Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 60 of 250
Found at i:18640226 original size:30 final size:30
Alignment explanation
Indices: 18640191--18640264 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
18640181 AGTTTTTCCC
18640191 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
18640221 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
18640251 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
18640265 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:18641929 original size:19 final size:18
Alignment explanation
Indices: 18641884--18641930 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
18641874 AAATTGATTG
*
18641884 AAAAA-AAAAATTCAAAA
1 AAAAAGAAAAATGCAAAA
*
18641901 AAAAGTGAAAAATAGCAAAA
1 AAAA-AGAAAAAT-GCAAAA
18641921 AAAAAGAAAA
1 AAAAAGAAAA
18641931 GAAAAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 4 0.17
19 11 0.46
20 9 0.38
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.09
Consensus pattern (18 bp):
AAAAAGAAAAATGCAAAA
Found at i:18643000 original size:11 final size:12
Alignment explanation
Indices: 18642984--18643019 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
18642974 AAAGAAATTG
18642984 AAAGAAAAC-AA
1 AAAGAAAACGAA
18642995 AAAGAAAACGAA
1 AAAGAAAACGAA
*
18643007 AAAGAAAAAGAA
1 AAAGAAAACGAA
18643019 A
1 A
18643020 TTGCAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.81, C:0.06, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:18643044 original size:17 final size:17
Alignment explanation
Indices: 18642970--18643044 Score: 66
Period size: 17 Copynumber: 4.5 Consensus size: 17
18642960 AGAAAGAGAT
**
18642970 TGAAAAAGAAATTGAAA
1 TGAAAAAGAAAAAGAAA
*
18642987 -G-AAAACAAAAAGAAAA
1 TGAAAAAGAAAAAG-AAA
*
18643003 CGAAAAAGAAAAAGAAA
1 TGAAAAAGAAAAAGAAA
*
18643020 TTG-CAAAGAAAAAGAAA
1 -TGAAAAAGAAAAAGAAA
18643037 TGAAAAAG
1 TGAAAAAG
18643045 TGAGAGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
15 8 0.17
16 6 0.13
17 21 0.46
18 11 0.24
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.08
Consensus pattern (17 bp):
TGAAAAAGAAAAAGAAA
Found at i:18643112 original size:33 final size:33
Alignment explanation
Indices: 18643075--18643137 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
18643065 AAAAGAAATT
18643075 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
18643108 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
18643138 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:18644941 original size:20 final size:20
Alignment explanation
Indices: 18644918--18644963 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
18644908 CCAGCTCGAA
*
18644918 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
18644938 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
18644958 TTAGCT
1 TTAGCT
18644964 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:18644945 original size:30 final size:30
Alignment explanation
Indices: 18644910--18644983 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
18644900 AGTTTTTCCC
18644910 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
18644940 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
18644970 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
18644984 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:18652675 original size:56 final size:55
Alignment explanation
Indices: 18652559--18652676 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
18652549 TGCATGCTTT
* * * *
18652559 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
18652613 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
18652669 CATTAAAT
1 CATTAAAT
18652677 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:18653326 original size:20 final size:20
Alignment explanation
Indices: 18653301--18653355 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
18653291 ACGAGTTAAA
* *
18653301 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
18653321 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
18653341 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
18653356 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:18654486 original size:56 final size:55
Alignment explanation
Indices: 18654370--18654487 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
18654360 TGCATGCTTT
* * * *
18654370 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
18654424 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
18654480 CATTAAAT
1 CATTAAAT
18654488 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:18655135 original size:20 final size:20
Alignment explanation
Indices: 18655110--18655164 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
18655100 ACGAGTTAAA
* *
18655110 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
18655130 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
18655150 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
18655165 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:18658337 original size:22 final size:21
Alignment explanation
Indices: 18658298--18658348 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
18658288 TTGAGAGTGA
*
18658298 AAAAGAAATTGAAGAAAGAAGAG
1 AAAAG-AATTGAAGAAAGAA-AC
18658321 AAAAGAATTAGAA-AAAGAAAC
1 AAAAGAATT-GAAGAAAGAAAC
18658342 AAAAGAA
1 AAAAGAA
18658349 AAAGACGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
22 10 0.38
23 8 0.31
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.08
Consensus pattern (21 bp):
AAAAGAATTGAAGAAAGAAAC
Found at i:18661047 original size:56 final size:55
Alignment explanation
Indices: 18660931--18661048 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
18660921 TGCATGCTTT
* * * *
18660931 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
18660985 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
18661041 CATTAAAT
1 CATTAAAT
18661049 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:18661697 original size:20 final size:20
Alignment explanation
Indices: 18661672--18661725 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
18661662 ACGAGTTAAA
* *
18661672 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
18661692 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
18661712 TTGAGCTCGAATGA
1 TTGAGCTCGAATGA
18661726 TTGAACCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:18662857 original size:56 final size:55
Alignment explanation
Indices: 18662741--18662858 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
18662731 TGCATGCTTT
* * * *
18662741 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
18662795 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
18662851 CATTAAAT
1 CATTAAAT
18662859 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:18663507 original size:20 final size:20
Alignment explanation
Indices: 18663482--18663535 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
18663472 ACGAGTTAAA
* *
18663482 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
18663502 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
18663522 TTGAGCTCGAATGA
1 TTGAGCTCGAATGA
18663536 ATTGAACCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:18664668 original size:56 final size:55
Alignment explanation
Indices: 18664552--18664669 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
18664542 TGCATGCTTT
* * * *
18664552 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
18664606 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
18664662 CATTAAAT
1 CATTAAAT
18664670 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:18665311 original size:20 final size:20
