Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold678
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1173314
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 74412 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:412059 original size:188 final size:183
Alignment explanation
Indices: 411712--412136 Score: 552
Period size: 188 Copynumber: 2.3 Consensus size: 183
411702 ATGCATGTAA
* *
411712 TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGCTGACAAGTATTGAGTCTTCTGTCTTA
1 TGACAAGTATTGAGTCTACTGAC-TT-TGTGACATTAGCTGACAAGTATTGAGTCTACTGACTTA
* * *
411777 ATGTGTCATTTGCTGCCAAGTATTGAGACTACTGTGTAATGACTTTATGAGTATTGAGTCTATTG
64 ATGTGTCATTTGCTGACAAGTATTAAGACTACTGTGTAATAACTTTATGAGTATTGAGTCTATTG
* *
411842 ACTGTGTGACATTAGCTGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
129 ACTGTGTGACATTAGCTGACAAGTATTGAGACTACTGACTTTATGTGACATTAGC
411897 TGACAAGTATTGAGTCTACTGACTTTGTGCAACATTAGCTGACAAGTATTGAGTCTACTGACTT-
1 TGACAAGTATTGAGTCTACTGACTTTGTG--ACATTAGCTGACAAGTATTGAGTCTACTGACTTA
* *
411961 TTGTGTCA-TTGCTGACAAGTATTAACTTAAGACTACTGTGTGATAACTTTATGAGTATTGAGTC
64 ATGTGTCATTTGCTGACAAG---T-A-TTAAGACTACTGTGTAATAACTTTATGAGTATTGAGTC
* ** * *
412025 TATTGACTGTGTGACATTAG-TTATTAGTTATTGAGACTGCTGTCTTTATGTGACATTAGC
124 TATTGACTGTGTGACATTAGCTGACAAG-TATTGAGACTACTGACTTTATGTGACATTAGC
* * * *
412085 TGATAAAGTAGTGAGTCTACTGACATGTGTGTCATTAGCTGAC-AGTATTGAG
1 TGA-CAAGTATTGAGTCTACTGAC-TTTGTGACATTAGCTGACAAGTATTGAG
412137 ACTCCTGTGT
Statistics
Matches: 212, Mismatches: 18, Indels: 18
0.85 0.07 0.07
Matches are distributed among these distances:
183 14 0.07
184 9 0.04
185 54 0.25
186 1 0.00
187 14 0.07
188 97 0.46
189 18 0.08
190 5 0.02
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (183 bp):
TGACAAGTATTGAGTCTACTGACTTTGTGACATTAGCTGACAAGTATTGAGTCTACTGACTTAAT
GTGTCATTTGCTGACAAGTATTAAGACTACTGTGTAATAACTTTATGAGTATTGAGTCTATTGAC
TGTGTGACATTAGCTGACAAGTATTGAGACTACTGACTTTATGTGACATTAGC
Found at i:418180 original size:16 final size:16
Alignment explanation
Indices: 418159--418193 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
418149 ATTGATGATT
418159 GACAGA-TGAACAGATG
1 GACAGATTG-ACAGATG
418175 GACAGATTGACAGATG
1 GACAGATTGACAGATG
418191 GAC
1 GAC
418194 TGAGAGACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.40, C:0.14, G:0.31, T:0.14
Consensus pattern (16 bp):
GACAGATTGACAGATG
Found at i:423648 original size:3 final size:3
Alignment explanation
Indices: 423640--423711 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
423630 CACACTACTG
423640 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
423688 GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA
423712 ACAAGAGCTG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:427448 original size:2 final size:2
Alignment explanation
Indices: 427443--427506 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
427433 CCCTAAATTT
427443 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
427485 GA GA GA GA GA GA GC GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
427507 TTATTAGACA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:428988 original size:21 final size:21
Alignment explanation
Indices: 428964--429080 Score: 148
Period size: 21 Copynumber: 5.6 Consensus size: 21
428954 TAGTCAACTG
*
428964 TAGTCAACTGTGTAACATCAA
1 TAGTCAACTGTATAACATCAA
*
428985 TAGTCAACGGTATAACATCAA
1 TAGTCAACTGTATAACATCAA
*
429006 TAGTCAACTGAATAACATCAA
1 TAGTCAACTGTATAACATCAA
* *
429027 TAGTCAACGGTATAACATCAG
1 TAGTCAACTGTATAACATCAA
*
429048 TAGTCAACCATGT-T-ACATCAG
1 TAGTCAA-C-TGTATAACATCAA
429069 TAGTCAACTGTA
1 TAGTCAACTGTA
429081 GTCAACTGTG
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
19 3 0.04
20 1 0.01
21 77 0.91
22 2 0.02
23 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (21 bp):
TAGTCAACTGTATAACATCAA
Found at i:429085 original size:31 final size:31
Alignment explanation
Indices: 429047--429111 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
429037 TATAACATCA
* *
429047 GTAGTCAACCATGTTACATCAGTAGTCAACT
1 GTAGTCAACCATGTAACATCAATAGTCAACT
** *
429078 GTAGTCAACTGTGTAACATTAATAGTCAACT
1 GTAGTCAACCATGTAACATCAATAGTCAACT
429109 GTA
1 GTA
429112 TAACATCAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (31 bp):
GTAGTCAACCATGTAACATCAATAGTCAACT
Found at i:429105 original size:21 final size:21
Alignment explanation
Indices: 429079--429173 Score: 95
Period size: 21 Copynumber: 4.5 Consensus size: 21
429069 TAGTCAACTG
* *
429079 TAGTCAACTGTGTAACATTAA
1 TAGTCAACTGTATAACATCAA
*
429100 TAGTCAACTGTATAACATCAG
1 TAGTCAACTGTATAACATCAA
* * *
429121 TAGTCAACTGAATAATATCAG
1 TAGTCAACTGTATAACATCAA
*
429142 TAGTCAACCATGT-T-ACATCAG
1 TAGTCAA-C-TGTATAACATCAA
429163 TAGTCAACTGT
1 TAGTCAACTGT
429174 TGTGATACCA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 3 0.05
20 1 0.02
21 57 0.88
22 2 0.03
23 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (21 bp):
TAGTCAACTGTATAACATCAA
Found at i:429105 original size:52 final size:52
Alignment explanation
Indices: 429027--429130 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
429017 ATAACATCAA
*
429027 TAGTCAACGGTATAACATCAGTAGTCAACCATGT-T-ACATCAGTAGTCAACTG
1 TAGTCAACGGTATAACATCAATAGTCAA-C-TGTATAACATCAGTAGTCAACTG
* * *
429079 TAGTCAACTGTGTAACATTAATAGTCAACTGTATAACATCAGTAGTCAACTG
1 TAGTCAACGGTATAACATCAATAGTCAACTGTATAACATCAGTAGTCAACTG
429131 AATAATATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
50 3 0.07
51 2 0.04
52 41 0.89
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (52 bp):
TAGTCAACGGTATAACATCAATAGTCAACTGTATAACATCAGTAGTCAACTG
Found at i:429115 original size:94 final size:94
Alignment explanation
Indices: 428985--429173 Score: 306
Period size: 94 Copynumber: 2.0 Consensus size: 94
428975 GTAACATCAA
*
428985 TAGTCAACGGTATAACATCAATAGTCAACTGAATAACATCAATAGTCAACGGTATAACATCAGTA
1 TAGTCAACGGTATAACATCAATAGTCAACTGAATAACATCAATAGTCAACGGAATAACATCAGTA
429050 GTCAACCATGTTACATCAGTAGTCAACTG
66 GTCAACCATGTTACATCAGTAGTCAACTG
* * * * * * *
429079 TAGTCAACTGTGTAACATTAATAGTCAACTGTATAACATCAGTAGTCAACTGAATAATATCAGTA
1 TAGTCAACGGTATAACATCAATAGTCAACTGAATAACATCAATAGTCAACGGAATAACATCAGTA
429144 GTCAACCATGTTACATCAGTAGTCAACTG
66 GTCAACCATGTTACATCAGTAGTCAACTG
429173 T
1 T
429174 TGTGATACCA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (94 bp):
TAGTCAACGGTATAACATCAATAGTCAACTGAATAACATCAATAGTCAACGGAATAACATCAGTA
GTCAACCATGTTACATCAGTAGTCAACTG
Found at i:429141 original size:73 final size:73
Alignment explanation
Indices: 429006--429149 Score: 202
Period size: 73 Copynumber: 2.0 Consensus size: 73
428996 ATAACATCAA
*
429006 TAGTCAACTGAATAACATCAATAGTCAACGGTATAACATCAGTAGTCAACCATGTTACATCAGTA
1 TAGTCAACTGAATAACATCAATAGTCAACGGTATAACATCAGTAGTCAACCATGTAACATCAGTA
429071 GTCAACTG
66 GTCAACTG
** * * *
429079 TAGTCAACTGTGTAACATTAATAGTCAACTGTATAACATCAGTAGTCAA-C-TGAATAATATCAG
1 TAGTCAACTGAATAACATCAATAGTCAACGGTATAACATCAGTAGTCAACCATG--TAACATCAG
429142 TAGTCAAC
64 TAGTCAAC
429150 CATGTTACAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
71 2 0.03
72 1 0.02
73 60 0.95
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (73 bp):
TAGTCAACTGAATAACATCAATAGTCAACGGTATAACATCAGTAGTCAACCATGTAACATCAGTA
GTCAACTG
Found at i:429160 original size:115 final size:115
Alignment explanation
Indices: 428949--429170 Score: 363
Period size: 115 Copynumber: 1.9 Consensus size: 115
428939 GAGATATCTG
428949 ATCAGTAGTCAACTGTAGTCAACTGTGTAACATCAATAGTCAACGGTATAACATCAATAGTCAAC
1 ATCAGTAGTCAACTGTAGTCAACTGTGTAACATCAATAGTCAACGGTATAACATCAATAGTCAAC
**
429014 TGAATAACATCAATAGTCAACGGTATAACATCAGTAGTCAACCATGTTAC
66 TGAATAACATCAATAGTCAACCATATAACATCAGTAGTCAACCATGTTAC
* * *
429064 ATCAGTAGTCAACTGTAGTCAACTGTGTAACATTAATAGTCAACTGTATAACATCAGTAGTCAAC
1 ATCAGTAGTCAACTGTAGTCAACTGTGTAACATCAATAGTCAACGGTATAACATCAATAGTCAAC
* * * *
429129 TGAATAATATCAGTAGTCAACCATGTTACATCAGTAGTCAAC
66 TGAATAACATCAATAGTCAACCATATAACATCAGTAGTCAAC
429171 TGTTGTGATA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 98 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (115 bp):
ATCAGTAGTCAACTGTAGTCAACTGTGTAACATCAATAGTCAACGGTATAACATCAATAGTCAAC
TGAATAACATCAATAGTCAACCATATAACATCAGTAGTCAACCATGTTAC
Found at i:430691 original size:27 final size:27
Alignment explanation
Indices: 430660--430715 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
430650 ATACATACAA
*
430660 ATATACATTGTATGCATACAAATATAC
1 ATATACATTGTATACATACAAATATAC
* *
430687 ATATACATTGTATACATATAAATGTAC
1 ATATACATTGTATACATACAAATATAC
430714 AT
1 AT
430716 TGCATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (27 bp):
ATATACATTGTATACATACAAATATAC
Found at i:430705 original size:21 final size:21
Alignment explanation
Indices: 430642--430737 Score: 86
Period size: 21 Copynumber: 4.3 Consensus size: 21
430632 ACATTTACAG
*
430642 TACATTGTATACATACAAATA
1 TACATTGTATACATATAAATA
*
430663 TACATTGTATGCATACAAATATACATA
1 TACATTG--T--ATAC--ATATAAATA
*
430690 TACATTGTATACATATAAATG
1 TACATTGTATACATATAAATA
*
430711 TACATTGCATA-ATTATAAATA
1 TACATTGTATACA-TATAAATA
430732 TACATT
1 TACATT
430738 AATATAAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.02
21 37 0.60
23 5 0.08
25 5 0.08
27 14 0.23
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (21 bp):
TACATTGTATACATATAAATA
Found at i:430731 original size:48 final size:48
Alignment explanation
Indices: 430642--430736 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
430632 ACATTTACAG
* *
430642 TACATTGTATACATACAAATATACATTGTATGCATACAAATATACATA
1 TACATTGTATACATACAAATATACATTGCATGAATACAAATATACATA
* * *
430690 TACATTGTATACATATAAATGTACATTGCAT-AATTATAAATATACAT
1 TACATTGTATACATACAAATATACATTGCATGAA-TACAAATATACAT
430737 TAATATAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
47 1 0.02
48 40 0.98
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (48 bp):
TACATTGTATACATACAAATATACATTGCATGAATACAAATATACATA
Found at i:437419 original size:21 final size:21
Alignment explanation
Indices: 437382--437421 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
437372 TACTACATGT
*
437382 ATCTGACAAGTCGACATAAAG
1 ATCTGACAAGTCAACATAAAG
*
437403 ATCTGACAAGTTAACATAA
1 ATCTGACAAGTCAACATAA
437422 TTTTCTGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (21 bp):
ATCTGACAAGTCAACATAAAG
Found at i:437512 original size:21 final size:21
Alignment explanation
Indices: 437483--437636 Score: 132
Period size: 21 Copynumber: 7.4 Consensus size: 21
437473 CATATTATAA
*
437483 GTCGACTTGTCAGATAATGAT
1 GTCGACTTGTCAGATAATTAT
* **
437504 GTTGACTTGTCAGAT-GCTAT
1 GTCGACTTGTCAGATAATTAT
* * *
437524 GTTGTCTTGTCAAATAATTAT
1 GTCGACTTGTCAGATAATTAT
*
437545 GTCGACTTGCCAGATAATTAT
1 GTCGACTTGTCAGATAATTAT
* *
437566 GTC-AGCTTGTCAAATAATGAT
1 GTCGA-CTTGTCAGATAATTAT
* *** *
437587 ATCGACTTAAAAGATGATTAT
1 GTCGACTTGTCAGATAATTAT
**
437608 GTCGACTTGTCAGATCCTTAT
1 GTCGACTTGTCAGATAATTAT
437629 GTCGACTT
1 GTCGACTT
437637 CTCAAAAATA
Statistics
Matches: 102, Mismatches: 28, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.16
21 85 0.83
22 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (21 bp):
GTCGACTTGTCAGATAATTAT
Found at i:437552 original size:41 final size:42
Alignment explanation
Indices: 437488--437594 Score: 119
Period size: 41 Copynumber: 2.6 Consensus size: 42
437478 TATAAGTCGA
* * * * *
437488 CTTGTCAGATAATGATGTTGACTTGTCAGAT-GCTATGT-TG
1 CTTGTCAAATAATGATGTCGACTTGCCAGATAACTATGTCAG
* *
437528 TCTTGTCAAATAATTATGTCGACTTGCCAGATAATTATGTCAG
1 -CTTGTCAAATAATGATGTCGACTTGCCAGATAACTATGTCAG
*
437571 CTTGTCAAATAATGATATCGACTT
1 CTTGTCAAATAATGATGTCGACTT
437595 AAAAGATGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
41 27 0.49
42 27 0.49
43 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (42 bp):
CTTGTCAAATAATGATGTCGACTTGCCAGATAACTATGTCAG
Found at i:437746 original size:21 final size:21
Alignment explanation
Indices: 437718--437809 Score: 85
Period size: 21 Copynumber: 4.4 Consensus size: 21
437708 CGTGAATAAG
437718 TGACAAGTCGACATAAAGATC
1 TGACAAGTCGACATAAAGATC
* * ***
437739 TTACAAGTCAACATATTTATC
1 TGACAAGTCGACATAAAGATC
* ** *
437760 TGACATGTCTTCATCAAGATC
1 TGACAAGTCGACATAAAGATC
**
437781 TGACAAGTCGACATAATTATC
1 TGACAAGTCGACATAAAGATC
437802 TGACAAGT
1 TGACAAGT
437810 GGTGGCAGAA
Statistics
Matches: 52, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (21 bp):
TGACAAGTCGACATAAAGATC
Found at i:448818 original size:39 final size:39
Alignment explanation
Indices: 448632--449124 Score: 156
Period size: 39 Copynumber: 13.0 Consensus size: 39
448622 ACATTTGACA
* **
448632 CATTTGATAAATTGTTGAGTTTTTTCCAC-CGTTTTAGCAT
1 CATTTGATACATACTTGAG-TTTTTCC-CTCGTTTTAGCAT
* * * * * *
448672 CATTTCACATATACTAGAGTTTTTCTCC-CATTTTTAGCTT
1 CATTTGATACATACTTGAGTTTTTC-CCTC-GTTTTAGCAT
* * * * *
448712 AACTTGACACAAACTTGAG-TTTTCCC-CCTGTTTAGCAT
1 CATTTGATACATACTTGAGTTTTTCCCTCGT-TTTAGCAT
* *
448750 CAATTG-T---TACATGAGTTGTTTCCCT-GTTTTAGCAT
1 CATTTGATACATACTTGAGTT-TTTCCCTCGTTTTAGCAT
* *
448785 CACTTT-ATACATACTTGAGTTTTTCGCTCGTTTTAGCAA
1 CA-TTTGATACATACTTGAGTTTTTCCCTCGTTTTAGCAT
* * *
448824 CATTTGATAC--A--TGAG--TTTCCCCCATTTTAGTAT
1 CATTTGATACATACTTGAGTTTTTCCCTCGTTTTAGCAT
* * *
448857 CATTTGATACATACATAAGTTTTTCTCTCGTTTTAGCAT
1 CATTTGATACATACTTGAGTTTTTCCCTCGTTTTAGCAT
* * * * * * * *
448896 TATTTTACATATACTTGAGTTTTACACC-CTTTTTTGTAT
1 CATTTGATACATACTTGAGTTTTTC-CCTCGTTTTAGCAT
*** * * ** * * *
448935 CACCCGGTACAAACTAAAGATTTCCCCTCGTTTTAGCAA
1 CATTTGATACATACTTGAGTTTTTCCCTCGTTTTAGCAT
* ** *
