Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 39 of 199
Found at i:11988547 original size:22 final size:23
Alignment explanation
Indices: 11988521--11988571 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
11988511 TTTAAAACTC
11988521 TTTTTATACA-AAAAAACAT-TT
1 TTTTTATACATAAAAAACATATT
*
11988542 ATTTTTATACATATAAAACATATT
1 -TTTTTATACATAAAAAACATATT
11988566 TTTTTA
1 TTTTTA
11988572 AAATTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 10 0.38
23 14 0.54
24 2 0.08
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTTATACATAAAAAACATATT
Found at i:11988580 original size:22 final size:23
Alignment explanation
Indices: 11988521--11988581 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
11988511 TTTAAAACTC
11988521 TTTTTATACAA-A-AAAACATTTA
1 TTTTTATA-AATATAAAACATTTA
*
11988543 TTTTTATACATATAAAACATATT-
1 TTTTTATAAATATAAAACAT-TTA
*
11988566 TTTTTA-AAATTTAAAA
1 TTTTTATAAATATAAAA
11988582 TTTATTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.03
22 17 0.52
23 13 0.39
24 2 0.06
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTTTATAAATATAAAACATTTA
Found at i:11988706 original size:26 final size:26
Alignment explanation
Indices: 11988677--11988728 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
11988667 AAACTATATT
11988677 ACACAAATTACATAATATATAAATAA
1 ACACAAATTACATAATATATAAATAA
11988703 ACACAAATTACATAATATATAAATAA
1 ACACAAATTACATAATATATAAATAA
11988729 TAAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (26 bp):
ACACAAATTACATAATATATAAATAA
Found at i:11988741 original size:26 final size:25
Alignment explanation
Indices: 11988686--11988757 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
11988676 TACACAAATT
*
11988686 ACATAATATATAAATAAACACA-AATT
1 ACATAATATATAAATAAA-A-ATAATA
11988712 ACATAATATATAAATAATAAATAATA
1 ACATAATATATAAATAA-AAATAATA
*
11988738 ACATATTAT-TAAATCAAAAA
1 ACATAATATATAAAT-AAAAA
11988758 ATAGATTAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 9 0.22
26 31 0.76
27 1 0.02
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
ACATAATATATAAATAAAAATAATA
Found at i:11994101 original size:11 final size:11
Alignment explanation
Indices: 11994085--11994111 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11994075 ATTTTCGTAG
11994085 TTAATTTAAAT
1 TTAATTTAAAT
11994096 TTAATTTAAAT
1 TTAATTTAAAT
11994107 TTAAT
1 TTAAT
11994112 ATGCACAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTAATTTAAAT
Found at i:12003114 original size:27 final size:22
Alignment explanation
Indices: 12003062--12003105 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12003052 CAGATGTACC
12003062 AAAAACAAATGATACGAGCTTA
1 AAAAACAAATGATACGAGCTTA
12003084 AAAAACAAATGATACGAGCTTA
1 AAAAACAAATGATACGAGCTTA
12003106 TGATAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.18
Consensus pattern (22 bp):
AAAAACAAATGATACGAGCTTA
Found at i:12004210 original size:14 final size:17
Alignment explanation
Indices: 12004179--12004215 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
12004169 ATTATAAAGG
12004179 ATATTATTAAATTAATT
1 ATATTATTAAATTAATT
12004196 ATATTA-TAAA-T-ATT
1 ATATTATTAAATTAATT
12004210 ATATTA
1 ATATTA
12004216 AGAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 4 0.20
17 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATTAAATTAATT
Found at i:12004391 original size:14 final size:14
Alignment explanation
Indices: 12004365--12004415 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
12004355 GAAAACAAAA
12004365 GAAATAAAATAAAG
1 GAAATAAAATAAAG
*
12004379 GAAATAAAGTAAAG
1 GAAATAAAATAAAG
* * *
12004393 TAAGTTAAAATAAAA
1 GAA-ATAAAATAAAG
12004408 G-AATAAAA
1 GAAATAAAA
12004416 GAAACAAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 5 0.17
14 16 0.55
15 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.18
Consensus pattern (14 bp):
GAAATAAAATAAAG
Found at i:12004426 original size:17 final size:16
Alignment explanation
Indices: 12004404--12004437 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12004394 AAGTTAAAAT
12004404 AAAAGAATAAAAGAAAC
1 AAAAGAA-AAAAGAAAC
*
12004421 AAAAGAAGAAAGAAAC
1 AAAAGAAAAAAGAAAC
12004437 A
1 A
12004438 GAATAGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAC
Found at i:12005590 original size:37 final size:39
Alignment explanation
Indices: 12005531--12005626 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
12005521 CGGATAGATT
* * * *
12005531 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
12005568 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
12005607 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
12005627 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:12011645 original size:50 final size:44
Alignment explanation
Indices: 12011607--12012080 Score: 190
Period size: 45 Copynumber: 10.5 Consensus size: 44
12011597 GTCACCGTAG
* *
12011607 CAAATCTTACCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTA
1 CAAATCTTACCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTA
* * * *
12011651 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAAATTTAAGATA
1 CAAATCTTACCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTA
** ** * * * * *
12011695 GTGAATCTTATTTCCTTGAAGTTGCAGCGG-GACATATTAAAGTTACAAGTTA
1 -CAAATCTTACCTCCCTGAAGTTACAGTGGAG-CAGATT---G----AAGCTA
* * * * * *
12011747 CAAATCTTATCTCTCTGAAGGTGCAATGGAGCAGATTAAAG---
1 CAAATCTTACCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTA
* * * * * *
12011788 CGAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTA
1 CAAATCTTACCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTA
* * * *
12011832 TAAATCTTATCC-CCCTGAAGTTGCAGTGGAGCAAATTGAAGATA
1 CAAATCTTA-CCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTA
* ** * ** *** * *
12011876 GCGAATCTTATTTTCCTGAAGTTGTAGCAAAACAGATTAAAGCTACAATTTA
1 -CAAATCTTACCTCCCTGAAGTTACAGTGGAGCAGATTGAAG---C----TA
* * * * * *
12011928 CAAATCTTATCTCCCTAAAGGTGCAGTGGAGCAGATTAAAGCGA
1 CAAATCTTACCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTA
* * *
12011972 -ACA--TTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
1 CAAATCTTACCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTA
** * * *
12012013 CAAAATCTTATATCCTTGAAGTTGCAGTGGAGCAGATTGAAGATA
1 C-AAATCTTACCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTA
**
12012058 GCAAATCTTATTTCCCTGAAGTT
1 -CAAATCTTACCTCCCTGAAGTT
12012081 CCAACGAAAT
Statistics
Matches: 328, Mismatches: 74, Indels: 55
0.72 0.16 0.12
Matches are distributed among these distances:
41 69 0.21
43 4 0.01
44 79 0.24
45 109 0.33
46 1 0.00
48 1 0.00
51 57 0.17
52 8 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
CAAATCTTACCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTA
Found at i:12011818 original size:41 final size:41
Alignment explanation
Indices: 12011747--12012080 Score: 191
Period size: 45 Copynumber: 7.5 Consensus size: 41
12011737 TTACAAGTTA
* * * *
12011747 CAAATCTTATCTCTCTGAAGGTGCAATGGAGCAGATTAAAG
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* *
12011788 CGAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAG
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * *
12011829 CTATAAATCTTATCCCCCTGAAGTTGCAGTGGAGCAAATTGAAGATAG
1 C---AAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--A-A-AG
* * * * * *** *
12011877 CGAATCTTATTTTCCTGAAGTTGTAGCAAAACAGATTAAAG
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* *
12011918 CTACAATTTACAAATCTTATCTCCCTAAAGGTGCAGTGGAGCAGATTAAAG
1 ---CAA---AC----CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * *
12011969 CGAACATTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAG
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * *
12012010 CTACAAAATCTTATATCCTTGAAGTTGCAGTGGAGCAGATTGAAGATAG
1 ---C-AAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--A-A-AG
* *
12012059 CAAATCTTATTTCCCTGAAGTT
1 CAAACCTTATCTCCCTGAAGTT
12012081 CCAACGAAAT
Statistics
Matches: 225, Mismatches: 43, Indels: 46
0.72 0.14 0.15
Matches are distributed among these distances:
41 70 0.31
42 1 0.00
43 1 0.00
44 36 0.16
45 77 0.34
46 2 0.01
47 3 0.01
48 6 0.03
49 2 0.01
51 27 0.12
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (41 bp):
CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
Found at i:12011820 original size:137 final size:137
Alignment explanation
Indices: 12011556--12011857 Score: 335
Period size: 137 Copynumber: 2.2 Consensus size: 137
12011546 CAGTGAAACC
* * * * * * *
12011556 ATAAATCCTATACCCCTGAAGTTGTAGTGGGACGA-ATTGAAGTCAC-CG-TAGCAAATCTTACC
1 ATAAATCTTATCCCCCTGAAGTTGCAGCGGGAC-ATATTAAAGTTACAAGTTA-CAAATCTTACC
* * * *
12011618 TCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGC
64 TCCTTGAAGGTGCAATGGAGCAGATTAAAG--ACAAACCTTATCTCCCTGAAGTTACAGTGGAGC
*
12011683 AAATTTAAGAT
127 AAATTAAAGAT
* ** * *
12011694 AGTGAATCTTATTTCCTTGAAGTTGCAGCGGGACATATTAAAGTTACAAGTTACAAATCTTATCT
1 A-TAAATCTTATCCCCCTGAAGTTGCAGCGGGACATATTAAAGTTACAAGTTACAAATCTTACCT
* *
12011759 -CTCTGAAGGTGCAATGGAGCAGATTAAAG-CGAACCTTATCTCCCTGAAGTTGCAGTGGAGCAA
65 CCT-TGAAGGTGCAATGGAGCAGATTAAAGACAAACCTTATCTCCCTGAAGTTACAGTGGAGCAA
*
12011822 ATTAAAGCT
129 ATTAAAGAT
12011831 ATAAATCTTATCCCCCTGAAGTTGCAG
1 ATAAATCTTATCCCCCTGAAGTTGCAG
12011858 TGGAGCAAAT
Statistics
Matches: 136, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
136 22 0.16
137 39 0.29
138 2 0.01
139 36 0.26
140 35 0.26
141 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (137 bp):
ATAAATCTTATCCCCCTGAAGTTGCAGCGGGACATATTAAAGTTACAAGTTACAAATCTTACCTC
CTTGAAGGTGCAATGGAGCAGATTAAAGACAAACCTTATCTCCCTGAAGTTACAGTGGAGCAAAT
TAAAGAT
Found at i:12011899 original size:45 final size:45
Alignment explanation
Indices: 12011793--12012150 Score: 246
Period size: 45 Copynumber: 7.8 Consensus size: 45
12011783 TAAAGCGAAC
* * *
12011793 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTA-TAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCAAAT
* * * *
12011837 CTTATCCCCCTGAAGTTGCAGTGGAGCAAATTGAAGATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCAAAT
* * * *** *
12011882 CTTATTTTCCTGAAGTTGTAGCAAAACAGATTAAAGCTACAATTTA-CAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-----A--TAGCAAAT
* * *
12011933 CTTATCTCCCTAAAGGTGCAGTGGAGCAGATT--A-A-AGCGAA-
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCAAAT
* *
12011973 CATTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA-CAAAAT
1 C-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGC-AAAT
* * *
12012019 CTTATATCCTTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCAAAT
* * ** * ** *
12012064 CTTATTTCCCTGAAGTTCCAACGAAATAGATTAAAGCTACAAGTTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--A-TAG---CAAAT
*
12012115 CTTATCTCCCTGAAGGTGCAGTGGAGCAGATTAAAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
12012151 TAACAAGTCC
Statistics
Matches: 237, Mismatches: 54, Indels: 39
0.72 0.16 0.12
Matches are distributed among these distances:
40 2 0.01
41 31 0.13
43 2 0.01
44 37 0.16
45 96 0.41
46 2 0.01
47 1 0.00
48 2 0.01
49 1 0.00
50 1 0.00
51 60 0.25
52 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCAAAT
Found at i:12011965 original size:51 final size:48
Alignment explanation
Indices: 12011793--12012372 Score: 276
Period size: 51 Copynumber: 12.4 Consensus size: 48
12011783 TAAAGCGAAC
*
12011793 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCT--AT--AAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACATACAAAT
* * * *
12011837 CTTATCCCCCTGAAGTTGCAGTGGAGCAAATTGAAG----ATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACATA-CAAAT
* * * *** *
12011882 CTTATTTTCCTGAAGTTGTAGCAAAACAGATTAAAGCTACAATTTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC-A--TACAAAT
* * *
12011933 CTTATCTCCCTAAAGGTGCAGTGGAGCAGATTAAAGC--GA-AC--A-
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACATACAAAT
*
