Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 21 of 141
Found at i:6436306 original size:44 final size:44
Alignment explanation
Indices: 6436243--6436468 Score: 111
Period size: 45 Copynumber: 5.1 Consensus size: 44
6436233 CCTTGAATTA
*
6436243 GCAGCGAAGCAGATGGAAGACACCAGCCTTGCCTCCCTGAGTTT
1 GCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
* * * * ** * *
6436287 GCAGCGGAGCAGA-CTGAAGATAGCAGATCTTATCT-TCTTA-TATT
1 GCAGCGAAGCAGATC-GAAGACACCAG-CCTTGCCTCCCTGAGT-TT
* * *
6436331 GGCAACAAAGCAGATCGAAGACACCAACCTTGCCTCCCTGAGTTT
1 -GCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
* * * * * * * * * * *
6436376 GTAGTGGAGCAGA-CTGAAAATAACAGATCTTGTCTTCCTGTA-CTG
1 GCAGCGAAGCAGATC-GAAGACACCAG-CCTTGCCTCCCTG-AGTTT
* * * *
6436421 GTAGTGAAGCAGATCGAAAACACCAGCCTTGCCTCTCTGAGTTT
1 GCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
6436465 GCAG
1 GCAG
6436469 TGGAGTAGGT
Statistics
Matches: 126, Mismatches: 44, Indels: 24
0.65 0.23 0.12
Matches are distributed among these distances:
43 3 0.02
44 59 0.47
45 60 0.48
46 4 0.03
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.23
Consensus pattern (44 bp):
GCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
Found at i:6436362 original size:89 final size:88
Alignment explanation
Indices: 6436187--6436473 Score: 335
Period size: 89 Copynumber: 3.2 Consensus size: 88
6436177 CTAATCCTAT
* * * * * *
6436187 CTCCCTGAAG-TTGCAGTGGAGCAGATTGAAGCTACAAATCCTATCTCCTTGA-ATTAGCAGCGA
1 CTCCCTG-AGTTTGCAGTGGAGCAGACTGAAGATACAGATCTTATCTTCTT-ATATTGGCAGCGA
*
6436250 AGCAGATGGAAGACACCAGCCTTGC
64 AGCAGATCGAAGACACCAGCCTTGC
* * *
6436275 CTCCCTGAGTTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTATCTTCTTATATTGGCAACAAA
1 CTCCCTGAGTTTGCAGTGGAGCAGACTGAAGATA-CAGATCTTATCTTCTTATATTGGCAGCGAA
*
6436340 GCAGATCGAAGACACCAACCTTGC
65 GCAGATCGAAGACACCAGCCTTGC
* * * * * * * *
6436364 CTCCCTGAGTTTGTAGTGGAGCAGACTGAAAATAACAGATCTTGTCTTCCTGTACTGGTAGTGAA
1 CTCCCTGAGTTTGCAGTGGAGCAGACTGAAGAT-ACAGATCTTATCTTCTTATATTGGCAGCGAA
*
6436429 GCAGATCGAAAACACCAGCCTTGC
65 GCAGATCGAAGACACCAGCCTTGC
*
6436453 CTCTCTGAGTTTGCAGTGGAG
1 CTCCCTGAGTTTGCAGTGGAG
6436474 TAGGTTGAAG
Statistics
Matches: 169, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
87 2 0.01
88 29 0.17
89 137 0.81
90 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (88 bp):
CTCCCTGAGTTTGCAGTGGAGCAGACTGAAGATACAGATCTTATCTTCTTATATTGGCAGCGAAG
CAGATCGAAGACACCAGCCTTGC
Found at i:6436757 original size:130 final size:133
Alignment explanation
Indices: 6436467--6436841 Score: 469
Period size: 130 Copynumber: 2.8 Consensus size: 133
6436457 CTGAGTTTGC
* * * *
6436467 AGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAATTGTGAAGCAGATCAG-ATACG
1 AGTGGAGTAGGTTGAAGATTGTACATCCTGTCTCCCTAAGCAATAGTGGAGCAGATCAGAAGACG
* * * * *
6436531 ACGAATCTTATCTTCCCAAGGTAGTA-AGGAAGCAAATTTAAGACAGCAGTCCTATCTCCGTGAG
66 ACGAATCTTATCTTCCC--GATAGTAGAGGAAGCAAATTTAAGCCACCAGTCCTATCCCCCTGAG
6436595 CAACT
129 CAACT
* * * * *
6436600 -GTGGAGTAGGTTGAAGATTGTACATCCTATCTTCCTAAGCAGTAGTGGAGGAGAT-AGAAGATG
1 AGTGGAGTAGGTTGAAGATTGTACATCCTGTCTCCCTAAGCAATAGTGGAGCAGATCAGAAGACG
* * *
6436663 ACAAATCTTATCTTCCCGATA-TAGAGGAAGCAAATTTAAGCCACCAGTCGTATCCCCCTGAG-T
66 ACGAATCTTATCTTCCCGATAGTAGAGGAAGCAAATTTAAGCCACCAGTCCTATCCCCCTGAGCA
*
6436726 AGT
131 ACT
*
6436729 AGTGGAGTAGGTTGAAGATTGTATATCCTGTCTCCCTAAGCAATAGTGGAGCAGATCA-AAGACG
1 AGTGGAGTAGGTTGAAGATTGTACATCCTGTCTCCCTAAGCAATAGTGGAGCAGATCAGAAGACG
* *
6436793 ACGAGTCTTATCTTCCCGAGGTAGTAG-GGAAGCAGATTTAAGCCACCAG
66 ACGAATCTTATCTTCCCGA--TAGTAGAGGAAGCAAATTTAAGCCACCAG
6436842 ACTTCTCTCC
Statistics
Matches: 208, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
129 4 0.02
130 108 0.52
131 3 0.01
132 90 0.43
133 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (133 bp):
AGTGGAGTAGGTTGAAGATTGTACATCCTGTCTCCCTAAGCAATAGTGGAGCAGATCAGAAGACG
ACGAATCTTATCTTCCCGATAGTAGAGGAAGCAAATTTAAGCCACCAGTCCTATCCCCCTGAGCA
ACT
Found at i:6440936 original size:37 final size:36
Alignment explanation
Indices: 6440858--6440949 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 36
6440848 TTAAATTTAA
6440858 TATTAAAATAATCACTTTAATATTAAATTAATAAAATAC
1 TATTAAAATAAT-A--TTAATATTAAATTAATAAAATAC
* *
6440897 TATTAAGATAAGTATTAA-ATTAAATTTAATATTAA-AC
1 TATTAAAATAA-TATTAATATTAAA-TTAATA-AAATAC
6440934 TATTAAAATAATATTA
1 TATTAAAATAATATTA
6440950 TTTTTGGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
36 11 0.23
37 22 0.47
38 2 0.04
39 11 0.23
40 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (36 bp):
TATTAAAATAATATTAATATTAAATTAATAAAATAC
Found at i:6442558 original size:17 final size:17
Alignment explanation
Indices: 6442536--6442576 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
6442526 AGATCTCTGA
6442536 CGAGCTTCCAAACCGAT
1 CGAGCTTCCAAACCGAT
*
6442553 CGAGCTTCCAAACCGGT
1 CGAGCTTCCAAACCGAT
6442570 CGAGCTT
1 CGAGCTT
6442577 TCGATAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.34, G:0.22, T:0.20
Consensus pattern (17 bp):
CGAGCTTCCAAACCGAT
Found at i:6442851 original size:20 final size:20
Alignment explanation
Indices: 6442824--6442875 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
6442814 TATGAACTAC
6442824 TCCATTTACTTACTTTACAT
1 TCCATTTACTTACTTTACAT
* * *
6442844 TTCATTTACTTTCTTTCCAT
1 TCCATTTACTTACTTTACAT
6442864 TCCATTTACTTA
1 TCCATTTACTTA
6442876 GCATAAGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (20 bp):
TCCATTTACTTACTTTACAT
Found at i:6459999 original size:15 final size:15
Alignment explanation
Indices: 6459976--6460010 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
6459966 AAAGAGTTCA
*
6459976 AGTATGATTAAACTT
1 AGTACGATTAAACTT
6459991 AGTACGATTAAACTT
1 AGTACGATTAAACTT
6460006 AGTAC
1 AGTAC
6460011 TTTAATACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (15 bp):
AGTACGATTAAACTT
Found at i:6461850 original size:16 final size:16
Alignment explanation
Indices: 6461829--6461859 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6461819 CTATGCATGT
*
6461829 AAAATATAAAAGACAA
1 AAAATAAAAAAGACAA
6461845 AAAATAAAAAAGACA
1 AAAATAAAAAAGACA
6461860 TAATAGTGAA
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:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATAAAAAAGACAA
Found at i:6463680 original size:50 final size:50
Alignment explanation
Indices: 6463626--6463730 Score: 158
Period size: 50 Copynumber: 2.1 Consensus size: 50
6463616 ATTGAGGTTG
*
6463626 TGAGAGGTCCCACGTAAGATCATGTCTGGGACATGGCATTGG-CACCGAGA
1 TGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCA-TGGACACCGAGA
* * *
6463676 TGAGAGGTCCCCCGTAAGACCCTGTCTGGGACATGGCATGGACACCGATA
1 TGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGACACCGAGA
6463726 TGAGA
1 TGAGA
6463731 ACTATCATGT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
49 3 0.06
50 47 0.94
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (50 bp):
TGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGACACCGAGA
Found at i:6463743 original size:50 final size:49
Alignment explanation
Indices: 6463635--6463811 Score: 135
Period size: 50 Copynumber: 3.6 Consensus size: 49
6463625 GTGAGAGGTC
* ** *
6463635 CCACGTAAGATCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
1 CCACGTAAGACCATGTCTGGGACATGGCA-TGGCACCGAGATGAGAACTA
* * *
6463685 CCCCGTAAGACCCTGTCTGGGACATGGCATGGACACCGATATGAGAACTA
1 CCACGTAAGACCATGTCTGGGACATGGCATGG-CACCGAGATGAGAACTA
* * * * * * * *
6463735 TCATGTAAGACCATATCTAGGATATGGCATTGGCA--GTACAAGA-AACATC
1 CCACGTAAGACCATGTCTGGGACATGGCA-TGGCACCG-AGATGAGAAC-TA
* *
6463784 CCATGTAAGACCATGTCTGTGACATGGC
1 CCACGTAAGACCATGTCTGGGACATGGC
6463812 TTTGGCATGT
Statistics
Matches: 101, Mismatches: 22, Indels: 9
0.77 0.17 0.07
Matches are distributed among these distances:
48 4 0.04
49 31 0.31
50 63 0.62
51 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.21
Consensus pattern (49 bp):
CCACGTAAGACCATGTCTGGGACATGGCATGGCACCGAGATGAGAACTA
Found at i:6464046 original size:20 final size:20
Alignment explanation
Indices: 6464021--6464069 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
6464011 TGAGTTATTT
6464021 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
6464041 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
6464061 AAG-AAGCAA
1 AAGTAAGCAA
6464070 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:6470736 original size:34 final size:34
Alignment explanation
Indices: 6470693--6470760 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
6470683 TCCTCTGTTT
6470693 TCACCTAGTGATGAAGATTAGGATAATTTTAATA
1 TCACCTAGTGATGAAGATTAGGATAATTTTAATA
*
6470727 TCACCTAGTGATGAAGATTGGGATAATTTTAATA
1 TCACCTAGTGATGAAGATTAGGATAATTTTAATA
6470761 CACTCATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (34 bp):
TCACCTAGTGATGAAGATTAGGATAATTTTAATA
Found at i:6471213 original size:23 final size:22
Alignment explanation
Indices: 6471178--6471223 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
6471168 ATTGATAATA
*
6471178 TGTTTTGATATAAAAAATTAAAG
1 TGTTTTGAAAT-AAAAATTAAAG
*
6471201 TGTTTTTAAATAAAAATTAAAG
1 TGTTTTGAAATAAAAATTAAAG
6471223 T
1 T
6471224 TGAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (22 bp):
TGTTTTGAAATAAAAATTAAAG
Found at i:6472942 original size:74 final size:75
Alignment explanation