Alignment explanation
Indices: 18665268--18665339 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
18665258 GAGCTAATAA
* * *
18665268 TGAGCTC-AACGAGTTAAAT
1 TGAGCTCGAATGAGCTAACT
* *
18665287 TGAGCTTGAATGAGCTGACT
1 TGAGCTCGAATGAGCTAACT
*
18665307 TGAGCACGAATGAGCTAACT
1 TGAGCTCGAATGAGCTAACT
18665327 TGAGCTCGAATGA
1 TGAGCTCGAATGA
18665340 ATTGAACCAC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 6 0.14
20 37 0.86
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (20 bp):
TGAGCTCGAATGAGCTAACT
Found at i:18666473 original size:56 final size:55
Alignment explanation
Indices: 18666357--18666474 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
18666347 TGCATGCTTT
* * * *
18666357 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
18666411 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
18666467 CATTAAAT
1 CATTAAAT
18666475 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:18667113 original size:20 final size:20
Alignment explanation
Indices: 18667090--18667152 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
18667080 CGAGCTCAAC
*
18667090 GAGCTAAATTGAGCTTGAAT
1 GAGCTAACTTGAGCTTGAAT
* *
18667110 GAGCTGACTTGAGCATGAAT
1 GAGCTAACTTGAGCTTGAAT
*
18667130 GAGCTAACTTGAGCTCGAAT
1 GAGCTAACTTGAGCTTGAAT
18667150 GAG
1 GAG
18667153 TTGAACCACA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (20 bp):
GAGCTAACTTGAGCTTGAAT
Found at i:18671937 original size:12 final size:12
Alignment explanation
Indices: 18671922--18671958 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
18671912 AAACAAAATA
18671922 AGATTGAAAAAG
1 AGATTGAAAAAG
18671934 AGATTGAAAAAG
1 AGATTGAAAAAG
*
18671946 AGAATGAAAAAG
1 AGATTGAAAAAG
18671958 A
1 A
18671959 AAAGGAGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (12 bp):
AGATTGAAAAAG
Found at i:18674055 original size:30 final size:30
Alignment explanation
Indices: 18674021--18674117 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
18674011 AGCTCACTCC
18674021 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * * *
18674051 TAGCTCAACTTCAACTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
18674081 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
18674111 TAGCTCA
1 TAGCTCA
18674118 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:18676747 original size:5 final size:5
Alignment explanation
Indices: 18676737--18676787 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
18676727 AAGAGAAAAC
*
18676737 AAAGA AAAGA AAAGA AAA-A GAAGAA AAAGA AAATGA AATA-A AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAG-A AAAGA AAA-GA AA-AGA AAAGA
18676783 AAAGA
1 AAAGA
18676788 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 4 0.10
5 26 0.67
6 8 0.21
7 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:18676766 original size:15 final size:16
Alignment explanation
Indices: 18676737--18676785 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
18676727 AAGAGAAAAC
18676737 AAAGAAA-AGAAAAGAA
1 AAAGAAAGA-AAAAGAA
18676753 AAAG-AAGAAAAAGAA
1 AAAGAAAGAAAAAGAA
* *
18676768 AATGAAATAAAAAGAA
1 AAAGAAAGAAAAAGAA
18676784 AA
1 AA
18676786 GAGAGGCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAGAAAGAAAAAGAA
Found at i:18676866 original size:13 final size:12
Alignment explanation
Indices: 18676835--18676866 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
18676825 TTGAGGGAAC
18676835 TTGAAAAAGCCT
1 TTGAAAAAGCCT
*
18676847 TTGAAAAATCCT
1 TTGAAAAAGCCT
18676859 TTGAAAAA
1 TTGAAAAA
18676867 CAAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:18676877 original size:6 final size:6
Alignment explanation
Indices: 18676868--18676901 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
18676858 TTTGAAAAAC
* *
18676868 AAAAAG AAAATG AAAATG AAAATG AGAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
18676902 AGAGTTTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (6 bp):
AAAATG
Found at i:18676881 original size:18 final size:18
Alignment explanation
Indices: 18676860--18676902 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
18676850 AAAAATCCTT
18676860 TGAAAAACAAAAAGAAAA
1 TGAAAAACAAAAAGAAAA
** * *
18676878 TGAAAATGAAAATGAGAA
1 TGAAAAACAAAAAGAAAA
18676896 TGAAAAA
1 TGAAAAA
18676903 GAGTTTGAGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.16, T:0.12
Consensus pattern (18 bp):
TGAAAAACAAAAAGAAAA
Found at i:18677957 original size:10 final size:10
Alignment explanation
Indices: 18677942--18677968 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
18677932 TACTCCTTCA
18677942 AGCTCAAATC
1 AGCTCAAATC
18677952 AGCTCAAATC
1 AGCTCAAATC
18677962 AGCTCAA
1 AGCTCAA
18677969 CTTCAACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:18677990 original size:10 final size:10
Alignment explanation
Indices: 18677942--18677990 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
18677932 TACTCCTTCA
*
18677942 AGCTCAAATC
1 AGCTCAACTC
*
18677952 AGCTCAAATC
1 AGCTCAACTC
18677962 AGCTCAACTTC
1 AGCTCAAC-TC
* *
18677973 AACTCAACTT
1 AGCTCAACTC
18677983 AGCTCAAC
1 AGCTCAAC
18677991 GAGCTCGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.37, C:0.33, G:0.08, T:0.22
Consensus pattern (10 bp):
AGCTCAACTC
Found at i:18680135 original size:4 final size:4
Alignment explanation
Indices: 18680116--18680152 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
18680106 GTTGTAAAGT
*
18680116 TTTA TTTT TATTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
18680153 CTTAGTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:18683926 original size:12 final size:13
Alignment explanation
Indices: 18683899--18683931 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
18683889 GTTGTAAAGT
*
18683899 TTTATTTTTATTA
1 TTTATTTATATTA
18683912 TTTATTTAT-TTA
1 TTTATTTATATTA
18683924 TTTATTTA
1 TTTATTTA
18683932 CTTAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATATTA
Found at i:18689606 original size:10 final size:10
Alignment explanation
Indices: 18689558--18689606 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
18689548 TACTCCTTCA
* *
18689558 AGCTCAAATC
1 AGCTCAACTT
*
18689568 AGCTCAAATT
1 AGCTCAACTT
18689578 AGCTCAACTT
1 AGCTCAACTT
*
18689588 CAACTCAACTT
1 -AGCTCAACTT
18689599 AGCTCAAC
1 AGCTCAAC
18689607 GAGCACGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.37, C:0.31, G:0.08, T:0.24
Consensus pattern (10 bp):
AGCTCAACTT
Found at i:18692283 original size:30 final size:30
Alignment explanation
Indices: 18692249--18692345 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
18692239 AGCTCACTCC
18692249 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
18692279 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
18692309 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
18692339 TAGCTCA
1 TAGCTCA
18692346 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:18694874 original size:22 final size:19
Alignment explanation
Indices: 18694832--18694875 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
18694822 GCTAGCTGAA
18694832 ATTATTATGTTAGATAGAT
1 ATTATTATGTTAGATAGAT
18694851 ATTATTATGTTAGATAGAT
1 ATTATTATGTTAGATAGAT
*
18694870 AATATT
1 ATTATT
18694876 TGATTTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.48
Consensus pattern (19 bp):
ATTATTATGTTAGATAGAT
Found at i:18695049 original size:33 final size:33
Alignment explanation
Indices: 18695008--18695084 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 33
18694998 TAAGGTTAGG
*
18695008 TGCATGCAC-AGTTTTATTTAATGAATGGGAAGA
1 TGCATGCACGA-TTTTATTCAATGAATGGGAAGA
