i:38647927 original size:85 final size:86
Alignment explanation
Indices: 38647815--38648002 Score: 220
Period size: 85 Copynumber: 2.2 Consensus size: 86
38647805 CGAGTCATAG
* ** * *
38647815 GTCTTCCTTTTAAATGTAATTTCATGCTCATTCCAAGAAATGAGTCTTCC-TTTAAAACATAA-T
1 GTCTTCCATTTAAACATAATTTCATGCTCATTCCAAGAAACGAATCTTCCATTT-AAACA-AATT
* *
38647878 CTCATTCTCATCCCGAGACATGA
64 CTCATGCTCAACCCGAGACATGA
* * ** *
38647901 GTCTTCC-TTTAAACATATTTTCATGCTCATTCCGAGTCACGAATCTTCCATTTATACAAATTCT
1 GTCTTCCATTTAAACATAATTTCATGCTCATTCCAAGAAACGAATCTTCCATTTAAACAAATTCT
38647965 CATGCTCAACCCGAGACATGA
66 CATGCTCAACCCGAGACATGA
*
38647986 GTCTTCCATTTATACAT
1 GTCTTCCATTTAAACAT
38648003 CAAGTGTTTC
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
84 2 0.02
85 67 0.77
86 18 0.21
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (86 bp):
GTCTTCCATTTAAACATAATTTCATGCTCATTCCAAGAAACGAATCTTCCATTTAAACAAATTCT
CATGCTCAACCCGAGACATGA
Found at i:38651731 original size:27 final size:27
Alignment explanation
Indices: 38651693--38651748 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
38651683 ATGAAAATTC
38651693 AAGGTAAAATTTGAGTACTAAAGTGTA
1 AAGGTAAAATTTGAGTACTAAAGTGTA
* *
38651720 AAGGTAAAATTTTAGTGCTAAAGTGTA
1 AAGGTAAAATTTGAGTACTAAAGTGTA
38651747 AA
1 AA
38651749 TAACACTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (27 bp):
AAGGTAAAATTTGAGTACTAAAGTGTA
Found at i:38660271 original size:28 final size:26
Alignment explanation
Indices: 38660240--38660304 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
38660230 TAGTGATTTA
38660240 ATATAAATATATAATTATTATTTAATAT
1 ATATAAATATATAA-TATT-TTTAATAT
* *
38660268 ATATAATTAATATAATATTTTTTATAT
1 ATATAAAT-ATATAATATTTTTAATAT
38660295 A-AT-AATATAT
1 ATATAAATATAT
38660305 TTGGGTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 4 0.12
25 2 0.06
26 2 0.06
27 8 0.24
28 11 0.33
29 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATAAATATATAATATTTTTAATAT
Found at i:38660278 original size:24 final size:25
Alignment explanation
Indices: 38660235--38660287 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
38660225 TGAATTAGTG
*
38660235 ATTTAATATAAATATATAAT-TATT
1 ATTTAATATAAATATATAATATAAT
*
38660259 ATTTAATATATATA-ATTAATATAAT
1 ATTTAATATAAATATA-TAATATAAT
38660284 ATTT
1 ATTT
38660288 TTTATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 17 0.68
25 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTAATATAAATATATAATATAAT
Found at i:38660283 original size:18 final size:18
Alignment explanation
Indices: 38660237--38660285 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 18
38660227 AATTAGTGAT
38660237 TTAATATAA-ATATATAA
1 TTAATATAATATATATAA
*
38660254 TTATTATTTAATATATATAA
1 TTA--ATATAATATATATAA
38660274 TTAATATAATAT
1 TTAATATAATAT
38660286 TTTTTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.11
18 8 0.30
19 5 0.19
20 11 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATATAATATATATAA
Found at i:38667732 original size:6 final size:6
Alignment explanation
Indices: 38667721--38667787 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
38667711 AATTTGATTG
** **
38667721 AATTTA AATTTA AA-GCA AATTTA AATTTAA AAGATA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA AATTTA
*
38667769 AA-ATA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
38667788 AATAAATTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
5 7 0.15
6 37 0.77
7 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (6 bp):
AATTTA
Found at i:38667762 original size:36 final size:35
Alignment explanation
Indices: 38667721--38667796 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 35
38667711 AATTTGATTG
*
38667721 AATTTAAATTTAAAGCAAATTTAAATTTAAAAGATA
1 AATTTAAATTTAAAACAAATTTAAATTTAAAA-ATA
*
38667757 AATTTAAATTTAAAATAAATTTAAATTTAAAAATA
1 AATTTAAATTTAAAACAAATTTAAATTTAAAAATA
38667792 AATTT
1 AATTT
38667797 GAATCAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 8 0.21
36 30 0.79
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (35 bp):
AATTTAAATTTAAAACAAATTTAAATTTAAAAATA