Indices: 6472816--6472964 Score: 239
Period size: 74 Copynumber: 2.0 Consensus size: 75
6472806 CATGTTGTGT
* * *
6472816 TAGTGATGTATGGTAAGGAAAATAAAATAATAAGCATGATAATTAAATAATG-AAAGGAAGGGTG
1 TAGTGATGTATGCTAAGAAAAATAAAATAATAAGCATGATAATTAAACAATGAAAAGGAAGGGTG
6472880 ATGAAAAAAA
66 ATGAAAAAAA
*
6472890 TAGTGATGTATGCTAAGAAAAATAAAATAA-AGAGCATGGTAATTAAACAATGAAAAGGAAGGGT
1 TAGTGATGTATGCTAAGAAAAATAAAATAATA-AGCATGATAATTAAACAATGAAAAGGAAGGGT
6472954 GATGAAAAAAA
65 GATGAAAAAAA
6472965 AATGGTCTCA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
73 1 0.01
74 46 0.67
75 22 0.32
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.21
Consensus pattern (75 bp):
TAGTGATGTATGCTAAGAAAAATAAAATAATAAGCATGATAATTAAACAATGAAAAGGAAGGGTG
ATGAAAAAAA
Found at i:6474450 original size:27 final size:27
Alignment explanation
Indices: 6474419--6474596 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
6474409 TAAATTGTAC
6474419 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
6474446 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
6474472 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
6474500 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
6474528 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
6474555 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
6474582 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6474597 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:6474533 original size:82 final size:81
Alignment explanation
Indices: 6474420--6474575 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
6474410 AAATTGTACA
* *
6474420 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
6474484 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
6474501 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
6474566 TGCGAGTTGA
65 TGCGAATTGA
6474576 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:6474587 original size:82 final size:81
Alignment explanation
Indices: 6474416--6474596 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
6474406 GATTAAATTG
* *
6474416 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
6474481 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
6474497 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
6474561 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
6474579 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
6474597 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:6479244 original size:24 final size:24
Alignment explanation
Indices: 6479200--6479271 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 24
6479190 TATAACAAGA
*
6479200 AGCTCACAAAGAG-CCTATAACGGGT
1 AGCTC-CAAAGAGTCAT-TAACGGGT
* *
6479225 AGCTCCAAAGAGTCATTAACAGAT
1 AGCTCCAAAGAGTCATTAACGGGT
**
6479249 AGCTCTGAAGAGAT-ATTAACGGG
1 AGCTCCAAAGAG-TCATTAACGGG
6479272 AAGCACCGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
24 30 0.79
25 8 0.21
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (24 bp):
AGCTCCAAAGAGTCATTAACGGGT
Found at i:6479345 original size:26 final size:27
Alignment explanation
Indices: 6479312--6479374 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
6479302 CAAGCGAGCA
6479312 TTAA-CGGGAAGCTCACAAAGAGCC-T
1 TTAATCGGGAAGCTCACAAAGAGCCAT
* * *
6479337 TTAATCGGGAATCTTACGAAGAGCCAT
1 TTAATCGGGAAGCTCACAAAGAGCCAT
*
6479364 ATAAT-GGGAAG
1 TTAATCGGGAAG
6479375 ATCATTGAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 4 0.13
26 22 0.71
27 5 0.16
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (27 bp):
TTAATCGGGAAGCTCACAAAGAGCCAT
Found at i:6483863 original size:27 final size:27
Alignment explanation
Indices: 6483833--6484010 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
6483823 ATATTGAGTC
* * * *
6483833 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
6483860 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
6483887 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
6483915 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
6483942 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
6483969 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
6483996 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
6484011 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:6483972 original size:82 final size:81
Alignment explanation
Indices: 6483854--6484009 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
6483844 TGCTATATAA
* *
6483854 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
6483919 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
6483936 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
6484000 CACTTAGTGC
65 CACTTAGTGC
6484010 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:6491926 original size:27 final size:27
Alignment explanation
Indices: 6491896--6492073 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
6491886 ATATTGAGTC
* * * *
6491896 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
6491923 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
6491950 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
6491978 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
6492005 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
6492032 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
6492059 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
6492074 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:6492035 original size:82 final size:81
Alignment explanation
Indices: 6491917--6492072 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
6491907 TGCTATATAA
* *
6491917 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
6491982 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
6491999 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
6492063 CACTTAGTGC
65 CACTTAGTGC
6492073 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:6496805 original size:24 final size:23
Alignment explanation
Indices: 6496778--6496822 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
6496768 AAGATTAAAT
* *
6496778 ACATACATTTCATATTATTATTTA
1 ACATACATGTCAGA-TATTATTTA
*
6496802 ACATTCATGTCAGATATTATT
1 ACATACATGTCAGATATTATT
6496823 CATAAAGTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (23 bp):
ACATACATGTCAGATATTATTTA
Found at i:6499322 original size:21 final size:23
Alignment explanation
Indices: 6499277--6499323 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6499267 TCACCTGCAA
* *
6499277 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
6499300 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
6499321 TAA
1 TAA
6499324 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:6504729 original size:15 final size:14
Alignment explanation
Indices: 6504663--6504730 Score: 86
Period size: 15 Copynumber: 4.8 Consensus size: 14
6504653 CTAGCCCTCT
6504663 TTTTTTTTTC--AA
1 TTTTTTTTTCAGAA
6504675 TTTTTTTTTCAGAA
1 TTTTTTTTTCAGAA
*
6504689 TTTTTTTTTTCAAAAA
1 -TTTTTTTTTC-AGAA
6504705 TTTTTTTTTCACGAA
1 TTTTTTTTTCA-GAA
6504720 TTTTTTTTTCA
1 TTTTTTTTTCA
6504731 ACTTGATATC
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
12 10 0.20
14 3 0.06
15 33 0.67
16 3 0.06
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTTTTTTTCAGAA
Found at i:6504731 original size:30 final size:30
Alignment explanation
Indices: 6504662--6504728 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
6504652 ACTAGCCCTC
6504662 TTTTTTTTTTC---AATTTTTTTTTCAGAA
1 TTTTTTTTTTCAAAAATTTTTTTTTCAGAA
6504689 TTTTTTTTTTCAAAAATTTTTTTTTCACGAA
1 TTTTTTTTTTCAAAAATTTTTTTTTCA-GAA
6504720 TTTTTTTTT
1 TTTTTTTTT
6504729 CAACTTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 11 0.31
30 13 0.36
31 12 0.33
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.70
Consensus pattern (30 bp):
TTTTTTTTTTCAAAAATTTTTTTTTCAGAA
Found at i:6504785 original size:12 final size:12
Alignment explanation
Indices: 6504768--6504816 Score: 82
Period size: 12 Copynumber: 4.2 Consensus size: 12
6504758 ATGGAAACAA
6504768 AATTTTTTTTTG
1 AATTTTTTTTTG
6504780 AATTTTTTTTTG
1 AATTTTTTTTTG
6504792 AA-TTTTTTTTG
1 AATTTTTTTTTG
*
6504803 AAATTTTTTTTG
1 AATTTTTTTTTG
6504815 AA
1 AA
6504817 GAAACTACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.31
12 25 0.69
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:6504797 original size:23 final size:23
Alignment explanation
Indices: 6504771--6504816 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
6504761 GAAACAAAAT
*
6504771 TTTTTTTTGAATTTTTTTTTGAA
1 TTTTTTTTGAAATTTTTTTTGAA
6504794 TTTTTTTTGAAATTTTTTTTGAA
1 TTTTTTTTGAAATTTTTTTTGAA
6504817 GAAACTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (23 bp):
TTTTTTTTGAAATTTTTTTTGAA
Found at i:6505851 original size:21 final size:23
Alignment explanation
Indices: 6505806--6505852 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6505796 TCACCTGCAA
* *
6505806 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
6505829 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
6505850 TAA
1 TAA
6505853 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:6506724 original size:21 final size:21
Alignment explanation
Indices: 6506700--6506739 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6506690 ATTTAACATG
* *
6506700 AATTGAATACAATTTACATTC
1 AATTCAATACAATTCACATTC
*