18695041 TGCATGCACGATTTTATTCAATGAATGGGAAGA
1 TGCATGCACGATTTTATTCAATGAATGGGAAGA
*
18695074 TTCATGCACGA
1 TGCATGCACGA
18695085 CCAGGTTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 40 0.98
34 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.31
Consensus pattern (33 bp):
TGCATGCACGATTTTATTCAATGAATGGGAAGA
Found at i:18695094 original size:33 final size:33
Alignment explanation
Indices: 18695027--18695094 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
18695017 AGTTTTATTT
****
18695027 AATGAATGGGAAGATGCATGCACGATTTTATTC
1 AATGAATGGGAAGATGCATGCACGACCAGATTC
* *
18695060 AATGAATGGGAAGATTCATGCACGACCAGGTTC
1 AATGAATGGGAAGATGCATGCACGACCAGATTC
18695093 AA
1 AA
18695095 AGCTAAGTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (33 bp):
AATGAATGGGAAGATGCATGCACGACCAGATTC
Found at i:18696468 original size:30 final size:30
Alignment explanation
Indices: 18696434--18696530 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
18696424 TAAACTAAAA
*
18696434 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * * *
18696464 TGAGCTGAGATTAAACTCCTAAGTTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
*
18696494 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
18696523 ATGAGCTA
1 -TGAGCTA
18696531 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:18699088 original size:23 final size:24
Alignment explanation
Indices: 18699058--18699102 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
18699048 AAGTTTTGAA
*
18699058 AAAAAAAAATT-CGAAAAAAAAGG
1 AAAAAAAAATTGCAAAAAAAAAGG
18699081 AAAAAAAAATTGCAAAAAAAAA
1 AAAAAAAAATTGCAAAAAAAAA
18699103 ATTGCATACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (24 bp):
AAAAAAAAATTGCAAAAAAAAAGG
Found at i:18699098 original size:14 final size:14
Alignment explanation
Indices: 18699081--18699108 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18699071 AAAAAAAAGG
18699081 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
18699095 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
18699109 TACGGTCTAG
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:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAAAATTGCA
Found at i:18701388 original size:24 final size:25
Alignment explanation
Indices: 18701361--18701414 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
18701351 ATGAGTGATA
*
18701361 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
18701385 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
18701409 AAAAAA
1 AAAAAA
18701415 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:18710874 original size:40 final size:40
Alignment explanation
Indices: 18710802--18710877 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
18710792 TATACATATA
*
18710802 TAGCCGAAGCTATCTCCAATCACACACCAAGTGCCACATT
1 TAGCCGAAGCTATCTCCAACCACACACCAAGTGCCACATT
* * * * *
18710842 TAGCCGAAGCTATTTCGAACCCCATACTAAGTGCCA
1 TAGCCGAAGCTATCTCCAACCACACACCAAGTGCCA
18710878 TTTTTTTAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.32, C:0.33, G:0.14, T:0.21
Consensus pattern (40 bp):
TAGCCGAAGCTATCTCCAACCACACACCAAGTGCCACATT
Found at i:18714463 original size:42 final size:42
Alignment explanation
Indices: 18714413--18714509 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
18714403 TGATGCCATG
* * * *
18714413 TCCCAGACATGGTCTTATACGAAATCACATATCGATGCCGCA
1 TCCCAGACATGGTCTTACACGAAATCACATACCGAAGCCACA
* * *
18714455 TCCCAGACATAGTCTTACACGAAATCTCATACCGAAGCCATA
1 TCCCAGACATGGTCTTACACGAAATCACATACCGAAGCCACA
*
18714497 TCCCAGATATGGT
1 TCCCAGACATGGT
18714510 TGATGTGAGC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAAATCACATACCGAAGCCACA
Found at i:18716217 original size:48 final size:48
Alignment explanation
Indices: 18716161--18716319 Score: 255
Period size: 48 Copynumber: 3.3 Consensus size: 48
18716151 CTTACATGTA
* *
18716161 ATCTCATATCGATGCTGATGTCATATCCCATATATGGTCTTACACAAG
1 ATCTCATATCGATGCTGATGACATATCCCAGATATGGTCTTACACAAG
*
18716209 ATCTCATATCGATGTTGATGACATATCCCAGATATGGTCTTACACAAG
1 ATCTCATATCGATGCTGATGACATATCCCAGATATGGTCTTACACAAG
* * * *
18716257 ATCTCGTATCGATGCTGATGCCATATCCCAGATATGGTCTTACATAGG
1 ATCTCATATCGATGCTGATGACATATCCCAGATATGGTCTTACACAAG
18716305 ATCTCATATCGATGC
1 ATCTCATATCGATGC
18716320 CATGTCCTAG
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 102 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (48 bp):
ATCTCATATCGATGCTGATGACATATCCCAGATATGGTCTTACACAAG
Found at i:18716394 original size:37 final size:37
Alignment explanation
Indices: 18716332--18716450 Score: 152
Period size: 37 Copynumber: 3.2 Consensus size: 37
18716322 TGTCCTAGAC
* *
18716332 ATGGTCTTACACGT-ATCACAATGCCATAGCCCAACA
1 ATGGTCTTACACGTCATCACGATGCCATAGCCCAACT
*
18716368 ATGGTCTTACATGTCATCACGATGCCATAGCCCAACT
1 ATGGTCTTACACGTCATCACGATGCCATAGCCCAACT
* * * *
18716405 ATGGTCTTACACG-CTATTATGATGCCATAGCCTAGCT
1 ATGGTCTTACACGTC-ATCACGATGCCATAGCCCAACT
18716442 ATGGTCTTA
1 ATGGTCTTA
18716451 TATATACCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
36 14 0.19
37 59 0.81
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (37 bp):
ATGGTCTTACACGTCATCACGATGCCATAGCCCAACT
Found at i:18720047 original size:30 final size:30
Alignment explanation
Indices: 18719952--18720048 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
18719942 AGCTCACTCC
* * *
18719952 TAGCTC-ACTTTCAACTCATGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
18719982 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
18720012 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
18720042 TAGCTCA
1 TAGCTCA
18720049 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:18722586 original size:21 final size:21
Alignment explanation
Indices: 18722552--18722607 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
18722542 ACATTCTTGT
18722552 AAAGAGAAAA-CAAAGAAAAG-A
1 AAAGA-AAAAGCAAA-AAAAGAA
*
18722573 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAGAA
18722594 AAAGAAAAAG-AAAA
1 AAAGAAAAAGCAAAA
18722608 TGAGATTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 12 0.38
21 20 0.62
ACGTcount: A:0.79, C:0.04, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAGCAAAAAAAGAA
Found at i:18722594 original size:15 final size:15
Alignment explanation
Indices: 18722563--18722605 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
18722553 AAGAGAAAAC
*
18722563 AAAGAAAAGAAAAGAA
1 AAAGAAAA-AGAAGAA
*
18722579 AAAGCAAAAGAAGAA
1 AAAGAAAAAGAAGAA
18722594 AAAGAAAAAGAA
1 AAAGAAAAAGAA
18722606 AATGAGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAGAA
Found at i:18722640 original size:24 final size:24
Alignment explanation
Indices: 18722572--18722660 Score: 62
Period size: 24 Copynumber: 3.8 Consensus size: 24
18722562 CAAAGAAAAG
18722572 AAAAGAAAAAGCAAAA-G-AA--GA
1 AAAAGAAAAAG-AAAATGAAATTGA
*
18722593 AAAAGAAAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGAAATTGA
* *
18722617 AAAAGAGAACGAAAA-GAAATTTGA
1 AAAAGAAAAAGAAAATGAAA-TTGA
* ** *
18722641 GAGTGAAAAAGAAGATGAAA
1 AAAAGAAAAAGAAAATGAAA
18722661 AAGAAATTGA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
20 4 0.08
21 12 0.23
22 1 0.02
23 3 0.06
24 28 0.54
25 4 0.08
ACGTcount: A:0.66, C:0.02, G:0.22, T:0.09
Consensus pattern (24 bp):
AAAAGAAAAAGAAAATGAAATTGA
Found at i:18722661 original size:30 final size:31
Alignment explanation
Indices: 18722597--18722668 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
18722587 AGAAGAAAAA
* *
18722597 GAAAAAGAAA-ATGAGATTGAAAAAGAGAAC
1 GAAAAAGAAATTTGAGAGTGAAAAAGAGAAC
*
18722627 G-AAAAGAAATTTGAGAGTGAAAAAGA-AGAT
