Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold141
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: 2772588
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 118404 characters in sequence are not A, C, G, or T
File 15 of 18
Found at i:2329733 original size:20 final size:20
Alignment explanation
Indices: 2329710--2329757 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
2329700 TCTCATGTGC
*
2329710 CGATACAATTGTCCATGTAT
1 CGATACAATTGACCATGTAT
*
2329730 CGATACAA-TGAGCATGTAT
1 CGATACAATTGACCATGTAT
2329749 CGATACAAT
1 CGATACAAT
2329758 GTATCGACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (20 bp):
CGATACAATTGACCATGTAT
Found at i:2336124 original size:3 final size:3
Alignment explanation
Indices: 2336111--2336140 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2336101 CTTCATCCGA
*
2336111 ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2336141 TTCCTCTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:2337862 original size:19 final size:19
Alignment explanation
Indices: 2337818--2337873 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
2337808 CTGCCAATTT
* *
2337818 CATGTATTGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
2337838 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
2337857 CATGTATCGATACAATG
1 CATGTATCGATACAATG
2337874 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:2337876 original size:13 final size:13
Alignment explanation
Indices: 2337858--2337883 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2337848 TACAATGAGC
2337858 ATGTATCGATACA
1 ATGTATCGATACA
2337871 ATGTATCGATACA
1 ATGTATCGATACA
2337884 TCTGGGTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2338625 original size:23 final size:23
Alignment explanation
Indices: 2338595--2338641 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2338585 AGCATGTTCA
2338595 TGCATGATTAATAGCTTGATAGG
1 TGCATGATTAATAGCTTGATAGG
2338618 TGCATGATTAATAGCTTGATAGG
1 TGCATGATTAATAGCTTGATAGG
2338641 T
1 T
2338642 TCCATGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.36
Consensus pattern (23 bp):
TGCATGATTAATAGCTTGATAGG
Found at i:2340160 original size:78 final size:78
Alignment explanation
Indices: 2340022--2340206 Score: 198
Period size: 78 Copynumber: 2.4 Consensus size: 78
2340012 GCATAAATTT
* * * * * *
2340022 TTTTTACAATCGGGGATATTCCAATCCCGTTATTTCCGAGGTATGCTCCAACCTCGGTTTTATTT
1 TTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCAAGGTATACTCCAACCTCCGTTTTATTT
*
2340087 CCAAAACAGT-GA-
66 CCAAAACA-TCAAC
* * *
2340099 TTTTCCACCATCGGGGATACTCTAACCCCGTTATTTCCAAAGGGT-TACTCCAACC-CCGTTTTT
1 TTTT-CACAATCGGGGATACTCCAACCCCGTTATTTCC-AA-GGTATACTCCAACCTCCGTTTTA
*
2340162 TTTCTAAAACATCAAC
63 TTTCCAAAACATCAAC
*
2340178 TTTTCACAATCGAGGATACTCCAACCCCG
1 TTTTCACAATCGGGGATACTCCAACCCCG
2340207 GTTTTATTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
77 5 0.06
78 67 0.75
79 14 0.16
80 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (78 bp):
TTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCAAGGTATACTCCAACCTCCGTTTTATTT
CCAAAACATCAAC
Found at i:2340203 original size:50 final size:51
Alignment explanation
Indices: 2340144--2340255 Score: 158
Period size: 51 Copynumber: 2.2 Consensus size: 51
2340134 TCCAAAGGGT
2340144 TACTCCAACCCC-GTTTT-TTTTCTAAAACA-TCAACTTTTCACAATCGAGGA
1 TACTCCAACCCCGGTTTTATTTTC-AAAACACT-AACTTTTCACAATCGAGGA
* * *
2340194 TACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTTCATAATCGGGGA
1 TACTCCAACCCCGGTTTTATTTTCAAAACACTAACTTTTCACAATCGAGGA
2340245 TACTCCAACCC
1 TACTCCAACCC
2340256 AGTTATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
50 12 0.21
51 38 0.68
52 6 0.11
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (51 bp):
TACTCCAACCCCGGTTTTATTTTCAAAACACTAACTTTTCACAATCGAGGA
Found at i:2340342 original size:130 final size:130
Alignment explanation
Indices: 2340058--2340675 Score: 767
Period size: 130 Copynumber: 4.7 Consensus size: 130
2340048 CCGTTATTTC
* * * * * * *
2340058 CGAGGTATGCTCCAACCTCGGTTTTATTTCCAAAACAGTGATTTTCCACCATCGGGGATACTCTA
1 CGAGG-ATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCA
* * * * *
2340123 ACCCCGTTATTTCCAAAGGGTTACTCCAACCC-CGTTTTTTTTCTAAAACATCAACTTTTCACAA
65 ACCCCGTTATTTCCAAGGGGATACTCCAACCCTAGTTTTATTTCTAAAACATCAACTTTCCACAA
2340187 T
130 T
* *
2340188 CGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTTCATAATCGGGGATACTCCAA
1 CGAGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAA
* * *
2340253 CCCAGTTATTTCCAAGGGGATACTCCAACCCTAGTTTTATTTCTAAAACATCAATTTTTCACAAT
66 CCCCGTTATTTCCAAGGGGATACTCCAACCCTAGTTTTATTTCTAAAACATCAACTTTCCACAAT
* * * * * * * * *
2340318 CGGGGATACTCTAACCCTGATTTTATTTCCAAAACAGTGATTTTCCACCATCGGGGATACTCTAA
1 CGAGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAA
* * **
2340383 CCCCGTTATTTCTAAGGGGTTACTCCAACCCCGGTTTTATTTCTAAAACATCAACTTTCCACAAT
66 CCCCGTTATTTCCAAGGGGATACTCCAACCCTAGTTTTATTTCTAAAACATCAACTTTCCACAAT
* ** * *
2340448 TGAGGATACTCCAACCTTGGTTTTATTTTCAAAACACTAATTTTTCATAATCGGGGATACTCCAA
1 CGAGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAA
*
2340513 CCCCGTTATTTCCAAGGGGATACTCCAA-CCTCAGTTTTATTTCTAAAACATCAATTTTCCACAA
66 CCCCGTTATTTCCAAGGGGATACTCCAACCCT-AGTTTTATTTCTAAAACATCAACTTTCCACAA
2340577 T
130 T
* * *
2340578 CGGGGATACTCCAACCCCGGTTTTATTTCCAAAACA-TCAATTTTTTTTACAATCGAGGATACTC
1 CGAGGATACTCCAACCCCGGTTTTATTTCCAAAACACT-AA--TTTTTCACAATCGGGGATACTC
* * * *
2340642 CAACCTCGATATTT-CATCGCGGATACTCCAACCC
63 CAACCCCGTTATTTCCA-AGGGGATACTCCAACCC
2340676 CATTATTTTT
Statistics
Matches: 419, Mismatches: 62, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
129 82 0.20
130 290 0.69
131 2 0.00
132 43 0.10
133 2 0.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (130 bp):
CGAGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAA
CCCCGTTATTTCCAAGGGGATACTCCAACCCTAGTTTTATTTCTAAAACATCAACTTTCCACAAT
Found at i:2340344 original size:51 final size:51
Alignment explanation
Indices: 2340268--2340385 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 51
2340258 TTATTTCCAA
* * *
2340268 GGGGATACTCCAACCCTAGTTTTATTTCTAAAACA-TCAATTTTTCACAATC
1 GGGGATACTCTAACCCTAGTTTTATTTCCAAAACAGT-AATTTTCCACAATC
* *
2340319 GGGGATACTCTAACCCT-GATTTTATTTCCAAAACAGTGATTTTCCACCATC
1 GGGGATACTCTAACCCTAG-TTTTATTTCCAAAACAGTAATTTTCCACAATC
2340370 GGGGATACTCTAACCC
1 GGGGATACTCTAACCC
2340386 CGTTATTTCT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 1 0.02
51 58 0.97
52 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
GGGGATACTCTAACCCTAGTTTTATTTCCAAAACAGTAATTTTCCACAATC
Found at i:2340463 original size:51 final size:51
Alignment explanation
Indices: 2340403--2340517 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 51
2340393 TCTAAGGGGT
*
2340403 TACTCCAACCCCGGTTTTA-TTTCTAAAACA-TCAACTTTCCACAATTGAGGA
1 TACTCCAACCCCGGTTTTATTTTC-AAAACACT-AACTTTCCACAATCGAGGA
** * * * *
2340454 TACTCCAACCTTGGTTTTATTTTCAAAACACTAATTTTTCATAATCGGGGA
1 TACTCCAACCCCGGTTTTATTTTCAAAACACTAACTTTCCACAATCGAGGA
2340505 TACTCCAACCCCG
1 TACTCCAACCCCG
2340518 TTATTTCCAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
51 48 0.91
52 5 0.09
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (51 bp):
TACTCCAACCCCGGTTTTATTTTCAAAACACTAACTTTCCACAATCGAGGA
Found at i:2340539 original size:260 final size:259
Alignment explanation
Indices: 2340067--2340613 Score: 943
Period size: 260 Copynumber: 2.1 Consensus size: 259
2340057 CCGAGGTATG
* *
2340067 CTCCAACCTCGGTTTTATTTCCAAAACAGTGATTTTCCACCATCGGGGATACTCTAACCCCGTTA
1 CTCCAACCCCGATTTTATTTCCAAAACAGTGATTTTCCACCATCGGGGATACTCTAACCCCGTTA
* *
2340132 TTTCCAAAGGGTTACTCCAACCCCGTTTTTTTTCTAAAACATCAACTTTTCACAATCGAGGATAC
66 TTTCCAAAGGGTTACTCCAACCCCGTTTTATTTCTAAAACATCAACTTTCCACAATCGAGGATAC
2340197 TCCAACCCCGGTTTTATTTTCAAAACACTAATTTTTCATAATCGGGGATACTCCAACCCAGTTAT
131 TCCAACCCCGGTTTTATTTTCAAAACACTAATTTTTCATAATCGGGGATACTCCAACCCAGTTAT
*
2340262 TTCCAAGGGGATACTCCAACC-CTAGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATA
196 TTCCAAGGGGATACTCCAACCTC-AGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATA
* *
2340326 CTCTAACCCTGATTTTATTTCCAAAACAGTGATTTTCCACCATCGGGGATACTCTAACCCCGTTA
1 CTCCAACCCCGATTTTATTTCCAAAACAGTGATTTTCCACCATCGGGGATACTCTAACCCCGTTA
* * *
2340391 TTTCTAAGGGGTTACTCCAACCCCGGTTTTATTTCTAAAACATCAACTTTCCACAATTGAGGATA
66 TTTCCAAAGGGTTACTCCAACCCC-GTTTTATTTCTAAAACATCAACTTTCCACAATCGAGGATA
** *
2340456 CTCCAACCTTGGTTTTATTTTCAAAACACTAATTTTTCATAATCGGGGATACTCCAACCCCGTTA
130 CTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTTCATAATCGGGGATACTCCAACCCAGTTA
2340521 TTTCCAAGGGGATACTCCAACCTCAGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATA
195 TTTCCAAGGGGATACTCCAACCTCAGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATA
*
2340586 CTCCAACCCCGGTTTTATTTCCAAAACA
1 CTCCAACCCCGATTTTATTTCCAAAACA
2340614 TCAATTTTTT
Statistics
Matches: 270, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
259 83 0.31
260 186 0.69
261 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (259 bp):
CTCCAACCCCGATTTTATTTCCAAAACAGTGATTTTCCACCATCGGGGATACTCTAACCCCGTTA
TTTCCAAAGGGTTACTCCAACCCCGTTTTATTTCTAAAACATCAACTTTCCACAATCGAGGATAC
TCCAACCCCGGTTTTATTTTCAAAACACTAATTTTTCATAATCGGGGATACTCCAACCCAGTTAT
TTCCAAGGGGATACTCCAACCTCAGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATA
Found at i:2340550 original size:79 final size:79
Alignment explanation
Indices: 2340451--2340596 Score: 224
Period size: 79 Copynumber: 1.8 Consensus size: 79
2340441 CCACAATTGA
** * *
2340451 GGATACTCCAACCTTGGTTTTATTT-TCAAAACA-CTAATTTTTCATAATCGGGGATACTCCAAC
1 GGATACTCCAACCTCAGTTTTATTTCT-AAAACATC-AATTTTCCACAATCGGGGATACTCCAAC
2340514 CCCGTTATTTCCAAGG
64 CCCGTTATTTCCAAGG
2340530 GGATACTCCAACCTCAGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAACCC
1 GGATACTCCAACCTCAGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAACCC
2340595 CG
66 CG
2340597 GTTTTATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
79 59 0.97
80 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (79 bp):
GGATACTCCAACCTCAGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAACCC
CGTTATTTCCAAGG
Found at i:2340593 original size:51 final size:52
Alignment explanation
Indices: 2340528--2340648 Score: 172
Period size: 51 Copynumber: 2.3 Consensus size: 52
2340518 TTATTTCCAA
*
2340528 GGGGATACTCCAACCTCAGTTTTATTTCTAAAACATCAA-TTTTCCACAATC
1 GGGGATACTCCAACCTCAGTTTTATTTCCAAAACATCAATTTTTCCACAATC
* * **
2340579 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTTTTACAATC
1 GGGGATACTCCAACCTCAGTTTTATTTCCAAAACATCAA-TTTTTCCACAATC
*
2340632 GAGGATACTCCAACCTC
1 GGGGATACTCCAACCTC
2340649 GATATTTCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 36 0.59
53 25 0.41
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCTCAGTTTTATTTCCAAAACATCAATTTTTCCACAATC
Found at i:2340682 original size:28 final size:27
Alignment explanation
Indices: 2340629--2340700 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
2340619 TTTTTTTACA
*
2340629 ATCGAGGATACTCCAACCTCGATATTT
1 ATCGAGGATACTCCAACCTCCATATTT
*
2340656 CATCGCGGATACTCCAACC-CCATTATTT
1 -ATCGAGGATACTCCAACCTCCA-TATTT
*
2340684 TTGCGAGGATACTCCAA
1 AT-CGAGGATACTCCAA