6506721 AATTCAATCCAATTCACAT
1 AATTCAATACAATTCACAT
6506740 CTTAGGCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (21 bp):
AATTCAATACAATTCACATTC
Found at i:6508040 original size:18 final size:18
Alignment explanation
Indices: 6507982--6508047 Score: 96
Period size: 18 Copynumber: 3.6 Consensus size: 18
6507972 TAACTAAGTA
*
6507982 AGTTAAAAGAACTTAGTG
1 AGTTTAAAGAACTTAGTG
* *
6508000 AGTTCAAAGAACCTAGTG
1 AGTTTAAAGAACTTAGTG
6508018 AGTTTAAAGAACTTAGTG
1 AGTTTAAAGAACTTAGTG
6508036 AGTTTAAGAGAA
1 AGTTTAA-AGAA
6508048 AGACATTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
18 39 0.91
19 4 0.09
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (18 bp):
AGTTTAAAGAACTTAGTG
Found at i:6509595 original size:27 final size:27
Alignment explanation
Indices: 6509498--6509596 Score: 128
Period size: 27 Copynumber: 3.6 Consensus size: 27
6509488 ACAAAATTTT
*
6509498 CCACAAAGGC-ATTCCTTTCAGAGTTCG
1 CCACAAAGGCTATT-CTTTCAGAGTTTG
* *
6509525 CCACAAAGGTTATTTCTTTCAGACTTTG
1 CCACAAAGGCTA-TTCTTTCAGAGTTTG
*
6509553 CCACAAAGTCTATTCTTTCAGAGTTTG
1 CCACAAAGGCTATTCTTTCAGAGTTTG
*
6509580 GCACAAAGGCTATTCTT
1 CCACAAAGGCTATTCTT
6509597 AGCTGTCATG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
27 38 0.61
28 22 0.35
29 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (27 bp):
CCACAAAGGCTATTCTTTCAGAGTTTG
Found at i:6510757 original size:28 final size:28
Alignment explanation
Indices: 6510725--6510781 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
6510715 TTCTCTTTAA
6510725 TACAGGGTAGAATATCAGAAAATCAAAT
1 TACAGGGTAGAATATCAGAAAATCAAAT
6510753 TACAGGGTAGAATATCAGAAAATCAAAT
1 TACAGGGTAGAATATCAGAAAATCAAAT
6510781 T
1 T
6510782 CTTACTTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.23
Consensus pattern (28 bp):
TACAGGGTAGAATATCAGAAAATCAAAT
Found at i:6520643 original size:40 final size:40
Alignment explanation
Indices: 6520606--6520791 Score: 241
Period size: 40 Copynumber: 4.7 Consensus size: 40
6520596 GCTACTCGTT
* *
6520606 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
6520646 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
6520686 CAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * * * *
6520726 CAAATGCCTTCGGGTCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
*
6520767 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
6520792 CATCATTCAA
Statistics
Matches: 132, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 122 0.92
41 10 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:6528655 original size:79 final size:81
Alignment explanation
Indices: 6528546--6528728 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
6528536 TACTCGTTCA
* *
6528546 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
6528609 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
6528626 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
6528689 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
6528705 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
6528729 CATCATTCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:6528728 original size:40 final size:40
Alignment explanation
Indices: 6528525--6528728 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
6528515 CGGAATTTAA
** *
6528525 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6528565 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6528605 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6528644 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
6528684 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
6528724 CCGGA
1 CCGGA
6528729 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:6537178 original size:39 final size:40
Alignment explanation
Indices: 6537077--6537186 Score: 134
Period size: 40 Copynumber: 2.8 Consensus size: 40
6537067 AAGGACACAT
* * * *
6537077 ATGTGCATACAGGGGTACTGAAGTACAAATAGGGTCATAG
1 ATGTGCATTCAAGGGTACCGAAGTACAAACAGGGTCATAG
** *
6537117 ATGTGCATTCAAATGTATCGAAGTACAAACAGAGG-CATAG
1 ATGTGCATTCAAGGGTACCGAAGTACAAACAG-GGTCATAG
6537157 AT-TGCATTCAAGGGTACCGAAGTACAAACA
1 ATGTGCATTCAAGGGTACCGAAGTACAAACA
6537187 TGGGCACTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 25 0.42
40 32 0.54
41 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (40 bp):
ATGTGCATTCAAGGGTACCGAAGTACAAACAGGGTCATAG
Found at i:6541017 original size:18 final size:18
Alignment explanation
Indices: 6540994--6541039 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
6540984 ATGTTGATTC
6540994 ATGAGGGGATTAGTGGAA
1 ATGAGGGGATTAGTGGAA
6541012 ATGAGGGGATTAGTGGAA
1 ATGAGGGGATTAGTGGAA
6541030 ATGAGGGGAT
1 ATGAGGGGAT
6541040 CAGTTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.46, T:0.22
Consensus pattern (18 bp):
ATGAGGGGATTAGTGGAA
Found at i:6543480 original size:22 final size:20
Alignment explanation
Indices: 6543437--6543475 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6543427 CAATTTAAAA
6543437 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
6543457 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
6543476 ATGTAAAAAC
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:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:6543598 original size:20 final size:20
Alignment explanation
Indices: 6543573--6543612 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6543563 AAATATTTTC
6543573 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
6543593 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
6543613 TCATTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:6544239 original size:24 final size:24
Alignment explanation
Indices: 6544207--6544278 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
6544197 TTTTACTGCA
6544207 ATATTCAGTGGCTTGACCACAACG
1 ATATTCAGTGGCTTGACCACAACG
*
6544231 ATATTCAGTGGCTTGACCACAATG
1 ATATTCAGTGGCTTGACCACAACG
* *
6544255 TTATTCAGTGGCTTGACCCCAACG
1 ATATTCAGTGGCTTGACCACAACG
6544279 TGCAGCTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (24 bp):
ATATTCAGTGGCTTGACCACAACG
Found at i:6549210 original size:21 final size:21
Alignment explanation
Indices: 6549164--6549210 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
6549154 TTCAGTGGTA
* *
6549164 ATTTTTATTTCTTTTGTTATT
1 ATTTTTATTTCTTATGTTACT
*
6549185 GTTTTTATTTACTTAT-TTACT
1 ATTTTTATTT-CTTATGTTACT
6549206 ATTTT
1 ATTTT
6549211 GCCTGGGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.72
Consensus pattern (21 bp):
ATTTTTATTTCTTATGTTACT
Found at i:6554213 original size:23 final size:25
Alignment explanation
Indices: 6554187--6554248 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 25
6554177 AGTTACATAC
*
6554187 AAAGAGAGCATTATATATC-ATT-T
1 AAAGAGAGCATTATATATCAATTAA
6554210 AAAG-GAGC-TGT-TATATCAATTAA
1 AAAGAGAGCAT-TATATATCAATTAA
6554233 AAAGGAGAGCATTATA
1 AAA-GAGAGCATTATA
6554249 CCTCCTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
21 7 0.23
22 8 0.26
23 7 0.23
24 1 0.03
25 5 0.16
26 3 0.10
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (25 bp):
AAAGAGAGCATTATATATCAATTAA
Found at i:6565495 original size:19 final size:19
Alignment explanation
Indices: 6565473--6565510 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6565463 TCAATCATCC
6565473 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
6565492 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
6565511 ACTCCCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:6567912 original size:50 final size:50
Alignment explanation
Indices: 6567784--6568069 Score: 296
Period size: 50 Copynumber: 5.7 Consensus size: 50
6567774 GATAATAACA
* * *
6567784 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGTAT--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-TGG
* * *
6567833 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATTGG
* * ** *
6567883 TGCCCATTCCATGTCCCAGACATGGTCTT--ATGGGGAACCTCTCATCTCT-G
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGG-AGTTCTCATAT-TGG
*
6567933 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATTGG
* * * ** * *
6567983 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATTGG
* *
6568033 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
6568070 CCTCTTTACC
Statistics
Matches: 195, Mismatches: 33, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
48 6 0.03
49 41 0.21
50 142 0.73
51 4 0.02
52 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATTGG
Found at i:6567964 original size:100 final size:100
Alignment explanation
Indices: 6567833--6568069 Score: 404
Period size: 100 Copynumber: 2.4 Consensus size: 100
6567823 TTTCCTGTAT
* * * *
6567833 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATTCCATGTC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTC
*
6567898 CCAGACATGGTCTTAT-GGGGAACCTCTCATCTCTG
66 CCAGACATGGTCTTATAGGGG-ACCTCTCATCTCGG
*
6567933 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTC
6567998 CCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
66 CCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
6568033 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGA
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGA
6568070 CCTCTTTACC
Statistics
Matches: 129, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
100 125 0.97
101 4 0.03