1 GAAAAAGAAATTTGAGAGTGAAAAAGAGA-AC
18722657 GAAAAAGAAATT
1 GAAAAAGAAATT
18722669 GAAACAAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 9 0.25
30 17 0.47
31 10 0.28
ACGTcount: A:0.61, C:0.01, G:0.24, T:0.14
Consensus pattern (31 bp):
GAAAAAGAAATTTGAGAGTGAAAAAGAGAAC
Found at i:18724762 original size:30 final size:31
Alignment explanation
Indices: 18724728--18724824 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
18724718 AGCTCACTCC
*
18724728 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
18724758 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
18724788 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
18724818 TAGCTCA
1 TAGCTCA
18724825 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:18736861 original size:23 final size:22
Alignment explanation
Indices: 18736809--18736861 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
18736799 TCCACGTCTT
*
18736809 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
18736831 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
18736854 TTTCTTTT
1 TTTCTTTT
18736862 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:18738166 original size:11 final size:9
Alignment explanation
Indices: 18738126--18738159 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
18738116 TTTTATTGAA
*
18738126 TTTTGCCTT
1 TTTTGACTT
18738135 TTTTGA-TT
1 TTTTGACTT
18738143 TTTTGACTT
1 TTTTGACTT
18738152 TTTTGACT
1 TTTTGACT
18738160 GATTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.09, C:0.12, G:0.12, T:0.68
Consensus pattern (9 bp):
TTTTGACTT
Found at i:18741570 original size:10 final size:10
Alignment explanation
Indices: 18741554--18741611 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
18741544 CAACTCCGAC
18741554 CAGCTCAATT
1 CAGCTCAATT
* *
18741564 GAGCTCATTT
1 CAGCTCAATT
18741574 CAGCTCAA-T
1 CAGCTCAATT
18741583 CGAGCTCAATT
1 C-AGCTCAATT
*
18741594 TAGCTACAATT
1 CAGCT-CAATT
18741605 CAGCTCA
1 CAGCTCA
18741612 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:18741577 original size:20 final size:20
Alignment explanation
Indices: 18741554--18741614 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
18741544 CAACTCCGAC
18741554 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
18741574 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
18741595 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
18741615 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:18748193 original size:28 final size:28
Alignment explanation
Indices: 18748138--18748214 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
18748128 ATCTTCGATG
*
18748138 TCTCGTACACTAAGTGCCATACTCAATA
1 TCTCGCACACTAAGTGCCATACTCAATA
* *
18748166 TCTCGCACACCAAGTGCCACTA-TTAATA
1 TCTCGCACACTAAGTGCCA-TACTCAATA
* **
18748194 TTTTTCACACTAAGTGCCATA
1 TCTCGCACACTAAGTGCCATA
18748215 TACATATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 2 0.05
28 37 0.90
29 2 0.05
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.30
Consensus pattern (28 bp):
TCTCGCACACTAAGTGCCATACTCAATA
Found at i:18749669 original size:23 final size:22
Alignment explanation
Indices: 18749635--18749680 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
18749625 AAAAGACACC
18749635 TGCAATTAACACA-TTAAAACA
1 TGCAATTAACACATTTAAAACA
18749656 TGCATATTAAACACATTTAAAACA
1 TGCA-ATT-AACACATTTAAAACA
18749680 T
1 T
18749681 AAAACACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.18
22 3 0.14
23 6 0.27
24 9 0.41
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.28
Consensus pattern (22 bp):
TGCAATTAACACATTTAAAACA
Found at i:18750653 original size:37 final size:37
Alignment explanation
Indices: 18750608--18750695 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 37
18750598 CTTGTTCATC
* *
18750608 GTCTTTTCTTTCTT-CAGTCTTTCTCTCTTTTTCAATTT
1 GTCTTTTCTTTCTTGAAATCTTT-T-TCTTTTTCAATTT
*
18750646 -TCTTTTCTTGCTTGAAATCTTTTTCTTTTTCAATTT
1 GTCTTTTCTTTCTTGAAATCTTTTTCTTTTTCAATTT
18750682 GT-TTTTCCTTTCTT
1 GTCTTTT-CTTTCTT
18750696 TCACTCTCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
36 17 0.40
37 20 0.47
38 6 0.14
ACGTcount: A:0.09, C:0.20, G:0.06, T:0.65
Consensus pattern (37 bp):
GTCTTTTCTTTCTTGAAATCTTTTTCTTTTTCAATTT
Found at i:18750717 original size:18 final size:18
Alignment explanation
Indices: 18750663--18750747 Score: 73
Period size: 18 Copynumber: 4.6 Consensus size: 18
18750653 TTGCTTGAAA
*
18750663 TCTTTTTCTTTTTCAATT
1 TCTTTTTCTTTTTCACTT
* *
18750681 TGTTTTTCCTTTCTTTCACTC
1 TCTTTTT-C-TT-TTTCACTT
18750702 TCTTTTTCTTTTTCACTT
1 TCTTTTTCTTTTTCACTT
** * *
18750720 TCTCATTCTTTTT-TCGT
1 TCTTTTTCTTTTTCACTT
18750737 TCTTTTTCTTT
1 TCTTTTTCTTT
18750748 CATTTTTCTC
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
17 11 0.21
18 24 0.45
19 3 0.06
20 3 0.06
21 12 0.23
ACGTcount: A:0.06, C:0.22, G:0.02, T:0.69
Consensus pattern (18 bp):
TCTTTTTCTTTTTCACTT
Found at i:18753756 original size:20 final size:20
Alignment explanation
Indices: 18753733--18753779 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18753723 GGGTTAAGAT
*
18753733 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
18753753 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
18753773 TGAGCTG
1 TGAGCTG
18753780 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:18754435 original size:16 final size:17
Alignment explanation
Indices: 18754402--18754435 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18754392 ACTAGACACA
18754402 ATAAAACATATATTAAT
1 ATAAAACATATATTAAT
*
18754419 ATAAGACATAT-TTAAT
1 ATAAAACATATATTAAT
18754435 A
1 A
18754436 CATTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAAAACATATATTAAT
Found at i:18757665 original size:23 final size:21
Alignment explanation
Indices: 18757628--18757688 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
18757618 TTTCTCACCT
18757628 TTTTCTCTTTTTTTTCCACTTTC
1 TTTTCT-TTTTTTTTCCA-TTTC
* *
18757651 TTTTCTTTTTCTTTTTCATTTT
1 TTTTCTTTTT-TTTTCCATTTC
*
18757673 TTTTCTTGCTTTTTTC
1 TTTTCTT-TTTTTTTC
18757689 TTTTGACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTCTTTTTTTTTCCATTTC
Found at i:18780868 original size:21 final size:21
Alignment explanation
Indices: 18780844--18780911 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
18780834 GATTTTGAAT
18780844 GAAATCGAGAGAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
*** *
18780865 GAAAAT-GAGAGAA-ACTTGAAT
1 G-AAATCGAGAGAAGA-AACAAA
*
18780886 GAAATCGAGAAAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
18780907 GAAAT
1 GAAAT
18780912 GAAAGAAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
20 5 0.15
21 24 0.71
22 5 0.15
ACGTcount: A:0.60, C:0.07, G:0.22, T:0.10
Consensus pattern (21 bp):
GAAATCGAGAGAAGAAACAAA
Found at i:18780884 original size:42 final size:42
Alignment explanation
Indices: 18780822--18780919 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
18780812 AGATTATGAG
* ** *
18780822 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAAACTTGAATGAAATCGAGAAAAGAAACAA
18780864 AGAAAATGAGAGAAACTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAAACTTGAATGAAATCGAGAAAAGAAACAA
*
18780906 AG-AAATGAAAGAAA
1 AGAAAATGAGAGAAA
18780920 AAGAAAATGA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 11 0.22
42 40 0.78
ACGTcount: A:0.58, C:0.05, G:0.23, T:0.13
Consensus pattern (42 bp):
AGAAAATGAGAGAAACTTGAATGAAATCGAGAAAAGAAACAA
Found at i:18780949 original size:24 final size:24
Alignment explanation
Indices: 18780913--18780972 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
18780903 CAAAGAAATG
*