12011975 -TTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTAC--A-AAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACATACAAAT
* * *
12012019 CTTATATCCTTGAAGTTGCAGTGGAGCAGATTGAAG----ATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACATA-CAAAT
* * ** * **
12012064 CTTATTTCCCTGAAGTTCCAACGAAATAGATTAAAGCTACAAGTTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC-A--TACAAAT
* *
12012115 CTTATCTCCCTGAAGGTGCAGTGGAGCAGATTAAAG-T--A-ACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACATACAAAT
* * * * ** *
12012159 CCTATAC-CTCTGAGGTTGCAGTGG-GTCAAATTAAATATACTATAGCAAGT
1 CTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTAAAGCTAC-ATA-CAAAT
** ** * *
12012209 CTTATCTCCCTGAAGTTATAGTGGAATAGACTAAAGTTACAAGCTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC-A--TACAAAT
* ** ** * * *
12012260 CTTATATCCCTGAAGTTGCAACGGAATAGGTTGAAG----ATACGAA-
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACATACAAAT
* ** *
12012303 --TATCTCCCTGAACTTGCAGTGGAATAGATTAAAGTTACAAGCTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC-A--TACAAAT
12012352 CTTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAG
12012373 CAGAATAGGT
Statistics
Matches: 401, Mismatches: 86, Indels: 91
0.69 0.15 0.16
Matches are distributed among these distances:
41 61 0.15
42 3 0.01
43 4 0.01
44 70 0.17
45 95 0.24
46 2 0.00
47 1 0.00
48 7 0.02
49 2 0.00
50 35 0.09
51 115 0.29
52 6 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (48 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACATACAAAT
Found at i:12012113 original size:182 final size:181
Alignment explanation
Indices: 12011617--12012150 Score: 798
Period size: 181 Copynumber: 2.9 Consensus size: 181
12011607 CAAATCTTAC
* * *
12011617 CTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAG
1 CTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAG
* * * ** * *
12011682 CAAATTTAAGATAGTGAATCTTATTTCCTTGAAGTTGCAGCGGGACATATTAAAGTTACAAGTTA
66 CAAATTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGCGAAACAGATTAAAGCTACAAGTTA
* * *
12011747 CAAATCTTATCTCTCTGAAGGTGCAATGGAGCAGATTAAAGCGAACCTTAT
131 CAAATCTTATCTCCCTGAAGGTGCAGTGGAGCAGATTAAAGCGAACATTAT
* * *
12011798 CTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTATAAATCTTATCCCCCTGAAGTTGCAGTGGAG
1 CTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAG
* * * *
12011863 CAAATTGAAGATAGCGAATCTTATTTTCCTGAAGTTGTAGCAAAACAGATTAAAGCTACAATTTA
66 CAAATTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGCGAAACAGATTAAAGCTACAAGTTA
*
12011928 CAAATCTTATCTCCCTAAAGGTGCAGTGGAGCAGATTAAAGCGAACATTAT
131 CAAATCTTATCTCCCTGAAGGTGCAGTGGAGCAGATTAAAGCGAACATTAT
* * *
12011979 CTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAAATCTTATATCCTTGAAGTTGCAGTGGA
1 CTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC-AAATCTTATCTCCCTGAAGTTGCAGTGGA
* * * * *
12012044 GCAGATTGAAGATAGCAAATCTTATTTCCCTGAAGTTCCAACGAAATAGATTAAAGCTACAAGTT
65 GCAAATTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGCGAAACAGATTAAAGCTACAAGTT
12012109 ACAAATCTTATCTCCCTGAAGGTGCAGTGGAGCAGATTAAAG
130 ACAAATCTTATCTCCCTGAAGGTGCAGTGGAGCAGATTAAAG
12012151 TAACAAGTCC
Statistics
Matches: 315, Mismatches: 37, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
181 192 0.61
182 123 0.39
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (181 bp):
CTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAG
CAAATTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGCGAAACAGATTAAAGCTACAAGTTA
CAAATCTTATCTCCCTGAAGGTGCAGTGGAGCAGATTAAAGCGAACATTAT
Found at i:12012325 original size:92 final size:92
Alignment explanation
Indices: 12012211--12012434 Score: 333
Period size: 92 Copynumber: 2.4 Consensus size: 92
12012201 TAGCAAGTCT
* * *
12012211 TATCTCCCTGAAGTTATAGTGGAATAGACTAAAGTTACAAGCTACAAATCTTATATCCCTGAAGT
1 TATCTCCCTGAAATTGTAGTGGAATAGATTAAAGTTACAAGCTACAAATCTTATATCCCTGAAGT
* *
12012276 TGCAACGGAATAGGTTGAAGATACGAA
66 TGCAACAGAATAGGTTGAAGATACAAA
* * *
12012303 TATCTCCCTGAACTTGCAGTGGAATAGATTAAAGTTACAAGCTACAAATCTTATCTCCCTGAAGT
1 TATCTCCCTGAAATTGTAGTGGAATAGATTAAAGTTACAAGCTACAAATCTTATATCCCTGAAGT
*
12012368 TGCAGCAGAATAGGTTGAAGATACAAA
66 TGCAACAGAATAGGTTGAAGATACAAA
* *
12012395 TATCT-CCTCGAAATTGTAGTGGAGTAGATTAAAATTACAA
1 TATCTCCCT-GAAATTGTAGTGGAATAGATTAAAGTTACAA
12012435 TTCTTACACC
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 3 0.03
92 116 0.97
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (92 bp):
TATCTCCCTGAAATTGTAGTGGAATAGATTAAAGTTACAAGCTACAAATCTTATATCCCTGAAGT
TGCAACAGAATAGGTTGAAGATACAAA
Found at i:12018513 original size:13 final size:13
Alignment explanation
Indices: 12018495--12018522 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12018485 CTATTTATCA
12018495 TATCTCAAAATCT
1 TATCTCAAAATCT
12018508 TATCTCAAAATCT
1 TATCTCAAAATCT
12018521 TA
1 TA
12018523 ATCAACCTAT
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:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (13 bp):
TATCTCAAAATCT
Found at i:12022637 original size:21 final size:22
Alignment explanation
Indices: 12022598--12022639 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
12022588 CTTTTGAATA
12022598 TTTTTATGATAATACATTATTAT
1 TTTTTATGATAATA-ATTATTAT
*
12022621 TTTTTATGATACT-ATTATT
1 TTTTTATGATAATAATTATT
12022640 CGTATATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
23 12 0.67
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTTTATGATAATAATTATTAT
Found at i:12022765 original size:3 final size:3
Alignment explanation
Indices: 12022757--12022781 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12022747 ATATGTTTAT
12022757 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
12022782 GTTTATGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12028143 original size:800 final size:800
Alignment explanation
Indices: 12026866--12028461 Score: 3138
Period size: 800 Copynumber: 2.0 Consensus size: 800
12026856 GTTTAAAATT
12026866 ATTACCCATATAATTTATTTGCTCATTCTCCATGCTAGGACCGAAGGGTAAATATTCTAAATTAT
1 ATTACCCATATAATTTATTTGCTCATTCTCCATGCTAGGACCGAAGGGTAAATATTCTAAATTAT
12026931 TTATTTCACCTCCATTAGCATCGCATTGCATCACCGGATGTACCTGCGTAGAAACACATAAACCA
66 TTATTTCACCTCCATTAGCATCGCATTGCATCACCGGATGTACCTGCGTAGAAACACATAAACCA
*
12026996 TCAATTTTTTATTTAAAAGTTCTACCTGATTCGATAACATGGTGACCGCATCTAAGTTAAAAACA
131 TCAATTTTTTATTTAAAAGTTCTACCTGATTCGATAACATGGTGACCACATCTAAGTTAAAAACA
12027061 CCGACTGCTTTTGTCGACTTTGTCCTCATGACTTGCCACTGATAATTATTCAATGACATCTCCTC
196 CCGACTGCTTTTGTCGACTTTGTCCTCATGACTTGCCACTGATAATTATTCAATGACATCTCCTC
*
12027126 TATAAACTCATAAGCTGCTTCAGGTGTTTTATTGTTCAGAGTACCACCGGCTGCTGCATCGATTA
261 TATAAACTCATAAGCTGCTTCAGGTGTTTTATTGTTCAGAGTAACACCGGCTGCTGCATCGATTA
12027191 ACTGCCTAGTTGAGGGATTCAAATCGTTGTAGAAGGTTTGAACTTGTAACCATAGAGGTAACCCA
326 ACTGCCTAGTTGAGGGATTCAAATCGTTGTAGAAGGTTTGAACTTGTAACCATAGAGGTAACCCA
12027256 TGGTGAGGGCACATTCTCAATAAATCCTTATACCTCTTACATGCATCATATAGCGTTTCTAAGTC
391 TGGTGAGGGCACATTCTCAATAAATCCTTATACCTCTTACATGCATCATATAGCGTTTCTAAGTC
*
12027321 AATCTGCACGAAGGAAGATATATCATTCCTCAGCTTAGCTGTCTTAGTCGGTGGAAAGTATTTTA
456 AATCTGCACGAAGGAAGATATATCATTCCTCAGCTTAGCTGTCTTAGTCGGTGGAAAGTACTTTA
12027386 GTAGGAATTTCTCGGTCATTTGATCTCATGTAGTGATAGAACCTCGTATATAAGGAGTTCAACCA
521 GTAGGAATTTCTCGGTCATTTGATCTCATGTAGTGATAGAACCTCGTATATAAGGAGTTCAACCA
*
12027451 CTGTTTAAATTTGTTTCTCAATGAGAAAGGGAATAATCGTAGGCGAATAGCATCGTAAGAAACTT
586 CTGTTTAAATTTGTTTCTCAATGAGAAAGGGAATAATCGTAGGCGAATAGCATCGTAAGAAACGT
12027516 CATTTATCTTGAAAGTATCACAAACTTTCAAAAAATTAGCCAAATAAGTATTTGGATCTTCGTCC
651 CATTTATCTTGAAAGTATCACAAACTTTCAAAAAATTAGCCAAATAAGTATTTGGATCTTCGTCC
12027581 TACAAACCATCGAACTAAACAAACTGTTGAATCATCTAAATAGTGTTCGGCTTCAGTTTGAAATT
716 TACAAACCATCGAACTAAACAAACTGTTGAATCATCTAAATAGTGTTCGGCTTCAGTTTGAAATT
12027646 ATTCGCAGTAATGGTGGGAA
781 ATTCGCAGTAATGGTGGGAA
*
12027666 ATTACCCATATAATTTATTTGCTCATTCTCCATGCTAGGACCGAAGGGTAAATATTCTGAATTAT
1 ATTACCCATATAATTTATTTGCTCATTCTCCATGCTAGGACCGAAGGGTAAATATTCTAAATTAT
12027731 TTATTTCACCTCCATTAGCATCGCATTGCATCACCGGATGTACCTGCGTAGAAACACATAAACCA
66 TTATTTCACCTCCATTAGCATCGCATTGCATCACCGGATGTACCTGCGTAGAAACACATAAACCA
*
12027796 TCAATTTTTTATTTAAAAGTTCTATCTGATTCGATAACATGGTGACCACATCTAAGTTAAAAACA
131 TCAATTTTTTATTTAAAAGTTCTACCTGATTCGATAACATGGTGACCACATCTAAGTTAAAAACA
12027861 CCGACTGCTTTTGTCGACTTTGTCCTCATGACTTGCCACTGATAATTATTCAATGACATCTCCTC
196 CCGACTGCTTTTGTCGACTTTGTCCTCATGACTTGCCACTGATAATTATTCAATGACATCTCCTC
12027926 TATAAACTCATAAGCTGCTTCAGGTGTTTTATTGTTCAGAGTAACACCGGCTGCTGCATCGATTA
261 TATAAACTCATAAGCTGCTTCAGGTGTTTTATTGTTCAGAGTAACACCGGCTGCTGCATCGATTA
12027991 ACTGCCTAGTTGAGGGATTCAAATCGTTGTAGAAGGTTTGAACTTGTAACCATAGAGGTAACCCA
326 ACTGCCTAGTTGAGGGATTCAAATCGTTGTAGAAGGTTTGAACTTGTAACCATAGAGGTAACCCA
12028056 TGGTGAGGGCACATTCTCAATAAATCCTTATACCTCTTACATGCATCATATAGCGTTTCTAAGTC
391 TGGTGAGGGCACATTCTCAATAAATCCTTATACCTCTTACATGCATCATATAGCGTTTCTAAGTC
12028121 AATCTGCACGAAGGAAGATATATCATTCCTCAGCTTAGCTGTCTTAGTCGGTGGAAAGTACTTTA
456 AATCTGCACGAAGGAAGATATATCATTCCTCAGCTTAGCTGTCTTAGTCGGTGGAAAGTACTTTA
12028186 GTAGGAATTTCTCGGTCATTTGATCTCATGTAGTGATAGAACCTCGTATATAAGGAGTTCAACCA
521 GTAGGAATTTCTCGGTCATTTGATCTCATGTAGTGATAGAACCTCGTATATAAGGAGTTCAACCA
12028251 CTGTTTAAATTTGTTTCTCAATGAGAAAGGGAATAATCGTAGGCGAATAGCATCGTAAGAAACGT
586 CTGTTTAAATTTGTTTCTCAATGAGAAAGGGAATAATCGTAGGCGAATAGCATCGTAAGAAACGT
12028316 CATTTATCTTGAAAGTATCACAAACTTTCAAAAAATTAGCCAAATAAGTATTTGGATCTTCGTCC
651 CATTTATCTTGAAAGTATCACAAACTTTCAAAAAATTAGCCAAATAAGTATTTGGATCTTCGTCC
12028381 TACAAACCATCGAACTAAACAAACTGTTGAATCATCTAAATAGTGTTCGGCTTCAGTTTGAAATT
716 TACAAACCATCGAACTAAACAAACTGTTGAATCATCTAAATAGTGTTCGGCTTCAGTTTGAAATT
12028446 ATTCGCAGTAATGGTG
781 ATTCGCAGTAATGGTG
12028462 TGTCTTACAA
Statistics
Matches: 790, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
800 790 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (800 bp):
ATTACCCATATAATTTATTTGCTCATTCTCCATGCTAGGACCGAAGGGTAAATATTCTAAATTAT
TTATTTCACCTCCATTAGCATCGCATTGCATCACCGGATGTACCTGCGTAGAAACACATAAACCA
TCAATTTTTTATTTAAAAGTTCTACCTGATTCGATAACATGGTGACCACATCTAAGTTAAAAACA
CCGACTGCTTTTGTCGACTTTGTCCTCATGACTTGCCACTGATAATTATTCAATGACATCTCCTC
TATAAACTCATAAGCTGCTTCAGGTGTTTTATTGTTCAGAGTAACACCGGCTGCTGCATCGATTA
ACTGCCTAGTTGAGGGATTCAAATCGTTGTAGAAGGTTTGAACTTGTAACCATAGAGGTAACCCA
TGGTGAGGGCACATTCTCAATAAATCCTTATACCTCTTACATGCATCATATAGCGTTTCTAAGTC
AATCTGCACGAAGGAAGATATATCATTCCTCAGCTTAGCTGTCTTAGTCGGTGGAAAGTACTTTA
GTAGGAATTTCTCGGTCATTTGATCTCATGTAGTGATAGAACCTCGTATATAAGGAGTTCAACCA
CTGTTTAAATTTGTTTCTCAATGAGAAAGGGAATAATCGTAGGCGAATAGCATCGTAAGAAACGT
CATTTATCTTGAAAGTATCACAAACTTTCAAAAAATTAGCCAAATAAGTATTTGGATCTTCGTCC
TACAAACCATCGAACTAAACAAACTGTTGAATCATCTAAATAGTGTTCGGCTTCAGTTTGAAATT
ATTCGCAGTAATGGTGGGAA
Found at i:12039952 original size:123 final size:124
Alignment explanation
Indices: 12039624--12039973 Score: 612
Period size: 125 Copynumber: 2.8 Consensus size: 124
12039614 TTATTTCGAG
*
12039624 TTGACGTTTCTGAGCAAATAGTATAAAATTGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * *
12039689 AAATCCCGCCCTCATGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATA-TATTTTT
12039749 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
12039814 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATA-ATTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATATTTTT
12039872 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
12039937 AAATCGCGCCATCGTGGACGCAATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
12039974 CAAGTTTGGG
Statistics
Matches: 215, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
123 103 0.48
125 112 0.52
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATATTTTT
Found at i:12040530 original size:27 final size:27
Alignment explanation
Indices: 12040489--12040591 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
12040479 TAGTATTGGC
*
12040489 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTAGAAGGCGCCAATGGTGGT
* * * *
12040516 GCCTATTTGGGAGGCGCCAATGATGGT
1 GCCTATCTAGAAGGCGCCAATGGTGGT