448974 CATTTGATACTTACTTGAG-CGTTCTCT-GTGTTTAAGCAT
1 CATTTGATACATACTTGAGTTTTTCCCTCGT-TTT-AGCAT
* * ** *
449013 TACTTGATATGTA-TT---TTTTTCTCC-CGTTTCAGCAT
1 CATTTGATACATACTTGAGTTTTTC-CCTCGTTTTAGCAT
* * * * *
449048 CATTTTATATATACTTGAGATTTTCCACT-GTTTTGGCAG
1 CATTTGATACATACTTGAGTTTTTCC-CTCGTTTTAGCAT
* * *
449087 CATTTGGTACATGCTTGAGTTTTTTTCC-CGTTTTAGCA
1 CATTTGATACATACTTGAG-TTTTTCCCTCGTTTTAGCA
449125 CCAGTTTCTC
Statistics
Matches: 319, Mismatches: 100, Indels: 69
0.65 0.20 0.14
Matches are distributed among these distances:
33 23 0.07
34 6 0.02
35 30 0.09
36 17 0.05
37 10 0.03
38 35 0.11
39 157 0.49
40 41 0.13
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.44
Consensus pattern (39 bp):
CATTTGATACATACTTGAGTTTTTCCCTCGTTTTAGCAT
Found at i:448835 original size:74 final size:72
Alignment explanation
Indices: 448742--448894 Score: 182
Period size: 72 Copynumber: 2.1 Consensus size: 72
448732 TTTCCCCCTG
* * * ** * *
448742 TTTAGCATCAATTGTTACATGAGTTGTTTCCCTGTTTTAGCATCACTTT-ATACATACTTGAGTT
1 TTTAGCAACAATTGATACATGAG-T-TTCCCCCATTTTAGCATCA-TTTGATACATACATAAGTT
448806 TTTCGCTCGT
63 TTTCGCTCGT
* *
448816 TTTAGCAACATTTGATACATGAGTTTCCCCCATTTTAGTATCATTTGATACATACATAAGTTTTT
1 TTTAGCAACAATTGATACATGAGTTTCCCCCATTTTAGCATCATTTGATACATACATAAGTTTTT
*
448881 CTCTCGT
66 CGCTCGT
448888 TTTAGCA
1 TTTAGCA
448895 TTATTTTACA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
71 3 0.04
72 44 0.65
73 1 0.01
74 20 0.29
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (72 bp):
TTTAGCAACAATTGATACATGAGTTTCCCCCATTTTAGCATCATTTGATACATACATAAGTTTTT
CGCTCGT
Found at i:450853 original size:138 final size:135
Alignment explanation
Indices: 450588--450856 Score: 416
Period size: 138 Copynumber: 2.0 Consensus size: 135
450578 CAAATTTTGT
* *
450588 GTACTTGATATACAGTATTCTATATATTTAGGCTATAAAAAACAACTCTAACTCAGTAGTTCAGT
1 GTACTTGATATACAGTATACTATATATTTAGGCTATAAAAAACAACTCAAACTCAGTAGTTCAGT
*
450653 TTTATTACAAAGCTAGAAAAAAAAATACAGACTCTCTTATTTCATTATCACAACCATAGTCAGTA
66 TTTATTACAAAGCTAG--AAAAAAATACAGACTCTCTGATTTCATTATCACAACCATAGTCAGTA
450718 ATGTTGA
129 ATGTTGA
450725 GTACTTGATATACAGTATACTATATATTTTAGGCTATTAAAAAAAACAACTCAAACTCAGTAGTT
1 GTACTTGATATACAGTATACTATATA-TTTAGGCTA-T--AAAAAACAACTCAAACTCAGTAGTT
* *
450790 CAGTTTTATTATAAAGCTAG-AAAAAATACAGACT-TCCTGATTTTATTATCACAACCATAGTCA
62 CAGTTTTATTACAAAGCTAGAAAAAAATACAGACTCT-CTGATTTCATTATCACAACCATAGTCA
450853 GTAA
126 GTAA
450857 AAGACAAAGA
Statistics
Matches: 122, Mismatches: 5, Indels: 9
0.90 0.04 0.07
Matches are distributed among these distances:
137 26 0.21
138 52 0.43
139 1 0.01
141 43 0.35
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (135 bp):
GTACTTGATATACAGTATACTATATATTTAGGCTATAAAAAACAACTCAAACTCAGTAGTTCAGT
TTTATTACAAAGCTAGAAAAAAATACAGACTCTCTGATTTCATTATCACAACCATAGTCAGTAAT
GTTGA
Found at i:454696 original size:39 final size:39
Alignment explanation
Indices: 454637--454823 Score: 266
Period size: 39 Copynumber: 4.8 Consensus size: 39
454627 AATTTAATAT
* * *
454637 ATACTTGAGTTTTCCCCCCGTTTTTGCATCATTTGATAC
1 ATACTTGAATTTTTCCCCCGTTTTAGCATCATTTGATAC
** *
454676 ATACTTGAATTTTTGTCCCGTTTTAGCATCATTTAATAC
1 ATACTTGAATTTTTCCCCCGTTTTAGCATCATTTGATAC
* * *
454715 ATATTTGAGTTTTTCCCCCGTTTTAGAATCATTTGATAC
1 ATACTTGAATTTTTCCCCCGTTTTAGCATCATTTGATAC
*
454754 ATTCTTGAATTTTTCCCCCGTTTTAGCATCATTTGATAC
1 ATACTTGAATTTTTCCCCCGTTTTAGCATCATTTGATAC
* *
454793 ATACTTGAGTTTTTCCCCTGTTTTAGCATCA
1 ATACTTGAATTTTTCCCCCGTTTTAGCATCA
454824 GTTCCTCCAT
Statistics
Matches: 129, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 129 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (39 bp):
ATACTTGAATTTTTCCCCCGTTTTAGCATCATTTGATAC
Found at i:454835 original size:78 final size:78
Alignment explanation
Indices: 454628--454823 Score: 302
Period size: 78 Copynumber: 2.5 Consensus size: 78
454618 TTTCAGTAAA
* * * * **
454628 ATTTAATATATACTTGAGTTTTCCCCCCGTTTTTGCATCATTTGATACATACTTGAATTTTTGTC
1 ATTTAATACATACTTGAGTTTTTCCCCCGTTTTAGCATCATTTGATACATTCTTGAATTTTTCCC
454693 CCGTTTTAGCATC
66 CCGTTTTAGCATC
* *
454706 ATTTAATACATATTTGAGTTTTTCCCCCGTTTTAGAATCATTTGATACATTCTTGAATTTTTCCC
1 ATTTAATACATACTTGAGTTTTTCCCCCGTTTTAGCATCATTTGATACATTCTTGAATTTTTCCC
454771 CCGTTTTAGCATC
66 CCGTTTTAGCATC
* *
454784 ATTTGATACATACTTGAGTTTTTCCCCTGTTTTAGCATCA
1 ATTTAATACATACTTGAGTTTTTCCCCCGTTTTAGCATCA
454824 GTTCCTCCAT
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 106 1.00
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.46
Consensus pattern (78 bp):
ATTTAATACATACTTGAGTTTTTCCCCCGTTTTAGCATCATTTGATACATTCTTGAATTTTTCCC
CCGTTTTAGCATC
Found at i:456998 original size:2 final size:2
Alignment explanation
Indices: 456991--457054 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
456981 GACCCAATGT
456991 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
457033 TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC
457055 AGCTCCCATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:457740 original size:41 final size:41
Alignment explanation
Indices: 457695--457822 Score: 193
Period size: 41 Copynumber: 3.1 Consensus size: 41
457685 ATCATGATTT
*
457695 CAACATACACATGTAAAAATAAACAATAAAAATTACCATGG
1 CAACATACACATGTAAAGATAAACAATAAAAATTACCATGG
* *
457736 CAACATACACATGTAAAGATAAACAATAAAAATTTCCTTGG
1 CAACATACACATGTAAAGATAAACAATAAAAATTACCATGG
** *
457777 CAACATACACATGTAAAGATAAACAAATGGAATTTACCATGG
1 CAACATACACATGTAAAGATAAAC-AATAAAAATTACCATGG
457819 CAAC
1 CAAC
457823 TTTGTGGCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 62 0.79
42 16 0.21
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (41 bp):
CAACATACACATGTAAAGATAAACAATAAAAATTACCATGG
Found at i:461611 original size:44 final size:44
Alignment explanation
Indices: 461548--461638 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
461538 TACCATATTC
* * *
461548 ATGGACCTTTGTCCTATTTGATATTCTGTTCTTTAATGTCATTG
1 ATGGACCTTTGTCCAATTTGATATTCTGTTATTTAATGTCACTG
461592 ATGGACCTTTGTCCAATTTGATATTCTGTTATTTAATGTCACTG
1 ATGGACCTTTGTCCAATTTGATATTCTGTTATTTAATGTCACTG
461636 ATG
1 ATG
461639 TTGAATATTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.47
Consensus pattern (44 bp):
ATGGACCTTTGTCCAATTTGATATTCTGTTATTTAATGTCACTG
Found at i:461657 original size:57 final size:57
Alignment explanation
Indices: 461588--461705 Score: 209
Period size: 57 Copynumber: 2.1 Consensus size: 57
461578 CTTTAATGTC
*
461588 ATTGATGGACCTTTGTCCAATTTGATATTCTGTTATTTAATGTCACTGATGTTGAAT
1 ATTGATGGACCTTTGTCCAATTTAATATTCTGTTATTTAATGTCACTGATGTTGAAT
* *
461645 ATTGATGGACCTTTGTCCTATTTAATATTCTGTTATTTAATGTCATTGATGTTGAAT
1 ATTGATGGACCTTTGTCCAATTTAATATTCTGTTATTTAATGTCACTGATGTTGAAT
461702 ATTG
1 ATTG
461706 TGAGGACTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (57 bp):
ATTGATGGACCTTTGTCCAATTTAATATTCTGTTATTTAATGTCACTGATGTTGAAT
Found at i:463130 original size:22 final size:22
Alignment explanation
Indices: 463100--463208 Score: 157
Period size: 22 Copynumber: 5.0 Consensus size: 22
463090 TAACTCTATC
*
463100 TCATATTGATCCTATAGACTTG
1 TCATGTTGATCCTATAGACTTG
*
463122 TCATGTTGATCCTATAAACTTG
1 TCATGTTGATCCTATAGACTTG
* * *
463144 TTATGTTGATCCTAAAGATTTG
1 TCATGTTGATCCTATAGACTTG
463166 TCAT-TTGATCCTATAGACTTG
1 TCATGTTGATCCTATAGACTTG
*
463187 TCATGTTGATCCTATATACTTG
1 TCATGTTGATCCTATAGACTTG
463209 CAGGGTTGTC
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
21 19 0.25
22 57 0.75
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (22 bp):
TCATGTTGATCCTATAGACTTG
Found at i:463186 original size:43 final size:44
Alignment explanation
Indices: 463100--463200 Score: 150
Period size: 43 Copynumber: 2.3 Consensus size: 44
463090 TAACTCTATC
* *
463100 TCATATTGATCCTATAGACTTGTCATGTTGATCCTATAAACTTG
1 TCATGTTGATCCTAAAGACTTGTCATGTTGATCCTATAAACTTG
* * *
463144 TTATGTTGATCCTAAAGATTTGTCAT-TTGATCCTATAGACTTG
1 TCATGTTGATCCTAAAGACTTGTCATGTTGATCCTATAAACTTG
463187 TCATGTTGATCCTA
1 TCATGTTGATCCTA
463201 TATACTTGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 29 0.57
44 22 0.43
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (44 bp):
TCATGTTGATCCTAAAGACTTGTCATGTTGATCCTATAAACTTG
Found at i:463416 original size:22 final size:22
Alignment explanation
Indices: 463381--463652 Score: 372
Period size: 22 Copynumber: 12.4 Consensus size: 22
463371 ACAACCCTGT
* *
463381 ACTTGTTATGTTGATCCTATAG
1 ACTTGTCATATTGATCCTATAG
463403 ACTTGTCATATTGATCCTATAG
1 ACTTGTCATATTGATCCTATAG
**
463425 ACTCATCATATTGATCCTATAG
1 ACTTGTCATATTGATCCTATAG
463447 ACTTGTCATATTGATCCTATAG
1 ACTTGTCATATTGATCCTATAG
**
463469 ACTCATCATATTGATCCTATAG
1 ACTTGTCATATTGATCCTATAG
* *
463491 ACTTGTTATGTTGATCCTATAG
1 ACTTGTCATATTGATCCTATAG
*
463513 ACTTGTCATATTAATCCTATAG
1 ACTTGTCATATTGATCCTATAG
463535 ACTTGTCATGA-TGATCCTATAG
1 ACTTGTCAT-ATTGATCCTATAG
463557 ACTTGTCATATTGATCCTATAG
1 ACTTGTCATATTGATCCTATAG
463579 ACTTGTCATGA-TGATCCT-TAAG
1 ACTTGTCAT-ATTGATCCTAT-AG
* *
463601 ACTTGT-ATGTTGATCCTATAT
1 ACTTGTCATATTGATCCTATAG
* *
463622 ACTTGTCCTATTGATCCTGTAG
1 ACTTGTCATATTGATCCTATAG
463644 ACTTGTCAT
1 ACTTGTCAT
463653 GTCTCATGTT
Statistics
Matches: 220, Mismatches: 23, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
21 18 0.08
22 200 0.91
23 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (22 bp):
ACTTGTCATATTGATCCTATAG
Found at i:467077 original size:33 final size:33
Alignment explanation
Indices: 467030--467187 Score: 262
Period size: 33 Copynumber: 4.8 Consensus size: 33
467020 TTTTGACTTG
* *
467030 ATAGATGTTGTGTAATTGTGAATCATTTACTCA
1 ATAGATTTTCTGTAATTGTGAATCATTTACTCA
467063 ATAGATTTTCTGTAATTGTGAATCATTTACTCA
1 ATAGATTTTCTGTAATTGTGAATCATTTACTCA
* *
467096 GTAGATTTTCTGTAATTGTGAGTCATTTACTCA
1 ATAGATTTTCTGTAATTGTGAATCATTTACTCA
467129 ATAGATTTTCTGTAATTGTGAATCATTTACTCA
1 ATAGATTTTCTGTAATTGTGAATCATTTACTCA
* *
467162 GTAGATTTTCTGTAATTGTGAGTCAT
1 ATAGATTTTCTGTAATTGTGAATCAT
467188 ATGTGTGTGC
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 117 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (33 bp):
ATAGATTTTCTGTAATTGTGAATCATTTACTCA
Found at i:467447 original size:2 final size:2
Alignment explanation
Indices: 467440--467492 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
467430 TGTTAGTCTG
467440 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
467482 GA GA GA GA GA G
1 GA GA GA GA GA G
467493 GCCAGTAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:467848 original size:43 final size:43
Alignment explanation
Indices: 467797--468391 Score: 1021
Period size: 43 Copynumber: 13.8 Consensus size: 43
467787 TTAAGGAGAC
* *
467797 TGGATGGTCAACAAACTAACCATCAGATCTACCTTAAGGAGGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
* * *
467840 TGGGTGGTCAACAAACTAACCATCAGATCTACCTTAAGGA-GAC
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATG-T
*
467883 TGGATGGTCAACAAACTAATCATCAGATCTACCTTATGGATGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
* *
467926 TGGAGGGTCTACAAACTAACCATCAGATCTACCTTATGGATGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
467969 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
*
468012 TGGAGGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
468055 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
* *
468098 TGGAGGGTCTACAAACTAACCATCAGATCTACCTTATGGATGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
* *
468141 TGGAGGGTCAACAAACTAACCATCAGATCTACCTTATGGAGGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
*
468184 TGGATGGTCAACAAACTAACCATCAGATCTACCTTAGGGATGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
468227 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
*
468270 TGGAGGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
468313 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
**
468356 TGGCGGGTCAACAAACTAACCATCAGATCTACCTTA
1 TGGATGGTCAACAAACTAACCATCAGATCTACCTTA
468392 AATTTTAAGT
Statistics
Matches: 525, Mismatches: 25, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
42 1 0.00
43 523 1.00
44 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (43 bp):
TGGATGGTCAACAAACTAACCATCAGATCTACCTTATGGATGT
Found at i:468883 original size:21 final size:21
Alignment explanation
Indices: 468857--468943 Score: 122
Period size: 21 Copynumber: 4.2 Consensus size: 21
468847 TTTTTCTAGC
*
468857 AAATATGTCGACATGCAAGAT
1 AAATATGTTGACATGCAAGAT
468878 AAATATGTTGACATGCAAGAT
1 AAATATGTTGACATGCAAGAT
* * *
468899 AATTATGTTAACATGCAACAT
1 AAATATGTTGACATGCAAGAT
*
468920 AATTATGTTGACATGCAAGA-
1 AAATATGTTGACATGCAAGAT
468940 AAAT
1 AAAT
468944 TGGAATCAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
20 3 0.05
21 56 0.95
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (21 bp):
AAATATGTTGACATGCAAGAT
Found at i:469085 original size:42 final size:42
Alignment explanation
Indices: 469033--469207 Score: 158
Period size: 42 Copynumber: 4.2 Consensus size: 42
469023 GTCGACATTA
* *
469033 AACTTATTTATGTTAACATGCAAGATAAATATGCTGACATGC
1 AACTTATTTATGTTGACATGCAAGATAAATATGTTGACATGC
* * * * * **
469075 AACTTATTTATGTCGACATGTAA-CTTATTAATGTCAACATGC
1 AACTTATTTATGTTGACATGCAAGATAAAT-ATGTTGACATGC
* *
469117 AAATCT-TTTATGTTGACATGCGAGATGAAA-ATGTTGACATGC
1 AACT-TATTTATGTTGACATGCAAGAT-AAATATGTTGACATGC
* * * **
469159 AACTTAGTTATGTTTACATGCGAGAGGAATATGTTGACATGC
1 AACTTATTTATGTTGACATGCAAGATAAATATGTTGACATGC
469201 AACTTAT
1 AACTTAT
469208 AAGTTGTAGG
Statistics
Matches: 103, Mismatches: 24, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
41 6 0.06
42 94 0.91
43 2 0.02
44 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (42 bp):