2340701 TCCCGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.08
28 35 0.92
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (27 bp):
ATCGAGGATACTCCAACCTCCATATTT
Found at i:2340760 original size:79 final size:80
Alignment explanation
Indices: 2340657--2340835 Score: 225
Period size: 79 Copynumber: 2.2 Consensus size: 80
2340647 TCGATATTTC
* ** * * *
2340657 ATCGCGGATACTCCAACCCCATTATTTTTGCGAGGATACTCCAATCCCGA-TTTTATTTTTAAAA
1 ATCGGGGATACTCCAACCCCATTATTTCCGAGAGGATACTCCAAACCCGATTTTTATTTCTAAAA
* *
2340721 CATCGATTTTCTATA
66 CACCGATTTTCCATA
* * *
2340736 ATCGGGGATACTCCAACCCTATTATTTCCGAGGGGATACTCCAAACCCGATTTTTATTTCTAGAA
1 ATCGGGGATACTCCAACCCCATTATTTCCGAGAGGATACTCCAAACCCGATTTTTATTTCTAAAA
*
2340801 CACCGATTTTCCATT
66 CACCGATTTTCCATA
* *
2340816 ATCAGGGATACTCCAGCCCC
1 ATCGGGGATACTCCAACCCC
2340836 TGTTATTATC
Statistics
Matches: 84, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
79 43 0.51
80 41 0.49
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCATTATTTCCGAGAGGATACTCCAAACCCGATTTTTATTTCTAAAA
CACCGATTTTCCATA
Found at i:2340776 original size:107 final size:108
Alignment explanation
Indices: 2340581--2340779 Score: 249
Period size: 107 Copynumber: 1.8 Consensus size: 108
2340571 CCACAATCGG
* *
2340581 GGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTTTTACAATCGAGGATACTCCAAC
1 GGATACTCCAACCCCGATTTTATTTCCAAAACATCAA-TTTTTCTACAATCGAGGATACTCCAAC
**
2340646 CTCGATATTTCATCGCGGATACTCCAACCCCATTATTTTTGCGA
65 CTCGATATTTCAGAGCGGATACTCCAACCCCATTATTTTTGCGA
* ** * * *
2340690 GGATACTCCAATCCCGATTTTATTTTTAAAACATCGA-TTTTCTATAATCGGGGATACTCCAACC
1 GGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCTACAATCGAGGATACTCCAACC
* * *
2340754 -CTATTATTTCCGAGGGGATACTCCAA
66 TCGA-TATTTCAGAGCGGATACTCCAA
2340780 ACCCGATTTT
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
106 2 0.03
107 42 0.55
109 32 0.42
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (108 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCTACAATCGAGGATACTCCAACC
TCGATATTTCAGAGCGGATACTCCAACCCCATTATTTTTGCGA
Found at i:2345120 original size:48 final size:42
Alignment explanation
Indices: 2345035--2345132 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 42
2345025 TTTCCTAGAT
2345035 TATGT-ATC-AGCATGTGATGTATCAGCTTTCAATGTAATCG
1 TATGTAATCAAGCATGTGATGTATCAGCTTTCAATGTAATCG
2345075 TATGTAATCAAGCAATGTGATTGTATCAGGCTTTTTCAAATGTAATCG
1 TATGTAATCAAGC-ATGTGA-TGTATCA-GC--TTTC-AATGTAATCG
2345123 TATGTAATCA
1 TATGTAATCA
2345133 GGACATGTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
40 5 0.10
41 3 0.06
42 3 0.06
43 6 0.12
44 7 0.14
45 2 0.04
47 4 0.08
48 20 0.40
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (42 bp):
TATGTAATCAAGCATGTGATGTATCAGCTTTCAATGTAATCG
Found at i:2349955 original size:19 final size:18
Alignment explanation
Indices: 2349930--2349994 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
2349920 ATTTCAATGA
2349930 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
2349948 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
2349964 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
2349980 TTTTGTATCGATACA
1 -TTTGTATCGATACA
2349995 ATGTATAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:2349969 original size:13 final size:13
Alignment explanation
Indices: 2349951--2349975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2349941 ACATAAGTGT
2349951 TGTATCGATACAA
1 TGTATCGATACAA
2349964 TGTATCGATACA
1 TGTATCGATACA
2349976 TAAGTTTTGT
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:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2349973 original size:32 final size:32
Alignment explanation
Indices: 2349932--2350000 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
2349922 TTCAATGATT
2349932 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
2349964 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2349996 TGTAT
1 TGTAT
2350001 AGTTACGAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2350065 original size:13 final size:13
Alignment explanation
Indices: 2350047--2350071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2350037 ATTACTCAAA
2350047 TGTATCGATACAT
1 TGTATCGATACAT
2350060 TGTATCGATACA
1 TGTATCGATACA
2350072 CTAATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2350126 original size:52 final size:52
Alignment explanation
Indices: 2350083--2350205 Score: 228
Period size: 52 Copynumber: 2.4 Consensus size: 52
2350073 TAATCTTTGA
* *
2350083 ATCGATACATGCAGGCAAATTTGCCCGGATGTATCGATGCACTATGAAATGT
1 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGT
2350135 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGT
1 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGT
2350187 ATCGATACATGCAGGCAAA
1 ATCGATACATGCAGGCAAA
2350206 ATTTCATATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (52 bp):
ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGT
Found at i:2356881 original size:8 final size:8
Alignment explanation
Indices: 2356868--2356925 Score: 64
Period size: 8 Copynumber: 7.0 Consensus size: 8
2356858 CATCTGACTT
2356868 TAAAAAAA
1 TAAAAAAA
2356876 TAAAAAAA
1 TAAAAAAA
2356884 TTAAAAAACA
1 -TAAAAAA-A
2356894 -AAAAAACA
1 TAAAAAA-A
*
2356902 AAAAAAAA
1 TAAAAAAA
2356910 TAAAAAAA
1 TAAAAAAA
*
2356918 CAAAAAAA
1 TAAAAAAA
2356926 ATGAAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
8 31 0.69
9 13 0.29
10 1 0.02
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.09
Consensus pattern (8 bp):
TAAAAAAA
Found at i:2356883 original size:9 final size:9
Alignment explanation
Indices: 2356869--2356937 Score: 63
Period size: 8 Copynumber: 7.8 Consensus size: 9
2356859 ATCTGACTTT
2356869 AAAAAAATA
1 AAAAAAATA
*
2356878 AAAAAATTA
1 AAAAAAATA
*
2356887 AAAAACA-A
1 AAAAAAATA
*
2356895 AAAAACA-A
1 AAAAAAATA
2356903 AAAAAAAT-
1 AAAAAAATA
*
2356911 AAAAAAACA
1 AAAAAAATA
2356920 AAAAAAATGA
1 AAAAAAAT-A
2356930 AGAAAAAA
1 A-AAAAAA
2356938 AGAGAGAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
8 22 0.44
9 20 0.40
10 2 0.04
11 6 0.12
ACGTcount: A:0.86, C:0.04, G:0.03, T:0.07
Consensus pattern (9 bp):
AAAAAAATA
Found at i:2356935 original size:18 final size:18
Alignment explanation
Indices: 2356869--2356926 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
2356859 ATCTGACTTT
*
2356869 AAAAAAAT-AAAAAA-AT
1 AAAAAAATAAAAAAACAA
* *
2356885 TAAAAAACAAAAAAACAA
1 AAAAAAATAAAAAAACAA
2356903 AAAAAAATAAAAAAACAA
1 AAAAAAATAAAAAAACAA
2356921 AAAAAA
1 AAAAAA
2356927 TGAAGAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 6 0.17
17 6 0.17
18 23 0.66
ACGTcount: A:0.88, C:0.05, G:0.00, T:0.07
Consensus pattern (18 bp):
AAAAAAATAAAAAAACAA
Found at i:2356935 original size:26 final size:25
Alignment explanation
Indices: 2356869--2356936 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 25
2356859 ATCTGACTTT
*
2356869 AAAAAAATAAAAAAATTAAAAAACA
1 AAAAAAATAAAAAAATAAAAAAACA
*
2356894 AAAAAACAAAAAAAAATAAAAAAACA
1 AAAAAA-ATAAAAAAATAAAAAAACA
2356920 AAAAAAATGAAGAAAAA
1 AAAAAAAT-AA-AAAAA
2356937 AAGAGAGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 7 0.19
26 25 0.68
27 5 0.14
ACGTcount: A:0.85, C:0.04, G:0.03, T:0.07
Consensus pattern (25 bp):
AAAAAAATAAAAAAATAAAAAAACA
Found at i:2356938 original size:1 final size:1
Alignment explanation
Indices: 2356869--2356926 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
2356859 ATCTGACTTT
* ** * * * *
2356869 AAAAAAATAAAAAAATTAAAAAACAAAAAAACAAAAAAAAATAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2356927 TGAAGAAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.88, C:0.05, G:0.00, T:0.07
Consensus pattern (1 bp):
A
Found at i:2358047 original size:55 final size:55
Alignment explanation
Indices: 2357970--2358239 Score: 272
Period size: 55 Copynumber: 4.8 Consensus size: 55
2357960 AAGCCCATAC
* * * *
2357970 AAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGATGCCTTTCAAAACCCACAT
1 AAGTTGGTGACACTTTTAAGTCCTCAAAGAGCAGGATGCCTTTCAAAACCCACAT
* * *
2358025 AAGTTGGTGACATTTTTAAGTCCTCAAAGAGCAGGGTGCCTCTCAAAACCCACAT
1 AAGTTGGTGACACTTTTAAGTCCTCAAAGAGCAGGATGCCTTTCAAAACCCACAT
* * * *
2358080 AAGTTGGTGACATTTTTAAGTCCTCAAAGAGCAGGGTGCCTCTT-AAAGCCCACAC
1 AAGTTGGTGACACTTTTAAGTCCTCAAAGAGCAGGATGCCT-TTCAAAACCCACAT
* ** * *
2358135 AAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACAC
1 AAGTTGGTGACACTTTTAAGTCCTCAAAGAGCAGGATGCCTT-T-C----AAAACCCACAT
* * * * *
2358196 AAGTTGGTGGCACTTTTCTAGCCCTCAAGGAGCAGGACGCCTTT
1 AAGTTGGTGACACTTTT-AAGTCCTCAAAGAGCAGGATGCCTTT
2358240 TCCTTTTAAA
Statistics
Matches: 186, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
54 1 0.01
55 135 0.73
56 1 0.01
61 28 0.15
62 21 0.11
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (55 bp):
AAGTTGGTGACACTTTTAAGTCCTCAAAGAGCAGGATGCCTTTCAAAACCCACAT
Found at i:2358285 original size:123 final size:122
Alignment explanation
Indices: 2357929--2358489 Score: 602
Period size: 123 Copynumber: 4.7 Consensus size: 122
2357919 CATTTTTCAA
* * ** * * *
2357929 TCCTTAAAGAGCAAGACACCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCACCTTTCAGTCCT
1 TCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCT
* * * * * * **
2357994 CAAAGAGTAGGATGCC-TTT-C----AAAACCCACATAAGTTGGTGACATTTTTAAG
66 CAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
* * * * * *
2358045 TCCTCAAAGAGCAGGGTGCC-TCT-C----AAAACCCACATAAGTTGGTGACATTTTTAAGTCCT
1 TCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCT
* *
2358104 CAAAGAGCAGG--G----TGCCTCTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
66 CAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
*
2358155 TCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGCCC
1 TCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCC
* * * *
2358220 TCAAGGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGCGGTATTTTCCAG
65 TCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
* * * * * *
2358278 TCCTCAAAGAGCAGGATGCTTTCTCCTTTTAAAGACCACTCGAGTTGGTGGCACTTTCCAGTCTT
1 TCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCT
* * * * *
2358343 CAAAAAGTAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT-CAG
66 CAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
* * *
2358399 TCCTCAAAAAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTGCAGTCCT
1 TCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCT
2358464 CAAAGAGCAGGACGCCTTTTCCTTTT
66 CAAAGAGCAGGACGCCTTTTCCTTTT
2358490 CTCCTTTGCC
Statistics
Matches: 366, Mismatches: 61, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
105 1 0.00
106 1 0.00
108 1 0.00
110 82 0.22
111 3 0.01
112 1 0.00
114 1 0.00
115 2 0.01
116 39 0.11
117 15 0.04
119 1 0.00
121 83 0.23
122 48 0.13
123 88 0.24
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (122 bp):
TCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCT
CAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
Found at i:2358305 original size:61 final size:60
Alignment explanation
Indices: 2357929--2358489 Score: 517
Period size: 61 Copynumber: 9.5 Consensus size: 60
2357919 CATTTTTCAA
* * * *
2357929 TCCTTAAAGAGCAAGACACCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCACCTTT-CAG
