Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 41 of 362
Found at i:11984365 original size:204 final size:204
Alignment explanation
Indices: 11984015--11984627 Score: 1208
Period size: 204 Copynumber: 3.0 Consensus size: 204
11984005 AGTAAAGTAG
11984015 CTAAAACTTCAGAACTAGTGATACATGCAACATTAAAGCTCCATATTTCCTTCATACTGAGATCC
1 CTAAAACTTCAGAACTAGTGATACATGCAACATTAAAGCTCCATATTTCCTTCATACTGAGATCC
11984080 ATTAAGCATGACAGAGCTGATTAATACTTTAGAATAAATCATTAAGCTAAATCAGGACTAGGACC
66 ATTAAGCATGACAGAGCTGATTAATACTTTAGAATAAATCATTAAGCTAAATCAGGACTAGGACC
11984145 AAGCATTAACATGTCAGGTGAAGAACAATCACCAAGTCATTATTCACAACCTCAAAGAACCAAAC
131 AAGCATTAACATGTCAGGTGAAGAACAATCACCAAGTCATTATTCACAACCTCAAAGAACCAAAC
11984210 AACAATTAC
196 AACAATTAC
11984219 CTAAAACTTCAGAACTAGTGATACATGCAACATTAAAGCTCCATATTTCCTTCATACTGAGATCC
1 CTAAAACTTCAGAACTAGTGATACATGCAACATTAAAGCTCCATATTTCCTTCATACTGAGATCC
11984284 ATTAAGCATGACAGAGCTGATTAATACTTTAGAATAAATCATTAAGCTAAATCAGGACTAGGACC
66 ATTAAGCATGACAGAGCTGATTAATACTTTAGAATAAATCATTAAGCTAAATCAGGACTAGGACC
11984349 AAGCATTAACATGTCAGGTGAAGAACAATCACCAAGTCATTATTCACAACCTCAAAGAACCAAAC
131 AAGCATTAACATGTCAGGTGAAGAACAATCACCAAGTCATTATTCACAACCTCAAAGAACCAAAC
11984414 AACAATTAC
196 AACAATTAC
11984423 CTAAAACTTCAGAACTAGTGATACATGCAACATTAAAGCTCCATATTTCCTTCATACTGAGATCC
1 CTAAAACTTCAGAACTAGTGATACATGCAACATTAAAGCTCCATATTTCCTTCATACTGAGATCC
11984488 ATTAAGCATGACAGAGCTGATTAATACTTTAGAATAAATCATTAAGCTAAATCAGGACTAGGACC
66 ATTAAGCATGACAGAGCTGATTAATACTTTAGAATAAATCATTAAGCTAAATCAGGACTAGGACC
* *
11984553 AAGCATTAACATGTCAGGTGAAGAACAATCACCAAGTCATTATTCAAAACCACAAAGAACCAAAC
131 AAGCATTAACATGTCAGGTGAAGAACAATCACCAAGTCATTATTCACAACCTCAAAGAACCAAAC
11984618 AACAATTAC
196 AACAATTAC
11984627 C
1 C
11984628 ATACATATGA
Statistics
Matches: 407, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 407 1.00
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (204 bp):
CTAAAACTTCAGAACTAGTGATACATGCAACATTAAAGCTCCATATTTCCTTCATACTGAGATCC
ATTAAGCATGACAGAGCTGATTAATACTTTAGAATAAATCATTAAGCTAAATCAGGACTAGGACC
AAGCATTAACATGTCAGGTGAAGAACAATCACCAAGTCATTATTCACAACCTCAAAGAACCAAAC
AACAATTAC
Found at i:11991853 original size:19 final size:19
Alignment explanation
Indices: 11991829--11991867 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
11991819 ATAATTTGAT
*
11991829 TTTTAAGTTAAAACTTTAA
1 TTTTAAATTAAAACTTTAA
* *
11991848 TTTTAAATTGAAATTTTAA
1 TTTTAAATTAAAACTTTAA
11991867 T
1 T
11991868 CTAATCTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTTAAATTAAAACTTTAA
Found at i:11993451 original size:21 final size:20
Alignment explanation
Indices: 11993425--11993468 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
11993415 AAGTTGTTTT
11993425 TATATATATTAATAAATTATA
1 TATATATATTAATAAATT-TA
11993446 TATATATATTAATAAATTTA
1 TATATATATTAATAAATTTA
11993466 TAT
1 TAT
11993469 TTTAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATATATTAATAAATTTA
Found at i:11993477 original size:21 final size:21
Alignment explanation
Indices: 11993425--11993477 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
11993415 AAGTTGTTTT
*
11993425 TATATATATTAATAAATTATA
1 TATATAAATTAATAAATTATA
*
11993446 TATATATATTAATAAATT-TA
1 TATATAAATTAATAAATTATA
*
11993466 TATTTTAAATTA
1 TA-TATAAATTA
11993478 TTTTTACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATAAATTAATAAATTATA
Found at i:11994943 original size:43 final size:43
Alignment explanation
Indices: 11994894--11995004 Score: 186
Period size: 43 Copynumber: 2.6 Consensus size: 43
11994884 TTAAAAAAAT
11994894 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGC
1 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGC
* *
11994937 GCCGCTAAAAGTCATGGCTTTTAGCGGCTTTTGTGGTAAAAGC
1 GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGC
* *
11994980 ACCGCTACAAGTCATGGCTTTTAGC
1 GCCGCTAAAAGTCATGGCTTTTAGC
11995005 TGTGCTTTTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (43 bp):
GCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGTGGGAAAAGC
Found at i:11995118 original size:31 final size:31
Alignment explanation
Indices: 11995083--11995163 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
11995073 TTTCCTGCAT
* *
11995083 TAAAATCCAACCAAATACAACAAATATAGTA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
* * *
11995114 TAAAATGCAGCCAAAAACAACAAATTTAGCA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
*
11995145 TAAAAAATACAACCAAAAA
1 T--AAAATCCAACCAAAAA
11995164 TATTAATTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 27 0.66
33 14 0.34
ACGTcount: A:0.60, C:0.19, G:0.05, T:0.16
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAGCA
Found at i:11995910 original size:13 final size:14
Alignment explanation
Indices: 11995885--11995913 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11995875 TGATTAATTG
11995885 AATTAAACAATTAT
1 AATTAAACAATTAT
11995899 AATTAAAC-ATTAT
1 AATTAAACAATTAT
11995912 AA
1 AA
11995914 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:12001208 original size:97 final size:97
Alignment explanation
Indices: 12001086--12001416 Score: 452
Period size: 97 Copynumber: 3.4 Consensus size: 97
12001076 TATTTAAGTA
* * * * * * * *
12001086 TTATGTAAGTTATGTAAGTTATATAAGTTATGATATGATATATATTTATGTAAGTAATAT-ATTT
1 TTATCTAAGTTATATAAGTTATATAAGTTATG-TAAGTTATATATTTATATAAGTTATCTAAGTT
*
12001150 ATCTAAGTTATAG-AAGTTATGTAAGTTATATAT
65 ATATAAGTTAT-GTAAGTTATGTAAGTTATATAT
* * * *
12001183 TTATCAAAGTTATATCAGTTATATAAGTTATGTAAGTTATATAAGTTATAT-ATTTATCTAAGTT
1 TTATCTAAGTTATATAAGTTATATAAGTTATGTAAGTTATAT-ATTTATATAAGTTATCTAAGTT
12001247 ATATAAGTTATGTAAGTTATGTAAGTTATATAT
65 ATATAAGTTATGTAAGTTATGTAAGTTATATAT
* *
12001280 TTATCTAAGTTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATCTAAGTTA
1 TTATCTAAGTTATATAAGTTATATAAGTTATGTAAGTTATATATTTATATAAGTTATCTAAGTTA
*
12001345 TATAAGTTATGTAAGTTATATAAGTTATATAT
66 TATAAGTTATGTAAGTTATGTAAGTTATATAT
* *
12001377 TTATCTAAGTTATATAAGTTATGTAAGTTTTGTAAGTTAT
1 TTATCTAAGTTATATAAGTTATATAAGTTATGTAAGTTAT
12001417 GTTAAATATT
Statistics
Matches: 209, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
96 20 0.10
97 189 0.90
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.47
Consensus pattern (97 bp):
TTATCTAAGTTATATAAGTTATATAAGTTATGTAAGTTATATATTTATATAAGTTATCTAAGTTA
TATAAGTTATGTAAGTTATGTAAGTTATATAT
Found at i:12001210 original size:53 final size:53
Alignment explanation
Indices: 12001086--12001418 Score: 312
Period size: 53 Copynumber: 6.6 Consensus size: 53
12001076 TATTTAAGTA
* * * * * *
12001086 TTATGTAAGTTATGTAAGTTATATAAGTTATGATATGATATATATTTATGTAAG
1 TTATATAAGTTATATAAGTTATGTAAGTTATG-TAAGTTATATATTTATCTAAG
* * * *
12001140 TAATAT-ATTTATCTAAGTTATAG-AAGTTATGTAAGTTATATATTTATCAAAG
1 TTATATAAGTTATATAAGTTAT-GTAAGTTATGTAAGTTATATATTTATCTAAG
* *
12001192 TTATATCAGTTATATAAGTTATGTAAGTTATATAAGTTATATATTTATC----
1 TTATATAAGTTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAG
12001241 -----TAAGTTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAG
1 TTATATAAGTTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAG
* * * * *
12001289 TTATATAAGTTATGTAAGTTATGTAAGTTATAT-ATTTATCTAAGTTATCTAAG
1 TTATATAAGTTATATAAGTTATGTAAGTTATGTAAGTTATAT-ATTTATCTAAG
*
12001342 ---------TTATATAAGTTATGTAAGTTATATAAGTTATATATTTATCTAAG
1 TTATATAAGTTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAG
* *
12001386 TTATATAAGTTATGTAAGTTTTGTAAGTTATGT
1 TTATATAAGTTATATAAGTTATGTAAGTTATGT
12001419 TAAATATTTA
Statistics
Matches: 229, Mismatches: 27, Indels: 47
0.76 0.09 0.16
Matches are distributed among these distances:
44 75 0.33
45 6 0.03
52 29 0.13
53 115 0.50
54 4 0.02
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (53 bp):
TTATATAAGTTATATAAGTTATGTAAGTTATGTAAGTTATATATTTATCTAAG
Found at i:12001413 original size:44 final size:44
Alignment explanation
Indices: 12001137--12001416 Score: 364
Period size: 44 Copynumber: 6.2 Consensus size: 44
12001127 ATATTTATGT
* * *
12001137 AAGTAATATATTTATCTAAGTTATAGAAGTTATGTAAGTTATAT
1 AAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGT
* * * * * *
12001181 -ATTTATCAAAGTTATATCAGTTATATAAGTTATGTAAGTTATAT
1 AAGTTAT-ATATTTATCTAAGTTATATAAGTTATGTAAGTTATGT
12001225 AAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGT
1 AAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGT
12001269 AAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGT
1 AAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGT
*
12001313 AAGTTATATATTTATCTAAGTTATCTAAGTTATATAAGTTATGTAAGTTATAT
1 AAG-T-TATA--TA--T---TTATCTAAGTTATATAAGTTATGTAAGTTATGT
*
12001366 AAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTTTGT
1 AAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGT
12001410 AAGTTAT
1 AAGTTAT
12001417 GTTAAATATT
Statistics
Matches: 209, Mismatches: 16, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
43 4 0.02
44 149 0.71
45 6 0.03
46 4 0.02
47 1 0.00
48 2 0.01
49 2 0.01
50 1 0.00
51 4 0.02
52 1 0.00
53 35 0.17
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.47
Consensus pattern (44 bp):
AAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGT
Found at i:12001548 original size:15 final size:15
Alignment explanation
Indices: 12001528--12001583 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
12001518 TAAGTTGCGG
12001528 ATTAAATAATATTTA
1 ATTAAATAATATTTA
*
12001543 ATTAAATAATATTGA
1 ATTAAATAATATTTA
*
12001558 A--AAAAAATATTTTA
1 ATTAAATAATA-TTTA
12001572 ATTAAATAATAT
1 ATTAAATAATAT
12001584 ACATGTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 16 0.47
16 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:12001789 original size:24 final size:24
Alignment explanation
Indices: 12001757--12001827 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
12001747 TTAACTTAAA
12001757 TGATAAAACGGACGATAATATTTG
1 TGATAAAACGGACGATAATATTTG
*
12001781 TGATAAAACGGACAATAATATTTG
1 TGATAAAACGGACGATAATATTTG
*
12001805 TGATAAAACGGACGAGAATATTT
1 TGATAAAACGGACGATAATATTT
12001828 CAATAATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (24 bp):
TGATAAAACGGACGATAATATTTG
Found at i:12002082 original size:64 final size:64