Found at i:38667788 original size:17 final size:18
Alignment explanation
Indices: 38667721--38667796 Score: 111
Period size: 17 Copynumber: 4.3 Consensus size: 18
38667711 AATTTGATTG
**
38667721 AATTTAAATTT-AAAGCA
1 AATTTAAATTTAAAAATA
38667738 AATTTAAATTTAAAAGATA
1 AATTTAAATTTAAAA-ATA
38667757 AATTTAAATTT-AAAATA
1 AATTTAAATTTAAAAATA
38667774 AATTTAAATTTAAAAATA
1 AATTTAAATTTAAAAATA
38667792 AATTT
1 AATTT
38667797 GAATCAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
17 25 0.46
18 17 0.31
19 12 0.22
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (18 bp):
AATTTAAATTTAAAAATA
Found at i:38668184 original size:52 final size:52
Alignment explanation
Indices: 38668122--38668370 Score: 163
Period size: 52 Copynumber: 5.2 Consensus size: 52
38668112 CTATCCAACT
*
38668122 TTACTTCAATTTCAAGAGGATAGGAAATGATATTTAATGCTTTTTCTAGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAATGATATTTAATGCTTTATCTAGCTC
* * *
38668174 TTACTTCAATTTC-AGAGAGAT---AAA-G--A-CT--TG--TTATCCAACT-
1 TTACTTCAATTTCAAGAG-GATAGGAAATGATATTTAATGCTTTATCTAGCTC
* * *
38668214 TTACTTCGATTTCAAAAGGATAGGAAATGATATTTAATGCTTCATCTAGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAATGATATTTAATGCTTTATCTAGCTC
* *
38668266 TTACTTCAATTTC-AGAGAGAT---AAA-G--A-CT--TG--TTATCCAGCTC
1 TTACTTCAATTTCAAGAG-GATAGGAAATGATATTTAATGCTTTATCTAGCTC
** * * *
38668307 -TACTTCAATTTCAAGAGGATAAAAAAATTATGTTTGATGCTTTATCTAGCTC
1 TTACTTCAATTTCAAGAGGAT-AGGAAATGATATTTAATGCTTTATCTAGCTC
38668359 TTACTTCAATTT
1 TTACTTCAATTT
38668371 TAGAGAGATA
Statistics
Matches: 149, Mismatches: 19, Indels: 57
0.66 0.08 0.25
Matches are distributed among these distances:
40 30 0.20
41 23 0.15
43 7 0.05
44 4 0.03
45 2 0.01
46 3 0.02
47 1 0.01
48 3 0.02
49 8 0.05
50 2 0.01
51 14 0.09
52 41 0.28
53 11 0.07
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (52 bp):
TTACTTCAATTTCAAGAGGATAGGAAATGATATTTAATGCTTTATCTAGCTC
Found at i:38668394 original size:93 final size:92
Alignment explanation
Indices: 38668070--38669035 Score: 631
Period size: 93 Copynumber: 10.4 Consensus size: 92
38668060 ATGTCGAGGT
* * * * *
38668070 TTTATCTTA-CTCTTACTACAACTTCAGAGATATAAAGGCTTGCTATCCAACTTTACTTCAATTT
1 TTTATC-TAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTT
**
38668134 CAAGAGGATAGGAAATGATATTTAATGC
65 CAAGAGGATAAAAAATGATATTTAATGC
* *
38668162 TTTTTCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTTCGATTTC
1 TTTATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTC
* **
38668227 AAAAGGATAGGAAATGATATTTAATGC
66 AAGAGGATAAAAAATGATATTTAATGC
* * *
38668254 TTCATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAGCTCTACTTCAATTTC
1 TTTATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTC
* * *
38668319 AAGAGGATAAAAAAATTATGTTTGATGC
66 AAGAGGAT-AAAAAATGATATTTAATGC
* **
38668347 TTTATCTAGCTCTTACTTCAATTTTAGAGAGATAAAGACTTGTTATCCATTTTTACTTCAATTTC
1 TTTATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTC
* **
38668412 AAGAGGATAAAAAATTGACATTTGAA-AA
66 AAGAGGATAAAAAA-TGATATTT-AATGC
* * * * * *
38668440 TTCATCTTGCTCTTACTAT-AACTTT-AGAGTGATGAAGA-TTCATTATCCATCTTTACTAT-AA
1 TTTATCTAGCTCTTACT-TCAA-TTTCAGAGAGATAAAGACTT-GTTATCCAACTTTACT-TCAA
* * **
38668501 CTTCAAGAGGATAAAAAAAATGACATTTGAA-AA
62 TTTCAAGAGGAT--AAAAAATGATATTT-AATGC
* * * * * * * *
38668534 TTCATCTTGCTCTTACTAT-AACTTCAGAGAGATGAATA-TTCATTATCAAACTTTACTAT-AAC
1 TTTATCTAGCTCTTACT-TCAATTTCAGAGAGATAAAGACTT-GTTATCCAACTTTACT-TCAAT
* **
38668596 TTCAAGAGGATAAAAAAATGACATTTGAA-AA
63 TTCAAGAGGAT-AAAAAATGATATTT-AATGC
* * * * * *
38668627 TTCATCTTGCTCTTACTAT-AACTTCAGAGAGATGAAGA-TTCATTATCCAACTTTACTAT-AAC
1 TTTATCTAGCTCTTACT-TCAATTTCAGAGAGATAAAGACTT-GTTATCCAACTTTACT-TCAAT
* * * **
38668689 TTCAAGAGGATAAAAATTTAACATTTGAA-AA
63 TTCAAGAGGATAAAAA-ATGATATTT-AATGC
* * * * * *
38668720 TTCATCTTGCTCTTACTAT-AACTTCAGAGAGATGAAGA-TTCATTATCCAACTTTACTAT-AAC
1 TTTATCTAGCTCTTACT-TCAATTTCAGAGAGATAAAGACTT-GTTATCCAACTTTACT-TCAAT
* * **
38668782 TTCAAGAGGATAAAAATTTGACATTTGAA-AA
63 TTCAAGAGGATAAAAA-ATGATATTT-AATGC
* * * * * * *
