Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 14 of 29
Found at i:1873289 original size:27 final size:27
Alignment explanation
Indices: 1873258--1873309 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1873248 TAATTAAATA
*
1873258 AATATAAAAAGACATAATTTATTAATT
1 AATATAAAAAGACATAAGTTATTAATT
*
1873285 AATATAAAAAGATATAAGTTATTAA
1 AATATAAAAAGACATAAGTTATTAA
1873310 ACATCTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (27 bp):
AATATAAAAAGACATAAGTTATTAATT
Found at i:1874955 original size:2 final size:2
Alignment explanation
Indices: 1874948--1874980 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1874938 GTAGTTCAAT
1874948 TA 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 TA T
1874981 TATTTCACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1875166 original size:13 final size:13
Alignment explanation
Indices: 1875142--1875184 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
1875132 ATTTGATATT
1875142 TATA-TTTT-ATA
1 TATATTTTTAATA
1875153 TATATTTTTAATA
1 TATATTTTTAATA
*
1875166 TATAATTTTTAAAA
1 TAT-ATTTTTAATA
1875180 TATAT
1 TATAT
1875185 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 4 0.14
12 4 0.14
13 8 0.29
14 12 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATATTTTTAATA
Found at i:1875191 original size:16 final size:15
Alignment explanation
Indices: 1875149--1875191 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1875139 ATTTATATTT
* *
1875149 TATATATATTTTTAA
1 TATATAAATTTTAAA
*
1875164 TATATAATTTTTAAAA
1 TATATAAATTTT-AAA
1875180 TATATAAATTTT
1 TATATAAATTTT
1875192 TTTAAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATAAATTTTAAA
Found at i:1876553 original size:18 final size:19
Alignment explanation
Indices: 1876523--1876560 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1876513 ATTTTTTAAA
1876523 AGTTTAAACTATG-GGTTT
1 AGTTTAAACTATGAGGTTT
1876541 AGTTTCAAA-TATGAGGTTT
1 AGTTT-AAACTATGAGGTTT
1876560 A
1 A
1876561 TAAGCACAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (19 bp):
AGTTTAAACTATGAGGTTT
Found at i:1885726 original size:19 final size:22
Alignment explanation
Indices: 1885702--1885748 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 22
1885692 ATAGATAATG
1885702 ATATAATAA-AAAT-AATTA-A
1 ATATAATAAGAAATGAATTATA
*
1885721 ATATAATAAGATATGAATTATA
1 ATATAATAAGAAATGAATTATA
1885743 ATATAA
1 ATATAA
1885749 ATACAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
20 3 0.12
21 5 0.21
22 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATAATAAGAAATGAATTATA
Found at i:1885815 original size:11 final size:10
Alignment explanation
Indices: 1885767--1885828 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
1885757 TAAATATATG
1885767 AATATATAAA
1 AATATATAAA
*
1885777 AATTTATATAA
1 AATATATA-AA
* * *
1885788 TATAAATTAAT
1 AATATA-TAAA
1885799 AATATATCAAA
1 AATATAT-AAA
*
1885810 AATATATATA
1 AATATATAAA
1885820 AATATATAA
1 AATATATAA
1885829 TATTTTAAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
10 18 0.46
11 19 0.49
12 2 0.05
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (10 bp):
AATATATAAA