Alignment explanation
Indices: 12001875--12002071 Score: 367
Period size: 64 Copynumber: 3.1 Consensus size: 64
12001865 ATATTTTATT
*
12001875 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATAATTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
12001939 AAATAATTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATAATTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
* *
12002003 AAATAATTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCATGATAG
1 AAATAATTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
12002067 AAATA
1 AAATA
12002072 TAGAAATATT
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 130 1.00
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.37
Consensus pattern (64 bp):
AAATAATTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
Found at i:12002879 original size:6 final size:7
Alignment explanation
Indices: 12002860--12002885 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12002850 ACTTATAAAC
12002860 GCAAAAA
1 GCAAAAA
12002867 GCAAAAA
1 GCAAAAA
12002874 GCAAAAA
1 GCAAAAA
12002881 GCAAA
1 GCAAA
12002886 TCTATAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (7 bp):
GCAAAAA
Found at i:12007779 original size:22 final size:21
Alignment explanation
Indices: 12007750--12007863 Score: 88
Period size: 22 Copynumber: 5.1 Consensus size: 21
12007740 TGCACTAATG
*
12007750 AACAGAGAGTACTGAAGTGCT
1 AACAGAGAGCACTGAAGTGCT
*
12007771 ATACAGAGAGCAC-AAATGTGCT
1 A-ACAGAGAGCACTGAA-GTGCT
*
12007793 AATCAGAGAGCACTGACGTGCT
1 AA-CAGAGAGCACTGAAGTGCT
*
12007815 AAATATCAGAGAGCAC-AAATGTGCT
1 --A-A-CAGAGAGCACTGAA-GTGCT
*
12007840 AATCAGAGAGCACTGATGTGCT
1 AA-CAGAGAGCACTGAAGTGCT
12007862 AA
1 AA
12007864 ATATTAGAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
21 4 0.05
22 50 0.66
23 3 0.04
24 2 0.03
25 17 0.22
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.19
Consensus pattern (21 bp):
AACAGAGAGCACTGAAGTGCT
Found at i:12007827 original size:25 final size:24
Alignment explanation
Indices: 12007752--12007926 Score: 173
Period size: 25 Copynumber: 7.4 Consensus size: 24
12007742 CACTAATGAA
* *
12007752 CAGAGAGTACTGAAGTGCT-ATA-
1 CAGAGAGCACTGATGTGCTAATAT
**
12007774 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGATGTGCTAATAT
*
12007796 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTGATGTGCT-AATAT
**
12007821 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGATGTGCTAATAT
12007843 CAGAGAGCACTGATGTGCTAAATAT
1 CAGAGAGCACTGATGTGCT-AATAT
* **
12007868 TAGAGAGCACTGGCGTGCTAATATT
1 CAGAGAGCACTGATGTGCTAATA-T
*
12007893 CAGAGAGCACTGGTGTGCTAATATT
1 CAGAGAGCACTGATGTGCTAATA-T
12007918 CAGAGAGCA
1 CAGAGAGCA
12007927 TGCTGAGGTC
Statistics
Matches: 128, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.01
22 51 0.40
23 1 0.01
24 6 0.05
25 69 0.54
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (24 bp):
CAGAGAGCACTGATGTGCTAATAT
Found at i:12007828 original size:47 final size:46
Alignment explanation
Indices: 12007752--12007926 Score: 201
Period size: 47 Copynumber: 3.7 Consensus size: 46
12007742 CACTAATGAA
* *
12007752 CAGAGAGTACTGAAGTGCT-ATA-CAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGATGTGCTAATATCAGAGAGCACAAATGTGCTAAT
*
12007796 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGATGTGCT-AATATCAGAGAGCACAAATGTGCTAAT
* ****
12007843 CAGAGAGCACTGATGTGCTAAATATTAGAGAGCACTGGCGTGCTAATATT
1 CAGAGAGCACTGATGTGCT-AATATCAGAGAGCACAAATGTGCT-A-A-T
*
12007893 CAGAGAGCACTGGTGTGCTAATATTCAGAGAGCA
1 CAGAGAGCACTGATGTGCTAATA-TCAGAGAGCA
12007927 TGCTGAGGTC
Statistics
Matches: 114, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
44 17 0.15
46 3 0.03
47 60 0.53
48 1 0.01
49 5 0.04
50 28 0.25
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (46 bp):
CAGAGAGCACTGATGTGCTAATATCAGAGAGCACAAATGTGCTAAT
Found at i:12011141 original size:18 final size:18
Alignment explanation
Indices: 12011118--12011162 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
12011108 AAGAATGGAA
12011118 GAAGAAGAAGATTACCTG
1 GAAGAAGAAGATTACCTG
*
12011136 GAAGAAGATGATTACCTG
1 GAAGAAGAAGATTACCTG
*
12011154 GATGAAGAA
1 GAAGAAGAA
12011163 AGAGATGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.44, C:0.09, G:0.29, T:0.18
Consensus pattern (18 bp):
GAAGAAGAAGATTACCTG
Found at i:12011215 original size:31 final size:31
Alignment explanation
Indices: 12011173--12011234 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
12011163 AGAGATGGGA
* * *
12011173 AAAGTTAAAGAATGGAAGAAAAAGAAAGCTT
1 AAAGTTAAAGAACGAAAGAAAAAAAAAGCTT
*
12011204 AAAGTTGAAGAACGAAAGAAAAAAAAAGCTT
1 AAAGTTAAAGAACGAAAGAAAAAAAAAGCTT
12011235 GCCTAGATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.60, C:0.05, G:0.21, T:0.15
Consensus pattern (31 bp):
AAAGTTAAAGAACGAAAGAAAAAAAAAGCTT
Found at i:12011509 original size:13 final size:13
Alignment explanation
Indices: 12011491--12011519 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12011481 AGTAGCAGGA
12011491 AAACCATCTCAAG
1 AAACCATCTCAAG
12011504 AAACCATCTCAAG
1 AAACCATCTCAAG
12011517 AAA
1 AAA
12011520 TAAAGCCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14
Consensus pattern (13 bp):
AAACCATCTCAAG
Found at i:12013522 original size:13 final size:13
Alignment explanation
Indices: 12013504--12013530 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12013494 GGAGTAATCG
12013504 CACACGGGCGTGT
1 CACACGGGCGTGT
12013517 CACACGGGCGTGT
1 CACACGGGCGTGT
12013530 C
1 C
12013531 CCTGCCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:12018761 original size:28 final size:28
Alignment explanation
Indices: 12018723--12018779 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
12018713 GAGTTTAAAG
12018723 AAAAACTAAATTGATTATTTTCGAATGA
1 AAAAACTAAATTGATTATTTTCGAATGA
* *
12018751 AAAAACTAAATTGATTGTTTTTGAATGA
1 AAAAACTAAATTGATTATTTTCGAATGA
12018779 A
1 A
12018780 CAATAATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (28 bp):
AAAAACTAAATTGATTATTTTCGAATGA
Found at i:12020530 original size:48 final size:47
Alignment explanation
Indices: 12020366--12020583 Score: 200
Period size: 48 Copynumber: 4.6 Consensus size: 47
12020356 GTATAATACT
* *
12020366 GATGCCATGTCCCAGACATGGTCTTACACTTG-CTCATCCATCAAGT--C
1 GATGCCATGTCCCAGACATGGTCTTACAC-TGACACAT-CAT-ACGTGCC
* * *
12020413 GATGCCATGTCCCAGACATGGTCTTACACTGAC-TATCGAAATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACATC-ATA-CG-TGCC
* * *
12020462 GACGCCATGTCCTAGACATGGTCTTACACTGACACCTCTATACGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACATC-ATACGTGCC
* *
12020510 GATGCCATGTCCCAAACATGGCCTTACACTGACACATC-T-CGTAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCATACGT-GCC
* *
12020556 GATG-CATGTCCCAGAAAT-GTCTCACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
12020584 AGCTCTAGTC
Statistics
Matches: 143, Mismatches: 20, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
44 8 0.06
45 17 0.12
46 14 0.10
47 30 0.21
48 36 0.25
49 34 0.24
50 4 0.03
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACACATCATACGTGCC
Found at i:12027089 original size:27 final size:27
Alignment explanation
Indices: 12027058--12027111 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
12027048 TCTATGGTCT
* *
12027058 GTGTCCCTTACACGGCTATGACATGCC
1 GTGTCCCTCACACGGCCATGACATGCC
12027085 GTGTCCCTCACACGGCCATGACATGCC
1 GTGTCCCTCACACGGCCATGACATGCC
12027112 CATGTCCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.37, G:0.22, T:0.22
Consensus pattern (27 bp):
GTGTCCCTCACACGGCCATGACATGCC
Found at i:12028236 original size:49 final size:47
Alignment explanation
Indices: 12028178--12028296 Score: 120
Period size: 45 Copynumber: 2.5 Consensus size: 47
12028168 CCGACCCTAT
* * * *
12028178 GTCCTAGACATGGTCTAACACTAGCTTTCACATATTCGT-GCTGATGCAA
1 GTCCCAGACAT-GTCTTACACTAGC-TACACATATT-GTAGCCGATGCAA
* *
12028227 GTCCCAGACATAGTCTTACACT-G--ACACATCTTGTAGCCGATGCAT
1 GTCCCAGACAT-GTCTTACACTAGCTACACATATTGTAGCCGATGCAA
12028272 GTCCCAGACATGTCTTACACTAGCT
1 GTCCCAGACATGTCTTACACTAGCT
12028297 CTCGTCTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
44 12 0.20
45 27 0.46
48 1 0.02
49 19 0.32
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (47 bp):
GTCCCAGACATGTCTTACACTAGCTACACATATTGTAGCCGATGCAA
Found at i:12034973 original size:27 final size:27
Alignment explanation
Indices: 12034935--12034989 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
12034925 GTTTGTAAAA
12034935 AAGAAAGATGGATCATTGAGGCTGTGC
1 AAGAAAGATGGATCATTGAGGCTGTGC
*
12034962 AAGAAAGATGGATCGTTGAGGCTGTGC
1 AAGAAAGATGGATCATTGAGGCTGTGC
12034989 A
1 A
12034990 TTGATTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.35, T:0.22
Consensus pattern (27 bp):
AAGAAAGATGGATCATTGAGGCTGTGC
Found at i:12047995 original size:25 final size:26
Alignment explanation
Indices: 12047940--12047989 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
12047930 AATAAAGTGC
12047940 AGAAAATCAGAAAGGATGAGAGAAAA
1 AGAAAATCAGAAAGGATGAGAGAAAA
12047966 AGAAAAT-AGAAAGGGATGAGAGAA
1 AGAAAATCAGAAA-GGATGAGAGAA
12047990 TTGAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.60, C:0.02, G:0.30, T:0.08
Consensus pattern (26 bp):
AGAAAATCAGAAAGGATGAGAGAAAA
Found at i:12050097 original size:13 final size:13
Alignment explanation
Indices: 12050079--12050106 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12050069 TACCACATTT
12050079 ATATCATCAAAAC
1 ATATCATCAAAAC
12050092 ATATCATCAAAAC
1 ATATCATCAAAAC
12050105 AT
1 AT
12050107 TATTCGAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (13 bp):
ATATCATCAAAAC
Found at i:12053128 original size:30 final size:31
Alignment explanation
Indices: 12053092--12053160 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
12053082 GGTTTCATTT
*
12053092 CAGTCACTCAAC-TTTTAAAAAA-TAACAAAA
1 CAGTCACT-AACATTATAAAAAAGTAACAAAA
* *
12053122 CAGTCACTAACATTATAAAAAAGTGACAAAG
1 CAGTCACTAACATTATAAAAAAGTAACAAAA
12053153 CAGTCACT
1 CAGTCACT
12053161 GATTAATACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 17 0.50
31 14 0.41
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.22
Consensus pattern (31 bp):