AACTTATTTATGTTGACATGCAAGATAAATATGTTGACATGC
Found at i:469171 original size:21 final size:20
Alignment explanation
Indices: 469019--469207 Score: 87
Period size: 21 Copynumber: 9.1 Consensus size: 20
469009 TGGTACCTTT
* **
469019 TTATGTCGACATTAAACTTA
1 TTATGTTGACATGCAACTTA
* * *
469039 TTTATGTTAACATGCAAGATAA
1 -TTATGTTGACATGCAA-CTTA
* *
469061 ATATGCTGACATGCAACTTA
1 TTATGTTGACATGCAACTTA
* *
469081 TTTATGTCGACATGTAACTTA
1 -TTATGTTGACATGCAACTTA
**
469102 TTAATGTCAACATGCAAATCTT-
1 TT-ATGTTGACATGC-AA-CTTA
*
469124 TTATGTTGACATGCGAGA-TGA
1 TTATGTTGACATGC-A-ACTTA
**
469145 AAATGTTGACATGCAACTTA
1 TTATGTTGACATGCAACTTA
* **
469165 GTTATGTTTACATGCGAGA-GGA
1 -TTATGTTGACATGC-A-ACTTA
*
469187 ATATGTTGACATGCAACTTA
1 TTATGTTGACATGCAACTTA
469207 T
1 T
469208 AAGTTGTAGG
Statistics
Matches: 122, Mismatches: 34, Indels: 25
0.67 0.19 0.14
Matches are distributed among these distances:
19 2 0.02
20 10 0.08
21 97 0.80
22 9 0.07
23 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (20 bp):
TTATGTTGACATGCAACTTA
Found at i:469245 original size:21 final size:21
Alignment explanation
Indices: 469206--469371 Score: 170
Period size: 21 Copynumber: 7.9 Consensus size: 21
469196 CATGCAACTT
* * *
469206 ATAAGTTGTAGGTCAACATAA
1 ATAAGTTGCATGTCGACATAA
**
469227 CGAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCGACATAA
* * *
469248 ATATGTTGCATGTCAACATAT
1 ATAAGTTGCATGTCGACATAA
* ** **
469269 TTATCTTGCATGTTAACATAA
1 ATAAGTTGCATGTCGACATAA
*
469290 CTAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCGACATAA
469311 ATAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCGACATAA
* **
469332 AGAAGTTGCATGTTAACATAA
1 ATAAGTTGCATGTCGACATAA
*
469353 ATAAGTTGCATGTTGACAT
1 ATAAGTTGCATGTCGACAT
469372 CAGTAGGTAG
Statistics
Matches: 120, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 120 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (21 bp):
ATAAGTTGCATGTCGACATAA
Found at i:469296 original size:63 final size:63
Alignment explanation
Indices: 469220--469371 Score: 214
Period size: 63 Copynumber: 2.4 Consensus size: 63
469210 GTTGTAGGTC
* * *** *
469220 AACATAACGAAGTTGCATGTCGACATAAATATGTTGCATGTCAACATATTTATCTTGCATGTT
1 AACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCAACATAAAGAACTTGCATGTT
* *
469283 AACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCGACATAAAGAAGTTGCATGTT
1 AACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCAACATAAAGAACTTGCATGTT
* *
469346 AACATAAATAAGTTGCATGTTGACAT
1 AACATAACTAAGTTGCATGTCGACAT
469372 CAGTAGGTAG
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 79 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (63 bp):
AACATAACTAAGTTGCATGTCGACATAAATAAGTTGCATGTCAACATAAAGAACTTGCATGTT
Found at i:469474 original size:21 final size:21
Alignment explanation
Indices: 469449--469534 Score: 82
Period size: 21 Copynumber: 4.1 Consensus size: 21
469439 TGTTTGATTG
*
469449 TAGTTTTCTTGCATGTCAACA
1 TAGTTATCTTGCATGTCAACA
* **
469470 TAGTTATGTTGCATGTTGACA
1 TAGTTATCTTGCATGTCAACA
** *
469491 TAACTATCTTGCATATCAACA
1 TAGTTATCTTGCATGTCAACA
* * *
469512 TATTTATCTTGAATGTCGACA
1 TAGTTATCTTGCATGTCAACA
469533 TA
1 TA
469535 ATTAATTGAA
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (21 bp):
TAGTTATCTTGCATGTCAACA
Found at i:469533 original size:42 final size:42
Alignment explanation
Indices: 469455--469535 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
469445 ATTGTAGTTT
* * * *
469455 TCTTGCATGTCAACATAGTTATGTTGCATGTTGACATAACTA
1 TCTTGCATATCAACATAGTTATCTTGAATGTCGACATAACTA
*
469497 TCTTGCATATCAACATATTTATCTTGAATGTCGACATAA
1 TCTTGCATATCAACATAGTTATCTTGAATGTCGACATAA
469536 TTAATTGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (42 bp):
TCTTGCATATCAACATAGTTATCTTGAATGTCGACATAACTA
Found at i:470098 original size:2 final size:2
Alignment explanation
Indices: 470091--470119 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
470081 AGGAACCGGG
470091 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
470120 GGGAAGGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:476376 original size:42 final size:43
Alignment explanation
Indices: 476178--476514 Score: 527
Period size: 43 Copynumber: 7.9 Consensus size: 43
476168 GTTTGAAACG
*
476178 TTAAGGAGGCTGAATGGTCAACAAACTAACCATCAGATCTACC
1 TTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATCTACC
* *
476221 TTAAGGAGACTGGATGGTCAACAGACTAACCATCAGATCTACC
1 TTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATCTACC
* *
476264 TTAAGGAGACTGGATGGTCAACAGACTAACCATCAGATCTACC
1 TTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATCTACC
* *
476307 TTAAGGAGACTGGATGGTCAACAAACTAACCATTAGATCTACC
1 TTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATCTACC
* * *
476350 TTAA-GAGGTTGGATGGTCAACAAACTAACCATTATATCTACC
1 TTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATCTACC
* *
476392 TTAA-GAGGTTGGATGGTCAACAGACTAACCATCAGATCTACC
1 TTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATCTACC
* *
476434 TTAA-GAGGTTGGATGGTCAACAGACTAACCATCAGATCTACC
1 TTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATCTACC
476476 TTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATC
1 TTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATC
476515 AACAAACTAA
Statistics
Matches: 280, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
42 120 0.43
43 160 0.57
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (43 bp):
TTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATCTACC
Found at i:476518 original size:20 final size:20
Alignment explanation
Indices: 476493--476534 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
476483 GGCTGGATGG
476493 TCAACAAACTAACCATCAGA
1 TCAACAAACTAACCATCAGA
476513 TCAACAAACTAACCATCAGA
1 TCAACAAACTAACCATCAGA
476533 TC
1 TC
476535 TACCTTAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.31, G:0.05, T:0.17
Consensus pattern (20 bp):
TCAACAAACTAACCATCAGA
Found at i:476549 original size:63 final size:63
Alignment explanation
Indices: 476450--476577 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
476440 GGTTGGATGG
*
476450 TCAACAGACTAACCATCAGATCTACCTTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGA
1 TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGA
476513 TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGA
1 TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGA
476576 TC
1 TC
476578 TACCTTAAGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (63 bp):
TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGA
Found at i:476574 original size:43 final size:43
Alignment explanation
Indices: 476513--476745 Score: 358
Period size: 43 Copynumber: 5.4 Consensus size: 43
476503 AACCATCAGA
476513 TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGG
1 TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGG
*
476556 TCAACAAACTAACCATCAGATCTACCTTAAGGAGACTGGATGG
1 TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGG
* *
476599 TCAACAAACTAACCATCAGATCTACCTTATGGAGACTGGATGG
1 TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGG
* * **
476642 TCAACAAATTAACCATTAGATCTTTCTTAAGGAGGCTGGATGG
1 TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGG
** * *
476685 TCAACAAACTAACCATTTGATCTCCCTTAAGGAGGCTAGATGG
1 TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGG
*
476728 TCAACAAACTAACAATCA
1 TCAACAAACTAACCATCA
476746 CTGGATGGTC
Statistics
Matches: 174, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 174 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (43 bp):
TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGG
Found at i:476595 original size:106 final size:105
Alignment explanation
Indices: 476408--476620 Score: 381
Period size: 106 Copynumber: 2.0 Consensus size: 105
476398 GGTTGGATGG
* * *
476408 TCAACAGACTAACCATCAGATCTACCTTAAGAGGTTGGATGGTCAACAGACTAACCATCAGATCT
1 TCAACAAACTAACCATCAGATCTACCTTAAGAGGCTGGATGGTCAACAAACTAACCATCAGATCT
*
476473 ACCTTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGA
66 ACCTTAAGGAGACTGGATGGTCAACAAACTAACCATCAGA
476513 TCAACAAACTAACCATCAGATCTACCTTAAGGAGGCTGGATGGTCAACAAACTAACCATCAGATC
1 TCAACAAACTAACCATCAGATCTACCTTAA-GAGGCTGGATGGTCAACAAACTAACCATCAGATC
476578 TACCTTAAGGAGACTGGATGGTCAACAAACTAACCATCAGA
65 TACCTTAAGGAGACTGGATGGTCAACAAACTAACCATCAGA
476619 TC
1 TC
476621 TACCTTATGG
Statistics
Matches: 103, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 29 0.28
106 74 0.72
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (105 bp):
TCAACAAACTAACCATCAGATCTACCTTAAGAGGCTGGATGGTCAACAAACTAACCATCAGATCT
ACCTTAAGGAGACTGGATGGTCAACAAACTAACCATCAGA
Found at i:476783 original size:155 final size:155
Alignment explanation
Indices: 476590--476900 Score: 437
Period size: 155 Copynumber: 2.0 Consensus size: 155
476580 CCTTAAGGAG
476590 ACTGGATGGTCAACAAACTAACCATCAGATCTACCTTA-TGGAGACTGGATGGTCAACAAATTAA
1 ACTGGATGGTCAACAAACTAACCATCAGATCTACCTTATTGG-GACTGGATGGTCAACAAATTAA
* * * * ** *
476654 CCATTAGATCTTTCTTAAGGAGGCTG-GATGGTCAACAAACTAACCATTTGATCTCCCTTAAGGA
65 CCATCAGATCTTCCTTAAGGAGACTGTG-TGATCAACAAACTAACCATCAGATCTACCTTAAGGA
* *
476718 GGCTAGATGGTCAACAAACTAACAATC
129 GACTAGATGGTCAACAAACCAACAATC
** **
476745 ACTGGATGGTCAACAAACTAACCATCAGATCTACCTTATTGGGGTTGGATGGTTTACAAATTAAC
1 ACTGGATGGTCAACAAACTAACCATCAGATCTACCTTATTGGGACTGGATGGTCAACAAATTAAC
* *
476810 CATCAGATCTTCCTTAAGGAGACTGTGTGATTAACAAATTAACCATCAGATCTACCTTAAGGAGA
66 CATCAGATCTTCCTTAAGGAGACTGTGTGATCAACAAACTAACCATCAGATCTACCTTAAGGAGA
* *
476875 CTGGATGGTCAACAAACCAACCATC
131 CTAGATGGTCAACAAACCAACAATC
476900 A
1 A
476901 AATCTACCTT
Statistics
Matches: 137, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
155 133 0.97
156 4 0.03
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (155 bp):
ACTGGATGGTCAACAAACTAACCATCAGATCTACCTTATTGGGACTGGATGGTCAACAAATTAAC
CATCAGATCTTCCTTAAGGAGACTGTGTGATCAACAAACTAACCATCAGATCTACCTTAAGGAGA
CTAGATGGTCAACAAACCAACAATC
Found at i:476810 original size:43 final size:43
Alignment explanation
Indices: 476746--477072 Score: 356
Period size: 43 Copynumber: 7.6 Consensus size: 43
476736 CTAACAATCA
* * *
476746 CTGGATGGTCAACAAACTAACCATCAGATCTACCTTATTGG-GG
1 CTGGATGGTTAACAAATTAACCATCAGATCTACCTTA-AGGAGG
* * * *
476789 TTGGATGGTTTACAAATTAACCATCAGATCTTCCTTAAGGAGA
1 CTGGATGGTTAACAAATTAACCATCAGATCTACCTTAAGGAGG
* *
476832 CTGTG-TGATTAACAAATTAACCATCAGATCTACCTTAAGGAGA
1 CTG-GATGGTTAACAAATTAACCATCAGATCTACCTTAAGGAGG
* ** * * *
476875 CTGGATGGTCAACAAACCAACCATCAAATCTACCTTATGGATG
1 CTGGATGGTTAACAAATTAACCATCAGATCTACCTTAAGGAGG
* *
476918 TTGGATGGTTAACAAATTAACCATCAGATCTTCCTTAAGGAGG
1 CTGGATGGTTAACAAATTAACCATCAGATCTACCTTAAGGAGG
* * * *
476961 CTGTG-TGATTAACAAATTAACCACCAGATCTACTTTAAGGATG
1 CTG-GATGGTTAACAAATTAACCATCAGATCTACCTTAAGGAGG
* * *
477004 CTGGATGGTCAACAAACTAACCATCAGATCTACCTTAAGGAGA
1 CTGGATGGTTAACAAATTAACCATCAGATCTACCTTAAGGAGG
* *
477047 CTGTG-TGGTCAACAAACTAACCATCA
1 CTG-GATGGTTAACAAATTAACCATCA
477073 TATTTATCCA
Statistics
Matches: 238, Mismatches: 40, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
42 4 0.02
43 231 0.97
44 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (43 bp):
CTGGATGGTTAACAAATTAACCATCAGATCTACCTTAAGGAGG
Found at i:476975 original size:129 final size:130
Alignment explanation
Indices: 476745--477040 Score: 499
Period size: 129 Copynumber: 2.3 Consensus size: 130
476735 ACTAACAATC
*
476745 ACTGGATGGTCAACAAACTAACCATCAGATCTACCTTATTGGGGTTGGATGGTTTACAAATTAAC
1 ACTGGATGGTCAACAAACTAACCATCAGATCTACCTTATTGGGGTTGGATGGTTAACAAATTAAC
*
476810 CATCAGATCTTCCTTAAGGAGACTGTGTGATTAACAAATTAACCATCAGATCTACCTTAAGGA-G
66 CATCAGATCTTCCTTAAGGAGACTGTGTGATTAACAAATTAACCACCAGATCTACCTTAAGGATG
* * *
476874 ACTGGATGGTCAACAAACCAACCATCAAATCTACCTTA-TGGATGTTGGATGGTTAACAAATTAA
1 ACTGGATGGTCAACAAACTAACCATCAGATCTACCTTATTGG-GGTTGGATGGTTAACAAATTAA
* *
476938 CCATCAGATCTTCCTTAAGGAGGCTGTGTGATTAACAAATTAACCACCAGATCTACTTTAAGGAT
65 CCATCAGATCTTCCTTAAGGAGACTGTGTGATTAACAAATTAACCACCAGATCTACCTTAAGGAT
477003 G
130 G
477004 -CTGGATGGTCAACAAACTAACCATCAGATCTACCTTA
1 ACTGGATGGTCAACAAACTAACCATCAGATCTACCTTA
477041 AGGAGACTGT
Statistics
Matches: 156, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
128 3 0.02
129 152 0.97
130 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (130 bp):
ACTGGATGGTCAACAAACTAACCATCAGATCTACCTTATTGGGGTTGGATGGTTAACAAATTAAC
CATCAGATCTTCCTTAAGGAGACTGTGTGATTAACAAATTAACCACCAGATCTACCTTAAGGATG
Found at i:481600 original size:20 final size:21
Alignment explanation
Indices: 481562--481600 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
481552 GACGTCATTT
481562 ACTTTATTCATTGATTAATTC
1 ACTTTATTCATTGATTAATTC
481583 ACTTTATTCATT-ATTAAT
1 ACTTTATTCATTGATTAAT
481601 AAATTATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.31, C:0.13, G:0.03, T:0.54
Consensus pattern (21 bp):
ACTTTATTCATTGATTAATTC
Found at i:484559 original size:59 final size:58
Alignment explanation
Indices: 484480--485522 Score: 316
Period size: 59 Copynumber: 17.5 Consensus size: 58
484470 TAAATGATAA
* * * *
484480 AAGTACAATGTCTATAATAAACGTTCAATGCATATAATAAACGTACCATGTATATAATG
1 AAGTACAATGTATAAAATAAACGTACAATGCATATAATAAA-GTACAATGTATATAATG
*
484539 AAGTACAATGTATAAAATAAATGTACAATGCATATAATAAAGTACAATGTATATAATG
1 AAGTACAATGTATAAAATAAACGTACAATGCATATAATAAAGTACAATGTATATAATG
* ** * * * * * *
484597 AAAATACAACATATACAATAAATGTACAATACTAATGTATATAATAAAAGTACATTGTCTAAAAT
1 -AAGTACAATGTATAAAAT-AA---AC-GTAC-AATGCATATAAT-AAAGTACAATGTATATAAT
*
484662 AA
58 -G
* ** * * * * *