*
12040543 GCCTATCTAGGAGGCGCCAATGGTGGT
1 GCCTATCTAGAAGGCGCCAATGGTGGT
12040570 GCCATAT-TAGAAGGCGCCAATG
1 GCC-TATCTAGAAGGCGCCAATG
12040592 CTGTGATTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 65 0.96
28 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.22
Consensus pattern (27 bp):
GCCTATCTAGAAGGCGCCAATGGTGGT
Found at i:12040571 original size:54 final size:54
Alignment explanation
Indices: 12040489--12040591 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
12040479 TAGTATTGGC
* *
12040489 GCCTATCTGGAAGGCGCCAATGGTGGTGCC-TATTTGGGAGGCGCCAATGATGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGTGCCATA-TTAGAAGGCGCCAATGATGGT
12040543 GCCTATCTAGG-AGGCGCCAATGGTGGTGCCATATTAGAAGGCGCCAATG
1 GCCTATCT-GGAAGGCGCCAATGGTGGTGCCATATTAGAAGGCGCCAATG
12040592 CTGTGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
54 41 0.91
55 4 0.09
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.22
Consensus pattern (54 bp):
GCCTATCTGGAAGGCGCCAATGGTGGTGCCATATTAGAAGGCGCCAATGATGGT
Found at i:12040701 original size:22 final size:21
Alignment explanation
Indices: 12040650--12040690 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
12040640 CAAAAACGGA
*
12040650 AGAAAGAAGAAGGAAGGAAGC
1 AGAAAAAAGAAGGAAGGAAGC
12040671 AGAAGAAAAGAAGGAAGGAA
1 AGAA-AAAAGAAGGAAGGAA
12040691 AAGAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.61, C:0.02, G:0.37, T:0.00
Consensus pattern (21 bp):
AGAAAAAAGAAGGAAGGAAGC
Found at i:12043742 original size:39 final size:38
Alignment explanation
Indices: 12043699--12043781 Score: 148
Period size: 39 Copynumber: 2.2 Consensus size: 38
12043689 AAAAAGTCAG
12043699 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAA-TTTTT
*
12043738 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
12043776 TTATAA
1 TTATAA
12043782 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 11 0.26
39 32 0.74
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:12044055 original size:49 final size:46
Alignment explanation
Indices: 12043922--12044171 Score: 187
Period size: 49 Copynumber: 5.4 Consensus size: 46
12043912 CAAATTAATT
*
12043922 ATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATATC
1 ATAAAA-AATTACAATATTCATAC--AAAATTATAATATTACAATAT-TC
**** * *
12043972 -CCCCACATTACAATATTCATACAAAATTACAATATTACAATATTC
1 ATAAAAAATTACAATATTCATACAAAATTATAATATTACAATATTC
*
12044017 ATAAAAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTC
1 AT---AAAAAATTACAATATTCATACAAAATTATAATATTACAATATTC
* * *
12044066 ATACAACATTACAATATTCATAAAAAAATTATAATATT-C-ATA--C
1 ATAAAAAATTACAATATTCAT-ACAAAATTATAATATTACAATATTC
* *
12044109 AAAATTACAATATTACAATATTCATAC-AAA--A-AA-ATTGCAATATTC
1 ATAA--A-AA-ATTACAATATTCATACAAAATTATAATATTACAATATTC
* *
12044154 ATACAAAATTATAATATT
1 ATAAAAAATTACAATATT
12044172 ACAATATTCA
Statistics
Matches: 164, Mismatches: 23, Indels: 35
0.74 0.10 0.16
Matches are distributed among these distances:
41 13 0.08
42 5 0.03
43 8 0.05
45 12 0.07
46 40 0.24
47 29 0.18
48 16 0.10
49 41 0.25
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (46 bp):
ATAAAAAATTACAATATTCATACAAAATTATAATATTACAATATTC
Found at i:12044055 original size:95 final size:97
Alignment explanation
Indices: 12043924--12044140 Score: 252
Period size: 95 Copynumber: 2.3 Consensus size: 97
12043914 AATTAATTAT
* * *
12043924 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATATC-CCCCACATTACAATAT
1 AAAAAAATTACAATATTCATAC-AAAAATTACAATATTACAATAT-TCACACAACATTACAATAT
*
12043988 TCAT-ACAAAATTACAATATTACAATATTCATAA
64 TCATAAAAAAATTACAATATTACAATATTCATAA
* * *
12044021 AAAAAAATTGCAATATTCATAC-AAAATTATAATATTACAATATTCATACAACATTACAATATTC
1 AAAAAAATTACAATATTCATACAAAAATTACAATATTACAATATTCACACAACATTACAATATTC
*
12044085 ATAAAAAAATTATAATATT-C-ATA--CA-AA
66 ATAAAAAAATTACAATATTACAATATTCATAA
* *
12044112 ATTACAATATTACAATATTCATACAAAAA
1 A--AAAAAATTACAATATTCATACAAAAA
12044141 AATTGCAATA
Statistics
Matches: 104, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
91 3 0.03
92 2 0.02
93 18 0.17
94 9 0.09
95 38 0.37
96 14 0.13
97 20 0.19
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.31
Consensus pattern (97 bp):
AAAAAAATTACAATATTCATACAAAAATTACAATATTACAATATTCACACAACATTACAATATTC
ATAAAAAAATTACAATATTACAATATTCATAA
Found at i:12044143 original size:30 final size:27
Alignment explanation
Indices: 12043978--12044318 Score: 294
Period size: 27 Copynumber: 14.1 Consensus size: 27
12043968 TATCCCCCAC
12043978 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
12044005 ATTACAATATTCATA-AAAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* *
12044027 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
*
12044054 ATTACAATATTCATACAACATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
*
12044081 ATT-C-ATA---A-A-AAAATT--AT-
1 ATTACAATATTCATACAAAATTACAAT
12044098 -----AATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
12044120 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* *
12044142 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
12044169 ATTACAATATTCATACAAAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* *
12044192 A-TATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTACAAT
12044218 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* * *
12044240 ATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAATTACAAT
12044267 ATTACAATATTCATAC-AAA--A-AAT
1 ATTACAATATTCATACAAAATTACAAT
*
12044290 -TTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
12044316 ATT
1 ATT
12044319 CATACAAAAA
Statistics
Matches: 261, Mismatches: 14, Indels: 78
0.74 0.04 0.22
Matches are distributed among these distances:
14 3 0.01
17 1 0.00
18 2 0.01
19 6 0.02
20 5 0.02
21 2 0.01
22 76 0.29
23 23 0.09
24 7 0.03
25 10 0.04
26 24 0.09
27 102 0.39
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.33
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:12044172 original size:49 final size:49
Alignment explanation
Indices: 12043978--12044318 Score: 393
Period size: 49 Copynumber: 7.1 Consensus size: 49
12043968 TATCCCCCAC
*
12043978 ATTACAATATTCATACAAAATTACAATATTACAATATTCATA-AAAA--A-AA-
1 ATTACAATATTCATAC-AAA--A-AA-ATTATAATATTCATACAAAATTACAAT
* * *
12044027 ATTGCAATATTCATAC---AAAATTATAATA-T--TACAATATTCATACAAC
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAA-AAT--TACAAT
12044073 ATTACAATATTCAT--AAAAAAATTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
** *
12044120 ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
* *
12044169 ATTACAATATTCATACAAAAAAAATATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
** * *
12044218 ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
*
12044267 ATTACAATATTCATACAAAAAATTTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
12044316 ATT
1 ATT
12044319 CATACAAAAA
Statistics
Matches: 251, Mismatches: 25, Indels: 32
0.81 0.08 0.10
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 2 0.01
41 8 0.03
42 2 0.01
43 1 0.00
44 1 0.00
45 2 0.01
46 13 0.05
47 31 0.12
48 1 0.00
49 181 0.72
50 5 0.02
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.33
Consensus pattern (49 bp):
ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAT
Found at i:12044222 original size:98 final size:98
Alignment explanation
Indices: 12044073--12044314 Score: 434
Period size: 98 Copynumber: 2.5 Consensus size: 98
12044063 TTCATACAAC
*
12044073 ATTACAATATTCAT--AAAAAAATTATAATATTCATACAAAATTACAATATTACAATATTCATAC
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAAATTACAATATTCATAC
*
12044136 AAAAAAATTGCAATATTCATACAAAATTATAAT
66 AAAAAAATTGCAATATTCATACAAAACTATAAT
*
12044169 ATTACAATATTCATACAAAAAAAATATAATATTCATACAAAATTACAAAATTACAATATTCATAC
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAAATTACAATATTCATAC
12044234 AAAAAAATTGCAATATTCATACAAAACTATAAT
66 AAAAAAATTGCAATATTCATACAAAACTATAAT
*
12044267 ATTACAATATTCATACAAAAAATTTATAATATTCATACAAAATTACAA
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAA
12044315 TATTCATACA
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
96 14 0.10
98 125 0.90
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (98 bp):
ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACAAAATTACAATATTCATAC
AAAAAAATTGCAATATTCATACAAAACTATAAT
Found at i:12044328 original size:41 final size:41
Alignment explanation
Indices: 12044267--12044452 Score: 170
Period size: 41 Copynumber: 4.5 Consensus size: 41
12044257 AAACTATAAT
12044267 ATTACAATATTCATACAAAAAATTTATAATATTCATAC-AAA
1 ATTACAATATTCATACAAAAAA-TTATAATATTCATACAAAA
* * *
12044308 ATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAA
1 ATTACAATATTCATACAAAAAATTA-TAATATTC-ATAC-AAAA
* * * *
12044350 A-TACAA-ATTTAATTATAAAATAATTACAATATTCATAC-AAC
1 ATTACAATA-TTCA-TACAAAA-AATTATAATATTCATACAAAA
12044391 ATTACAATATTCATA-AAAAAATTATAATATTCATACAAAAA
1 ATTACAATATTCATACAAAAAATTATAATATTCATAC-AAAA
*
12044432 ATTTAAAATATTCATACAAAA
1 A-TTACAATATTCATACAAAA
12044453 TTCTAATCTA
Statistics
Matches: 116, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
39 19 0.16
40 12 0.10
41 38 0.33
42 30 0.26
43 14 0.12
44 3 0.03
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (41 bp):
ATTACAATATTCATACAAAAAATTATAATATTCATACAAAA
Found at i:12044441 original size:22 final size:21
Alignment explanation
Indices: 12044215--12044452 Score: 100
Period size: 22 Copynumber: 11.1 Consensus size: 21
12044205 ACAAAATTAC
*
12044215 AAAATTACAATATTCATACAAA
1 AAAATTAAAATATTCATAC-AA
**
12044237 AAAATTGCAATATTCATAC--
1 AAAATTAAAATATTCATACAA
* *
12044256 AAAACTATAATATTACAATATTCATACA
1 AAAATTAAAATATT-C-ATA--C--A-A
*
12044284 AAAAATTTATAATATTCATAC--
1 AAA-A-TTAAAATATTCATACAA
*
12044305 AAAATTACAATATTCATACAA
1 AAAATTAAAATATTCATACAA
** * * *
12044326 AAAATTACTA-ATCCAAAACTA
1 AAAATTAAAATATTC-ATACAA
* * *
12044347 TAAA-TACAAAT-TTAATTATAA
1 AAAATTA-AAATATTCA-TACAA
*
12044368 AATAATTACAATATTCATAC--
1 AA-AATTAAAATATTCATACAA
* *
12044388 AACATTACAATATTCATA-AA
1 AAAATTAAAATATTCATACAA
*
12044408 AAAATTATAATATTCATACAA
1 AAAATTAAAATATTCATACAA
12044429 AAAATTTAAAATATTCATACAA
1 AAAA-TTAAAATATTCATACAA
12044451 AA
1 AA
12044453 TTCTAATCTA
Statistics
Matches: 166, Mismatches: 26, Indels: 48
0.69 0.11 0.20
Matches are distributed among these distances:
19 40 0.24
20 26 0.16
21 33 0.20
22 43 0.26
23 6 0.04
26 1 0.01
28 6 0.04
29 2 0.01
30 9 0.05
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTAAAATATTCATACAA
Found at i:12044454 original size:20 final size:20
Alignment explanation
Indices: 12044377--12044454 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
12044367 AAATAATTAC
* *
12044377 AATATTCATACAACA-TTAC
1 AATATTCATACAAAATTTAA
* * *
12044396 AATATTCATAAAAAAATTAT
1 AATATTCATACAAAATTTAA
12044416 AATATTCATACAAAAAATTTAA
1 AATATTCATAC--AAAATTTAA
12044438 AATATTCATACAAAATT
1 AATATTCATACAAAATT
12044455 CTAATCTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 13 0.26
20 19 0.38
22 18 0.36
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATTCATACAAAATTTAA
Found at i:12044638 original size:14 final size:13
Alignment explanation
Indices: 12044616--12044646 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
12044606 CCTTTTTTCT
12044616 TTCTTTCTTCTTC
1 TTCTTTCTTCTTC
12044629 TTCTTCTCTTCTTC
1 TTCTT-TCTTCTTC
12044643 TTCT
1 TTCT
12044647 CCTTTCTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
TTCTTTCTTCTTC
Found at i:12044658 original size:14 final size:14
Alignment explanation
Indices: 12044621--12044658 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
12044611 TTTCTTTCTT
*
12044621 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTCC
12044635 TCTTCTTCTTCTCC
1 TCTTCTTCTTCTCC
12044649 T-TTCTCTCTT
1 TCTTCT-TCTT
12044659 TTTTTTTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
TCTTCTTCTTCTCC
Found at i:12044658 original size:17 final size:17
Alignment explanation