CAGTCACTAACATTATAAAAAAGTAACAAAA
Found at i:12053342 original size:3 final size:3
Alignment explanation
Indices: 12053336--12053383 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
12053326 GAGGAGGAGG
*
12053336 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
12053384 GACTGTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12056412 original size:26 final size:26
Alignment explanation
Indices: 12056382--12056485 Score: 190
Period size: 26 Copynumber: 4.0 Consensus size: 26
12056372 TGAAATTCCC
12056382 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
12056408 ATCATGGAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACCCATT
*
12056434 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12056460 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12056486 GTCAATTTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12062071 original size:26 final size:26
Alignment explanation
Indices: 12062041--12062200 Score: 302
Period size: 26 Copynumber: 6.2 Consensus size: 26
12062031 TGAAATTCCC
12062041 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12062067 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12062093 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12062119 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12062145 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
12062171 ATCATGGAACATTTATCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
12062197 ATCA
1 ATCA
12062201 ATTTGTATCA
Statistics
Matches: 132, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 132 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12063896 original size:3 final size:3
Alignment explanation
Indices: 12063888--12063918 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12063878 GAAGAGAGCC
12063888 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
12063919 GAAAAGACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12071551 original size:49 final size:49
Alignment explanation
Indices: 12071492--12071599 Score: 207
Period size: 49 Copynumber: 2.2 Consensus size: 49
12071482 GATTGGTGTT
*
12071492 CCTTTCCAGTATACGTTGAGCAAGTGAGTGAAATCGAATCATTTAATTA
1 CCTTTCCAGTATACGTTGAGCAAGTGAGTGAAATCAAATCATTTAATTA
12071541 CCTTTCCAGTATACGTTGAGCAAGTGAGTGAAATCAAATCATTTAATTA
1 CCTTTCCAGTATACGTTGAGCAAGTGAGTGAAATCAAATCATTTAATTA
12071590 CCTTTCCAGT
1 CCTTTCCAGT
12071600 TTCCATTTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 58 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (49 bp):
CCTTTCCAGTATACGTTGAGCAAGTGAGTGAAATCAAATCATTTAATTA
Found at i:12080795 original size:6 final size:6
Alignment explanation
Indices: 12080766--12080795 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
12080756 ATATTAATTA
*
12080766 TATATA TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT
12080796 GAATTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:12092656 original size:25 final size:26
Alignment explanation
Indices: 12092628--12092681 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
12092618 TAATTAGTAT
*
12092628 AAAATATT-AATAATTCAAT-AAATTG
1 AAAA-ATTAAATAATTAAATAAAATTG
12092653 AAAAATTAAATAATTAAATAAAATTG
1 AAAAATTAAATAATTAAATAAAATTG
12092679 AAA
1 AAA
12092682 TTTAGGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.12
25 14 0.54
26 9 0.35
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (26 bp):
AAAAATTAAATAATTAAATAAAATTG
Found at i:12093342 original size:14 final size:15
Alignment explanation
Indices: 12093314--12093345 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
12093304 ATTTTCTATT
12093314 AATTTATTAAAATAA
1 AATTTATTAAAATAA
12093329 AATTTATT-AAATAA
1 AATTTATTAAAATAA
12093343 AAT
1 AAT
12093346 ATGATCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTATTAAAATAA
Found at i:12093414 original size:16 final size:15
Alignment explanation
Indices: 12093389--12093422 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
12093379 AAAGTTGATA
*
12093389 ATAATTAATATATATT
1 ATAATAAATATA-ATT
12093405 ATAATAAATATAATT
1 ATAATAAATATAATT
12093420 ATA
1 ATA
12093423 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:12093546 original size:31 final size:30
Alignment explanation
Indices: 12093490--12093547 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
12093480 CTTTTGAAAA
* *
12093490 TATTTACAAAAAGAGACATCTAATTTTTAC
1 TATTTACAAAAAGAGACACCAAATTTTTAC
12093520 TATTTACAAAAA-AGAGCAACCAAATTTT
1 TATTTACAAAAAGAGA-C-ACCAAATTTT
12093548 GAAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.12
30 13 0.54
31 8 0.33
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (30 bp):
TATTTACAAAAAGAGACACCAAATTTTTAC
Found at i:12098892 original size:33 final size:33
Alignment explanation
Indices: 12098854--12098962 Score: 123
Period size: 33 Copynumber: 3.3 Consensus size: 33
12098844 GGTGTACATT
**
12098854 CCTTTTCAAGTGGTACACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTACACACAAAGTATACCTAA
* *
12098887 CCTTTTCATA-TGGTATACAAAAAGTATACCTAA
1 CCTTTTCA-AGTGGTACACACAAAGTATACCTAA
* * * *
12098920 CCTTTCCATGT-GTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGGTACACACAAAGTATACCTAA
12098952 CCTTTTCAAGT
1 CCTTTTCAAGT
12098963 TGCACAATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
32 26 0.42
33 35 0.56
34 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (33 bp):
CCTTTTCAAGTGGTACACACAAAGTATACCTAA
Found at i:12106262 original size:33 final size:33
Alignment explanation
Indices: 12106224--12106332 Score: 123
Period size: 33 Copynumber: 3.3 Consensus size: 33
12106214 GGTGTACATT
**
12106224 CCTTTTCAAGTGGTACACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTACACACAAAGTATACCTAA
* * *
12106257 CCTTTT-AATATGGTATACAAAAAGTATACCTAA
1 CCTTTTCAA-GTGGTACACACAAAGTATACCTAA
* * *
12106290 CCTTTCCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGGTACACACAAAGTATACCTAA
12106322 CCTTTTCAAGT
1 CCTTTTCAAGT
12106333 TGCACAATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
32 29 0.47
33 31 0.50
34 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (33 bp):
CCTTTTCAAGTGGTACACACAAAGTATACCTAA
Found at i:12112292 original size:58 final size:57
Alignment explanation
Indices: 12112202--12112350 Score: 169
Period size: 57 Copynumber: 2.6 Consensus size: 57
12112192 TTGACCTTAT
* * *
12112202 TATAGAAAGTATTTTGCCTGGACTGGTAATCCTGATATAAGCTCTCT-TGAGCATATGA
1 TATAGAAAGGATTTAGCCTGGACAGGTAATCCTGAT-TAAGCTCT-TATGAGCATATGA
* *
12112260 TATAGATAGGATTTAGCCTGGACAGGTAATCCTGATTAAGCTCTTATGAGCATATGT
1 TATAGAAAGGATTTAGCCTGGACAGGTAATCCTGATTAAGCTCTTATGAGCATATGA
* * *
12112317 TGA-ACGCAA-GATTTAGCTTGGACAAGTAATCCTG
1 T-ATA-GAAAGGATTTAGCCTGGACAGGTAATCCTG
12112351 TTATATGATA
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
56 1 0.01
57 43 0.54
58 35 0.44
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (57 bp):
TATAGAAAGGATTTAGCCTGGACAGGTAATCCTGATTAAGCTCTTATGAGCATATGA
Found at i:12112340 original size:57 final size:58
Alignment explanation
Indices: 12112202--12112315 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
12112192 TTGACCTTAT
* * * *
12112202 TATAGAAAGTATTTTGCCTGGACTGGTAATCCTGATATAAGCTCTCTTGAGCATATGA
1 TATAGATAGGATTTAGCCTGGACAGGTAATCCTGATATAAGCTCTCTTGAGCATATGA
12112260 TATAGATAGGATTTAGCCTGGACAGGTAATCCTGAT-TAAGCTCT-TATGAGCATATG
1 TATAGATAGGATTTAGCCTGGACAGGTAATCCTGATATAAGCTCTCT-TGAGCATATG
12112316 TTGAACGCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 1 0.02
57 18 0.35
58 32 0.63
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (58 bp):
TATAGATAGGATTTAGCCTGGACAGGTAATCCTGATATAAGCTCTCTTGAGCATATGA
Found at i:12112909 original size:29 final size:29
Alignment explanation
Indices: 12112877--12112935 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
12112867 GCATGTATAG
* *
12112877 GTTAACTTAACCATGGATGGCTTGAATAT
1 GTTAACTTAACCATGGATGACTTAAATAT
12112906 GTTAACTTAACCATGGATGACTTAAATAT
1 GTTAACTTAACCATGGATGACTTAAATAT
12112935 G
1 G
12112936 CTATTTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (29 bp):
GTTAACTTAACCATGGATGACTTAAATAT
Found at i:12114075 original size:46 final size:46
Alignment explanation
Indices: 12114017--12114111 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
12114007 ATGAAATTAA
12114017 AATAATCACTTGTACATATCTCTATGCCAATTCAAAAAATTAATTC
1 AATAATCACTTGTACATATCTCTATGCCAATTCAAAAAATTAATTC
* *
12114063 AATAATCTCTTGTACATATCTCTATGCCAATTCAAAGAATTAATTC
1 AATAATCACTTGTACATATCTCTATGCCAATTCAAAAAATTAATTC
12114109 AAT
1 AAT
12114112 CACATAAGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (46 bp):
AATAATCACTTGTACATATCTCTATGCCAATTCAAAAAATTAATTC
Found at i:12114155 original size:21 final size:21
Alignment explanation
Indices: 12114131--12114174 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
12114121 ACATAAAAGA
12114131 TTACATGAGGTAACAATGTAT
1 TTACATGAGGTAACAATGTAT
*
12114152 TTACGTGAGGTAACAATGTAT
1 TTACATGAGGTAACAATGTAT
12114173 TT
1 TT
12114175 CTACCTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.36
Consensus pattern (21 bp):
TTACATGAGGTAACAATGTAT
Found at i:12115381 original size:45 final size:44
Alignment explanation
Indices: 12115317--12115407 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 44
12115307 TGCCGAGCTG
*
12115317 TTTTTCGCCTTTTGTACAAATCTGTTAAAAAATAATCATAATTTA
1 TTTTTCGCCCTTTGTACAAATCTGTT-AAAAATAATCATAATTTA
* *
12115362 TTTTTTGCCCTTTGTACAAATCTGTTGAAAATAATCATAATTTA
1 TTTTTCGCCCTTTGTACAAATCTGTTAAAAATAATCATAATTTA
12115406 TT
1 TT
12115408 ATGAAATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
44 19 0.44
45 24 0.56
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (44 bp):
TTTTTCGCCCTTTGTACAAATCTGTTAAAAATAATCATAATTTA
Found at i:12115981 original size:15 final size:16
Alignment explanation
Indices: 12115949--12115981 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12115939 TTTTGATTAA
*
12115949 AATAATATAAGGTAAT
1 AATAATATAAGCTAAT
12115965 AATAATA-AAGCTAAT
1 AATAATATAAGCTAAT
12115980 AA
1 AA
12115982 AAGTTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (16 bp):
AATAATATAAGCTAAT
Found at i:12117573 original size:10 final size:10