1 TCCTCAAAGAGCAGGAC-GCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAG
* * * * * * * **
2357990 TCCTCAAAGAGTAGGA-----TGCCTTTCAAAACCCACATAAGTTGGTGACATTTTTAAG
1 TCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
* * * * * * * **
2358045 TCCTCAAAGAGCAGG--G---TGCCTCTCAAAACCCACATAAGTTGGTGACATTTTTAAG
1 TCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
* *
2358100 TCCTCAAAGAGCAGG--G---TGCCTCTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
1 TCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
* * *
2358155 TCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAG
1 TCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCCAG
* * * * *
2358217 CCCTCAAGGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGCGGTATTTTCCAG
1 TCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
* * * *
2358278 TCCTCAAAGAGCAGGATGCTTTCTCCTTTTAAAGACCACTCGAGTTGGTGGCACTTTCCAG
1 TCCTCAAAGAGCAGGACGCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
* * * * * *
2358339 TCTTCAAAAAGTAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT-CAG
1 TCCTCAAAGAGCAGGAC-GCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
* * *
2358399 TCCTCAAAAAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTGCAG
1 TCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
2358460 TCCTCAAAGAGCAGGACGCCTTTTCCTTTT
1 TCCTCAAAGAGCAGGACG-CTTTTCCTTTT
2358490 CTCCTTTGCC
Statistics
Matches: 428, Mismatches: 59, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
54 3 0.01
55 142 0.33
57 1 0.00
60 57 0.13
61 168 0.39
62 57 0.13
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (60 bp):
TCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAG
Found at i:2358550 original size:37 final size:38
Alignment explanation
Indices: 2358460--2358640 Score: 134
Period size: 42 Copynumber: 4.5 Consensus size: 38
2358450 CACTTTGCAG
*
2358460 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTCTCCTTTG
1 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTCTCCTTTA
* ** *
2358498 CCCTC-TTGAGCAGGACGCC-TTTCCTTTTTTCCTTTA
1 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTCTCCTTTA
* *
2358534 TCCTCAAAGAGTAGGACGCACTTCATTTCCTTCTTTTTCCTTCTA
1 TCCTCAAAGAGCAGGACGC-C-T--TTTCC-T-TTTCTCCTT-TA
* * *
2358579 GTTCTCAAAGAGCAGGACGCACTTTATTTTCCTTTT-TCTTTTG
1 -TCCTCAAAGAGCAGGACGC-C----TTTTCCTTTTCTCCTTTA
2358622 TCCTCAAAGAGCAGGACGC
1 TCCTCAAAGAGCAGGACGC
2358641 ATTTCATTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
36 19 0.17
37 22 0.19
38 5 0.04
42 23 0.20
43 2 0.02
44 13 0.11
45 5 0.04
46 20 0.17
47 5 0.04
49 1 0.01
ACGTcount: A:0.18, C:0.29, G:0.15, T:0.38
Consensus pattern (38 bp):
TCCTCAAAGAGCAGGACGCCTTTTCCTTTTCTCCTTTA
Found at i:2358563 original size:42 final size:43
Alignment explanation
Indices: 2358517--2358657 Score: 178
Period size: 42 Copynumber: 3.2 Consensus size: 43
2358507 GCAGGACGCC
*
2358517 TTTCCTTTTTTCCTTTATCCTCAAAGAGTAGGACGCACTTCA-
1 TTTCCTTTTTTCCTTTATCCTCAAAGAGCAGGACGCACTTCAT
* *
2358559 TTTCCTTCTTTTTCCTTCTAGTTCTCAAAGAGCAGGACGCACTTTAT
1 TTTCC-T-TTTTTCCTT-TA-TCCTCAAAGAGCAGGACGCACTTCAT
* * *
2358606 TTTCC-TTTTTCTTTTGTCCTCAAAGAGCAGGACGCATTTCAT
1 TTTCCTTTTTTCCTTTATCCTCAAAGAGCAGGACGCACTTCAT
2358648 TTTCCTTTTT
1 TTTCCTTTTT
2358658 CCTCGAAAAG
Statistics
Matches: 85, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
42 33 0.39
43 6 0.07
44 17 0.20
45 2 0.02
46 22 0.26
47 5 0.06
ACGTcount: A:0.18, C:0.25, G:0.12, T:0.45
Consensus pattern (43 bp):
TTTCCTTTTTTCCTTTATCCTCAAAGAGCAGGACGCACTTCAT
Found at i:2358590 original size:46 final size:45
Alignment explanation
Indices: 2358523--2358654 Score: 164
Period size: 46 Copynumber: 3.0 Consensus size: 45
2358513 CGCCTTTCCT
*
2358523 TTTTTCCTTTA-TCCTCAAAGAGTAGGACGCACTTCATTTCCTTC
1 TTTTTCCTTTAGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTC
* * *
2358567 TTTTTCCTTCTAGTTCTCAAAGAGCAGGACGCACTTTATTT--TCC
1 TTTTTCCTT-TAGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTC
* *
2358611 TTTTT-CTTTTGTCCTCAAAGAGCAGGACGCATTTCATTTTCCTT
1 TTTTTCCTTTAGTCCTCAAAGAGCAGGACGCACTTCA-TTTCCTT
2358655 TTTCCTCGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
42 24 0.32
43 6 0.08
44 16 0.22
45 3 0.04
46 25 0.34
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (45 bp):
TTTTTCCTTTAGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTC
Found at i:2358661 original size:35 final size:36
Alignment explanation
Indices: 2358606--2358674 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
2358596 CGCACTTTAT
* *
2358606 TTTCCTTTTTCTTTTGTCCTC-AAAGAGCAGGACGCA
1 TTTCATTTTCCTTTTGTCCTCGAAA-AGCAGGACGCA
*
2358642 TTTCATTTTCCTTTT-TCCTCGAAAAGCTGGACG
1 TTTCATTTTCCTTTTGTCCTCGAAAAGCAGGACG
2358675 TACTCCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 13 0.45
36 16 0.55
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCATTTTCCTTTTGTCCTCGAAAAGCAGGACGCA
Found at i:2361761 original size:51 final size:50
Alignment explanation
Indices: 2361700--2361796 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 50
2361690 TTCATCTTGA
*
2361700 GGATACTCCAA-TCTCGATTTCATTTCCAAAACATCAATTTTTCTTTATCGG
1 GGATACTCCAACT-TCGATTTCATTTCCAAAACATAAATTTTT-TTTATCGG
* * *
2361751 GGATACTCCAACTTCGATTTTATTTCTAAAGCATAAATTTTTTTTA
1 GGATACTCCAACTTCGATTTCATTTCCAAAACATAAATTTTTTTTA
2361797 CAATCGAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
50 4 0.10
51 36 0.88
52 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (50 bp):
GGATACTCCAACTTCGATTTCATTTCCAAAACATAAATTTTTTTTATCGG
Found at i:2361903 original size:51 final size:51
Alignment explanation
Indices: 2361830--2361945 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
2361820 TTATTTTCAA
* ** * * ** *
2361830 GGGATACTCCAACCTTGGTTTTATTTCTAAATCATCAATTTTTTAGAATCG
1 GGGATACTCTAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATCG
* *
2361881 GGGATACTCTAACCCCGATTTTATTTCTAAAACATCGATTTTCCACCATCG
1 GGGATACTCTAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATCG
2361932 GGGATACTCTAACC
1 GGGATACTCTAACC
2361946 TCGTTATTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
GGGATACTCTAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATCG
Found at i:2362010 original size:130 final size:131
Alignment explanation
Indices: 2361700--2362236 Score: 573
Period size: 130 Copynumber: 4.1 Consensus size: 131
2361690 TTCATCTTGA
* * * * * * *** **
2361700 GGATACTCCAATCTCGATTTCATTTCCAAAACATCAATTTTTCTTTATCGGGGATACTCCAACTT
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAACCC
* * * * *
2361765 CGATTTTATTTCTAAAGCATAAATTTTTTTTACAATCGAAGATACTCCAACCTCGTTATTTTCAA
66 CGATTTTATTTCTAAAACATCAA-TTTTTTCACAATCGGAGATACTCCAACCTCGTTATTTCCAA
2361830 -G
130 GG
** * ** * *
2361831 GGATACTCCAACCTTGGTTTTATTTCTAAATCATCAATTTTTTAGAATCGGGGATACTCTAACCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAACCC
* * * * *
2361896 CGATTTTATTTCTAAAACATCGA-TTTTCCACCATCGGGGATACTCTAACCTCGTTATTTCCAAG
66 CGATTTTATTTCTAAAACATCAATTTTTTCACAATCGGAGATACTCCAACCTCGTTATTTCCAAG
2361960 G
131 G
* * * *
2361961 GGTTACTCCAACCGCGGTTTTATTTCTAAAACATCAACTTTCCACAATCGGGGATACTTCAACCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAACCC
* * ** *
2362026 TGGTTTTATTT-TCAAAACGCCAA-TTTTTCATAATCGGAGATACTCCAACC-CTGTTATTTCCA
66 CGATTTTATTTCT-AAAACATCAATTTTTTCACAATCGGAGATACTCCAACCTC-GTTATTTCCA
**
2362088 AAA
129 AGG
*
2362091 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACAATCGAGGATACTCCAACCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAACCC
* * * * *
2362156 CGATTTTTTTTCCAAAACATCAATTTTTTTTACAATCGGGGATACTCCAACCTTGTTATTT-CAT
66 CGATTTTATTTCTAAAACATCAA-TTTTTTCACAATCGGAGATACTCCAACCTCGTTATTTCCA-
*
2362220 CGG
129 AGG
2362223 GGATACTCCAACCC
1 GGATACTCCAACCC
2362237 TATTATTTTC
Statistics
Matches: 335, Mismatches: 63, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
129 35 0.10
130 181 0.54
131 74 0.22
132 45 0.13
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (131 bp):
GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACAATCGGGGATACTCCAACCC
CGATTTTATTTCTAAAACATCAATTTTTTCACAATCGGAGATACTCCAACCTCGTTATTTCCAAG
G
Found at i:2362031 original size:51 final size:51
Alignment explanation
Indices: 2361959--2362078 Score: 136
Period size: 51 Copynumber: 2.4 Consensus size: 51
2361949 TTATTTCCAA
* *
2361959 GGGGTTACTCCAACCGC-GGTTTTA-TTTCTAAAACATCAACTTTCCACAATC
1 GGGGATACTCCAACC-CTGGTTTTATTTTC-AAAACACCAACTTTCCACAATC
* * * * *
2362010 GGGGATACTTCAACCCTGGTTTTATTTTCAAAACGCCAATTTTTCATAATC
1 GGGGATACTCCAACCCTGGTTTTATTTTCAAAACACCAACTTTCCACAATC
*
2362061 GGAGATACTCCAACCCTG
1 GGGGATACTCCAACCCTG
2362079 TTATTTCCAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
50 1 0.02
51 53 0.91
52 4 0.07
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCTGGTTTTATTTTCAAAACACCAACTTTCCACAATC
Found at i:2362154 original size:51 final size:52
Alignment explanation
Indices: 2362090--2362207 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 52
2362080 TATTTCCAAA
* *
2362090 AGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAA-TTTTCCACAATCG
1 AGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCCACAATCG
* **
2362141 AGGATACTCCAACCCCGATTTTTTTTCCAAAACATCAATTTTTTTTACAATCG
1 AGGATACTCCAACCCCGATTTTATTTCCAAAACATCAA-TTTTTCCACAATCG
*
2362194 GGGATACTCCAACC
1 AGGATACTCCAACC
2362208 TTGTTATTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 35 0.59
53 24 0.41
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (52 bp):
AGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCCACAATCG
Found at i:2362230 original size:28 final size:27
Alignment explanation
Indices: 2362190--2362261 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
2362180 TTTTTTTACA
* *
2362190 ATCGGGGATACTCCAACCTTGTTATTT
1 ATCGGGGATACTCCAACCCTATTATTT
2362217 CATCGGGGATACTCCAACCCTATTATTT
1 -ATCGGGGATACTCCAACCCTATTATTT
2362245 -TCGCAGGGATACTCCAA
1 ATCG--GGGATACTCCAA
2362262 TCCCAATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 3 0.08
28 37 0.93
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCTATTATTT
Found at i:2362310 original size:79 final size:80
Alignment explanation
Indices: 2362218--2362389 Score: 212
Period size: 79 Copynumber: 2.2 Consensus size: 80
2362208 TTGTTATTTC
*
2362218 ATCGGGGATACTCCAACCCTATTATTT-TCGCAGG-GATACTCCAATCCC-AA-TTTTATTT-TC
1 ATCGAGGATACTCCAACCCTATTATTTCT-G-AGGAGATACTCCAA-CCCTAATTTTTATTTCT-
*
2362278 AAAACATCGATTTTCTATA
62 AAAACATCAATTTTCTATA
* * *
2362297 ATCGAGGATACTCCAACCCTTTTATTTCTGAGGAGATACTCCAACCCTGATTTTTATTTCTAGAA
1 ATCGAGGATACTCCAACCCTATTATTTCTGAGGAGATACTCCAACCCTAATTTTTATTTCTAAAA
2362362 CATCAATTTTCTATA
66 CATCAATTTTCTATA
2362377 ATC-AGGGATACTC
1 ATCGA-GGATACTC
2362390 TAGCCCCGTT
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
78 6 0.07
79 38 0.46
80 37 0.45
81 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (80 bp):
ATCGAGGATACTCCAACCCTATTATTTCTGAGGAGATACTCCAACCCTAATTTTTATTTCTAAAA
CATCAATTTTCTATA
Found at i:2362335 original size:107 final size:108
Alignment explanation
Indices: 2362142--2362344 Score: 272
Period size: 107 Copynumber: 1.9 Consensus size: 108
2362132 CCACAATCGA
* * *
2362142 GGATACTCCAACCCCGATTTTTTTTCCAAAACATCAATTTTTTTTACAATCGGGGATACTCCAAC