18780913 AAAGAAAAAGAAAATGAGATTGAA
1 AAAGAAAAAGAAAAAGAGATTGAA
* * * *
18780937 AAAGAGAATGAAAAAGAGTTTGAG
1 AAAGAAAAAGAAAAAGAGATTGAA
*
18780961 AGAGAAAAAGAA
1 AAAGAAAAAGAA
18780973 TGTGAATAAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.12
Consensus pattern (24 bp):
AAAGAAAAAGAAAAAGAGATTGAA
Found at i:18781001 original size:18 final size:19
Alignment explanation
Indices: 18780965--18781003 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
18780955 TTTGAGAGAG
*
18780965 AAAAAGAATGTGAATAAGA
1 AAAAAGAATGTGAAAAAGA
*
18780984 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
18781002 AA
1 AA
18781004 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:18786380 original size:33 final size:35
Alignment explanation
Indices: 18786343--18786413 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 35
18786333 TCTTTTTCAA
18786343 TCTCAATCTCAAATTCTTTTT-TCTT-TTTCTTTT
1 TCTCAATCTCAAATTCTTTTTCTCTTATTTCTTTT
* ** *
18786376 TCTCACTCTCATTTTCTTTTTCTTTTATTTCTTTT
1 TCTCAATCTCAAATTCTTTTTCTCTTATTTCTTTT
18786411 TCT
1 TCT
18786414 TTTTCTCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 18 0.56
34 3 0.09
35 11 0.34
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (35 bp):
TCTCAATCTCAAATTCTTTTTCTCTTATTTCTTTT
Found at i:18786406 original size:15 final size:14
Alignment explanation
Indices: 18786387--18786437 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 14
18786377 CTCACTCTCA
18786387 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
18786401 TATTTCTTTTTCTTT
1 T-TTTCTTTTTCTTT
* *
18786416 TTCTCTCATTTCTTT
1 TTTTCT-TTTTCTTT
18786431 TTTTCTT
1 TTTTCTT
18786438 CTCTCAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.16
15 26 0.84
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:18786442 original size:22 final size:21
Alignment explanation
Indices: 18786362--18786448 Score: 97
Period size: 21 Copynumber: 4.2 Consensus size: 21
18786352 CAAATTCTTT
*
18786362 TTTCTTTTTCTTTTTCTCAC-
1 TTTCTTTTTCTTTTTCTCTCA
* * * *
18786382 TCTCATTTTCTTTTTCTTTTA
1 TTTCTTTTTCTTTTTCTCTCA
18786403 TTTCTTTTTCTTTTTCTCTCA
1 TTTCTTTTTCTTTTTCTCTCA
*
18786424 TTTCTTTTT-TTCTTCTCTCAA
1 TTTCTTTTTCTTTTTCTCTC-A
18786445 TTTC
1 TTTC
18786449 ATTCAAGATT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 24 0.44
21 31 0.56
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTTTTTCTTTTTCTCTCA
Found at i:18787299 original size:29 final size:30
Alignment explanation
Indices: 18787257--18787325 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
18787247 CAATCACTCT
* *
18787257 TTTTTTTTTCAATTTTGATTTTTTTTCTTC
1 TTTTTTTTTCAATTCTGAATTTTTTTCTTC
18787287 TTTTTTTTT-AATTCTGAATTTTTTTCTTC
1 TTTTTTTTTCAATTCTGAATTTTTTTCTTC
18787316 TTTTTTTTTC
1 TTTTTTTTTC
18787326 TTCAATACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (30 bp):
TTTTTTTTTCAATTCTGAATTTTTTTCTTC
Found at i:18787389 original size:15 final size:14
Alignment explanation
Indices: 18787369--18787416 Score: 71
Period size: 15 Copynumber: 3.4 Consensus size: 14
18787359 GAATACAAAC
18787369 TTTTTTTTT-GAAT
1 TTTTTTTTTCGAAT
*
18787382 TTTTTTTTTCAAAAT
1 TTTTTTTTTC-GAAT
18787397 TTTTTTTTTCGAAT
1 TTTTTTTTTCGAAT
18787411 TTTTTT
1 TTTTTT
18787417 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 9 0.29
14 9 0.29
15 13 0.42
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTCGAAT
Found at i:18792455 original size:27 final size:26
Alignment explanation
Indices: 18792411--18792463 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
18792401 TTAAAATATG
* * *
18792411 TTAATATGTCTAGCTTAGGACATAATT
1 TTAAAATGTCTAACTTAGAACA-AATT
*
18792438 TTAAAATGTCTAATTTAGAACAAATT
1 TTAAAATGTCTAACTTAGAACAAATT
18792464 AATTAGCTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (26 bp):
TTAAAATGTCTAACTTAGAACAAATT
Found at i:18794048 original size:21 final size:21
Alignment explanation
Indices: 18794022--18794065 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
18794012 CCAATACGTC
18794022 CCTTTCATCTCGAGTATTCCT
1 CCTTTCATCTCGAGTATTCCT
18794043 CCTTTCATCTCGAGTATTCCT
1 CCTTTCATCTCGAGTATTCCT
18794064 CC
1 CC
18794066 ATTTAAGTAG
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:0.14, C:0.36, G:0.09, T:0.41
Consensus pattern (21 bp):
CCTTTCATCTCGAGTATTCCT
Found at i:18794292 original size:93 final size:93
Alignment explanation
Indices: 18794179--18794350 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
18794169 GCCCATAAGT
* *
18794179 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
18794244 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
18794272 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
18794337 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
18794351 CAAATATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:18794346 original size:46 final size:46
Alignment explanation
Indices: 18794171--18794346 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
18794161 TGTAACCCGC
* * *
18794171 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
18794217 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
18794263 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
18794310 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
18794347 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 69 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:18797808 original size:17 final size:17
Alignment explanation
Indices: 18797788--18797820 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18797778 AAAAGAGTGT
18797788 GAAAGAAAAAAAGAAAA
1 GAAAGAAAAAAAGAAAA
*
18797805 GAAAGAAAAAGAGAAA
1 GAAAGAAAAAAAGAAA
18797821 GACTGTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAAAAGAAAA
Found at i:18800567 original size:20 final size:19
Alignment explanation
Indices: 18800544--18800608 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
18800534 AAGCTCAAAC
18800544 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
18800564 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
18800584 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
18800604 GAGCT
1 GAGCT
18800609 GGGGAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:18802423 original size:33 final size:33
Alignment explanation
Indices: 18802385--18802447 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
18802375 GATTACTCAC
18802385 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
18802418 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
18802448 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:18802474 original size:21 final size:21
Alignment explanation
Indices: 18802445--18802500 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
18802435 CAAGCTCTCT
*
18802445 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
18802466 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
18802487 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
18802501 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:18802493 original size:14 final size:14
Alignment explanation
Indices: 18802444--18802500 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
18802434 TCAAGCTCTC
18802444 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
18802457 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
18802471 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
18802485 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
18802499 TT
1 TT
18802501 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:18802560 original size:18 final size:18
Alignment explanation
Indices: 18802462--18802565 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