Indices: 12044614--12044658 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
12044604 TACCTTTTTT
* *
12044614 CTTTCTTTCTTCTTCTT
1 CTTTCTCTCTTCTTCTC
12044631 C-TTCTCTTCTTCTTCTC
1 CTTTCTC-TCTTCTTCTC
12044648 CTTTCTCTCTT
1 CTTTCTCTCTT
12044659 TTTTTTTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 15 0.62
18 5 0.21
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
CTTTCTCTCTTCTTCTC
Found at i:12044859 original size:13 final size:13
Alignment explanation
Indices: 12044841--12044865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12044831 ACCCGACCCG
12044841 ACCCGTATTTTTA
1 ACCCGTATTTTTA
12044854 ACCCGTATTTTT
1 ACCCGTATTTTT
12044866 TTCAAAAAAA
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:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (13 bp):
ACCCGTATTTTTA
Found at i:12047710 original size:10 final size:10
Alignment explanation
Indices: 12047695--12047719 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12047685 CAAATCTAAC
12047695 ATTATGTAAA
1 ATTATGTAAA
12047705 ATTATGTAAA
1 ATTATGTAAA
12047715 ATTAT
1 ATTAT
12047720 TAAGTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:12047802 original size:29 final size:29
Alignment explanation
Indices: 12047768--12047973 Score: 334
Period size: 29 Copynumber: 7.3 Consensus size: 29
12047758 AAATTATGTA
*
12047768 AAATTAGGTTAGGGTTAAGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
12047797 AAATTAGGTTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATT
*
12047827 AAATTAGGTTATGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
12047856 AAATTAGGTTAGGGTTAGGATTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
12047885 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
12047914 AAATTAGG-T----TTAGGG-TTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
12047937 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
12047966 AAATTAGG
1 AAATTAGG
12047974 GTTTTTATTA
Statistics
Matches: 165, Mismatches: 5, Indels: 14
0.90 0.03 0.08
Matches are distributed among these distances:
23 16 0.10
24 7 0.04
28 7 0.04
29 108 0.65
30 27 0.16
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:12048059 original size:36 final size:36
Alignment explanation
Indices: 12048019--12048133 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
12048009 ATATCAAATA
*
12048019 ATATCAAAATAACTCGAAAAAATTTCTATGCCTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
* **** * * *
12048055 ATATC-AAATAAACTTCTATTTTATTAC-AT-CAAATA
1 ATATCAAAAT-AAC-TCGAAAAAATTTCTATGCATATT
*
12048090 ATATCAAAATAACTCGAAAAAATTTCTATGCGTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
*
12048126 ACATCAAA
1 ATATCAAA
12048134 TAAACTTCTA
Statistics
Matches: 55, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
34 7 0.13
35 17 0.31
36 24 0.44
37 7 0.13
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (36 bp):
ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
Found at i:12048085 original size:25 final size:25
Alignment explanation
Indices: 12048051--12048161 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
12048041 TTTCTATGCC
*
12048051 TATTATATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
*
12048076 TATTACATCAAAT-AA-TATC-A--A
1 TATTACATCAAATAAACT-TCTATTT
* * * **
12048097 AATAAC-TCGAAA-AAATTTCTATGCG
1 TATTACATC-AAATAAACTTCTAT-TT
12048122 TATTACATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
12048147 TATTACATCAAATAA
1 TATTACATCAAATAA
12048162 TAAATTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.03
21 11 0.17
22 2 0.03
23 2 0.03
24 4 0.06
25 34 0.52
26 11 0.17
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (25 bp):
TATTACATCAAATAAACTTCTATTT
Found at i:12048086 original size:71 final size:71
Alignment explanation
Indices: 12047979--12048163 Score: 334
Period size: 71 Copynumber: 2.6 Consensus size: 71
12047969 TTAGGGTTTT
*
12047979 TATTACATCAAATAGAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTACATCAAATA-AACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTT
12048044 CTATGCC
65 CTATGCC
*
12048051 TATTATATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
*
12048116 TATGCG
66 TATGCC
12048122 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
12048164 AATTTAAATA
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
71 96 0.88
72 13 0.12
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
TATGCC
Found at i:12048591 original size:18 final size:18
Alignment explanation
Indices: 12048564--12048599 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12048554 CGGAAAAGGA
* *
12048564 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
12048582 TACATATAAGGGCTAGGG
1 TACATATAAGGGCTAGGG
12048600 AACACACCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.36, T:0.25
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:12048673 original size:13 final size:13
Alignment explanation
Indices: 12048655--12048691 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
12048645 TGTTGAATTG
12048655 CTGCGTCAGGTGA
1 CTGCGTCAGGTGA
12048668 CTGCGTCAGGTGA
1 CTGCGTCAGGTGA
12048681 CTGCGTC-GGTG
1 CTGCGTCAGGTG
12048692 CTCTCGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.11, C:0.24, G:0.41, T:0.24
Consensus pattern (13 bp):
CTGCGTCAGGTGA
Found at i:12049052 original size:15 final size:15
Alignment explanation
Indices: 12049032--12049062 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12049022 TTTTGTGGTG
12049032 ATCGTCAAACACCTC
1 ATCGTCAAACACCTC
12049047 ATCGTCAAACACCTC
1 ATCGTCAAACACCTC
12049062 A
1 A
12049063 GGGTTCGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.39, G:0.06, T:0.19
Consensus pattern (15 bp):
ATCGTCAAACACCTC
Found at i:12049290 original size:7 final size:7
Alignment explanation
Indices: 12049278--12049302 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12049268 TTATGTACAT
12049278 AATACTA
1 AATACTA
12049285 AATACTA
1 AATACTA
12049292 AATACTA
1 AATACTA
12049299 AATA
1 AATA
12049303 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:12050352 original size:21 final size:21
Alignment explanation
Indices: 12050313--12050352 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12050303 TGAAAATATA
* **
12050313 AAAAAATTTAAAATTATTTTT
1 AAAAAATATAAAAAAATTTTT
12050334 AAAAAATATAAAAAAATTT
1 AAAAAATATAAAAAAATTT
12050353 AAATTATTTT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAATATAAAAAAATTTTT
Found at i:12050357 original size:30 final size:30
Alignment explanation
Indices: 12050305--12050369 Score: 114
Period size: 31 Copynumber: 2.2 Consensus size: 30
12050295 GCCATTGCTG
12050305 AAAATATAAAAAAATTTAAAATTATTTTTAA
1 AAAATATAAAAAAATTTAAAATTA-TTTTAA
12050336 AAAATATAAAAAAATTT-AAATTATTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAA
12050365 AAAAT
1 AAAAT
12050370 GAAATTGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.32
30 6 0.18
31 17 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
AAAATATAAAAAAATTTAAAATTATTTTAA
Found at i:12050425 original size:29 final size:29
Alignment explanation
Indices: 12050393--12050476 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 29
12050383 AATTGAAATT
12050393 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
* * **
12050422 AAAT-T-GA---GAG-GAA-ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
12050444 AAATATGGGTTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
12050473 AAAT
1 AAAT
12050477 TGAGAGGATT
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
22 9 0.23
23 4 0.10
24 4 0.10
27 5 0.13
28 4 0.10
29 13 0.33
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:12050426 original size:51 final size:51
Alignment explanation
Indices: 12050370--12050484 Score: 212
Period size: 51 Copynumber: 2.3 Consensus size: 51
12050360 TTTAAAAAAT
*
12050370 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
12050421 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
12050472 GAAATTGAGAGGA
1 GAAATTGAGAGGA
12050485 TTAGAGAGGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:12052484 original size:23 final size:23
Alignment explanation
Indices: 12052445--12052492 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12052435 CTGTAAATCT
12052445 TATAAAAATAGTAAAAAATTATA
1 TATAAAAATAGTAAAAAATTATA
* *
12052468 TATAAATATA-TATAAAAATTTTA
1 TATAAAAATAGTA-AAAAATTATA
12052491 TA
1 TA
12052493 AGGTAGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TATAAAAATAGTAAAAAATTATA
Found at i:12052735 original size:10 final size:10
Alignment explanation
Indices: 12052715--12052804 Score: 62
Period size: 10 Copynumber: 9.4 Consensus size: 10
12052705 TTTGATATAC
*
12052715 TTTATAGTTT
1 TTTATAATTT
*
12052725 TTTATGA-TT
1 TTTATAATTT
**
12052734 TTTATAAAAT
1 TTTATAATTT
*
12052744 TTTAAAATTT
1 TTTATAATTT
*
12052754 TTTATAATAT
1 TTTATAATTT
**
12052764 TTTACGA-TT
1 TTTATAATTT
12052773 TTTATAA-TT
1 TTTATAATTT
12052782 TTT-TAATTT
1 TTTATAATTT
* *
12052791 TTAATAAATT
1 TTTATAATTT
12052801 TTTA
1 TTTA
12052805 ATATTTTTAT
Statistics
Matches: 60, Mismatches: 17, Indels: 6
0.72 0.20 0.07
Matches are distributed among these distances:
8 3 0.05
9 23 0.38
10 34 0.57
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTATAATTT
Found at i:12052737 original size:19 final size:19
Alignment explanation
Indices: 12052724--12052814 Score: 80
Period size: 19 Copynumber: 4.8 Consensus size: 19
12052714 CTTTATAGTT
* *
12052724 TTTTATGATTTTTATAAAA
1 TTTTAAGATTTTTATAATA
*
12052743 TTTTAAAATTTTTTATAATA
1 TTTTAAGA-TTTTTATAATA
*
12052763 TTTTACGATTTTTATAAT-
1 TTTTAAGATTTTTATAATA
*
12052781 TTTTTA-ATTTTTAATAA-A
1 TTTTAAGATTTTT-ATAATA
*
12052799 TTTTTAATATTTTTAT
1 -TTTTAAGATTTTTAT
12052815 TAAAATTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
17 6 0.10
18 8 0.14
19 23 0.39
20 22 0.37
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTAAGATTTTTATAATA
Found at i:12052830 original size:20 final size:21
Alignment explanation
Indices: 12052785--12052830 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
12052775 TATAATTTTT
*
12052785 TAATTTTTAATAAATTTTTAA
1 TAATTTTTAATAAATATTTAA
*
12052806 T-ATTTTTATTAAA-ATTTAA
1 TAATTTTTAATAAATATTTAA
12052825 TAATTT
1 TAATTT
12052831 AATATGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 6 0.27
20 15 0.68
21 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTTTAATAAATATTTAA
Found at i:12060171 original size:31 final size:31
Alignment explanation
Indices: 12060135--12060203 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
12060125 ATAAAATGAC
* *
12060135 TACTGAACAATTC-GAAAGTTTTCATTTAAAT
1 TACTGAACAATTCAAAAACTTTT-ATTTAAAT
* *
12060166 TACTGAACTATTCAAAAACTTTTATTTAAGT
1 TACTGAACAATTCAAAAACTTTTATTTAAAT
12060197 TACTGAA
1 TACTGAA
12060204 TTATTAAGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (31 bp):
TACTGAACAATTCAAAAACTTTTATTTAAAT
Found at i:12067422 original size:12 final size:12
Alignment explanation
Indices: 12067407--12067435 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
12067397 TTACTGTTTT
12067407 ATTTAATATTTC
1 ATTTAATATTTC
12067419 ATTTAATATTTC
1 ATTTAATATTTC
12067431 ATTTA
1 ATTTA
12067436 TTTATTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTAATATTTC
Found at i:12069493 original size:19 final size:19
Alignment explanation
Indices: 12069469--12069515 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
12069459 AACGTCTCTT
*
12069469 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
12069488 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
12069507 TATGCATTA
1 TTTGCATTA
12069516 AAGACTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:12071108 original size:40 final size:39
Alignment explanation
Indices: 12071054--12071213 Score: 219
Period size: 40 Copynumber: 4.3 Consensus size: 39
12071044 AAATATATTT
* *
12071054 ATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
12071093 ATTTTTTTAAATTTTAAAATATTTTTAAAATAC---TTT-