1 GGATACTCCAACCCCAATTTTTTTTCCAAAACATCAA-TTTTTCTACAATCGAGGATACTCCAAC
2362207 CTTGTTATTTCATCGGGGATACTCCAACCCTATTATTTTCGCAG
65 CTTGTTATTTCATCGGGGATACTCCAACCCTATTATTTTCGCAG
* * *
2362251 GGATACTCCAATCCCAATTTTATTTT-CAAAACATCGA-TTTTCTATAATCGAGGATACTCCAAC
1 GGATACTCCAACCCCAATTTT-TTTTCCAAAACATCAATTTTTCTACAATCGAGGATACTCCAA-
2362314 CCTT-TTATTTC-T-GAGGAGATACTCCAACCCT
64 CCTTGTTATTTCATCG-GG-GATACTCCAACCCT
2362345 GATTTTTATT
Statistics
Matches: 84, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
105 1 0.01
106 3 0.04
107 43 0.51
108 4 0.05
109 29 0.35
110 4 0.05
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (108 bp):
GGATACTCCAACCCCAATTTTTTTTCCAAAACATCAATTTTTCTACAATCGAGGATACTCCAACC
TTGTTATTTCATCGGGGATACTCCAACCCTATTATTTTCGCAG
Found at i:2363404 original size:28 final size:28
Alignment explanation
Indices: 2363364--2364014 Score: 559
Period size: 28 Copynumber: 23.3 Consensus size: 28
2363354 GTTGCGACAT
* *
2363364 AAGTCAACAACTCCGTGGCACCCGTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTA
*
2363392 AAGTCCACAACTCTGTGGCATTCCCTTTT-
1 AAGTCCACAACTCCGTGGCA--CCCTTTTA
** *
2363421 AAGTCCACAACTTTGTAGCAACCC-TTTA
1 AAGTCCACAACTCCGTGGC-ACCCTTTTA
* *
2363449 AAG-CCTAAAACTCTGTGGCACCCTTTTA
1 AAGTCC-ACAACTCCGTGGCACCCTTTTA
* *
2363477 AAGTCCACAACTTCGTGGCACCCTTTAA
1 AAGTCCACAACTCCGTGGCACCCTTTTA
* **
2363505 AAGTCCGCAACTCTATGGCACCCTTTT-
1 AAGTCCACAACTCCGTGGCACCCTTTTA
* * * *
2363532 AAGTCCATAACTCCATGTCA-CCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTA
* ** * *
2363559 TAGTCCACAACTTAGTGGCACCTTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTA
*
2363587 AAGTCCACAACTCCCTGGCACCCGTTTT-
1 AAGTCCACAACTCCGTGGCACCC-TTTTA
* * *
2363615 AAGTCCACAACTCAGTGGCA-TCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTA
* * **
2363642 ATGTCCATAACTTTGTGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTA
* * *
2363670 AAGCCCATAACTCCGTGGCACCTTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTA
*
2363698 AAGTCCACTA-TCCGTGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTA
* * *
2363725 AAGTCCACAACTCTGTGGCA-TCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTA
* * * *
2363752 AAGTCCACAATTTCGTAGCACCTTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTA
2363780 AAGTCCACAACTCCGTGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTA
*
2363808 AAGTCCATAACTCCGTGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTA
* *
2363836 AAGTCCATAACTTCGTGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTA
* * *
2363864 AAGTCCATAACTCGGTGGCACACTTTT-
1 AAGTCCACAACTCCGTGGCACCCTTTTA
**
2363891 AAGTCCACAACTTTGTGGCACCCTTTT-
1 AAGTCCACAACTCCGTGGCACCCTTTTA
* ** * * *
2363918 AAGTCAATGAGTCAGTGGCATTCCCTTCTA
1 AAGTCCACAACTCCGTGGCA--CCCTTTTA
* * * ** *
2363948 AAGCCCATAAGTTAGTGGCACCCCTTTCA
1 AAGTCCACAACTCCGTGGCA-CCCTTTTA
* * * *
2363977 AAGCCCACAAGTCAGTGGCACTCTTTTCA
1 AAGTCCACAACTCCGTGGCACCCTTTT-A
2364006 AAGTCCACA
1 AAGTCCACA
2364015 CAGGTTGGTG
Statistics
Matches: 511, Mismatches: 94, Indels: 35
0.80 0.15 0.05
Matches are distributed among these distances:
26 10 0.02
27 139 0.27
28 277 0.54
29 62 0.12
30 23 0.05
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (28 bp):
AAGTCCACAACTCCGTGGCACCCTTTTA
Found at i:2363503 original size:55 final size:56
Alignment explanation
Indices: 2363364--2364014 Score: 583
Period size: 55 Copynumber: 11.7 Consensus size: 56
2363354 GTTGCGACAT
* *
2363364 AAGTCAACAACTCCGTGGCACCCGTTTAAAGTCCACAACTCTGTGGCATTCCCTTTT-
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCA--CCCTTTTA
** * *
2363421 AAGTCCACAACTTTGTAGCAACCC-TTTAAAG-CCTAAAACTCTGTGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGC-ACCCTTTTAAAGTCC-ACAACTCTGTGGCACCCTTTTA
* * * *
2363477 AAGTCCACAACTTCGTGGCACCCTTTAAAAGTCCGCAACTCTATGGCACCCTTTT-
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTA
* * * ** * *
2363532 AAGTCCATAACTCCATGTCA-CCTTTTTTAGTCCACAACT-TAGTGGCACCTTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCT-GTGGCACCCTTTTA
* * * *
2363587 AAGTCCACAACTCCCTGGCACCCGTTTT-AAGTCCACAACTCAGTGGCA-TCTTTTT
1 AAGTCCACAACTCCGTGGCACCC-TTTTAAAGTCCACAACTCTGTGGCACCCTTTTA
* * ** * * * *
2363642 ATGTCCATAACTTTGTGGCACCCTTTTAAAGCCCATAACTCCGTGGCACCTTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTA
* * *
2363698 AAGTCCACTA-TCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCA-TCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTA
* * * * *
2363752 AAGTCCACAATTTCGTAGCACCTTTTTAAAGTCCACAACTCCGTGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTA
* *
2363808 AAGTCCATAACTCCGTGGCACCCTTTTAAAGTCCATAACT-TCGTGGCACCCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCT-GTGGCACCCTTTTA
* * * *
2363864 AAGTCCATAACTCGGTGGCACACTTTT-AAGTCCACAACTTTGTGGCACCCTTTT-
1 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTA
* ** * * * * * * *
2363918 AAGTCAATGAGTCAGTGGCATTCCCTTCTAAAGCCCATAAGT-TAGTGGCACCCCTTTCA
1 AAGTCCACAACTCCGTGGCA--CCCTTTTAAAGTCCACAACTCT-GTGGCA-CCCTTTTA
* * * *
2363977 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGTCCACA
1 AAGTCCACAACTCCGTGGCACCCTTTT-AAAGTCCACA
2364015 CAGGTTGGTG
Statistics
Matches: 486, Mismatches: 85, Indels: 45
0.79 0.14 0.07
Matches are distributed among these distances:
53 1 0.00
54 59 0.12
55 173 0.36
56 158 0.33
57 61 0.13
58 18 0.04
59 16 0.03
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (56 bp):
AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTA
Found at i:2363660 original size:83 final size:83
Alignment explanation
Indices: 2363364--2363919 Score: 518
Period size: 83 Copynumber: 6.7 Consensus size: 83
2363354 GTTGCGACAT
* * * * *
2363364 AAGTCAACAACTCCGTGGCACCCGTTTAAAGTCCACAACTCTGTGGCATTCCCTTTT-AAGTCCA
1 AAGTCCACAACTCAGTGGCA-CCTTTTTAAGTCCACAACTTTGTGGCA--CCCTTTTAAAGTCCA
** *
2363428 CAACTTTGTAGCAACCC-TTTA
63 CAACTCCGTGGC-ACCCTTTTA
* * * * * *
2363449 AAG-CCTAAAACTCTGTGGCACCCTTTTAAAGTCCACAACTTCGTGGCACCCTTTAAAAGTCCGC
1 AAGTCC-ACAACTCAGTGGCA-CCTTTTTAAGTCCACAACTTTGTGGCACCCTTTTAAAGTCCAC
**
2363513 AACTCTATGGCACCCTTTT-
64 AACTCCGTGGCACCCTTTTA
* * * * * *
2363532 AAGTCCATAACTCCA-TGTCACCTTTTTTAGTCCACAACTTAGTGGCACCTTTTTTAAGTCCACA
1 AAGTCCACAACT-CAGTGGCACCTTTTTAAGTCCACAACTTTGTGGCACCCTTTTAAAGTCCACA
*
2363596 ACTCCCTGGCACCCGTTTT-
65 ACTCCGTGGCACCC-TTTTA
* * * * *
2363615 AAGTCCACAACTCAGTGGCATCTTTTTATGTCCATAACTTTGTGGCACCCTTTTAAAGCCCATAA
1 AAGTCCACAACTCAGTGGCACCTTTTTAAGTCCACAACTTTGTGGCACCCTTTTAAAGTCCACAA
*
2363680 CTCCGTGGCACCTTTTTA
66 CTCCGTGGCACCCTTTTA
* * * * * *
2363698 AAGTCCACTA-TCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGCA-TCTTTTTAAGTCCACA
1 AAGTCCACAACTCAGTGGCA-CCTTTTTAAGTCCACAACTTTGTGGCACCCTTTTAAAGTCCACA
* * * *
2363761 ATTTCGTAGCACCTTTTTA
65 ACTCCGTGGCACCCTTTTA
* * * ** *
2363780 AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAAGTCCATA
1 AAGTCCACAACTCAGTGGCA-CCTTTTTAAGTCCACAACTTTGTGGCACCCTTTTAAAGTCCACA
*
2363845 ACTTCGTGGCACCCTTTTA
65 ACTCCGTGGCACCCTTTTA
* *
2363864 AAGTCCATAACTCGGTGGCACAC-TTTTAAGTCCACAACTTTGTGGCACCCTTTTAA
1 AAGTCCACAACTCAGTGGCAC-CTTTTTAAGTCCACAACTTTGTGGCACCCTTTTAA
2363920 GTCAATGAGT
Statistics
Matches: 394, Mismatches: 65, Indels: 26
0.81 0.13 0.05
Matches are distributed among these distances:
82 100 0.25
83 184 0.47
84 70 0.18
85 40 0.10
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (83 bp):
AAGTCCACAACTCAGTGGCACCTTTTTAAGTCCACAACTTTGTGGCACCCTTTTAAAGTCCACAA
CTCCGTGGCACCCTTTTA
Found at i:2364071 original size:28 final size:28
Alignment explanation
Indices: 2363927--2364387 Score: 447
Period size: 28 Copynumber: 16.0 Consensus size: 28
2363917 TAAGTCAATG
* *
2363927 AGTCAGTGGCATTCCCTTCTAAAGCCCATA
1 AGTCAGTGGCA-TCCTTTC-AAAGCCCACA
* *
2363957 AGTTAGTGGCACCCCTTTCAAAGCCCACA
1 AGTCAGTGGCA-TCCTTTCAAAGCCCACA
*
2363986 AGTCAGTGGCACTCTTTTCAAAGTCCACACA
1 AGTCAGTGGCA-TCCTTTCAAAG-CC-CACA
* ** * *
2364017 GGTTGGTGGCAACTCATTTCAAAGCCCATA
1 AGTCAGTGGC-A-TCCTTTCAAAGCCCACA
* * *
2364047 AGTTAGTGGCATCATTTCAAGGCCCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * * *
2364075 AGCCAGTGGCATCTTTTCAATGACCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* *
2364103 AG-CAGTGGCATCTTTTCAAAGCTCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * **
2364130 AGTCAGTAGCATCCTTTTAAAGCCCTTA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
2364158 AGTCAGTGGCATCCTTTCAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* *
2364186 AGTTAGTGGCATCATTTCAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* *
2364214 AGTTAGTGGCATCCTTTTAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * *
2364242 AGACAGTGACATCCTTTCAAAGCTCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
* * *
2364270 AGTTATTGGCATCATTTCAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
*
2364298 AGTCAGTGGCATCTTTTCAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAGCCCACA
*
2364326 AGTCAATGGCATACCCTTTCAAAGCCCACACA
1 AGTCAGTGGCAT--CCTTTCAAAG-CC-CACA
* **
2364358 AGTCGGTGGCAACTTTTTTCAAAGCCCACA
1 AGTCAGTGGC-A-TCCTTTCAAAGCCCACA
2364388 CAAGTTAGTG
Statistics
Matches: 362, Mismatches: 59, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
27 24 0.07
28 216 0.60
29 30 0.08
30 41 0.11
31 17 0.05
32 32 0.09
33 1 0.00
34 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (28 bp):
AGTCAGTGGCATCCTTTCAAAGCCCACA
Found at i:2364176 original size:56 final size:56
Alignment explanation
Indices: 2363656--2364387 Score: 426
Period size: 56 Copynumber: 12.9 Consensus size: 56
2363646 CCATAACTTT
* * * * * * * *
2363656 GTGGCACCCTTTTAAAGCCCATAACTCCGTGGCA-CCTTTTTAAAGTCCACTA-TCC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTTAAAGCCCACAAGTCA
* * * * * * * *
2363711 GTGGCACCCTTTTAAAGTCCACAACTCTGTGGCAT-CTTTTTAAGTCCACAATTTC-
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAA-GTCA
* * * * * * * * * *
2363766 GTAGCA-CCTTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCATAACTCC
1 GTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCA
* * * * * * * * * *
2363822 GTGGCACCCTTTTAAAGTCCATAACTTC-GTGGCACCCTTTTAAAGTCCATAACTCG
1 GTGGCATCCTTTCAAAGCCCACAA-GTCAGTGGCATCCTTTTAAAGCCCACAAGTCA
* * * ** * * * **
2363878 GTGGCA-CACTTT-TAAGTCCACAACTTTGTGGCACCCTTTT-AAGTCAATGAGTCA
1 GTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCA
* * * * *
2363932 GTGGCATTCCCTTCTAAAGCCCATAAGTTAGTGGCACCCCTTTCAAAGCCCACAAGTCA
1 GTGGCA-TCCTTTC-AAAGCCCACAAGTCAGTGGCA-TCCTTTTAAAGCCCACAAGTCA
* * ** * * * *
2363991 GTGGCACTCTTTTCAAAGTCCACACAGGTTGGTGGCAACTCATTTCAAAGCCCATAAGTTA
1 GTGGCA-TCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-TCCTTTTAAAGCCCACAAGTCA
* * * * *
2364052 GTGGCATCATTTCAAGGCCCACAAGCCAGTGGCAT-CTTTTCAATGACCACAAG-CA
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTT-AAAGCCCACAAGTCA
* * * **
2364107 GTGGCATCTTTTCAAAGCTCACAAGTCAGTAGCATCCTTTTAAAGCCCTTAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCA
* * * *
2364163 GTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCA
* * * * * *
2364219 GTGGCATCCTTTTAAAGCCCACAAGACAGTGACATCCTTTCAAAGCTCACAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCA
* *
2364275 TTGGCATCATTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTT-AAAGCCCACAAGTCA
* * * *
