Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 123 of 325
Found at i:38315033 original size:18 final size:20
Alignment explanation
Indices: 38314992--38315036 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
38314982 ATTTTTTTGT
* *
38314992 ATTTTTATGAAAATTTTTAT
1 ATTTTTAAGAAAATTTTTAA
38315012 ATTTTTAAG-AAA-TTTTAA
1 ATTTTTAAGAAAATTTTTAA
38315030 ATTTTTA
1 ATTTTTA
38315037 CACTGACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 12 0.52
19 3 0.13
20 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
ATTTTTAAGAAAATTTTTAA
Found at i:38315332 original size:13 final size:14
Alignment explanation
Indices: 38315305--38315331 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38315295 TTCGCCTATG
38315305 TATTGATGAAAAAA
1 TATTGATGAAAAAA
38315319 TATTGATGAAAAA
1 TATTGATGAAAAA
38315332 TGGGGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
TATTGATGAAAAAA
Found at i:38321688 original size:61 final size:61
Alignment explanation
Indices: 38321593--38321710 Score: 227
Period size: 61 Copynumber: 1.9 Consensus size: 61
38321583 ATCATGTCCA
*
38321593 TGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGCAAAGTCAACCAACATCT
1 TGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAACATCT
38321654 TGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAAC
1 TGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAAC
38321711 TTCATAACTC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (61 bp):
TGTGTATACTCATATTTAAAAATATAGTCCTTTAAGCAAATTGAAAAGTCAACCAACATCT
Found at i:38329975 original size:17 final size:19
Alignment explanation
Indices: 38329933--38329977 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
38329923 CTCAAAGTAA
*
38329933 AGAAAATAAGCATAACAAT
1 AGAAAATAAGCACAACAAT
*
38329952 AGAAAATAAG-ACAACCAT
1 AGAAAATAAGCACAACAAT
38329970 -GAAAATAA
1 AGAAAATAA
38329978 AGCTTGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.13
Consensus pattern (19 bp):
AGAAAATAAGCACAACAAT
Found at i:38332831 original size:14 final size:15
Alignment explanation
Indices: 38332806--38332834 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38332796 AATATTTGTA
38332806 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
38332821 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
38332835 TACCATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:38339881 original size:36 final size:39
Alignment explanation
Indices: 38339737--38339945 Score: 199
Period size: 40 Copynumber: 5.6 Consensus size: 39
38339727 AGCTCTTGTT
*
38339737 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAG-CCGGATT-TAGTAACTCGCA
* *
38339777 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTT-AGCCGGATTTAGTAACTCGCA
* *
38339817 CAAATG-CTTTGGGACTTAACC-GATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCGGATTTAGTAACTCGCA
* *
38339854 C-AATGCCTTCGGG-C-TAGCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCGGATTTAGTAACTCGCA
* * * *
38339890 CAAATG-CTTC-GGATTTAGTCCGGATATGGT-ACT--TA
1 CAAATGCCTTCGGGACTTAG-CCGGATTTAGTAACTCGCA
38339925 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
38339946 CGGACATCAT
Statistics
Matches: 142, Mismatches: 17, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
34 1 0.01
35 17 0.12
36 31 0.22
37 32 0.23
38 11 0.08
39 10 0.07
40 37 0.26
41 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCGGATTTAGTAACTCGCA
Found at i:38339945 original size:73 final size:74
Alignment explanation
Indices: 38339763--38339945 Score: 178
Period size: 73 Copynumber: 2.5 Consensus size: 74
38339753 ATAGCCCGGT
* * * *
38339763 TATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCTTTG
1 TATAGTAACTC-CACAA-AGCCTTCGGGACTT-AGCCGGAATTAGTAACTCGCACAAATGCTTTC
38339828 GGACTTAACCGA
63 GGACTTAACCGA
* * *
38339840 TTTAGTAACTCGCACAATGCCTTCGGG-C-TAGCCGGAATTAGTATCTCGCACAAATGC-TTCGG
1 TATAGTAACTC-CACAAAGCCTTCGGGACTTAGCCGGAATTAGTAACTCGCACAAATGCTTTCGG
* *
38339902 ATTTAGTCCGGA
65 ACTTA-ACC-GA
* *
38339914 TATGGT-ACT-TACAAAGCCTTCGGGACTTAGCC
1 TATAGTAACTCCACAAAGCCTTCGGGACTTAGCC
38339946 CGGACATCAT
Statistics
Matches: 91, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
71 13 0.14
72 9 0.10
73 35 0.38
74 7 0.08
75 1 0.01
76 10 0.11
77 16 0.18
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (74 bp):
TATAGTAACTCCACAAAGCCTTCGGGACTTAGCCGGAATTAGTAACTCGCACAAATGCTTTCGGA
CTTAACCGA
Found at i:38347757 original size:39 final size:40
Alignment explanation
Indices: 38347666--38347888 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
38347656 GCTCCTCGTT
*
38347666 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
38347706 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACT-GCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
38347745 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
38347785 C-AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
38347823 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
38347864 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38347889 CATCATTCAA
Statistics
Matches: 163, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 25 0.15
39 60 0.37
40 65 0.40
41 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:38347769 original size:79 final size:80
Alignment explanation
Indices: 38347666--38347888 Score: 287
Period size: 79 Copynumber: 2.8 Consensus size: 80
38347656 GCTCCTCGTT
* *
38347666 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
38347731 ATTTAGTAACT-GCA
66 AATTAGTAACTCGCA
*
38347745 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCAC-AATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
38347807 GAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
* * * * *
38347823 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
38347886 GGA
64 GGA
38347889 CATCATTCAA
Statistics
Matches: 126, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
77 22 0.17
78 39 0.31
79 50 0.40
80 15 0.12
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:38349545 original size:28 final size:25
Alignment explanation
Indices: 38349490--38349548 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
38349480 ACATTTGTAT
* * *
38349490 TTTATTTAATATTACTATAATTATA
1 TTTATTTAATAATAATATAATTAAA
38349515 TTTATTTAATAATAATATAAAATTTAAA
1 TTTATTTAATAATAATAT--AA-TTAAA
38349543 TTTATT
1 TTTATT
38349549 ATTATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 16 0.57
27 2 0.07
28 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTATTTAATAATAATATAATTAAA
Found at i:38349653 original size:17 final size:17
Alignment explanation
Indices: 38349631--38349667 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
38349621 TTTTTATTTA
38349631 TATATATTTAAAATATT
1 TATATATTTAAAATATT
* *
38349648 TATATATTTTATATATT
1 TATATATTTAAAATATT
38349665 TAT
1 TAT
38349668 TTGAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATATTTAAAATATT
Found at i:38351040 original size:52 final size:55
Alignment explanation
Indices: 38350933--38351052 Score: 174
Period size: 52 Copynumber: 2.2 Consensus size: 55
38350923 GTAACGGTTT
* *
38350933 ATTTTAAATTTTGAATATTATTTAATATTTTTTTTCATTTCTGTAATTTTAATTA
1 ATTTTAATTTTTGAATATTATTTAATATTTTTTTTCATTTATGTAATTTTAATTA
*
38350988 ATTTTAATTTTTGAATATTATTT-A-A-TTTTTTTCATTTATGTAATTTTCATTA
1 ATTTTAATTTTTGAATATTATTTAATATTTTTTTTCATTTATGTAATTTTAATTA
*
38351040 ATTTGTATTTTTT
1 ATTT-TAATTTTT
38351053 TTATTATAGT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
52 29 0.48
53 8 0.13
54 1 0.02
55 22 0.37
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.64
Consensus pattern (55 bp):
ATTTTAATTTTTGAATATTATTTAATATTTTTTTTCATTTATGTAATTTTAATTA
Found at i:38351990 original size:7 final size:7
Alignment explanation
Indices: 38351978--38352009 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
38351968 AGTCGCTTCA
38351978 TATTTAG
1 TATTTAG
38351985 TATTTAG
1 TATTTAG
38351992 TATTTAG
1 TATTTAG
38351999 TATTTAG
1 TATTTAG
38352006 TATT
1 TATT
38352010 ATTTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:38353090 original size:27 final size:26
Alignment explanation
Indices: 38353060--38353119 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
38353050 TATTGTTTCA
38353060 TTTAATAAAAAAATAATTTTTTTATAT
1 TTTAATAAAAAAATAATTTTTTTAT-T
** *
38353087 TTTAATAGTAAATTAATTTTTTTATT
1 TTTAATAAAAAAATAATTTTTTTATT
38353113 TTATAAT
1 TT-TAAT
38353120 TTTAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTAATAAAAAAATAATTTTTTTATT
Found at i:38353143 original size:33 final size:31
Alignment explanation
Indices: 38353079--38353143 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
38353069 AAAATAATTT
*
38353079 TTTTATATTTTAATAGTAAATTAATTTTTTTA
1 TTTTATATTTTAATAG-AAATTAATTCTTTTA
38353111 TTTTATAATTTTAATA-AAATATAAGTTCTTTTA
1 TTTTAT-ATTTTAATAGAAAT-TAA-TTCTTTTA
38353144 AATAAGGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 4 0.14
32 9 0.31
33 16 0.55
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTTATATTTTAATAGAAATTAATTCTTTTA
Found at i:38356653 original size:24 final size:24
Alignment explanation
Indices: 38356621--38356675 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
38356611 GTTGGGACAT
*
38356621 ATTAAATTCGTCCACCAGCAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
38356645 ATTAAATTCGTCAACCAGCAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