1 ATTTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTA
12071129 A----TTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTA
12071165 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
*
12071204 AATTTTTTAA
1 ATTTTTTTAA
12071214 AAATTTTAAA
Statistics
Matches: 108, Mismatches: 3, Indels: 20
0.82 0.02 0.15
Matches are distributed among these distances:
31 24 0.22
32 3 0.03
35 3 0.03
36 2 0.02
37 3 0.03
39 24 0.22
40 49 0.45
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:12071140 original size:31 final size:31
Alignment explanation
Indices: 12071102--12071169 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
12071092 AATTTTTTTA
12071102 AATTTTAAAATATTTTTAAAATACTTTATTT
1 AATTTTAAAATATTTTTAAAATACTTTATTT
*
12071133 AATTTTAAAATATTTTTAAAATACTTTTTTT
1 AATTTTAAAATATTTTTAAAATACTTTATTT
12071164 AATTTT
1 AATTTT
12071170 TTTAATTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (31 bp):
AATTTTAAAATATTTTTAAAATACTTTATTT
Found at i:12071140 original size:71 final size:70
Alignment explanation
Indices: 12071056--12071226 Score: 258
Period size: 71 Copynumber: 2.4 Consensus size: 70
12071046 ATATATTTAT
* *
12071056 TTTTTTAATTTTAAAATATTTTTTACATAC-TTTTTTAATTTTTTTAAATTTTAAAATATTTTTA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTT-AATTTTAAAATATTTTTA
12071120 AAATAC
65 AAATAC
12071126 TTTATTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTTA
1 TTT-TTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTTA
12071191 AAATAC
65 AAATAC
12071197 TTTTTTAAATTTTTTAAAA-A-TTTTAAAATA
1 TTTTTT-AA--TTTTAAAATATTTTTAAAATA
12071227 AAAATAGGCC
Statistics
Matches: 94, Mismatches: 2, Indels: 9
0.90 0.02 0.09
Matches are distributed among these distances:
70 6 0.06
71 64 0.68
72 16 0.17
73 8 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (70 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAA
AATAC
Found at i:12071206 original size:12 final size:11
Alignment explanation
Indices: 12071104--12071226 Score: 86
Period size: 11 Copynumber: 11.9 Consensus size: 11
12071094 TTTTTTTAAA
12071104 TTTTAAAATAT
1 TTTTAAAATAT
12071115 TTTTAAAATA-
1 TTTTAAAATAT
* ** *
12071125 CTTT-ATTTAA
1 TTTTAAAATAT
12071135 TTTTAAAATAT
1 TTTTAAAATAT
12071146 TTTTAAAATACT
1 TTTTAAAATA-T
**
12071158 TTTTTTAAT-T
1 TTTTAAAATAT
*
12071168 TTTT----TAA
1 TTTTAAAATAT
12071175 TTTTAAAATAT
1 TTTTAAAATAT
12071186 TTTTAAAATACT
1 TTTTAAAATA-T
*
12071198 TTTTTAAAT-T
1 TTTTAAAATAT
12071208 TTTTAAAA-A-
1 TTTTAAAATAT
12071217 TTTTAAAATA
1 TTTTAAAATA
12071227 AAAATAGGCC
Statistics
Matches: 88, Mismatches: 13, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
9 11 0.12
10 20 0.23
11 35 0.40
12 17 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:12072271 original size:6 final size:6
Alignment explanation
Indices: 12072262--12072320 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
12072252 GAAAATGATG
* * * *
12072262 GAAAAA G-AAAA GAAAAG GAAAAAA AAGAAAA GGAAAG GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA G-AAAAA GA-AAAA GAAAAA GAAAAA GAAAAA
12072311 G-AAAA GAAAA
1 GAAAAA GAAAA
12072321 GGATAGGCCA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
5 10 0.24
6 23 0.56
7 8 0.20
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:12072274 original size:5 final size:5
Alignment explanation
Indices: 12072264--12072321 Score: 64
Period size: 5 Copynumber: 11.0 Consensus size: 5
12072254 AAATGATGGA
*
12072264 AAAAG AAAAG AAAAGG AAAA- AAAAG AAAAGG AAAGG AAAAAG AAAAAG
1 AAAAG AAAAG AAAA-G AAAAG AAAAG AAAA-G AAAAG -AAAAG -AAAAG
12072312 AAAAG AAAAG
1 AAAAG AAAAG
12072322 GATAGGCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
4 4 0.09
5 24 0.51
6 19 0.40
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:12072302 original size:37 final size:36
Alignment explanation
Indices: 12072239--12072320 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
12072229 AAAAAATAAA
* * * *
12072239 AAAACAAAAAAATGAAAATGATGGAAAAAG-AAAAG
1 AAAAGAAAAAAAAGAAAAGGAAGGAAAAAGAAAAAG
12072274 AAAAGGAAAAAAAAGAAAAGGAAAGGAAAAAGAAAAAG
1 AAAA-GAAAAAAAAGAAAAGG-AAGGAAAAAGAAAAAG
12072312 AAAAGAAAA
1 AAAAGAAAA
12072321 GGATAGGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
35 4 0.10
36 13 0.32
37 14 0.35
38 9 0.22
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.04
Consensus pattern (36 bp):
AAAAGAAAAAAAAGAAAAGGAAGGAAAAAGAAAAAG
Found at i:12074673 original size:44 final size:43
Alignment explanation
Indices: 12074602--12074810 Score: 125
Period size: 44 Copynumber: 4.8 Consensus size: 43
12074592 TTAAGCCACC
* * * * * *
12074602 AATCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAGAATGT
1 AATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAATGT
* * * ** *
12074645 ACATCTTGTCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGCG
1 A-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAATG-T
* * * * * **
12074690 AATCTTATCTTCCC-AAGGTAGTAGCGAAGCAGATTTAAGCCA-CC
1 AATCTTATC-TCCCTAA-GCAGTAGTGGAGCAGATTGAAG-AATGT
* * * *
12074734 AATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAAATGT
1 AATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAATGT
* *
12074777 AGATCTTGTCTCCCTAAGCAATAGTGGAGCAGAT
1 A-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
12074811 CAAAGACGGT
Statistics
Matches: 121, Mismatches: 37, Indels: 15
0.70 0.21 0.09
Matches are distributed among these distances:
42 1 0.01
43 21 0.17
44 76 0.63
45 23 0.19
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (43 bp):
AATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAATGT
Found at i:12074776 original size:132 final size:132
Alignment explanation
Indices: 12074535--12074876 Score: 549
Period size: 132 Copynumber: 2.6 Consensus size: 132
12074525 CTGTACTGAC
*
12074535 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCTCAAGGTAGTAGGGAAGCAGATTTAAGCCA
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCA
* * * *
12074600 CCAATCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAGAATGTACATCTTGTCTCCCTAAGTA
66 CCAATCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAATGTACATCTTGTCTCCCTAAGCA
*
12074665 GT
131 AT
*
12074667 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGCGAAGCAGATTTAAGCCA
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCA
* *
12074732 CCAATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAAATGTAGATCTTGTCTCCCTAAGCA
66 CCAATCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAATGTACATCTTGTCTCCCTAAGCA
12074797 AT
131 AT
* * * *
12074799 AGTGGAGCAGATCAAAGACGGTGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAACCA
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCA
* *
12074864 CCAGTCATATCTC
66 CCAATCCTATCTC
12074877 TTTGGCATTA
Statistics
Matches: 194, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 194 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (132 bp):
AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCA
CCAATCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAATGTACATCTTGTCTCCCTAAGCA
AT
Found at i:12076848 original size:12 final size:12
Alignment explanation
Indices: 12076833--12076861 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
12076823 TTACTGTTTT
12076833 ATTTAATATTTC
1 ATTTAATATTTC
12076845 ATTTAATATTTC
1 ATTTAATATTTC
12076857 ATTTA
1 ATTTA
12076862 TTTATTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTAATATTTC
Found at i:12108681 original size:20 final size:20
Alignment explanation
Indices: 12108643--12108682 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12108633 TTTTGAACTA
*
12108643 AATTATTTTTATTTATTTAT
1 AATTATTTTTAATTATTTAT
12108663 AATTATTTTGTAATT-TTTAT
1 AATTATTTT-TAATTATTTAT
12108683 GTAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
AATTATTTTTAATTATTTAT
Found at i:12108709 original size:20 final size:20
Alignment explanation
Indices: 12108673--12108710 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12108663 AATTATTTTG
*
12108673 TAATTTTTATGTAATAAAAA
1 TAATTTTTATATAATAAAAA
12108693 TAATATTTTATAT-ATAAA
1 TAAT-TTTTATATAATAAA
12108711 TTATGCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TAATTTTTATATAATAAAAA
Found at i:12110702 original size:16 final size:16
Alignment explanation
Indices: 12110681--12110722 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
12110671 ATGCTTTCTT
12110681 ATATATATATATATTC
1 ATATATATATATATTC
*
12110697 ATATATATGTATATTC
1 ATATATATATATATTC
12110713 ATATATATAT
1 ATATATATAT
12110723 TTTTATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATATATATATATTC
Found at i:12111236 original size:13 final size:13
Alignment explanation
Indices: 12111209--12111257 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
12111199 ACACTCAAAA
*
12111209 TTTTCAAAAGTAC
1 TTTTCAAAAGCAC
* *
12111222 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
*
12111235 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
12111248 TTTTCAAAAG
1 TTTTCAAAAG
12111258 TAATGAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:12118693 original size:21 final size:21
Alignment explanation
Indices: 12118667--12118711 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
12118657 AATTAAATAA
* *
12118667 TTTATT-TAAATTTTATTTTAT
1 TTTATTCTAAAATTAATTTT-T
12118688 TTTATTCTAAAATTAATTTTT
1 TTTATTCTAAAATTAATTTTT
12118709 TTT
1 TTT
12118712 GAAAATTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTATTCTAAAATTAATTTTT
Found at i:12127583 original size:19 final size:20
Alignment explanation
Indices: 12127559--12127603 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
12127549 AGGGTTGGTT
12127559 TTTAATTTTT-AATAATTTA
1 TTTAATTTTTAAATAATTTA
12127578 TTTAATTTTTAAATAATTTA
1 TTTAATTTTTAAATAATTTA
12127598 TTTAAT
1 TTTAAT
12127604 CAAATCCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAATTTTTAAATAATTTA
Found at i:12128012 original size:21 final size:22
Alignment explanation
Indices: 12127965--12128013 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
12127955 AATTGAACTT
**
12127965 AAATTGAATGAGATAAAATTCTTA
1 AAATTGAATGAGAT--AATTCAGA
12127989 AAATTGAATGAGAT-ATTCAGA
1 AAATTGAATGAGATAATTCAGA
12128010 AAAT
1 AAAT
12128014 CGCACGACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
24 14 0.61
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (22 bp):
AAATTGAATGAGATAATTCAGA
Found at i:12131368 original size:18 final size:17
Alignment explanation
Indices: 12131342--12131377 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12131332 TTTGGTTATA
12131342 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
12131360 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
12131377 T
1 T
12131378 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:12133583 original size:99 final size:102
Alignment explanation
Indices: 12133386--12133589 Score: 238
Period size: 99 Copynumber: 2.0 Consensus size: 102
12133376 TTTGCAAAAT
** *
12133386 GCGCCGCAAAAATATCTTAACCGAAACGCATTGTTTTGGTCTTGATGTATCCTAGAATTAGTGGC
1 GCGCCGCAAAAATATCTTAACCGAAACGCAGAGTTTTGGTCTTGAGGTATCCTAGAATTAGTGGC
**** *
12133451 GCTTAAGGGAAAACGCCGTTAAGGCATAATATTAGCG
66 GCTTAAGGGAAAACGCAACAAAAGCATAATATTAGCG
* * **
12133488 GCGCCGC-AAAATATCTTAACC-AAATGTAGAG-TTTGGTCTTGAGGTATGTTAGAATTAGTGGC
1 GCGCCGCAAAAATATCTTAACCGAAACGCAGAGTTTTGGTCTTGAGGTATCCTAGAATTAGTGGC
*
12133550 GCTTATA-GGAAAACGCAACAAACAG-ATAGTATTAGCG
66 GCTTA-AGGGAAAACGCAACAAA-AGCATAATATTAGCG
12133587 GCG
1 GCG
12133590 GTTTTTGAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
99 58 0.67
100 8 0.09
101 14 0.16
102 7 0.08
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (102 bp):
GCGCCGCAAAAATATCTTAACCGAAACGCAGAGTTTTGGTCTTGAGGTATCCTAGAATTAGTGGC
GCTTAAGGGAAAACGCAACAAAAGCATAATATTAGCG
Found at i:12134121 original size:229 final size:228
Alignment explanation
Indices: 12133519--12134125 Score: 587