484664 AAGTAAAATGTATATTAT-GA-GATACAATGTATATAATAGAGTACAATGTCTATAATAA
1 AAGTACAATGTATAAAATAAACG-TACAATGCATATAATAAAGTACAATGTATATAAT-G
* * * * ** * * *
484722 AAGTACCATGTCTATAATAAAAG-AGCAATGGTTATAATAAAAGTACAATGTCTATAGTAA
1 AAGTACAATGTATAAAATAAACGTA-CAATGCATATAAT-AAAGTACAATGTATATAAT-G
* * ** * ** *
484782 AAGTACAATTTCTATTATAAA-GTACAATGTATATTTTAAAGTACAATGTATA-AATTA
1 AAGTACAATGTATAAAATAAACGTACAATGCATATAATAAAGTACAATGTATATAA-TG
** * * * *
484839 AATGTACAATGTATTTAATAGAA-GTACAATGTATATGATAAAAGTACAATGTATGTAATAA
1 AA-GTACAATGTATAAAATA-AACGTACAATGCATATAAT-AAAGTACAATGTATATAAT-G
** * *
484900 AAGTACAATGTATGTAATAAA-GTACAATGTATATAATAAAAGTATAATGTGCA-ATAA--
1 AAGTACAATGTATAAAATAAACGTACAATGCATATAAT-AAAGTACAATGT--ATATAATG
* * * * * * *
484957 AAGTTCATTGTCTATAATAAAAGTACAATGCATAAAATAAAAGTACAATGTATATAATAA
1 AAGTACAATGTATAAAATAAACGTACAATGCATATAAT-AAAGTACAATGTATATAAT-G
* * * * * * * * * * * *
485017 AAG-AGCAGTTTTTATAATAAAAGTACACTGTC-TAGAATAAAGGTACTATATTTATAGTT
1 AAGTA-CAATGTATAAAATAAACGTACAATG-CATATAATAAA-GTACAATGTATATAATG
* ** * * *
485076 ATAGTAAAATGTATATGATAAA-GTATAATGTATATAATAAAAGTACAATGTATATAATAA
1 A-AGTACAATGTATAAAATAAACGTACAATGCATATAAT-AAAGTACAATGTATATAAT-G
* ** * * * * ** * *
485136 AAGTACAATATATGTATTAAAAGTA-AAT-CTTTTATAATAAAAATACTCTGTATGTAATAA
1 AAGTACAATGTATAAAATAAACGTACAATGC--ATATAAT-AAAGTACAATGTATATAAT-G
* * * * ** * *
485196 AAGTACAATGTTTATAATAAAAGTACAATGTATATGGTAAAATACAATGTTTTGATAA--
1 AAGTACAATGTATAAAATAAACGTACAATGCATATAATAAAGTACAATG-TAT-ATAATG
* * * * * * * * *
485254 AAGTACAACGTATATAAGAAA-GTACAAAGTATTTAATTTAAGTACAATGTATTTAATTT
1 AAGTACAATGTATAAAATAAACGTACAATGCATATAA-TAAAGTACAATGTATATAA-TG
* * * * * * * *
485313 AAGTACAATGCATATAATAAA-GTACAATGTATATAATAATAAAAGTACACTTTCTAGAATAA
1 AAGTACAATGTATAAAATAAACGTACAATG--CAT-ATAAT-AAAGTACAATGTATATAAT-G
* * ** * * *
485375 AATTACAATGTATATAA-AAA-GTA-AATATATATAACAAAAATGAACAATGTATATAATA
1 AAGTACAATGTATAAAATAAACGTACAATGCATAT-A-ATAAA-GTACAATGTATATAATG
* * ** * * * *
485433 AAGTACAATATCTAAAATAAAAATTCAATGTATATAATCAAAGTTA-AATGAATATAATTA
1 AAGTACAATGTATAAAATAAACGTACAATGCATATAAT-AAAG-TACAATGTATATAA-TG
*
485493 AAGTACAATGCATAAAATTAAA-GTACAATG
1 AAGTACAATGTATAAAA-TAAACGTACAATG
485523 TATTATTACA
Statistics
Matches: 764, Mismatches: 158, Indels: 123
0.73 0.15 0.12
Matches are distributed among these distances:
56 4 0.01
57 40 0.05
58 152 0.20
59 236 0.31
60 221 0.29
61 38 0.05
62 30 0.04
63 1 0.00
64 3 0.00
65 11 0.01
66 28 0.04
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (58 bp):
AAGTACAATGTATAAAATAAACGTACAATGCATATAATAAAGTACAATGTATATAATG
Found at i:484808 original size:118 final size:116
Alignment explanation
Indices: 484420--485525 Score: 595
Period size: 118 Copynumber: 9.3 Consensus size: 116
484410 GAAAGTCACT
* * * * * * *
484420 AAGTACAATGTATATGATAAAAGAAAAATGTCTGTAATAAAATTTCAATGTA-AATGATAAAAGT
1 AAGTACAATGTATATAAT-AAAGTACAATGTATATAAT-AAAGTACAATGTATAA--ATAAAAGT
* * * ** * * *
484484 ACAATGTCTATAATAAACGTTCAATGCATATAATAAACGTACCATGTATATAAT-G
62 ACCATGTCTATAATAAAAG-ACAATGGTTATAATAAAAGTACAATGTATATAATAA
* *
484539 AAGTACAATGTATAAAATAAATGTACAATGCATATAATAAAGTACAATGTATATAATGAAAA-TA
1 AAGTACAATGTATATAATAAA-GTACAATGTATATAATAAAGTACAATGTATA-AAT-AAAAGTA
* * * * * * *
484603 CAACATATACAATAAATGTACAATACTAAT-GTATATAATAAAAGTACATTGTCTAAAATAA
63 C--CATGT-CTAT-AA--TAAAAGAC-AATGGT-TATAATAAAAGTACAATGTATATAATAA
* * * * *
484664 AAGTAAAATGTATATTAT-GAGATACAATGTATATAATAGAGTACAATGTCTATAATAAAAGTAC
1 AAGTACAATGTATATAATAAAG-TACAATGTATATAATAAAGTACAATGTATA-AATAAAAGTAC
* *
484728 CATGTCTATAATAAAAGAGCAATGGTTATAATAAAAGTACAATGTCTATAGTAA
64 CATGTCTATAATAAAAGA-CAATGGTTATAATAAAAGTACAATGTATATAATAA
* * * ** * *
484782 AAGTACAATTTCTATTATAAAGTACAATGTATATTTTAAAGTACAATGTATAAATTAAATGTACA
1 AAGTACAATGTATATAATAAAGTACAATGTATATAATAAAGTACAATGTATAAA-TAAAAGTACC
* * * * *
484847 ATGTATTTAATAGAAGTACAAT-GTATATGATAAAAGTACAATGTATGTAATAA
65 ATGTCTATAATAAAAG-ACAATGGT-TATAATAAAAGTACAATGTATATAATAA
* * ** *
484900 AAGTACAATGTATGTAATAAAGTACAATGTATATAATAAAAGTATAATGT-GCAATAAAAGT-TC
1 AAGTACAATGTATATAATAAAGTACAATGTATATAAT-AAAGTACAATGTATAAATAAAAGTACC
** *
484963 ATTGTCTATAATAAAAGTACAATGCATAAAATAAAAGTACAATGTATATAATAA
65 A-TGTCTATAATAAAAG-ACAATGGTTATAATAAAAGTACAATGTATATAATAA
* * * * * * * * * *
485017 AAG-AGCAGTTTTTATAATAAAAGTACACTGTCTAGAATAAAGGTACTATATTTAT-AGTTATAG
1 AAGTA-CAATGTATATAAT-AAAGTACAATGTATATAATAAA-GTAC-A-ATGTATAAATAAAAG
** * * *
485080 TAAAATGTATATGAT-AAAGTATAAT-GTATATAATAAAAGTACAATGTATATAATAA
61 TACCATGTCTATAATAAAAG-ACAATGGT-TATAATAAAAGTACAATGTATATAATAA
* * * * * * ** *
485136 AAGTACAATATATGTATTAAAAGTA-AATCTTTTATAATAAAAATACTCTGTATGTAATAAAAGT
1 AAGTACAATGTATATAAT-AAAGTACAAT-GTATATAAT-AAAGTACAATGTAT-AAATAAAAGT
* * ** * *
485200 ACAATGTTTATAATAAAAGTACAAT-GTATATGGTAAAA-TACAATGT-TTTGATAA
62 ACCATGTCTATAATAAAAG-ACAATGGT-TATAATAAAAGTACAATGTATATAATAA
* * * * * * **
485254 AAGTACAACGTATATAAGAAAGTACAAAGTATTTAATTTAAGTACAATGTATTTAATTTAAGTAC
1 AAGTACAATGTATATAATAAAGTACAATGTATATAA-TAAAGTACAATGTA-TAAATAAAAGTAC
* * * * * *
485319 AATG-CATATAAT-AAAGTACAATGTATATAATAATAAAAGTACACTTTCTAGAATAA
64 CATGTC-TATAATAAAAG-ACAATG-GT-T-ATAATAAAAGTACAATGTATATAATAA
* * * *
485375 AATTACAATGTATATAA-AAAGTA-AATATATATAACAAAAATGAACAATGTATATAAT-AAAGT
1 AAGTACAATGTATATAATAAAGTACAATGTATAT-A-ATAAA-GTACAATGTATA-AATAAAAGT
* * * * * *
485437 ACAATATCTAAAATAAAA-ATTCAAT-GTATATAATCAAAGTTA-AATGAATATAATTA
62 ACCATGTCTATAATAAAAGA--CAATGGT-TATAATAAAAG-TACAATGTATATAATAA
* *
485493 AAGTACAATGCATAAAATTAAAGTACAATGTAT
1 AAGTACAATGTATATAA-TAAAGTACAATGTAT
485526 TATTACAAGA
Statistics
Matches: 760, Mismatches: 168, Indels: 116
0.73 0.16 0.11
Matches are distributed among these distances:
116 12 0.02
117 112 0.15
118 253 0.33
119 157 0.21
120 83 0.11
121 54 0.07
122 6 0.01
123 6 0.01
124 62 0.08
125 15 0.02
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (116 bp):
AAGTACAATGTATATAATAAAGTACAATGTATATAATAAAGTACAATGTATAAATAAAAGTACCA
TGTCTATAATAAAAGACAATGGTTATAATAAAAGTACAATGTATATAATAA
Found at i:485151 original size:24 final size:20
Alignment explanation
Indices: 484420--485525 Score: 849
Period size: 20 Copynumber: 55.6 Consensus size: 20
484410 GAAAGTCACT
*
484420 AAGTACAATGTATATGATAA
1 AAGTACAATGTATATAATAA
* * * *
484440 AAGAAAAATGTCTGTAATAA
1 AAGTACAATGTATATAATAA
* * * *
484460 AATTTCAATGTAAATGATAA
1 AAGTACAATGTATATAATAA
*
484480 AAGTACAATGTCTATAATAA
1 AAGTACAATGTATATAATAA
* * *
484500 ACGTTCAATGCATATAATAA
1 AAGTACAATGTATATAATAA
* * *
484520 ACGTACCATGTATATAAT-G
1 AAGTACAATGTATATAATAA
*
484539 AAGTACAATGTATAAAATAA
1 AAGTACAATGTATATAATAA
* *
484559 ATGTACAATGCATATAAT-A
1 AAGTACAATGTATATAATAA
484578 AAGTACAATGTATATAATGAA
1 AAGTACAATGTATATAAT-AA
** *
484599 AA-TACAACATATACAATAAA
1 AAGTACAATGTATATAAT-AA
*
484619 TGTACAATACTAATGTATATAATAA
1 ---A-AGTAC-AATGTATATAATAA
* * *
484644 AAGTACATTGTCTAAAATAA
1 AAGTACAATGTATATAATAA
* * *
484664 AAGTAAAATGTATATTATGA
1 AAGTACAATGTATATAATAA
*
484684 GA-TACAATGTATATAAT-A
1 AAGTACAATGTATATAATAA
* *
484702 GAGTACAATGTCTATAATAA
1 AAGTACAATGTATATAATAA
* *
484722 AAGTACCATGTCTATAATAA
1 AAGTACAATGTATATAATAA
484742 AAG-AGCAATGGT-TATAATAA
1 AAGTA-CAAT-GTATATAATAA
* *
484762 AAGTACAATGTCTATAGTAA
1 AAGTACAATGTATATAATAA
* * *
484782 AAGTACAATTTCTATTAT-A
1 AAGTACAATGTATATAATAA
* *
484801 AAGTACAATGTATAT-TTTA
1 AAGTACAATGTATATAATAA
484820 AAGTACAATGTATA-AATTAA
1 AAGTACAATGTATATAA-TAA
* * *
484840 ATGTACAATGTATTTAATAG
1 AAGTACAATGTATATAATAA
*
484860 AAGTACAATGTATATGATAA
1 AAGTACAATGTATATAATAA
*
484880 AAGTACAATGTATGTAATAA
1 AAGTACAATGTATATAATAA
*
484900 AAGTACAATGTATGTAAT-A
1 AAGTACAATGTATATAATAA
484919 AAGTACAATGTATATAATAA
1 AAGTACAATGTATATAATAA
* **
484939 AAGTATAATG--TGCAATAA
1 AAGTACAATGTATATAATAA
* * *
484957 AAGTTCATTGTCTATAATAA
1 AAGTACAATGTATATAATAA
* *
484977 AAGTACAATGCATAAAATAA
1 AAGTACAATGTATATAATAA
484997 AAGTACAATGTATATAATAA
1 AAGTACAATGTATATAATAA
* * *
485017 AAG-AGCAGTTTTTATAATAA
1 AAGTA-CAATGTATATAATAA
* * *
485037 AAGTACACTGTCTAGAATAA
1 AAGTACAATGTATATAATAA
* * * * * *
485057 AGGTACTATATTTATAGTTA
1 AAGTACAATGTATATAATAA
* * *
485077 TAGTAAAATGTATATGAT-A
1 AAGTACAATGTATATAATAA
*
485096 AAGTATAATGTATATAATAA
1 AAGTACAATGTATATAATAA
485116 AAGTACAATGTATATAATAA
1 AAGTACAATGTATATAATAA
* * *
485136 AAGTACAATATATGTATTAA
1 AAGTACAATGTATATAATAA
* *
485156 AAGTA-AATCTTTTATAATAA
1 AAGTACAAT-GTATATAATAA
* ** *
485176 AAATACTCTGTATGTAATAA
1 AAGTACAATGTATATAATAA
*
485196 AAGTACAATGTTTATAATAA
1 AAGTACAATGTATATAATAA
**
485216 AAGTACAATGTATATGGTAA
1 AAGTACAATGTATATAATAA
* *
485236 AA-TACAATGT-TTTGATAA
1 AAGTACAATGTATATAATAA
* *
485254 AAGTACAACGTATATAA-GA
1 AAGTACAATGTATATAATAA
* * **
485273 AAGTACAAAGTATTTAATTT
1 AAGTACAATGTATATAATAA
* **
485293 AAGTACAATGTATTTAATTT
1 AAGTACAATGTATATAATAA
*
485313 AAGTACAATGCATATAAT-A
1 AAGTACAATGTATATAATAA
485332 AAGTACAATGTATATAATAATAA
1 AAGTACAATG--TAT-ATAATAA
* * * *
485355 AAGTACACTTTCTAGAATAA
1 AAGTACAATGTATATAATAA
*
485375 AATTACAATGTATAT-A-AA
1 AAGTACAATGTATATAATAA
* *
485393 AAGTA-AATATATATAACAAA
1 AAGTACAATGTATATAA-TAA
*
485413 AATGAACAATGTATATAAT-A
1 AA-GTACAATGTATATAATAA
* * *
485433 AAGTACAATATCTAAAATAA
1 AAGTACAATGTATATAATAA
* * *
485453 AAATTCAATGTATATAATCA
1 AAGTACAATGTATATAATAA
* *
485473 AAGTTA-AATGAATATAATTA
1 AAG-TACAATGTATATAATAA
* * *
485493 AAGTACAATGCATAAAATTA
1 AAGTACAATGTATATAATAA
485513 AAGTACAATGTAT
1 AAGTACAATGTAT
485526 TATTACAAGA
Statistics
Matches: 857, Mismatches: 187, Indels: 84
0.76 0.17 0.07
Matches are distributed among these distances:
17 8 0.01
18 32 0.04
19 185 0.22
20 570 0.67
21 21 0.02
22 16 0.02
23 10 0.01
24 1 0.00
25 5 0.01
26 9 0.01
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (20 bp):
AAGTACAATGTATATAATAA
Found at i:485675 original size:29 final size:29
Alignment explanation
Indices: 485632--487085 Score: 2287
Period size: 29 Copynumber: 50.1 Consensus size: 29
485622 ATATTGAAAT
* * *
485632 AAAACCCATCCCTATTAACTTAGGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
* *
485661 GAAACCAATCCCTATTAACTTATATATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
485690 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
**
485719 AAAACTGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
** *
485748 AAAACTGATCCCTATTAACTTATATATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
**
485777 AAAACTGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
** *
485806 AAAACTGATCCCTATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
*
485835 AAAACCAATCCCTATTAACTTATGTATGC
1 AAAACCAATCCCTATTAACTTATGTATAC
* * *
485864 AAAACCAGTCCCAATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
** *
485893 AAAACTGATCCCTATTAACTTATATATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
*
485922 AAAACCAATCCCTATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
** *
485951 AAAACTGATCCCTATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
*
485980 AAAACCAGTCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
**
486009 AAAACTGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
* *
486038 AAAACCAGTCCCTATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
**
486067 AAAACTGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486096 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
*
486125 AAAACCAATCCCTATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
**
486154 AAAACTGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486183 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486212 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486241 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486270 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486299 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486328 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486357 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486386 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486415 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486444 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486473 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486502 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486531 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486560 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
**
486589 AAAACTGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
** *
486618 AAAACTGATCCCTATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
**
486647 AAAACTGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
*
486676 AAAACCGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486705 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
*
486734 AAAACCAATCCCTATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
**
486763 AAAACTGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
*
486792 AAAACCGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
486821 AAAACCAATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
*
486850 AAAACCAATCCCTATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
** *
486879 AAAACTGATCCCTATTAACTTATATATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
*
486908 AAAACCAATCCCTATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
**
486937 AAAACTGATCCCTATTAACTTATGTATAC
1 AAAACCAATCCCTATTAACTTATGTATAC
*
486966 AAAACCAATCCCTATTAACTTATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
* * *
486995 AAAACCTATCCCTATTAACTTATGAACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
* ** *