38356669 ATTAAAT
1 ATTAAAT
38356676 CTGTCCAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (24 bp):
ATTAAATTCGTCAACCAGCAGCTC
Found at i:38356769 original size:17 final size:18
Alignment explanation
Indices: 38356749--38356783 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
38356739 TGTACACACA
38356749 AATTAATTCAG-CACATT
1 AATTAATTCAGACACATT
*
38356766 AATTAATTTAGACACATT
1 AATTAATTCAGACACATT
38356784 TAAAAATTAT
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:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTAATTCAGACACATT
Found at i:38356916 original size:14 final size:14
Alignment explanation
Indices: 38356905--38356934 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38356895 GCAATTAATA
38356905 AATTTGTCTTAAGT
1 AATTTGTCTTAAGT
38356919 AATTTGTCTTAAGT
1 AATTTGTCTTAAGT
38356933 AA
1 AA
38356935 GACTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (14 bp):
AATTTGTCTTAAGT
Found at i:38358888 original size:25 final size:24
Alignment explanation
Indices: 38358847--38358894 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
38358837 ACAATTGACC
*
38358847 AAACTAAGATATGGGAAGCTTTTAA
1 AAACTAAGATATCGGAA-CTTTTAA
38358872 AAACTAAG-TCATCGGAACTTTTA
1 AAACTAAGAT-ATCGGAACTTTTA
38358895 TCGACAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (24 bp):
AAACTAAGATATCGGAACTTTTAA
Found at i:38359167 original size:15 final size:15
Alignment explanation
Indices: 38359147--38359175 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38359137 GTTCTGTTCA
38359147 CTCATTTCTTTTTCT
1 CTCATTTCTTTTTCT
38359162 CTCATTTCTTTTTC
1 CTCATTTCTTTTTC
38359176 AAACTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.66
Consensus pattern (15 bp):
CTCATTTCTTTTTCT
Found at i:38361620 original size:24 final size:24
Alignment explanation
Indices: 38361588--38361642 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
38361578 GTTGGGACAT
* *
38361588 ATTAAATTCGTCCACCAGCAGCTC
1 ATTAAATTCGTCAACCAACAGCTC
38361612 ATTAAATTCGTCAACCAACAGCTC
1 ATTAAATTCGTCAACCAACAGCTC
38361636 ATTAAAT
1 ATTAAAT
38361643 CTGTCCAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (24 bp):
ATTAAATTCGTCAACCAACAGCTC
Found at i:38363169 original size:126 final size:126
Alignment explanation
Indices: 38362944--38363318 Score: 518
Period size: 126 Copynumber: 3.0 Consensus size: 126
38362934 GGCCAAGTAT
* * *
38362944 GAACTACTGTAGAAAAAGAGCATCCATGTGAGAGCTTTTTTT-AGAAATTTTGATAACATTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCATGTGGGAG-TTTTTTTCAGAAATTTTGATGACATTGCAT
* *
38363008 CCTACTTGAAGCGTTTTTGACACTATATGTTCAAAAACGTCTTCTTAAAATTATTTTTTCAA
65 CCTACTTGAAGCGTTTTTGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAA
* * * *
38363070 GAACTACTGTAGTAAAAGAGCGTCTATGTGGGAGTTTTTTTCAGAAATTTTAATGACATTACATC
1 GAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGTTTTTTTCAGAAATTTTGATGACATTGCATC
* * * *
38363135 CTGCTTGAAGTGTTTTTGATACTATTTGTTCAAAAACGTCTTCTCAAAATTACTTTTTCAA
66 CTACTTGAAGCGTTTTTGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAA
* * * * * * * * *
38363196 GAACTATTATAGCAAAAGAGTGTCCACGTGGGAGCTTTTTGCAAAAAATTTGATGACATTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGTTTTTTTCAGAAATTTTGATGACATTGCATC
* *
38363261 CTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTT
66 CTACTTGAAGCGTTTTTGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTT
38363319 AGGGTAAAAA
Statistics
Matches: 217, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
125 7 0.03
126 210 0.97
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGTTTTTTTCAGAAATTTTGATGACATTGCATC
CTACTTGAAGCGTTTTTGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAA
Found at i:38363410 original size:28 final size:30
Alignment explanation
Indices: 38363378--38363457 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
38363368 AAAAAAAACT
**
38363378 AAACCCTAATTTAATTAAT-TTTAACCC-A
1 AAACCCTAATTTAATTAATCTAAAACCCTA
*
38363406 AAACCCTAATTTAATTTATCTAAAACCCTA
1 AAACCCTAATTTAATTAATCTAAAACCCTA
* *
38363436 GAACCCTAATTTACTTAATCTA
1 AAACCCTAATTTAATTAATCTA
38363458 TTTAAAAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
28 18 0.41
29 6 0.14
30 20 0.45
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.35
Consensus pattern (30 bp):
AAACCCTAATTTAATTAATCTAAAACCCTA
Found at i:38363433 original size:22 final size:22
Alignment explanation
Indices: 38363405--38363571 Score: 76
Period size: 22 Copynumber: 7.4 Consensus size: 22
38363395 ATTTTAACCC
38363405 AAAACCCTAATTTAATTTATCT
1 AAAACCCTAATTTAATTTATCT
**
38363427 AAAACCCTAGAACCCTAATTTA-CT
1 AAAACCCT--AA-TTTAATTTATCT
* * **
38363451 -TAA-TCT-ATTTAA-AAATCAT
1 AAAACCCTAATTTAATTTATC-T
* * *
38363470 AA-ACCTTAATTTAATTTGTTT
1 AAAACCCTAATTTAATTTATCT
* *
38363491 TAAATCCTAATTTAATTTATCT
1 AAAACCCTAATTTAATTTATCT
* *
38363513 AAAACCCTAATTTAATTAATTTTAACCC
1 AAAACCCTAA--T--TTAA-TTT-ATCT
38363541 AAAACCCTAATTTAATTTATCT
1 AAAACCCTAATTTAATTTATCT
*
38363563 AAAATCCTA
1 AAAACCCTA
38363572 GAACCCTAAT
Statistics
Matches: 102, Mismatches: 27, Indels: 32
0.63 0.17 0.20
Matches are distributed among these distances:
17 1 0.01
18 4 0.04
19 3 0.03
20 1 0.01
21 8 0.08
22 44 0.43
23 5 0.05
24 9 0.09
25 7 0.07
26 5 0.05
27 3 0.03
28 12 0.12
ACGTcount: A:0.41, C:0.18, G:0.01, T:0.40
Consensus pattern (22 bp):
AAAACCCTAATTTAATTTATCT
Found at i:38363483 original size:64 final size:63
Alignment explanation
Indices: 38363404--38363633 Score: 178
Period size: 64 Copynumber: 3.5 Consensus size: 63
38363394 AATTTTAACC
38363404 CAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAT
1 CAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAT
* * * * * ** * *
38363467 CATAAACCTTAATTTAATTTGTTTTAAATCCT--AA-TTTAATTTATCTAAAACCCTAATTTAAT
1 CA-AAACCCTAATTTAATTTATCTAAAACCCTAGAACCCTAATTTA-CT-TAA-TCT-ATTT-A-
*
38363529 TAATTTTAACC
59 -AA----AA-T
*
38363540 CAAAACCCTAATTTAATTTATCTAAAATCCTAGAACCCTAATTTACTTAATCTATTTAAAAAT
1 CAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAT
* * * *
38363603 AAAAAATCCTAATTTAATTTATTTTAAACCC
1 -CAAAACCCTAATTTAATTTATCTAAAACCC
38363634 CAATTTAATT
Statistics
Matches: 126, Mismatches: 24, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
61 7 0.06
62 4 0.03
63 4 0.03
64 53 0.42
65 4 0.03
66 1 0.01
68 4 0.03
70 1 0.01
71 4 0.03
72 29 0.23
73 4 0.03
74 4 0.03
75 7 0.06
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.39
Consensus pattern (63 bp):
CAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAT
Found at i:38363616 original size:136 final size:136
Alignment explanation
Indices: 38363378--38363658 Score: 483
Period size: 136 Copynumber: 2.1 Consensus size: 136
38363368 AAAAAAAACT
38363378 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
1 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
* * * * *
38363443 AATTTACTTAATCTATTTAAAAATCATAAACCTTAATTTAATTTGTTTTAAATCCTAATTTAATT
66 AATTTACTTAATCTATTTAAAAATAAAAAACCTTAATTTAATTTATTTTAAACCCCAATTTAATT
38363508 TATCTA
131 TATCTA
*
38363514 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAATCCTAGAACCCT
1 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
38363579 AATTTACTTAATCTATTTAAAAATAAAAAATCC-TAATTTAATTTATTTTAAACCCCAATTTAAT
66 AATTTACTTAATCTATTTAAAAATAAAAAA-CCTTAATTTAATTTATTTTAAACCCCAATTTAAT
38363643 TTATCTA
130 TTATCTA
*
38363650 AAATCCTAA
1 AAACCCTAA
38363659 AACCCTAATT
Statistics
Matches: 137, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
136 135 0.99
137 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.39
Consensus pattern (136 bp):
AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
AATTTACTTAATCTATTTAAAAATAAAAAACCTTAATTTAATTTATTTTAAACCCCAATTTAATT
TATCTA
Found at i:38363647 original size:86 final size:86
Alignment explanation
Indices: 38363542--38363705 Score: 283
Period size: 86 Copynumber: 1.9 Consensus size: 86
38363532 TTTTAACCCA
* *
38363542 AAACCCTAATTTAATTTATCTAAAATCCTAGAACCCTAATTTACTTAATCTATTTAAAAATAAAA
1 AAACCCCAATTTAATTTATCTAAAATCCTAAAACCCTAATTTACTTAATCTATTTAAAAATAAAA
*
38363607 AATCCTAATTTAATTTATTTT
66 AACCCTAATTTAATTTATTTT
* *
38363628 AAACCCCAATTTAATTTATCTAAAATCCTAAAACCCTAATTTACTTAATCTATTTAAAAATCATA
1 AAACCCCAATTTAATTTATCTAAAATCCTAAAACCCTAATTTACTTAATCTATTTAAAAATAAAA
38363693 AACCCTAATTTAA
66 AACCCTAATTTAA
38363706 ATAATTTTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.38
Consensus pattern (86 bp):
AAACCCCAATTTAATTTATCTAAAATCCTAAAACCCTAATTTACTTAATCTATTTAAAAATAAAA
AACCCTAATTTAATTTATTTT
Found at i:38363686 original size:34 final size:34
Alignment explanation
Indices: 38363638--38363704 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
38363628 AAACCCCAAT
* *
38363638 TTAATTTATCT-AAAATCCTAAAACCCTAATTTAC
1 TTAATCTATCTAAAAATCAT-AAACCCTAATTTAC
*
38363672 TTAATCTATTTAAAAATCATAAACCCTAATTTA
1 TTAATCTATCTAAAAATCATAAACCCTAATTTA
38363705 AATAATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 22 0.76
35 7 0.24
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (34 bp):
TTAATCTATCTAAAAATCATAAACCCTAATTTAC
Found at i:38364458 original size:19 final size:19
Alignment explanation
Indices: 38364430--38364481 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
38364420 ATTTGACTTC
38364430 TTCATATTTAATTTTT-AA
1 TTCATATTTAATTTTTCAA
38364448 TTCAGTATTTAATTTTTCAA