Period size: 229 Copynumber: 2.7 Consensus size: 228
12133509 AAATGTAGAG
* * ** * * * ** *
12133519 TTTGGTCTTGAGGTATGTTAGAATTAGTGGCGCTTATAGGAAAACGCAAC-AAACAGATAGTATT
1 TTTGGTCTGGATGTATACTAGAATTAGTGGCGCTTACAGTAAAACACCGCTAAA-TGATAGTATT
* * * * ** * ** * * *
12133583 AGCGGCGGTTT-TTGAAAGCTCCGTGAAATATCTGGACCAAAACGCATCGTTTTGGTTTTGCT-T
65 AGCGGCGATTTGGTAAAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTTGGTCTTGATGT
* * * *
12133646 ATCTAGAATTAGTGGCGTTTACCGAAAACGCCGCTACAGCATAGTATTAGCGGCGAGTAGTGGCT
130 ATCTAGAATTAGTGGCGCTTACCGAAAACGCAGCTAAAGCATAGTATTAGCGGCGAGTAGTGGAT
* *
12133711 GTCGCCGCAAAATATCTTAACCAAAACACAGCGT
195 GTCACCGCAAAATATCTAAACCAAAACACAGCGT
* ** *
12133745 TTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACAGTAAAATGCCGTTAAATGATAGTATTA
1 TTTGGTCTGGATGTATACTAGAATTAGTGGCGCTTACAGTAAAACACCGCTAAATGATAGTATTA
* * * * *
12133810 GCGGCGCTTTGGTAAAAGCGCTGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGAGGTA
66 GCGGCGATTTGGTAAAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTA
* ** ** * * ** **
12133875 TGTTAGCGTTAGTGGCGCTTATTGGAAAATGCAGCTAAAGGATAGTATTAGCGGCGCTTTTTGGA
131 T-CTAGAATTAGTGGCGCTTA-CCGAAAACGCAGCTAAAGCATAGTATTAGCGGCGAGTAGTGGA
*
12133940 TG-CACCGCAAAATATCTAAACCAAAACGCAGCGT
194 TGTCACCGCAAAATATCTAAACCAAAACACAGCGT
* * * * *
12133974 TTTGGTCTGGATGTATATTTGAATTATTGGCGCTTACGGTGAAACACCGCTAAA-GCATAGTATT
1 TTTGGTCTGGATGTATACTAGAATTAGTGGCGCTTACAGTAAAACACCGCTAAATG-ATAGTATT
***
12134038 AGCGGCGATTT-GTGGCTAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTTGGTCTTGATG
65 AGCGGCGATTTGGT-AAAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTTGGTCTTGATG
* *
12134102 TATACTAAAATTTGTGGCGCTTAC
129 TAT-CTAGAATTAGTGGCGCTTAC
12134126 GGGAAACCGC
Statistics
Matches: 308, Mismatches: 66, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
226 60 0.19
227 41 0.13
228 6 0.02
229 167 0.54
230 34 0.11
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (228 bp):
TTTGGTCTGGATGTATACTAGAATTAGTGGCGCTTACAGTAAAACACCGCTAAATGATAGTATTA
GCGGCGATTTGGTAAAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTA
TCTAGAATTAGTGGCGCTTACCGAAAACGCAGCTAAAGCATAGTATTAGCGGCGAGTAGTGGATG
TCACCGCAAAATATCTAAACCAAAACACAGCGT
Found at i:12134144 original size:115 final size:114
Alignment explanation
Indices: 12133488--12134145 Score: 621
Period size: 115 Copynumber: 5.8 Consensus size: 114
12133478 AATATTAGCG
* * * * **
12133488 GCGCCGCAAAATATCTTAACC-AAATGTAGAG-TTTGGTCTTGAGGTATGTTAGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
** ** * * * * *
12133551 CTTATAGGAAAACGCAACAAACAG-ATAGTATTAGCGGCGGTTTTTGAAA
66 CTTACGGGAAAACGCCGCTAA-AGCATAGTATTAGCGGCGATTTGTGGAT
* ** ** * * *
12133600 GCTCCGTGAAATATCTGGACCAAAACGCATCGTTTTGGTTTTGCT-TAT-CTAGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* * * * * *
12133663 TTTAC-CGAAAACGCCGCTACAGCATAGTATTAGCGGCGAGTAGTGGCT
66 CTTACGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTGGAT
*
12133711 GTCGCCGCAAAATATCTTAACCAAAACACAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
1 G-CGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* * * * * ** *
12133776 GCTTACAGTAAAATGCCGTTAAATG-ATAGTATTAGCGGCGCTTTGGTAAAA
65 GCTTACGGGAAAACGCCGCTAAA-GCATAGTATTAGCGGCGATTT-GTGGAT
* * * ** **
12133827 GCGCTGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGAGGTATGTTAGCGTTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
** * * * * *
12133892 CTTATTGGAAAATGCAGCTAAAGGATAGTATTAGCGGCGCTTTTTGGAT
66 CTTACGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTGGAT
* * * * * *
12133941 GCACCGCAAAATATCTAAACCAAAACGCAGCGTTTTGGTCTGGATGTATATTTGAATTATTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* *
12134006 CTTACGGTG-AAACACCGCTAAAGCATAGTATTAGCGGCGATTTGTGGCT
66 CTTACGG-GAAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTGGAT
* * *
12134055 AGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAAAATTTGTGGC
1 -GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* *
12134120 GCTTACGGGAAACCGCCGCGAAAGCA
65 GCTTACGGGAAAACGCCGCTAAAGCA
12134146 AATTGTTAAA
Statistics
Matches: 435, Mismatches: 98, Indels: 23
0.78 0.18 0.04
Matches are distributed among these distances:
110 2 0.00
111 29 0.07
112 68 0.16
113 12 0.03
114 124 0.29
115 196 0.45
116 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (114 bp):
GCGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
CTTACGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTGGAT
Found at i:12134980 original size:8 final size:8
Alignment explanation
Indices: 12134963--12135023 Score: 58
Period size: 8 Copynumber: 8.0 Consensus size: 8
12134953 AAGATTTAAA
12134963 GTTT-AGG
1 GTTTAAGG
12134970 GTTTAAGG
1 GTTTAAGG
12134978 GTTT-AGCG
1 GTTTAAG-G
12134986 GTTT-AGG
1 GTTTAAGG
* *
12134993 ATTTTAGG
1 GTTTAAGG
*
12135001 GTTTAGGG
1 GTTTAAGG
12135009 GTTTAA-G
1 GTTTAAGG
12135016 GTTTAAGG
1 GTTTAAGG
12135024 TTAAATCCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
7 17 0.38
8 28 0.62
ACGTcount: A:0.20, C:0.02, G:0.38, T:0.41
Consensus pattern (8 bp):
GTTTAAGG
Found at i:12134981 original size:15 final size:15
Alignment explanation
Indices: 12134963--12135023 Score: 70
Period size: 15 Copynumber: 4.0 Consensus size: 15
12134953 AAGATTTAAA
12134963 GTTTAGGGTTTAAGG
1 GTTTAGGGTTTAAGG
12134978 GTTTAGCGGTTT-AGG
1 GTTTAG-GGTTTAAGG
* *
12134993 ATTTTAGGGTTTAGGG
1 -GTTTAGGGTTTAAGG
*
12135009 GTTTAAGGTTTAAGG
1 GTTTAGGGTTTAAGG
12135024 TTAAATCCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 26 0.68
16 12 0.32
ACGTcount: A:0.20, C:0.02, G:0.38, T:0.41
Consensus pattern (15 bp):
GTTTAGGGTTTAAGG
Found at i:12135001 original size:23 final size:23
Alignment explanation
Indices: 12134963--12135023 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
12134953 AAGATTTAAA
*
12134963 GTTTAGGGTTTAAGGGTTTAGCG
1 GTTTAGGATTTAAGGGTTTAGCG
* *
12134986 GTTTAGGATTTTAGGGTTTAGGG
1 GTTTAGGATTTAAGGGTTTAGCG
12135009 GTTTAAGG-TTTAAGG
1 GTTT-AGGATTTAAGG
12135024 TTAAATCCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 30 0.91
24 3 0.09
ACGTcount: A:0.20, C:0.02, G:0.38, T:0.41
Consensus pattern (23 bp):
GTTTAGGATTTAAGGGTTTAGCG
Found at i:12135644 original size:148 final size:148
Alignment explanation
Indices: 12135490--12135772 Score: 379
Period size: 148 Copynumber: 1.9 Consensus size: 148
12135480 TTTACTACGA
* * *
12135490 GTTGAGGAAACGGCACCGTTTCCTACTTTTATTAGTGGCGCTTCAGGTAAAGCGCCGCAAAAATA
1 GTTGAGGAAACGACACCGTTTCCTACTTTTATTAGTGGCGCTTCAGATAAAACGCCGCAAAAATA
* * *
12135555 TTTAAGGTTATCTGATAACAGTGCCGTTTTGTCCATGTTATTAGTGGCGTTTTTACTGC-AAGCG
66 TTTAAGGTTATCTAATAACAGTGCCATTTTGTCCATGGTATTAGTGGCGTTTTTACT-CTAAGCG
12135619 CCACAAATATTTATTAGTG
130 CCACAAATATTTATTAGTG
* ** * ** ** *
12135638 GTTGAGGTAACGATGCCGTTTCCTATTTTTATTAGTGGCGCTTTTGATAAAACGCCTTAAAAATG
1 GTTGAGGAAACGACACCGTTTCCTACTTTTATTAGTGGCGCTTCAGATAAAACGCCGCAAAAATA
* * * *
12135703 TTTATGGTTATCTAATAACAGTGTCATTTTGTCCATGGTATTTGTGGCGTTTTTGCTCTAAGCGC
66 TTTAAGGTTATCTAATAACAGTGCCATTTTGTCCATGGTATTAGTGGCGTTTTTACTCTAAGCGC
12135768 CACAA
131 CACAA
12135773 GTTTTAGCTT
Statistics
Matches: 115, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
147 1 0.01
148 114 0.99
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (148 bp):
GTTGAGGAAACGACACCGTTTCCTACTTTTATTAGTGGCGCTTCAGATAAAACGCCGCAAAAATA
TTTAAGGTTATCTAATAACAGTGCCATTTTGTCCATGGTATTAGTGGCGTTTTTACTCTAAGCGC
CACAAATATTTATTAGTG
Found at i:12135806 original size:148 final size:147
Alignment explanation
Indices: 12135490--12135827 Score: 346
Period size: 148 Copynumber: 2.3 Consensus size: 147
12135480 TTTACTACGA
** * *
12135490 GTTGAGGAAACGGCACCGTTTCCTACTTTTATTAGTGGCGCTTCAGGTAAAGCGCCGCAAAAATA
1 GTTGA-GAAACGGCTGCGTTTCCTACTTTTATTAGTGGCGCTTCAGATAAAACGCCGCAAAAATA
* * *
12135555 TTTAAGGTTATCTGATAACAGTGCCGTTTTGTCCATGTTATTAGTGGCGTTTTTACTGCAAGCGC
65 TTTAAGGTTATCTAATAACAGTGCCATTTTGTCCATGGTATTAGTGGCGTTTTTACTGCAAGCGC
*
12135620 CACAAATATTTATTAGTG
130 CACAAATATTTATTAATG
* * * ** **
12135638 GTTGAGGTAAC-GATGCCGTTTCCTATTTTTATTAGTGGCGCTTTTGATAAAACGCCTTAAAAAT
1 GTTGA-GAAACGGCTG-CGTTTCCTACTTTTATTAGTGGCGCTTCAGATAAAACGCCGCAAAAAT
* * * * *
12135702 GTTTATGGTTATCTAATAACAGTGTCATTTTGTCCATGGTATTTGTGGCGTTTTTGCT-CTAAGC
64 ATTTAAGGTTATCTAATAACAGTGCCATTTTGTCCATGGTATTAGTGGCGTTTTTACTGC-AAGC
*
12135766 GCCACAAGT-TTTAGCTTAAT-
128 GCCACAAATATTTA--TTAATG
* **
12135786 GTGTGTA-AAACGGCTGCGTTT-GTACTGATATTAGTGGCGCTT
1 GT-TG-AGAAACGGCTGCGTTTCCTACTTTTATTAGTGGCGCTT
12135828 ATTTATAAGC
Statistics
Matches: 156, Mismatches: 27, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
147 23 0.15
148 123 0.79
149 9 0.06
150 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (147 bp):
GTTGAGAAACGGCTGCGTTTCCTACTTTTATTAGTGGCGCTTCAGATAAAACGCCGCAAAAATAT
TTAAGGTTATCTAATAACAGTGCCATTTTGTCCATGGTATTAGTGGCGTTTTTACTGCAAGCGCC
ACAAATATTTATTAATG
Found at i:12136285 original size:14 final size:14
Alignment explanation
Indices: 12136266--12136320 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
12136256 TATATTCCAG
12136266 TTGCTGGAATATAC
1 TTGCTGGAATATAC
12136280 TTGCTGGAATATA-
1 TTGCTGGAATATAC
* ***
12136293 TGGCCAAATATATAC
1 TTGCTGGA-ATATAC
12136308 TTGCTGGAATATA
1 TTGCTGGAATATA
12136321 TACTTTACTA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
13 4 0.13
14 23 0.74
15 4 0.13
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (14 bp):
TTGCTGGAATATAC
Found at i:12136320 original size:16 final size:16
Alignment explanation
Indices: 12136235--12136325 Score: 59
Period size: 16 Copynumber: 5.9 Consensus size: 16
12136225 CTTATAACTT
* *
12136235 TGGAGTATATACTTGT
1 TGGAATATATACTTGC
*
12136251 TGGAATATATTCCAGTTGC
1 TGGAATATA-T--ACTTGC
12136270 TGG-A-ATATACTTGC
1 TGGAATATATACTTGC
*
12136284 TGG-A-ATATA-TGGC
1 TGGAATATATACTTGC
**
12136297 -CAAATATATACTTGC
1 TGGAATATATACTTGC
12136312 TGGAATATATACTT
1 TGGAATATATACTT
12136326 TACTAAAATC
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
13 4 0.07
14 19 0.33
15 3 0.05
16 20 0.34
17 4 0.07
18 1 0.02
19 7 0.12
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (16 bp):
TGGAATATATACTTGC
Found at i:12137820 original size:21 final size:21
Alignment explanation
Indices: 12137791--12137843 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
12137781 ACATCTTTGA
* *
12137791 TATATATATTTATATACATTTT
1 TATATATATTTAT-TAAAATTT
*
12137813 TA-ATATATATATTAAAATTT
1 TATATATATTTATTAAAATTT
12137833 TATATATATTT
1 TATATATATTT
12137844 GAAAAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATATATTTATTAAAATTT
Found at i:12137837 original size:19 final size:19
Alignment explanation
Indices: 12137810--12137854 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
12137800 TTATATACAT
12137810 TTTTAATATATATATT-AAAA
1 TTTT-ATATATAT-TTGAAAA
12137830 TTTTATATATATTTGAAAA
1 TTTTATATATATTTGAAAA
*
12137849 ATTTAT
1 TTTTAT
12137855 CAATCATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTATATATATTTGAAAA
Found at i:12137929 original size:12 final size:12
Alignment explanation
Indices: 12137912--12138206 Score: 114
Period size: 12 Copynumber: 25.1 Consensus size: 12
12137902 TACACAACAC
12137912 ATAACTTACATA
1 ATAACTTACATA
12137924 ATAACTTAC---
1 ATAACTTACATA
*
12137933 ATAACTTATAT-
1 ATAACTTACATA
*
12137944 ATAAACTTATAT-
1 AT-AACTTACATA
12137956 ATAACTTACATA
1 ATAACTTACATA
12137968 CATAACTTA-AGTA
1 -ATAACTTACA-TA
* *
12137981 A-AATTTATAT-
1 ATAACTTACATA
12137991 ATAAACTTAAACA-A
1 AT-AACTT--ACATA
*
12138005 CACAACTTACATA
1 -ATAACTTACATA
*
12138018 ATAACTTATATA
1 ATAACTTACATA
*
12138030 ATAAC-T-CA-C
1 ATAACTTACATA
*
12138039 ATAACTTATAT-
1 ATAACTTACATA
12138050 ATAACTTACATAA
1 ATAACTTACAT-A
*
12138063 ATAACTTAAATA
1 ATAACTTACATA
* *
12138075 A-AATTTATAT-
1 ATAACTTACATA
*
12138085 ATAAACTTACACAACA
1 AT-AACTT--AC-ATA
12138101 CATAACTTACATA
1 -ATAACTTACATA
12138114 ATAACTTAC---
1 ATAACTTACATA
12138123 ATAACTT--ATA
1 ATAACTTACATA
* *
12138133 CATGACTTATAT-