487024 AAAACCAGTCATTATTAACTTATGTAGAC
1 AAAACCAATCCCTATTAACTTATGTATAC
** * ** *
487053 AAAACTGATCCCTTTTAACCAATGTACAC
1 AAAACCAATCCCTATTAACTTATGTATAC
487082 AAAA
1 AAAA
487086 AGCCTTAATT
Statistics
Matches: 1326, Mismatches: 99, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 1326 1.00
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAACCAATCCCTATTAACTTATGTATAC
Found at i:488680 original size:2 final size:2
Alignment explanation
Indices: 488673--488708 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
488663 TTTTTAGCGG
488673 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
488709 GCCGTCATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:489260 original size:43 final size:43
Alignment explanation
Indices: 489210--489295 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
489200 TAGACGGCTC
*
489210 GGCTTCGCCTCGCCATCTATGAGATTGATCAACCCAATATATT
1 GGCTTCGCCTCGCCATCTATGAGATTGATCAAACCAATATATT
*
489253 GGCTTCGCCTGGCCATCTATGAGATTGATCAAACCAATATATT
1 GGCTTCGCCTCGCCATCTATGAGATTGATCAAACCAATATATT
489296 TCCGTAGTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (43 bp):
GGCTTCGCCTCGCCATCTATGAGATTGATCAAACCAATATATT
Found at i:489539 original size:86 final size:84
Alignment explanation
Indices: 489407--489973 Score: 672
Period size: 86 Copynumber: 6.8 Consensus size: 84
489397 ATTTTTTTTT
* * * * *
489407 AGATATCGCCATGTTTTTAAGTGTTTATCAGATATCACCATATTCTTAATCTTTATCAGATATCA
1 AGATATCACCATGTTCTT-AGTCTTTATCAGATATCACCATGTTCTTAGTCTTTATCAGATATCA
489472 CCATGTTCTATAGTCTTTATC
65 CCATGTTCT-TAGTCTTTATC
* * * *
489493 AGAAATCACCATGTTCTTAGTCTTTTTTTAGATATCACCATGTTCTTGGTCTTTATCAGATATCA
1 AGATATCACCATGTTCTTAGTC-TTTATCAGATATCACCATGTTCTTAGTCTTTATCAGATATCA
*
489558 CCATGTTCTTTAGTCTTTGTC
65 CCATGTTC-TTAGTCTTTATC
** *
489579 AGATATCACCATGTTCTATAGTCTTTATTTGATATCACCATGTTCTTAATCTTTATCAGATATCA
1 AGATATCACCATGTTCT-TAGTCTTTATCAGATATCACCATGTTCTTAGTCTTTATCAGATATCA
* *
489644 CCATGTTCTTAATCTTTATT
65 CCATGTTCTTAGTCTTTATC
* * **
489664 ACATATCACCATGTTCTAAGTCTTTATCAGATATCTTCATGTTCTTAGTC--T-T----TAT---
1 AGATATCACCATGTTCTTAGTCTTTATCAGATATCACCATGTTCTTAGTCTTTATCAGATATCAC
*
489719 CATGTTCTTAGTCTTTATT
66 CATGTTCTTAGTCTTTATC
** * * * *
489738 AGATATCACCATACTCTTAGTATTTATCAGATATCACCATGTTCTTAGTCTTTATTAGATTTTAC
1 AGATATCACCATGTTCTTAGTCTTTATCAGATATCACCATGTTCTTAGTCTTTATCAGATATCAC
*
489803 CATGTTCTTAGTCTTTATT
66 CATGTTCTTAGTCTTTATC
* * * *
489822 ATATATCACCACGTTCTATAGTCTTTATCAGATATCACCATGTTCTAAAGTCTTTATCAGGTATC
1 AGATATCACCATGTTCT-TAGTCTTTATCAGATATCACCATGTTCT-TAGTCTTTATCAGATATC
489887 ACCATGTTCTATAGTCTTTATC
64 ACCATGTTCT-TAGTCTTTATC
*
489909 AGATATCA-CATTGTTCTTTAGTCTCTATCAGATATCACCATGTT-TTAGTCTTTATCAGATATC
1 AGATATCACCA-TGTTC-TTAGTCTTTATCAGATATCACCATGTTCTTAGTCTTTATCAGATATC
489972 AC
64 AC
489974 TGTTTTAGAC
Statistics
Matches: 413, Mismatches: 50, Indels: 37
0.83 0.10 0.07
Matches are distributed among these distances:
74 61 0.15
76 1 0.00
77 4 0.01
81 3 0.01
82 1 0.00
84 59 0.14
85 73 0.18
86 158 0.38
87 52 0.13
88 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.44
Consensus pattern (84 bp):
AGATATCACCATGTTCTTAGTCTTTATCAGATATCACCATGTTCTTAGTCTTTATCAGATATCAC
CATGTTCTTAGTCTTTATC
Found at i:489687 original size:28 final size:28
Alignment explanation
Indices: 489407--489720 Score: 364
Period size: 28 Copynumber: 11.0 Consensus size: 28
489397 ATTTTTTTTT
* * *
489407 AGATATCGCCATGTTTTTAAGTGTTTATC
1 AGATATCACCATG-TTCTAAGTCTTTATC
*
489436 AGATATCACCATATTCTTAA-TCTTTATC
1 AGATATCACCATGTTC-TAAGTCTTTATC
489464 AGATATCACCATGTTCTATAGTCTTTATC
1 AGATATCACCATGTTCTA-AGTCTTTATC
* * * *
489493 AGAAATCACCATGTTCTTAGTCTTTTTTT
1 AGATATCACCATGTTCTAAGTC-TTTATC
**
489522 AGATATCACCATGTTCTTGGTCTTTATC
1 AGATATCACCATGTTCTAAGTCTTTATC
* *
489550 AGATATCACCATGTTCTTTAGTCTTTGTC
1 AGATATCACCATGTTC-TAAGTCTTTATC
*
489579 AGATATCACCATGTTCTATAGTCTTTATT
1 AGATATCACCATGTTCTA-AGTCTTTATC
*
489608 TGATATCACCATGTTCTTAA-TCTTTATC
1 AGATATCACCATGTTC-TAAGTCTTTATC
*
489636 AGATATCACCATGTTCTTAA-TCTTTATT
1 AGATATCACCATGTTC-TAAGTCTTTATC
*
489664 ACATATCACCATGTTCTAAGTCTTTATC
1 AGATATCACCATGTTCTAAGTCTTTATC
** *
489692 AGATATCTTCATGTTCTTAGTCTTTATC
1 AGATATCACCATGTTCTAAGTCTTTATC
489720 A
1 A
489721 TGTTCTTAGT
Statistics
Matches: 249, Mismatches: 28, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
27 5 0.02
28 130 0.52
29 112 0.45
30 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (28 bp):
AGATATCACCATGTTCTAAGTCTTTATC
Found at i:489723 original size:18 final size:18
Alignment explanation
Indices: 489700--489736 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
489690 TCAGATATCT
489700 TCATGTTCTTAGTCTTTA
1 TCATGTTCTTAGTCTTTA
489718 TCATGTTCTTAGTCTTTA
1 TCATGTTCTTAGTCTTTA
489736 T
1 T
489737 TAGATATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.57
Consensus pattern (18 bp):
TCATGTTCTTAGTCTTTA
Found at i:489735 original size:74 final size:74
Alignment explanation
Indices: 489645--489965 Score: 268
Period size: 74 Copynumber: 4.0 Consensus size: 74
489635 CAGATATCAC
* **
489645 CATGTTCTTAATCTTTATTACATATCACCATGTTCTAAGTCTTTATCAGATATCTTCATGTTCTT
1 CATGTTCTTAGTCTTTATTACATATCACCATGTTCTAAGTCTTTATCAGATATCACCATGTTCTT
489710 AGTCTTTAT
66 AGTCTTTAT
* ** * *
489719 CATGTTCTTAGTCTTTATTAGATATCACCATACTCTTAGTATTTATCAGATATCACCATGTTCTT
1 CATGTTCTTAGTCTTTATTACATATCACCATGTTCTAAGTCTTTATCAGATATCACCATGTTCTT
489784 AGTCTTTATTAGATTTT
66 AGTC--T-TT--A---T
* *
489801 ACCATGTTCTTAGTCTTTATTATATATCACCACGTTCTATAGTCTTTATCAGATATCACCATGTT
1 --CATGTTCTTAGTCTTTATTACATATCACCATGTTCTA-AGTCTTTATCAGATATCACCATGTT
*
489866 CTAAAGTCTTTATCAGGTAT
63 CT-TAGTC--T-T----TAT
* * * *
489886 CACCATGTTCTATAGTCTTTATCAGATATCA-CATTGTTCTTTAGTCTCTATCAGATATCACCAT
1 ---CATGTTCT-TAGTCTTTATTACATATCACCA-TGTTC-TAAGTCTTTATCAGATATCACCAT
489950 GTT-TTAGTCTTTAT
60 GTTCTTAGTCTTTAT
489964 CA
1 CA
489966 GATATCACTG
Statistics
Matches: 206, Mismatches: 21, Indels: 39
0.77 0.08 0.15
Matches are distributed among these distances:
74 61 0.30
75 2 0.01
76 1 0.00
77 2 0.01
78 3 0.01
79 1 0.00
82 2 0.01
83 1 0.00
84 32 0.16
85 31 0.15
86 22 0.11
87 45 0.22
88 2 0.01
90 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (74 bp):
CATGTTCTTAGTCTTTATTACATATCACCATGTTCTAAGTCTTTATCAGATATCACCATGTTCTT
AGTCTTTAT
Found at i:489756 original size:46 final size:46
Alignment explanation
Indices: 489673--489766 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
489663 TACATATCAC
** ** *
489673 CATGTTCTAAGTCTTTATCAGATATCTTCATGTTCTTAGTCTTTAT
1 CATGTTCTAAGTCTTTATCAGATATCACCATACTCTTAGTATTTAT
* *
489719 CATGTTCTTAGTCTTTATTAGATATCACCATACTCTTAGTATTTAT
1 CATGTTCTAAGTCTTTATCAGATATCACCATACTCTTAGTATTTAT
489765 CA
1 CA
489767 GATATCACCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (46 bp):
CATGTTCTAAGTCTTTATCAGATATCACCATACTCTTAGTATTTAT
Found at i:489807 original size:102 final size:102
Alignment explanation
Indices: 489617--489938 Score: 290
Period size: 102 Copynumber: 3.0 Consensus size: 102
489607 TTGATATCAC
** * *
489617 CATGTTCTTAATCTTTATCAGATATCACCATGTTCTTAATCTTTATTACATATCACCATGTTCTA
1 CATGTTCTTAATCTTTATCAGATATCACCATACTCTTAATATTTATCACATATCACCATGTTCTA
489682 AGTCTTTATCAGATATCTTCATGTTCTTAGTCTTTAT
66 AGTCTTTATCAGATATCTTCATGTTCTTAGTCTTTAT
* * * * *
489719 CATGTTCTTAGTCTTTATTAGATATCACCATACTCTTAGTATTTATCAGATATCACCATGTTCTT
1 CATGTTCTTAATCTTTATCAGATATCACCATACTCTTAATATTTATCACATATCACCATGTTCTA
*
489784 AGTCTTTATTAGAT-T-TTACCATGTTCTTAGTCTTTATTATATAT
66 AGTCTTTATCAGATATCTT--CATGTTCTTAGTC-----T-T-TAT
* * ** * * **
489828 CACCACGTTCTATAGTCTTTATCAGATATCACCATGTTCTAAAGTCTTTATCAGGTATCACCATG
1 ---CATGTTCT-TAATCTTTATCAGATATCACCATACTCTTAA-TATTTATCACATATCACCATG
* *
489893 TTCTATAGTCTTTATCAGATATC-ACATTGTTCTTTAGTCTCTAT
61 TTCTA-AGTCTTTATCAGATATCTTCA-TGTTC-TTAGTCTTTAT
489937 CA
1 CA
489939 GATATCACCA
Statistics
Matches: 179, Mismatches: 22, Indels: 34
0.76 0.09 0.14
Matches are distributed among these distances:
100 2 0.01
101 1 0.01
102 82 0.46
106 2 0.01
107 1 0.01
108 1 0.01
109 6 0.03
111 1 0.01
112 7 0.04
113 26 0.15
114 25 0.14
115 18 0.10
116 7 0.04
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (102 bp):
CATGTTCTTAATCTTTATCAGATATCACCATACTCTTAATATTTATCACATATCACCATGTTCTA
AGTCTTTATCAGATATCTTCATGTTCTTAGTCTTTAT
Found at i:489838 original size:130 final size:132
Alignment explanation
Indices: 489588--489973 Score: 384
Period size: 130 Copynumber: 2.9 Consensus size: 132
489578 CAGATATCAC
* ** *
489588 CATGTTCTATAGTCTTTATTTGATATCACCATGTTCTTAATCTTTATCAGATATCACCATGTTCT
1 CATGTTCTATAGTCTTTATTAGATATCACCATACTCTTAATATTTATCAGATATCACCATGTTCT
** *
489653 TAATCTTTATTACATATCACCATGTTCTAAGTCTTTATCAGATATCTTCATGTTCT-TAGTCTTT
66 TAATCTTTATTACATATCACCATGTTCTAAGTCTTTATCAGATATCACCACGTTCTATAGTCTTT
489717 AT
131 AT
*
489719 CATGTTCT-TAGTCTTTATTAGATATCACCATACTCTTAGTATTTATCAGATATCACCATGTTCT
1 CATGTTCTATAGTCTTTATTAGATATCACCATACTCTTAATATTTATCAGATATCACCATGTTCT
* * * * * * *
489783 TAGTCTTTATTAGATTTTACCATGTTCTTAGTCTTTATTATATATCACCACGTTCTATAGTCTTT
66 TAATCTTTATTACATATCACCATGTTCTAAGTCTTTATCAGATATCACCACGTTCTATAGTC--T
489848 ATCAGATAT
129 -T----TAT
* * * ** * *
489857 CACCATGTTCTAAAGTCTTTATCAGGTATCACCATGTTCTATAGTCTTTATCAGATATCA-CATT
1 ---CATGTTCTATAGTCTTTATTAGATATCACCATACTCT-TAATATTTATCAGATATCACCA-T
* * * * *
489921 GTTCTTTAGTCTCTATCAGATATCACCATGTT-TTAGTCTTTATCAGATATCAC
61 GTTC-TTAATCTTTATTACATATCACCATGTTCTAAGTCTTTATCAGATATCAC
489974 TGTTTTAGAC
Statistics
Matches: 213, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
130 97 0.46
131 13 0.06
133 1 0.00
134 1 0.00
138 3 0.01
141 8 0.04
142 25 0.12
143 42 0.20
144 23 0.11
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (132 bp):
CATGTTCTATAGTCTTTATTAGATATCACCATACTCTTAATATTTATCAGATATCACCATGTTCT
TAATCTTTATTACATATCACCATGTTCTAAGTCTTTATCAGATATCACCACGTTCTATAGTCTTT
AT
Found at i:489856 original size:29 final size:28
Alignment explanation
Indices: 489719--489973 Score: 334
Period size: 29 Copynumber: 9.0 Consensus size: 28
489709 TAGTCTTTAT
*
489719 CATGTTCTTAGTCTTTATTAGATATCAC
1 CATGTTCTTAGTCTTTATCAGATATCAC
** *
489747 CATACTCTTAGTATTTATCAGATATCAC
1 CATGTTCTTAGTCTTTATCAGATATCAC
* * *
489775 CATGTTCTTAGTCTTTATTAGATTTTAC
1 CATGTTCTTAGTCTTTATCAGATATCAC
* *
489803 CATGTTCTTAGTCTTTATTATATATCAC
1 CATGTTCTTAGTCTTTATCAGATATCAC
*
489831 CACGTTCTATAGTCTTTATCAGATATCAC
1 CATGTTCT-TAGTCTTTATCAGATATCAC
* *
489860 CATGTTCTAAAGTCTTTATCAGGTATCAC
1 CATGTTCT-TAGTCTTTATCAGATATCAC
489889 CATGTTCTATAGTCTTTATCAGATATCA-
1 CATGTTCT-TAGTCTTTATCAGATATCAC
*
489917 CATTGTTCTTTAGTCTCTATCAGATATCAC
1 CA-TGTTC-TTAGTCTTTATCAGATATCAC
489947 CATGTT-TTAGTCTTTATCAGATATCAC
1 CATGTTCTTAGTCTTTATCAGATATCAC
489974 TGTTTTAGAC
Statistics
Matches: 200, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
27 20 0.10
28 80 0.40
29 97 0.49
30 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (28 bp):
CATGTTCTTAGTCTTTATCAGATATCAC
Found at i:495744 original size:2 final size:2
Alignment explanation
Indices: 495737--495776 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
495727 TTATAAGATT
495737 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
495777 ATCCCCCCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:504599 original size:17 final size:17
Alignment explanation
Indices: 504577--504610 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
504567 CCCCCCCCCC
*
504577 GTTTGAATTAGCTTCCG
1 GTTTGAATTACCTTCCG
504594 GTTTGAATTACCTTCCG
1 GTTTGAATTACCTTCCG
504611 ACGCCACTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (17 bp):
GTTTGAATTACCTTCCG
Found at i:505048 original size:21 final size:21
Alignment explanation
Indices: 505024--505132 Score: 101
Period size: 21 Copynumber: 5.0 Consensus size: 21
505014 TTTATTTTAT
*
505024 TAATTTGTTATAACAGATTAG
1 TAATTTGTTATAACAAATTAG
* *
505045 TAATTTGTTGTAACAAATTAT
1 TAATTTGTTATAACAAATTAG
505066 TAATTTGTTATAACAAATTATCATG
1 TAATTTGTTATAACAAA-T-T-A-G
* * *
505091 ATAATCTGTTATATCAAATTAC
1 -TAATTTGTTATAACAAATTAG
* *
505113 TAATATGTTATGACAAATTA
1 TAATTTGTTATAACAAATTA
505133 ATAAAAAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
21 51 0.71
22 1 0.01
23 2 0.03
24 2 0.03
25 1 0.01
26 15 0.21
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.43
Consensus pattern (21 bp):
TAATTTGTTATAACAAATTAG
Found at i:510942 original size:30 final size:30
Alignment explanation
Indices: 510906--511035 Score: 233
Period size: 30 Copynumber: 4.3 Consensus size: 30
510896 AATCAAGGCT
*
510906 ATTGTACGTAAAGCTGAATTAGATGGTACA
1 ATTGTACGTAAAGCTGAACTAGATGGTACA
510936 ATTGTACGTAAAGCTGAACTAGATGGTACA
1 ATTGTACGTAAAGCTGAACTAGATGGTACA
510966 ATTGTACGTAAAGCTGAACTAGATGGTACA
1 ATTGTACGTAAAGCTGAACTAGATGGTACA
*
510996 ATTGTACGTAAAGCTAAACTAGATGGTACA
1 ATTGTACGTAAAGCTGAACTAGATGGTACA
*
511026 ATTGCACGTA
1 ATTGTACGTA
511036 TAAACAAATC
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 97 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (30 bp):
ATTGTACGTAAAGCTGAACTAGATGGTACA
Found at i:511578 original size:14 final size:14
Alignment explanation
Indices: 511559--511585 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
511549 AATATGCTTA
511559 TTTATTTTCTACAG
1 TTTATTTTCTACAG
511573 TTTATTTTCTACA
1 TTTATTTTCTACA
511586 ACACCAGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.04, T:0.59
Consensus pattern (14 bp):
TTTATTTTCTACAG
Found at i:514047 original size:25 final size:25
Alignment explanation
Indices: 514019--514124 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 25