38668813 TTCATCTTGCGCTTACTAT-AACTTCAGAGAGATGAAGA-TTCATTATCCAACTTTACTAT-AAC
1 TTTATCTAGCTCTTACT-TCAATTTCAGAGAGATAAAGACTT-GTTATCCAACTTTACT-TCAAT
*
38668875 TTCAAGAGGATAAAAAATTGACATTTGAA-GC
63 TTCAAGAGGATAAAAAA-TGATATTT-AATGC
* * * *
38668906 TTTATCTTA-CGCTTACTAT-AACTTCAGAGAGATAAAGA-TTCATTATCCATCTTTACTAT-AA
1 TTTATC-TAGCTCTTACT-TCAATTTCAGAGAGATAAAGACTT-GTTATCCAACTTTACT-TCAA
* * * *
38668967 CTTCAAGAGGATAAAAATTGACATTTGAA-AC
62 TTTCAAGAGGATAAAAAATGATATTT-AATGC
* * *
38668998 TTCATCTTGCTCTTACTAT-AACTTCAGAGAGATAAAGA
1 TTTATCTAGCTCTTACT-TCAATTTCAGAGAGATAAAGA
38669036 TTTTTCCCTT
Statistics
Matches: 799, Mismatches: 60, Indels: 30
0.90 0.07 0.03
Matches are distributed among these distances:
91 3 0.00
92 206 0.26
93 499 0.62
94 85 0.11
95 6 0.01
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (92 bp):
TTTATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTC
AAGAGGATAAAAAATGATATTTAATGC
Found at i:38668684 original size:40 final size:39
Alignment explanation
Indices: 38668639--38668882 Score: 137
Period size: 40 Copynumber: 5.5 Consensus size: 39
38668629 CATCTTGCTC
38668639 TTACTATAACTTCAGAGAGATGAAGATTCATTATCCAACT
1 TTACTATAACTTCA-AGAGATGAAGATTCATTATCCAACT
* * **
38668679 TTACTATAACTTCAAGAGGATAAAAATTTAACATTTGAAAATTCATCTTGCT
1 TTACTATAACTTCAAGA-GATGAAGA-TT--CA-TT----A-TC--C-AACT
38668731 CTTACTATAACTTCAGAGAGATGAAGATTCATTATCCAACT
1 -TTACTATAACTTCA-AGAGATGAAGATTCATTATCCAACT
* * * *
38668772 TTACTATAACTTCAAGAGGATAAAAATTTGACATTTGAAAATTCATCTT
1 TTACTATAACTTCAAGA-GATGAAGA-TT--CA-TT----ATCCAAC-T
38668821 GCGCTTACTATAACTTCAGAGAGATGAAGATTCATTATCCAACT
1 ----TTACTATAACTTCA-AGAGATGAAGATTCATTATCCAACT
38668865 TTACTATAACTTCAAGAG
1 TTACTATAACTTCAAGAG
38668883 GATAAAAAAT
Statistics
Matches: 158, Mismatches: 16, Indels: 61
0.67 0.07 0.26
Matches are distributed among these distances:
39 10 0.06
40 54 0.34
41 6 0.04
42 1 0.01
43 4 0.03
44 7 0.04
45 6 0.04
48 6 0.04
49 7 0.04
50 4 0.03
51 1 0.01
52 6 0.04
53 40 0.25
54 6 0.04
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (39 bp):
TTACTATAACTTCAAGAGATGAAGATTCATTATCCAACT
Found at i:38668734 original size:373 final size:370
Alignment explanation
Indices: 38668184--38669037 Score: 1087
Period size: 373 Copynumber: 2.3 Consensus size: 370
38668174 TTACTTCAAT
* * * * * ** *
38668184 TTCAGAGAGATAAAGACTT-GTTATCCAACTTTACT-TCGATTTCAAAAGGATAGGAAATGATAT
1 TTCAGAGAGATAAAGA-TTCATTATCAAACTTTACTAT-AACTTCAAGAGGATAAAAAATGACAT
** * * * *
38668247 TT-AATGCTTCATCTAGCTCTTACT-TCAATTTCAGAGAGATAAAGACTTGTTATCCAGCTCTAC
64 TTGAA-AATTCATCTTGCTCTTACTAT-AACTTCAGAGAGATAAAGA-TTATTATCCAACTCTAC
* ** *** * * *
38668310 TTCAATTTCAAGAGGATAAAAAAATTATGTTTGATGCTTTATCTAGCTCTTACT-TCAATTTTAG
126 TTCAACTTCAAGAGGATAAAAAAATTACATTTGAAAATTCATCTAGCTCTTACTAT-AACTTCAG
* ** *
38668374 AGAGATAAAGACTT-GTTATCCATTTTTACT-TCAATTTCAAGAGGATAAAAAATTGACATTTGA
190 AGAGATAAAGA-TTCATTATCCAACTTTACTAT-AACTTCAAGAGGATAAAAAATTGACATTTGA
* * * *
38668437 AAATTCATCTTGCTCTTACTATAACTTTAGAGTGATGAAGATTCATTATCCATCTTTACTATAAC
253 AAATTCATCTTGCGCTTACTATAACTTCAGAGAGATGAAGATTCATTATCCAACTTTACTATAAC
* *
38668502 TTCAAGAGGATAAAAAAAATGACATTTGAAAATTCATCTTGCTCTTACTATAAC
318 TTCAAGAGGAT-AAAAAAATGACATTTGAAAATTCATCTTACGCTTACTATAAC
* *
38668556 TTCAGAGAGATGAATATTCATTATCAAACTTTACTATAACTTCAAGAGGATAAAAAAATGACATT
1 TTCAGAGAGATAAAGATTCATTATCAAACTTTACTATAACTTCAAGAGGAT-AAAAAATGACATT
* *
38668621 TGAAAATTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGATTCATTATCCAACTTTACTAT
65 TGAAAATTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATT-ATTATCCAACTCTACT-T
* *
38668686 -AACTTCAAGAGGAT-AAAAATTTAACATTTGAAAATTCATCTTGCTCTTACTATAACTTCAGAG
128 CAACTTCAAGAGGATAAAAAAATT-ACATTTGAAAATTCATCTAGCTCTTACTATAACTTCAGAG
* *
38668749 AGATGAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGATAAAAATTTGACATTTGAAAAT
192 AGATAAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGATAAAAAATTGACATTTGAAAAT
38668814 TCATCTTGCGCTTACTATAACTTCAGAGAGATGAAGATTCATTATCCAACTTTACTATAACTTCA
257 TCATCTTGCGCTTACTATAACTTCAGAGAGATGAAGATTCATTATCCAACTTTACTATAACTTCA
* ** *