2364331 ATGGCATACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTTTTTTCAAAGCCCACA
1 GTGGCAT--CCTTTCAAAG-CC-CACAAGTCAGTGGCATC-CTTTT-AAAGCCCACA
2364388 CAAGTTAGTG
Statistics
Matches: 555, Mismatches: 93, Indels: 51
0.79 0.13 0.07
Matches are distributed among these distances:
54 32 0.06
55 135 0.24
56 236 0.43
57 21 0.04
58 29 0.05
59 27 0.05
60 34 0.06
61 26 0.05
62 15 0.03
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (56 bp):
GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCA
Found at i:2364388 original size:32 final size:32
Alignment explanation
Indices: 2363972--2364445 Score: 223
Period size: 28 Copynumber: 16.2 Consensus size: 32
2363962 GTGGCACCCC
2363972 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* * ** *
2364001 TTTCAAAGTCCACACAGGTTGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* * *
2364033 TTTCAAAG-CC-CATAAGTTAGTGGC-A-TCA
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* *
2364061 TTTC-AAGGCC-CACAAGCCAGTGGC-A-TCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* *
2364089 TTTCAATG-AC-CACAAG-CAGTGGC-A-TCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* * *
2364116 TTTCAAAG--CTCACAAGTCAGTAGCATC-CT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
** *
2364145 TTT-AAAG-CC-CTTAAGTCAGTGGC-A-TCC
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* *
2364172 TTTCAAAG-CC-CACAAGTTAGTGGC-A-TCA
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* *
2364200 TTTCAAAG-CC-CACAAGTTAGTGGCATC-CT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* * *
2364229 TTT-AAAG-CC-CACAAGACAGTGAC-A-TCC
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* * * *
2364256 TTTCAAAG--CTCACAAGTTATTGGC-A-TCA
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
2364284 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* *
2364312 TTTCAAAG-CC-CACAAGTCAATGGCATAC-CC
1 TTTCAAAGCCCACACAAGTCAGTGGCA-ACTCT
* *
2364342 TTTCAAAGCCCACACAAGTCGGTGGCAACTTT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
* * *
2364374 TTTCAAAGCCCACACAAGTTAGTGGCACCTATT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACT-CT
* ** * * *
2364407 TTTTAAAGCCCACGTAAGTCGGTGGTAACCCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
2364439 TTTCAAA
1 TTTCAAA
2364446 TCACCACTTT
Statistics
Matches: 361, Mismatches: 59, Indels: 47
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.00
27 36 0.10
28 179 0.50
29 22 0.06
30 23 0.06
31 17 0.05
32 59 0.16
33 24 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCAGTGGCAACTCT
Found at i:2364415 original size:33 final size:32
Alignment explanation
Indices: 2364284--2364419 Score: 133
Period size: 32 Copynumber: 4.4 Consensus size: 32
2364274 ATTGGCATCA
*
2364284 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTTT
* **
2364312 TTTCAAAG-CC-CACAAGTCAATGGCATAC-CC
1 TTTCAAAGCCCACACAAGTCAGTGGCA-ACTTT
*
2364342 TTTCAAAGCCCACACAAGTCGGTGGCAACTTT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACTTT
* *
2364374 TTTCAAAGCCCACACAAGTTAGTGGCACCTATT
1 TTTCAAAGCCCACACAAGTCAGTGGCAACT-TT
*
2364407 TTTTAAAGCCCAC
1 TTTCAAAGCCCAC
2364420 GTAAGTCGGT
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
28 23 0.25
30 10 0.11
31 4 0.04
32 40 0.44
33 14 0.15
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.25
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCAGTGGCAACTTT
Found at i:2365460 original size:10 final size:10
Alignment explanation
Indices: 2365445--2365482 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2365435 CTTCTCTTAT
2365445 AAATCTAAAA
1 AAATCTAAAA
2365455 AAATCTAAAA
1 AAATCTAAAA
*
2365465 AGAAT-TAGAA
1 A-AATCTAAAA
2365475 AAATCTAA
1 AAATCTAA
2365483 CACCATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.75
11 3 0.12
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (10 bp):
AAATCTAAAA
Found at i:2372809 original size:31 final size:33
Alignment explanation
Indices: 2372768--2372842 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
2372758 TAAAAATGTA
2372768 TATATTTATATAAATTATGA-ATG-TTA-ATAGTT
1 TATA-TTATATAAATTATGATATGTTTATATA-TT
* *
2372800 TATATTATATAGATTTTGATATGTTTATATATT
1 TATATTATATAAATTATGATATGTTTATATATT
*
2372833 TATGTTATAT
1 TATATTATAT
2372843 TGTATTATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 13 0.35
32 7 0.19
33 14 0.38
34 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (33 bp):
TATATTATATAAATTATGATATGTTTATATATT
Found at i:2373203 original size:90 final size:89
Alignment explanation
Indices: 2373098--2373266 Score: 232
Period size: 90 Copynumber: 1.9 Consensus size: 89
2373088 ATGTACTACT
* * * * *
2373098 AATAAAAAGAATGATTGAGTTTGGTGTTACTTAACTCAATCATACTAATTCAGTTTATAAAAT-T
1 AATAAAAAGAATGATTGAGCTTGGTGTCACTTAACACAATCACACTAACTCAGTTTAT-AAATGT
2373162 ATATAAATATTTGAATCTATGCTATC
65 AT-TAAATATTTGAATCTATGCTATC
* * * *
2373188 AATAAAACGAGTGATTGAGCTTGGTGTCACTTAACACAATGACACTAACTCAGTTTATAAATGTC
1 AATAAAAAGAATGATTGAGCTTGGTGTCACTTAACACAATCACACTAACTCAGTTTATAAATGTA
2373253 TTAAATATTTGAAT
66 TTAAATATTTGAAT
2373267 TAAATTTTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
89 17 0.25
90 52 0.75
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (89 bp):
AATAAAAAGAATGATTGAGCTTGGTGTCACTTAACACAATCACACTAACTCAGTTTATAAATGTA
TTAAATATTTGAATCTATGCTATC
Found at i:2378609 original size:58 final size:57
Alignment explanation
Indices: 2378519--2378963 Score: 259
Period size: 58 Copynumber: 7.7 Consensus size: 57
2378509 TAAATGGCCT
* * * * *
2378519 TAAAATGCATGAAAA-TACAAAAATAGTCCTAAATCATGAGAAATTATTAAGATGACTC
1 TAAAATGCAT-AAAATTAC-ATAATAGTCCTAAATCATGAAAAATAACTAAAATGACTC
* * * *
2378577 TAAAATGCATAAAATTGCATAAATGGTCCTAAATCATGAAAAAATTACTAAAATAACTC
1 TAAAATGCATAAAATTACAT-AATAGTCCTAAATCATG-AAAAATAACTAAAATGACTC
* * * *
2378636 TAAAATG--TAAGAATTTGCATAATTGTCCTTAAATCATAAAAAATAATTAAAATGA-TC
1 TAAAATGCATAA-AA-TTACATAATAGTCC-TAAATCATGAAAAATAACTAAAATGACTC
* * *
2378693 TTAAAATGCATGAAGTTACATAATAGTCTTTAAATCAT-AGAAAATAACTAAAATGAACT-
1 -TAAAATGCATAAAATTACATAATAGTC-CTAAATCATGA-AAAATAACTAAAATG-ACTC
* * * ** *
2378752 TAAAATACATAAAATTAC-TAATAGTCCTAAATCAT--CAAATGACTAATGTGACAC
1 TAAAATGCATAAAATTACATAATAGTCCTAAATCATGAAAAATAACTAAAATGACTC
* * * * * * * * *
2378806 TAAAATGCATGAATTTGCTTAATGGTCTTTAAATCTTAGAATATGATAA-AAAAAT--CT-
1 TAAAATGCATAAAATTACATAATAGTC-CTAAATCAT-GAA-A-AATAACTAAAATGACTC
* * * * * * *
2378863 TAAAATGTATGAAATTACATGATAGTCTTAAAACATGAAAAATGACTAAAATAACTC
1 TAAAATGCATAAAATTACATAATAGTCCTAAATCATGAAAAATAACTAAAATGACTC
* * * *
2378920 TAAATTGCATGAAATGACATAATAGTGCTTAACATGCATGAAAA
1 TAAAATGCATAAAATTACATAATAGT-CCTAA-AT-CATGAAAA
2378964 TAATATAAAA
Statistics
Matches: 302, Mismatches: 57, Indels: 54
0.73 0.14 0.13
Matches are distributed among these distances:
53 5 0.02
54 31 0.10
55 10 0.03
56 24 0.08
57 62 0.21
58 112 0.37
59 40 0.13
60 15 0.05
61 3 0.01
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (57 bp):
TAAAATGCATAAAATTACATAATAGTCCTAAATCATGAAAAATAACTAAAATGACTC
Found at i:2378727 original size:117 final size:115
Alignment explanation
Indices: 2378544--2378757 Score: 263
Period size: 117 Copynumber: 1.8 Consensus size: 115
2378534 TACAAAAATA
* * * * * *
2378544 GTCCTAAATCATGAGAAATTATTAAGATGACTCTAAAATGCATAAAATTGCATAAATGGTCCTAA
1 GTCCTAAATCATAAAAAATAATTAAAATGACTCTAAAATGCATAAAATTACATAAATAGTCCTAA
*
2378609 ATCATGAAAAAATTACTAAAAT-AACTCTAAAATGTAAGAATTTGCATAATT
66 ATCAT-AAAAAATAACTAAAATGAACT-TAAAATGTAAGAATTTGCATAATT
* * *
2378660 GTCCTTAAATCATAAAAAATAATTAAAATGA-TCTTAAAATGCATGAAGTTACAT-AATAGTCTT
1 GTCC-TAAATCATAAAAAATAATTAAAATGACTC-TAAAATGCATAAAATTACATAAATAGTC-C
*
2378723 TAAATCATAGAAAATAACTAAAATGAACTTAAAAT
63 TAAATCATAAAAAATAACTAAAATGAACTTAAAAT
2378758 ACATAAAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
116 32 0.39
117 51 0.61
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (115 bp):
GTCCTAAATCATAAAAAATAATTAAAATGACTCTAAAATGCATAAAATTACATAAATAGTCCTAA
ATCATAAAAAATAACTAAAATGAACTTAAAATGTAAGAATTTGCATAATT
Found at i:2378945 original size:169 final size:170
Alignment explanation
Indices: 2378635--2378945 Score: 387
Period size: 169 Copynumber: 1.8 Consensus size: 170
2378625 TAAAATAACT
* * **
2378635 CTAAAATGTAAGAATTTGCATAATTGTCCTTAAATCATAAAAAATAATTAAAATGATCTTAAAAT
1 CTAAAATGCAAGAATTTGCATAATGGTCCTTAAATCATAAAAAATAATTAAAAAAATCTTAAAAT
* *
2378700 GCATGAAGTTACATAATAGTCTTTAAATCATAGAAAATAACTAAAATGAACTTAAAATACATAAA
66 GCATGAAATTACATAATAGTCTTTAAAACATAGAAAATAACTAAAATGAACTTAAAATACATAAA
*
2378765 ATTACTAATAGTCCTAAATCATCAAATGACTAATGTGACA
131 ATGACTAATAGTCCTAAATCATCAAATGACTAATGTGACA
* * * * * * *
2378805 CTAAAATGCATGAATTTGCTTAATGGTCTTTAAATCTTAGAATATGA-TAAAAAAATCTTAAAAT
1 CTAAAATGCAAGAATTTGCATAATGGTCCTTAAATCATAAAAAATAATTAAAAAAATCTTAAAAT
* * * * * *
2378869 GTATGAAATTACATGATAGTC-TTAAAACAT-GAAAAATGACTAAAAT-AACTCTAAATTGCATG
66 GCATGAAATTACATAATAGTCTTTAAAACATAG-AAAATAACTAAAATGAACT-TAAAATACATA
2378931 AAATGACATAATAGT
129 AAATGAC-TAATAGT
2378946 GCTTAACATG
Statistics
Matches: 118, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
167 5 0.04
168 35 0.30
169 40 0.34
170 38 0.32
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (170 bp):
CTAAAATGCAAGAATTTGCATAATGGTCCTTAAATCATAAAAAATAATTAAAAAAATCTTAAAAT
GCATGAAATTACATAATAGTCTTTAAAACATAGAAAATAACTAAAATGAACTTAAAATACATAAA
ATGACTAATAGTCCTAAATCATCAAATGACTAATGTGACA
Found at i:2389654 original size:17 final size:17
Alignment explanation
Indices: 2389632--2389666 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2389622 TTCCTCTTAA
2389632 TTTTTCCCTCTTTTTCT
1 TTTTTCCCTCTTTTTCT
* *
2389649 TTTTTCTCTTTTTTTCT
1 TTTTTCCCTCTTTTTCT
2389666 T
1 T
2389667 CTCTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCCCTCTTTTTCT
Found at i:2389670 original size:13 final size:12
Alignment explanation
Indices: 2389648--2389678 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
2389638 CCTCTTTTTC
2389648 TTTTTTCTCTTT
1 TTTTTTCTCTTT
2389660 TTTTCTTCTCTTT
1 TTTT-TTCTCTTT
2389673 TTTTTT
1 TTTTTT
2389679 TTTTTTGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:2390503 original size:19 final size:19
Alignment explanation
Indices: 2390481--2390518 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2390471 TTGGTAGTAG
*
2390481 CCAAATTTGTATCGATACA
1 CCAAATATGTATCGATACA
*
2390500 CCAAGTATGTATCGATACA
1 CCAAATATGTATCGATACA
2390519 TGTATACACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (19 bp):
CCAAATATGTATCGATACA
Found at i:2396719 original size:13 final size:13
Alignment explanation
Indices: 2396701--2396739 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2396691 ATATCTTTCT
*
2396701 TTGTATTGATACA
1 TTGTATCGATACA
2396714 TTGTATCGATACA
1 TTGTATCGATACA
*
2396727 CTGTATCGATACA
1 TTGTATCGATACA
2396740 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2400761 original size:19 final size:18
Alignment explanation
Indices: 2400727--2400765 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
2400717 GTAGTTCACC
2400727 ATTTTATTTATTTTTATT
1 ATTTTATTTATTTTTATT
*
2400745 ATTTTATATTCTTTTTATT
1 ATTTTAT-TTATTTTTATT
2400764 AT
1 AT
2400766 GACCTTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTATTTATTTTTATT
Found at i:2400911 original size:2 final size:2