1 TTCA-TATTTAATTTTTCAA
*
38364468 TTTATCATTTAATT
1 TTCAT-ATTTAATT
38364482 AACGATTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 4 0.13
19 13 0.43
20 13 0.43
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (19 bp):
TTCATATTTAATTTTTCAA
Found at i:38369927 original size:93 final size:88
Alignment explanation
Indices: 38369825--38370024 Score: 210
Period size: 93 Copynumber: 2.2 Consensus size: 88
38369815 TTACAAAAAT
* * **
38369825 AATTTAATACAAATAATTT-TTTTTCCGTCATGCACATGTCAT-A-AACTTTAATACAAAGAAA-
1 AATTTAATACAAATAATTTATTTTT--GTCATACACATGAC-TGACAA-TAAAATACAAAGAAAT
* *
38369886 TCTATTTTTGTCATGTACAATAATAACCAAAC
62 TC-ATTTCTATCATGT---ATAATAA-CAAAC
*
38369918 AATTTAATACAAATAAATTTATTTTTGTCCTACACATGACTGACAATAAAATACAAAGAAATTCA
1 AATTTAATACAAAT-AATTTATTTTTGTCATACACATGACTGACAATAAAATACAAAGAAATTCA
38369983 TTTCTATCATGTATAATAACAAAC
65 TTTCTATCATGTATAATAACAAAC
*
38370007 AATTTAATACAAACAATT
1 AATTTAATACAAATAATT
38370025 CAAATATGAT
Statistics
Matches: 94, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
88 4 0.04
89 18 0.19
90 7 0.07
92 1 0.01
93 50 0.53
94 9 0.10
95 5 0.05
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.35
Consensus pattern (88 bp):
AATTTAATACAAATAATTTATTTTTGTCATACACATGACTGACAATAAAATACAAAGAAATTCAT
TTCTATCATGTATAATAACAAAC
Found at i:38370020 original size:14 final size:15
Alignment explanation
Indices: 38369996--38370024 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38369986 CTATCATGTA
38369996 TAATAACAAACAATT
1 TAATAACAAACAATT
38370011 TAAT-ACAAACAATT
1 TAATAACAAACAATT
38370025 CAAATATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATAACAAACAATT
Found at i:38374080 original size:10 final size:10
Alignment explanation
Indices: 38374065--38374093 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
38374055 GATGCCCTTT
38374065 GAGAGAGAGG
1 GAGAGAGAGG
38374075 GAGAGAGAGG
1 GAGAGAGAGG
38374085 GAGAGAGAG
1 GAGAGAGAG
38374094 AGAACGGAAT
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:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (10 bp):
GAGAGAGAGG
Found at i:38377524 original size:20 final size:20
Alignment explanation
Indices: 38377499--38377564 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
38377489 TATTTTTTAG
38377499 TTAATTATTAAGTTATAATT
1 TTAATTATTAAGTTATAATT
*
38377519 TTAATTAGGTAA-TTATAATT
1 TTAATTA-TTAAGTTATAATT
* * * *
38377539 TTAA-AATTTAGATACAATT
1 TTAATTATTAAGTTATAATT
38377558 TTAATTA
1 TTAATTA
38377565 AATAAAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.31
20 20 0.56
21 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (20 bp):
TTAATTATTAAGTTATAATT
Found at i:38383810 original size:354 final size:355
Alignment explanation
Indices: 38383142--38383850 Score: 1168
Period size: 354 Copynumber: 2.0 Consensus size: 355
38383132 TTCAAATTGT
* *
38383142 CCAAATCCTTTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTTTGGACATCGA
1 CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTCTGGACATCGA
*
38383207 CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGATCGATCCATTTTTCTAGCTCCAAACTT
66 CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGATCGATCCATTTTTCTAGCTCCAAACTC
*
38383272 TTTCTCTCAAAATCTTATTTAATGATCTCTAACTCAGATGGGATCACCTTCAAGTGTTCTTCCAT
131 TTTCTCTCAAAATCTTATTTAATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
*
38383337 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCGCTGATCCTCTAACCCCACCATTAGT
196 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCGCTGATCCTCTAACCCCACCATCAGT
* *
38383402 CATACTCAGGGGTAGTCATTGGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGGCA
261 CATACTCAGGGGTAGTCATTAGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGACA
38383467 TTCGATATCTCACGAAATTTCTTTTTGTAA
326 TTCGATATCTCACGAAATTTCTTTTTGTAA
* *
38383497 CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTTAGCTTTT-AGCTTCTAGTTTCTGGACATTGA
1 CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTCTGGACATCGA
* * * ** * * * *
38383561 CATCTAGCCCCAGCTGTATTTTTTCTCCCTTTAATTGCTGGATCCTTTTTTCTAGCTCCGAACTC
66 CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGATCGATCCATTTTTCTAGCTCCAAACTC
* * *
38383626 TTTCTCTCGAAATCTTGTTTGATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
131 TTTCTCTCAAAATCTTATTTAATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
* *
38383691 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCGTTGATCCTCTGACCCCACCATCAGT
196 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCGCTGATCCTCTAACCCCACCATCAGT
* * *
38383756 CATACTCAGGGGTGGTCATTAGATTAGCAGCAAACCTTTTCATTTTATGAGTTTGGTTCTAGACA
261 CATACTCAGGGGTAGTCATTAGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGACA
*
38383821 TTCGATATCTCACGAACTTTCTTTTTGTAA
326 TTCGATATCTCACGAAATTTCTTTTTGTAA
38383851 TTATCTCCCT
Statistics
Matches: 327, Mismatches: 27, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
354 288 0.88
355 39 0.12
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (355 bp):
CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTCTGGACATCGA
CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGATCGATCCATTTTTCTAGCTCCAAACTC
TTTCTCTCAAAATCTTATTTAATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCGCTGATCCTCTAACCCCACCATCAGT
CATACTCAGGGGTAGTCATTAGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGACA
TTCGATATCTCACGAAATTTCTTTTTGTAA
Found at i:38386723 original size:3 final size:3
Alignment explanation
Indices: 38386717--38386751 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
38386707 TAATAGTAAG
38386717 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
38386752 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:38387960 original size:21 final size:21
Alignment explanation
Indices: 38387930--38387982 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
38387920 TAATTTTTGG
*
38387930 GTTTTAGGTTTAGGTTGGTTT
1 GTTTTGGGTTTAGGTTGGTTT
** *
38387951 -TTATTGGGTTGGGGTTTGTTT
1 GTT-TTGGGTTTAGGTTGGTTT
38387972 GTTTTGGGTTT
1 GTTTTGGGTTT
38387983 GATGGTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.06, C:0.00, G:0.36, T:0.58
Consensus pattern (21 bp):
GTTTTGGGTTTAGGTTGGTTT
Found at i:38389670 original size:20 final size:20
Alignment explanation
Indices: 38389579--38389705 Score: 92
Period size: 20 Copynumber: 6.3 Consensus size: 20
38389569 GAGGAGGAAG
* * *
38389579 TACTGATAGTTTATCTGCAT
1 TACTGGTAGTTTGTCTACAT
* * * * *
38389599 TTCTGGTGGCTTGTCCACAA
1 TACTGGTAGTTTGTCTACAT
* ** *
38389619 TACTGGCAACTTGTCTACAA
1 TACTGGTAGTTTGTCTACAT
* *
38389639 TACTGGCAGTTTATCTACAT
1 TACTGGTAGTTTGTCTACAT
*
38389659 TACTGGTGGTTTGTCTACAT
1 TACTGGTAGTTTGTCTACAT
* * *
38389679 TATTGGTAGCTTGTCTGCAT
1 TACTGGTAGTTTGTCTACAT
38389699 TACTGGT
1 TACTGGT
38389706 GGCTTGTTCA
Statistics
Matches: 82, Mismatches: 25, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
TACTGGTAGTTTGTCTACAT
Found at i:38389674 original size:40 final size:39
Alignment explanation
Indices: 38389628--38389763 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
38389618 ATACTGGCAA
*
38389628 CTTGTCTACAATACTGGCAGTTTATCTACATTACTGGTGG
1 CTTGTCTACAATA-TGGCAGTTTATCTGCATTACTGGTGG
* * * * *
38389668 TTTGTCTACATTATTGGTAGCTTGTCTGCATTACTGGTGG
1 CTTGTCTACAATA-TGGCAGTTTATCTGCATTACTGGTGG
* *
38389708 CTTGT-TCACATTTATGGCAGTTTATCTGTATTACTGGTGG
1 CTTGTCT-ACA-ATATGGCAGTTTATCTGCATTACTGGTGG
* *
38389748 CTTGTCCACAAAATGG
1 CTTGTCTACAATATGG
38389764 TGTGTTATTG
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
39 5 0.06
40 70 0.90
41 3 0.04
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (39 bp):
CTTGTCTACAATATGGCAGTTTATCTGCATTACTGGTGG
Found at i:38389719 original size:20 final size:20
Alignment explanation
Indices: 38389596--38389712 Score: 99
Period size: 20 Copynumber: 5.8 Consensus size: 20
38389586 AGTTTATCTG
* *
38389596 CATTTCTGGTGGCTTGTCCA
1 CATTACTGGTGGCTTGTCTA
* ***
38389616 CAATACTGGCAACTTGTCTA
1 CATTACTGGTGGCTTGTCTA
* ** * *
38389636 CAATACTGGCAGTTTATCTA
1 CATTACTGGTGGCTTGTCTA
*
38389656 CATTACTGGTGGTTTGTCTA
1 CATTACTGGTGGCTTGTCTA
* * *
38389676 CATTATTGGTAGCTTGTCTG
1 CATTACTGGTGGCTTGTCTA
38389696 CATTACTGGTGGCTTGT
1 CATTACTGGTGGCTTGT
38389713 TCACATTTAT
Statistics
Matches: 78, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
CATTACTGGTGGCTTGTCTA
Found at i:38392388 original size:10 final size:10
Alignment explanation
Indices: 38392367--38392401 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
38392357 AATTAAATTC
38392367 TAAAAGATAAA
1 TAAAA-ATAAA
38392378 TAAAAATAAA
1 TAAAAATAAA
*
38392388 TAAAGATAAA
1 TAAAAATAAA
38392398 TAAA
1 TAAA
38392402 TATTAAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:38393654 original size:26 final size:26
Alignment explanation
Indices: 38393618--38393670 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
38393608 AACCACCAAG
38393618 TATATCCCATTGTGATTGAAATAATT
1 TATATCCCATTGTGATTGAAATAATT
*
38393644 TATATCTCATTGTGATTGAAATAATT
1 TATATCCCATTGTGATTGAAATAATT
38393670 T
1 T
38393671 TGCAAGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (26 bp):
TATATCCCATTGTGATTGAAATAATT
Found at i:38397741 original size:21 final size:21
Alignment explanation
Indices: 38397715--38397755 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
38397705 ATCTGCTCAA
*