38668879 AGAGGATAAAAAATTGACATTTGAAGCTTTATCTTACGCTTACTATAAC
322 AGAGGATAAAAAAATGACATTTGAAAATTCATCTTACGCTTACTATAAC
* * *
38668928 TTCAGAGAGATAAAGATTCATTATCCATCTTTACTATAACTTCAAGAGGATAAAAATTGACATTT
1 TTCAGAGAGATAAAGATTCATTATCAAACTTTACTATAACTTCAAGAGGATAAAAAATGACATTT
*
38668993 GAAACTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATT
66 GAAAATTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATT
38669038 TTTCCCTTTT
Statistics
Matches: 419, Mismatches: 52, Indels: 23
0.85 0.11 0.05
Matches are distributed among these distances:
371 58 0.14
372 133 0.32
373 222 0.53
374 6 0.01
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (370 bp):
TTCAGAGAGATAAAGATTCATTATCAAACTTTACTATAACTTCAAGAGGATAAAAAATGACATTT
GAAAATTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTATTATCCAACTCTACTTCAA
CTTCAAGAGGATAAAAAAATTACATTTGAAAATTCATCTAGCTCTTACTATAACTTCAGAGAGAT
AAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGATAAAAAATTGACATTTGAAAATTCAT
CTTGCGCTTACTATAACTTCAGAGAGATGAAGATTCATTATCCAACTTTACTATAACTTCAAGAG
GATAAAAAAATGACATTTGAAAATTCATCTTACGCTTACTATAAC
Found at i:38668806 original size:186 final size:187
Alignment explanation
Indices: 38668170--38669037 Score: 1082
Period size: 186 Copynumber: 4.7 Consensus size: 187
38668160 GCTTTTTCTA
* * * * *
38668170 GCTCTTACT-TCAATTTCAGAGAGATAAAGACTT-GTTATCCAACTTTACT-TCGATTTCAAAAG
1 GCTCTTACTAT-AACTTCAGAGAGATAAAGA-TTCATTATCCAACTTTACTAT-AACTTCAAGAG
** * ** * * *
38668232 GATAGGAAA-TGATATTT-AATGCTTCATCTAGCTCTTACT-TCAATTTCAGAGAGATAAAGACT
63 GATAAAAAATTGACATTTGAA-AATTCATCTTGCTCTTACTAT-AACTTCAGAGAGATGAAGA-T
* * * * ** *** * *
38668294 T-GTTATCCAGCTCTACT-TCAATTTCAAGAGGATAAAAAAATT-ATGTTTGATGCTTTATCTA
125 TCATTATCCAACTTTACTAT-AACTTCAAGAGGATAAAAAAATTGACATTTGAAAATTCATCTT
* * * ** *
38668355 GCTCTTACT-TCAATTTTAGAGAGATAAAGACTT-GTTATCCATTTTTACT-TCAATTTCAAGAG
1 GCTCTTACTAT-AACTTCAGAGAGATAAAGA-TTCATTATCCAACTTTACTAT-AACTTCAAGAG
* *
38668417 GATAAAAAATTGACATTTGAAAATTCATCTTGCTCTTACTATAACTTTAGAGTGATGAAGATTCA
63 GATAAAAAATTGACATTTGAAAATTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGATTCA
* *
38668482 TTATCCATCTTTACTATAACTTCAAGAGGATAAAAAAAATGACATTTGAAAATTCATCTT
128 TTATCCAACTTTACTATAACTTCAAGAGGATAAAAAAATTGACATTTGAAAATTCATCTT
* * *
38668542 GCTCTTACTATAACTTCAGAGAGATGAATATTCATTATCAAACTTTACTATAACTTCAAGAGGAT
1 GCTCTTACTATAACTTCAGAGAGATAAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGAT
*
38668607 AAAAAAATGACATTTGAAAATTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGATTCATTA
66 AAAAAATTGACATTTGAAAATTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGATTCATTA
* *
38668672 TCCAACTTTACTATAACTTCAAGAGGAT-AAAAATTTAACATTTGAAAATTCATCTT
131 TCCAACTTTACTATAACTTCAAGAGGATAAAAAAATTGACATTTGAAAATTCATCTT
*
38668728 GCTCTTACTATAACTTCAGAGAGATGAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGAT
1 GCTCTTACTATAACTTCAGAGAGATAAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGAT
* *
38668793 AAAAATTTGACATTTGAAAATTCATCTTGCGCTTACTATAACTTCAGAGAGATGAAGATTCATTA
66 AAAAAATTGACATTTGAAAATTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGATTCATTA
** *
38668858 TCCAACTTTACTATAACTTCAAGAGGAT-AAAAAATTGACATTTGAAGCTTTATCTT
131 TCCAACTTTACTATAACTTCAAGAGGATAAAAAAATTGACATTTGAAAATTCATCTT
* * *
38668914 ACGCTTACTATAACTTCAGAGAGATAAAGATTCATTATCCATCTTTACTATAACTTCAAGAGGAT
1 GCTCTTACTATAACTTCAGAGAGATAAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGAT
* *
38668979 -AAAAATTGACATTTGAAACTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATT
66 AAAAAATTGACATTTGAAAATTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGATT
38669038 TTTCCCTTTT
Statistics
Matches: 613, Mismatches: 61, Indels: 18
0.89 0.09 0.03
Matches are distributed among these distances:
185 121 0.20
186 336 0.55
187 154 0.25
188 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (187 bp):
GCTCTTACTATAACTTCAGAGAGATAAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGAT
AAAAAATTGACATTTGAAAATTCATCTTGCTCTTACTATAACTTCAGAGAGATGAAGATTCATTA
TCCAACTTTACTATAACTTCAAGAGGATAAAAAAATTGACATTTGAAAATTCATCTT