Alignment explanation
Indices: 2400904--2400935 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2400894 AGCAAAAGAT
2400904 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2400936 CATCTACCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2401771 original size:2 final size:2
Alignment explanation
Indices: 2401764--2401798 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2401754 TAAAAATTTA
2401764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2401799 AATAAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2403257 original size:18 final size:18
Alignment explanation
Indices: 2403226--2403262 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2403216 GGTTTTAAAA
*
2403226 TGAAGGTCTCTACAAGGT
1 TGAAGATCTCTACAAGGT
*
2403244 TGAAGATCTTTACAAGGT
1 TGAAGATCTCTACAAGGT
2403262 T
1 T
2403263 TGCTATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (18 bp):
TGAAGATCTCTACAAGGT
Found at i:2405308 original size:21 final size:22
Alignment explanation
Indices: 2405266--2405308 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
2405256 GAATAACTCA
**
2405266 CAAAATTAAAAATAGATCACAT
1 CAAAATTAAAAATAGAAAACAT
*
2405288 CAAAA-TAAAAATTGAAAACAT
1 CAAAATTAAAAATAGAAAACAT
2405309 ACCAAAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.21
Consensus pattern (22 bp):
CAAAATTAAAAATAGAAAACAT
Found at i:2406420 original size:15 final size:15
Alignment explanation
Indices: 2406400--2406432 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2406390 TTGCTGTTCG
2406400 TCTTGCTGTTTTGTT
1 TCTTGCTGTTTTGTT
*
2406415 TCTTGCTGTTTTTTT
1 TCTTGCTGTTTTGTT
2406430 TCT
1 TCT
2406433 CTTCTTGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (15 bp):
TCTTGCTGTTTTGTT
Found at i:2406439 original size:20 final size:21
Alignment explanation
Indices: 2406414--2406463 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
2406404 GCTGTTTTGT
*
2406414 TTCTTGCTGTTTTTTTTC-TC
1 TTCTTGCTGTTTTGTTTCTTC
2406434 TTCTTGCTGTTTTGTTTCTTC
1 TTCTTGCTGTTTTGTTTCTTC
2406455 TTCGTTGCT
1 TTC-TTGCT
2406464 TGTTGTTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 17 0.63
21 5 0.19
22 5 0.19
ACGTcount: A:0.00, C:0.20, G:0.14, T:0.66
Consensus pattern (21 bp):
TTCTTGCTGTTTTGTTTCTTC
Found at i:2406469 original size:21 final size:20
Alignment explanation
Indices: 2406414--2406470 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
2406404 GCTGTTTTGT
* *
2406414 TTCTTGCTGTTTTTTTTCTC
1 TTCTTGCTGTGTTGTTTCTC
*
2406434 TTCTTGCTGTTTTGTTTCTTC
1 TTCTTGCTGTGTTGTTTC-TC
2406455 TTCGTTGCT-TGTTGTT
1 TTC-TTGCTGTGTTGTT
2406471 GCTGCTGCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 17 0.52
21 11 0.33
22 5 0.15
ACGTcount: A:0.00, C:0.18, G:0.16, T:0.67
Consensus pattern (20 bp):
TTCTTGCTGTGTTGTTTCTC
Found at i:2406543 original size:5 final size:5
Alignment explanation
Indices: 2406527--2406623 Score: 53
Period size: 5 Copynumber: 19.4 Consensus size: 5
2406517 CTCTTGTTGT
* * *
2406527 CTTTG CTGTG CTTTG CTGTTT CGTTT- C-TTG C-TTG CTGTTT CTTTG
1 CTTTG CTTTG CTTTG CT-TTG C-TTTG CTTTG CTTTG CT-TTG CTTTG
* *
2406572 CTTTG CTTTG CTGTTT CATTT- C-TTG C-TTG CTGTTT CTTTG CTTTG
1 CTTTG CTTTG CT-TTG C-TTTG CTTTG CTTTG CT-TTG CTTTG CTTTG
2406617 CTTTG CT
1 CTTTG CT
2406624 GTTTCGTTTC
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
3 4 0.05
4 10 0.14
5 40 0.54
6 18 0.24
7 2 0.03
ACGTcount: A:0.01, C:0.21, G:0.20, T:0.59
Consensus pattern (5 bp):
CTTTG
Found at i:2406563 original size:19 final size:18
Alignment explanation
Indices: 2406539--2406647 Score: 137
Period size: 19 Copynumber: 5.6 Consensus size: 18
2406529 TTGCTGTGCT
2406539 TTGCTGTTTCGTTTCTTGC
1 TTGCTGTTTC-TTTCTTGC
2406558 TTGCTGTTTCTTTGCTTTGC
1 TTGCTGTTTCTTT-C-TTGC
2406578 TTTGCTGTTTCATTTCTTGC
1 -TTGCTGTTTC-TTTCTTGC
2406598 TTGCTGTTTCTTTGCTTTGC
1 TTGCTGTTTCTTT-C-TTGC
2406618 TTTGCTGTTTCGTTTCTTGC
1 -TTGCTGTTTC-TTTCTTGC
2406638 TTGCTGTTTC
1 TTGCTGTTTC
2406648 ATTCATCAGC
Statistics
Matches: 82, Mismatches: 0, Indels: 16
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.07
19 32 0.39
20 16 0.20
21 22 0.27
22 6 0.07
ACGTcount: A:0.01, C:0.20, G:0.19, T:0.60
Consensus pattern (18 bp):
TTGCTGTTTCTTTCTTGC
Found at i:2406570 original size:40 final size:40
Alignment explanation
Indices: 2406521--2406647 Score: 227
Period size: 40 Copynumber: 3.1 Consensus size: 40
2406511 TTCCTTCTCT
*
2406521 TGTTGTCTTTGCTGTGCTTTGCTGTTTCGTTTCTTGCTTGC
1 TGTT-TCTTTGCTTTGCTTTGCTGTTTCGTTTCTTGCTTGC
*
2406562 TGTTTCTTTGCTTTGCTTTGCTGTTTCATTTCTTGCTTGC
1 TGTTTCTTTGCTTTGCTTTGCTGTTTCGTTTCTTGCTTGC
2406602 TGTTTCTTTGCTTTGCTTTGCTGTTTCGTTTCTTGCTTGC
1 TGTTTCTTTGCTTTGCTTTGCTGTTTCGTTTCTTGCTTGC
2406642 TGTTTC
1 TGTTTC
2406648 ATTCATCAGC
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
40 79 0.95
41 4 0.05
ACGTcount: A:0.01, C:0.20, G:0.20, T:0.59
Consensus pattern (40 bp):
TGTTTCTTTGCTTTGCTTTGCTGTTTCGTTTCTTGCTTGC
Found at i:2406572 original size:15 final size:14
Alignment explanation
Indices: 2406549--2406647 Score: 61
Period size: 14 Copynumber: 7.4 Consensus size: 14
2406539 TTGCTGTTTC
2406549 GTTTCTTGCTTGCT
1 GTTTCTTGCTTGCT
2406563 GTTTCTTTGCTTTGCT
1 GTTTC-TTGC-TTGCT
* *
2406579 -TTGC-TG-TTTC-
1 GTTTCTTGCTTGCT
*
2406589 ATTTCTTGCTTGCT
1 GTTTCTTGCTTGCT
2406603 GTTTCTTTGCTTTGCT
1 GTTTC-TTGC-TTGCT
* *
2406619 -TTGC-TG-TTTC-
1 GTTTCTTGCTTGCT
2406629 GTTTCTTGCTTGCT
1 GTTTCTTGCTTGCT
2406643 GTTTC
1 GTTTC
2406648 ATTCATCAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 24
0.66 0.09 0.25
Matches are distributed among these distances:
11 12 0.19
12 4 0.06
13 10 0.16
14 14 0.22
15 14 0.22
16 10 0.16
ACGTcount: A:0.01, C:0.20, G:0.19, T:0.60
Consensus pattern (14 bp):
GTTTCTTGCTTGCT
Found at i:2406683 original size:80 final size:80
Alignment explanation
Indices: 2406521--2406673 Score: 197
Period size: 80 Copynumber: 1.9 Consensus size: 80
2406511 TTCCTTCTCT
* ** **
2406521 TGTTGTCTTTGCTGTGCTTTGCTGTTTCGTTTCTTGCTTGCTGTTTCTTTGCTTTGCTTTGCTGT
1 TGTTGTCTTTGCTGTGCTTTGCTGTTTCGTTTCTTGCTTGCTGTTTCATTGCTCAGC-TTGCAAT
2406586 TTCATTTCTTGCTTGC
65 TTCATTTCTTGCTTGC
*
2406602 TGTT-TCTTTGCTTTGCTTTGCTGTTTCGTTTCTTGCTTGCTGTTTCATT-CATCAGC-TGCCAA
1 TGTTGTCTTTGCTGTGCTTTGCTGTTTCGTTTCTTGCTTGCTGTTTCATTGC-TCAGCTTG-CAA
2406664 TTTC-TTTCTT
64 TTTCATTTCTT
2406674 ATTTTTGCTG
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
78 8 0.12
79 6 0.09
80 46 0.72
81 4 0.06
ACGTcount: A:0.04, C:0.21, G:0.18, T:0.57
Consensus pattern (80 bp):
TGTTGTCTTTGCTGTGCTTTGCTGTTTCGTTTCTTGCTTGCTGTTTCATTGCTCAGCTTGCAATT
TCATTTCTTGCTTGC
Found at i:2406957 original size:42 final size:43
Alignment explanation
Indices: 2406891--2407055 Score: 181
Period size: 42 Copynumber: 3.9 Consensus size: 43
2406881 TTCTGTTTCT
* * * * *
2406891 TCTTCATCAGCTTCAAAACCGAATTGAATTGCTTTGCT-TCAAC
1 TCTTCTTCAGC-TCCAAATCGAATTGCATTGCTTTGCTGTCAGC
* * *
2406934 TCTTCTTCAGTTTCAAATCGAATTGCATTGCTTTGCTGT-TGC
1 TCTTCTTCAGCTCCAAATCGAATTGCATTGCTTTGCTGTCAGC
* * * *
2406976 TTTTCTTCAGTTCCAAATCAAATTGCATTGCTTTGCTGCCAGC
1 TCTTCTTCAGCTCCAAATCGAATTGCATTGCTTTGCTGTCAGC
* *
2407019 TCTTCTTCAGCTCCAAATCGAATTGCCTTCCTTTGCT
1 TCTTCTTCAGCTCCAAATCGAATTGCATTGCTTTGCT
2407056 TTTTTTTTTT
Statistics
Matches: 102, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 58 0.57
43 44 0.43
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (43 bp):
TCTTCTTCAGCTCCAAATCGAATTGCATTGCTTTGCTGTCAGC
Found at i:2407382 original size:2 final size:2
Alignment explanation
Indices: 2407377--2407407 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2407367 TTTTTTTCTT
2407377 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2407408 TTTATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2407447 original size:10 final size:10
Alignment explanation
Indices: 2407376--2407447 Score: 53
Period size: 12 Copynumber: 7.0 Consensus size: 10
2407366 TTTTTTTTCT
2407376 TTATATATATA
1 TTATATAT-TA
2407387 TATATATATATA
1 T-TATATAT-TA
2407399 TATATATATT-
1 T-TATATATTA
2407409 TTATA-ATT-
1 TTATATATTA
2407417 TTATTATATTA
1 TTA-TATATTA
*
2407428 -TATTTAATTA
1 TTATAT-ATTA
2407438 TTATATATTA
1 TTATATATTA
2407448 GACATACCAC
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
8 6 0.11
9 8 0.15
10 14 0.26
11 6 0.11
12 19 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATATATTA
Found at i:2410235 original size:48 final size:47
Alignment explanation
Indices: 2410183--2410335 Score: 137
Period size: 48 Copynumber: 3.2 Consensus size: 47
2410173 TTTTAGGATT
* * *
2410183 ATTTTGTACTTTCCTTCAAAATTGACTAAAATATGTCTTTTAATGTTA
1 ATTTTGTACTTTCCATCAAAACTGACTAAAATATGTCTTTTGA-GTTA
* * * *
2410231 ATTTTGAATTTTCAATCAAAACCGACTAAAAT-TGAGTCTTTTGAGTTA
1 ATTTTGTACTTTCCATCAAAACTGACTAAAATAT--GTCTTTTGAGTTA
* * * * * *
2410279 GTTTTGTACTTTTCATCAAAACTAATTAAAATCAAGTCTTTTGGGGTTA
1 ATTTTGTACTTTCCATCAAAACTGACTAAAAT-ATGTCTTTT-GAGTTA
2410328 ATTTTGTA
1 ATTTTGTA
2410336 TTTTTTGTCA
Statistics
Matches: 82, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
47 1 0.01
48 61 0.74
49 20 0.24
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (47 bp):
ATTTTGTACTTTCCATCAAAACTGACTAAAATATGTCTTTTGAGTTA
Found at i:2410348 original size:97 final size:95
Alignment explanation
Indices: 2410111--2410389 Score: 249
Period size: 96 Copynumber: 2.9 Consensus size: 95
2410101 GAGTTTTAGG
* * * * * *
2410111 TTAAAATTGAGTCTTTTAGGGTTATTTTTATATTTTTTGTTAAAATCAACCAAAATCGAGTGTTT
1 TTAAAA-TAAGTCTTTTAGGGTTAATTTTGTATTTTTTGTCAAAA-CAACTAAAATCGAGTCTTT
* * * *
2410176 TAGGATTA-TTTTGTACTTTCCTTCAAAATTGA
64 TAGG-TTAGTTTTGTACTTTTCATCAAAACTAA
* * ** * *** * *
2410208 CTAAAATATGTCTTTTAATGTTAATTTTGAATTTTCAATCAAAACCGACTAAAATTGAGTCTTTT
1 TTAAAATAAGTCTTTTAGGGTTAATTTTGTATTTTTTGTCAAAA-CAACTAAAATCGAGTCTTTT
2410273 -GAGTTAGTTTTGTACTTTTCATCAAAACTAA
65 AG-GTTAGTTTTGTACTTTTCATCAAAACTAA
* *
2410304 TTAAAATCAAGTCTTTTGGGGTTAATTTTGTATTTTTTGTCAAAACTAA-TCACAATCGAGTCTT
1 TTAAAAT-AAGTCTTTTAGGGTTAATTTTGTATTTTTTGTCAAAAC-AACT-AAAATCGAGTC-T
*
2410368 TTTAGGTTAGTTTTGCACTTTT
62 TTTAGGTTAGTTTTGTACTTTT
2410390 TGACAAAATC
Statistics
Matches: 141, Mismatches: 34, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
95 4 0.03
96 72 0.51
97 44 0.31
98 20 0.14
99 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (95 bp):
TTAAAATAAGTCTTTTAGGGTTAATTTTGTATTTTTTGTCAAAACAACTAAAATCGAGTCTTTTA
GGTTAGTTTTGTACTTTTCATCAAAACTAA
Found at i:2410350 original size:49 final size:48
Alignment explanation
Indices: 2410265--2410397 Score: 149
Period size: 49 Copynumber: 2.7 Consensus size: 48
2410255 ACTAAAATTG
* ** *
2410265 AGTCTTTTGAGTTAGTTTTGTACTTTTCATCAAAACTAATTAAAATCA
1 AGTCTTTTGGGTTAGTTTTGTACTTTTTGTCAAAACTAATCAAAATCA
* * * *
2410313 AGTCTTTTGGGGTTAATTTTGTATTTTTTGTCAAAACTAATCACAATCG
1 AGTCTTTT-GGGTTAGTTTTGTACTTTTTGTCAAAACTAATCAAAATCA
* * *
2410362 AGTCTTTTTAGGTTAGTTTTGCACTTTTTGACAAAA
1 AGTC-TTTTGGGTTAGTTTTGTACTTTTTGTCAAAA
2410398 TCAATCTAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
48 8 0.11
49 58 0.83
50 4 0.06
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (48 bp):
AGTCTTTTGGGTTAGTTTTGTACTTTTTGTCAAAACTAATCAAAATCA
Found at i:2411794 original size:65 final size:65
Alignment explanation