38397715 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
38397736 ACTCCACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
38397756 TCGCTCGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:38400576 original size:16 final size:16
Alignment explanation
Indices: 38400551--38400581 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38400541 CACCACTTGG
*
38400551 ATTGTTTGCCATTAAA
1 ATTGTCTGCCATTAAA
38400567 ATTGTCTGCCATTAA
1 ATTGTCTGCCATTAA
38400582 TCATAATGTT
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:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (16 bp):
ATTGTCTGCCATTAAA
Found at i:38403678 original size:31 final size:31
Alignment explanation
Indices: 38403642--38403707 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
38403632 TTTTTTAGCT
*
38403642 AAATTTGACCATAAATCTTTTAAAAACAGTC
1 AAATTTGACCATAAACCTTTTAAAAACAGTC
* **
38403673 AAATTTGACTATAAACCTTTTAAAAGGAGTC
1 AAATTTGACCATAAACCTTTTAAAAACAGTC
38403704 AAAT
1 AAAT
38403708 AGTTGCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (31 bp):
AAATTTGACCATAAACCTTTTAAAAACAGTC
Found at i:38403811 original size:7 final size:8
Alignment explanation
Indices: 38403799--38403836 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
38403789 TTTATACTTT
38403799 TTTTTA-A
1 TTTTTATA
38403806 TTTTTATA
1 TTTTTATA
38403814 TTTTTATA
1 TTTTTATA
38403822 TTTTTGAATA
1 TTTTT--ATA
38403832 TTTTT
1 TTTTT
38403837 TTATCATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 6 0.21
8 14 0.50
10 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (8 bp):
TTTTTATA
Found at i:38403845 original size:21 final size:20
Alignment explanation
Indices: 38403814--38403855 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
38403804 AATTTTTATA
*
38403814 TTTTTATATTTTTGAATATT
1 TTTTTATATTTTTAAATATT
38403834 TTTTTATCATTTTTAAATATT
1 TTTTTAT-ATTTTTAAATATT
38403855 T
1 T
38403856 GTTGACGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTATATTTTTAAATATT
Found at i:38412027 original size:16 final size:16
Alignment explanation
Indices: 38412008--38412064 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
38411998 ATTGGAATAT
38412008 AGGCGTAATGGATTAG
1 AGGCGTAATGGATTAG
38412024 AGGCGTAATGGATTAG
1 AGGCGTAATGGATTAG
*
38412040 AGGCGTAATGGAATAG
1 AGGCGTAATGGATTAG
*
38412056 ATGCGTAAT
1 AGGCGTAAT
38412065 AGCAAATCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.07, G:0.35, T:0.25
Consensus pattern (16 bp):
AGGCGTAATGGATTAG
Found at i:38412107 original size:45 final size:44
Alignment explanation
Indices: 38412044--38412133 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
38412034 GATTAGAGGC
*
38412044 GTAATGGAATAGATGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
38412089 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
38412133 G
1 G
38412134 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.44
45 22 0.54
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:38412315 original size:16 final size:16
Alignment explanation
Indices: 38412278--38412319 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
38412268 TTAATCATAT
*
38412278 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
38412294 TT-AAATATATTATAA
1 TTAAAATATATTATAA
38412309 TTAAAATATAT
1 TTAAAATATAT
38412320 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:38412326 original size:14 final size:15
Alignment explanation
Indices: 38412287--38412328 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38412277 TTTAAACATA
*
38412287 ATTATTATTAAATAT
1 ATTATAATTAAATAT
38412302 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
38412316 A-TATAATTTAATA
1 ATTATAATTAAATA
38412329 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:38412439 original size:18 final size:17
Alignment explanation
Indices: 38412418--38412452 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38412408 TTATTATTAA
*
38412418 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38412436 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38412453 TCTAATAATC
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:38412510 original size:60 final size:60
Alignment explanation
Indices: 38412326--38412512 Score: 159
Period size: 60 Copynumber: 3.1 Consensus size: 60
38412316 ATATAATTTA
* * *
38412326 ATAAAATTCTTAATAGTCAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTC-TAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
** * * * * ** * * * *
38412387 ATAAAA-GATAATTTAA-C-ATAATTATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAATTCTAA--TAATCAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
38412445 AATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
38412506 ATAAAAT
1 ATAAAAT
38412513 ATAATTTGAA
Statistics
Matches: 91, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
58 4 0.04
59 38 0.42
60 40 0.44
61 9 0.10
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (60 bp):
ATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:38412517 original size:119 final size:121
Alignment explanation
Indices: 38412276--38412572 Score: 501
Period size: 119 Copynumber: 2.5 Consensus size: 121
38412266 ATTTAATCAT
*
38412276 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
38412341 GTCAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 ATCAAAATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATA
38412397 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATA
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
38412460 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 ATCAAAATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATA
* * *
38412516 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
38412573 TAAAATAATT
Statistics
Matches: 168, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 109 0.65
120 55 0.33
121 4 0.02
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAAAATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATA
Found at i:38412571 original size:59 final size:58
Alignment explanation
Indices: 38412374--38412561 Score: 173
Period size: 59 Copynumber: 3.2 Consensus size: 58
38412364 CTCAAATCAT
*
38412374 AATATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTAA-ATAATTATTATTAAATATATTTTAATTAA
* * * * * * * * * ** * *
38412433 AATATATAAT-TTAATAAAATTCTAATAATCAAT-ATTCTTATATGAATTTACTAAAATCAT
1 AATATATGATACT-ATAAAA-TATAAT-TTAAATAATTATTAT-TAAATATATTTTAATTAA
*
38412493 AATATATGATACTATAAAATATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTT-AAATAATTATTATTAAATATATTTTAATTAA
38412552 AATATATGAT
1 AATATATGAT
38412562 TTAATAAAAT
Statistics
Matches: 94, Mismatches: 28, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
58 2 0.02
59 51 0.54
60 38 0.40
61 3 0.03
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (58 bp):
AATATATGATACTATAAAATATAATTTAAATAATTATTATTAAATATATTTTAATTAA
Found at i:38417899 original size:46 final size:46
Alignment explanation
Indices: 38417780--38418020 Score: 204
Period size: 46 Copynumber: 5.1 Consensus size: 46
38417770 GAAATCTTAC
* *
38417780 ACATATCGATGCCGATGCTATATCCCAGATATGGTCTTACACTGGCTCTT
1 ACATATCGATGCCGATGC-ATGTCCCAGACAT-GTCTTACACTGG--CTT
* * *
38417830 ACATATCCG-TGTCGATGCTTGTCCCAAACATGTCTTACACTGGCTT
1 ACATAT-CGATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
* * *
38417876 ACATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACTAG--T
1 ACATATCGATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
* * * *
38417920 ACTCGTCTCAATGCCGATGCCATGTCCCAGGCATGGTCTTACACTGGCTT
1 A--CATATCGATGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTT
* * * *
38417970 TCATAAT--ATGGCCGATGCATGTCCTAGACATGTCTTGCACTGGCTC
1 ACAT-ATCGAT-GCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
38418016 ACATA
1 ACATA
38418021 ATAGTAGTGT
Statistics
Matches: 157, Mismatches: 24, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
44 2 0.01
45 3 0.02
46 66 0.42
47 27 0.17
48 32 0.20
49 10 0.06
50 15 0.10
51 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (46 bp):
ACATATCGATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
Found at i:38423266 original size:19 final size:19
Alignment explanation
Indices: 38423242--38423280 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
38423232 AATAATAATT
38423242 AATTTATCAATATGCTTTC
1 AATTTATCAATATGCTTTC
38423261 AATTTATCAATATGCTTTC
1 AATTTATCAATATGCTTTC
38423280 A
1 A
38423281 CCAATTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (19 bp):
AATTTATCAATATGCTTTC
Found at i:38424490 original size:46 final size:46
Alignment explanation
Indices: 38424329--38424612 Score: 249
Period size: 46 Copynumber: 6.1 Consensus size: 46
38424319 GAAATCTTAC
* * * *
38424329 ACATATCGATGCCAATGCCATATCCCAGATATGGTCTTACACTGGCTCTT
1 ACATCTCGATGCCGATG-CATGTCCCAGACAT-GTCTTACACTGG--CTT
* * * *
38424379 ACATATCCATGCCGATGCATGTCCCAAACATGTCTTACACTAGC--
1 ACATCTCGATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
38424423 ACATCTCG-TAGCCGATGCATGTCCC-GAACATGTCTTACACTGGCTT
1 ACATCTCGAT-GCCGATGCATGTCCCAG-ACATGTCTTACACTGGCTT
* * *
38424469 ACATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACCGGCACT
1 ACATCTCGATGCCGATGCATGTCCCAGACATGTCTTACACTGGC-TT
* *
38424516 -CATCTCAATGCCGATGCCATGTCCCAGACATGGTCTTCCACTGGCTT
1 ACATCTCGATGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTT
* * ** * *
38424563 TCATAAT--ATGGCCGATGCATGTGGCAGACATGTCTTGCACTGGCTC
1 ACAT-CTCGAT-GCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
38424609 ACAT
1 ACAT
38424613 AACAGCAGTG
Statistics
Matches: 198, Mismatches: 24, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
43 1 0.01
44 37 0.19
46 70 0.35
47 31 0.16
48 32 0.16
49 12 0.06
50 15 0.08
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
ACATCTCGATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
Found at i:38424584 original size:94 final size:91
Alignment explanation
Indices: 38424328--38424598 Score: 284
Period size: 94 Copynumber: 2.9 Consensus size: 91
38424318 GGAAATCTTA
* * * *
38424328 CACATATCGATGCCAATGCCATATCCCAGATATGGTCTTACACTGGCTCTTACATATCCAT-GCC
1 CACATCTC-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TT-CATAT-CATGGCC
* *
38424392 GATGCATGTCCCAAACATGTCTTACACTAG
62 GATGCATGTCCCAGACATGTCTTACACCAG
* * *
38424422 CACATCTCGTAGCCGATG-CATGTCCC-GAACAT-GTCTTACACTGGCTTACATCTCGA-GGCCG
1 CACATCTCAT-GCCGATGCCATGTCCCAG-ACATGGTCTTACACTGGCTTTCATATC-ATGGCCG
*
38424483 ATGCATGTCCCAGACATGTCTTACACCGG
63 ATGCATGTCCCAGACATGTCTTACACCAG
*
38424512 CACTCATCTCAATGCCGATGCCATGTCCCAGACATGGTCTTCCACTGGCTTTCATAAT-ATGGCC
1 CA--CATCTC-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCAT-ATCATGGCC
**
38424576 GATGCATGTGGCAGACATGTCTT
62 GATGCATGTCCCAGACATGTCTT
38424599 GCACTGGCTC
Statistics
Matches: 149, Mismatches: 16, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
89 1 0.01
90 37 0.25
91 1 0.01
92 28 0.19
93 25 0.17
94 56 0.38
95 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (91 bp):
CACATCTCATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATCATGGCCGATG
CATGTCCCAGACATGTCTTACACCAG
Found at i:38437836 original size:22 final size:21
Alignment explanation
Indices: 38437817--38437857 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38437807 AATATGTTCT
*
38437817 GCATCTGTATCTGAACTGTTTA
1 GCATCT-TACCTGAACTGTTTA
*
38437839 GCGTCTTACCTGAACTGTT
1 GCATCTTACCTGAACTGTT
38437858 ACGATAGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (21 bp):
GCATCTTACCTGAACTGTTTA
Found at i:38442250 original size:93 final size:93
Alignment explanation
Indices: 38442142--38442312 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
38442132 GCCCCTAAGT
* * *
38442142 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
38442207 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
38442235 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
38442300 CGAGTTCGGATGC
66 CGAGTTCGGATGC
38442313 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:38442309 original size:46 final size:46
Alignment explanation
Indices: 38442137--38442309 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
38442127 AACCCGCCCC
* * * *
38442137 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
38442183 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
38442231 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
38442276 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
38442310 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:38454792 original size:23 final size:23
Alignment explanation
Indices: 38454693--38454808 Score: 101
Period size: 23 Copynumber: 4.9 Consensus size: 23
38454683 AACTCACCGT
38454693 AGCTCG-TATGAGCTTACTGATATATC
1 AGCTCGTTA-GAGCTTACTG-T-T-TC
*
38454719 AGCTCGTAAGAGCTTACTGTTCTC
1 AGCTCGTTAGAGCTTACTGTT-TC
**
38454743 AGCTCG-TATGAGCTTACTAATTC
1 AGCTCGTTA-GAGCTTACTGTTTC
* *
38454766 AGCTCGTTAGAGCTTATTGTTTT
1 AGCTCGTTAGAGCTTACTGTTTC
**
38454789 AGCTCAATAGAGCTTACTGT
1 AGCTCGTTAGAGCTTACTGT
38454809 CCATTAGCTC
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
23 36 0.48
24 21 0.28
25 1 0.01
26 16 0.21
27 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
AGCTCGTTAGAGCTTACTGTTTC
Found at i:38455799 original size:30 final size:30
Alignment explanation
Indices: 38455756--38455819 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
38455746 ACGGGAAGAG
* *
38455756 ACACCGGCGTGTGTCTCAG-CAGTGTGTGAC
1 ACACCGGCCTGTGTCTCAGCCA-TGTGCGAC
*
38455786 ACACGGGCCTGTGTCTCAGCCATGTGCGAC
1 ACACCGGCCTGTGTCTCAGCCATGTGCGAC
38455816 ACAC
1 ACAC
38455820 AGTTATGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.20
Consensus pattern (30 bp):
ACACCGGCCTGTGTCTCAGCCATGTGCGAC
Found at i:38458489 original size:24 final size:24
Alignment explanation
Indices: 38458460--38458508 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
38458450 AATCCCTCAA
38458460 TAACTCAACACTTTAAATCAATAG
1 TAACTCAACACTTTAAATCAATAG
38458484 TAACTCAACACTTTAAATCAATAG
1 TAACTCAACACTTTAAATCAATAG
38458508 T
1 T
38458509 TTCAGAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (24 bp):
TAACTCAACACTTTAAATCAATAG
Found at i:38463320 original size:55 final size:53
Alignment explanation
Indices: 38463179--38463587 Score: 309
Period size: 55 Copynumber: 7.7 Consensus size: 53
38463169 TTTTCCTTTT
* * * *
38463179 TGAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTA
1 TGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTA
* * *
38463232 TGAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGTCTTA
1 TGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTA
** ** *** *
38463285 TAGTAACTCTTCAATTTCATGTCTTGACATGGTCTTACATGATTTCCTAGCCTTA
1 T-G-AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTA
* * * * *
38463340 TAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACAT--GAT--AT-CCTTA
1 T-GAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTA
* *** * *
38463389 T--CCT-ACCATATGCCATGTTCCAAACATGGTCTTAAATGGTATCCTTGCCTTA
1 TGAACTCACCA-ATGCCATG-TCTTGACATGGTCTTACATGGGATCCTTGCCTTA
*
38463441 TGAACTCACCAATGCCATGCCTTCG-CATGGTCTTACATGGGA-CCTTTGCCTTA
1 TGAACTCACCAATGCCATGTCTT-GACATGGTCTTACATGGGATCC-TTGCCTTA
* * ***
38463494 TAGTAACTCATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCTTGCCTTA
1 T-G-AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTA
* * * * *
38463549 TAGAACTTATCAATGCCATGCCTTGGCATGGTTTTACAT
1 T-GAACTCACCAATGCCATGTCTTGACATGGTCTTACAT
38463588 CATATCCTTA
Statistics
Matches: 280, Mismatches: 56, Indels: 39
0.75 0.15 0.10
Matches are distributed among these distances:
45 3 0.01
46 10 0.04
47 13 0.05
49 8 0.03
51 1 0.00
52 11 0.04
53 69 0.25
54 74 0.26
55 87 0.31
56 4 0.01
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (53 bp):
TGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTA
Found at i:38463377 original size:109 final size:108
Alignment explanation
Indices: 38463191--38463587 Score: 488
Period size: 109 Copynumber: 3.7 Consensus size: 108
38463181 AACTTACCAT
* *
38463191 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
* *
38463256 GCATGGTCTTACATGGGACCTTTGTCTTATAGTAACTCTTCAA
66 GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
** * * * *
38463299 TTTCATGTCTTGACATGGTCTTACATGATTTCCTAGCCTTATAGAACTTATCAATGCCATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTT
* **
38463364 GGCATGGTCTTACAT--GA--TAT-CCTTATCCT-AC-CAT--A
65 GGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
*** * *
38463399 TGCCATGTTCCAAACATGGTCTTAAATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTT
1 TGCCATG-TCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTT
*
38463464 CGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
65 GGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
* * * *
38463508 TGCCATGTCTTGACATAGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTT
*
38463573 GGCATGGTTTTACAT
65 GGCATGGTCTTACAT
38463588 CATATCCTTA
Statistics
Matches: 238, Mismatches: 39, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
100 40 0.17
101 28 0.12
102 4 0.02
103 2 0.01
104 8 0.03
105 9 0.04
106 2 0.01
107 5 0.02
108 64 0.27
109 76 0.32
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (108 bp):
TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
Found at i:38463563 original size:209 final size:209
Alignment explanation
Indices: 38463203--38463649 Score: 750
Period size: 209 Copynumber: 2.1 Consensus size: 209
38463193 CCATGTCTTG
* *
38463203 ACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGCATGGTCTTAC
1 ACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTCGCATGGTCTTAC
* * ** *
38463268 ATGGGACCTTTGTCTTATAGTAACTCTTCAATTTCATGTCTTGACATGGTCTTACATGATTTCCT
66 ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCT
* *
38463333 AGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCCTACCAT
131 AGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATCATATCCTTATCCTACCAA
38463398 ATGCCATGTTCCAA
196 ATGCCATGTTCCAA
*
38463412 ACATGGTCTTAAATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTCGCATGGTCTTAC
1 ACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTCGCATGGTCTTAC
38463477 ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCT
66 ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCT
* * *
38463542 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTTTTACATCATATCCTTATCTTACCAA
131 AGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATCATATCCTTATCCTACCAA
*
38463607 ATGTCATGTTCCAA
196 ATGCCATGTTCCAA
* *
38463621 ACATAGTCTTACATGGTATCCTTGTCTTA
1 ACATGGTCTTACATGGTATCCTTGCCTTA
38463650 GTGCCAATGC
Statistics
Matches: 221, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