Alignment explanation
Indices: 12117560--12117595 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
12117550 TAAGCTCGGT
12117560 TGAGCTCAAA
1 TGAGCTCAAA
*
12117570 TGAGCTGAAA
1 TGAGCTCAAA
*
12117580 CGAGCTCAAA
1 TGAGCTCAAA
12117590 TGAGCT
1 TGAGCT
12117596 GAGTCGAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.19
Consensus pattern (10 bp):
TGAGCTCAAA
Found at i:12119398 original size:12 final size:11
Alignment explanation
Indices: 12119381--12119443 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 11
12119371 TCGATCTCTT
12119381 TTTCTTTTTCAC
1 TTTCTTTTTC-C
12119393 TTTCTTTTTCC
1 TTTCTTTTTCC
12119404 GTTTCATTTTT-C
1 -TTTC-TTTTTCC
*
12119416 -TT-TTTCTCAC
1 TTTCTTTTTC-C
*
12119426 TTTCTTTTTGC
1 TTTCTTTTTCC
12119437 TTTCTTT
1 TTTCTTT
12119444 CAAATTCTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
8 4 0.10
10 3 0.07
11 11 0.26
12 19 0.45
13 5 0.12
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.70
Consensus pattern (11 bp):
TTTCTTTTTCC
Found at i:12119440 original size:19 final size:18
Alignment explanation
Indices: 12119340--12119460 Score: 65
Period size: 18 Copynumber: 6.8 Consensus size: 18
12119330 CTTTTTCAAT
*
12119340 TTTCTTTTTC-TTCTTAC
1 TTTCTTTTTCTTTCTCAC
* **
12119357 ATTCTTTTTCACTCTCGA-
1 TTTCTTTTTCTTTCTC-AC
* *
12119375 TCTCTTTTTCTTTTTCAC
1 TTTCTTTTTCTTTCTCAC
*
12119393 TTTCTTTTTCCGTT-TCA-
1 TTTCTTTTT-CTTTCTCAC
*
12119410 TTT-TTCTT-TTTCTCAC
1 TTTCTTTTTCTTTCTCAC
*
12119426 TTTCTTTTTGCTTTCTTTCAA
1 TTTCTTTTT-CTTTC--TCAC
*
12119447 ATTCTTTTTCTTTC
1 TTTCTTTTTCTTTC
12119461 ATTTCCTTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
14 2 0.03
15 3 0.04
16 7 0.09
17 17 0.22
18 25 0.32
19 8 0.10
20 5 0.06
21 11 0.14
ACGTcount: A:0.08, C:0.24, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTCTTTTTCTTTCTCAC
Found at i:12119458 original size:16 final size:16
Alignment explanation
Indices: 12119437--12119486 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
12119427 TTCTTTTTGC
12119437 TTTCTTTCAAATTCTT
1 TTTCTTTCAAATTCTT
*
12119453 TTTCTTTC-ATTTCCTTT
1 TTTCTTTCAAATT-C-TT
*
12119470 TTTCTTTTAAATTCTT
1 TTTCTTTCAAATTCTT
12119486 T
1 T
12119487 CTCACTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 3 0.11
16 12 0.43
17 10 0.36
18 3 0.11
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTCTTTCAAATTCTT
Found at i:12124499 original size:43 final size:43
Alignment explanation
Indices: 12124446--12124528 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
12124436 GAGATATGTG
*
12124446 GCATCCGAGCTCGTTGAGAGGTCCGAGTTTATTATGGATGCAA
1 GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCAA
*
12124489 GCATCCGAGCTCGTTGAGAGGTCTGAGTTCATTATGGATG
1 GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
12124529 TGTTACATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (43 bp):
GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCAA
Found at i:12126006 original size:23 final size:23
Alignment explanation
Indices: 12125979--12126028 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
12125969 TCCCAATGCG
*
12125979 CACGTGCGTGCGCATTGCCTTCA
1 CACGTGCGTGCGCATTGCCTCCA
*
12126002 CACGTGCGTGTGCATTGCCTCCA
1 CACGTGCGTGCGCATTGCCTCCA
12126025 CACG
1 CACG
12126029 GGTGTGTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.14, C:0.36, G:0.26, T:0.24
Consensus pattern (23 bp):
CACGTGCGTGCGCATTGCCTCCA
Found at i:12126035 original size:23 final size:23
Alignment explanation
Indices: 12125979--12126036 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
12125969 TCCCAATGCG
* * *
12125979 CACGTGCGTGCGCATTGCCTTCA
1 CACGGGCGTGTGCATTGCCTCCA
*
12126002 CACGTGCGTGTGCATTGCCTCCA
1 CACGGGCGTGTGCATTGCCTCCA
*
12126025 CACGGGTGTGTG
1 CACGGGCGTGTG
12126037 AGGTTTAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.12, C:0.31, G:0.31, T:0.26
Consensus pattern (23 bp):
CACGGGCGTGTGCATTGCCTCCA
Found at i:12136096 original size:40 final size:39
Alignment explanation
Indices: 12136012--12136196 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 39
12136002 TTGAATGATG
* * * *
12136012 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
12136052 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
12136092 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
12136131 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
12136172 -CCGGGCTATA-TCCCGAAGGCATTTG
1 TCCGGGCTA-AGT-CCGAAGGCATTTG
12136197 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 35 0.28
40 78 0.63
41 11 0.09
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:12136148 original size:79 final size:80
Alignment explanation
Indices: 12136012--12136196 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 80
12136002 TTGAATGATG
* *
12136012 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
12136076 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
12136091 TTCCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
*
12136154 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
12136171 ACCGGGCTATATCCCGAAGGCATTTG
1 TCCGGGCTA-AGCCCGAAGGCATTTG
12136197 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 34 0.37
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATA
Found at i:12136218 original size:79 final size:79
Alignment explanation
Indices: 12136065--12136229 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
12136055 GGACTAAGAT
* * **
12136065 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
12136130 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
12136144 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATATCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTA-AGCCCGAAGGCATTTGAACGAGTTA-C
* *
12136207 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
12136223 CCGAAGG
1 CCGAAGG
12136230 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.62
80 26 0.35
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:12144037 original size:79 final size:81
Alignment explanation
Indices: 12143897--12144081 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
12143887 TTGAATGATG
* *
12143897 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
12143961 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * *
12143976 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCTGG-TTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCC-GGACTAAGAT-CCGAAGGC
*
12144037 AATTGTGCGAGTTACTATA
63 AATTGTGCGAGATACTATA
* *
12144056 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
12144082 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 1 0.01
79 55 0.60
80 35 0.38
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:12144095 original size:40 final size:40
Alignment explanation
Indices: 12143898--12144081 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
12143888 TGAATGATGT
* * * *
12143898 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
12143938 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
12143978 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* * *
12144016 TCCTGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
12144057 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
12144082 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:12144103 original size:79 final size:79
Alignment explanation
Indices: 12143950--12144114 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
12143940 GGACTAAGAT
* * **
12143950 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
12144015 ATCCTGGTTAAGTC
66 ATCCTGGTTAAATC
* *
12144029 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
12144092 TATATCC-GGTTAAATT
63 TAAATCCTGGTTAAATC
12144108 CCGAAGG
1 CCGAAGG
12144115 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCTGGTTAAATC
Found at i:12151365 original size:43 final size:43
Alignment explanation
Indices: 12151267--12151391 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
12151257 AACTAAGATG
* * * * *
12151267 TCCGAGCTCGTTGAGTGGTCTGGGTTC-TTGAGATATGTG-GCA
1 TCCGAGCTCGTTGAGAGGTCTGAGTTCATT-ATAGATGCGAGCA
12151309 TCCGAGCTCGTTGAGAGGTCTGAGTTCATTATAGATGCGAGCA
1 TCCGAGCTCGTTGAGAGGTCTGAGTTCATTATAGATGCGAGCA
* * * *
12151352 TCCGAGCTCGTTGAAAGGTCCGAGTTCATAATGGATGCGA
1 TCCGAGCTCGTTGAGAGGTCTGAGTTCATTATAGATGCGA
12151392 TTTATGTAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
42 31 0.43
43 41 0.57
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (43 bp):
TCCGAGCTCGTTGAGAGGTCTGAGTTCATTATAGATGCGAGCA
Found at i:12152185 original size:18 final size:19
Alignment explanation
Indices: 12152162--12152197 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12152152 TTGTTGATCA
*
12152162 ATGAA-TGTATGGTAAAGT
1 ATGAATTGTATGCTAAAGT
12152180 ATGAATTGTATGCTAAAG
1 ATGAATTGTATGCTAAAG
12152198 GATAAGGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (19 bp):
ATGAATTGTATGCTAAAGT
Found at i:12158185 original size:22 final size:21
Alignment explanation
Indices: 12158157--12158198 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12158147 ATGTCATTAG
12158157 GGTTCAAACGGAAAAAGGAAAT
1 GGTTC-AACGGAAAAAGGAAAT
**
12158179 GGTTCAATTGAAAAAGGAAA
1 GGTTCAACGGAAAAAGGAAA
12158199 ACAAGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.50, C:0.07, G:0.26, T:0.17
Consensus pattern (21 bp):
GGTTCAACGGAAAAAGGAAAT
Found at i:12165513 original size:35 final size:35
Alignment explanation
Indices: 12165462--12165583 Score: 183
Period size: 35 Copynumber: 3.5 Consensus size: 35
12165452 ATAAAGAAAA
*
12165462 CCATACTGA-TATGTGAAACGTAGGTATGGCATTTT
1 CCATACTGAGT-TGTGAAACGTAGGTATGGTATTTT
* *
12165497 CCATACCGAGTGGTGAAACGTAGGTATGGTATTTT
1 CCATACTGAGTTGTGAAACGTAGGTATGGTATTTT
* *
12165532 TCATACTGAGTTGTGAAACGTAGGTATGATATTTT
1 CCATACTGAGTTGTGAAACGTAGGTATGGTATTTT
12165567 CCATACTGAGTTGTGAA
1 CCATACTGAGTTGTGAA
12165584 TGTGGCACTA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
35 77 0.99
36 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (35 bp):
CCATACTGAGTTGTGAAACGTAGGTATGGTATTTT
Found at i:12167096 original size:22 final size:19
Alignment explanation
Indices: 12167060--12167099 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