514009 TATGTCTAGT
* * *
514019 CGTGCATAGAAATCAGGTGTCTCAC
1 CGTGCATACAAGTCACGTGTCTCAC
* * * *
514044 CGTGCAAACATGTTACGTGTCTCAT
1 CGTGCATACAAGTCACGTGTCTCAC
514069 CGTGCATACAAGTCACGTGTCTCAC
1 CGTGCATACAAGTCACGTGTCTCAC
* * * * *
514094 CATGCAAACATGTTACGTGTCTCAT
1 CGTGCATACAAGTCACGTGTCTCAC
514119 CGTGCA
1 CGTGCA
514125 AACATGTTAC
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (25 bp):
CGTGCATACAAGTCACGTGTCTCAC
Found at i:514065 original size:50 final size:50
Alignment explanation
Indices: 514018--514124 Score: 178
Period size: 50 Copynumber: 2.1 Consensus size: 50
514008 ATATGTCTAG
* * *
514018 TCGTGCATAGAAATCAGGTGTCTCACCGTGCAAACATGTTACGTGTCTCA
1 TCGTGCATACAAATCACGTGTCTCACCATGCAAACATGTTACGTGTCTCA
*
514068 TCGTGCATACAAGTCACGTGTCTCACCATGCAAACATGTTACGTGTCTCA
1 TCGTGCATACAAATCACGTGTCTCACCATGCAAACATGTTACGTGTCTCA
514118 TCGTGCA
1 TCGTGCA
514125 AACATGTTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (50 bp):
TCGTGCATACAAATCACGTGTCTCACCATGCAAACATGTTACGTGTCTCA
Found at i:514125 original size:25 final size:25
Alignment explanation
Indices: 514035--514140 Score: 149
Period size: 25 Copynumber: 4.2 Consensus size: 25
514025 TAGAAATCAG
514035 GTGTCTCACCGTGCAAACATGTTAC
1 GTGTCTCACCGTGCAAACATGTTAC
* * * *
514060 GTGTCTCATCGTGCATACAAGTCAC
1 GTGTCTCACCGTGCAAACATGTTAC
*
514085 GTGTCTCACCATGCAAACATGTTAC
1 GTGTCTCACCGTGCAAACATGTTAC
*
514110 GTGTCTCATCGTGCAAACATGTTAC
1 GTGTCTCACCGTGCAAACATGTTAC
*
514135 ATGTCT
1 GTGTCT
514141 TATATGCATC
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 69 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (25 bp):
GTGTCTCACCGTGCAAACATGTTAC
Found at i:514140 original size:50 final size:50
Alignment explanation
Indices: 514036--514140 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
514026 AGAAATCAGG
* * *
514036 TGTCTCACCGTGCAAACATGTTACGTGTCTCATCGTGCATACAAGTCACG
1 TGTCTCACCATGCAAACATGTTACGTGTCTCATCGTGCAAACAAGTCACA
* *
514086 TGTCTCACCATGCAAACATGTTACGTGTCTCATCGTGCAAACATGTTACA
1 TGTCTCACCATGCAAACATGTTACGTGTCTCATCGTGCAAACAAGTCACA
514136 TGTCT
1 TGTCT
514141 TATATGCATC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (50 bp):
TGTCTCACCATGCAAACATGTTACGTGTCTCATCGTGCAAACAAGTCACA
Found at i:519999 original size:210 final size:207
Alignment explanation
Indices: 519582--520002 Score: 754
Period size: 210 Copynumber: 2.0 Consensus size: 207
519572 CATCAGATTC
** *
519582 ATTGATACTTTAATTTTTCAGTAGCCTGTCCGACTGCGTATGGGCATTTTACACGCCTTATCCCT
1 ATTGATACTTTAATTTTTCAGTAGCCTGTCCGACCACGTATGGGCATTTTACACGCATTATCCCT
*
519647 CCATCTTCTTCAAATATTTCAACTTTAAAATAATTTTCAAATATTATCGCAATTTATTATAAAAT
66 CCAACTTCTTCAAATATTTCAACTTTAAAATAATTTTCAAATATTATCGCAATTTATTATAAAAT
519712 ATAGAAAAAAATCATCTATTTTAGCTTTAAGACTTGAATATTTTCCTTTATCTTAGGACAAAGTT
131 ATAGAAAAAAATCATCTATTTTAGCTTTAAGACTTGAATATTTTCCTTTATCTTAGGACAAAGTT
519777 CTTTTAAAGGAT
196 CTTTTAAAGGAT
519789 ATTGATACTTTAATTTTTCAGTAGCCTGTCCGACCACGTATGGGCATTTTACACGCATATTATCC
1 ATTGATACTTTAATTTTTCAGTAGCCTGTCCGACCACGTATGGGCATTTTACACGC--ATTATCC
519854 AC-CCAACTTCTTCAAATATTTCAACTTTAAAATAATTTTCAAATATTATCGCAATTTATTATAA
64 -CTCCAACTTCTTCAAATATTTCAACTTTAAAATAATTTTCAAATATTATCGCAATTTATTATAA
519918 AATATAGAAAAAAAATCATCTATTTTAGCTTTAAGACTTGAATATTTTCCTTTATCTTAGGACAA
128 AATATAG-AAAAAAATCATCTATTTTAGCTTTAAGACTTGAATATTTTCCTTTATCTTAGGACAA
*
519983 AGTTCTTTTCAAGGAT
192 AGTTCTTTTAAAGGAT
519999 ATTG
1 ATTG
520003 CTATAGACGT
Statistics
Matches: 205, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
207 54 0.26
209 74 0.36
210 77 0.38
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (207 bp):
ATTGATACTTTAATTTTTCAGTAGCCTGTCCGACCACGTATGGGCATTTTACACGCATTATCCCT
CCAACTTCTTCAAATATTTCAACTTTAAAATAATTTTCAAATATTATCGCAATTTATTATAAAAT
ATAGAAAAAAATCATCTATTTTAGCTTTAAGACTTGAATATTTTCCTTTATCTTAGGACAAAGTT
CTTTTAAAGGAT
Found at i:520915 original size:14 final size:15
Alignment explanation
Indices: 520873--520918 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
520863 TCACCGAGAC
*
520873 GAGACATCACCCTTAT
1 GAGAC-TCACCTTTAT
520889 GAGACTTCACCTTTAT
1 GAGAC-TCACCTTTAT
520905 GAGAC-CACCTTTAT
1 GAGACTCACCTTTAT
520919 CATATGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 9 0.32
16 19 0.68
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (15 bp):
GAGACTCACCTTTAT
Found at i:521142 original size:20 final size:20
Alignment explanation
Indices: 521119--521184 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
521109 ATTTGACCAC
521119 ATAATACAATATTATAATAT
1 ATAATACAATATTATAATAT
*
521139 ATAAAACAATA-TAGT-AT-T
1 ATAATACAATATTA-TAATAT
* * * *
521157 ATATTACAATATCATATTAC
1 ATAATACAATATTATAATAT
521177 ATAATACA
1 ATAATACA
521185 TCATAACATA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
18 11 0.31
19 6 0.17
20 18 0.51
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAATACAATATTATAATAT
Found at i:521752 original size:177 final size:176
Alignment explanation
Indices: 521408--521980 Score: 791
Period size: 177 Copynumber: 3.2 Consensus size: 176
521398 GCACATATTT
* * * *
521408 CAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCAAGCATCCGAAACCTATAGCTCAAATT
1 CAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCAGAAACCTATAGCTCAGATT
* * * *
521473 ---CATTCAAGCCTGTCTGGTGCATCAGTATCATAAGACGCACCATCCATGGAAGTCTGGTGAAG
66 CAGCATCCAAGCCT-TCTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG
* * * *
521535 TTA-GGACAAGTAGTAACTAAGATATAAT-C-ATCAGAGGGCACCTGCAA
130 -TACGGACCAGCAGTAACTTAGATAT--TGCTATCAAAGGGCACCTGCAA
* ** *
521582 CAAAACCTTTAACCAGCTCCAAAAACCTTAACCTCCTTTAGCATCAGTAACCTATAGCTCAGATT
1 CAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCAGAAACCTATAGCTCAGATT
* *
521647 CAGCATCCAAGCCTTCCTGGTGCATCAGTATCATTAGACACACCATCAATGCAAGTTTGGTGAAG
66 CAGCATCCAAGCCTT-CTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG
521712 TACGGACCAGCAGTAACTTAGATATTGCTATCAAAGGGCACCTGCAA
130 TACGGACCAGCAGTAACTTAGATATTGCTATCAAAGGGCACCTGCAA
* *
521759 CAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATT
1 CAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCAGAAACCTATAGCTCAGATT
* * *
521824 CAGCACCCAAGCCTTACTGGTGCATCAGTTTCATAAGACACACCATCCATGCAAGTTTGGTGACG
66 CAGCATCCAAGCCTT-CTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG
521889 TACGGACCTA-CAGTAACTTAGATAATTGCTATCAAAGGGCACCTGCAA
130 TACGGACC-AGCAGTAACTTAGAT-ATTGCTATCAAAGGGCACCTGCAA
* * *
521937 CAAAAACTTTAACCTGGTCCAACAACCTTAACCTCCTCCAGCAT
1 CAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCAT
521981 ATTAAATTTA
Statistics
Matches: 359, Mismatches: 31, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
174 58 0.16
175 1 0.00
176 4 0.01
177 229 0.64
178 67 0.19
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (176 bp):
CAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCAGAAACCTATAGCTCAGATT
CAGCATCCAAGCCTTCTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGT
ACGGACCAGCAGTAACTTAGATATTGCTATCAAAGGGCACCTGCAA
Found at i:521775 original size:19 final size:19
Alignment explanation
Indices: 521751--521792 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
521741 ATCAAAGGGC
*
521751 ACCTGCAACAAAAACTTTA
1 ACCTGCAACAAAAACCTTA
**
521770 ACCTGCTCCAAAAACCTTA
1 ACCTGCAACAAAAACCTTA
521789 ACCT
1 ACCT
521793 CCTCCAGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.21
Consensus pattern (19 bp):
ACCTGCAACAAAAACCTTA
Found at i:521797 original size:19 final size:19
Alignment explanation
Indices: 521759--521798 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
521749 GCACCTGCAA
* *
521759 CAAAAACTTTAACCTGCTC
1 CAAAAACCTTAACCTCCTC
521778 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
521797 CA
1 CA
521799 GCATCCGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.38, G:0.03, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:522051 original size:178 final size:174
Alignment explanation
Indices: 521408--522066 Score: 667
Period size: 177 Copynumber: 3.7 Consensus size: 174
521398 GCACATATTT
* * * * * *
521408 CAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCAAGCATCCGAAACCTATAGCTCAAATT
1 CAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCCTCCAGCATACTAAA--TATAGCTCAGATT
* * * *
521473 ---CATTCAAGCCTGT-CTGGTGCATCAGTA-TCATAAGACGCACCATCCATGGAAGTCTGGTGA
64 CAGCATCCAAGCCT-TACTGGTGCATC-GTAGTCA-AAGACACACCATCCATGCAAGTTTGGTGA
* * * *
521533 AGTTA-GGACAAGTAGTAACTAAGATATAAT-C-ATCAGAGGGCACCTGCAA
126 AG-TACGGACCAGCAGTAACTTAGATAT--TGCTATCAAAGGGCACCTGCAA
* * ** * *
521582 CAAAACCTTTAACCAGCTCCAAAAACCTTAACCTCCTTTAGCATCAGTAACCTATAGCTCAGATT
1 CAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCCTCCAGCAT-ACTAA-ATATAGCTCAGATT
* * *
521647 CAGCATCCAAGCCTTCCTGGTGCATCAGTA-TCATTAGACACACCATCAATGCAAGTTTGGTGAA
64 CAGCATCCAAGCCTTACTGGTGCATC-GTAGTCA-AAGACACACCATCCATGCAAGTTTGGTGAA
521711 GTACGGACCAGCAGTAACTTAGATATTGCTATCAAAGGGCACCTGCAA
127 GTACGGACCAGCAGTAACTTAGATATTGCTATCAAAGGGCACCTGCAA
* *
521759 CAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATT
1 CAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCCTCCAGCATACTAAA--TATAGCTCAGATT
* * *
521824 CAGCACCCAAGCCTTACTGGTGCATCAGT-TTCATAAGACACACCATCCATGCAAGTTTGGTGAC
64 CAGCATCCAAGCCTTACTGGTGCATC-GTAGTCA-AAGACACACCATCCATGCAAGTTTGGTGAA
521888 GTACGGACCTA-CAGTAACTTAGATAATTGCTATCAAAGGGCACCTGCAA
127 GTACGGACC-AGCAGTAACTTAGAT-ATTGCTATCAAAGGGCACCTGCAA
* * * *
521937 CAAAAACTTTAACCTGGTCCAACAACCTTAACCTCCTCCAGCATATTAAATTTAGGACTCAGATT
1 CAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCCTCCAGCATACTAAATATA-G-CTCAGATT
* * ** * * ** *
522002 CAGCATCCAAGTCTTTCAAGTCCATACGTAGGTC-CAGATGCATCATCCATGCAAGTTTGGTGAA
64 CAGCATCCAAGCCTTACTGGTGCAT-CGTA-GTCAAAGACACACCATCCATGCAAGTTTGGTGAA
522066 G
127 G
522067 ACATGACAAG
Statistics
Matches: 416, Mismatches: 50, Indels: 34
0.83 0.10 0.07
Matches are distributed among these distances:
174 52 0.12
175 3 0.01
176 9 0.02
177 224 0.54
178 125 0.30
179 1 0.00
180 2 0.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (174 bp):
CAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCCTCCAGCATACTAAATATAGCTCAGATTCA
GCATCCAAGCCTTACTGGTGCATCGTAGTCAAAGACACACCATCCATGCAAGTTTGGTGAAGTAC
GGACCAGCAGTAACTTAGATATTGCTATCAAAGGGCACCTGCAA
Found at i:522060 original size:355 final size:350
Alignment explanation
Indices: 521408--522066 Score: 821
Period size: 355 Copynumber: 1.9 Consensus size: 350
521398 GCACATATTT
*
521408 CAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCAAGCATCCGAAACCTATAGCTCAAATT
1 CAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCAAGCATCCGAAACCTATAGCTCAAATT
** * *
521473 CATTCAAGCCTGTCTGGTGCATCAGTATCATAAGACGCACCATCCATGGAAGTCTGGTGAAGTTA
66 CACCCAAGCCTGTCTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTCTGGTGAAGTTA
* * *
521538 GGACAAGTAGTAACTAAGATATAATCATCAGAGGGCACCTGCAACAAAACCTTTAACCAGCTCCA
131 GGACAAGCAGTAACTAAGATATAATCATCAAAGGGCACCTGCAACAAAAACTTTAACCAGCTCCA
** * **
521603 AAAACCTTAACCTCCTTTAGCATCAGTAACCTATAGCTCAGATTCAGCATCCAAGCCTTCCTGGT
196 AAAACCTTAACCTCCTCCAGCATCAGTAACATATAGCTCAGATTCAGCATCCAAGCCTTCCAAGT
* *
521668 GCATCAGTATCATTAGACACACCATCAATGCAAGTTTGGTGAAGTACGGACCAGCAGTAACTTAG
261 CCATCAGTATCA-CAGACACACCATCAATGCAAGTTTGGTGAAGTACGGACCAGCAGTAACTTAG
521733 ATATTGCTATCAAAGGGCACCTGCAA
325 ATATTGCTATCAAAGGGCACCTGCAA
* * *
521759 CAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATT
1 CAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCAAGCATCCGAAACCTATAGCTCAAATT
* * *
521824 CAGCACCCAAGCCT-TACTGGTGCATCAGTTTCATAAGACACACCATCCATGCAAGTTTGGTGAC
66 ---CACCCAAGCCTGT-CTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTCTGGTGAA
* * *
521888 G-TACGGACCTA-CAGTAACTTAGATA-ATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAAC
127 GTTA-GGA-CAAGCAGTAACTAAGATATAAT-C-ATCAAAGGGCACCTGCAACAAAAACTTTAAC
* * * * *
521950 CTGGTCCAACAACCTTAACCTCCTCCAGCAT-ATTAA-ATTTAGGACTCAGATTCAGCATCCAAG
188 CAGCTCCAAAAACCTTAACCTCCTCCAGCATCAGTAACATATA-G-CTCAGATTCAGCATCCAAG
* * ** * *
522013 TCTTTCAAGTCCAT-ACGTAGGTC-CAGATGCATCATCCATGCAAGTTTGGTGAAG
251 CCTTCCAAGTCCATCA-GTA--TCACAGACACACCATCAATGCAAGTTTGGTGAAG
522067 ACATGACAAG
Statistics
Matches: 260, Mismatches: 35, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
351 61 0.23
353 8 0.03
354 75 0.29
355 114 0.44
357 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (350 bp):
CAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCAAGCATCCGAAACCTATAGCTCAAATT
CACCCAAGCCTGTCTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTCTGGTGAAGTTA
GGACAAGCAGTAACTAAGATATAATCATCAAAGGGCACCTGCAACAAAAACTTTAACCAGCTCCA
AAAACCTTAACCTCCTCCAGCATCAGTAACATATAGCTCAGATTCAGCATCCAAGCCTTCCAAGT
CCATCAGTATCACAGACACACCATCAATGCAAGTTTGGTGAAGTACGGACCAGCAGTAACTTAGA
TATTGCTATCAAAGGGCACCTGCAA
Found at i:527616 original size:2 final size:2
Alignment explanation
Indices: 527609--527656 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
527599 ACTTACTTAT
527609 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
527651 TC TC TC
1 TC TC TC
527657 GTAAATTAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:528380 original size:37 final size:36
Alignment explanation
Indices: 528339--528442 Score: 99
Period size: 37 Copynumber: 2.9 Consensus size: 36
528329 TTTACTAGCT
528339 TTACTTTTTAAAACAAAGTAATGGTAATGGTAATGCA
1 TTACTTTTTAAAAC-AAGTAATGGTAATGGTAATGCA
** *
528376 TTAC--TTT-ACTCATGTAATGGTAAT-GTAATGCA
1 TTACTTTTTAAAACAAGTAATGGTAATGGTAATGCA
***
528408 TTACTTCAAGAAAATCAAGTAATGGTAATGGTAAT
1 TTACTT-TTTAAAA-CAAGTAATGGTAATGGTAAT
528443 TTAATGCCCA