209 221 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (209 bp):
ACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTCGCATGGTCTTAC
ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCT
AGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATCATATCCTTATCCTACCAA
ATGCCATGTTCCAA
Found at i:38463596 original size:54 final size:54
Alignment explanation
Indices: 38463191--38463596 Score: 354
Period size: 54 Copynumber: 7.6 Consensus size: 54
38463181 AACTTACCAT
* * * * *
38463191 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
** * *
38463244 TGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGTCTTATAGTAACTCTTCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCC-TTGCCTTATAG-AACTCATCAA
** * * * * *
38463299 TTTCATGTCTTGACATGGTCTTACATGATTTCCTAGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
*
38463353 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCC---T---AC-CAT--A
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTT-GCCTTATAGAACTCATCAA
*** * * *
38463399 TGCCATGTTCC-AAACATGGTCTTAAATGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATG--CCTTGGCATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* **
38463453 TGCCATGCCTTCGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCC-TTGCCTTATAG-AACTCATCAA
* * * * *
38463508 TGCCATGTCTTGACATAGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* *
38463562 TGCCATGCCTTGGCATGGTTTTACATCATATCCTT
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTT
38463597 ATCTTACCAA
Statistics
Matches: 280, Mismatches: 53, Indels: 39
0.75 0.14 0.10
Matches are distributed among these distances:
46 10 0.04
47 20 0.07
48 4 0.01
49 3 0.01
51 2 0.01
52 9 0.03
53 58 0.21
54 85 0.30
55 85 0.30
56 4 0.01
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
Found at i:38465343 original size:20 final size:21
Alignment explanation
Indices: 38465315--38465354 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
38465305 GCTTTAGTTT
*
38465315 AGCTTTTTCAAG-TTCTGTTC
1 AGCTCTTTCAAGCTTCTGTTC
*
38465335 AGCTCTTTCGAGCTTCTGTT
1 AGCTCTTTCAAGCTTCTGTT
38465355 AAACTCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.47
Consensus pattern (21 bp):
AGCTCTTTCAAGCTTCTGTTC
Found at i:38465353 original size:21 final size:21
Alignment explanation
Indices: 38465294--38465389 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
38465284 CTTTCTATTT
* *
38465294 AGCTCTTTCGTGCTT-TAGTTT
1 AGCTCTTTCGAGCTTCT-GTTA
* * *
38465315 AGCTTTTTCAAG-TTCTGTTC
1 AGCTCTTTCGAGCTTCTGTTA
38465335 AGCTCTTTCGAGCTTCTGTTA
1 AGCTCTTTCGAGCTTCTGTTA
* *
38465356 AACTCTTAT-GAGTTTCTGTTA
1 AGCTCTT-TCGAGCTTCTGTTA
38465377 AG--CTTTCGAGCTT
1 AGCTCTTTCGAGCTT
38465390 TTGTCGGTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
18 1 0.02
19 8 0.13
20 15 0.25
21 35 0.58
22 1 0.02
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
AGCTCTTTCGAGCTTCTGTTA
Found at i:38473323 original size:20 final size:20
Alignment explanation
Indices: 38473298--38473351 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
38473288 GGGATTGCAC
38473298 TTTGGTGTCTCTATTAGCAT
1 TTTGGTGTCTCTATTAGCAT
38473318 TTTGGTGTCTCTATTAGCAT
1 TTTGGTGTCTCTATTAGCAT
*
38473338 TTTGATGCTCTCTA
1 TTTGGTG-TCTCTA
38473352 GTGTGTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.15, C:0.17, G:0.19, T:0.50
Consensus pattern (20 bp):
TTTGGTGTCTCTATTAGCAT
Found at i:38475135 original size:20 final size:20
Alignment explanation
Indices: 38475088--38475138 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 20
38475078 TGCTCTATAT
*
38475088 ATTATTT-TATT-TTTTTGA
1 ATTATTTATATTATTTTTAA
38475106 A-TA-TTA-ATTATTTTTAA
1 ATTATTTATATTATTTTTAA
38475123 ATTATTTATATTATTT
1 ATTATTTATATTATTT
38475139 ACTTTAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 5 0.19
17 9 0.33
18 3 0.11
19 3 0.11
20 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTATTTATATTATTTTTAA
Found at i:38475157 original size:25 final size:26
Alignment explanation
Indices: 38475125--38475197 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
38475115 ATTTTTAAAT
38475125 TATTTATATTATTTACTTTAAA-CTGT-
1 TATTTATATTATTTA-TTTAAACCT-TA
* *
38475151 T-TTTATAGTATCTATTTTAAACCTTA
1 TATTTATATTATTTA-TTTAAACCTTA
*
38475177 TATATATATTATTTATTTAAA
1 TATTTATATTATTTATTTAAA
38475198 ATTATCTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 18 0.47
26 10 0.26
27 10 0.26
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (26 bp):
TATTTATATTATTTATTTAAACCTTA
Found at i:38476981 original size:3 final size:3
Alignment explanation
Indices: 38476973--38477007 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
38476963 TAGGTTAAGT
38476973 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
38477008 GCTTCAACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:38477571 original size:22 final size:23
Alignment explanation
Indices: 38477546--38477609 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 23
38477536 ATTATCTTTT
38477546 TTTAATA-ATATTATTTTAAAAA
1 TTTAATATATATTATTTTAAAAA
*
38477568 TTTAAATCATATATTTCTTTTAAAAA
1 TTT-AAT-ATATA-TTATTTTAAAAA
* *
38477594 TATAATATATCTTATT
1 TTTAATATATATTATT
38477610 ATTACATCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
22 3 0.09
23 7 0.21
24 5 0.15
25 6 0.18
26 13 0.38
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAATATATATTATTTTAAAAA
Found at i:38478449 original size:16 final size:16
Alignment explanation
Indices: 38478428--38478477 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
38478418 AGTTAATTAT
38478428 TAAATTTATATAAATA
1 TAAATTTATATAAATA
*
38478444 TAAA-TTAT-TAATTTA
1 TAAATTTATATAA-ATA
38478459 TTAAATTTTATATAAATA
1 -TAAA-TTTATATAAATA
38478477 T
1 T
38478478 TTTATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.11
15 6 0.22
16 8 0.30
17 1 0.04
18 6 0.22
19 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATTTATATAAATA
Found at i:38483351 original size:20 final size:20
Alignment explanation
Indices: 38483291--38483351 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
38483281 ACACTTTAAT
38483291 TACATAGTATTTTCAACCAA
1 TACATAGTATTTTCAACCAA
*
38483311 AACATAGTATTTTCAACCAA
1 TACATAGTATTTTCAACCAA
38483331 TACATAGTATTTTCAACCAA
1 TACATAGTATTTTCAACCAA
38483351 T
1 T
38483352 TTCAAACATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (20 bp):
TACATAGTATTTTCAACCAA
Found at i:38484279 original size:42 final size:42
Alignment explanation
Indices: 38484179--38484340 Score: 184
Period size: 43 Copynumber: 3.8 Consensus size: 42
38484169 AGCTTGTACA
* * * *
38484179 ATGCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATA-CG
* *
38484222 ATGTCACTGTCCCAGACAG-GGTCTTACACGAAATCAAATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGAAATCAAATACG
*
38484264 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATAAGT-CG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-AAATCA-AA-TACG
* *
38484308 GTGCCAAAGTCCCAGACGTGGTCTTACACGAAA
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAA
38484341 CACATATCGG
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
42 28 0.27
43 41 0.40
44 32 0.31
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATACG
Found at i:38491645 original size:13 final size:14
Alignment explanation
Indices: 38491603--38491647 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
38491593 TAATAATGAT
38491603 TAAAGTATATTATAA
1 TAAAGTA-ATTATAA
38491618 TAATA-TAA-TATAA
1 TAA-AGTAATTATAA
38491631 TAAAGTAATTA-AA
1 TAAAGTAATTATAA
38491644 TAAA
1 TAAA
38491648 AAATAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 17 0.63
14 3 0.11
15 5 0.19
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAAAGTAATTATAA
Found at i:38491739 original size:16 final size:19
Alignment explanation
Indices: 38491698--38491740 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
38491688 GAAACAGAGC
38491698 AAGGAAAGAAAGAAAGAAA
1 AAGGAAAGAAAGAAAGAAA
38491717 AAGGGAAAG-AA-AAAG-AA
1 AA-GGAAAGAAAGAAAGAAA
38491734 AAGGAAA
1 AAGGAAA
38491741 ATTTAGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 4 0.17
18 4 0.17
19 4 0.17
20 6 0.26
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (19 bp):
AAGGAAAGAAAGAAAGAAA
Found at i:38493497 original size:20 final size:20
Alignment explanation
Indices: 38493468--38493514 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
38493458 GGTCTGACCC
*
38493468 CACGGCCATGTCCCAAGCCA
1 CACGGGCATGTCCCAAGCCA
*
38493488 CACGGGCATGTCCCAGGCCA
1 CACGGGCATGTCCCAAGCCA
38493508 CACGGGC
1 CACGGGC
38493515 GTGTGCTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.43, G:0.28, T:0.09
Consensus pattern (20 bp):
CACGGGCATGTCCCAAGCCA
Found at i:38496850 original size:38 final size:37
Alignment explanation
Indices: 38496799--38496875 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 37
38496789 AATGGGATTA
38496799 TACAAATTTTGCTGAGTTGGAGAATTC-TTCCTGGATGT
1 TACAAATTTTGCTGAGTTGGAG-A-TCATTCCTGGATGT
38496837 TACAAATTTTGCTGAGTTGGAGATCATTTCCTGGATGT
1 TACAAATTTTGCTGAGTTGGAGATCA-TTCCTGGATGT
38496875 T
1 T
38496876 GGATCTACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
36 2 0.05
37 1 0.03
38 34 0.92
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (37 bp):
TACAAATTTTGCTGAGTTGGAGATCATTCCTGGATGT
Found at i:38502782 original size:20 final size:21