Found at i:1891787 original size:4 final size:4
Alignment explanation
Indices: 1891778--1891829 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
1891768 AGTAAGGAAC
* * * * *
1891778 ATAT ATAT ATAT ATAT GTAT GTAT ATAT GTAT ATAT ATGT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1891826 ATAT
1 ATAT
1891830 TATGAGGAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:1891802 original size:12 final size:11
Alignment explanation
Indices: 1891778--1891823 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
1891768 AGTAAGGAAC
*
1891778 ATATATATA-T
1 ATATATGTATT
1891788 ATATATGTATGT
1 ATATATGTAT-T
1891800 ATATATGTA-T
1 ATATATGTATT
1891810 ATATATGTA-T
1 ATATATGTATT
1891820 ATAT
1 ATAT
1891824 GTATATTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
10 23 0.70
12 10 0.30
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (11 bp):
ATATATGTATT
Found at i:1891804 original size:18 final size:17
Alignment explanation
Indices: 1891781--1891833 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
1891771 AAGGAACATA
*
1891781 TATATATATATATGTATG
1 TATATATGTATAT-TATG
1891799 TATATATGTATATATATG
1 TATATATGTATAT-TATG
1891817 TATATATGTATATTATG
1 TATATATGTATATTATG
1891834 AGGAAAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
17 4 0.12
18 29 0.88
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (17 bp):
TATATATGTATATTATG
Found at i:1892834 original size:10 final size:10
Alignment explanation
Indices: 1892819--1892844 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1892809 CTCAAAACAA
1892819 ATATATATTT
1 ATATATATTT
1892829 ATATATATTT
1 ATATATATTT
1892839 ATATAT
1 ATATAT
1892845 GGAAAAGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATATATATTT
Found at i:1894876 original size:86 final size:86
Alignment explanation
Indices: 1894786--1894959 Score: 330
Period size: 86 Copynumber: 2.0 Consensus size: 86
1894776 TATGTCAATT
*
1894786 AATCAACTCCCTTATGGACTTCATAATTACTATAAAGAGATATTGTTGTTAATTTATTTATTAAT
1 AATCAACTCCCTTATGGACTTCATAATTACCATAAAGAGATATTGTTGTTAATTTATTTATTAAT
*
1894851 TGAATTTAGTATTATTAAATC
66 GGAATTTAGTATTATTAAATC
1894872 AATCAACTCCCTTATGGACTTCATAATTACCATAAAGAGATATTGTTGTTAATTTATTTATTAAT
1 AATCAACTCCCTTATGGACTTCATAATTACCATAAAGAGATATTGTTGTTAATTTATTTATTAAT
1894937 GGAATTTAGTATTATTAAATC
66 GGAATTTAGTATTATTAAATC
1894958 AA
1 AA
1894960 ATAAAACTAA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (86 bp):
AATCAACTCCCTTATGGACTTCATAATTACCATAAAGAGATATTGTTGTTAATTTATTTATTAAT
GGAATTTAGTATTATTAAATC
Found at i:1895232 original size:3 final size:3
Alignment explanation
Indices: 1895224--1895277 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
1895214 ACTACATTAC
1895224 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1895272 ATT ATT
1 ATT ATT
1895278 TTCTATATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1895897 original size:21 final size:22
Alignment explanation
Indices: 1895862--1895906 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1895852 AAATAAAAAA
**
1895862 TATTTATATTTATAT-TTTTTT
1 TATTTATATAGATATATTTTTT
1895883 TATTTATATAGATATAATTTTTT