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
32 12 0.23
33 12 0.23
34 2 0.04
35 3 0.06
36 1 0.02
37 17 0.33
38 5 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (36 bp):
TTACTTTTTAAAACAAGTAATGGTAATGGTAATGCA
Found at i:528619 original size:65 final size:65
Alignment explanation
Indices: 528513--528764 Score: 495
Period size: 65 Copynumber: 3.9 Consensus size: 65
528503 CCCAAGCCTG
*
528513 CTCTGTACACATACAGATGTACACATTCCCAACAATTCAATCTATGACACTGTCATAGCTCTACA
1 CTCTGTACACATACAGATGTACACATTCCCAACAATACAATCTATGACACTGTCATAGCTCTACA
528578 CTCTGTACACATACAGATGTACACATTCCCAACAATACAATCTATGACACTGTCATAGCTCTACA
1 CTCTGTACACATACAGATGTACACATTCCCAACAATACAATCTATGACACTGTCATAGCTCTACA
528643 CTCTGTACACATACAGATGTACACATTCCCAACAATACAATCTATGACACTGTCATAGCTCTACA
1 CTCTGTACACATACAGATGTACACATTCCCAACAATACAATCTATGACACTGTCATAGCTCTACA
528708 CTCTGTACACATACAGATGTACACATTCCCAACAATACAATCTATGACACTGTCATA
1 CTCTGTACACATACAGATGTACACATTCCCAACAATACAATCTATGACACTGTCATA
528765 CTGTTACAGC
Statistics
Matches: 186, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 186 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (65 bp):
CTCTGTACACATACAGATGTACACATTCCCAACAATACAATCTATGACACTGTCATAGCTCTACA
Found at i:535452 original size:22 final size:22
Alignment explanation
Indices: 535373--536146 Score: 641
Period size: 22 Copynumber: 35.4 Consensus size: 22
535363 ACGCTCCTCA
*
535373 GGTCCTAACTGGAGACT-CAGG
1 GGTCCTAACTGGAGACTCCATG
*
535394 GGTCCTAACTGGAGGCTCCATG
1 GGTCCTAACTGGAGACTCCATG
* * *
535416 TGTCCCAAATGGAGACTCCATG
1 GGTCCTAACTGGAGACTCCATG
* * * *
535438 GGTTCAAACTTGAGACTCCATC
1 GGTCCTAACTGGAGACTCCATG
*** **
535460 GGTAAAAACTGGAGACTTTATG
1 GGTCCTAACTGGAGACTCCATG
**
535482 GGTCCTAACTAAAGACTCCATG
1 GGTCCTAACTGGAGACTCCATG
** *
535504 GGTCCTAACTGGAGGTTCCAGG
1 GGTCCTAACTGGAGACTCCATG
* *
535526 GGTCCTAACT-TACGACTCCATC
1 GGTCCTAACTGGA-GACTCCATG
*** **
535548 GGTAAAAACTGGAGACTTAATG
1 GGTCCTAACTGGAGACTCCATG
**
535570 GGTCCTAACTAAAGACTCCATG
1 GGTCCTAACTGGAGACTCCATG
** *
535592 GGTCCTAACTGGAGGTTCCAGG
1 GGTCCTAACTGGAGACTCCATG
*
535614 GGTCCTAACTGGAGACTCTACT-
1 GGTCCTAACTGGAGACTCCA-TG
** *
535636 GGTCCTAACAAGAGACTCCACG
1 GGTCCTAACTGGAGACTCCATG
**
535658 GGTCCTAACCAGAGACTCCATG
1 GGTCCTAACTGGAGACTCCATG
* *
535680 GGTCCTAACTGGAGGCTCCAGG
1 GGTCCTAACTGGAGACTCCATG
* * *
535702 GGTCCCAAATGGAGACTCCAGG
1 GGTCCTAACTGGAGACTCCATG
* *
535724 GGTCCCAAATGGAGACTCCATG
1 GGTCCTAACTGGAGACTCCATG
* *
535746 GGTTCTAACTGGAGACTCCAGG
1 GGTCCTAACTGGAGACTCCATG
* * * *
535768 GGTCATAACTAGAAACTCCAGG
1 GGTCCTAACTGGAGACTCCATG
*
535790 GGTCCTAACTGGAGACTCCAGG
1 GGTCCTAACTGGAGACTCCATG
*
535812 GGTCCTAACTAGAGACTCCATG
1 GGTCCTAACTGGAGACTCCATG
*
535834 GGTCCTAACT-TACGACTCCA-G
1 GGTCCTAACTGGA-GACTCCATG
*** * **
535855 CGGTAAAAATTGGAGACTTTATG
1 -GGTCCTAACTGGAGACTCCATG
**
535878 GGTCCTAACTAAAGACTCCATG
1 GGTCCTAACTGGAGACTCCATG
** *
535900 GGTCCTAACTGGAGGTTCCAGG
1 GGTCCTAACTGGAGACTCCATG
*
535922 GGTCCTAACTGGAGACTCTACT-
1 GGTCCTAACTGGAGACTCCA-TG
*
535944 GGTCCTAAC--GAGACTCCACG
1 GGTCCTAACTGGAGACTCCATG
** *
535964 GGTCCTAACCAGAGACTCCTTG
1 GGTCCTAACTGGAGACTCCATG
*
535986 GGTCCTAACTGGAGACTCCAGG
1 GGTCCTAACTGGAGACTCCATG
*
536008 GGTCCTAACTAGAGACTCCATG
1 GGTCCTAACTGGAGACTCCATG
** * *
536030 GGTCCTAACTTAAGACTTCACG
1 GGTCCTAACTGGAGACTCCATG
* *
536052 GGTCCTAACTGGAGTCTTCA-G
1 GGTCCTAACTGGAGACTCCATG
* * **
536073 GGTCTTAACTGGAGACTCTACA
1 GGTCCTAACTGGAGACTCCATG
** * *
536095 GGTCCTAACAAGAAACTCTACT-
1 GGTCCTAACTGGAGACTCCA-TG
* *
536117 GGTACTAACTGGAGACTCCACG
1 GGTCCTAACTGGAGACTCCATG
536139 GGTCCTAA
1 GGTCCTAA
536147 ATGGGTTCTA
Statistics
Matches: 593, Mismatches: 144, Indels: 31
0.77 0.19 0.04
Matches are distributed among these distances:
20 17 0.03
21 36 0.06
22 537 0.91
23 3 0.01
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.22
Consensus pattern (22 bp):
GGTCCTAACTGGAGACTCCATG
Found at i:539631 original size:24 final size:25
Alignment explanation
Indices: 539544--539663 Score: 120
Period size: 24 Copynumber: 4.9 Consensus size: 25
539534 TTTTAGGCCT
* *
539544 TCACTGTGCTATATTTAACAGGAAA
1 TCACTGTGCTCTATTTAACAGGACA
* * **
539569 TCATTGTGCTCTA-ATAACAGGATT
1 TCACTGTGCTCTATTTAACAGGACA
539593 TCACTGTGCTCTATTTAACAGGA-A
1 TCACTGTGCTCTATTTAACAGGACA
* *
539617 TCACTATGCTCTATTTTACA-GACA
1 TCACTGTGCTCTATTTAACAGGACA
* *
539641 TTAACTGTGGTCTATTTAACAGG
1 -TCACTGTGCTCTATTTAACAGG
539664 CGTTCATTGT
Statistics
Matches: 77, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
23 2 0.03
24 39 0.51
25 35 0.45
26 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (25 bp):
TCACTGTGCTCTATTTAACAGGACA
Found at i:539648 original size:49 final size:49
Alignment explanation
Indices: 539546--539663 Score: 132
Period size: 49 Copynumber: 2.4 Consensus size: 49
539536 TTAGGCCTTC
* * * * *
539546 ACTGTGCTATATTTAACAGGAAATCATTGTGCTCTAATAACAGGATTTC
1 ACTGTGCTCTATTTAACAGGAAATCACTATGCTCTAATAACAGGAATTA
* *
539595 ACTGTGCTCTATTTAACAGG-AATCACTATGCTCTATTTTACA-GACATTA
1 ACTGTGCTCTATTTAACAGGAAATCACTATGCTCTA-ATAACAGGA-ATTA
*
539644 ACTGTGGTCTATTTAACAGG
1 ACTGTGCTCTATTTAACAGG
539664 CGTTCATTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 15 0.25
49 44 0.75
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (49 bp):
ACTGTGCTCTATTTAACAGGAAATCACTATGCTCTAATAACAGGAATTA
Found at i:539733 original size:27 final size:27
Alignment explanation
Indices: 539676--539737 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 27
539666 TTCATTGTGT
*
539676 TGTGCTCTATTTTTTACAGCCGATCAC
1 TGTGCTCTATCTTTTACAGCCGATCAC
* *
539703 --TGCTCTATCTTTTACAGGCGTTCAC
1 TGTGCTCTATCTTTTACAGCCGATCAC
539728 TGTGCTCTAT
1 TGTGCTCTAT
539738 TTGACACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 22 0.73
27 8 0.27
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (27 bp):
TGTGCTCTATCTTTTACAGCCGATCAC
Found at i:540666 original size:26 final size:26
Alignment explanation
Indices: 540623--541032 Score: 454
Period size: 26 Copynumber: 15.8 Consensus size: 26
540613 TTGTAAGCAC
540623 ACTAGATGGGGAGGTGTCATTATGAG
1 ACTAGATGGGGAGGTGTCATTATGAG
* *
540649 ACAAGATGGGGAGTTGTCATTATGAG
1 ACTAGATGGGGAGGTGTCATTATGAG
* *
540675 ACAAGATGGGGAGTTGTCATTATGAG
1 ACTAGATGGGGAGGTGTCATTATGAG
* *
540701 ACAAGATGGGGAGTTGTCATTATGAG
1 ACTAGATGGGGAGGTGTCATTATGAG
* * * * *
540727 ACAAAAAGGGGGGGGGGGTCATTATGAG
1 AC-TAGA-TGGGGAGGTGTCATTATGAG
540755 ACTAGATGGGGAGGTGTC---ATGAG
1 ACTAGATGGGGAGGTGTCATTATGAG
* * *
540778 ACTAGATGGGTAGATGTCACTATGA-
1 ACTAGATGGGGAGGTGTCATTATGAG
* * *
540803 ATTTAGATGGGTAGATGTCATTAT-AGG
1 A-CTAGATGGGGAGGTGTCATTATGA-G
* *
540830 ACAAGATGGTGAGGTGTCATTATGAG
1 ACTAGATGGGGAGGTGTCATTATGAG
*
540856 ACAAGATGGGGAGGTGTCATTATGAG
1 ACTAGATGGGGAGGTGTCATTATGAG
540882 ACTAGATGGGGAGGTGTCATTATGAG
1 ACTAGATGGGGAGGTGTCATTATGAG
* *
540908 ACTAGATGGGGAGTTGTCATTATGAC
1 ACTAGATGGGGAGGTGTCATTATGAG
** * *
540934 TTTAGATGGGGGGGTGTCATTATGAC
1 ACTAGATGGGGAGGTGTCATTATGAG
**
540960 TTTAGATGGGGAGGTGTCATT-TGGAG
1 ACTAGATGGGGAGGTGTCATTAT-GAG
* *
540986 ACCAGATGGGGAGGTGTCATTAGGAG
1 ACTAGATGGGGAGGTGTCATTATGAG
*
541012 ACCAGATGGGGAGGTGTCATT
1 ACTAGATGGGGAGGTGTCATT
541033 TTGACTGATT
Statistics
Matches: 338, Mismatches: 35, Indels: 22
0.86 0.09 0.06
Matches are distributed among these distances:
23 21 0.06
25 3 0.01
26 289 0.86
27 7 0.02
28 18 0.05
ACGTcount: A:0.28, C:0.08, G:0.37, T:0.27
Consensus pattern (26 bp):
ACTAGATGGGGAGGTGTCATTATGAG
Found at i:542853 original size:27 final size:27
Alignment explanation
Indices: 542813--542864 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
542803 AGGAGTTCTT
*
542813 TGTAGGATAAACTCTGTAAGAGCTATA
1 TGTAGGATAAACTCTATAAGAGCTATA
** *
542840 TGTAGGATTCACTCTATAGGAGCTA
1 TGTAGGATAAACTCTATAAGAGCTA
542865 CTGTGGAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (27 bp):
TGTAGGATAAACTCTATAAGAGCTATA
Found at i:546306 original size:15 final size:16
Alignment explanation
Indices: 546277--546309 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
546267 TACTACAGGT
546277 AACTCTCGATGGCTCG
1 AACTCTCGATGGCTCG
*
546293 AACT-TCGATTGCTCG
1 AACTCTCGATGGCTCG
546308 AA
1 AA
546310 GTTCTTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (16 bp):
AACTCTCGATGGCTCG
Found at i:549265 original size:30 final size:30
Alignment explanation
Indices: 549225--549324 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
549215 TACGTTACCA
*
549225 GTCCAGTAGATCGGAGTCTATTGACCGGCG
1 GTCCAATAGATCGGAGTCTATTGACCGGCG
*
549255 GTCCAATAGATC-GATGTCTATTGACCGGTG
1 GTCCAATAGATCGGA-GTCTATTGACCGGCG
* * * * *
549285 G-CCGAATAGATTGCAGTCTGTTGACCAGCA
1 GTCC-AATAGATCGGAGTCTATTGACCGGCG
*
549315 GTTCAATAGA
1 GTCCAATAGA
549325 ACGGTTTCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
29 4 0.07
30 51 0.89
31 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (30 bp):
GTCCAATAGATCGGAGTCTATTGACCGGCG
Found at i:550003 original size:98 final size:98
Alignment explanation
Indices: 549887--550311 Score: 561
Period size: 98 Copynumber: 4.3 Consensus size: 98
549877 TTTTTCATAA
* * * * * *
549887 TGTATTTAACAGGACATGGTTAAAAGAAGTATTATGTTTATATACATTTATTACACTC-TCACAC
1 TGTATTTTACAGGACATGGTCAAAAGAAGGATCATATCTATATACATTTATTACACTCAT-ACAC
*
549951 TTAATGTTGTCAAATGTTTGACACTTTTTGACCC
65 TTAATGTTGTCAAATGTTTTACACTTTTTGACCC
* *
549985 TGTGTTTTACAGGACATGGTCAAAATAAGGATCATATCTATATACATTTATTA-ATCTCATACAC
1 TGTATTTTACAGGACATGGTCAAAAGAAGGATCATATCTATATACATTTATTACA-CTCATACAC
550049 TTAATGTTGTCAAATGTTTTACACTTTTTTG-CCC
65 TTAATGTTGTCAAATGTTTTACAC-TTTTTGACCC
* * * *
550083 TGTATTTTACAAGACA-GGATCAAAATAAGGATCACATCTATATACATGTATTACACTCATACAC
1 TGTATTTTACAGGACATGG-TCAAAAGAAGGATCATATCTATATACATTTATTACACTCATACAC
*
550147 TTAATGTTGTCAAATGTTTTACACTTTTTTACCC
65 TTAATGTTGTCAAATGTTTTACACTTTTTGACCC
* * * * *
550181 TGTGTTTTACAGGACATGGTCAATAGAAGGGTCATATCTGTTTACATTTATTACACTCATACACT
1 TGTATTTTACAGGACATGGTCAAAAGAAGGATCATATCTATATACATTTATTACACTCATACACT
* * *
550246 TTATGTTGTCAAATGTATTACACTTTTTGACAC
66 TAATGTTGTCAAATGTTTTACACTTTTTGACCC
* * *
550279 TGTATTTGACAGGACATGGTCAACAGGAGGATC
1 TGTATTTTACAGGACATGGTCAAAAGAAGGATC
550312 TCTATGGACA
Statistics
Matches: 288, Mismatches: 32, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
97 8 0.03
98 270 0.94
99 10 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (98 bp):
TGTATTTTACAGGACATGGTCAAAAGAAGGATCATATCTATATACATTTATTACACTCATACACT
TAATGTTGTCAAATGTTTTACACTTTTTGACCC
Found at i:564426 original size:15 final size:15
Alignment explanation
Indices: 564397--564425 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
564387 CAAAGAGTAC
564397 CTTTTTTTTCTTTTT
1 CTTTTTTTTCTTTTT
564412 CTTTTTTTT-TTTTT
1 CTTTTTTTTCTTTTT
564426 TGATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
CTTTTTTTTCTTTTT
Found at i:564673 original size:17 final size:17
Alignment explanation
Indices: 564651--564685 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
564641 CCCATGTTGC
*
564651 AACCACTATTGAAATAA
1 AACCACTACTGAAATAA
564668 AACCACTACTGAAATAA
1 AACCACTACTGAAATAA
564685 A
1 A
564686 TTTTTAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.20, G:0.06, T:0.20
Consensus pattern (17 bp):
AACCACTACTGAAATAA
Found at i:564826 original size:84 final size:82
Alignment explanation
Indices: 564647--564846 Score: 238
Period size: 84 Copynumber: 2.4 Consensus size: 82
564637 GATACCCATG
* * * *
564647 TTGCAACCACTATTGAAATAAAACCACTACTGAAATAAATTTTTAATAGTGCTTGGAAATGTATT
1 TTGCAACCACTATTGAAATACAACCACTATTGAAAAAAATTTTTAATAGTGCTTGGAAACGTATT
564712 TCATTAGAAAAATAACC
66 TCATTAGAAAAATAACC
* * * **
564729 TTGCAACTACTATTGAAATACAACCACTATTGAAAAAAATTATTTCATTAGTGGTTGGGGACGTA
1 TTGCAACCACTATTGAAATACAACCACTATTGAAAAAAATT-TTT-AATAGTGCTTGGAAACGTA
* * * *
564794 TTTCATTAGGAGAATCACT
64 TTTCATTAGAAAAATAACC
* **
564813 TTGCAACCACTATTGCAATACAAATACTATTGAA
1 TTGCAACCACTATTGAAATACAACCACTATTGAA
564847 GTAATGTTGA
Statistics
Matches: 99, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
82 37 0.37
83 3 0.03
84 59 0.60
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (82 bp):
TTGCAACCACTATTGAAATACAACCACTATTGAAAAAAATTTTTAATAGTGCTTGGAAACGTATT
TCATTAGAAAAATAACC
Found at i:565573 original size:57 final size:54
Alignment explanation
Indices: 565488--565747 Score: 237
Period size: 53 Copynumber: 4.8 Consensus size: 54
565478 TGAATATCAC
* * * * * * * *
565488 TATTGAGATAAATAATTTCTATAGTGGTTGGGGATGTACTTCATTATTACCAACAT
1 TATTGAAATAATTTATTTCAATAGTGGTTGGGTATGCATTTCATTATAACC-AC-T
* *
565544 TGAATGAAATAATTTATTTCAATAGTGGTTGGGTATGCGTTTCATTATAACCACT
1 T-ATTGAAATAATTTATTTCAATAGTGGTTGGGTATGCATTTCATTATAACCACT
* *
565599 T-TTGAAATAAATTT-TTTCAATAGTGGTTAGGTATGCATTTCATTACAACC-CT
1 TATTGAAAT-AATTTATTTCAATAGTGGTTGGGTATGCATTTCATTATAACCACT
* * * *
565651 TATTGAAATATTTTATTTCAATAGTGGATAAGGG--TGCAGTTCATTACAACCA-T
1 TATTGAAATAATTTATTTCAATAGTGG-T-TGGGTATGCATTTCATTATAACCACT
** * *
565704 TATTGAAATAAAATATTTCAATAGTGGTAGGG-ATGCATGTCATT
1 TATTGAAATAATTTATTTCAATAGTGGTTGGGTATGCATTTCATT
565748 TTAATGCCTA
Statistics
Matches: 173, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
51 4 0.02
52 17 0.10
53 99 0.57
54 6 0.03
55 4 0.02
56 3 0.02
57 40 0.23
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (54 bp):
TATTGAAATAATTTATTTCAATAGTGGTTGGGTATGCATTTCATTATAACCACT
Found at i:565694 original size:106 final size:104
Alignment explanation
Indices: 565548--565747 Score: 262
Period size: 106 Copynumber: 1.9 Consensus size: 104
565538 CAACATTGAA
* * *
565548 TGAAATAATTTATTTCAATAGTGGTTGGGTATGCGTTTCATTATAACCACTT-TTGAAATAAATT