Found at i:38669254 original size:100 final size:99
Alignment explanation
Indices: 38669080--38669259 Score: 247
Period size: 100 Copynumber: 1.8 Consensus size: 99
38669070 GCCGTTGCGA
* * *
38669080 TCTTAGATCTTTCCCGTCGTGTCTTTGAGGTACACGGTCCGCCGTTGCGACTTAGACCTTTCCCT
1 TCTTAGATCTTTCCCATCATGTCTTTGAGGTACACGGTCCGCCATTGCGACTTAGACCTTTCCCT
*
38669145 TTTCTGTTTTTGTGGTACTAGATTCACCATTGTGG
66 TTTC-GGTTTTGTGGTACTAGATTCACCATTGTGG
* * *
38669180 TCTTAGATCTTTCCCATCATG-CTTCTGAGGTACATGGTCTGCCATTGTGACTTAGACCTTT-CC
1 TCTTAGATCTTTCCCATCATGTCTT-TGAGGTACACGGTCCGCCATTGCGACTTAGACCTTTCCC
*
38669243 TTGTTGGGTTTTGTGGT
65 TT-TTCGGTTTTGTGGT
38669260 GCTGAGACCT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
99 17 0.24
100 53 0.76
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.41
Consensus pattern (99 bp):
TCTTAGATCTTTCCCATCATGTCTTTGAGGTACACGGTCCGCCATTGCGACTTAGACCTTTCCCT
TTTCGGTTTTGTGGTACTAGATTCACCATTGTGG
Found at i:38670539 original size:8 final size:9
Alignment explanation
Indices: 38670512--38670551 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
38670502 CTATTTTGTT
*
38670512 TTTTTCTTG
1 TTTTTCTTC
38670521 TTTTTGCTTC
1 TTTTT-CTTC
38670531 TTTTT-TTC
1 TTTTTCTTC
38670539 TTTTTCTTC
1 TTTTTCTTC
38670548 TTTT
1 TTTT
38670552 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 8 0.29
9 12 0.43
10 8 0.29
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:38677953 original size:6 final size:6
Alignment explanation
Indices: 38677942--38678008 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
38677932 AATTTGATTG
** **
38677942 AATTTA AATTTA AA-GCA AATTTA AATTTAA AAGATA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA AATTTA
*
38677990 AA-ATA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
38678009 AATAAATTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
5 7 0.15
6 37 0.77
7 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (6 bp):
AATTTA
Found at i:38677983 original size:36 final size:35
Alignment explanation
Indices: 38677942--38678017 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 35
38677932 AATTTGATTG
*
38677942 AATTTAAATTTAAAGCAAATTTAAATTTAAAAGATA
1 AATTTAAATTTAAAACAAATTTAAATTTAAAA-ATA
*
38677978 AATTTAAATTTAAAATAAATTTAAATTTAAAAATA
1 AATTTAAATTTAAAACAAATTTAAATTTAAAAATA
38678013 AATTT
1 AATTT
38678018 GAATCAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 8 0.21
36 30 0.79
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (35 bp):
AATTTAAATTTAAAACAAATTTAAATTTAAAAATA
Found at i:38678009 original size:17 final size:18
Alignment explanation
Indices: 38677942--38678017 Score: 111
Period size: 17 Copynumber: 4.3 Consensus size: 18
38677932 AATTTGATTG
**
38677942 AATTTAAATTT-AAAGCA
1 AATTTAAATTTAAAAATA
38677959 AATTTAAATTTAAAAGATA
1 AATTTAAATTTAAAA-ATA
38677978 AATTTAAATTT-AAAATA
1 AATTTAAATTTAAAAATA
38677995 AATTTAAATTTAAAAATA
1 AATTTAAATTTAAAAATA
38678013 AATTT
1 AATTT
38678018 GAATCAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
17 25 0.46
18 17 0.31
19 12 0.22
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (18 bp):
AATTTAAATTTAAAAATA
Found at i:38681645 original size:23 final size:23
Alignment explanation
Indices: 38681608--38681664 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
38681598 GAGAATAAAG
* *
38681608 TGACATATCGTAAGTTAGGAGCA
1 TGACATCTCGAAAGTTAGGAGCA
38681631 TGACATCTCGAAAGTTAGGAGCA
1 TGACATCTCGAAAGTTAGGAGCA
*
38681654 CGACATCTCGA
1 TGACATCTCGA
38681665 GTACTCGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (23 bp):
TGACATCTCGAAAGTTAGGAGCA
Found at i:38682763 original size:30 final size:32
Alignment explanation
Indices: 38682697--38682763 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
38682687 TTAAACATAA
* * *
38682697 TTTTTTTAAAAAAAATCATTTGAACACTTGTT
1 TTTTTTTAAAAAAAATCATTTCAAAACTTGTC
38682729 TTTTTTTAAAAAAAA-C-TTTCAAAACTT-TC
1 TTTTTTTAAAAAAAATCATTTCAAAACTTGTC
*
38682758 CTTTTT
1 TTTTTT
38682764 CTGTCCCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 6 0.19
30 9 0.29
31 1 0.03
32 15 0.48