Alignment explanation
Indices: 38502739--38502784 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
38502729 ACTGTTTTGT
38502739 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
38502759 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
38502778 TATGGGC
1 TATGGGC
38502785 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:38502851 original size:60 final size:60
Alignment explanation
Indices: 38502777--38502911 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 60
38502767 AACTGTGTTA
* * *
38502777 ATATGGGCAAGGCCCAATATA-TCTCA-ACTTGTAATAGGGCTACGGCCTAGATTGATACTG
1 ATATGGGCTAGGCCCAATATACTCTCATAC-TGTAA-AGGGCTACGGCCCAGATTAATACTG
* * * *
38502837 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATACTCTCATACTGTAAAGGGCTACGGCCCAGATTAATACTG
38502897 ATATGGGCTAAGGCC
1 ATATGGGCT-AGGCC
38502912 AGTTAACTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
60 49 0.75
61 14 0.22
62 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (60 bp):
ATATGGGCTAGGCCCAATATACTCTCATACTGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:38503608 original size:16 final size:16
Alignment explanation
Indices: 38503587--38503625 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
38503577 GTTTTCAATG
*
38503587 AAAACATAGTTTTCGA
1 AAAACACAGTTTTCGA
*
38503603 AAAACACGGTTTTCGA
1 AAAACACAGTTTTCGA
38503619 AAAACAC
1 AAAACAC
38503626 TTTAATGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (16 bp):
AAAACACAGTTTTCGA
Found at i:38510864 original size:47 final size:47
Alignment explanation
Indices: 38510807--38510936 Score: 170
Period size: 47 Copynumber: 2.8 Consensus size: 47
38510797 ACAATCGATA
* *
38510807 AGTACCTATACCATCGCCCATAGCCAAATCAAGGTAACTTATCTCGG
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCTCGG
* * * * *
38510854 AGTACTTATACCATGGCCTATAGTCAAATCAAGGTAACTCCTCTCTG
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCTCGG
* * *
38510901 AATACCTATACCATGGACCGTAGCCAAATCAAGGTA
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTA
38510937 TTATTCACAC
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCTCGG
Found at i:38516862 original size:13 final size:13
Alignment explanation
Indices: 38516844--38516872 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38516834 TTTAGTTTAA
38516844 TTAGTTAATTAGT
1 TTAGTTAATTAGT
38516857 TTAGTTAATTAGT
1 TTAGTTAATTAGT
38516870 TTA
1 TTA
38516873 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:38522330 original size:27 final size:27
Alignment explanation
Indices: 38522299--38522476 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38522289 TAAATTGTAC
38522299 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
38522326 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
38522352 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
38522380 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
38522408 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
38522435 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
38522462 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
38522477 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:38522413 original size:82 final size:81
Alignment explanation
Indices: 38522300--38522455 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38522290 AAATTGTACA
* *
38522300 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
38522364 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
38522381 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
38522446 TGCGAGTTGA
65 TGCGAATTGA
38522456 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:38522467 original size:82 final size:81
Alignment explanation
Indices: 38522296--38522476 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
38522286 GATTAAATTG
* *
38522296 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
38522361 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
38522377 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
38522441 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
38522459 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
38522477 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:38525574 original size:6 final size:6
Alignment explanation
Indices: 38525563--38525601 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
38525553 TCCTCCTATC
38525563 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
38525602 CAATTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:38525607 original size:18 final size:18
Alignment explanation
Indices: 38525568--38525607 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
38525558 CTATCTTTTT
**
38525568 ATTTTTATTTTTATTTTT
1 ATTTTTATTTTTATTTCA
38525586 ATTTTTATTTTTATTTCA
1 ATTTTTATTTTTATTTCA
38525604 ATTT
1 ATTT
38525608 AATTATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTTTATTTTTATTTCA
Found at i:38528563 original size:13 final size:13
Alignment explanation
Indices: 38528545--38528573 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38528535 TTTAGTTTAA
38528545 TTAGTTAATTAGT
1 TTAGTTAATTAGT
38528558 TTAGTTAATTAGT
1 TTAGTTAATTAGT
38528571 TTA
1 TTA
38528574 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:38532261 original size:71 final size:67
Alignment explanation
Indices: 38532184--38532325 Score: 176
Period size: 67 Copynumber: 2.1 Consensus size: 67
38532174 TCACCAGATA
* * * **
38532184 CAGATATTATGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGTGA
1 CAGATATTATGACGAAGCCACCAGAAC--A-A-ATATATGTGGCGAAGCCACCAGATTGCAGCAA
38532249 GGCTGC
62 GGCTGC
* * *
38532255 CAGATATTGTGACGAAGTCACCAGAACAAATATATGTGGCGAGGCCACCAGATTGCAGCAAGGCT
1 CAGATATTATGACGAAGCCACCAGAACAAATATATGTGGCGAAGCCACCAGATTGCAGCAAGGCT
38532320 GC
66 GC
38532322 CAGA
1 CAGA
38532326 ACGCTTCATC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
67 39 0.62
68 1 0.02
69 1 0.02
71 22 0.35
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (67 bp):
CAGATATTATGACGAAGCCACCAGAACAAATATATGTGGCGAAGCCACCAGATTGCAGCAAGGCT
GC
Found at i:38537434 original size:62 final size:62
Alignment explanation
Indices: 38537337--38537461 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
38537327 CATTTGAGAC
38537337 TTAGTTTTTCATGCATTACTAAAGCGGTGAAGTTTCTTGGGGGCTAGAGTTCATCACTAGAT
1 TTAGTTTTTCATGCATTACTAAAGCGGTGAAGTTTCTTGGGGGCTAGAGTTCATCACTAGAT
38537399 TTAGTTTTTCATGCATTACTAAAGCGGTGAAGTTTCTTGGGGGCTAGAGTTCATCACTAGAT
1 TTAGTTTTTCATGCATTACTAAAGCGGTGAAGTTTCTTGGGGGCTAGAGTTCATCACTAGAT
38537461 T
1 T
38537462 ATCTAATGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (62 bp):
TTAGTTTTTCATGCATTACTAAAGCGGTGAAGTTTCTTGGGGGCTAGAGTTCATCACTAGAT
Found at i:38538972 original size:24 final size:24
Alignment explanation
Indices: 38538945--38538996 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
38538935 AATCAAAGTC
* *
38538945 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
38538969 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
38538993 AAAT
1 AAAT
38538997 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:38543525 original size:50 final size:49
Alignment explanation
Indices: 38543409--38543589 Score: 272
Period size: 49 Copynumber: 3.7 Consensus size: 49
38543399 CTAGTACGCA
* *
38543409 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGATACACG
** *
38543458 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGATACACG
* * * *
38543508 TAGTAGCCTACACTTAGTACTACAAATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGATACACG
38543557 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
38543590 TCATAATAGA
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 73 0.63
50 43 0.37
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGATACACG
Found at i:38543580 original size:99 final size:99
Alignment explanation
Indices: 38543409--38543590 Score: 328
Period size: 99 Copynumber: 1.8 Consensus size: 99
38543399 CTAGTACGCA
* *
38543409 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTACACTTAGTACTACAAATGCGACCAATTATCCGATACACGTAGTAGCCTGCACTTA
38543474 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGTGACCTAACCATCTGATACACG
* *
38543508 TAGTAGCCTACACTTAGTACTACAAATGTGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTACACTTAGTACTACAAATGCGACCAATTATCCGATACACGTAGTAGCCTGCACTTA
38543573 GTACTACACACGTGACCT
66 GTACTACACACGTGACCT
38543591 CATAATAGAT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 79 1.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTACACTTAGTACTACAAATGCGACCAATTATCCGATACACGTAGTAGCCTGCACTTA
GTACTACACACGTGACCTAACCATCTGATACACG
Found at i:38543857 original size:29 final size:30
Alignment explanation
Indices: 38543815--38543876 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
38543805 GGTACAACCA
* *
38543815 ATGTAATAGTAATTTAACATTCAA-TTCAC
1 ATGTAACAATAATTTAACATTCAATTTCAC
**
38543844 ATGTAACAATAATTTGTCATTCAATTTCAC
1 ATGTAACAATAATTTAACATTCAATTTCAC
38543874 ATG
1 ATG
38543877 ACACAACAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (30 bp):
ATGTAACAATAATTTAACATTCAATTTCAC
Found at i:38546631 original size:24 final size:24
Alignment explanation
Indices: 38546604--38546667 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
38546594 AAACCTAATC
38546604 CTAATCAAAGTC-AAATATATTATT
1 CTAAT-AAAGTCTAAATATATTATT
* *
38546628 CTAATAAATTCTAAATATATTATA