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (100 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTC
CCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
Found at i:6568074 original size:150 final size:149
Alignment explanation
Indices: 6567784--6568062 Score: 364
Period size: 150 Copynumber: 1.9 Consensus size: 149
6567774 GATAATAACA
* * *
6567784 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTATTGCCAATGTCATATCC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATATATTGCCAATGCCATATCC
* * ** * * ** *
6567849 CAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATTCCATGTCCCAGACATGGTCTTAT
66 CAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATATCCCAGACATGGTCTTAT
6567914 GGGGAACCTCTCATCTCTG
131 GGGGAACCTCTCATCTCTG
* * *
6567933 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-TGGTGCCCATGCCATG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCATATAT--TGCCAATGCCATA
* *
6567996 TCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAACGCCATATCCCAGACATGGTCT
63 TCCCAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATATCCCAGACATGGTCT
6568061 TA
128 TA
6568063 CATGGGACCT
Statistics
Matches: 110, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
148 4 0.04
149 40 0.36
150 66 0.60
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (149 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATATATTGCCAATGCCATATCC
CAGACATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATATCCCAGACATGGTCTTAT
GGGGAACCTCTCATCTCTG
Found at i:6574476 original size:50 final size:50
Alignment explanation
Indices: 6574413--6574586 Score: 249
Period size: 50 Copynumber: 3.5 Consensus size: 50
6574403 CAATGTCATA
* * *
6574413 TCCCAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGGGAGTTCTCATATTGGTGCCAACGCCATG
*** ** * *
6574463 TCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGAGTTCTCATATTGGTGCCAACGCCATG
6574513 TCCCAGACATGGTCTTACATGGGAGTTCTCATATTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGAGTTCTCATATTGGTGCCAACGCCATG
*
6574563 TCCCAAACATGGTCTTACATGGGA
1 TCCCAGACATGGTCTTACATGGGA
6574587 CCTCTTTACC
Statistics
Matches: 106, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 106 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGAGTTCTCATATTGGTGCCAACGCCATG
Found at i:6579648 original size:18 final size:18
Alignment explanation
Indices: 6579625--6579680 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
6579615 AAAGTTACAT
6579625 GGGCACGGACACGGGTTG
1 GGGCACGGACACGGGTTG
*
6579643 GGGCACGGACACGGATTG
1 GGGCACGGACACGGGTTG
*
6579661 GGGCACAGACACGGGTTG
1 GGGCACGGACACGGGTTG
6579679 GG
1 GG
6579681 ACATGGCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.20, C:0.21, G:0.48, T:0.11
Consensus pattern (18 bp):
GGGCACGGACACGGGTTG
Found at i:6581735 original size:132 final size:132
Alignment explanation
Indices: 6581342--6581739 Score: 724
Period size: 132 Copynumber: 3.0 Consensus size: 132
6581332 AATGGAGAAA
* *
6581342 GTTCTTCGCAGTTCAATAATCGACTGGTAATGGGAGAAAATGGGGTTGATACGGGCTCTTTACCC
1 GTTCTTCGCAGTTCAATAGTCGACTGGTAATGGGAGAAAATGGGGTCGATACGGGCTCTTTACCC
* *
6581407 CTATTAAAATATCAAAAATTGGGCCCATTGCGCAAACCCAACCTTTACAAGTCTTTGTCAAATTA
66 CTATTAAAATATCAAAAATTGGGCCCATTGCCCAAACCCAACCTTTACAAGTCTTTGTCAAATTG
6581472 TG
131 TG
*
6581474 ATTCTTCGCAGTTCAATAGTCGACTGGTAATGGGAGAAAATGGGGTCGATACGGGCTCTTTACCC
1 GTTCTTCGCAGTTCAATAGTCGACTGGTAATGGGAGAAAATGGGGTCGATACGGGCTCTTTACCC
6581539 CTATTAAAATATCAAAAATTGGGCCCATTGCCCAAACCCAACCTTTACAAGTCTTTGTCAAATTG
66 CTATTAAAATATCAAAAATTGGGCCCATTGCCCAAACCCAACCTTTACAAGTCTTTGTCAAATTG
6581604 TG
131 TG
* *
6581606 GTTCTTCGCAGTTCAATAGTCGACTGGTAATGGGAGAAAATGGGGTCAATGCGGGCTCTTTACCC
1 GTTCTTCGCAGTTCAATAGTCGACTGGTAATGGGAGAAAATGGGGTCGATACGGGCTCTTTACCC
*
6581671 CTATTAAAATATCAAAAATTGGGCCCATTGCCCAAACCCAACCTTTACTAGTCTTTGTCAAATTG
66 CTATTAAAATATCAAAAATTGGGCCCATTGCCCAAACCCAACCTTTACAAGTCTTTGTCAAATTG
6581736 TG
131 TG
6581738 GT
1 GT
6581740 CTAATTCTTT
Statistics
Matches: 257, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 257 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (132 bp):
GTTCTTCGCAGTTCAATAGTCGACTGGTAATGGGAGAAAATGGGGTCGATACGGGCTCTTTACCC
CTATTAAAATATCAAAAATTGGGCCCATTGCCCAAACCCAACCTTTACAAGTCTTTGTCAAATTG
TG
Found at i:6584073 original size:9 final size:9
Alignment explanation
Indices: 6584069--6584144 Score: 98
Period size: 9 Copynumber: 8.4 Consensus size: 9
6584059 AAATTACCCA
6584069 AATTAACCG
1 AATTAACCG
* *
6584078 GATTACCCG
1 AATTAACCG
6584087 AATTAACCG
1 AATTAACCG
* *
6584096 GATTACCCG
1 AATTAACCG
6584105 AATTAACCG
1 AATTAACCG
*
6584114 AATTACCCG
1 AATTAACCG
*
6584123 AATTAACCA
1 AATTAACCG
6584132 AATTAACCG
1 AATTAACCG
6584141 AATT
1 AATT
6584145 GAATCACTAC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:6584084 original size:18 final size:18
Alignment explanation
Indices: 6584061--6584144 Score: 123
Period size: 18 Copynumber: 4.7 Consensus size: 18
6584051 TTGGTTAAAA
*
6584061 ATTACCCAAATTAACCGG
1 ATTACCCGAATTAACCGG
6584079 ATTACCCGAATTAACCGG
1 ATTACCCGAATTAACCGG
*
6584097 ATTACCCGAATTAACCGA
1 ATTACCCGAATTAACCGG
**
6584115 ATTACCCGAATTAACCAA
1 ATTACCCGAATTAACCGG
*
6584133 ATTAACCGAATT
1 ATTACCCGAATT
6584145 GAATCACTAC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (18 bp):
ATTACCCGAATTAACCGG
Found at i:6584100 original size:27 final size:27
Alignment explanation
Indices: 6584060--6584144 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
6584050 TTTGGTTAAA
* * * *
6584060 AATTACCCAAATTAACCGGATTACCCG
1 AATTAACCGAATTAACCGAATTAACCG
* *
6584087 AATTAACCGGATTACCCGAATTAACCG
1 AATTAACCGAATTAACCGAATTAACCG
* *
6584114 AATTACCCGAATTAACCAAATTAACCG
1 AATTAACCGAATTAACCGAATTAACCG
6584141 AATT
1 AATT
6584145 GAATCACTAC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.24
Consensus pattern (27 bp):
AATTAACCGAATTAACCGAATTAACCG
Found at i:6599349 original size:27 final size:27
Alignment explanation
Indices: 6599316--6599369 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
6599306 AAATTGTTTC
*
6599316 TTGTTCTATTTTTAATTCATGATTGTT
1 TTGTTCTATGTTTAATTCATGATTGTT
* *
6599343 TTGTTCTGTGTTTGATTCATGATTGTT
1 TTGTTCTATGTTTAATTCATGATTGTT
6599370 CAAGCAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.07, G:0.17, T:0.61
Consensus pattern (27 bp):
TTGTTCTATGTTTAATTCATGATTGTT
Found at i:6613577 original size:27 final size:27
Alignment explanation
Indices: 6613542--6613614 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
6613532 TACAGAATAT
*
6613542 GCCACAAAGGCTATTCATTCATAGTAC
1 GCCACAAAGGCTATTCATTCAGAGTAC
*
6613569 GCCATAAAGGCTATTCATTCAGAGTAC
1 GCCACAAAGGCTATTCATTCAGAGTAC
6613596 GCCACAAAGGCTATTCATT
1 GCCACAAAGGCTATTCATT
6613615 ACTATCGTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (27 bp):
GCCACAAAGGCTATTCATTCAGAGTAC
Found at i:6616040 original size:12 final size:12
Alignment explanation
Indices: 6616002--6616043 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
6615992 ATTGGTCATA
6616002 GAGAGATTTGAG
1 GAGAGATTTGAG
6616014 GAGGGAGATTT--G
1 GA--GAGATTTGAG
6616026 GAGAGATTTGAG
1 GAGAGATTTGAG
6616038 GAGAGA
1 GAGAGA
6616044 ATATTGGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 7 0.27
12 12 0.46
14 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.45, T:0.21
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:6616688 original size:27 final size:27
Alignment explanation
Indices: 6616658--6616915 Score: 286
Period size: 27 Copynumber: 9.6 Consensus size: 27
6616648 TTACACTATT
* *
6616658 ATGACTGAAATACCCCCACAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAGA
* * *
6616685 ATGACCGAAGTACCCCCATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAGA
* * *
6616712 ATGACCAAAATACCCTCATAGGATAGA
1 ATGACCGAAATACCCCCATAGGGTAGA
* * * *
6616739 ATGACCGAAACAGCCTCATAAGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAGA
** *
6616766 ATGACCGAAATACTTCCATAGGATAGA
1 ATGACCGAAATACCCCCATAGGGTAGA
* *
6616793 ATGACTGAAATA-CCCGATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAGA
* *
6616819 ATGACCGAAATACCCCTATAAGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAGA
* * *
6616846 ATAACCAAAATACCCCCATAAGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAGA
6616873 ATGACCGAAATACCCCCATAGGGTA-A
1 ATGACCGAAATACCCCCATAGGGTAGA
*
6616899 AGTGACCAAAATACCCC
1 A-TGACCGAAATACCCC
6616916 TGTAGGATAA
Statistics
Matches: 191, Mismatches: 38, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
26 23 0.12
27 168 0.88
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.17
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAGA
Found at i:6616922 original size:134 final size:135
Alignment explanation
Indices: 6616658--6616930 Score: 356
Period size: 134 Copynumber: 2.0 Consensus size: 135
6616648 TTACACTATT
* *
6616658 ATGACTGAAATACCCCCACAGGGTAGAATGACCGAAGTACCCCCATAAGGTAAAATGACCAAAAT
1 ATGACTGAAATACCCCCACAGGGTAGAATGACCGAAATACCCCCATAAGGTAAAATAACCAAAAT
* * * * *
6616723 ACCCTCATAGGATAGAATGACCGAAACAGCCTCATAAGGTAGAATGACCGAAATACTTCCATAGG
66 ACCCCCATAGGATAGAATGACCGAAACACCCCCATAAGGTAGAATGACCAAAATACTCCCATAGG
*
6616788 ATAGA
131 ATAAA
* * * *
6616793 ATGACTGAAATA-CCCGATAGGGTAGAATGACCGAAATACCCCTATAAGGTAGAATAACCAAAAT
1 ATGACTGAAATACCCCCACAGGGTAGAATGACCGAAATACCCCCATAAGGTAAAATAACCAAAAT
* * *