12167050 TTTTATTTCT
12167060 TTTTATTTATTATTTTATG
1 TTTTATTTATTATTTTATG
12167079 TTTTATGTTATATAATTTTAT
1 TTTTAT-TTAT-T-ATTTTAT
12167100 AATAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 1 0.06
22 7 0.39
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTTATTATTTTATG
Found at i:12169036 original size:45 final size:45
Alignment explanation
Indices: 12168914--12169037 Score: 142
Period size: 45 Copynumber: 2.8 Consensus size: 45
12168904 ACCAGAAACA
* * *
12168914 AGTAAGACCATAACTGAAAGACGTTATGGCATCATGATTTTAATG
1 AGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATTCTAATG
* **
12168959 AATAAGACCATAGCAAAAAGATGTTATGGCATCATGATTCT-ATCG
1 AGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATTCTAAT-G
* * * *
12169004 AGTAAGACCATAGTTGAACGATGCTATAGCATCA
1 AGTAAGACCATAGCTGAAAGATGTTATGGCATCA
12169038 CGAATCAAAC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 2 0.03
45 63 0.97
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (45 bp):
AGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATTCTAATG
Found at i:12169156 original size:45 final size:46
Alignment explanation
Indices: 12169060--12169158 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 46
12169050 ATAAAACTAT
* *
12169060 AGTTGAAAGACACTATGACAGCACGACAAAAAGTAAATAAGACCAT
1 AGTTGAAAGACACTATGACAGCAAGACAAAAAGTAAATAAGACCAC
* * * * * *
12169106 GGTTGAAAGACACTATGGCATCAAGTCAAGAA-TAAATTAGACCAC
1 AGTTGAAAGACACTATGACAGCAAGACAAAAAGTAAATAAGACCAC
12169151 AGTTGAAA
1 AGTTGAAA
12169159 AGCACCATGG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
45 18 0.41
46 26 0.59
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.18
Consensus pattern (46 bp):
AGTTGAAAGACACTATGACAGCAAGACAAAAAGTAAATAAGACCAC
Found at i:12176815 original size:68 final size:67
Alignment explanation
Indices: 12176743--12176892 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
12176733 CATCATGTGT
* * * *
12176743 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
12176805 ATGTAG
62 ATGTAG
** * *
12176811 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
12176876 AG
66 AG
12176878 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
12176893 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:12176848 original size:64 final size:64
Alignment explanation
Indices: 12176767--12176950 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
12176757 AGACATTATG
* *
12176767 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
12176831 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
12176896 AA
63 AA
* * * *
12176898 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
12176951 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:12198755 original size:55 final size:55
Alignment explanation
Indices: 12198670--12198784 Score: 131
Period size: 55 Copynumber: 2.1 Consensus size: 55
12198660 TGTATATATG
* * *
12198670 CGCACACCCATGTTATTTTGACAGTATCGACCACGGCTGGTGGGCACGGGCGTGT
1 CGCACACCCATGTTATTTTGACAGTATCGACCACGGCTGATAGACACGGGCGTGT
* * ** * * * *
12198725 CGCACACTCGTGTTATTTTGGTAGTTTCGACCATGGTTTATAGACACGGGCGTGT
1 CGCACACCCATGTTATTTTGACAGTATCGACCACGGCTGATAGACACGGGCGTGT
12198780 CGCAC
1 CGCAC
12198785 TGCCGTGGCA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.28
Consensus pattern (55 bp):
CGCACACCCATGTTATTTTGACAGTATCGACCACGGCTGATAGACACGGGCGTGT
Found at i:12206041 original size:17 final size:18
Alignment explanation
Indices: 12206014--12206047 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12206004 AATTAAATAT
12206014 ATGCATATTAAATTATTA
1 ATGCATATTAAATTATTA
*
12206032 ATGC-TATTAATTTATT
1 ATGCATATTAAATTATT
12206048 TAAACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
ATGCATATTAAATTATTA
Found at i:12208877 original size:28 final size:28
Alignment explanation
Indices: 12208811--12208938 Score: 150
Period size: 28 Copynumber: 4.5 Consensus size: 28
12208801 CATGAGATTG
* * **
12208811 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
12208840 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
12208868 GCACTAAGTGTGTGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
12208897 GCACTAAGTGTGCGAGTTAT-ATTATATA
1 GCACTAAGTGTGCGAGTT-TGATTATATA
*
12208925 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
12208939 GACTTACTAT
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
28 44 0.51
29 41 0.48
30 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:12219363 original size:44 final size:44
Alignment explanation
Indices: 12219241--12219371 Score: 131
Period size: 50 Copynumber: 2.8 Consensus size: 44
12219231 TGAGGTATAA
* *
12219241 TGCCGAAGCCATATCCCAGACATGGTCTTACACTGACTTTAACATATTTG
1 TGCCGATGCCATATCCAAGACATGGTCTTACACTG------ACATATTTG
* *
12219291 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACATATCTTG
1 TGCCGATGCCATATCCAAGACATGGTCTTACACTGACATAT-TTG
*
12219336 TAGCTGATG-CATATCCAAGACAT-GTCTTACACTGAC
1 T-GCCGATGCCATATCCAAGACATGGTCTTACACTGAC
12219372 TTACATCTCG
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
44 19 0.26
45 16 0.22
46 6 0.08
50 33 0.45
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (44 bp):
TGCCGATGCCATATCCAAGACATGGTCTTACACTGACATATTTG
Found at i:12219404 original size:46 final size:47
Alignment explanation
Indices: 12219254--12219508 Score: 174
Period size: 46 Copynumber: 5.4 Consensus size: 47
12219244 CGAAGCCATA
* *
12219254 TCCCAGACATGGTCTTACACTGACTTTAACATATTTG-TGCCGATGCCATG
1 TCCCAGACATGGTCTTACACTGAC-TT-ACAT-CTTGAGGCCGATG-CATG
* * *
12219304 TCCCAGACATGGTCTTACACTGAC--ATATCTTGTA-GCTGATGCATA
1 TCCCAGACATGGTCTTACACTGACTTACATCTTG-AGGCCGATGCATG
* *
12219349 TCCAAGACAT-GTCTTACACTGACTTACATCTCGAGGCCGATGCATG
1 TCCCAGACATGGTCTTACACTGACTTACATCTTGAGGCCGATGCATG
* * * * *
12219395 TCCCAGACAT-GCCTTACACT-AGCTCT-CGT-TTCAATGCTGATGCCATG
1 TCCCAGACATGGTCTTACACTGA-CT-TACATCTT-GAGGCCGATG-CATG
* * * *
12219442 TCCCAGACATGGTCTTACACTGGC-T-CTTGTAATGTGGCCGATGCATG
1 TCCCAGACATGGTCTTACACTGACTTACATCT--TGAGGCCGATGCATG
*
12219489 TCCCAGACAT-GTCGTACACT
1 TCCCAGACATGGTCTTACACT
12219509 AGCACACAAT
Statistics
Matches: 167, Mismatches: 24, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
44 13 0.08
45 18 0.11
46 65 0.39
47 30 0.18
48 16 0.10
49 1 0.01
50 24 0.14
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
TCCCAGACATGGTCTTACACTGACTTACATCTTGAGGCCGATGCATG
Found at i:12219457 original size:94 final size:93
Alignment explanation
Indices: 12219238--12219512 Score: 262
Period size: 94 Copynumber: 2.9 Consensus size: 93
12219228 ACATGAGGTA
* * * *
12219238 TAATGCCGAAGCCATATCCCAGACATGGTCTTACACTGACTTTAACATATTTGTGCCGATGCCAT
1 TAATGCTGATGCCATATCCCAGACATGGTCTTACACTGAC-TT-ACAT-CTTGGGCCGATG-CAT
12219303 GTCCCAGACATGGTCTTACACT-GACATATCTTG
62 GTCCCAGACAT-GTCTTACACTAG-CATATCTTG
* *
12219336 T-A-GCTGATG-CATATCCAAGACAT-GTCTTACACTGACTTACATCTCGAGGCCGATGCATGTC
1 TAATGCTGATGCCATATCCCAGACATGGTCTTACACTGACTTACATCTTG-GGCCGATGCATGTC
* *
12219397 CCAGACATGCCTTACACTAGC-TCTCGTT-
65 CCAGACATGTCTTACACTAGCATATC-TTG
* * * *
12219425 TCAATGCTGATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CTTGTAATGTGGCCGATGCAT
1 T-AATGCTGATGCCATATCCCAGACATGGTCTTACACTGACTTACATCT--TG-GGCCGATGCAT
*
12219488 GTCCCAGACATGTCGTACACTAGCA
62 GTCCCAGACATGTCTTACACTAGCA
12219513 CACAATTAAC
Statistics
Matches: 149, Mismatches: 17, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
89 4 0.03
90 12 0.08
91 18 0.12
92 21 0.14
93 15 0.10
94 59 0.40
95 13 0.09
96 5 0.03
97 1 0.01
98 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (93 bp):
TAATGCTGATGCCATATCCCAGACATGGTCTTACACTGACTTACATCTTGGGCCGATGCATGTCC
CAGACATGTCTTACACTAGCATATCTTG
Found at i:12226377 original size:44 final size:44
Alignment explanation
Indices: 12226314--12226402 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
12226304 CATTCTAAGG
*
12226314 TAAAGATTTTCGTTGCTTAAAGGGTTATCCATTACGGTATAGTT
1 TAAAGATTTTCGTTGCTTAAAGGGTTATCCATTACAGTATAGTT
*
12226358 TAAAGATTTTCGTTGCTTAAAGGGTTATCCATTACAGTTTAGTT
1 TAAAGATTTTCGTTGCTTAAAGGGTTATCCATTACAGTATAGTT
12226402 T
1 T
12226403 GGTTTAGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (44 bp):
TAAAGATTTTCGTTGCTTAAAGGGTTATCCATTACAGTATAGTT
Found at i:12236894 original size:12 final size:12
Alignment explanation
Indices: 12236877--12236901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12236867 ATGTAAGTGA
12236877 TCTTGATGATTT
1 TCTTGATGATTT
12236889 TCTTGATGATTT
1 TCTTGATGATTT
12236901 T
1 T
12236902 TACATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:12237780 original size:47 final size:46
Alignment explanation
Indices: 12237617--12237932 Score: 234
Period size: 44 Copynumber: 6.8 Consensus size: 46
12237607 TGAATTGTGC
* * * *
12237617 GCCAGTGTAAGACGTGTCTGGGACACGCATCGG--CTAAGA-GTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAAAGATG-AGT
* * * * * *
12237661 GCTAGTGTAAGACATGTCTGGGGCATGTATCAGCACACATAAATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACA-A-AGATGAGT
12237709 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAAAGATGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACAAAGATGAGT
** *
12237757 GCCAAAGTAAGACATGTCTGGGACATGCATCGGCCTCAACAGA-GA-T
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-CACAA-AGATGAGT
* ** * *
12237803 AGCCAGTGTAAGACGTGTCTGGGACACACATCGG--CTAAGA-GTTGT
1 -GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAAAGATG-AGT
* * * * * *
12237848 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCATATATAAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCA--CAAAGATGAGT
*
12237896 GCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
12237933 ATATATCCCA
Statistics
Matches: 213, Mismatches: 40, Indels: 32
0.75 0.14 0.11
Matches are distributed among these distances:
43 4 0.02
44 57 0.27
45 1 0.00
46 9 0.04
47 49 0.23
48 48 0.23
49 29 0.14
50 16 0.08
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.21
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAAAGATGAGT
Found at i:12244073 original size:4 final size:4
Alignment explanation
Indices: 12244057--12244090 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