1 TGAAATAATTTATTTCAATAGTGGTAGGG-ATGCGTTTCATTACAACCA-TTATTGAAATAAAAT
* * *
565612 TTTTCAATAGTGGTTAGGTATGCATTTCATTACAACCCTTAT
64 ATTTCAATAGTGG-TAGGGATGCATGTCATTACAACCCTTAT
*
565654 TGAAATATTTTATTTCAATAGTGGATAAGGG-TGCAG-TTCATTACAACCATTATTGAAATAAAA
1 TGAAATAATTTATTTCAATAGTGG-T-AGGGATGC-GTTTCATTACAACCATTATTGAAATAAAA
565717 TATTTCAATAGTGGTAGGGATGCATGTCATT
63 TATTTCAATAGTGGTAGGGATGCATGTCATT
565748 TTAATGCCTA
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
105 17 0.20
106 61 0.73
107 2 0.02
108 3 0.04
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (104 bp):
TGAAATAATTTATTTCAATAGTGGTAGGGATGCGTTTCATTACAACCATTATTGAAATAAAATAT
TTCAATAGTGGTAGGGATGCATGTCATTACAACCCTTAT
Found at i:565956 original size:17 final size:17
Alignment explanation
Indices: 565930--565964 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
565920 ATTGAAGTAA
565930 TTTATGTCAATAGTGGT
1 TTTATGTCAATAGTGGT
*
565947 TTTATTTCAATAGTGGT
1 TTTATGTCAATAGTGGT
565964 T
1 T
565965 GCAACATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51
Consensus pattern (17 bp):
TTTATGTCAATAGTGGT
Found at i:574469 original size:2 final size:2
Alignment explanation
Indices: 574462--574488 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
574452 TTGCAGAGTG
574462 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
574489 TGGGACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:579321 original size:21 final size:21
Alignment explanation
Indices: 579291--579335 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
579281 TTTTAGATTC
579291 GCACGAGCTCTCCCATACGTT
1 GCACGAGCTCTCCCATACGTT
* * *
579312 GCACGGGCTCTCGCATTCGTT
1 GCACGAGCTCTCCCATACGTT
579333 GCA
1 GCA
579336 TGCCTTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.36, G:0.24, T:0.24
Consensus pattern (21 bp):
GCACGAGCTCTCCCATACGTT
Found at i:581377 original size:83 final size:83
Alignment explanation
Indices: 581104--581390 Score: 331
Period size: 83 Copynumber: 3.5 Consensus size: 83
581094 TATGGATACG
* * * **
581104 ATATCGATTTTACATTGTCAACATTGCCGATATTTCTTTGCCGTTAACATCGTCGACATTGCAAC
1 ATATCGAGTTTACATCGTCAACATAGCCGATATTTCTTTAACGTTAACATCGTCGACATTGCAAC
* *
581169 GTTGACGATGTTGAACCT
66 GTCGACGATGTTGAACCA
* * * * * * * **
581187 ATATCGAGTTAACATTGGCGACATAGCCAATTTTTATTTAAAATTAACATCGTCGACATTGCAAC
1 ATATCGAGTTTACATCGTCAACATAGCCGATATTTCTTTAACGTTAACATCGTCGACATTGCAAC
* *
581252 GTCGACGGTGTTGAACCG
66 GTCGACGATGTTGAACCA
* * * * * *
581270 ATATCTAGTTTACATCATCGACATAGCCGATGTTTCTTTAACGTTTACATCGTCGACATCGCAAC
1 ATATCGAGTTTACATCGTCAACATAGCCGATATTTCTTTAACGTTAACATCGTCGACATTGCAAC
*
581335 GTCGACGATGTTAAACCA
66 GTCGACGATGTTGAACCA
* *
581353 ATATCGATTTTACATCGTCAACATACCCGATATTTCTT
1 ATATCGAGTTTACATCGTCAACATAGCCGATATTTCTT
581391 AAATGTCAAC
Statistics
Matches: 168, Mismatches: 36, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
83 168 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (83 bp):
ATATCGAGTTTACATCGTCAACATAGCCGATATTTCTTTAACGTTAACATCGTCGACATTGCAAC
GTCGACGATGTTGAACCA
Found at i:583562 original size:14 final size:15
Alignment explanation
Indices: 583543--583571 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
583533 TTAAAAGTTA
583543 AGATTTTAT-ATTTT
1 AGATTTTATAATTTT
583557 AGATTTTATAATTTT
1 AGATTTTATAATTTT
583572 GCAGATTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
AGATTTTATAATTTT
Found at i:585864 original size:21 final size:21
Alignment explanation
Indices: 585840--585913 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
585830 AATCCTATCA
585840 TATCGTGCGTGTATACTGTTC
1 TATCGTGCGTGTATACTGTTC
* * *
585861 TATCGTGCGT-TAATTCTATAC
1 TATCGTGCGTGT-ATACTGTTC
585882 TATCGTGCGTGTATACTGTTC
1 TATCGTGCGTGTATACTGTTC
585903 TATCGTGCGTG
1 TATCGTGCGTG
585914 AATCCTATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.96
22 1 0.02
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (21 bp):
TATCGTGCGTGTATACTGTTC
Found at i:585886 original size:42 final size:42
Alignment explanation
Indices: 585830--585921 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
585820 ATCGTGTATC
*
585830 AATCCTAT-CATATCGTGCGTGTATACTGTTCTATCGTGCGTT
1 AATCCTATAC-TATCGTGCGTGTATACTGTTCTATCGTGCGTG
*
585872 AATTCTATACTATCGTGCGTGTATACTGTTCTATCGTGCGTG
1 AATCCTATACTATCGTGCGTGTATACTGTTCTATCGTGCGTG
585914 AATCCTAT
1 AATCCTAT
585922 CAGGTTTATC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (42 bp):
AATCCTATACTATCGTGCGTGTATACTGTTCTATCGTGCGTG
Found at i:587638 original size:21 final size:22
Alignment explanation
Indices: 587613--587723 Score: 115
Period size: 21 Copynumber: 5.3 Consensus size: 22
587603 AATCCTATCA
*
587613 TATCGTGCGTGT-ATACTGTTC
1 TATCGTGCGTGTAATACTATTC
* *
587634 CATCGTGCGT-TAATCCTATTC
1 TATCGTGCGTGTAATACTATTC
* *
587655 TTTCGTGCGTGT-ATACTGTTC
1 TATCGTGCGTGTAATACTATTC
*
587676 TATCGTGCGT-TAATGCTATTC
1 TATCGTGCGTGTAATACTATTC
* *
587697 TATCGTGCGTG-AATCCTATCC
1 TATCGTGCGTGTAATACTATTC
587718 TATCGT
1 TATCGT
587724 TTATCTTGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
20 2 0.03
21 71 0.96
22 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (22 bp):
TATCGTGCGTGTAATACTATTC
Found at i:587721 original size:42 final size:42
Alignment explanation
Indices: 587589--587723 Score: 148
Period size: 42 Copynumber: 3.2 Consensus size: 42
587579 GTTTATCCTT
** * *
587589 TCCTATCGTGTATCAATCCTA-TCATATCGTGCGTGTATACTGT
1 TCCTATCGTGCGTTAATCCTATTC-TATCGTGCGTGTATACT-A
* *
587632 TCC-ATCGTGCGTTAATCCTATTCTTTCGTGCGTGTATACTG
1 TCCTATCGTGCGTTAATCCTATTCTATCGTGCGTGTATACTA
* * * *
587673 TTCTATCGTGCGTTAATGCTATTCTATCGTGCGTGAATCCTA
1 TCCTATCGTGCGTTAATCCTATTCTATCGTGCGTGTATACTA
587715 TCCTATCGT
1 TCCTATCGT
587724 TTATCTTGTA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 71 0.91
43 5 0.06
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (42 bp):
TCCTATCGTGCGTTAATCCTATTCTATCGTGCGTGTATACTA
Found at i:589280 original size:17 final size:17
Alignment explanation
Indices: 589254--589286 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
589244 AACTCTCAGT
589254 TTAGCAGATAACTGGTC
1 TTAGCAGATAACTGGTC
*
589271 TTAGCCGATAACTGGT
1 TTAGCAGATAACTGGT
589287 ACAGTACCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCAGATAACTGGTC
Found at i:591629 original size:20 final size:20
Alignment explanation
Indices: 591606--591739 Score: 205
Period size: 20 Copynumber: 6.6 Consensus size: 20
591596 AAAAATTCTT
*
591606 ATTTGTTCGGACGAATTACG
1 ATTTGTTCGGACGAATTAGG
* *
591626 ATTTGTTCGGACGAATAAGTT
1 ATTTGTTCGGACGAATTAG-G
591647 ATTTGTTCGGACGAATTAGG
1 ATTTGTTCGGACGAATTAGG
591667 ATTTGTTCGGACGAATTAGG
1 ATTTGTTCGGACGAATTAGG
* *
591687 ATTTGTTCGGACGAATAAGTT
1 ATTTGTTCGGACGAATTAG-G
591708 ATTTGTTCGGACGAATTAGG
1 ATTTGTTCGGACGAATTAGG
591728 ATTTGTTCGGAC
1 ATTTGTTCGGAC
591740 NNNNNNNNNN
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
20 67 0.65
21 36 0.35
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (20 bp):
ATTTGTTCGGACGAATTAGG
Found at i:591661 original size:41 final size:40
Alignment explanation
Indices: 591606--591739 Score: 198
Period size: 41 Copynumber: 3.3 Consensus size: 40
591596 AAAAATTCTT
* * *
591606 ATTTGTTCGGACGAATTACGATTTGTTCGGACGAATAAGTT
1 ATTTGTTCGGACGAATTAAGATTTGTTCGGACGAATTAG-G
*
591647 ATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGG
1 ATTTGTTCGGACGAATTAAGATTTGTTCGGACGAATTAGG
591687 ATTTGTTCGGACGAA-TAAGTTATTTGTTCGGACGAATTAGG
1 ATTTGTTCGGACGAATTAAG--ATTTGTTCGGACGAATTAGG
591728 ATTTGTTCGGAC
1 ATTTGTTCGGAC
591740 NNNNNNNNNN
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
39 3 0.03
40 15 0.17
41 69 0.79
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (40 bp):
ATTTGTTCGGACGAATTAAGATTTGTTCGGACGAATTAGG
Found at i:591679 original size:61 final size:61
Alignment explanation
Indices: 591606--591739 Score: 259
Period size: 61 Copynumber: 2.2 Consensus size: 61
591596 AAAAATTCTT
591606 ATTTGTTCGGACGAATTACGATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGG
1 ATTTGTTCGGACGAATTACGATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGG
*
591667 ATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGG
1 ATTTGTTCGGACGAATTACGATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGG
591728 ATTTGTTCGGAC
1 ATTTGTTCGGAC
591740 NNNNNNNNNN
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 72 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (61 bp):
ATTTGTTCGGACGAATTACGATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGG
Found at i:594767 original size:2 final size:2
Alignment explanation
Indices: 594760--594790 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
594750 NNNNNNNNNN
594760 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
594791 GTATATATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:595147 original size:15 final size:15
Alignment explanation
Indices: 595124--595156 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
595114 ACGTCAGAAT
595124 CAACAATTATATCAG
1 CAACAATTATATCAG
*
595139 CAACTATTATATCAG
1 CAACAATTATATCAG
595154 CAA
1 CAA
595157 TAAGTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.27
Consensus pattern (15 bp):
CAACAATTATATCAG
Found at i:597335 original size:2 final size:2
Alignment explanation
Indices: 597328--597359 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
597318 CTGCACATCA
597328 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
597360 AGTAACGCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:603827 original size:2 final size:2
Alignment explanation
Indices: 603822--603863 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
603812 ACACAACATG
603822 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
603864 ATTTGCATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:604796 original size:17 final size:17
Alignment explanation
Indices: 604761--604796 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
604751 ATCACCTTGC
*
604761 AACCACTATTGAAATAA
1 AACCACTATTGAAAAAA
604778 AACCACTATTGAAAAAA
1 AACCACTATTGAAAAAA
604795 AA
1 AA
604797 ATATTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (17 bp):
AACCACTATTGAAAAAA
Found at i:604839 original size:85 final size:85
Alignment explanation
Indices: 604673--604875 Score: 250
Period size: 85 Copynumber: 2.4 Consensus size: 85
604663 GATATCGATG
* ** * * * *
604673 TTGCAACCACTATTGAAATAAAACCAATACAG-AAATAAATTATTTCAAAATTGGTTGGGAATGT
1 TTGCAACCACTATTGAAATAAAACCACTATTGAAAAAAAAATATTTCAAAAGTGGTTGGGAACGT
*
604737 ATTTCATTGGTAAAATCACC
66 ATTTCATTGATAAAATCACC
*
604757 TTGCAACCACTATTGAAATAAAACCACTATTGAAAAAAAAATATTTCAATAGTGGTTTGGG-ACG
1 TTGCAACCACTATTGAAATAAAACCACTATTGAAAAAAAAATATTTCAAAAGTGG-TTGGGAACG
*
604821 TATTTCATT-ATAAGAATCACT
65 TATTTCATTGATAA-AATCACC
* * *
604842 TTGCAACCACTATTGCAATACAACTACTATTGAA
1 TTGCAACCACTATTGAAATAAAACCACTATTGAA
604876 GTAAAGATTG
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
84 32 0.31
85 66 0.64
86 5 0.05
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (85 bp):
TTGCAACCACTATTGAAATAAAACCACTATTGAAAAAAAAATATTTCAAAAGTGGTTGGGAACGT
ATTTCATTGATAAAATCACC
Found at i:605631 original size:51 final size:52
Alignment explanation
Indices: 605512--605698 Score: 171
Period size: 51 Copynumber: 3.5 Consensus size: 52
605502 TTATGAATAT
* * * * * *
605512 CACTATTGAGATAAATAATTTCAATAGTGGTTGGGGGTGTACTTCATTATTACCAA
1 CACTATTGAAATAAATTATTTCAATAGTGGTTAGGGATGCATTTCA-T-TT--CAA
* * * * * *
605568 CATTGAATGAAATAAATTATTTTAATAGTGGTTTGGTATGCGTTTCATTAT-AA
1 CACT-ATTGAAATAAATTATTTCAATAGTGGTTAGGGATGCATTTCATT-TCAA
*
605621 -ACTTTTGAAATAAATTATTTCAATAGTGGTTAGGGATGCATTTCATTTCAA
1 CACTATTGAAATAAATTATTTCAATAGTGGTTAGGGATGCATTTCATTTCAA
*
605672 CCACTATTGAAATAATTTATTTCAATA
1 -CACTATTGAAATAAATTATTTCAATA
605699 AATAAATGAA
Statistics
Matches: 106, Mismatches: 20, Indels: 13
0.76 0.14 0.09
Matches are distributed among these distances:
50 1 0.01
51 40 0.38
52 2 0.02
53 25 0.24
55 1 0.01
56 5 0.05
57 32 0.30
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (52 bp):
CACTATTGAAATAAATTATTTCAATAGTGGTTAGGGATGCATTTCATTTCAA
Found at i:605762 original size:17 final size:16
Alignment explanation
Indices: 605736--605770 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
605726 ATTGAAATAA
605736 TTTTTTTCAATAGTGG
1 TTTTTTTCAATAGTGG
605752 TTTTATTTCAATAGTGG
1 TTTT-TTTCAATAGTGG
605769 TT
1 TT
605771 GCAAGGTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (16 bp):
TTTTTTTCAATAGTGG
Found at i:605930 original size:83 final size:84
Alignment explanation
Indices: 605703--605941 Score: 354
Period size: 84 Copynumber: 2.9 Consensus size: 84
605693 TCAATAAATA
* *
605703 AATGAAATACATTTCCAGCCCCTATTGAAATAATTTTTTTCAATAGTGGTTTTATTTCAATAGTG
1 AATGAAATACATTCCCAACCCCTATTGAAATAATTTTTTTCAATAGTGGTTTTATTTCAATAGTG
605768 GTTGCAAGGTGATTTTTCT
66 GTTGCAAGGTGATTTTTCT
* * * * * *
605787 AATGAAATACGTCCCCAACCACTTTTGAAATATTTTTTTTCAATAGTGGTTTTATATCAATAGTG
1 AATGAAATACATTCCCAACCCCTATTGAAATAATTTTTTTCAATAGTGGTTTTATTTCAATAGTG
**
605852 GTTGCGTGGTGATTTTTCT
66 GTTGCAAGGTGATTTTTCT
* * *
605871 AATGAAATAC-TTCCCAACCCCTATTGAAATAATTTATGTCAATAGTGGTTTTATTTCAATAGTA
1 AATGAAATACATTCCCAACCCCTATTGAAATAATTTTTTTCAATAGTGGTTTTATTTCAATAGTG
605935 GTTGCAA
66 GTTGCAA
605942 CATACCCATA
Statistics
Matches: 135, Mismatches: 20, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
83 51 0.38
84 84 0.62
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (84 bp):
AATGAAATACATTCCCAACCCCTATTGAAATAATTTTTTTCAATAGTGGTTTTATTTCAATAGTG
GTTGCAAGGTGATTTTTCT
Done.