6616857 ACCCCCATAAGG-TAGAATGACCGAAATACCCCCATAGGGTA-AAGTGACCAAAATAC-CCCTGT
66 ACCCCCAT-AGGATAGAATGACCGAAACACCCCCATAAGGTAGAA-TGACCAAAATACTCCC-AT
6616919 AGGATAAA
128 AGGATAAA
6616927 ATGA
1 ATGA
6616931 TTGTTATACC
Statistics
Matches: 120, Mismatches: 15, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
133 4 0.03
134 101 0.84
135 15 0.12
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.17
Consensus pattern (135 bp):
ATGACTGAAATACCCCCACAGGGTAGAATGACCGAAATACCCCCATAAGGTAAAATAACCAAAAT
ACCCCCATAGGATAGAATGACCGAAACACCCCCATAAGGTAGAATGACCAAAATACTCCCATAGG
ATAAA
Found at i:6631949 original size:5 final size:5
Alignment explanation
Indices: 6631939--6631964 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6631929 AAACATATTA
6631939 AAACC AAACC AAACC AAACC AAACC A
1 AAACC AAACC AAACC AAACC AAACC A
6631965 TTCATATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:6638282 original size:38 final size:39
Alignment explanation
Indices: 6638205--6638291 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 39
6638195 TATAATTGCC
* * *
6638205 ATAATTATAATAATGTTTGACCAAAAAATTACAATTACA
1 ATAATTATAATAATATTCGACCAAAAAATTACAACTACA
* * *
6638244 ATAATTATAATAATATTCGATC-ATAAATTATAACTACA
1 ATAATTATAATAATATTCGACCAAAAAATTACAACTACA
6638282 ATAATTATAA
1 ATAATTATAA
6638292 CAAGGATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 23 0.55
39 19 0.45
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (39 bp):
ATAATTATAATAATATTCGACCAAAAAATTACAACTACA
Found at i:6639592 original size:13 final size:13
Alignment explanation
Indices: 6639574--6639598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6639564 TAATGGTATA
6639574 TTGAATCCATGAC
1 TTGAATCCATGAC
6639587 TTGAATCCATGA
1 TTGAATCCATGA
6639599 AAATTTAGTA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:6640176 original size:27 final size:27
Alignment explanation
Indices: 6640145--6640322 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
6640135 TAAATTGTAC
6640145 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
6640172 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
6640198 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
6640226 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
6640254 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
6640281 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
6640308 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6640323 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:6640259 original size:82 final size:81
Alignment explanation
Indices: 6640146--6640301 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
6640136 AAATTGTACA
* *
6640146 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
6640210 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
6640227 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
6640292 TGCGAGTTGA
65 TGCGAATTGA
6640302 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:6640313 original size:82 final size:81
Alignment explanation
Indices: 6640142--6640322 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
6640132 GATTAAATTG
* *
6640142 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
6640207 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
6640223 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
6640287 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
6640305 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
6640323 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:6640333 original size:27 final size:27
Alignment explanation
Indices: 6640227--6640333 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
6640217 TGACCATGCG
* * * *
6640227 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
6640255 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
6640282 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
6640309 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
6640334 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:6654572 original size:27 final size:27
Alignment explanation
Indices: 6654534--6654712 Score: 166
Period size: 27 Copynumber: 6.6 Consensus size: 27
6654524 TAAATTGTAC
6654534 AGCACTAAGTGTGCGGTTTGACTATGT
1 AGCACTAAGTGTGCGGTTTGACTATGT
* *** *
6654561 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGGTTTGACTATGT
** *
6654587 ATGCACTAAGTGTGCGAATTGA-TCATGC
1 A-GCACTAAGTGTGCGGTTTGACT-ATGT
*
6654615 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCG-GTTTGACTATGT
* * *
6654643 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGGTTTGACTATGT
* *
6654670 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCG-GTTTGACTATGT
*
6654697 AGCACTGAGTGTGCGG
1 AGCACTAAGTGTGCGG
6654713 GCTCAATATA
Statistics
Matches: 127, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.02
27 103 0.81
28 21 0.17
29 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGGTTTGACTATGT
Found at i:6654702 original size:82 final size:81
Alignment explanation
Indices: 6654531--6654712 Score: 240
Period size: 82 Copynumber: 2.2 Consensus size: 81
6654521 GATTAAATTG
* *
6654531 TACAGCACTAAGTGTGCGGTTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
6654596 GTGTGCGAATTGATCA
66 GTGTGCGAATTGATCA
* * ** *
6654612 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCG-GTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* *
6654676 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGATCA
* *
6654694 TATAGCACTGAGTGTGCGG
1 TACAGCACTAAGTGTGCGG
6654713 GCTCAATATA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
81 18 0.21
82 68 0.79
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGATCA
Found at i:6655459 original size:105 final size:106
Alignment explanation
Indices: 6655336--6655545 Score: 413
Period size: 106 Copynumber: 2.0 Consensus size: 106
6655326 TGAATTATGG
6655336 CATGTAAACTTTAAGCCATGCGAAAATGGCACGAATGTT-CGATTGAGTTGGATCAAGGGTAGGC
1 CATGTAAACTTTAAGCCATGCGAAAATGGCACGAATGTTCCGATTGAGTTGGATCAAGGGTAGGC
6655400 ATGAAATGGACCTAGTTACTTTCGTAACAGATGCTGGCAGC
66 ATGAAATGGACCTAGTTACTTTCGTAACAGATGCTGGCAGC
6655441 CATGTAAACTTTAAGCCATGCGAAAATGGCACGAATGTTCCGATTGAGTTGGATCAAGGGTAGGC
1 CATGTAAACTTTAAGCCATGCGAAAATGGCACGAATGTTCCGATTGAGTTGGATCAAGGGTAGGC
6655506 ATGAAATGGACCTAGTTACTTTCGTAACAGATGCTGGCAG
66 ATGAAATGGACCTAGTTACTTTCGTAACAGATGCTGGCAG
6655546 TAGCAGTGTC
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
105 39 0.38
106 65 0.62
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (106 bp):
CATGTAAACTTTAAGCCATGCGAAAATGGCACGAATGTTCCGATTGAGTTGGATCAAGGGTAGGC
ATGAAATGGACCTAGTTACTTTCGTAACAGATGCTGGCAGC
Found at i:6656073 original size:100 final size:100
Alignment explanation
Indices: 6655917--6656116 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
6655907 TGCAACTTGG
*
6655917 GAGACTTTGACTAATAAACTGTACTAATTGGCCCGACCAAAAATTCTAGAAAAAAATACATAGAT
1 GAGACTTTGACTAAAAAACTGTACTAATTGGCCCGACCAAAAATTCTAGAAAAAAATACATAGAT
6655982 GGGCACATGAGTCTAGTTTCTGGGAAAAATTACGA
66 GGGCACATGAGTCTAGTTTCTGGGAAAAATTACGA
6656017 GAGACTTTGACTAAAAAACTGTACTAATTGGCCCGACCAAAAATTCTAGAAAAAAATACATAGAT
1 GAGACTTTGACTAAAAAACTGTACTAATTGGCCCGACCAAAAATTCTAGAAAAAAATACATAGAT
*
6656082 GTGCACATGAGTCTAGTTTCTGGGAAAAATTACGA
66 GGGCACATGAGTCTAGTTTCTGGGAAAAATTACGA
6656117 AACTGATTTT
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (100 bp):
GAGACTTTGACTAAAAAACTGTACTAATTGGCCCGACCAAAAATTCTAGAAAAAAATACATAGAT
GGGCACATGAGTCTAGTTTCTGGGAAAAATTACGA
Found at i:6660700 original size:50 final size:50
Alignment explanation
Indices: 6660641--6660741 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
6660631 GTGTTTCTTA
*
6660641 AAGTTTCGCCTTGGAAAAAGGTATTCAGATTTGGCCGAAAGGGCAAGTTG
1 AAGTTTCGCCTTGGAAAAAGGTACTCAGATTTGGCCGAAAGGGCAAGTTG
6660691 AAGTTTCGCCTTGGAAAAAGGTACTCAGATTTGGCCGAAAGGGCAAGTTG
1 AAGTTTCGCCTTGGAAAAAGGTACTCAGATTTGGCCGAAAGGGCAAGTTG
6660741 A
1 A
6660742 GTCCGAGATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.25
Consensus pattern (50 bp):
AAGTTTCGCCTTGGAAAAAGGTACTCAGATTTGGCCGAAAGGGCAAGTTG
Found at i:6661713 original size:20 final size:20
Alignment explanation
Indices: 6661688--6661730 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6661678 TAGGACTAAA
* *
6661688 TCAGAAACATATAGAAATTT
1 TCAGAAAAAGATAGAAATTT
*
6661708 TCAGAAAAAGATGGAAATTT
1 TCAGAAAAAGATAGAAATTT
6661728 TCA
1 TCA
6661731 AACTACAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (20 bp):
TCAGAAAAAGATAGAAATTT
Found at i:6670710 original size:48 final size:49
Alignment explanation
Indices: 6670608--6670800 Score: 168
Period size: 48 Copynumber: 4.0 Consensus size: 49
6670598 ATAGATTTTG
* * * * * * *
6670608 CGGTGGTCTGCACACAG-TCTGTGCCACCTTTGTGTAATAATA-GATTCT
1 CGGTGGCCTGCACACAGTTC-GTGCCACCCTTGTATCATAACAGGAATAT
* * * *
6670656 CAGTGGCCTGCACATAGTTCGTGCCACCCTTGTATCTTAACAGGTCA-AT
1 CGGTGGCCTGCACACAGTTCGTGCCACCCTTGTATCATAACAGG-AATAT
* *
6670705 -GGTGGCCTGCACACAGTCCGTGCCACCCTT-TAATCGTAACA-GAATAT
1 CGGTGGCCTGCACACAGTTCGTGCCACCCTTGT-ATCATAACAGGAATAT
*
6670752 CGGTGGCCTGTACACAG-TCTGTGCCACCCTTGTATCATAACA-GAATAT
1 CGGTGGCCTGCACACAGTTC-GTGCCACCCTTGTATCATAACAGGAATAT
6670800 C
1 C
6670801 TGTACGCAAA
Statistics
Matches: 118, Mismatches: 19, Indels: 16
0.77 0.12 0.10
Matches are distributed among these distances:
46 1 0.01
47 5 0.04
48 107 0.91
49 5 0.04