Indices: 2411688--2411840 Score: 159
Period size: 65 Copynumber: 2.4 Consensus size: 65
2411678 TCTTAAGTCA
* * * * *
2411688 AACC-AATTTTCCTAGAAAGAGGTCGAACCTCGAAACCAAATTAAAGTCTTTTTCGTTTTAAGCT
1 AACCTAATTTTCTTAGAAATAGGTCGAACCTCGAAACCAAATTAAAGTC-CTTTCCTTTTAAGAT
2411752 G
65 G
** * * ** * *
2411753 AA-CTCGTTTTCTTAGAAATAGGTCGAGCTTCGAAATGAAATTGAGGTCCTTTCCTTTTAAGATG
1 AACCTAATTTTCTTAGAAATAGGTCGAACCTCGAAACCAAATTAAAGTCCTTTCCTTTTAAGATG
2411817 AACCTAATTTT-TTAGAAATAGGTC
1 AACCTAATTTTCTTAGAAATAGGTC
2411841 TAGCCTAAGA
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
64 29 0.41
65 42 0.59
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (65 bp):
AACCTAATTTTCTTAGAAATAGGTCGAACCTCGAAACCAAATTAAAGTCCTTTCCTTTTAAGATG
Found at i:2411917 original size:63 final size:64
Alignment explanation
Indices: 2411765--2411971 Score: 183
Period size: 64 Copynumber: 3.2 Consensus size: 64
2411755 CTCGTTTTCT
* * ** * * * *
2411765 TAGAAATAGGTCGAGCTTCGAAATGAAATTGAGGTCCTTTCCTTTTAAGATGAACCTAAT-TT-T
1 TAGAAATAGGTCAAGCATAAAAATGAAATCGAGGTCCTTTTCTTTTAAG-TCAAAC--ATGTTCT
2411828 T-
63 TC
* * * * *
2411829 TAGAAATAGGTCTAGCCTAAGAATGAAATCGAGTTCCTTTTC-TTTAAGGTCAAACTTGTT-TTC
1 TAGAAATAGGTCAAGCATAAAAATGAAATCGAGGTCCTTTTCTTTTAA-GTCAAACATGTTCTT-
2411892 C
64 C
* *
2411893 TAG-AATAGGTCAAGCATAAAAATGAAATCGAGGTCTTTTTCTTTTTAAGTCAAACATGTTCTTT
1 TAGAAATAGGTCAAGCATAAAAATGAAATCGAGGTCCTTTTC-TTTTAAGTCAAACATGTTCTTC
2411957 TAGAAATAGGTCAAG
1 TAGAAATAGGTCAAG
2411972 TTTCAACACG
Statistics
Matches: 117, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
61 1 0.01
62 4 0.03
63 42 0.36
64 52 0.44
65 18 0.15
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (64 bp):
TAGAAATAGGTCAAGCATAAAAATGAAATCGAGGTCCTTTTCTTTTAAGTCAAACATGTTCTTC
Found at i:2412915 original size:28 final size:31
Alignment explanation
Indices: 2412876--2412952 Score: 81
Period size: 33 Copynumber: 2.5 Consensus size: 31
2412866 TGATTAAGTT
2412876 GTTATATATTTATA-TA-AT-AATTTTAAAA
1 GTTATATATTTATATTATATAAATTTTAAAA
2412904 GTTA-ATAGTTTATATTATATAAATTTTAATATA
1 GTTATATA-TTTATATTATATAAATTTTAA-A-A
* *
2412937 TTTTTATATTTATATT
1 GTTATATATTTATATT
2412953 GTATTCGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 3 0.08
28 10 0.25
29 2 0.05
30 2 0.05
31 8 0.20
32 1 0.03
33 11 0.28
34 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (31 bp):
GTTATATATTTATATTATATAAATTTTAAAA
Found at i:2414730 original size:26 final size:26
Alignment explanation
Indices: 2414682--2414731 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
2414672 ATATGGTCGA
* *
2414682 AACTTAACAACGAAGGGATATCAAGC
1 AACTTAACAACGAACGGAAATCAAGC
* *
2414708 AACTTAACAACGGACTGAAATCAA
1 AACTTAACAACGAACGGAAATCAA
2414732 ATATTATGTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (26 bp):
AACTTAACAACGAACGGAAATCAAGC
Found at i:2415261 original size:52 final size:53
Alignment explanation
Indices: 2415205--2415314 Score: 177
Period size: 54 Copynumber: 2.1 Consensus size: 53
2415195 TTAGTTTATG
*
2415205 TTTTTTTTTAAATATTTATA-TTTGACATACTTTAAGATGTTAATATAAATCA
1 TTTTTTTTTAAATATTTATATTTTAACATACTTTAAGATGTTAATATAAATCA
* *
2415257 TTTTTTTTTAAATATTTATATTTTTAACATGCTTTGAGATGTTAATATAAATCA
1 TTTTTTTTTAAATATTTATA-TTTTAACATACTTTAAGATGTTAATATAAATCA
2415311 TTTT
1 TTTT
2415315 AGAAACACGA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
52 20 0.38
54 33 0.62
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (53 bp):
TTTTTTTTTAAATATTTATATTTTAACATACTTTAAGATGTTAATATAAATCA
Found at i:2417347 original size:19 final size:19
Alignment explanation
Indices: 2417303--2417349 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2417293 TTGTTTAATT
*
2417303 TTAAATTAACTATTTTATC
1 TTAAATTAACTATTTTATA
* *
2417322 TTTAATTAA-TAATTTTTTA
1 TTAAATTAACT-ATTTTATA
2417341 TTAAATTAA
1 TTAAATTAA
2417350 AATATAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAAATTAACTATTTTATA
Found at i:2420025 original size:13 final size:13
Alignment explanation
Indices: 2420007--2420036 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2419997 ACATTTCACC
2420007 ATGTATCGATACA
1 ATGTATCGATACA
2420020 ATGTATCGATACA
1 ATGTATCGATACA
2420033 ATGT
1 ATGT
2420037 GAGTTTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2420791 original size:21 final size:21
Alignment explanation
Indices: 2420767--2420808 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2420757 CAATATATAA
2420767 CTCCCCCTTAATAAAATTTTT
1 CTCCCCCTTAATAAAATTTTT
*
2420788 CTCCCTCTTAATAAAATTTTT
1 CTCCCCCTTAATAAAATTTTT
2420809 AATGCTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (21 bp):
CTCCCCCTTAATAAAATTTTT
Found at i:2420932 original size:20 final size:20
Alignment explanation
Indices: 2420897--2420951 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
2420887 TTTCAAAATA
* *
2420897 TCTCTCCCTTTTTTTATTAAC
1 TCTCTCCC-CTTTTTATCAAC
2420918 TCTCTCCCCTTTTTATCAAC
1 TCTCTCCCCTTTTTATCAAC
*
2420938 TCT-TCGCCTTTTTA
1 TCTCTCCCCTTTTTA
2420952 CAAATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 10 0.32
20 13 0.42
21 8 0.26
ACGTcount: A:0.13, C:0.33, G:0.02, T:0.53
Consensus pattern (20 bp):
TCTCTCCCCTTTTTATCAAC
Found at i:2426357 original size:34 final size:34
Alignment explanation
Indices: 2426300--2426518 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 34
2426290 AAGTGGGAGA
*
2426300 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2426333 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2426367 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * **
2426401 ATTGTTAATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2426435 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
2426469 ATTGTTAACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
2426503 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2426519 TGGTTTTTAT
Statistics
Matches: 158, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
33 17 0.11
34 140 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2426443 original size:102 final size:101
Alignment explanation
Indices: 2426300--2426518 Score: 330
Period size: 102 Copynumber: 2.2 Consensus size: 101
2426290 AAGTGGGAGA
** * * * *
2426300 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
*
2426365 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTAACTAAATGGGAGATTTGGTAGCTTACC
*
2426401 ATTGTTAATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
2426466 ACCATTGTTAACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTAACTAAATGGGAGATTTGGTAGCTTACC
2426503 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2426519 TGGTTTTTAT
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTAACTAAATGGGAGATTTGGTAGCTTACC
Found at i:2426954 original size:14 final size:15
Alignment explanation
Indices: 2426935--2426963 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2426925 TTTAATTTTT
2426935 AATTTTA-TATTAAA
1 AATTTTATTATTAAA
2426949 AATTTTATTATTAAA
1 AATTTTATTATTAAA
2426964 TTAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTTATTATTAAA
Found at i:2427497 original size:20 final size:20
Alignment explanation
Indices: 2427468--2427512 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2427458 TTAACTTAAT
*
2427468 TTATATATT-ATGTAATATCA
1 TTATAAATTAATGTAATAT-A
*
2427488 TTATAAATTAATTTAATATA
1 TTATAAATTAATGTAATATA
2427508 TTATA
1 TTATA
2427513 TATAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTATAAATTAATGTAATATA
Found at i:2427540 original size:21 final size:21
Alignment explanation
Indices: 2427507--2427546 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2427497 AATTTAATAT
*
2427507 ATTATATATAAAAATTAATTGA
1 ATTATATA-AAAAAATAATTGA
2427529 ATTA-ATAAAAAAATAATT
1 ATTATATAAAAAAATAATT
2427547 TATATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 3 0.18
22 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTATATAAAAAAATAATTGA
Found at i:2427577 original size:22 final size:23
Alignment explanation
Indices: 2427542--2427586 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2427532 AATAAAAAAA
*
2427542 TAATTTATATATTTTTAATATTT
1 TAATTAATATATTTTTAATATTT
*
2427565 TAATTAAT-TATTTTTTATATTT
1 TAATTAATATATTTTTAATATTT
2427587 AATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TAATTAATATATTTTTAATATTT
Found at i:2427598 original size:17 final size:18
Alignment explanation
Indices: 2427568--2427626 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 18
2427558 AATATTTTAA
2427568 TTAATTATTTTTT-ATAT
1 TTAATTATTTTTTAATAT
2427585 TTAA-TATTTATTTAATAT
1 TTAATTATTT-TTTAATAT
*
2427603 TAAAATTATTTTTTAAATAT
1 T-TAATTATTTTTT-AATAT
2427623 TTAA
1 TTAA
2427627 AAATTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 5 0.14
17 7 0.20
18 5 0.14
19 7 0.20
20 11 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAATTATTTTTTAATAT
Found at i:2427670 original size:22 final size:23
Alignment explanation
Indices: 2427628--2427681 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
2427618 AATATTTAAA
*
2427628 AATTTTAATTATAATAAATTAATT
1 AATTTAAATTAT-ATAAATTAATT
2427652 AATTTAAATTAT-TAAATTAATT
1 AATTTAAATTATATAAATTAATT
*
2427674 AAATTAAA
1 AATTTAAA
2427682 AATTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 17 0.61
24 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTTAAATTATATAAATTAATT
Found at i:2427674 original size:9 final size:9
Alignment explanation
Indices: 2427632--2427680 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
2427622 TTTAAAAATT
2427632 TTAATTATAA
1 TTAATTA-AA
*
2427642 TAAATT-AA
1 TTAATTAAA
2427650 TTAATTTAAA
1 TTAA-TTAAA
2427660 TT-ATTAAA
1 TTAATTAAA
2427668 TTAATTAAA
1 TTAATTAAA
2427677 TTAA
1 TTAA
2427681 AAATTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
8 12 0.35
9 13 0.38
10 9 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAATTAAA
Found at i:2427681 original size:14 final size:14
Alignment explanation
Indices: 2427632--2427681 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2427622 TTTAAAAATT
2427632 TTAATTATAA-TAAA
1 TTAATTA-AATTAAA
*
2427646 TTAATTAATTTAAA
1 TTAATTAAATTAAA
2427660 TT-ATTAAATT-AA
1 TTAATTAAATTAAA
2427672 TTAAATTAAA
1 TT-AATTAAA
2427682 AATTAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 4 0.13
13 8 0.26
14 19 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAATTAAATTAAA
Found at i:2427692 original size:31 final size:32
Alignment explanation
Indices: 2427623--2427693 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
2427613 TTTTAAATAT
*
2427623 TTAAAAATT-TTAATTATAATAAATTAATTAA
1 TTAAAAATTATTAATTATAATAAATTAATAAA
* *
2427654 TT-TAAATTATTAAATTA-ATTAAATTAA-AAA
1 TTAAAAATTATT-AATTATAATAAATTAATAAA
2427684 TTAAAAATTA
1 TTAAAAATTA
2427694 AAAATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 9 0.27
31 19 0.58
32 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TTAAAAATTATTAATTATAATAAATTAATAAA
Found at i:2427698 original size:21 final size:22
Alignment explanation
Indices: 2427665--2427706 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
2427655 TTAAATTATT
*
2427665 AAATTAATTAAATTAAAAATTAA
1 AAATTAA-TAAATAAAAAATTAA
2427688 AAATTAA-AAATAAAAAATT
1 AAATTAATAAATAAAAAATT