12244047 GATAGAAAAA
* *
12244057 TTAT TTTT TTAT TTAT TTAT TTAT GTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
12244091 CTATGAGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:12244504 original size:12 final size:12
Alignment explanation
Indices: 12244487--12244511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12244477 ATGTAAGTTA
12244487 TCTTGATGATTT
1 TCTTGATGATTT
12244499 TCTTGATGATTT
1 TCTTGATGATTT
12244511 T
1 T
12244512 TACATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:12245270 original size:44 final size:44
Alignment explanation
Indices: 12245208--12245469 Score: 168
Period size: 44 Copynumber: 5.7 Consensus size: 44
12245198 TGAATTGTGA
* * * *
12245208 GCTAGTGTAAGACGTGTCTGGGACACACATCGGCTAATAGTTGT
1 GCTAGTGTAAGACATGTCTAGGACACGCATCGGCTAAGAGTTGT
* * * * * * *
12245252 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCACACATAAATGAGA
1 GCTAGTGTAAGACATGTCTAGGACACGCATCGGC-TA-A-GAGT-TGT
* * * * *
12245300 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-ACAGAGATGAAT
1 GCTAGTGTAAGA-CATGTCTAGGACA-CGCATCGGCTA-AGAGTTG--T
* * * * *
12245348 GCTAGAGTAAGACATGTCTAGGACATGCATCAGCCTTAACAGAGAT-A
1 GCTAGTGTAAGACATGTCTAGGACACGCATC-GGC-T-A-AGAGTTGT
* * *
12245395 GCCAGTGTAAAACATGTCTGGGACACGCATCGGCTAAGAGTTGT
1 GCTAGTGTAAGACATGTCTAGGACACGCATCGGCTAAGAGTTGT
*
12245439 GCTAGTGTAAGACATGTCTAGGACATGCATC
1 GCTAGTGTAAGACATGTCTAGGACACGCATC
12245470 AGCACGCATA
Statistics
Matches: 167, Mismatches: 38, Indels: 26
0.72 0.16 0.11
Matches are distributed among these distances:
43 5 0.03
44 57 0.34
45 2 0.01
46 9 0.05
47 43 0.26
48 25 0.15
49 12 0.07
50 14 0.08
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (44 bp):
GCTAGTGTAAGACATGTCTAGGACACGCATCGGCTAAGAGTTGT
Found at i:12245312 original size:48 final size:48
Alignment explanation
Indices: 12245255--12245519 Score: 210
Period size: 47 Copynumber: 5.6 Consensus size: 48
12245245 TAGTTGTGCT
12245255 AGTGTAAGACATGTCTAGGACATGCATCAGCACACATAAATGAGAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCAGCACACATAAATGAGAGCC
* * * *
12245303 AGTGTAAGACCATGTCTGGGACATGGCATC-G-ACACAGAGATGA-ATGCT
1 AGTGTAAGA-CATGTCTAGGACAT-GCATCAGCACACATAAATGAGA-GCC
* *
12245351 AGAGTAAGACATGTCTAGGACATGCATCAG--C-CTTAACA-GAGATAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCAGCACACATAA-ATGAG--AGCC
* * * * * * * * * *
12245398 AGTGTAAAACATGTCTGGGACACGCATCGGC-TA-A-GAGT-TGTGCT
1 AGTGTAAGACATGTCTAGGACATGCATCAGCACACATAAATGAGAGCC
* *
12245442 AGTGTAAGACATGTCTAGGACATGCATCAGCACGCATATATGAGAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCAGCACACATAAATGAGAGCC
*
12245490 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTAGGACAT-GCATC
12245520 GGCAATATAT
Statistics
Matches: 165, Mismatches: 35, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
44 29 0.18
45 4 0.02
46 9 0.05
47 44 0.27
48 42 0.25
49 27 0.16
50 10 0.06
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (48 bp):
AGTGTAAGACATGTCTAGGACATGCATCAGCACACATAAATGAGAGCC
Found at i:12245466 original size:91 final size:90
Alignment explanation
Indices: 12245206--12245522 Score: 361
Period size: 93 Copynumber: 3.4 Consensus size: 90
12245196 GGTGAATTGT
* * * * *
12245206 GAGCTAGTGTAAGACGTGTCTGGGACACACATCGGCTAATAGTTGTGCTAGTGTAAGACATGTCT
1 GAGCCAGTGTAAAACATGTCTGGGACACGCATCGGCTAAGAGTTGTGCTAGTGTAAGACATGTCT
12245271 AGGACATGCATCAGCACACATAAATGA
66 AGGACATGCATCAG--CACATAAATGA
* * * * *
12245298 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-ACAGAGATGAATGCTAGAGTAAGACA
1 GAGCCAGTGTAA-AACATGTCTGGGACA-CGCATCGGCTA-AGAGTTG--TGCTAGTGTAAGACA
*
12245362 TGTCTAGGACATGCATCAGC-CTTAACA-GA
61 TGTCTAGGACATGCATCAGCACATAA-ATGA
12245391 GATAGCCAGTGTAAAACATGTCTGGGACACGCATCGGCTAAGAGTTGTGCTAGTGTAAGACATGT
1 G--AGCCAGTGTAAAACATGTCTGGGACACGCATCGGCTAAGAGTTGTGCTAGTGTAAGACATGT
*
12245456 CTAGGACATGCATCAGCACGCATATATGA
64 CTAGGACATGCATCAGCA--CATAAATGA
* *
12245485 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GAGCCAGTGTAA-AACATGTCTGGGACA-CGCATCGGC
12245523 AATATATCCC
Statistics
Matches: 190, Mismatches: 20, Indels: 28
0.80 0.08 0.12
Matches are distributed among these distances:
91 34 0.18
92 22 0.12
93 48 0.25
94 42 0.22
95 11 0.06
96 33 0.17
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (90 bp):
GAGCCAGTGTAAAACATGTCTGGGACACGCATCGGCTAAGAGTTGTGCTAGTGTAAGACATGTCT
AGGACATGCATCAGCACATAAATGA
Found at i:12253967 original size:6 final size:7
Alignment explanation
Indices: 12253950--12253974 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12253940 AGCAATTTCT
12253950 TTTTTTA
1 TTTTTTA
12253957 TTTTTTA
1 TTTTTTA
12253964 TTTTTTA
1 TTTTTTA
12253971 TTTT
1 TTTT
12253975 ATTCATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:12255466 original size:13 final size:14
Alignment explanation
Indices: 12255448--12255476 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12255438 ATTTTTTTAC
12255448 TTAAACTTATT-TT
1 TTAAACTTATTATT
12255461 TTAAACTTATTATT
1 TTAAACTTATTATT
12255475 TT
1 TT
12255477 TTAAATAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAAACTTATTATT
Found at i:12255468 original size:19 final size:19
Alignment explanation
Indices: 12255418--12255481 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 19
12255408 AAAGCCCAGT
* *
12255418 TTATTTTTTAAAC-GAATC
1 TTATTTTTTAAACTTAAAC
*
12255436 TTATTTTTT-TACTTAAAC
1 TTATTTTTTAAACTTAAAC
12255454 TTATTTTTTAAACTT--A-
1 TTATTTTTTAAACTTAAAC
12255470 TTATTTTTTAAA
1 TTATTTTTTAAA
12255482 TAGGCATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
16 12 0.30
17 3 0.08
18 21 0.52
19 4 0.10
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (19 bp):
TTATTTTTTAAACTTAAAC
Found at i:12256476 original size:21 final size:21
Alignment explanation
Indices: 12256450--12256489 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12256440 AAAATAGACA
12256450 AGAAAATG-GATGTTTTGTTTG
1 AGAAAATGTGAT-TTTTGTTTG
12256471 AGAAAATGTGATTTTTGTT
1 AGAAAATGTGATTTTTGTT
12256490 GTACAGGGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (21 bp):
AGAAAATGTGATTTTTGTTTG
Found at i:12258421 original size:30 final size:30
Alignment explanation
Indices: 12258387--12258449 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
12258377 ATTTATTTTA
*
12258387 TTGTTAATTTTCTTATTATTTTAAAGGCAT
1 TTGTTAATTTTCTTATTATTTTAAAAGCAT
*
12258417 TTGTTAATTTTTTTATTATTTTAAAAGCAT
1 TTGTTAATTTTCTTATTATTTTAAAAGCAT
12258447 TTG
1 TTG
12258450 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAAAAGCAT
Found at i:12263911 original size:14 final size:14
Alignment explanation
Indices: 12263892--12263919 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12263882 AACTCTGTAA
12263892 ACGTGGTTAAGAAT
1 ACGTGGTTAAGAAT
12263906 ACGTGGTTAAGAAT
1 ACGTGGTTAAGAAT
12263920 TATTATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (14 bp):
ACGTGGTTAAGAAT
Found at i:12264405 original size:11 final size:11
Alignment explanation
Indices: 12264391--12264416 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12264381 AAAAGTAATT
12264391 AAAATTTAAAA
1 AAAATTTAAAA
12264402 AAAATTTAAAA
1 AAAATTTAAAA
12264413 AAAA
1 AAAA
12264417 CCCTAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:12264987 original size:5 final size:5
Alignment explanation
Indices: 12264977--12265016 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
12264967 TACTTAAGAA
* *
12264977 TATAT TATAT TGTAT TATAT TATAT TATAT TATAT AATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
12265017 AAATAAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:12265103 original size:17 final size:19
Alignment explanation
Indices: 12265077--12265118 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
12265067 GAAAAAGAGA
*
12265077 AGAAAA-AGAAA-GAAAGG
1 AGAAAAGAGAAATAAAAGG
12265094 A-AAAAGAGAAATAAAAGG
1 AGAAAAGAGAAATAAAAGG
12265112 AGAAAAG
1 AGAAAAG
12265119 TTAGGGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 6 0.29
18 6 0.29
19 5 0.24
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (19 bp):
AGAAAAGAGAAATAAAAGG
Found at i:12265400 original size:8 final size:9
Alignment explanation
Indices: 12265369--12265397 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
12265359 ATTAGGGACT
12265369 AAATTTTGA
1 AAATTTTGA
12265378 AAATTTTGA
1 AAATTTTGA
12265387 AAATTTTGA
1 AAATTTTGA
12265396 AA
1 AA
12265398 TTTATGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (9 bp):
AAATTTTGA
Found at i:12267171 original size:23 final size:23
Alignment explanation
Indices: 12267145--12267241 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
12267135 ATAAGTGCCA
12267145 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12267168 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12267191 CACTG--ATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12267212 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12267235 CACTGAT
1 CACTGAT
12267242 CAATAACACT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
21 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:12267210 original size:44 final size:44
Alignment explanation
Indices: 12267152--12267241 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
12267142 CCACACTGAT
* *
12267152 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
12267196 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
12267240 AT
1 AT
12267242 CAATAACACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (44 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
Found at i:12274514 original size:23 final size:23
Alignment explanation
Indices: 12274488--12274585 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
12274478 ATAAGTGCCA
*
12274488 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
*
12274511 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
*
12274534 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
*
12274556 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
12274579 CACTGAT
1 CACTGAT
12274586 CAATAACACT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 20 0.29
23 50 0.71