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (49 bp):
CGGTGGCCTGCACACAGTTCGTGCCACCCTTGTATCATAACAGGAATAT
Found at i:6678017 original size:48 final size:48
Alignment explanation
Indices: 6677928--6678067 Score: 156
Period size: 48 Copynumber: 2.9 Consensus size: 48
6677918 ATAGATTTCG
* * * * * ***
6677928 CGGTGGTCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATTCT
1 CGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGACAAT
* *
6677976 CGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGGACAAT
1 CGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACA-GACAAT
* *
6678025 -GTTGGCCTGCACACAGTCCGTGCCACCCTTGTATCGTAACAGA
1 CGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGA
6678068 ATCCGTACCA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
47 2 0.03
48 73 0.94
49 3 0.04
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (48 bp):
CGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGACAAT
Found at i:6678141 original size:48 final size:47
Alignment explanation
Indices: 6678101--6678191 Score: 146
Period size: 48 Copynumber: 1.9 Consensus size: 47
6678091 ACAGATTCTC
* *
6678101 GGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGGACAAT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCGTAACA-GACAAT
*
6678149 GTTGGCCTGCACACAGTCCGTGCCACCCTTGTATCGTAACAGA
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCGTAACAGA
6678192 ATATCGGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 2 0.05
48 38 0.95
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (47 bp):
GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCGTAACAGACAAT
Found at i:6678165 original size:124 final size:124
Alignment explanation
Indices: 6677945--6678193 Score: 498
Period size: 124 Copynumber: 2.0 Consensus size: 124
6677935 CTGCACACAG
6677945 TCCGTACCACCTTTGTGTAATAACAGATTCTCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTA
1 TCCGTACCACCTTTGTGTAATAACAGATTCTCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTA
6678010 TCTTAACAGGACAATGTTGGCCTGCACACAGTCCGTGCCACCCTTGTATCGTAACAGAA
66 TCTTAACAGGACAATGTTGGCCTGCACACAGTCCGTGCCACCCTTGTATCGTAACAGAA
6678069 TCCGTACCACCTTTGTGTAATAACAGATTCTCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTA
1 TCCGTACCACCTTTGTGTAATAACAGATTCTCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTA
6678134 TCTTAACAGGACAATGTTGGCCTGCACACAGTCCGTGCCACCCTTGTATCGTAACAGAA
66 TCTTAACAGGACAATGTTGGCCTGCACACAGTCCGTGCCACCCTTGTATCGTAACAGAA
6678193 T
1 T
6678194 ATCGGTATGC
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (124 bp):
TCCGTACCACCTTTGTGTAATAACAGATTCTCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTA
TCTTAACAGGACAATGTTGGCCTGCACACAGTCCGTGCCACCCTTGTATCGTAACAGAA
Found at i:6690550 original size:21 final size:20
Alignment explanation
Indices: 6690524--6690565 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
6690514 TCACACCGCG
6690524 CCTTGC-TACTCGCACCAACAC
1 CCTTGCTTA-TCGCACC-ACAC
6690545 CCTTGCTTATCGCACCACAC
1 CCTTGCTTATCGCACCACAC
6690565 C
1 C
6690566 ATCAAGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 13 0.65
22 2 0.10
ACGTcount: A:0.21, C:0.48, G:0.10, T:0.21
Consensus pattern (20 bp):
CCTTGCTTATCGCACCACAC
Found at i:6690703 original size:17 final size:18
Alignment explanation
Indices: 6690674--6690708 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6690664 TTCTCCTAAA
*
6690674 TTTCAATTTTATTTAATT
1 TTTCAATTTTATTGAATT
6690692 TTTCAA-TTTATTGAATT
1 TTTCAATTTTATTGAATT
6690709 ATTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTCAATTTTATTGAATT
Found at i:6701456 original size:18 final size:18
Alignment explanation
Indices: 6701427--6701479 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
6701417 TGAATGAGTG
*
6701427 TAAAATTATAAAAATATTA
1 TAAAATTCTAAAAAT-TTA
*
6701446 -ATAATTCTAAAAATTTA
1 TAAAATTCTAAAAATTTA
6701463 TAAAATTCATAAAAATT
1 TAAAATTC-TAAAAATT
6701480 ATGAACTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 3 0.10
18 18 0.62
19 8 0.28
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTCTAAAAATTTA
Found at i:6701605 original size:18 final size:16
Alignment explanation
Indices: 6701578--6701619 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
6701568 TAAAAATATA
*
6701578 TTTTTTATATTTTTAT
1 TTTTTTATATTTTAAT
6701594 CTTTTTTCATATTTTAAT
1 -TTTTTT-ATATTTTAAT
6701612 TTTTTTAT
1 TTTTTTAT
6701620 GTCAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 9 0.39
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATATTTTAAT
Found at i:6705015 original size:22 final size:22
Alignment explanation
Indices: 6704985--6705065 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 22
6704975 AACATGCAGC
6704985 AAACAAATTTCTTCTCCATAAG
1 AAACAAATTTCTTCTCCATAAG
* *
6705007 AAACCAATTT-TCTCATCAATATGCAG
1 AAACAAATTTCT-TC-TCCATA---AG
* *
6705033 CAAACAAAATTCTTATCCATAAG
1 -AAACAAATTTCTTCTCCATAAG
*
6705056 AAACCAATTT
1 AAACAAATTT
6705066 TCTCATTGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
21 1 0.02
22 19 0.43
23 7 0.16
26 7 0.16
27 9 0.20
28 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (22 bp):
AAACAAATTTCTTCTCCATAAG
Found at i:6705068 original size:23 final size:23
Alignment explanation
Indices: 6704992--6705068 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
6704982 AGCAAACAAA
*
6704992 TTTCTTCTCCATAAGAAACCAAT
1 TTTCTTATCCATAAGAAACCAAT
* * *
6705015 TTTCTCATCAATATGCAGCAAA-CAAA
1 TTTCTTATCCATA---AG-AAACCAAT
*
6705041 ATTCTTATCCATAAGAAACCAAT
1 TTTCTTATCCATAAGAAACCAAT
6705064 TTTCT
1 TTTCT
6705069 CATTGATTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 3 0.08
23 19 0.47
26 15 0.38
27 3 0.08
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (23 bp):
TTTCTTATCCATAAGAAACCAAT
Found at i:6705092 original size:49 final size:49
Alignment explanation
Indices: 6704973--6705071 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
6704963 CTATCTCCCC
* * *
6704973 TCAACATGCAGCAAACAAATTTCTTCTCCATAAGAAACCAATTTTCTCA
1 TCAATATGCAGCAAACAAAATTCTTATCCATAAGAAACCAATTTTCTCA
6705022 TCAATATGCAGCAAACAAAATTCTTATCCATAAGAAACCAATTTTCTCA
1 TCAATATGCAGCAAACAAAATTCTTATCCATAAGAAACCAATTTTCTCA
6705071 T
1 T
6705072 TGATTCAATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.29
Consensus pattern (49 bp):
TCAATATGCAGCAAACAAAATTCTTATCCATAAGAAACCAATTTTCTCA
Found at i:6705131 original size:13 final size:13
Alignment explanation
Indices: 6705113--6705140 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6705103 TCAAATCGAC
6705113 GTTGTAGCAATAG
1 GTTGTAGCAATAG
6705126 GTTGTAGCAATAG
1 GTTGTAGCAATAG
6705139 GT
1 GT
6705141 ATAATTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.32
Consensus pattern (13 bp):
GTTGTAGCAATAG
Found at i:6706781 original size:17 final size:17
Alignment explanation
Indices: 6706759--6706792 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6706749 ATGGGGTAAG
6706759 ATGCTAATCTAATATTC
1 ATGCTAATCTAATATTC
*
6706776 ATGCTATTCTAATATTC
1 ATGCTAATCTAATATTC
6706793 TTGACATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (17 bp):
ATGCTAATCTAATATTC
Found at i:6706889 original size:17 final size:17
Alignment explanation
Indices: 6706867--6706900 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6706857 ATGGGGTAAG
6706867 ATGCTAATCTAATATTC
1 ATGCTAATCTAATATTC
*
6706884 ATGCTATTCTAATATTC
1 ATGCTAATCTAATATTC
6706901 TTGACATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (17 bp):
ATGCTAATCTAATATTC
Found at i:6706916 original size:108 final size:108
Alignment explanation
Indices: 6706735--6706949 Score: 421
Period size: 108 Copynumber: 2.0 Consensus size: 108
6706725 TCATGATTGA
6706735 ACAGTATGCCCGGGATGGGGTAAGATGCTAATCTAATATTCATGCTATTCTAATATTCTTGACAT
1 ACAGTATGCCCGGGATGGGGTAAGATGCTAATCTAATATTCATGCTATTCTAATATTCTTGACAT
6706800 CTTACTTTCTATATCTTACGCACACGTTATGACTAATGATAAT
66 CTTACTTTCTATATCTTACGCACACGTTATGACTAATGATAAT
6706843 ACAGTATGCCCGGGATGGGGTAAGATGCTAATCTAATATTCATGCTATTCTAATATTCTTGACAT
1 ACAGTATGCCCGGGATGGGGTAAGATGCTAATCTAATATTCATGCTATTCTAATATTCTTGACAT
*
6706908 CTTACTTTCTATATCTTACGCACACGTTATGACTAATTATAA
66 CTTACTTTCTATATCTTACGCACACGTTATGACTAATGATAA
6706950 CCATGTTATT
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (108 bp):
ACAGTATGCCCGGGATGGGGTAAGATGCTAATCTAATATTCATGCTATTCTAATATTCTTGACAT
CTTACTTTCTATATCTTACGCACACGTTATGACTAATGATAAT
Found at i:6707908 original size:15 final size:14
Alignment explanation
Indices: 6707868--6707896 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6707858 TTTTTGTATC
6707868 AATTTAATTATTCT
1 AATTTAATTATTCT
6707882 AATTTAATTATTCT
1 AATTTAATTATTCT
6707896 A
1 A
6707897 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:6711848 original size:11 final size:11
Alignment explanation
Indices: 6711829--6711861 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
6711819 AAATTGTAGT
6711829 TTCAAAAAAAA
1 TTCAAAAAAAA
6711840 -TCGAAAAAAAA
1 TTC-AAAAAAAA
6711851 TTCAAAAAAAA
1 TTCAAAAAAAA
6711862 GGATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.15
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:6714116 original size:29 final size:30
Alignment explanation
Indices: 6714066--6714123 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
6714056 GAGTGATAAA
*
6714066 AAAAAGAGAGAGTGATTCAAAA-GAAAAAG