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.49
Consensus pattern (32 bp):
TTTTTTTAAAAAAAATCATTTCAAAACTTGTC
Found at i:38683908 original size:42 final size:42
Alignment explanation
Indices: 38683844--38684048 Score: 270
Period size: 42 Copynumber: 4.9 Consensus size: 42
38683834 ATAACCCAGG
* ** * * *
38683844 TTCAATCTGCCCTCTGAATGGGGTAAAAGATTAGATGGTGCC
1 TTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATGGTGTC
* * * *
38683886 TTCAATCTGCCCTCTGGTTGGGGTAAAAGATTGGATGGTTTG
1 TTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATGGTGTC
* *
38683928 TTCAATCTGCCCTTTGGCTAGGGTAAAAGATTAGATGGTGTC
1 TTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATGGTGTC
*
38683970 TTTAATCTGCCCTTTGGTTAGGGTAAAAGATTGGAT-G-GTC
1 TTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATGGTGTC
*
38684010 TTCAATGTGCCCTTTGGTTAGGGTAAAAGATTGGATGGT
1 TTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATGGT
38684049 AGCTCCGCTT
Statistics
Matches: 144, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
40 37 0.26
41 2 0.01
42 105 0.73
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (42 bp):
TTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATGGTGTC
Found at i:38688851 original size:21 final size:21
Alignment explanation
Indices: 38688827--38688894 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
38688817 TCCTTTATTA
38688827 TTCTTACTGCTTCGACCATTT
1 TTCTTACTGCTTCGACCATTT
** * *
38688848 TTC-TACT--TAAGTCCTTTAT
1 TTCTTACTGCTTCGACCATT-T
38688867 TATTCTTACTGCTTCGACCATTT
1 T--TCTTACTGCTTCGACCATTT
38688890 TTCTT
1 TTCTT
38688895 GAAACACCCG
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 6 0.18
19 2 0.06
20 4 0.12
21 9 0.27
22 4 0.12
23 2 0.06
24 6 0.18
ACGTcount: A:0.16, C:0.25, G:0.07, T:0.51
Consensus pattern (21 bp):
TTCTTACTGCTTCGACCATTT
Found at i:38688856 original size:42 final size:42
Alignment explanation
Indices: 38688809--38688893 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
38688799 ACAGCATTGA
38688809 TACTTAAGTCCTTTATTATTCTTACTGCTTCGACCATTTTTC
1 TACTTAAGTCCTTTATTATTCTTACTGCTTCGACCATTTTTC
38688851 TACTTAAGTCCTTTATTATTCTTACTGCTTCGACCATTTTTC
1 TACTTAAGTCCTTTATTATTCTTACTGCTTCGACCATTTTTC
38688893 T
1 T
38688894 TGAAACACCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.19, C:0.24, G:0.07, T:0.51
Consensus pattern (42 bp):
TACTTAAGTCCTTTATTATTCTTACTGCTTCGACCATTTTTC
Found at i:38697721 original size:10 final size:10
Alignment explanation
Indices: 38697706--38697734 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
38697696 AAGAATCATT
38697706 ATTTATATTA
1 ATTTATATTA
38697716 ATTTATATTA
1 ATTTATATTA
38697726 ATTTATATT
1 ATTTATATT
38697735 TCATGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTATATTA
Found at i:38699900 original size:14 final size:14
Alignment explanation
Indices: 38699881--38699908 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38699871 ATATTAAAAT
38699881 GGAAATAAATTAAG
1 GGAAATAAATTAAG
38699895 GGAAATAAATTAAG
1 GGAAATAAATTAAG
38699909 TTTGATAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (14 bp):
GGAAATAAATTAAG
Found at i:38700394 original size:16 final size:16
Alignment explanation
Indices: 38700373--38700403 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38700363 AAATTTGAGA
*
38700373 TTTAATTTTTATATAT
1 TTTAATTTTGATATAT
38700389 TTTAATTTTGATATA
1 TTTAATTTTGATATA
38700404 ATTTGATACC
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:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTAATTTTGATATAT
Found at i:38701315 original size:3 final size:3
Alignment explanation
Indices: 38701307--38701361 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
38701297 AAATGAAATA
38701307 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38701355 AAT AAT A
1 AAT AAT A
38701362 TAAGTTTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:38702804 original size:23 final size:23
Alignment explanation
Indices: 38702778--38702821 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
38702768 CCGTACGCTG
38702778 AGTATTTCATACTCAATGGTACA