1 -ATAACTTACATA
*
12138145 ATAACTTTCATA
1 ATAACTTACATA
*
12138157 ACTTACTT--ATA
1 A-TAACTTACATA
12138168 ATAACTTACATA
1 ATAACTTACATA
* *
12138180 ACTTACTTATAATA
1 A-TAACTTA-CATA
12138194 ATAACTTACATA
1 ATAACTTACATA
12138206 A
1 A
12138207 CTTATTAATA
Statistics
Matches: 216, Mismatches: 29, Indels: 76
0.67 0.09 0.24
Matches are distributed among these distances:
9 20 0.09
10 9 0.04
11 53 0.25
12 69 0.32
13 42 0.19
14 14 0.06
15 2 0.01
16 5 0.02
17 2 0.01
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:12137990 original size:96 final size:95
Alignment explanation
Indices: 12137879--12138171 Score: 439
Period size: 94 Copynumber: 3.1 Consensus size: 95
12137869 TTTACATACA
*
12137879 TAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAACTTATAT
1 TAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAACTTATAC
*
12137944 ATAAACTTATATATAACTTACATACATAACT
66 AT-AACTTATATATAACTTACATAAATAACT
* * * *
12137975 TAAGTAAAATTTATATATAAACTTAAACAACAC--AACTTACATAATAACTTATATAA-TAACTC
1 TAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAACTTA-T-
12138037 ACATAACTTATATATAACTTACATAAATAACT
64 ACATAACTTATATATAACTTACATAAATAACT
12138069 TAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAACTTATAC
1 TAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAACTTATAC
* * * *
12138134 ATGACTTATATATAACTTTCATAACTTACT
66 ATAACTTATATATAACTTACATAAATAACT
12138164 TATAATAA
1 TA-AATAA
12138172 CTTACATAAC
Statistics
Matches: 177, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
93 2 0.01
94 81 0.46
95 33 0.19
96 59 0.33
97 2 0.01
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.34
Consensus pattern (95 bp):
TAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATAACTTATAC
ATAACTTATATATAACTTACATAAATAACT
Found at i:12138114 original size:9 final size:9
Alignment explanation
Indices: 12138088--12138210 Score: 57
Period size: 9 Copynumber: 13.7 Consensus size: 9
12138078 TTTATATATA
*
12138088 AACTTACAC
1 AACTTACAT
12138097 AAC--ACAT
1 AACTTACAT
12138104 AACTTACATAAT
1 AACTTAC---AT
12138116 AACTTACAT
1 AACTTACAT
12138125 AACTTATACAT
1 AAC-T-TACAT
* *
12138136 GACTTATATAT
1 AAC-T-TACAT
*
12138147 AACTTTCAT
1 AACTTACAT
12138156 AACTTAC-T
1 AACTTACAT
*
12138164 TA--TA-AT
1 AACTTACAT
12138170 AACTTACAT
1 AACTTACAT
12138179 AACTTACTTAT
1 AACTTAC--AT
12138190 AA--TA-AT
1 AACTTACAT
12138196 AACTTACAT
1 AACTTACAT
12138205 AACTTA
1 AACTTA
12138211 TTAATATTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 32
0.68 0.07 0.25
Matches are distributed among these distances:
6 8 0.09
7 6 0.07
8 6 0.07
9 38 0.43
10 2 0.02
11 20 0.22
12 9 0.10
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.36
Consensus pattern (9 bp):
AACTTACAT
Found at i:12138140 original size:11 final size:11
Alignment explanation
Indices: 12138100--12138161 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
12138090 CTTACACAAC
12138100 ACATAACTTACAT
1 ACATAACTT--AT
12138113 A-ATAAC-T-T
1 ACATAACTTAT
12138121 ACATAACTTAT
1 ACATAACTTAT
*
12138132 ACATGACTTAT
1 ACATAACTTAT
*
12138143 ATATAACTT-T
1 ACATAACTTAT
12138153 -CATAACTTA
1 ACATAACTTA
12138162 CTTATAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 2 0.05
9 12 0.29
10 2 0.05
11 19 0.46
12 5 0.12
13 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.37
Consensus pattern (11 bp):
ACATAACTTAT
Found at i:12138151 original size:31 final size:32
Alignment explanation
Indices: 12138100--12138180 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
12138090 CTTACACAAC
12138100 ACATAACTTACATAATAACTTACATAACTTAT
1 ACATAACTTACATAATAACTTACATAACTTAT
* * *
12138132 ACATGACTTATAT-ATAACTTTCATAACTTACTT
1 ACATAACTTACATAATAACTTACATAACTTA--T
*
12138165 ATAATAACTTACATAA
1 A-CATAACTTACATAA
12138181 CTTACTTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
31 16 0.41
32 11 0.28
33 2 0.05
34 9 0.23
35 1 0.03
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.37
Consensus pattern (32 bp):
ACATAACTTACATAATAACTTACATAACTTAT
Found at i:12138167 original size:84 final size:79
Alignment explanation
Indices: 12138018--12138211 Score: 194
Period size: 84 Copynumber: 2.4 Consensus size: 79
12138008 AACTTACATA
* * * *
12138018 ATAACTTATATAATAACTCACATAACTTATATATAACTTACATAAATAACTTAAATAAAATTTAT
1 ATAACTTAAATAATAACTTACATAACTTATACATAACTTA-ATAAATAACTTAAATAAAACTTAT
12138083 ATATAAACTTACACAACAC
65 A-AT-AACTTACA-AA-AC
* * * ** *
12138102 ATAACTTACATAATAACTTACATAACTTATACATGACTT-ATATATAACTTTCATAACTTACTTA
1 ATAACTTAAATAATAACTTACATAACTTATACATAACTTAATAAATAACTTAAATAA--AACTTA
*
12138166 TAATAACTTACATAAC
64 TAATAACTTACAAAAC
*
12138182 -TTACTTATAATAATAACTTACATAACTTAT
1 ATAACTTA-AATAATAACTTACATAACTTAT
12138212 TAATATTTAT
Statistics
Matches: 95, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
79 6 0.06
80 23 0.24
81 1 0.01
82 22 0.23
83 2 0.02
84 41 0.43
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.37
Consensus pattern (79 bp):
ATAACTTAAATAATAACTTACATAACTTATACATAACTTAATAAATAACTTAAATAAAACTTATA
ATAACTTACAAAAC
Found at i:12138201 original size:26 final size:25
Alignment explanation
Indices: 12138137--12138210 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 25
12138127 CTTATACATG
*
12138137 ACTTATAT-ATAACTTTCATAACTT
1 ACTTATATAATAACTTACATAACTT
12138161 AC-T-TATAATAACTTACATAACTT
1 ACTTATATAATAACTTACATAACTT
12138184 ACTTATAATAATAACTTACATAACTT
1 ACTTAT-ATAATAACTTACATAACTT
12138210 A
1 A
12138211 TTAATATTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
22 3 0.07
23 18 0.40
24 3 0.07
25 1 0.02
26 20 0.44
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (25 bp):
ACTTATATAATAACTTACATAACTT
Found at i:12138215 original size:23 final size:24
Alignment explanation
Indices: 12138008--12138216 Score: 106
Period size: 26 Copynumber: 8.9 Consensus size: 24
12137998 TAAACAACAC
*
12138008 AACTTACATAA-TAACTTATATAAT
1 AACTTACATAACTTACTTA-ATAAT
*
12138032 AACTCACATAACTTA--T-AT-AT
1 AACTTACATAACTTACTTAATAAT
* *
12138052 AACTTACATAAATAACTTAAATAA-
1 AACTTACATAACTTACTT-AATAAT
* * ** *
12138076 AATTTATATATAAACTTACACAACACAT
1 AA-CT-TACAT-AACTTACTTAATA-AT
* *
12138104 AACTTACATAA-TAACTT-A-CAT
1 AACTTACATAACTTACTTAATAAT
*
12138125 AACTT--AT-ACATGACTT-ATATAT
1 AACTTACATAAC-TTACTTAATA-AT
*
12138147 AACTTTCATAACTTACTT-ATAAT
1 AACTTACATAACTTACTTAATAAT
12138170 AACTTACATAACTTACTTATAATAAT
1 AACTTACATAACTTAC-T-TAATAAT
12138196 AACTTACATAACTTA-TTAATA
1 AACTTACATAACTTACTTAATA
12138217 TTTATATGGA
Statistics
Matches: 142, Mismatches: 22, Indels: 43
0.69 0.11 0.21
Matches are distributed among these distances:
18 1 0.01
19 2 0.01
20 20 0.14
21 9 0.06
22 8 0.06
23 24 0.17
24 29 0.20
25 9 0.06
26 31 0.22
27 7 0.05
28 2 0.01
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.36
Consensus pattern (24 bp):
AACTTACATAACTTACTTAATAAT
Found at i:12138610 original size:21 final size:21
Alignment explanation
Indices: 12138584--12138654 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
12138574 CTACAACTTA
*
12138584 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
12138605 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
12138626 AAGCAGAGGCTGCAACGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
12138647 AAGCAGAG
1 AAGCAGAG
12138655 CAGAGCAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:12139139 original size:49 final size:49
Alignment explanation
Indices: 12139065--12139162 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
12139055 AAAAATGCCG
12139065 CTAAAGACCATGTTCTTTAGAGGCGCTT-AGAAAAAAACGCCGCTAAAGA
1 CTAAAGACCATGTTCTTTAGAGGCGCTTAAG-AAAAAACGCCGCTAAAGA
* *
12139114 CTAAAGACTATGTTCTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAGA
1 CTAAAGACCATGTTCTTTAGAGGCGCTTAAGAAAAAACGCCGCTAAAGA
12139163 ACATGATCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 44 0.96
50 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (49 bp):
CTAAAGACCATGTTCTTTAGAGGCGCTTAAGAAAAAACGCCGCTAAAGA
Found at i:12139177 original size:42 final size:42
Alignment explanation
Indices: 12138971--12139179 Score: 242
Period size: 42 Copynumber: 4.8 Consensus size: 42
12138961 GTTTTTGTAT
* *
12138971 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCAGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
* *
12139013 AAAAATGCCGCTAAAGATA-ATGTTCTTTAGCGGCGCTTAGAC
1 AAAAACGCCGCTAAAGA-ACATGTTCTTTAGCGGCGCTTAGAA
* * *
12139055 AAAAATGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
12139097 AAAAACGCCGCTAAAGACTAAAGACTATGTTCTTTAGCGGCGCTTA-AGA
1 AAAAACGCCGCTAAAG-----A-AC-ATGTTCTTTAGCGGCGCTTAGA-A
* *
12139146 AAAAACGCCGCTAAAGAACATGATCTCTAGCGGC
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
12139180 ATTTTTCTCT
Statistics
Matches: 145, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
42 102 0.70
43 3 0.02
44 1 0.01
47 1 0.01
48 2 0.01
49 36 0.25
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:12139350 original size:22 final size:22
Alignment explanation
Indices: 12139319--12139362 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12139309 TAGTGGCGTT
* *
12139319 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAACACCGCTAAAGACCTA
12139341 AAAAAACACCGCTAAAGACCTA
1 AAAAAACACCGCTAAAGACCTA
12139363 TTTTGATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.27, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACACCGCTAAAGACCTA
Found at i:12144624 original size:31 final size:32
Alignment explanation
Indices: 12144553--12144624 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
12144543 AAATGATTTA
12144553 AAGTTTAGGGATTGATTTAAAAAGAATATTAT
1 AAGTTTAGGGATTGATTTAAAAAGAATATTAT
*
12144585 AAGTTTAGGGATTGATTTAAAAAGAATGTTAT
1 AAGTTTAGGGATTGATTTAAAAAGAATATTAT
12144617 -AGTTTAGG
1 AAGTTTAGG
12144625 CATGTATGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 8 0.21
32 31 0.79
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (32 bp):
AAGTTTAGGGATTGATTTAAAAAGAATATTAT
Found at i:12148962 original size:21 final size:21
Alignment explanation
Indices: 12148938--12148990 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12148928 CATTATTTCT
*
12148938 AATCTCACCGCTACAATATCC
1 AATCTCACCGCTACAATAACC
* *
12148959 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAATAACC
12148980 AATCTCACCGC
1 AATCTCACCGC
12148991 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.38, G:0.08, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:12149720 original size:129 final size:130
Alignment explanation
Indices: 12149507--12149769 Score: 474
Period size: 129 Copynumber: 2.0 Consensus size: 130
12149497 ATTGCGAAGC
12149507 CTTGTCTTCACAACTTTTATGGCTGAAAATGCTTATTCGGTTGTTGCAGTAGACACGATAAGAGT
1 CTTGTCTTCACAACTTTTATGGCTGAAAATGCTTATTCGGTTGTTGCAGTAGACACGATAAGAGT
* *
12149572 TAGTACAAGACGAACAATTCTATCAAGAAGATGATAAATAATTAACTTCTTTGTCTTAGCTAGCA
66 TAGCACAAGACAAACAATTCTATCAAGAAGATGATAAATAATTAACTTCTTTGTCTTAGCTAGCA
* *
12149637 CTTGTCTTCACAATTTTTATGGCTG-AAATGTTTATTCGGTTGTTGCAGTAGACACGATAAGAGT
1 CTTGTCTTCACAACTTTTATGGCTGAAAATGCTTATTCGGTTGTTGCAGTAGACACGATAAGAGT
*
12149701 TAGCACAAGACAAATAATTCTATCAAGAAGATGATAAATAATTAACTTCTTTGTCTTAGCTAGCA
66 TAGCACAAGACAAACAATTCTATCAAGAAGATGATAAATAATTAACTTCTTTGTCTTAGCTAGCA
12149766 CTTG
1 CTTG
12149770 ACATAACTCG
Statistics
Matches: 128, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
129 104 0.81
130 24 0.19
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (130 bp):
CTTGTCTTCACAACTTTTATGGCTGAAAATGCTTATTCGGTTGTTGCAGTAGACACGATAAGAGT
TAGCACAAGACAAACAATTCTATCAAGAAGATGATAAATAATTAACTTCTTTGTCTTAGCTAGCA
Found at i:12151874 original size:30 final size:30
Alignment explanation
Indices: 12151822--12151940 Score: 105
Period size: 30 Copynumber: 3.8 Consensus size: 30
12151812 AAGAATGTTT
* * *
12151822 AGGATCTTGAGAAGACCCGATATCTCATTC
1 AGGAGCTTGAGAAGATCTGATATCTCATTC
*
12151852 AGGAGCTTGGGAAGA-CTTGATATCTCATTC
1 AGGAGCTTGAGAAGATC-TGATATCTCATTC
* *