1 AAAAAGAAAGAGTGATTCAAAATGAAAAAG
*
6714095 AAAAAGAAACGAGTGA-TGAAAATGAAAAA
1 AAAAAGAAA-GAGTGATTCAAAATGAAAAA
6714124 AGAGTTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.64, C:0.03, G:0.22, T:0.10
Consensus pattern (30 bp):
AAAAAGAAAGAGTGATTCAAAATGAAAAAG
Found at i:6717181 original size:18 final size:18
Alignment explanation
Indices: 6717155--6717192 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6717145 ATCCCAATGA
* *
6717155 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
6717173 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
6717191 TC
1 TC
6717193 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:6717199 original size:18 final size:18
Alignment explanation
Indices: 6717158--6717199 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6717148 CCAATGATCG
* *
6717158 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
6717176 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
6717194 CCACCA
1 CCACCA
6717200 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:6717919 original size:12 final size:12
Alignment explanation
Indices: 6717902--6717978 Score: 77
Period size: 12 Copynumber: 6.4 Consensus size: 12
6717892 ACTAGTTTTT
*
6717902 TACTAACAATAA
1 TACTAATAATAA
*
6717914 TACTAAGTAA-CA
1 TACTAA-TAATAA
6717926 T-CTTAATAATAA
1 TAC-TAATAATAA
*
6717938 TAATAATAATAA
1 TACTAATAATAA
*
6717950 TAATAATAATAA
1 TACTAATAATAA
*
6717962 TAATAATAATAA
1 TACTAATAATAA
6717974 TACTA
1 TACTA
6717979 TAACATCCTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
11 4 0.07
12 50 0.89
13 2 0.04
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.32
Consensus pattern (12 bp):
TACTAATAATAA
Found at i:6717937 original size:3 final size:3
Alignment explanation
Indices: 6717929--6717975 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
6717919 AGTAACATCT
6717929 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6717976 CTATAACATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6718835 original size:1 final size:1
Alignment explanation
Indices: 6718829--6718880 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
6718819 TCAGTTCAGG
* * * * *
6718829 TTTTTTTTTCTTTTTTTATTTTTTTTTGTTTTTTTGTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6718881 ATATATTTTG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.02, C:0.02, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:6718852 original size:18 final size:18
Alignment explanation
Indices: 6718829--6718880 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
6718819 TCAGTTCAGG
*
6718829 TTTTTTTTTCTTTTTTTA
1 TTTTTTTTTGTTTTTTTA
*
6718847 TTTTTTTTTGTTTTTTTG
1 TTTTTTTTTGTTTTTTTA
6718865 TTTTTTTTTGTTTTTT
1 TTTTTTTTTGTTTTTT
6718881 ATATATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.02, C:0.02, G:0.06, T:0.90
Consensus pattern (18 bp):
TTTTTTTTTGTTTTTTTA
Found at i:6718910 original size:27 final size:27
Alignment explanation
Indices: 6718880--6718947 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
6718870 TTTTGTTTTT
6718880 TATATATTTTGGTAAATAAAAAAATTA
1 TATATATTTTGGTAAATAAAAAAATTA
* *
6718907 TATATTTTTTGGTAAATAAAAAAGTTA
1 TATATATTTTGGTAAATAAAAAAATTA
*
6718934 TA-ATATTTTAGTAA
1 TATATATTTTGGTAA
6718948 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 10 0.27
27 27 0.73
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (27 bp):
TATATATTTTGGTAAATAAAAAAATTA
Found at i:6720113 original size:15 final size:16
Alignment explanation
Indices: 6720088--6720117 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6720078 TATATTATTA
6720088 AATTATTATTTTAAAT
1 AATTATTATTTTAAAT
6720104 AATT-TTATTTTAAA
1 AATTATTATTTTAAA
6720118 AAGTTTCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTATTATTTTAAAT
Found at i:6720333 original size:27 final size:26
Alignment explanation
Indices: 6720286--6720337 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
6720276 TTTTAAATAA
*
6720286 ATAATAATATAGTTATGAAATTCAAAC
1 ATAATAATATAGTAATGAAA-TCAAAC
*
6720313 ATAATAATATA-TAACTTAAATCAAA
1 ATAATAATATAGTAA-TGAAATCAAA
6720338 TAATTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (26 bp):
ATAATAATATAGTAATGAAATCAAAC
Found at i:6724733 original size:22 final size:24
Alignment explanation
Indices: 6724681--6724733 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
6724671 ATAATACAAG
*
6724681 TATTTTTTTTATAAAAAGATTAAA
1 TATTTTTTTTATAAAAACATTAAA
6724705 TAGTTTTTTTTA-AAAGAACA-T-AA
1 TA-TTTTTTTTATAAA-AACATTAAA
6724728 TATTTT
1 TATTTT
6724734 CTAAATGACG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 6 0.23
25 12 0.46
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (24 bp):
TATTTTTTTTATAAAAACATTAAA
Found at i:6728922 original size:28 final size:28
Alignment explanation
Indices: 6728890--6728945 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
6728880 TCGGCTTGAC
* *
6728890 TTAGACATCATTAA-AGCATGTAATAAAA
1 TTAGACA-CATTAATAACATATAATAAAA
6728918 TTAGACACATTAATAACATATAATAAAA
1 TTAGACACATTAATAACATATAATAAAA
6728946 ACACATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29
Consensus pattern (28 bp):
TTAGACACATTAATAACATATAATAAAA
Found at i:6733838 original size:14 final size:15
Alignment explanation
Indices: 6733821--6733850 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6733811 GTTTTCTCAC
6733821 TCTAT-TTTTCTTTT
1 TCTATCTTTTCTTTT
6733835 TCTATCTTTTCTTTT
1 TCTATCTTTTCTTTT
6733850 T
1 T
6733851 GCTCCTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (15 bp):
TCTATCTTTTCTTTT
Found at i:6742089 original size:22 final size:22
Alignment explanation
Indices: 6742022--6742096 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
6742012 CAAAAGTGTT
*
6742022 ATTAGTGGTAGCTT-ATCTACAA
1 ATTAGTGGTAG-TTCATCTGCAA
* * *
6742044 ACTAGTGGCAGTTCATCTGTAA
1 ATTAGTGGTAGTTCATCTGCAA
*
6742066 ATTAGTGGTAGTTCATATGCAA
1 ATTAGTGGTAGTTCATCTGCAA
*
6742088 ATCAGTGGT
1 ATTAGTGGT
6742097 GGCTTGTTCA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
21 2 0.05
22 41 0.95
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (22 bp):
ATTAGTGGTAGTTCATCTGCAA
Found at i:6749418 original size:340 final size:340
Alignment explanation
Indices: 6748798--6749477 Score: 1360
Period size: 340 Copynumber: 2.0 Consensus size: 340
6748788 ATGTGTTCAC
6748798 ACGATTTGGGACACCAAGAGCTATTATTAGTGATGAAGGTTCTCACTTTGTGAACAAATGACTTA
1 ACGATTTGGGACACCAAGAGCTATTATTAGTGATGAAGGTTCTCACTTTGTGAACAAATGACTTA
6748863 AGTGGTTGCGTGACAAATATGATGTGAAGCATAAGATTGGTACTGCCTATCACCCCTAGTGTAAT
66 AGTGGTTGCGTGACAAATATGATGTGAAGCATAAGATTGGTACTGCCTATCACCCCTAGTGTAAT
6748928 GAGCAAGTTGAAAGAGTGAATCACGAAATCAAAGGTATCCTTGAAAAGGTAGTACGCCCTAGCAG
131 GAGCAAGTTGAAAGAGTGAATCACGAAATCAAAGGTATCCTTGAAAAGGTAGTACGCCCTAGCAG
6748993 AAAATATTGGTCTCGAAGGCTCGATGATGCATTATGGGCCTATCGAACATCATTTAAGACTCCGT
196 AAAATATTGGTCTCGAAGGCTCGATGATGCATTATGGGCCTATCGAACATCATTTAAGACTCCGT
6749058 TAGGAATGACTCCTTATCGATTAGTCTTTGGAAAGGCATGTCATTTGCCATTAGAGTTGGAAAAT
261 TAGGAATGACTCCTTATCGATTAGTCTTTGGAAAGGCATGTCATTTGCCATTAGAGTTGGAAAAT
6749123 AAAGCTCACTGGGCT
326 AAAGCTCACTGGGCT
6749138 ACGATTTGGGACACCAAGAGCTATTATTAGTGATGAAGGTTCTCACTTTGTGAACAAATGACTTA
1 ACGATTTGGGACACCAAGAGCTATTATTAGTGATGAAGGTTCTCACTTTGTGAACAAATGACTTA
6749203 AGTGGTTGCGTGACAAATATGATGTGAAGCATAAGATTGGTACTGCCTATCACCCCTAGTGTAAT
66 AGTGGTTGCGTGACAAATATGATGTGAAGCATAAGATTGGTACTGCCTATCACCCCTAGTGTAAT
6749268 GAGCAAGTTGAAAGAGTGAATCACGAAATCAAAGGTATCCTTGAAAAGGTAGTACGCCCTAGCAG
131 GAGCAAGTTGAAAGAGTGAATCACGAAATCAAAGGTATCCTTGAAAAGGTAGTACGCCCTAGCAG
6749333 AAAATATTGGTCTCGAAGGCTCGATGATGCATTATGGGCCTATCGAACATCATTTAAGACTCCGT
196 AAAATATTGGTCTCGAAGGCTCGATGATGCATTATGGGCCTATCGAACATCATTTAAGACTCCGT
6749398 TAGGAATGACTCCTTATCGATTAGTCTTTGGAAAGGCATGTCATTTGCCATTAGAGTTGGAAAAT
261 TAGGAATGACTCCTTATCGATTAGTCTTTGGAAAGGCATGTCATTTGCCATTAGAGTTGGAAAAT
6749463 AAAGCTCACTGGGCT
326 AAAGCTCACTGGGCT
6749478 TTAAAGCAGT
Statistics
Matches: 340, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
340 340 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (340 bp):
ACGATTTGGGACACCAAGAGCTATTATTAGTGATGAAGGTTCTCACTTTGTGAACAAATGACTTA
AGTGGTTGCGTGACAAATATGATGTGAAGCATAAGATTGGTACTGCCTATCACCCCTAGTGTAAT
GAGCAAGTTGAAAGAGTGAATCACGAAATCAAAGGTATCCTTGAAAAGGTAGTACGCCCTAGCAG
AAAATATTGGTCTCGAAGGCTCGATGATGCATTATGGGCCTATCGAACATCATTTAAGACTCCGT
TAGGAATGACTCCTTATCGATTAGTCTTTGGAAAGGCATGTCATTTGCCATTAGAGTTGGAAAAT
AAAGCTCACTGGGCT
Found at i:6766004 original size:15 final size:15
Alignment explanation
Indices: 6765984--6766015 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6765974 TTTTACTTAG
*
6765984 TAGTTTTATTTAATT
1 TAGTTTAATTTAATT
6765999 TAGTTTAATTTAATT
1 TAGTTTAATTTAATT
6766014 TA
1 TA
6766016 TACAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TAGTTTAATTTAATT
Found at i:6768069 original size:26 final size:26
Alignment explanation
Indices: 6768040--6768126 Score: 111
Period size: 26 Copynumber: 3.3 Consensus size: 26
6768030 CCCATAGCTT
* *
6768040 GTGTGAGCAGACCCATTTCACAACTC
1 GTGTGAGCATACCTATTTCACAACTC
* * *
6768066 GTGTAAGCATACCTATTTCATAGCTC
1 GTGTGAGCATACCTATTTCACAACTC
*
6768092 GTGTGAACATACCTATTTCACAACTC
1 GTGTGAGCATACCTATTTCACAACTC
*
6768118 ATGTGAGCA
1 GTGTGAGCA
6768127 ACTATGTATA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (26 bp):
GTGTGAGCATACCTATTTCACAACTC