18802452 TCTTTTTTCG
18802462 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
18802481 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
18802501 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
18802519 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
18802537 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
18802555 CTTTTTGTTTT
1 CTTTTTCTTTT
18802566 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:18802582 original size:6 final size:6
Alignment explanation
Indices: 18802462--18802569 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
18802452 TCTTTTTTCG
* * * **
18802462 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
18802513 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
18802561 -GTTTT CTTT
1 CTTTTT CTTT
18802570 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:18803446 original size:15 final size:16
Alignment explanation
Indices: 18803418--18803452 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
18803408 TGCTGCTTAA
18803418 GGGTCGGTTTCAAAAT
1 GGGTCGGTTTCAAAAT
18803434 GGGTCGG-TTCAAAAT
1 GGGTCGGTTTCAAAAT
18803449 GGGT
1 GGGT
18803453 TACAAGGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.23, C:0.11, G:0.37, T:0.29
Consensus pattern (16 bp):
GGGTCGGTTTCAAAAT
Found at i:18805303 original size:20 final size:19
Alignment explanation
Indices: 18805280--18805344 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
18805270 AAGCTCAAAC
18805280 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
18805300 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
18805320 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
18805340 GAGCT
1 GAGCT
18805345 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:18807159 original size:33 final size:33
Alignment explanation
Indices: 18807121--18807183 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
18807111 GATTACTCAC
18807121 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
18807154 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
18807184 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:18807210 original size:21 final size:21
Alignment explanation
Indices: 18807181--18807236 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
18807171 CAAGCTCTCT
*
18807181 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
18807202 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
18807223 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
18807237 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:18807229 original size:14 final size:14
Alignment explanation
Indices: 18807180--18807236 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
18807170 TCAAGCTCTC
18807180 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
18807193 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
18807207 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
18807221 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
18807235 TT
1 TT
18807237 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:18807264 original size:18 final size:18
Alignment explanation
Indices: 18807243--18807300 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
18807233 TTTTCTCTCA
18807243 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
18807261 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
18807279 CTTTTT-GTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
18807296 GTTTT
1 CTTTT
18807301 CTTTCAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 13 0.38
18 21 0.62
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.74
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:18807291 original size:11 final size:11
Alignment explanation
Indices: 18807275--18807304 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
18807265 TGCAATTTCT
18807275 TTTTCTTTTTG
1 TTTTCTTTTTG
18807286 TTTTCTTTTTG
1 TTTTCTTTTTG
18807297 TTTTCTTT
1 TTTTCTTT
18807305 CAATTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:18807317 original size:6 final size:6
Alignment explanation
Indices: 18807198--18807304 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
18807188 TCTTTTTTCG
* * * **
18807198 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
18807249 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT -GTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
18807296 -GTTTT CTTT
1 CTTTTT CTTT
18807305 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 25, Indels: 8
0.69 0.24 0.08
Matches are distributed among these distances:
5 8 0.11
6 52 0.72
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:18812473 original size:22 final size:24
Alignment explanation
Indices: 18812411--18812509 Score: 134
Period size: 22 Copynumber: 4.3 Consensus size: 24
18812401 AAGTAAGTGA
*
18812411 AAAAAAAGTTTCGACAAAAAGTTC
1 AAAAAAAGTTTCGAAAAAAAGTTC
18812435 AAAAAAAGTTTCGAAAAAAAGTTC
1 AAAAAAAGTTTCGAAAAAAAGTTC
*
18812459 AAAAAAAG-TTC-AAAAAAATTTC
1 AAAAAAAGTTTCGAAAAAAAGTTC
* *
18812481 AAAAAAA-TTTC-AAAAAAATTTT
1 AAAAAAAGTTTCGAAAAAAAGTTC
18812503 AAAAAAA
1 AAAAAAA
18812510 AATTGAAACT
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
22 37 0.52
23 3 0.04
24 31 0.44
ACGTcount: A:0.63, C:0.08, G:0.07, T:0.22
Consensus pattern (24 bp):
AAAAAAAGTTTCGAAAAAAAGTTC
Found at i:18812510 original size:12 final size:11
Alignment explanation
Indices: 18812411--18812509 Score: 117
Period size: 11 Copynumber: 8.6 Consensus size: 11
18812401 AAGTAAGTGA
18812411 AAAAAAAGTTTC
1 AAAAAAA-TTTC
* *
18812423 GACAAAAAGTTC
1 -AAAAAAATTTC
18812435 AAAAAAAGTTTC
1 AAAAAAA-TTTC
*
18812447 GAAAAAAAGTTC
1 -AAAAAAATTTC
*
18812459 AAAAAAAGTTC
1 AAAAAAATTTC
18812470 AAAAAAATTTC
1 AAAAAAATTTC
18812481 AAAAAAATTTC
1 AAAAAAATTTC
*
18812492 AAAAAAATTTT
1 AAAAAAATTTC
18812503 AAAAAAA
1 AAAAAAA
18812510 AATTGAAACT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
11 55 0.71
12 9 0.12
13 13 0.17
ACGTcount: A:0.63, C:0.08, G:0.07, T:0.22
Consensus pattern (11 bp):
AAAAAAATTTC
Found at i:18814590 original size:16 final size:17
Alignment explanation
Indices: 18814571--18814607 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
18814561 AGAAGATTGT
*
18814571 AAAAAAATAA-AAGAAG
1 AAAAAAATAAGAAAAAG
18814587 AAAAAAATAAGAAAAAG
1 AAAAAAATAAGAAAAAG
18814604 AAAA
1 AAAA
18814608 CAAAAGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAAAAATAAGAAAAAG
Found at i:18817257 original size:4 final size:4
Alignment explanation
Indices: 18817248--18817274 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18817238 AAGTTTTATT
18817248 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
18817275 TACTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:18819671 original size:17 final size:18
Alignment explanation
Indices: 18819634--18819671 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
18819624 GATTGAGAGT
* *
18819634 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
18819652 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
18819669 GAA
1 GAA
18819672 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:18819684 original size:13 final size:12
Alignment explanation
Indices: 18819653--18819707 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
18819643 TGTGAAACAG
*
18819653 AAAAGAAATTGA
1 AAAAGAAGTTGA
18819665 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
18819677 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
18819689 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
18819701 AAAAGAA
1 AAAAGAA