12151882 AAGATCTTGAGATTGAGAAGATCTGATATCTCGTTC
1 -AG-----GAGCTTGAGAAGATCTGATATCTCATTC
*
12151918 AGGAGCTTGGGAAGATCTGATAT
1 AGGAGCTTGAGAAGATCTGATAT
12151941 TTGATTTTTC
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
29 1 0.01
30 44 0.60
31 2 0.03
35 2 0.03
36 23 0.32
37 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (30 bp):
AGGAGCTTGAGAAGATCTGATATCTCATTC
Found at i:12153424 original size:21 final size:19
Alignment explanation
Indices: 12153384--12153427 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
12153374 AAATTACAAA
*
12153384 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATATTT
*
12153403 AAAATTCTAAAATTTATATTT
1 AAAATTC-AAAA-TAATATTT
12153424 AAAA
1 AAAA
12153428 ATATTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
21 10 0.48
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTCAAAATAATATTT
Found at i:12164686 original size:20 final size:20
Alignment explanation
Indices: 12164643--12164687 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
12164633 TTTGGATTAA
12164643 AATTTTTATATCATTTATTT
1 AATTTTTATATCATTTATTT
*
12164663 -ATTTTT-TATCATTTTTTTT
1 AATTTTTATATCA-TTTATTT
12164682 AATTTT
1 AATTTT
12164688 ACTTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
AATTTTTATATCATTTATTT
Found at i:12167341 original size:29 final size:29
Alignment explanation
Indices: 12167291--12167350 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
12167281 ATAGCAATCT
* **
12167291 AACTATAATCCAGATATTTATA-ATAAAAA
1 AACTATAATCCAAATAAATATAGA-AAAAA
12167320 AACTATAATCCAAATAAATATAGAAAAAA
1 AACTATAATCCAAATAAATATAGAAAAAA
12167349 AA
1 AA
12167351 TCCAAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (29 bp):
AACTATAATCCAAATAAATATAGAAAAAA
Found at i:12184235 original size:124 final size:124
Alignment explanation
Indices: 12184040--12184389 Score: 594
Period size: 124 Copynumber: 2.8 Consensus size: 124
12184030 TAATTTCGAG
* * *
12184040 TTGACATTTCTGATCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTCAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
12184105 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAAT-AATTTTTT
12184165 TTGACGTTTCTGAGCAAATAGTAT-AAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * *
12184229 AAATCGCGCCCTCGTGGACGCGCTTTTGCAACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTTTTT
* * *
12184288 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGTTATTTGAAAAGAATCTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
12184353 AAATCGCGCCCTTGTGGACGCGCTTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
12184390 CATGTTTGGG
Statistics
Matches: 213, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
123 32 0.15
124 159 0.75
125 22 0.10
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTTTTT
Found at i:12187302 original size:5 final size:5
Alignment explanation
Indices: 12187286--12187316 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
12187276 AAAATAATAA
12187286 GCCCG AGCCCG GCCCG GCCCG GCCCG GCCCG
1 GCCCG -GCCCG GCCCG GCCCG GCCCG GCCCG
12187317 ATTTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.03, C:0.58, G:0.39, T:0.00
Consensus pattern (5 bp):
GCCCG
Found at i:12188046 original size:115 final size:116
Alignment explanation
Indices: 12187839--12188077 Score: 408
Period size: 115 Copynumber: 2.1 Consensus size: 116
12187829 TGATAAATTG
* *
12187839 TATTAACTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAACTCAAAAAATTGTATTAATGGTTACTAAAATTATCAAATTATATAAAATAATTAATTGT
* * * *
12187904 TAGTATCAGTCAAAACATTTTTTCAAATCTAACA-TATGTGAATGTAAAAT
66 TACTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
*
12187954 TATTAACTCTAAAAATTGTATTAATGGTTACTAAAATTATCAAATTATATAAAATAATTAATTGT
1 TATTAACTCAAAAAATTGTATTAATGGTTACTAAAATTATCAAATTATATAAAATAATTAATTGT
12188019 TACTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
66 TACTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
12188070 TATTAACT
1 TATTAACT
12188078 TAGTTTAGGA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
115 93 0.80
116 23 0.20
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (116 bp):
TATTAACTCAAAAAATTGTATTAATGGTTACTAAAATTATCAAATTATATAAAATAATTAATTGT
TACTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
Found at i:12188136 original size:21 final size:21
Alignment explanation
Indices: 12188107--12188259 Score: 150
Period size: 21 Copynumber: 7.0 Consensus size: 21
12188097 AAATTAGGTT
* *
12188107 AGGGGTAGGGTTTTAAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
12188128 AGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
12188149 AGGGGTTAGGGTTTTTAA-TTAA
1 A-GGGTTAGGGTTTTTAAGTT-A
* *
12188171 ATTAGGTTAGAGTTTTTAAAGTTA
1 A--GGGTTAGGGTTTTT-AAGTTA
*
12188195 AGGTTTAGGGTTTTTAA-TTAA
1 AGGGTTAGGGTTTTTAAGTT-A
*
12188216 ATTAGGTTAGGGTTTTTAAGTTA
1 A--GGGTTAGGGTTTTTAAGTTA
*
12188239 AGGTTTAGGGTTTTTAA-TTA
1 AGGGTTAGGGTTTTTAAGTTA
12188259 A
1 A
12188260 ATTAGGTTAG
Statistics
Matches: 111, Mismatches: 12, Indels: 19
0.78 0.08 0.13
Matches are distributed among these distances:
20 6 0.05
21 40 0.36
22 29 0.26
23 28 0.25
24 6 0.05
25 2 0.02
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (21 bp):
AGGGTTAGGGTTTTTAAGTTA
Found at i:12188288 original size:21 final size:22
Alignment explanation
Indices: 12188263--12188306 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12188253 TAATTAAATT
*
12188263 AGGTT-AGGGTTAGGGTTTTTA
1 AGGTTAAGGGTTAGGATTTTTA
*
12188284 AGGTTAAGGTTTAGGATTTTTA
1 AGGTTAAGGGTTAGGATTTTTA
12188306 A
1 A
12188307 TTAAATTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (22 bp):
AGGTTAAGGGTTAGGATTTTTA
Found at i:12188321 original size:45 final size:44
Alignment explanation
Indices: 12188130--12188321 Score: 276
Period size: 45 Copynumber: 4.2 Consensus size: 44
12188120 TAAAGTTAAG
*
12188130 GGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAAGTTAA-GGTTTAGGGTTTTTAATTAAATTA
*
12188175 GGTTAGAGTTTTTAAAGTTAAGGTTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTT-AAGTTAAGGTTTAGGGTTTTTAATTAAATTA
12188220 GGTTAGGGTTTTTAAGTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAAGTTAAGGTTTAGGGTTTTTAATT-AA--A--TTA
*
12188269 GGGTTAGGGTTTTTAAGGTTAAGGTTTAGGATTTTTAATTAAATTA
1 -GGTTAGGGTTTTTAA-GTTAAGGTTTAGGGTTTTTAATTAAATTA
12188315 GGTTAGG
1 GGTTAGG
12188322 ATTAGGGTTT
Statistics
Matches: 135, Mismatches: 4, Indels: 16
0.87 0.03 0.10
Matches are distributed among these distances:
44 25 0.19
45 56 0.41
46 10 0.07
47 1 0.01
48 1 0.01
49 3 0.02
50 17 0.13
51 22 0.16
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (44 bp):
GGTTAGGGTTTTTAAGTTAAGGTTTAGGGTTTTTAATTAAATTA
Found at i:12188332 original size:29 final size:29
Alignment explanation
Indices: 12188284--12188643 Score: 367
Period size: 29 Copynumber: 12.6 Consensus size: 29
12188274 AGGGTTTTTA
* *
12188284 AGGTTAAGGTTTAGGATTTTTAATTAAATT
1 AGGTT-AGGGTTAGGGTTTTTAATTAAATT
*
12188314 AGGTTAGGATTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAAATT
12188343 AGGTTAGGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAAATT
12188372 AGGTTAGGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAAATT
* *
12188401 AGGTTAGGGGTAGGATTTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAAATT
*
12188430 AGGTTAGGGGTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAAATT
*
12188459 AGGTTAGGGGTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAAATT
12188488 A----A--GTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAAATT
*
12188511 AGGTTAGGG-T----TTTGT-ATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAAATT
** *
12188534 AGGTTAGGGTTTTTAAAGTTAAGGTTTAGGGTT---TT
1 AGGTTAGGG---TTAGGGTT----TTTA--ATTAAATT
* *
12188569 AAGTTAAGGTTTAGGG-TTTTAATTAAATT
1 AGGTT-AGGGTTAGGGTTTTTAATTAAATT
12188598 AGGTTAGGGTTAGGG-TTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAAATT
*
12188626 AGGTCAGGGTTTAGGGTT
1 AGGTTAGGG-TTAGGGTT
12188644 AAATTAGGTT
Statistics
Matches: 285, Mismatches: 18, Indels: 54
0.80 0.05 0.15
Matches are distributed among these distances:
23 38 0.13
24 4 0.01
25 1 0.00
26 2 0.01
27 2 0.01
28 35 0.12
29 177 0.62
30 6 0.02
31 2 0.01
32 1 0.00
33 4 0.01
35 8 0.03
36 3 0.01
38 2 0.01
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (29 bp):
AGGTTAGGGTTAGGGTTTTTAATTAAATT
Found at i:12188574 original size:20 final size:20
Alignment explanation
Indices: 12188537--12188594 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
12188527 TTAAATTAGG
12188537 TTAGGGTTTTTAAAGTTAAGGT
1 TTAGGG-TTTT-AAGTTAAGGT
12188559 TTAGGGTTTTAAGTTAAGGT
1 TTAGGGTTTTAAGTTAAGGT
12188579 TTAGGGTTTTAA-TTAA
1 TTAGGGTTTTAAGTTAA
12188595 ATTAGGTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.11
20 22 0.61
21 4 0.11
22 6 0.17
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (20 bp):
TTAGGGTTTTAAGTTAAGGT
Found at i:12188656 original size:28 final size:29
Alignment explanation
Indices: 12188576--12188643 Score: 120
Period size: 28 Copynumber: 2.4 Consensus size: 29
12188566 TTTAAGTTAA
*
12188576 GGTTTAGGGTTTTAATTAAATTAGGTTAG
1 GGTTTAGGGTTTTAATTAAATTAGGTCAG
12188605 GG-TTAGGGTTTTAATTAAATTAGGTCAG
1 GGTTTAGGGTTTTAATTAAATTAGGTCAG
12188633 GGTTTAGGGTT
1 GGTTTAGGGTT
12188644 AAATTAGGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 27 0.73
29 10 0.27
ACGTcount: A:0.25, C:0.01, G:0.31, T:0.43
Consensus pattern (29 bp):
GGTTTAGGGTTTTAATTAAATTAGGTCAG
Found at i:12188687 original size:25 final size:25
Alignment explanation
Indices: 12188659--12188771 Score: 114
Period size: 25 Copynumber: 4.7 Consensus size: 25
12188649 AGGTTAGGAT
12188659 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
12188684 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * *
12188707 --AAATAAC-TCGAAA-AAATTTCTA
1 TTTTATTACATC-AAATAAACTTCTA
*
12188729 TTTTATTACATCAAATAAACTTTTA
1 TTTTATTACATCAAATAAACTTCTA
12188754 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
12188772 TATCAAAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
20 2 0.03
21 11 0.15
22 2 0.03
23 2 0.03
24 11 0.15
25 43 0.61
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:12188738 original size:70 final size:69
Alignment explanation
Indices: 12188659--12188815 Score: 278
Period size: 70 Copynumber: 2.3 Consensus size: 69
12188649 AGGTTAGGAT
12188659 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAAT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTC-AAAAAAT
12188724 TTCTA
65 TTCTA
*
12188729 TTTTATTACATCAAATAAACTTTTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
12188794 TCTA
66 TCTA
* *
12188798 TTTTTTTACATAAAATAA
1 TTTTATTACATCAAATAA
12188816 TATCAAAATA
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
69 28 0.33
70 56 0.67
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.41
Consensus pattern (69 bp):
TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
TCTA
Found at i:12188807 original size:44 final size:45
Alignment explanation
Indices: 12188739--12188825 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
12188729 TTTTATTACA
*
12188739 TCAAATAAACTTTTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTTTATTTTATTACATAAAATAATATCAAAATAAC
*
12188784 TCAAA-AAA-TTTCTATTTTTTTACATAAAATAATATCAAAATA
1 TCAAATAAACTTT-TATTTTATTACATAAAATAATATCAAAATA
12188826 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 3 0.08
44 31 0.79
45 5 0.13
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.39
Consensus pattern (45 bp):
TCAAATAAACTTTTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:12189265 original size:18 final size:18
Alignment explanation
Indices: 12189242--12189276 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12189232 CAGAAAAGGA
*
12189242 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
*
12189260 TACATATGAGGGCTAGG
1 TACATATAAGGGCTAGG
12189277 AAACGCACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Done.