1 TATTTATATAGATAT-ATTTTTT
1895906 T
1 T
1895907 TGTTTGACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTTATATAGATATATTTTTT
Found at i:1897561 original size:34 final size:34
Alignment explanation
Indices: 1897479--1897561 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 34
1897469 AGTGTTAGTT
* *
1897479 TTGTTGACTAAATGAGTGATTTGGTAGTTTATTA
1 TTGTTGACTAAATGGGTGATTTGGTAGTTTATCA
*
1897513 TTGTTGATTAAATGGGTGATTTGGTA-TTTCATCA
1 TTGTTGACTAAATGGGTGATTTGGTAGTTT-ATCA
1897547 TTGTTGACTAAATGG
1 TTGTTGACTAAATGG
1897562 TTAAAAGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 3 0.07
34 41 0.93
ACGTcount: A:0.25, C:0.05, G:0.24, T:0.46
Consensus pattern (34 bp):
TTGTTGACTAAATGGGTGATTTGGTAGTTTATCA
Found at i:1897897 original size:28 final size:28
Alignment explanation
Indices: 1897861--1897918 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1897851 ATGACCCTGC
1897861 TCTACCTATCATTGCACTAATAATGGTA
1 TCTACCTATCATTGCACTAATAATGGTA
* *
1897889 TCTATCTATCATTGCACTAATAGTGGTA
1 TCTACCTATCATTGCACTAATAATGGTA
1897917 TC
1 TC
1897919 AGAGCTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (28 bp):
TCTACCTATCATTGCACTAATAATGGTA
Found at i:1902092 original size:34 final size:34
Alignment explanation
Indices: 1902022--1902300 Score: 265
Period size: 34 Copynumber: 8.5 Consensus size: 34
1902012 AAGTGAGAGA
* * *
1902022 ATTGTTAACTAAATGGGTGATTTGAT-GTTTGCC
1 ATTGTTGACTAAATGGGTGATTTGGTGGTTTGTC
1902055 ATTGTTGACTAAATGGGTGATTTGGTGGTTTGTC
1 ATTGTTGACTAAATGGGTGATTTGGTGGTTTGTC
* * * * ** *
1902089 ATTGTTGATTAAAT--CTCCA---AGTGG-GAG-A
1 ATTGTTGACTAAATGGGT-GATTTGGTGGTTTGTC
*
1902117 ATTGTTAACTAAATGGGTGATTTGGTGGTTTG-C
1 ATTGTTGACTAAATGGGTGATTTGGTGGTTTGTC
**
1902150 TATTGTTGACTAAATGGGTGATTTGGTGGTTTAAC
1 -ATTGTTGACTAAATGGGTGATTTGGTGGTTTGTC
* * *
1902185 ATTGTTGATTAAATAGGTGATTTGGT-GTTTGTT
1 ATTGTTGACTAAATGGGTGATTTGGTGGTTTGTC
1902218 ATTGTTGACTAAAT-GGTGATTTGGTGGTTTGTC
1 ATTGTTGACTAAATGGGTGATTTGGTGGTTTGTC
** * *
1902251 ACGGTTGATTAAATGGGTGATTTGATGGTTTGTC
1 ATTGTTGACTAAATGGGTGATTTGGTGGTTTGTC
* *
1902285 ATTATTAACTAAATGG
1 ATTGTTGACTAAATGG
1902301 CTAAAAGATA
Statistics
Matches: 198, Mismatches: 36, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
28 12 0.06
29 2 0.01
30 5 0.03
32 16 0.08
33 60 0.30
34 102 0.52
35 1 0.01
ACGTcount: A:0.23, C:0.06, G:0.28, T:0.43
Consensus pattern (34 bp):
ATTGTTGACTAAATGGGTGATTTGGTGGTTTGTC
Found at i:1902188 original size:96 final size:95
Alignment explanation
Indices: 1902004--1902198 Score: 336
Period size: 96 Copynumber: 2.0 Consensus size: 95
1901994 GTTCACAATC
1902004 AAATCTCCAAGTGAGAGAATTGTTAACTAAATGGGTGATTTGATGTTTGCCATTGTTGACTAAAT
1 AAATCTCCAAGTGAGAGAATTGTTAACTAAATGGGTGATTTGATGTTTGCCATTGTTGACTAAAT
**
1902069 GGGTGATTTGGTGGTTTGTCATTGTTGATT
66 GGGTGATTTGGTGGTTTAACATTGTTGATT
* * *
1902099 AAATCTCCAAGTGGGAGAATTGTTAACTAAATGGGTGATTTGGTGGTTTGCTATTGTTGACTAAA
1 AAATCTCCAAGTGAGAGAATTGTTAACTAAATGGGTGATTTGAT-GTTTGCCATTGTTGACTAAA
1902164 TGGGTGATTTGGTGGTTTAACATTGTTGATT
65 TGGGTGATTTGGTGGTTTAACATTGTTGATT
1902195 AAAT
1 AAAT
1902199 AGGTGATTTG
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