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCAAAGCTAC
Found at i:12274553 original size:45 final size:45
Alignment explanation
Indices: 12274495--12274583 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
12274485 CCACACTGAT
* * *
12274495 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCAAAGCTACCACTGG
12274540 ATGTAGCCAAAGCTACCACTGAAATGTAGCCAAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCAAAGCTACCACTG
12274584 ATCAATAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCAAAGCTACCACTGG
Found at i:12278556 original size:21 final size:21
Alignment explanation
Indices: 12278530--12278573 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
12278520 TTTTGAAAGC
12278530 TAAGTTGGTTTGTGATATTTG
1 TAAGTTGGTTTGTGATATTTG
12278551 TAAGTTGGTTTGTGATATTTG
1 TAAGTTGGTTTGTGATATTTG
12278572 TA
1 TA
12278574 GCAATAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.52
Consensus pattern (21 bp):
TAAGTTGGTTTGTGATATTTG
Found at i:12282331 original size:37 final size:37
Alignment explanation
Indices: 12282286--12282357 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 37
12282276 ATCCATATGA
12282286 TTGGTTATGAATGAAAT-AGAAAGAATAAAAGAATATT
1 TTGGTTATGAATGAAATGA-AAAGAATAAAAGAATATT
12282323 TTGGTTATGAATGAAATGAAAAGAATAAAAGAATA
1 TTGGTTATGAATGAAATGAAAAGAATAAAAGAATA
12282358 CTTGCTCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 33 0.97
38 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (37 bp):
TTGGTTATGAATGAAATGAAAAGAATAAAAGAATATT
Found at i:12284122 original size:19 final size:19
Alignment explanation
Indices: 12284098--12284136 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12284088 TGTTGATCGA
12284098 ACAACCTTACCAAAAAATC
1 ACAACCTTACCAAAAAATC
12284117 ACAACCTTACCAAAAAATC
1 ACAACCTTACCAAAAAATC
12284136 A
1 A
12284137 ATTAACACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (19 bp):
ACAACCTTACCAAAAAATC
Found at i:12284466 original size:35 final size:35
Alignment explanation
Indices: 12284405--12284490 Score: 129
Period size: 35 Copynumber: 2.5 Consensus size: 35
12284395 AGTGCCACAA
*
12284405 TTCACAACTCAGTAT-GGAAATACCATACTTACGT
1 TTCACAACTCAGTATGGGAAATACCATACCTACGT
* *
12284439 TTCACAACTCAGTATGGGAAATGCCATACCTATGT
1 TTCACAACTCAGTATGGGAAATACCATACCTACGT
*
12284474 TTCATAACTCAGTATGG
1 TTCACAACTCAGTATGG
12284491 TTTTCTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 15 0.32
35 32 0.68
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (35 bp):
TTCACAACTCAGTATGGGAAATACCATACCTACGT
Found at i:12286667 original size:24 final size:24
Alignment explanation
Indices: 12286639--12286912 Score: 109
Period size: 24 Copynumber: 11.2 Consensus size: 24
12286629 ACAAAATATT
* * *
12286639 ATATAAAACAATTTGAAGTCAATA
1 ATATAAAACAATTTCAAATAAATA
12286663 ATATAAAACAATTTCAAATAAATA
1 ATATAAAACAATTTCAAATAAATA
*
12286687 ATATGTAAAACAAATTTAAAATAAAT-
1 ATA--TAAAAC-AATTTCAAATAAATA
* *
12286713 A-ATAAGACAATTTTAAATGAATAATA
1 ATATAAAACAATTTCAAAT--A-AATA
* * **
12286739 TATAGAAAAACAAGTTTAAAATGGATA
1 -ATA-TAAAACAA-TTTCAAATAAATA
*
12286766 CTATAAAAAGCAATTT-AAAGTAAATA
1 ATAT-AAAA-CAATTTCAAA-TAAATA
* * * *
12286792 GTATAAAACAATTTAAAATCATTA
1 ATATAAAACAATTTCAAATAAATA
* * *
12286816 ATATACAA-AATAATAAAAT-AAT-
1 ATATAAAACAAT-TTCAAATAAATA
* * * *
12286838 ATATAGAGCAACTTAAAATAAATA
1 ATATAAAACAATTTCAAATAAATA
* *
12286862 ATTTATAAAACAATTTAAAAT-AACA
1 A--TATAAAACAATTTCAAATAAATA
*
12286887 A-AT-AAA-AAGTTCAAAATAAATA
1 ATATAAAACAATTTC-AAATAAATA
12286909 ATAT
1 ATAT
12286913 GTGAAAAATA
Statistics
Matches: 193, Mismatches: 33, Indels: 49
0.70 0.12 0.18
Matches are distributed among these distances:
20 4 0.02
21 7 0.04
22 27 0.14
23 17 0.09
24 48 0.25
25 18 0.09
26 38 0.20
27 20 0.10
28 1 0.01
29 6 0.03
30 7 0.04
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.29
Consensus pattern (24 bp):
ATATAAAACAATTTCAAATAAATA
Found at i:12286702 original size:27 final size:25
Alignment explanation
Indices: 12286632--12286946 Score: 154
Period size: 26 Copynumber: 12.5 Consensus size: 25
12286622 ATATGCAACA
* * *
12286632 AAATATTATATAAAACAATTTGAAGT
1 AAATAATAT-TAAAACAATTTAAAAT
* *
12286658 CAATAATA-TAAAACAATTTCAAAT
1 AAATAATATTAAAACAATTTAAAAT
12286682 AAATAATATGTAAAACAAATTTAAAAT
1 AAATAATAT-TAAAAC-AATTTAAAAT
* *
12286709 AAAT-A-A-TAAGACAATTTTAAAT
1 AAATAATATTAAAACAATTTAAAAT
*
12286731 GAATAATATATAGAAAAACAAGTTTAAAAT
1 AAATAATAT-T---AAAACAA-TTTAAAAT
** * * *
12286761 GGATACTATAAAAAGCAATTTAAAGT
1 AAATAATATTAAAA-CAATTTAAAAT
*
12286787 AAATAGTA-TAAAACAATTTAAAAT
1 AAATAATATTAAAACAATTTAAAAT
* * * *
12286811 CATTAATA-TACAA-AA--TAATA-
1 AAATAATATTAAAACAATTTAAAAT
* * *
12286831 AAATAATATATAGAGCAACTTAAAAT
1 AAATAATAT-TAAAACAATTTAAAAT
*
12286857 AAATAATTTATAAAACAATTTAAAAT
1 AAATAATAT-TAAAACAATTTAAAAT
* * *
12286883 -AACAA-A-TAAAA-AGTTCAAAAT
1 AAATAATATTAAAACAATTTAAAAT
*
12286904 AAATAATATGTGAAAAATAAATTTAAAAT
1 AAATAATAT-T--AAAA-CAATTTAAAAT
12286933 AAATAATATATAAA
1 AAATAATAT-TAAA
12286947 TATATATACA
Statistics
Matches: 221, Mismatches: 42, Indels: 51
0.70 0.13 0.16
Matches are distributed among these distances:
20 6 0.03
21 12 0.05
22 24 0.11
23 11 0.05
24 41 0.19
25 14 0.06
26 52 0.24
27 23 0.10
29 24 0.11
30 14 0.06
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (25 bp):
AAATAATATTAAAACAATTTAAAAT
Found at i:12286947 original size:26 final size:25
Alignment explanation
Indices: 12286632--12287161 Score: 145
Period size: 26 Copynumber: 21.6 Consensus size: 25
12286622 ATATGCAACA
* * *
12286632 AAATATTATATAAAACAATTTGAAGT
1 AAATAATATATAAAA-AATTTAAAAT
* * *
12286658 CAATAATATA-AAACAATTTCAAAT
1 AAATAATATATAAAAAATTTAAAAT
*
12286682 AAATAATATGTAAAACAAATTTAAAAT
1 AAATAATATAT-AAA-AAATTTAAAAT
* * *
12286709 AAAT-A-ATA-AGACAATTTTAAAT
1 AAATAATATATAAAAAATTTAAAAT
*
12286731 GAATAATATATAGAAAAACAAGTTTAAAAT
1 AAATAATATAT---AAAA-AA-TTTAAAAT
** * *
12286761 GGATACTATA-AAAAGCAATTTAAAGT
1 AAATAATATATAAAA--AATTTAAAAT
* *
12286787 AAATAGTATA-AAACAATTTAAAAT
1 AAATAATATATAAAAAATTTAAAAT
* * *
12286811 CATTAATATACAAAATAA--TAAAAT
1 AAATAATATATAAAA-AATTTAAAAT
* ** *
12286835 -AAT-ATATA-GAGCAACTTAAAAT
1 AAATAATATATAAAAAATTTAAAAT
*
12286857 AAATAATTTATAAAACAATTTAAAAT
1 AAATAATATATAAAA-AATTTAAAAT
* * *
12286883 -AA-CA-A-ATAAAAAGTTCAAAAT
1 AAATAATATATAAAAAATTTAAAAT
*
12286904 AAATAATATGTGAAAAATAAATTTAAAAT
1 AAATAATA--T-ATAAA-AAATTTAAAAT
* *
12286933 AAATAATATAT---AAATAT-ATAT
1 AAATAATATATAAAAAATTTAAAAT
* * * *
12286954 ACAT-ATATA-AAACAGTTTAATAT
1 AAATAATATATAAAAAATTTAAAAT
* *
12286977 AATTAATATAT--GAAATCTTAAAAT
1 AAATAATATATAAAAAAT-TTAAAAT
** *
12287001 --A-AATA-ATAAAAGGTTTACAAT
1 AAATAATATATAAAAAATTTAAAAT
*
12287022 AAATAATA-A-AAAGAATTT-AAAT
1 AAATAATATATAAAAAATTTAAAAT
** * * * * *
12287044 CAGTTAACATATAAAACA-GTATGACT
1 -AAATAATATATAAAAAATTTA-AAAT
*
12287070 AAATAACATAT--AAAATTTAAAAT
1 AAATAATATATAAAAAATTTAAAAT
* *
12287093 AGATAATATATATAAAATAGTTTAAAGT
1 AAATAATATATA-AAAA-A-TTTAAAAT
*
12287121 AAATAACATATAAAAATATTTAAAAT
1 AAATAATATATAAAAA-ATTTAAAAT
*
12287147 AAATAATATGTAAAA
1 AAATAATATATAAAA
12287162 CTGGTTAAAA
Statistics
Matches: 363, Mismatches: 90, Indels: 102
0.65 0.16 0.18
Matches are distributed among these distances:
20 9 0.02
21 25 0.07
22 44 0.12
23 43 0.12
24 67 0.18
25 24 0.07
26 70 0.19
27 24 0.07
28 23 0.06
29 19 0.05
30 15 0.04
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (25 bp):
AAATAATATATAAAAAATTTAAAAT
Found at i:12287169 original size:26 final size:26
Alignment explanation
Indices: 12287069--12287178 Score: 100
Period size: 26 Copynumber: 4.2 Consensus size: 26
12287059 ACAGTATGAC
*
12287069 TAAATAACATAT-AAAA--TTTAAAA
1 TAAATAATATATAAAAATGTTTAAAA
* *
12287092 TAGATAATATATATAAAATAGTTTAAAG
1 TAAATAATATATA-AAAAT-GTTTAAAA
* *
12287120 TAAATAACATATAAAAATATTTAAAA
1 TAAATAATATATAAAAATGTTTAAAA
* * *
12287146 TAAATAATATGTAAAACTGGTTAAAA
1 TAAATAATATATAAAAATGTTTAAAA
12287172 TGAAATA
1 T-AAATA
12287179 TTTATATATA
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
23 10 0.14
25 4 0.06
26 28 0.41
27 10 0.14
28 17 0.25
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (26 bp):
TAAATAATATATAAAAATGTTTAAAA
Found at i:12288411 original size:17 final size:17
Alignment explanation
Indices: 12288369--12288419 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
12288359 AGGTTTGTAA
*
12288369 TTGGGTTTTAACTTTGGG
1 TTGGGTTTT-AGTTTGGG
*
12288387 TT-GG-TTTAGTTTGGT
1 TTGGGTTTTAGTTTGGG
12288402 TTGGGTTTTAGTTTGGG
1 TTGGGTTTTAGTTTGGG
12288419 T
1 T
12288420 CATCTGCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 8 0.29
16 5 0.18
17 13 0.46
18 2 0.07
ACGTcount: A:0.08, C:0.02, G:0.35, T:0.55
Consensus pattern (17 bp):
TTGGGTTTTAGTTTGGG
Found at i:12288890 original size:44 final size:45
Alignment explanation
Indices: 12288855--12289287 Score: 178
Period size: 44 Copynumber: 9.8 Consensus size: 45
12288845 TTGTTGCTTT
12288855 AATCTACTCCAATGCAACTTCAGGAAGATAAGATTTGCTATCTTC
1 AATCTACTCCAATGCAACTTCAGGAAGATAAGATTTGCTATCTTC
* * * * * * *
12288900 AGTCTGCTCCACTGCAACTACAGGGAGATAAGA-CT-CTTAACTTC
1 AATCTACTCCAATGCAACTTCAGGAAGATAAGATTTGC-TATCTTC
* * * * ** *
12288944 AACCT-GTCCCACTGCAACTTTAGGGGGATAAGGTTTGCTATCTTC
1 AATCTACT-CCAATGCAACTTCAGGAAGATAAGATTTGCTATCTTC
* * * * * * * *
12288989 GATCTACTCCACTGCAGCTCCAGGAGGATCAGATCTG-TAACTTC
1 AATCTACTCCAATGCAACTTCAGGAAGATAAGATTTGCTATCTTC
* * *
12289033 AATCTACTCCACTACAAC-TCTAGGGAGATAAGACTCTTG--A-CTTC
1 AATCTACTCCAATGCAACTTC-AGGAAGATAAGA-T-TTGCTATCTTC
* * * * * *
12289077 AA-CTTGCCCCACTGCAACTTCAGGGAGATAAGGTTTACTATCTTC
1 AATC-TACTCCAATGCAACTTCAGGAAGATAAGATTTGCTATCTTC
* ** *** *
12289122 AATCTACTCCACTGCAAC-TCTAGGGGGATAAGACCAG-TAACTTC
1 AATCTACTCCAATGCAACTTC-AGGAAGATAAGATTTGCTATCTTC
* * * * * **
12289166 AATTTACTCCACTGCAACTTTAGGGAGATAAGATTAG-TGGCTTC
1 AATCTACTCCAATGCAACTTCAGGAAGATAAGATTTGCTATCTTC
* * * * * **
12289210 AATTTGCTCC-CTGCAAC-TCTAGGGAGATAAGATTAG-TGGCTTC
1 AATCTACTCCAATGCAACTTC-AGGAAGATAAGATTTGCTATCTTC
* * *
12289253 AATATGCTCCACTGCAACTTCAGAGAA-ATAAGATT
1 AATCTACTCCAATGCAACTTCAG-GAAGATAAGATT
12289288 CGCCATGGTG
Statistics
Matches: 308, Mismatches: 60, Indels: 41