1 AGTATTTCATACTCAATGGTACA
*
38702801 AGTATTTCATACTCAGTGGTA
1 AGTATTTCATACTCAATGGTA
38702822 TTACTATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (23 bp):
AGTATTTCATACTCAATGGTACA
Found at i:38704069 original size:14 final size:15
Alignment explanation
Indices: 38704043--38704071 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38704033 TGTTCTTTCC
38704043 TTCTTTGTTTCTTTT
1 TTCTTTGTTTCTTTT
38704058 TTCTTT-TTTCTTTT
1 TTCTTTGTTTCTTTT
38704072 ATTTCTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (15 bp):
TTCTTTGTTTCTTTT
Found at i:38710074 original size:23 final size:23
Alignment explanation
Indices: 38710047--38710091 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
38710037 ACCGTACGCT
38710047 GAGTATTTCATACTCAGTGGTAC
1 GAGTATTTCATACTCAGTGGTAC
38710070 GAGTATTTCATACTCAGTGGTA
1 GAGTATTTCATACTCAGTGGTA
38710092 TTACTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (23 bp):
GAGTATTTCATACTCAGTGGTAC
Found at i:38710604 original size:25 final size:24
Alignment explanation
Indices: 38710576--38710623 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38710566 CAGCCCGACT
*
38710576 AATTAATAGGGACTTTCAATTTTAC
1 AATTAATA-GCACTTTCAATTTTAC
* *
38710601 AATTCATATCACTTTCAATTTTA
1 AATTAATAGCACTTTCAATTTTA
38710624 ATTTCACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (24 bp):
AATTAATAGCACTTTCAATTTTAC
Found at i:38724963 original size:18 final size:15
Alignment explanation
Indices: 38724939--38724983 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
38724929 GTTCAAAGTG
38724939 TAATTAATTTAAAATTT
1 TAATTAA-TTAAAA-TT
38724956 TCAATTAATT-AAATT
1 T-AATTAATTAAAATT
38724971 TAATTAATTAAAA
1 TAATTAATTAAAA
38724984 ACCTACTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.31
15 6 0.23
16 3 0.12
17 3 0.12
18 6 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTAATTAAAATT
Found at i:38726155 original size:2 final size:2
Alignment explanation
Indices: 38726148--38726175 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38726138 GAATTACTAG
38726148 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38726176 GATTAGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38735785 original size:32 final size:31
Alignment explanation
Indices: 38735728--38735795 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
38735718 TTGATACTTG
*
38735728 AACTTGACACTTTTTCCTAATTTGGTACCTA
1 AACTTGACACTTTTTCCTAAGTTGGTACCTA
** *
38735759 AACTTGACACTTTTTTTTCAAGTTGGTACTTA
1 AACTTGACACTTTTTCCT-AAGTTGGTACCTA
38735791 AACTT
1 AACTT
38735796 TTTGGGGTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 16 0.50
32 16 0.50
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.44
Consensus pattern (31 bp):
AACTTGACACTTTTTCCTAAGTTGGTACCTA
Found at i:38735858 original size:60 final size:60
Alignment explanation
Indices: 38735744--38735857 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
38735734 ACACTTTTTC
* * *
38735744 CTAATTTGGTACCTAAACTTGACACTTTTTTTTCAAGTTGGTACTTAAACTTTTTGGGGT
1 CTAATTTGGTACCTAAACTTGACACTATTTTTCCAAGTTGGTACGTAAACTTTTTGGGGT
* * *
38735804 CTAATTTGGTACCTGAACTTGA-A-TATTTTTCCTAATTTGGTACGTAATCTTTTT
1 CTAATTTGGTACCTAAACTTGACACTATTTTTCC-AAGTTGGTACGTAAACTTTTT
38735858 TAATATTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 7 0.15
59 19 0.40
60 21 0.45
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (60 bp):
CTAATTTGGTACCTAAACTTGACACTATTTTTCCAAGTTGGTACGTAAACTTTTTGGGGT
Found at i:38736162 original size:12 final size:13
Alignment explanation
Indices: 38736145--38736184 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
38736135 TAAAACCCAA
38736145 TTTTATTT-TTAT
1 TTTTATTTATTAT
38736157 TTTTATTTATT-T
1 TTTTATTTATTAT
*
38736169 ATTTATTTATTAT
1 TTTTATTTATTAT
38736182 TTT
1 TTT
38736185 ATAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTAT
Found at i:38737482 original size:17 final size:16
Alignment explanation
Indices: 38737451--38737481 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38737441 TTCTTTTAAC
38737451 AAATTAAATCCTTTTA
1 AAATTAAATCCTTTTA