18819708 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:18822501 original size:93 final size:93
Alignment explanation
Indices: 18822389--18822559 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
18822379 GCCCAGAAGT
* *
18822389 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
18822454 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCAGATGCCTAGTTACATCTCTC
*
18822482 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
18822547 CGAGTTCAGATGC
66 CGAGCTCAGATGC
18822560 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCAGATGCCTAGTTACATCTCTC
Found at i:18822553 original size:46 final size:45
Alignment explanation
Indices: 18822385--18822550 Score: 201
Period size: 46 Copynumber: 3.6 Consensus size: 45
18822375 ACCCGCCCAG
*
18822385 AAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT
1 AAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCATCCAT
* *
18822431 AAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTTACAT
1 AAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--TCCAT
*** *
18822477 CTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
1 AAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCAT
18822524 AAGTGAACTCGGACTCAACTCAACGAG
1 AAGTGAACTCGGACTCAACTCAACGAG
18822551 TTCAGATGCT
Statistics
Matches: 101, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 58 0.57
47 32 0.32
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (45 bp):
AAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCAT
Found at i:18822575 original size:46 final size:46
Alignment explanation
Indices: 18822386--18822575 Score: 117
Period size: 46 Copynumber: 4.1 Consensus size: 46
18822376 CCCGCCCAGA
* ** * *
18822386 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGCTCAGATGCTCAACCATCC-T
*
18822431 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAGTTA-CATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGCTCAGATGCTC-A---ACCATC-CT
* * * * * * *
18822481 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGCTC--AGATGCTCAACCATCCT
*
18822525 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCAGATGCTCAACCATCCT
18822571 AGTGA
1 AGTGA
18822576 CATGTCACTT
Statistics
Matches: 113, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
44 10 0.09
45 1 0.01
46 63 0.56
47 28 0.25
49 4 0.04
50 6 0.05
51 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCAGATGCTCAACCATCCT
Found at i:18824943 original size:14 final size:14
Alignment explanation
Indices: 18824924--18824985 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
18824914 CAAAGATAAC
18824924 AAGAAAACCGAATA
1 AAGAAAACCGAATA
* *
18824938 AAGAAATCC-AAGA
1 AAGAAAACCGAATA
*
18824951 TAGAGAAACCGAAATA
1 AAGA-AAACCG-AATA
*
18824967 AAGAAATCCAGAATA
1 AAGAAAACC-GAATA
18824982 AAGA
1 AAGA
18824986 GATCCAGGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
13 6 0.16
14 12 0.32
15 12 0.32
16 7 0.19
ACGTcount: A:0.61, C:0.13, G:0.16, T:0.10
Consensus pattern (14 bp):
AAGAAAACCGAATA
Found at i:18824983 original size:15 final size:15
Alignment explanation
Indices: 18824924--18825002 Score: 76
Period size: 15 Copynumber: 5.4 Consensus size: 15
18824914 CAAAGATAAC
*
18824924 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
18824938 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
18824953 GAGAAA-CC-GAAATA
1 AAGAAATCCAG-AATA
18824967 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
18824982 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
18824997 AAGAAA
1 AAGAAA
18825003 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
14 19 0.36
15 33 0.62
16 1 0.02
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:18825011 original size:15 final size:15
Alignment explanation
Indices: 18824935--18825011 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
18824925 AGAAAACCGA
18824935 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
18824950 ATAGAGAAA-CCGAA-
1 ATAAAGAAATCC-AAG
18824964 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
18824978 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
18824994 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
18825009 ATA
1 ATA
18825012 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 38 0.76
16 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:18828038 original size:93 final size:93
Alignment explanation
Indices: 18827923--18828093 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
18827913 GCCCAGAAGT
* *
18827923 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAAATCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAAATCAA
18827988 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
18828016 GAACTCGGACTCAGCTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAAATCAA
*
18828081 CGAGTTCGGATGC
66 CGAGCTCGGATGC
18828094 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAAATCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:18828090 original size:46 final size:46
Alignment explanation
Indices: 18827919--18828090 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
18827909 ACCCGCCCAG
* *
18827919 AAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT
1 AAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT
* * *
18827965 AAGTGAACTCGGACTCAAATCAACGAGCTCGG--ATGC-CTAGTTACAT
1 AAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--TCCAT
*** * *
18828011 CTCTCGAACTCGGACTCAGCTCAACGAGTTCGGACATTCGCATCCAT
1 AAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT
*
18828058 AAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 AAGTGAACTCGGACTCAACTCAACGAGCTCGGA
18828091 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 64 0.62
47 30 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
AAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT
Found at i:18832084 original size:64 final size:64
Alignment explanation
Indices: 18832003--18832185 Score: 185
Period size: 64 Copynumber: 2.8 Consensus size: 64
18831993 AGACATTATG
* *
18832003 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
18832067 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTA-ACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
18832131 AA
63 AA
* * * *
18832133 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
18832186 CGAACTATAT
Statistics
Matches: 96, Mismatches: 17, Indels: 13
0.76 0.13 0.10
Matches are distributed among these distances:
62 9 0.09
63 11 0.11
64 24 0.25
65 18 0.19
66 21 0.22
67 13 0.14
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:18832163 original size:65 final size:66
Alignment explanation
Indices: 18832036--18832163 Score: 170
Period size: 65 Copynumber: 1.9 Consensus size: 66
18832026 TACTATGTGT
* * * *
18832036 ACACCATGTAGACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAA
1 ACACCATGTAGACAAGAGAGCTACGAGATAAATG-AGCTAGGTCACATGCGTGGTACCAAGTGAA
18832101 GG
65 GG
* *
18832103 ACACCATGTA-ACAAGAGAGCTACGAGATAAACTG-GCTAGGTCACATGGGTGGTACTAAGTG
1 ACACCATGTAGACAAGAGAGCTACGAGATAAA-TGAGCTAGGTCACATGCGTGGTACCAAGTG
18832164 TTCACCATGT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
65 23 0.43
66 19 0.35
67 12 0.22
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (66 bp):
ACACCATGTAGACAAGAGAGCTACGAGATAAATGAGCTAGGTCACATGCGTGGTACCAAGTGAAG
G
Found at i:18844101 original size:15 final size:15
Alignment explanation
Indices: 18844077--18844153 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
18844067 GAATGAAGTG
* *
18844077 GAAAAAGAAAGATAA
1 GAAAATGAAAAATAA
*
18844092 GAAAATGAAAAAGAA
1 GAAAATGAAAAATAA
* *
18844107 AAAAATGAGAAA-AA
1 GAAAATGAAAAATAA
*