1 CTAATAAAGTCTAAATATATTATT
*
38546652 CTCATAAA-TACTAAAT
1 CTAATAAAGT-CTAAAT
38546668 CTTCTAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.17
24 29 0.83
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (24 bp):
CTAATAAAGTCTAAATATATTATT
Found at i:38548138 original size:13 final size:13
Alignment explanation
Indices: 38548100--38548138 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
38548090 TTTTTTCATT
38548100 TATTTATTTTTAA
1 TATTTATTTTTAA
* **
38548113 TAATTATAATTAA
1 TATTTATTTTTAA
38548126 TATTTATTTTTAA
1 TATTTATTTTTAA
38548139 AACAAATTTA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTATTTTTAA
Found at i:38549436 original size:22 final size:22
Alignment explanation
Indices: 38549411--38549453 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38549401 TATCCAAACA
38549411 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
38549433 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
38549454 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:38551196 original size:21 final size:20
Alignment explanation
Indices: 38551155--38551198 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
38551145 GACGTTCTAT
* *
38551155 GTTTAGGTTCGGGATTTAAG
1 GTTTAGGTTCGAGATTCAAG
*
38551175 GTTTAGGGTTCGAGCTTCAAG
1 GTTTA-GGTTCGAGATTCAAG
38551196 GTT
1 GTT
38551199 CAAAGGTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.18, C:0.09, G:0.34, T:0.39
Consensus pattern (20 bp):
GTTTAGGTTCGAGATTCAAG
Found at i:38552313 original size:11 final size:11
Alignment explanation
Indices: 38552294--38552328 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
38552284 TGCAACCAAA
*
38552294 TTTTGTGCACT
1 TTTTGTGCAAT
*
38552305 TTTTATGCAAT
1 TTTTGTGCAAT
38552316 TTTTGTGCAAT
1 TTTTGTGCAAT
38552327 TT
1 TT
38552329 ATTTCATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.57
Consensus pattern (11 bp):
TTTTGTGCAAT
Found at i:38554495 original size:12 final size:12
Alignment explanation
Indices: 38554480--38554507 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38554470 TTTTGTTTCC
38554480 TTTAGCATACAT
1 TTTAGCATACAT
38554492 TTTAGCATACAT
1 TTTAGCATACAT
38554504 TTTA
1 TTTA
38554508 ATTTTGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (12 bp):
TTTAGCATACAT
Found at i:38570887 original size:26 final size:26
Alignment explanation
Indices: 38570856--38570905 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
38570846 TCCTGTACAT
* *
38570856 ATATGCTCACATGAGCTGTGAAATCA
1 ATATGCTCACACGAGATGTGAAATCA
38570882 ATATGCTCACACGAGATGTGAAAT
1 ATATGCTCACACGAGATGTGAAAT
38570906 GGGCTTGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (26 bp):
ATATGCTCACACGAGATGTGAAATCA
Found at i:38607422 original size:31 final size:31
Alignment explanation
Indices: 38607360--38607422 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
38607350 ACAACATTTC
**
38607360 AAAAAGAAAATCTAAAAAATGAAATCTTGAG
1 AAAAAGAAAATCTAAAAAATGAAATAATGAG
* *
38607391 AAAAAGAAAATTTAATAAATG-AATAAATGAG
1 AAAAAGAAAATCTAAAAAATGAAAT-AATGAG
38607422 A
1 A
38607423 CATTTATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.63, C:0.03, G:0.13, T:0.21
Consensus pattern (31 bp):
AAAAAGAAAATCTAAAAAATGAAATAATGAG
Found at i:38613772 original size:6 final size:6
Alignment explanation
Indices: 38613755--38613785 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
38613745 CTGTGCTTTG
38613755 TTATTT TT-TTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TT
38613786 TACCCTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTATTT
Found at i:38615750 original size:16 final size:15
Alignment explanation
Indices: 38615724--38615762 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
38615714 ATTGAATTAT
* *
38615724 TTATATTTTATATAA
1 TTATATATTATAAAA
38615739 TTGATATATTATAAAA
1 TT-ATATATTATAAAA
38615755 TTATATAT
1 TTATATAT
38615763 GATTTAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TTATATATTATAAAA
Found at i:38623355 original size:33 final size:36
Alignment explanation
Indices: 38623286--38623369 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 36
38623276 CTATACCCAT
* * *
38623286 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCATA-ACACATACACATATATTCAC
38623323 CTATGCCGAATGCAT-ACACATA-A-ATATATTCAC
1 CTATGCCGAATGCATAACACATACACATATATTCAC
38623356 CTATGCCGAATGCA
1 CTATGCCGAATGCA
38623370 ACATTATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 22 0.50
34 1 0.02
35 6 0.14
37 15 0.34
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.29
Consensus pattern (36 bp):
CTATGCCGAATGCATAACACATACACATATATTCAC
Found at i:38623642 original size:41 final size:41
Alignment explanation
Indices: 38623597--38623752 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
38623587 ACCGGCTCTT
*
38623597 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
38623638 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
38623679 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
38623720 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
38623753 TAACGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:38630976 original size:33 final size:33
Alignment explanation
Indices: 38630907--38631004 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
38630897 CTATACCCAT
* * *
38630907 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
38630944 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
38630977 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
38631005 ACATATCTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:38631264 original size:41 final size:41
Alignment explanation
Indices: 38631219--38631374 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
38631209 ACCGGCTCTT
*
38631219 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
38631260 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
38631301 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
38631342 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
38631375 TAACGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:38631885 original size:21 final size:23
Alignment explanation
Indices: 38631861--38631908 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
38631851 TATATATATA
38631861 TATTTC-AC-TCATACTTTTAAT
1 TATTTCAACATCATACTTTTAAT
*
38631882 TATTTCAACTATCATATTTTTAAT
1 TATTTCAAC-ATCATACTTTTAAT
38631906 TAT
1 TAT
38631909 ATTTCATCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
24 15 0.65
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTCAACATCATACTTTTAAT
Found at i:38636046 original size:35 final size:35
Alignment explanation
Indices: 38636000--38636067 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
38635990 AGCTCCTGAG
38636000 TTAGCTAGATTAAGCTACAATGATCGCAAAAACAC
1 TTAGCTAGATTAAGCTACAATGATCGCAAAAACAC
38636035 TTAGCTAGATTAAGCTACAATGATCGCAAAAAC
1 TTAGCTAGATTAAGCTACAATGATCGCAAAAAC
38636068 CTAAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (35 bp):
TTAGCTAGATTAAGCTACAATGATCGCAAAAACAC
Found at i:38640275 original size:25 final size:25
Alignment explanation
Indices: 38640227--38640275 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38640217 CATTATTCTA
* *
38640227 AATATTCAAAAATTTATAATTATAG
1 AATATTAAAAAATTTATAAATATAG
38640252 AATATTAAATAAATTTA-AAATATA
1 AATATTAAA-AAATTTATAAATATA
38640276 AAAACAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
AATATTAAAAAATTTATAAATATAG
Found at i:38640364 original size:8 final size:8
Alignment explanation
Indices: 38640338--38640395 Score: 50
Period size: 8 Copynumber: 7.1 Consensus size: 8
38640328 AACTCAACCA
38640338 TTAATAATT
1 TTAAT-ATT
38640347 TT-ATATTT
1 TTAATA-TT
38640355 TTAATATT
1 TTAATATT
38640363 TTAATATT
1 TTAATATT
38640371 TT-ATAATT
1 TTAAT-ATT
*
38640379 ATAAT-TT
1 TTAATATT
38640386 TTAAATATT
1 TT-AATATT
38640395 T
1 T
38640396 AGAATAATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
8 25 0.61
9 10 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTAATATT
Found at i:38640365 original size:16 final size:18
Alignment explanation
Indices: 38640338--38640377 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
38640328 AACTCAACCA
38640338 TTAATAATTTT-ATATTT
1 TTAATAATTTTAATATTT
38640355 TTAAT-ATTTTAATATTT
1 TTAATAATTTTAATATTT
38640372 TATAAT
1 T-TAAT
38640378 TATAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 12 0.57
18 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATAATTTTAATATTT
Found at i:38640392 original size:24 final size:24
Alignment explanation
Indices: 38640344--38640395 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
38640334 ACCATTAATA
* * *
38640344 ATTTTATATTTTTAATATTTTAAT
1 ATTTTATAATTATAATATTTAAAT
*
38640368 ATTTTATAATTATAATTTTTAAAT
1 ATTTTATAATTATAATATTTAAAT
38640392 ATTT
1 ATTT
38640396 AGAATAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTTTATAATTATAATATTTAAAT
Found at i:38640856 original size:15 final size:15
Alignment explanation
Indices: 38640838--38640885 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
38640828 TTAAATTATG
38640838 AAAATTATAAAATAT
1 AAAATTATAAAATAT
*
38640853 AAAATTATAAAACA-
1 AAAATTATAAAATAT
*
38640867 AAAATAAATAAAAT-T
1 AAAAT-TATAAAATAT
38640882 AAAA
1 AAAA
38640886 AAAAAAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATTATAAAATAT
Done.