0.75 0.15 0.10
Matches are distributed among these distances:
42 3 0.01
43 44 0.14
44 159 0.52
45 97 0.31
46 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (45 bp):
AATCTACTCCAATGCAACTTCAGGAAGATAAGATTTGCTATCTTC
Found at i:12288974 original size:89 final size:89
Alignment explanation
Indices: 12288858--12289286 Score: 279
Period size: 89 Copynumber: 4.9 Consensus size: 89
12288848 TTGCTTTAAT
* * *
12288858 CTACTCCAATGCAACTTCAGGAAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTACAG
1 CTACTCCACTGCAACTTTAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTACAG
12288923 GGAGATAAGACTCT-TAACTTCAAC
66 GGAGATAAGA-TCTGTAACTTCAAC
* * * * * *
12288947 CT-GTCCCACTGCAACTTTAGGGGGATAAGGTTTGCTATCTTC-GATCTACTCCACTGCAGCTCC
1 CTACT-CCACTGCAACTTTAGGGAGATAAGATTTGCTATCTTCAG-TCTGCTCCACTGCAACTAC
* *
12289010 A-GGAGGATCAGATCTGTAACTTCAAT
64 AGGGA-GATAAGATCTGTAACTTCAAC
* * * * *
12289036 CTACTCCACTACAACTCTAGGGAGATAAGACTCTTG--A-CTTCA-ACTTGCCCCACTGCAACTT
1 CTACTCCACTGCAACTTTAGGGAGATAAGA-T-TTGCTATCTTCAGTC-TGCTCCACTGCAACTA
* * * * *
12289097 CAGGGAGATAAGGTTTACTATCTTCAAT
63 CAGGGAGATAAGATCT-GTAACTTCAAC
* * *** * * * * **
12289125 CTACTCCACTGCAACTCTAGGGGGATAAGACCAG-TAACTTCAATTTACTCCACTGCAACTTTAG
1 CTACTCCACTGCAACTTTAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTACAG
** *
12289189 GGAGATAAGAT-TAGTGGCTTCAAT
66 GGAGATAAGATCT-GTAACTTCAAC
* * * * ** * * *
12289213 TTGCTCC-CTGCAACTCTAGGGAGATAAGATTAG-TGGCTTCAATATGCTCCACTGCAACTTCAG
1 CTACTCCACTGCAACTTTAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTACAG
* *
12289276 AGAAATAAGAT
66 GGAGATAAGAT
12289287 TCGCCATGGT
Statistics
Matches: 274, Mismatches: 52, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
87 59 0.22
88 49 0.18
89 161 0.59
90 2 0.01
91 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (89 bp):
CTACTCCACTGCAACTTTAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTACAG
GGAGATAAGATCTGTAACTTCAAC
Found at i:12289058 original size:133 final size:133
Alignment explanation
Indices: 12288855--12289198 Score: 456
Period size: 133 Copynumber: 2.6 Consensus size: 133
12288845 TTGTTGCTTT
* * * * * * *
12288855 AATCTACTCCAATGCAACTTCAGGAAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTA
1 AATCTACTCCACTGCAACTCCAGGAGGATAAGATCTG-TAACTTCAATCTACTCCACTGCAACT-
* * * *
12288920 C-AGGGAGATAAGACTCTTAACTTCAACCTGTCCCACTGCAACTTTAGGGGGATAAGGTTTGCTA
64 CTAGGGAGATAAGACTCTTAACTTCAACCTGCCCCACTGCAACTTCAGGGAGATAAGGTTTACTA
12288984 TCTTC
129 TCTTC
* * * *
12288989 GATCTACTCCACTGCAGCTCCAGGAGGATCAGATCTGTAACTTCAATCTACTCCACTACAACTCT
1 AATCTACTCCACTGCAACTCCAGGAGGATAAGATCTGTAACTTCAATCTACTCCACTGCAACTCT
* *
12289054 AGGGAGATAAGACTCTTGACTTCAACTTGCCCCACTGCAACTTCAGGGAGATAAGGTTTACTATC
66 AGGGAGATAAGACTCTTAACTTCAACCTGCCCCACTGCAACTTCAGGGAGATAAGGTTTACTATC
12289119 TTC
131 TTC
* * * * * *
12289122 AATCTACTCCACTGCAACTCTAGGGGGATAAGACCAGTAACTTCAATTTACTCCACTGCAACTTT
1 AATCTACTCCACTGCAACTCCAGGAGGATAAGATCTGTAACTTCAATCTACTCCACTGCAACTCT
12289187 AGGGAGATAAGA
66 AGGGAGATAAGA
12289199 TTAGTGGCTT
Statistics
Matches: 182, Mismatches: 27, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
132 1 0.01
133 151 0.83
134 30 0.16
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (133 bp):
AATCTACTCCACTGCAACTCCAGGAGGATAAGATCTGTAACTTCAATCTACTCCACTGCAACTCT
AGGGAGATAAGACTCTTAACTTCAACCTGCCCCACTGCAACTTCAGGGAGATAAGGTTTACTATC
TTC
Found at i:12289210 original size:133 final size:133
Alignment explanation
Indices: 12288855--12289271 Score: 444
Period size: 133 Copynumber: 3.1 Consensus size: 133
12288845 TTGTTGCTTT
* * * *** * * *
12288855 AATCTACTCCAATGCAACTTCAGGAAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTA
1 AATCTACTCCACTGCAACTCCAGGAGGATAAGACCAG-TAACTTCAATCTACTCCACTGCAACTA
* * * * * * *
12288920 CAGGGAGATAAGACTCTTAACTTCAACCTGTCCCACTGCAACTTTAGGGGGATAAGGTTTGCTAT
65 TAGGGAGATAAGACTCTTGACTTCAACTTGCCCCACTGCAACTTCAGGGAGATAAGGTTTACTAT
12288985 CTTC
130 CTTC
* * * * * * *
12288989 GATCTACTCCACTGCAGCTCCAGGAGGATCAGATCTGTAACTTCAATCTACTCCACTACAACTCT
1 AATCTACTCCACTGCAACTCCAGGAGGATAAGACCAGTAACTTCAATCTACTCCACTGCAACTAT
12289054 AGGGAGATAAGACTCTTGACTTCAACTTGCCCCACTGCAACTTCAGGGAGATAAGGTTTACTATC
66 AGGGAGATAAGACTCTTGACTTCAACTTGCCCCACTGCAACTTCAGGGAGATAAGGTTTACTATC
12289119 TTC
131 TTC
* * * *
12289122 AATCTACTCCACTGCAACTCTAGGGGGATAAGACCAGTAACTTCAATTTACTCCACTGCAACTTT
1 AATCTACTCCACTGCAACTCCAGGAGGATAAGACCAGTAACTTCAATCTACTCCACTGCAACTAT
* ** * * * * * **
12289187 AGGGAGATAAGATTAGTGGCTTCAATTTGCTCC-CTGCAAC-TCTAGGGAGATAA-GATTAGTGG
66 AGGGAGATAAGACTCTTGACTTCAACTTGCCCCACTGCAACTTC-AGGGAGATAAGGTTTACTAT
12289249 CTTC
130 CTTC
* *
12289253 AATATGCTCCACTGCAACT
1 AATCTACTCCACTGCAACT
12289272 TCAGAGAAAT
Statistics
Matches: 241, Mismatches: 41, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
131 28 0.12
132 17 0.07
133 166 0.69
134 30 0.12
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (133 bp):
AATCTACTCCACTGCAACTCCAGGAGGATAAGACCAGTAACTTCAATCTACTCCACTGCAACTAT
AGGGAGATAAGACTCTTGACTTCAACTTGCCCCACTGCAACTTCAGGGAGATAAGGTTTACTATC
TTC
Found at i:12292248 original size:37 final size:37
Alignment explanation
Indices: 12292203--12292274 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 37
12292193 ATCCATATGA
12292203 TTGGTTATGAATGAAAT-AGAAAGAATAAAAGAATATT
1 TTGGTTATGAATGAAATGA-AAAGAATAAAAGAATATT
12292240 TTGGTTATGAATGAAATGAAAAGAATAAAAGAATA
1 TTGGTTATGAATGAAATGAAAAGAATAAAAGAATA
12292275 CTTGCTCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 33 0.97
38 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (37 bp):
TTGGTTATGAATGAAATGAAAAGAATAAAAGAATATT
Found at i:12302196 original size:24 final size:23
Alignment explanation
Indices: 12302164--12302215 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
12302154 CGTTATGTTG
*
12302164 AAAATGTTTACAATAAATAATAA
1 AAAAGGTTTACAATAAATAATAA
12302187 TAAAAGGTTTACAATAAATAATAA
1 -AAAAGGTTTACAATAAATAATAA
12302211 AAAAG
1 AAAAG
12302216 AATTTAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.27
Consensus pattern (23 bp):
AAAAGGTTTACAATAAATAATAA
Found at i:12302221 original size:24 final size:24
Alignment explanation
Indices: 12302170--12302221 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
12302160 GTTGAAAATG
*
12302170 TTTACAATAAATAATAATAAAAGG
1 TTTACAATAAATAATAATAAAAGA
12302194 TTTACAATAAATAATAA-AAAAGAA
1 TTTACAATAAATAATAATAAAAG-A
12302218 TTTA
1 TTTA
12302222 AATCAGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (24 bp):
TTTACAATAAATAATAATAAAAGA
Found at i:12302323 original size:26 final size:26
Alignment explanation
Indices: 12302250--12302359 Score: 118
Period size: 26 Copynumber: 4.2 Consensus size: 26
12302240 ACAGTATGAC
12302250 TAAATAACATAT--AAA-ATTTAAAA
1 TAAATAACATATAAAAATATTTAAAA
* *
12302273 TAGATAATATATATAAAATAGTTTAAAA
1 TAAATAACATATA-AAAATA-TTTAAAA
12302301 TAAATAACATATAAAAATATTTAAAA
1 TAAATAACATATAAAAATATTTAAAA
* * * *
12302327 TAAATAATATGTAAAACTGTTTAAAA
1 TAAATAACATATAAAAATATTTAAAA
12302353 TGAAATA
1 T-AAATA
12302360 TTTATATATA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.14
26 33 0.45
27 12 0.16
28 18 0.25
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (26 bp):
TAAATAACATATAAAAATATTTAAAA
Found at i:12302367 original size:54 final size:54
Alignment explanation
Indices: 12302250--12302359 Score: 149
Period size: 54 Copynumber: 2.1 Consensus size: 54
12302240 ACAGTATGAC
*
12302250 TAAATAACATAT--AAA-ATTTAAAATAGATAATATATATAAAATAGTTTAAAA
1 TAAATAACATATAAAAATATTTAAAATAAATAATATATATAAAATAGTTTAAAA
* *
12302301 TAAATAACATATAAAAATATTTAAAATAAATAATATGTA-AAACT-GTTTAAAA
1 TAAATAACATATAAAAATATTTAAAATAAATAATATATATAAAATAGTTTAAAA
12302353 TGAAATA
1 T-AAATA
12302360 TTTATATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
51 12 0.23
52 9 0.17
53 12 0.23
54 19 0.37
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (54 bp):
TAAATAACATATAAAAATATTTAAAATAAATAATATATATAAAATAGTTTAAAA
Found at i:12306534 original size:104 final size:104
Alignment explanation
Indices: 12306210--12306527 Score: 595
Period size: 104 Copynumber: 3.1 Consensus size: 104
12306200 TAACCGTTAT
* * *
12306210 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
12306275 AATCAGCACATAGCAACCCCCTTT--CATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
12306312 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
12306377 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
12306416 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
12306481 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
12306520 TGGTGGAT
1 TGGTGGAT
12306528 CACGCACCAT
Statistics
Matches: 211, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
102 86 0.41
104 125 0.59
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:12306956 original size:29 final size:29
Alignment explanation
Indices: 12306923--12306986 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
12306913 TAATCCACCA
12306923 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
12306952 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
12306982 CCCAA
1 CCCAA
12306987 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:12306960 original size:30 final size:30
Alignment explanation
Indices: 12306930--12306986 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12306920 CCACCCAACT
12306930 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
12306959 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
12306987 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:12310327 original size:34 final size:35
Alignment explanation
Indices: 12310250--12310329 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
12310240 GAAAATATAC
*
12310250 TGAGTTGTGAAACGTAGGTATGACATTTCCCATAT
1 TGAGTTGTGAAACGTAGGTATGACATGTCCCATAT
* **
12310285 TGATTTGTGAAACGTAGGTATGGTATGT-CCATAT
1 TGAGTTGTGAAACGTAGGTATGACATGTCCCATAT
12310319 TGAGTTGTGAA
1 TGAGTTGTGAA
12310330 TGGTGGCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 16 0.40
35 24 0.60
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (35 bp):
TGAGTTGTGAAACGTAGGTATGACATGTCCCATAT
Done.