18844121 GAAAGT-AAAAAT-A
1 GAAAATGAAAAATAA
*
18844134 GAAAAAGAAAGAA-AA
1 GAAAATGAAA-AATAA
18844149 GAAAA
1 GAAAA
18844154 AATGAGAGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
13 9 0.19
14 9 0.19
15 30 0.62
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.06
Consensus pattern (15 bp):
GAAAATGAAAAATAA
Found at i:18844154 original size:24 final size:24
Alignment explanation
Indices: 18844100--18844177 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
18844090 AAGAAAATGA
18844100 AAAAGAAAAAAATGAG--AA-AAAG
1 AAAAG-AAAAAATGAGAAAAGAAAG
*
18844122 -AAAGTAAAAAT-AGAAAAAGAAAG
1 AAAAGAAAAAATGAG-AAAAGAAAG
*
18844145 AAAAGAAAAAATGAGAGAAGAAA-
1 AAAAGAAAAAATGAGAAAAGAAAG
18844168 AACAAGAAAA
1 AA-AAGAAAA
18844178 TGAAAATGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 2 0.04
20 6 0.13
21 4 0.09
22 2 0.04
23 6 0.13
24 24 0.52
25 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (24 bp):
AAAAGAAAAAATGAGAAAAGAAAG
Found at i:18844195 original size:57 final size:56
Alignment explanation
Indices: 18844077--18844199 Score: 135
Period size: 57 Copynumber: 2.2 Consensus size: 56
18844067 GAATGAAGTG
* *
18844077 GAAAAAGAAAGATAAGAAAATGAAAAAGAAAAAAATGAGAAAAAGAAAGTAAAAATA
1 GAAAAAGAAAGAAAAGAAAATGAAAAAGAAAAAAA-GAGAAAAAGAAAATAAAAATA
* * * *
18844134 GAAAAAGAAAGAAAAGAAAAAATGAGAGAAGAAAAACA-AGAAAATGAAAATGAAAAT-
1 GAAAAAGAAAGAAAAG--AAAATGA-AAAAGAAAAAAAGAGAAAAAGAAAATAAAAATA
18844191 G-AAAAGAAA
1 GAAAAAGAAA
18844200 AGCTTGATTG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
56 8 0.14
57 16 0.28
58 16 0.28
59 7 0.12
60 10 0.18
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (56 bp):
GAAAAAGAAAGAAAAGAAAATGAAAAAGAAAAAAAGAGAAAAAGAAAATAAAAATA
Found at i:18845283 original size:45 final size:45
Alignment explanation
Indices: 18845188--18845348 Score: 211
Period size: 45 Copynumber: 3.6 Consensus size: 45
18845178 CGGTATTTCA
* *
18845188 CCTGCTAGGCTCGAA-GCTCG-ATA-TCATTTCACCGACATTATAG
1 CCTGCTAGGCTCAAAGGCTCGAATAGT-ATCTCACCGACATTATAG
* * * *
18845231 CCTGCTAGGCTCGAAGGCCCGAATAGTATCTCACTGGCATTATAG
1 CCTGCTAGGCTCAAAGGCTCGAATAGTATCTCACCGACATTATAG
*
18845276 CCTGCTAGGCTCAAAGGCTCGAATAGTATCTCACCGACATCATAG
1 CCTGCTAGGCTCAAAGGCTCGAATAGTATCTCACCGACATTATAG
* *
18845321 CCTGCTAGGTTCAAAAGCTCGAATAGTA
1 CCTGCTAGGCTCAAAGGCTCGAATAGTA
18845349 CCGTACGATA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
43 15 0.14
44 4 0.04
45 84 0.81
46 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (45 bp):
CCTGCTAGGCTCAAAGGCTCGAATAGTATCTCACCGACATTATAG
Found at i:18846515 original size:13 final size:13
Alignment explanation
Indices: 18846497--18846521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18846487 TGGTCATCAT
18846497 GGTGTGAACACAA
1 GGTGTGAACACAA
18846510 GGTGTGAACACA
1 GGTGTGAACACA
18846522 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:18847100 original size:30 final size:30
Alignment explanation
Indices: 18847004--18847088 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
18846994 TAAACTAAAA
* *
18847004 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * *
18847034 TGAGCTGAGATTAAACTCCTAAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
*
18847064 TGAGCTAAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCGTGAGCT
18847089 GAATATGAGC
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:18848087 original size:20 final size:20
Alignment explanation
Indices: 18848064--18848129 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
18848054 AGCTCCGTGC
18848064 AGCTCAACTCAGCTTATTTG
1 AGCTCAACTCAGCTTATTTG
** * **
18848084 AGCTCATTTTAGCTCGTTTG
1 AGCTCAACTCAGCTTATTTG
*
18848104 AGCTCAAC-CGAGCTTACTTTC
1 AGCTCAACTC-AGCTTA-TTTG
18848125 AGCTC
1 AGCTC
18848130 CTTCTTTCTT
Statistics
Matches: 33, Mismatches: 11, Indels: 3
0.70 0.23 0.06
Matches are distributed among these distances:
20 25 0.76
21 8 0.24
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (20 bp):
AGCTCAACTCAGCTTATTTG
Found at i:18851179 original size:10 final size:10
Alignment explanation
Indices: 18851164--18851220 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
18851154 CACCTGAGCA
18851164 CGTTTCAGCT
1 CGTTTCAGCT
18851174 CGTTTCAGCT
1 CGTTTCAGCT
*
18851184 CGTTTGAGCT
1 CGTTTCAGCT
* *
18851194 TGATTTTAGCT
1 CG-TTTCAGCT
18851205 CGTTTCAGCT
1 CGTTTCAGCT
*
18851215 TGTTTC
1 CGTTTC
18851221 TTTTCCATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
10 32 0.80
11 8 0.20
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (10 bp):
CGTTTCAGCT
Found at i:18856092 original size:21 final size:21
Alignment explanation
Indices: 18856057--18856110 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
18856047 GCTAGGAGTG
*
18856057 AGCTCGATTT-AGCTC-AGACA
1 AGCTGGATTTGAGCTCGA-ACA
* *
18856077 AGTTGGATTTGAGCTCGAATA
1 AGCTGGATTTGAGCTCGAACA
18856098 AGCTGGATTTGAG
1 AGCTGGATTTGAG
18856111 TTGGACGGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.29
21 19 0.68
22 1 0.04
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
AGCTGGATTTGAGCTCGAACA
Found at i:18859956 original size:19 final size:19
Alignment explanation
Indices: 18859932--18859971 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
18859922 AGCTCCCATG
18859932 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
18859951 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
18859970 TA
1 TA
18859972 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:18861233 original size:14 final size:14
Alignment explanation
Indices: 18861211--18861258 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
18861201 ACCTAAACCG
* *
18861211 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
18861225 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
*
18861239 ACCCTTTTGTTCCT
1 ACCATTTTGTTCCT
18861253 ACCATT
1 ACCATT
18861259 CCATTCGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:18861660 original size:30 final size:29
Alignment explanation
Indices: 18861617--18861692 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
18861607 TTTAATCTCT
*
18861617 TTTTCAATTTCTTTTTCACTCTCAAATTT-A
1 TTTTC-ATTTCTTTTTCAATCTC-AATTTCA
* *
18861647 TTTTCATTCTCTTTTTCAATCTCATTTTCT
1 TTTTCATT-TCTTTTTCAATCTCAATTTCA
18861677 TTTTCATTTTCTTTTT
1 TTTTCA-TTTCTTTTT
18861693 GCTTTTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 7 0.17
30 31 0.77
31 2 0.05
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTCATTTCTTTTTCAATCTCAATTTCA
Found at i:18861692 original size:18 final size:18
Alignment explanation
Indices: 18861646--18861698 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
18861636 TCTCAAATTT
*
18861646 ATTTTCATTCTCTTTTTC
1 ATTTTCATTTTCTTTTTC
* *
18861664 AATCTCATTTTCTTTTTC
1 ATTTTCATTTTCTTTTTC
*
18861682 ATTTTCTTTTTGCTTTT
1 ATTTTCATTTT-CTTTT
18861699 CAAAGGCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (18 bp):
ATTTTCATTTTCTTTTTC
Found at i:18861699 original size:12 final size:12
Alignment explanation
Indices: 18861668--18861692 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18861658 TTTTTCAATC
18861668 TCATTTTCTTTT
1 TCATTTTCTTTT
18861680 TCATTTTCTTTT
1 TCATTTTCTTTT
18861692 T
1 T
18861693 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:18861710 original size:12 final size:12
Alignment explanation
Indices: 18861695--18861722 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18861685 TTCTTTTTGC
18861695 TTTTCAAAGGCT
1 TTTTCAAAGGCT
18861707 TTTTCAAAGGCT
1 TTTTCAAAGGCT
18861719 TTTT
1 TTTT
18861723 GAAGTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (12 bp):
TTTTCAAAGGCT
Done.