*
38737467 AAATTTAATCCTTTT
1 AAATTAAATCCTTTT
38737482 TTTTTACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTAAATCCTTTTA
Found at i:38738046 original size:21 final size:22
Alignment explanation
Indices: 38738022--38738064 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
38738012 ATTTTCTAGA
*
38738022 TTTT-GAAAACTAAATTGTTTT
1 TTTTAGAAAACTAAAATGTTTT
* *
38738043 TTTTATAAAATTAAAATGTTTT
1 TTTTAGAAAACTAAAATGTTTT
38738065 AAGGTGCTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (22 bp):
TTTTAGAAAACTAAAATGTTTT
Found at i:38751174 original size:14 final size:15
Alignment explanation
Indices: 38751155--38751183 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38751145 AAAAAGTGCA
38751155 AGGAGGAA-AAGAAG
1 AGGAGGAAGAAGAAG
38751169 AGGAGGAAGAAGAAG
1 AGGAGGAAGAAGAAG
38751184 CACCGTGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (15 bp):
AGGAGGAAGAAGAAG
Found at i:38751722 original size:31 final size:31
Alignment explanation
Indices: 38751686--38751746 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
38751676 CCACTGTGAG
*
38751686 TGTATTGTGAATTGTTCAAGGGGAACACTCT
1 TGTATTGTGAACTGTTCAAGGGGAACACTCT
*
38751717 TGTATTGTTAACTGTTCAAGGGGAACACTC
1 TGTATTGTGAACTGTTCAAGGGGAACACTC
38751747 CAATGCAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (31 bp):
TGTATTGTGAACTGTTCAAGGGGAACACTCT
Found at i:38754209 original size:7 final size:7
Alignment explanation
Indices: 38754193--38754279 Score: 79
Period size: 7 Copynumber: 12.3 Consensus size: 7
38754183 CCAAAAAAAG
38754193 AAAG-AA
1 AAAGAAA
38754199 AAAGAAA
1 AAAGAAA
*
38754206 AAAGAGA
1 AAAGAAA
*
38754213 AAGGAAA
1 AAAGAAA
*
38754220 AAAAAAA
1 AAAGAAA
*
38754227 AAAAAAA
1 AAAGAAA
38754234 AAAGAGAA
1 AAAGA-AA
38754242 AGAAGAAA
1 A-AAGAAA
*
38754250 GAAGAAA
1 AAAGAAA
*
38754257 GAA-AAA
1 AAAGAAA
38754263 AAAGAGAA
1 AAAGA-AA
38754271 AAAGAAA
1 AAAGAAA
38754278 AA
1 AA
38754280 GGAGTGGTCA
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
6 9 0.13
7 43 0.63
8 12 0.18
9 4 0.06
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:38754220 original size:29 final size:28
Alignment explanation
Indices: 38754187--38754280 Score: 111
Period size: 28 Copynumber: 3.2 Consensus size: 28
38754177 TTTCACCCAA
38754187 AAAAAGAAAGAAAAAGAAAAAAGAGAAAGG
1 AAAAAGAAAGAAAAA-AAAAAAGAGAAA-G
*
38754217 AAAAA-AAAAAAAAAAAAAAAGAGAAAG
1 AAAAAGAAAGAAAAAAAAAAAGAGAAAG
38754244 AAGAAAG-AAGAAAGAAAAAAAAGAGAAAAAG
1 AA-AAAGAAAGAAA-AAAAAAAAGAG--AAAG
38754275 AAAAAG
1 AAAAAG
38754281 GAGTGGTCAA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.05
28 20 0.35
29 19 0.33
30 9 0.16
31 6 0.11
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (28 bp):
AAAAAGAAAGAAAAAAAAAAAGAGAAAG
Found at i:38754236 original size:35 final size:36
Alignment explanation
Indices: 38754185--38754279 Score: 115
Period size: 35 Copynumber: 2.6 Consensus size: 36
38754175 AATTTCACCC
*
38754185 AAAAAAAGAAAGAAAAAGAAAAAAG-AGAAAGGAA-A
1 AAAAAAAAAAAGAAAAAGAAAAAAGAAGAAA-GAAGA
* *
38754220 AAAAAAAAAAAAAAAAAG-AGAAAGAAGAAAGAAGA
1 AAAAAAAAAAAGAAAAAGAAAAAAGAAGAAAGAAGA
38754255 AAGAAAAAAAAGAGAAAAAGAAAAA
1 AA-AAAAAAAA-AGAAAAAGAAAAA
38754280 GGAGTGGTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
34 8 0.16
35 24 0.48
36 8 0.16
37 7 0.14
38 3 0.06
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (36 bp):
AAAAAAAAAAAGAAAAAGAAAAAAGAAGAAAGAAGA
Found at i:38754238 original size:41 final size:43
Alignment explanation
Indices: 38754185--38754280 Score: 126
Period size: 41 Copynumber: 2.3 Consensus size: 43
38754175 AATTTCACCC
*
38754185 AAAAAAAGAAAGAAAAAGAAAAAAG-AGAAAGGAAAAAAAA-A-
1 AAAAAAAAAAAGAAAAAGAAAAAAGAAGAAA-GAAAAAAAAGAG
* *
38754226 AAAAAAAAAAAGAGAAAGAAGAAAGAAGAAAGAAAAAAAAGAG
1 AAAAAAAAAAAGAAAAAGAAAAAAGAAGAAAGAAAAAAAAGAG
*
38754269 AAAAAGAAAAAG
1 AAAAAAAAAAAG
38754281 GAGTGGTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
41 31 0.65
42 6 0.12
43 11 0.23
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (43 bp):
AAAAAAAAAAAGAAAAAGAAAAAAGAAGAAAGAAAAAAAAGAG
Done.