Found at i:6773873 original size:20 final size:20
Alignment explanation
Indices: 6773848--6773886 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6773838 TTATACAAGA
6773848 TTGCACATTGGTGCCTCTGT
1 TTGCACATTGGTGCCTCTGT
*
6773868 TTGCACATTGGTGTCTCTG
1 TTGCACATTGGTGCCTCTG
6773887 CTTACACTTC
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:0.10, C:0.23, G:0.26, T:0.41
Consensus pattern (20 bp):
TTGCACATTGGTGCCTCTGT
Found at i:6774879 original size:22 final size:20
Alignment explanation
Indices: 6774854--6774905 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
6774844 ATAGGTAAGT
6774854 TTATGTACTATAAATATATGGC
1 TTATG-ACT-TAAATATATGGC
**
6774876 TTATGACTTATTTATATGGC
1 TTATGACTTAAATATATGGC
*
6774896 TTGTGACTTA
1 TTATGACTTA
6774906 TTTATATGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 19 0.70
21 3 0.11
22 5 0.19
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (20 bp):
TTATGACTTAAATATATGGC
Found at i:6774893 original size:20 final size:20
Alignment explanation
Indices: 6774868--6774918 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
6774858 GTACTATAAA
6774868 TATATGGCTTATGACTTATT
1 TATATGGCTTATGACTTATT
*
6774888 TATATGGCTTGTGACTTATT
1 TATATGGCTTATGACTTATT
6774908 TATATGTGCTT
1 TATATG-GCTT
6774919 GAAGTGGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.51
Consensus pattern (20 bp):
TATATGGCTTATGACTTATT
Found at i:6779083 original size:20 final size:20
Alignment explanation
Indices: 6779054--6779096 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6779044 TTGAAATGCT
6779054 AACAGAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
* * *
6779074 AACAGTGGCATCGAAGTGCA
1 AACAGAGGCACCAAAGTGCA
6779094 AAC
1 AAC
6779097 CCATACAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (20 bp):
AACAGAGGCACCAAAGTGCA
Found at i:6780434 original size:25 final size:25
Alignment explanation
Indices: 6780405--6780524 Score: 177
Period size: 25 Copynumber: 4.8 Consensus size: 25
6780395 GTATTGTATT
*
6780405 TGAAATGAATCCTTTGTGGCATATC
1 TGAAATGAAGCCTTTGTGGCATATC
* ** *
6780430 TGAAATGAAGCATTTGTGGTGTATT
1 TGAAATGAAGCCTTTGTGGCATATC
6780455 TGAAATGAAGCCTTTGTGGCATATC
1 TGAAATGAAGCCTTTGTGGCATATC
*
6780480 TGAAATGAAGCCTCTGTGGCATATC
1 TGAAATGAAGCCTTTGTGGCATATC
*
6780505 TGAAATGAAGCCTTTATGGC
1 TGAAATGAAGCCTTTGTGGC
6780525 GTATTGATAA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 83 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (25 bp):
TGAAATGAAGCCTTTGTGGCATATC
Found at i:6782551 original size:41 final size:40
Alignment explanation
Indices: 6782500--6782654 Score: 229
Period size: 41 Copynumber: 3.8 Consensus size: 40
6782490 TTCAGGTTAC
* *
6782500 CGAAGCACAAACAGGGGCACGTAAGTTCAATTTAGGGGTA
1 CGAAGTACAAACAGGGGCACGTAAGTGCAATTTAGGGGTA
* * *
6782540 TCGAAGTACAAACAGGGGCATGTAAGTGTAATTAAGGGGTA
1 -CGAAGTACAAACAGGGGCACGTAAGTGCAATTTAGGGGTA
6782581 CCGAAGTACAAACAGGGGCACGTAAGTGCAATTTAGGGGTA
1 -CGAAGTACAAACAGGGGCACGTAAGTGCAATTTAGGGGTA
*
6782622 CTGAAGTACAAACGGGGGCACGTAAGTGCAATT
1 C-GAAGTACAAACAGGGGCACGTAAGTGCAATT
6782655 CAGAGAATAG
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
40 1 0.01
41 102 0.99
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (40 bp):
CGAAGTACAAACAGGGGCACGTAAGTGCAATTTAGGGGTA
Found at i:6782566 original size:20 final size:20
Alignment explanation
Indices: 6782506--6782566 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
6782496 TTACCGAAGC
*
6782506 ACAAACAGGGGCACGTAAGT
1 ACAAACAGGGGCATGTAAGT
* ** *
6782526 TCAATTTAGGGGTATCG-AAGT
1 ACAA-ACAGGGGCAT-GTAAGT
6782547 ACAAACAGGGGCATGTAAGT
1 ACAAACAGGGGCATGTAAGT
6782567 GTAATTAAGG
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 13 0.45
22 1 0.03
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.20
Consensus pattern (20 bp):
ACAAACAGGGGCATGTAAGT
Found at i:6782607 original size:20 final size:20
Alignment explanation
Indices: 6782506--6782648 Score: 78
Period size: 21 Copynumber: 7.0 Consensus size: 20
6782496 TTACCGAAGC
6782506 ACAAACAGGGGCACGTAAGT
1 ACAAACAGGGGCACGTAAGT
* ** *
6782526 TCAATTTAGGGGTATCG-AAGT
1 ACAA-ACAGGGGCA-CGTAAGT
*
6782547 ACAAACAGGGGCATGTAAGT
1 ACAAACAGGGGCACGTAAGT
** *
6782567 GTAATTA-AGGGGTACCG-AAGT
1 ACAA--ACAGGGGCA-CGTAAGT
6782588 ACAAACAGGGGCACGTAAGT
1 ACAAACAGGGGCACGTAAGT
* ** *
6782608 GCAATTTAGGGGTAC-TGAAGT
1 ACAA-ACAGGGGCACGT-AAGT
*
6782629 ACAAACGGGGGCACGTAAGT
1 ACAAACAGGGGCACGTAAGT
6782649 GCAATTCAGA
Statistics
Matches: 87, Mismatches: 25, Indels: 22
0.65 0.19 0.16
Matches are distributed among these distances:
19 4 0.05
20 39 0.45
21 40 0.46
22 4 0.05
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (20 bp):
ACAAACAGGGGCACGTAAGT
Found at i:6782613 original size:82 final size:82
Alignment explanation
Indices: 6782497--6782654 Score: 255
Period size: 82 Copynumber: 1.9 Consensus size: 82
6782487 GTATTCAGGT
* *
6782497 TACCGAAGCACAAACAGGGGCACGTAAGTTCAATTTAGGGGTA-TCGAAGTACAAACAGGGGCAT
1 TACCGAAGCACAAACAGGGGCACGTAAGTGCAATTTAGGGGTACT-GAAGTACAAACAGGGGCAC
*
6782561 GTAAGTGTAATTAAGGGG
65 GTAAGTGCAATTAAGGGG
* *
6782579 TACCGAAGTACAAACAGGGGCACGTAAGTGCAATTTAGGGGTACTGAAGTACAAACGGGGGCACG
1 TACCGAAGCACAAACAGGGGCACGTAAGTGCAATTTAGGGGTACTGAAGTACAAACAGGGGCACG
6782644 TAAGTGCAATT
66 TAAGTGCAATT
6782655 CAGAGAATAG
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
82 69 0.99
83 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (82 bp):
TACCGAAGCACAAACAGGGGCACGTAAGTGCAATTTAGGGGTACTGAAGTACAAACAGGGGCACG
TAAGTGCAATTAAGGGG
Found at i:6789554 original size:27 final size:27
Alignment explanation
Indices: 6789516--6789874 Score: 319
Period size: 27 Copynumber: 13.3 Consensus size: 27
6789506 ATTCATGGGC
*
6789516 AAATGACTGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCCCGAAGGGTA
* *
6789543 AAATGATCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCCCGAAGGGTA
* * * *
6789570 AAATGACCGAACTACCCTCGAAAGTTA
1 AAATGACCGAAATACCCCCGAAGGGTA
* *
6789597 AAATGGCCGAAATACCCCC-ATAGGATA
1 AAATGACCGAAATACCCCCGA-AGGGTA
* * * * *
6789624 AAATG-CCAAAAATATCCTCGATGGATA
1 AAATGACC-GAAATACCCCCGAAGGGTA
* ** *
6789651 AAATGATCGAAATACCCCTAAAGAGTA
1 AAATGACCGAAATACCCCCGAAGGGTA
* * *
6789678 AAATGAACGAAATACACCCGAAAGGTA
1 AAATGACCGAAATACCCCCGAAGGGTA
* **
6789705 AACTGACCGAAATACCTTCGAAGGGTA
1 AAATGACCGAAATACCCCCGAAGGGTA
* * * * *
6789732 AAATCACTGAAATACCTCTGAATGGTA
1 AAATGACCGAAATACCCCCGAAGGGTA
* *
6789759 AAATGACCTAAATA-CCCCAAAGGGTA
1 AAATGACCGAAATACCCCCGAAGGGTA
* ** *
6789785 AAACGACTAAAATACCCCCCGTAGGGTA
1 AAATGACCGAAATA-CCCCCGAAGGGTA
*
6789813 AAATGACCAAAATACCCCCTGAAGGGTA
1 AAATGACCGAAATACCCCC-GAAGGGTA
**
6789841 AAATGATTGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCCCGAAGGGTA
6789868 AAATGAC
1 AAATGAC
6789875 TGTTATACCC
Statistics
Matches: 263, Mismatches: 62, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
26 22 0.08
27 194 0.74
28 47 0.18
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCGAAGGGTA
Found at i:6790078 original size:26 final size:26
Alignment explanation
Indices: 6790049--6790116 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
6790039 ATTGTTTCTA
*
6790049 GCAGCTTTGTTGCGATGCTGA-TACTG
1 GCAGCTTTGCTGCGATGCT-ACTACTG
* *
6790075 GCAGCTCTACTGCGATGCTACTACTG
1 GCAGCTTTGCTGCGATGCTACTACTG
*
6790101 GCAGCTTTGCTACGAT
1 GCAGCTTTGCTGCGAT
6790117 ATTGGTGTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 1 0.03
26 34 0.97
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (26 bp):
GCAGCTTTGCTGCGATGCTACTACTG
Found at i:6802028 original size:17 final size:16
Alignment explanation
Indices: 6802000--6802052 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
6801990 TTTGGTTCAC
6802000 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6802016 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
6802033 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6802049 TGTA
1 TGTA
6802053 ATAGCAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:6802309 original size:18 final size:17
Alignment explanation
Indices: 6802288--6802322 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6802278 TTATTATTAA
*
6802288 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
6802306 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
6802323 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:6802376 original size:157 final size:157
Alignment explanation
Indices: 6802175--6802491 Score: 571
Period size: 157 Copynumber: 2.0 Consensus size: 157
6802165 TAGAATACCC
* * *
6802175 TTAGCATAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTCAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
6802240 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAAATATTATTAAATATATTTAAATTAAAA
6802305 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
6802332 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
6802397 ATATCAATAATAAATAATTTAATCATATTTAAACATAAATATTATTAAATATATTTAAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAAATATTATTAAATATATTTAAATTAAAA
6802462 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
6802489 TTA
1 TTA
6802492 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 153 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAAATATTATTAAATATATTTAAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Done.