2427707 TAATCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATTAATAAATAAAAAATTAA
Found at i:2427703 original size:6 final size:7
Alignment explanation
Indices: 2427674--2427706 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2427664 TAAATTAATT
2427674 AAATTAA
1 AAATTAA
2427681 AAATTAA
1 AAATTAA
2427688 AAATTAA
1 AAATTAA
*
2427695 AAATAAA
1 AAATTAA
2427702 AAATT
1 AAATT
2427707 TAATCAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATTAA
Found at i:2428762 original size:10 final size:10
Alignment explanation
Indices: 2428747--2428771 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2428737 TTAATATAAA
2428747 AATAATTTTT
1 AATAATTTTT
2428757 AATAATTTTT
1 AATAATTTTT
2428767 AATAA
1 AATAA
2428772 AAATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AATAATTTTT
Found at i:2429502 original size:27 final size:26
Alignment explanation
Indices: 2429471--2429554 Score: 73
Period size: 28 Copynumber: 3.1 Consensus size: 26
2429461 TTGTAAAAAA
2429471 ATCTTTTATTATATTTTTAATTTTTAT
1 ATCTTTTATTATATTTTT-ATTTTTAT
*
2429498 ATC--TTAGTTATATTATTTTATTTTAAT
1 ATCTTTTA-TTATA-T-TTTTATTTTTAT
* *
2429525 ATAATATTTATTTTATTTTTATTTTTAT
1 AT-CT-TTTATTATATTTTTATTTTTAT
2429553 AT
1 AT
2429555 TTTAATGTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
25 3 0.07
26 5 0.11
27 13 0.28
28 17 0.37
29 1 0.02
30 4 0.09
31 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (26 bp):
ATCTTTTATTATATTTTTATTTTTAT
Found at i:2431761 original size:12 final size:12
Alignment explanation
Indices: 2431746--2431770 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2431736 ATAATTTAAA
2431746 TAAATATTTTAT
1 TAAATATTTTAT
2431758 TAAATATTTTAT
1 TAAATATTTTAT
2431770 T
1 T
2431771 TTAATTTTTA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAATATTTTAT
Found at i:2431888 original size:9 final size:9
Alignment explanation
Indices: 2431876--2432018 Score: 63
Period size: 9 Copynumber: 15.0 Consensus size: 9
2431866 ATAATTTTTT
2431876 AAATTAAAA
1 AAATTAAAA
*
2431885 AAATTTAAA
1 AAATTAAAA
* *
2431894 AAATTCATA
1 AAATTAAAA
* **
2431903 ATATTTTAA
1 AAATTAAAA
* *
2431912 ATATAAAATA
1 AAATTAAA-A
*
2431922 AAATTTTAAA
1 AAA-TTAAAA
2431932 AAA-TAAAA
1 AAATTAAAA
*
2431940 AAATTAATA
1 AAATTAAAA
2431949 AAATTCAAAAA
1 AAATT--AAAA
*
2431960 TCAAAATAAAA
1 --AAATTAAAA
*
2431971 AAATTATAA
1 AAATTAAAA
* *
2431980 AAATTTATA
1 AAATTAAAA
2431989 AAATTCAAAA
1 AAATT-AAAA
*
2431999 AACTTAAAA
1 AAATTAAAA
2432008 TAAACTTAAAA
1 -AAA-TTAAAA
2432019 TTTTAAAATA
Statistics
Matches: 98, Mismatches: 26, Indels: 18
0.69 0.18 0.13
Matches are distributed among these distances:
8 7 0.07
9 56 0.57
10 15 0.15
11 16 0.16
13 4 0.04
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.29
Consensus pattern (9 bp):
AAATTAAAA
Found at i:2431910 original size:34 final size:38
Alignment explanation
Indices: 2431866--2431935 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 38
2431856 AAATATAAGA
*
2431866 ATAATTTTTTAAAT-T-AAA-AAAA-TTTAAAAAATTC
1 ATAATATTTTAAATATAAAATAAAATTTTAAAAAATTC
2431900 ATAATATTTTAAATATAAAATAAAATTTTAAAAAAT
1 ATAATATTTTAAATATAAAATAAAATTTTAAAAAAT
2431936 AAAAAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 13 0.42
35 1 0.03
36 3 0.10
37 4 0.13
38 10 0.32
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (38 bp):
ATAATATTTTAAATATAAAATAAAATTTTAAAAAATTC
Found at i:2431922 original size:19 final size:19
Alignment explanation
Indices: 2431856--2431931 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 19
2431846 AAGTCAACAA
*
2431856 AAATATAAGAATAATTTTTT
1 AAATATAA-AATAATATTTT
*
2431876 AAAT-TAAAA-AA-ATTTA
1 AAATATAAAATAATATTTT
* **
2431892 AAAAAT-TCATAATATTTT
1 AAATATAAAATAATATTTT
*
2431910 AAATATAAAATAAAATTTT
1 AAATATAAAATAATATTTT
2431929 AAA
1 AAA
2431932 AAATAAAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
16 7 0.17
17 5 0.12
18 11 0.26
19 15 0.36
20 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
AAATATAAAATAATATTTT
Found at i:2431939 original size:20 final size:19
Alignment explanation
Indices: 2431900--2431939 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2431890 TAAAAAATTC
* *
2431900 ATAATATTTTAAATATAAA
1 ATAAAATTTTAAAAATAAA
2431919 ATAAAATTTTAAAAAATAAA
1 ATAAAATTTT-AAAAATAAA
2431939 A
1 A
2431940 AAATTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAATTTTAAAAATAAA
Found at i:2431983 original size:31 final size:33
Alignment explanation
Indices: 2431931--2431998 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 33
2431921 AAAATTTTAA
2431931 AAAATAAAAAAATTAATAAAATTCA-AAAA-TC
1 AAAATAAAAAAATTAATAAAATTCATAAAATTC
*
2431962 AAAATAAAAAAATT-ATAAAAATTTATAAAATTC
1 AAAATAAAAAAATTAAT-AAAATTCATAAAATTC
2431995 AAAA
1 AAAA
2431999 AACTTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 2 0.06
31 21 0.64
32 4 0.12
33 6 0.18
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (33 bp):
AAAATAAAAAAATTAATAAAATTCATAAAATTC
Found at i:2432090 original size:16 final size:16
Alignment explanation
Indices: 2432070--2432114 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2432060 AATATATAAT
2432070 TAAAATTAATAAAAATA
1 TAAAATTAA-AAAAATA
*
2432087 -AAAATTACAAAAATA
1 TAAAATTAAAAAAATA
*
2432102 TTAAATTAAAAAA
1 TAAAATTAAAAAA
2432115 GAAGAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAATTAAAAAAATA
Found at i:2432350 original size:12 final size:12
Alignment explanation
Indices: 2432304--2432354 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
2432294 AAGAAAATGA
* *
2432304 GAAAGGGAAAAG
1 GAAAGAGAAAGG
* *
2432316 GAAAGAAAAAGA
1 GAAAGAGAAAGG
2432328 GAAAGAG--AGG
1 GAAAGAGAAAGG
2432338 GAAAGAGAAAGG
1 GAAAGAGAAAGG
2432350 GAAAG
1 GAAAG
2432355 GGGGAGAGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 9 0.29
12 22 0.71
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
GAAAGAGAAAGG
Found at i:2432796 original size:10 final size:11
Alignment explanation
Indices: 2432770--2432795 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2432760 AATGCTAAGT
2432770 TTTTTAAATAA
1 TTTTTAAATAA
2432781 TTTTTAAATAA
1 TTTTTAAATAA
2432792 TTTT
1 TTTT
2432796 AGGGTTTTAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTTAAATAA
Found at i:2432883 original size:18 final size:17
Alignment explanation
Indices: 2432862--2432906 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2432852 TTTTTTATAT
2432862 ATTTTTAATTATATTTAA
1 ATTTTTAATTAT-TTTAA
*
2432880 ATTTTTAAATATTTTAA
1 ATTTTTAATTATTTTAA
*
2432897 ATTTTAAATT
1 ATTTTTAATT
2432907 TTAATAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTAATTATTTTAA
Found at i:2432893 original size:16 final size:16
Alignment explanation
Indices: 2432862--2432910 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
2432852 TTTTTTATAT
2432862 ATTTTTAATTATATTTAA
1 ATTTTTAA--ATATTTAA
2432880 ATTTTTAAATATTTTAA
1 ATTTTTAAATA-TTTAA
2432897 A-TTTTAAAT-TTTAA
1 ATTTTTAAATATTTAA
2432911 TAATATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.17
16 11 0.37
17 6 0.20
18 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTAAATATTTAA
Found at i:2433349 original size:13 final size:13
Alignment explanation
Indices: 2433326--2433359 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2433316 TTTAAAAAAA
2433326 ATAATTAAATATTT
1 ATAATT-AATATTT
*
2433340 TTAATTAATATTT
1 ATAATTAATATTT
2433353 ATAATTA
1 ATAATTA
2433360 TGCATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATAATTAATATTT
Found at i:2447600 original size:79 final size:79
Alignment explanation
Indices: 2447469--2447744 Score: 360
Period size: 79 Copynumber: 3.5 Consensus size: 79
2447459 TGTAACCCCA
* * *
2447469 ATTTTATTTCTAAAATACTGATTTTTCACCATC-AGGGATACTCCAACCCCGTTATTTTTGAGAG
1 ATTTTATTTCTAAAACACCGATTTTCCACCATCGA-GGATACTCCAACCCCGTTATTTTTGAGAG
2447533 GATACTCCAAACCT-G
65 GATACTCC-AACCTCG
* * * *
2447548 ATTTTATTTTTAAAACACCGATTTTCCACCATCGAGGATACTCTAACCCCGTTATTTCTGAGGGG
1 ATTTTATTTCTAAAACACCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTTGAGAGG
* *
2447613 ATACTTCAACCTCA
66 ATACTCCAACCTCG
* * * *
2447627 ATTTTATTTTTAAAACACCTACTTTT-CACCATCGGGGAGACTCCAACCCCGTTATTTTTGAGAG
1 ATTTTATTTCTAAAACACCGA-TTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTTGAGAG
*
2447691 GGTACTCCAACCTCG
65 GATACTCCAACCTCG
* *
2447706 ATTTTATTTCTAAAACATCGATTTTCCACCATCGGGGAT
1 ATTTTATTTCTAAAACACCGATTTTCCACCATCGAGGAT
2447745 GTAGACACCT
Statistics
Matches: 171, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
78 9 0.05
79 157 0.92
80 5 0.03
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (79 bp):
ATTTTATTTCTAAAACACCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTTGAGAGG
ATACTCCAACCTCG
Found at i:2448072 original size:33 final size:33
Alignment explanation
Indices: 2448035--2448101 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2448025 TTCTACGATT
2448035 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2448068 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2448101 T
1 T
2448102 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2448073 original size:13 final size:13
Alignment explanation
Indices: 2448055--2448079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2448045 CATAAAATGT
2448055 TGTATCGATACAA
1 TGTATCGATACAA
2448068 TGTATCGATACA
1 TGTATCGATACA
2448080 TATTTTTTTG
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:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2448160 original size:13 final size:13
Alignment explanation
Indices: 2448142--2448166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2448132 ATTACTCAAA
2448142 TGTATCGATACAT
1 TGTATCGATACAT
2448155 TGTATCGATACA
1 TGTATCGATACA
2448167 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2448268 original size:52 final size:52
Alignment explanation
Indices: 2448175--2448298 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
2448165 CACTGATCTT
*
2448175 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
2448226 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
2448278 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2448299 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:2451515 original size:79 final size:79
Alignment explanation
Indices: 2451384--2451630 Score: 307
Period size: 79 Copynumber: 3.1 Consensus size: 79
2451374 CGTTACGACA
** * * * **
2451384 GGGGATACTCCAACCCTATTATTTCTAAAATGATACTTTAACCCCGATTTTATTTTTAAAAAACT
1 GGGGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCGATTTTATTTTTAAAAAACT
* *
2451449 GATTTTTCACCATT
66 AATTTTTCACCATC
* * * * *
2451463 GGGGATACTCCAATCCCGTTATTTTTGAGAGGATACTCCAACTCCGATTTTATTTCTAAAACACT
1 GGGGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCGATTTTATTTTTAAAAAACT
2451528 AATTTTTCACCATC
66 AATTTTTCACCATC
* * * *
2451542 GGGGATATTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTTCAAAATA-T
1 GGGGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCGATTTTATTTTTAAAAAACT
*
2451606 CAACTTTTCACCATC
66 -AATTTTTCACCATC
2451621 GGGGATACTC
1 GGGGATACTC
2451631 TGACCCTATT
Statistics
Matches: 143, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
78 1 0.01
79 142 0.99
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCGATTTTATTTTTAAAAAACT
AATTTTTCACCATC
Done.