95 42 0.45
96 52 0.55
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.39
Consensus pattern (95 bp):
AAATCTCCAAGTGAGAGAATTGTTAACTAAATGGGTGATTTGATGTTTGCCATTGTTGACTAAAT
GGGTGATTTGGTGGTTTAACATTGTTGATT
Found at i:1902283 original size:67 final size:67
Alignment explanation
Indices: 1902126--1902300 Score: 244
Period size: 67 Copynumber: 2.6 Consensus size: 67
1902116 AATTGTTAAC
* **
1902126 TAAATGGGTGATTTGGTGGTTTGCTATTGTTGACTAAATGGGTGATTTGGTGGTTTAACATTGTT
1 TAAATGGGTGATTTGGTGGTTTGTTATTGTTGACTAAAT-GGTGATTTGGTGGTTTAACACGGTT
1902191 GAT
65 GAT
* **
1902194 TAAATAGGTGATTTGGT-GTTTGTTATTGTTGACTAAATGGTGATTTGGTGGTTTGTCACGGTTG
1 TAAATGGGTGATTTGGTGGTTTGTTATTGTTGACTAAATGGTGATTTGGTGGTTTAACACGGTTG
1902258 AT
66 AT
* * * *
1902260 TAAATGGGTGATTTGATGGTTTGTCATTATTAACTAAATGG
1 TAAATGGGTGATTTGGTGGTTTGTTATTGTTGACTAAATGG
1902301 CTAAAAGATA
Statistics
Matches: 95, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
66 39 0.41
67 40 0.42
68 16 0.17
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (67 bp):
TAAATGGGTGATTTGGTGGTTTGTTATTGTTGACTAAATGGTGATTTGGTGGTTTAACACGGTTG
AT
Found at i:1902298 original size:100 final size:101
Alignment explanation
Indices: 1902117--1902298 Score: 251
Period size: 100 Copynumber: 1.8 Consensus size: 101
1902107 AAGTGGGAGA
** *
1902117 ATTGTTAACTAAATGGGTGATTTGGTGGTTTGCTATTGTTGACTAAATGGGTGATTTGGTGGTTT
1 ATTGTTAACTAAATGGGTGATTTGGTGGTTTGCTACGGTTGACTAAATGGGTGATTTGATGGTTT
* * *
1902182 AACATTGTTGATTAAATAGGTGATTTGGTGTTTGTT
66 AACATTATTAACTAAATAGGTGATTTGGTGTTTGTT
* *
1902218 ATTGTTGACTAAAT-GGTGATTTGGTGGTTTG-TCACGGTTGATTAAATGGGTGATTTGATGGTT
1 ATTGTTAACTAAATGGGTGATTTGGTGGTTTGCT-ACGGTTGACTAAATGGGTGATTTGATGGTT
**
1902281 TGTCATTATTAACTAAAT
65 TAACATTATTAACTAAAT
1902299 GGCTAAAAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
99 1 0.01
100 56 0.80
101 13 0.19
ACGTcount: A:0.23, C:0.05, G:0.27, T:0.45
Consensus pattern (101 bp):
ATTGTTAACTAAATGGGTGATTTGGTGGTTTGCTACGGTTGACTAAATGGGTGATTTGATGGTTT
AACATTATTAACTAAATAGGTGATTTGGTGTTTGTT
Found at i:1903190 original size:26 final size:26
Alignment explanation
Indices: 1903161--1903219 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1903151 GAAATAAATT
*
1903161 ATTTTAATTTTAATTAATTTATTT-A-A
1 ATTTTAATTTAAATT-A-TTATTTAATA
*
1903187 ATTTAAATTTAAATTATTATTTAATA
1 ATTTTAATTTAAATTATTATTTAATA
1903213 ATTTTAA
1 ATTTTAA
1903220 ATCAAATCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 6 0.21
25 2 0.07
26 20 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTTTAATTTAAATTATTATTTAATA
Found at i:1903921 original size:17 final size:17
Alignment explanation
Indices: 1903895--1903950 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
1903885 AAAATATAAC
1903895 TAAAATATAATATAATA
1 TAAAATATAATATAATA
*
1903912 TAAAAAATAATATAA-A
1 TAAAATATAATATAATA
*
1903928 TACAATATAA-AT-ATA
1 TAAAATATAATATAATA
1903943 T-AAATATA
1 TAAAATATA
1903951 TTAAAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 7 0.21
15 4 0.12
16 9 0.26
17 14 0.41
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATATAATATAATA
Found at i:1903928 original size:28 final size:28
Alignment explanation
Indices: 1903883--1904051 Score: 84
Period size: 28 Copynumber: 5.9 Consensus size: 28
1903873 AAATGAGATG
1903883 TAAAAATATAACTA-AAATATAATATAATA
1 TAAAAA-ATAA-TATAAATATAATATAATA
*
1903912 TAAAAAATAATATAAATACAATATAAATA
1 TAAAAAATAATATAAATATAATAT-AATA
* * * *
1903941 TATAAATATATTA-AAAT-TTATATTATA
1 TA-AAAAATAATATAAATATAATATAATA
* * *
1903968 TTAAATATTAATATATAA-A-AAT-TTATA
1 -TAAAAAATAATATA-AATATAATATAATA
* * *
1903995 TAAATATATTACACATTAAACATAATTATAATA
1 TAAA-A-AATA-ATA-TAAATATAA-TATAATA
1904028 T-AAAAA-AATATAAATATAATATAA
1 TAAAAAATAATATAAATATAATATAA
1904052 ATATGTAATT
Statistics
Matches: 108, Mismatches: 17, Indels: 33
0.68 0.11 0.21
Matches are distributed among these distances:
26 9 0.08
27 24 0.22
28 29 0.27
29 23 0.21
30 12 0.11
31 3 0.03
32 3 0.03
33 5 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAAAAATAATATAAATATAATATAATA
Found at i:1903938 original size:11 final size:11
Alignment explanation
Indices: 1903887--1904055 Score: 81
Period size: 11 Copynumber: 16.0 Consensus size: 11
1903877 GAGATGTAAA
* *
1903887 AATATAACTAA
1 AATATAAATAT
1903898 AATAT-AATAT
1 AATATAAATAT
*
1903908 AATATAAAAAAT
1 AATAT-AAATAT
*
1903920 AATATAAATAC
1 AATATAAATAT
1903931 AATAT-AA-AT
1 AATATAAATAT
1903940 -ATATAAATAT
1 AATATAAATAT
*
1903950 ATTA-AAAT-T
1 AATATAAATAT
* *
1903959 TATAT-TATATT
1 AATATAAATA-T
*
1903970 AAATATTAATAT
1 -AATATAAATAT
*
1903982 -ATAAAAAT-T
1 AATATAAATAT
*
1903991 TATATAAATAT
1 AATATAAATAT
* * *
1904002 ATTACACAT-T
1 AATATAAATAT
* *
1904012 AAACATAATTAT
1 -AATATAAATAT
*
1904024 AATATAAA-AA
1 AATATAAATAT
1904034 AATATAAATAT
1 AATATAAATAT
1904045 AATATAAATAT
1 AATATAAATAT
1904056 GTAATTAAAT
Statistics
Matches: 115, Mismatches: 28, Indels: 30
0.66 0.16 0.17
Matches are distributed among these distances:
8 4 0.03
9 9 0.08
10 39 0.34
11 45 0.39
12 15 0.13
13 3 0.03
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAAATAT
Found at i:1903975 original size:12 final size:13
Alignment explanation
Indices: 1903960--1904001 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1903950 ATTAAAATTT
1903960 ATATTATAT-TAA
1 ATATTATATATAA
1903972 ATATTAATATATAA
1 ATATT-ATATATAA
*
1903986 AAATT-TATATAA
1 ATATTATATATAA
1903998 ATAT
1 ATAT
1904002 ATTACACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 15 0.58
13 4 0.15
14 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATTATATATAA
Found at i:1904365 original size:14 final size:14
Alignment explanation
Indices: 1904346--1904380 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1904336 TAGTATCATT
1904346 GTTAAAAAAATTGG
1 GTTAAAAAAATTGG
*
1904360 GTTAAAAAAATTTG
1 GTTAAAAAAATTGG
1904374 G-TAAAAA
1 GTTAAAAA
1904381 TATGATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (14 bp):
GTTAAAAAAATTGG
Found at i:1905899 original size:9 final size:9
Alignment explanation
Indices: 1905885--1905934 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
1905875 TAATATATCA
1905885 TATTATATT
1 TATTATATT
1905894 TATTATATT
1 TATTATATT
*
1905903 AATTTTATATT
1 --TATTATATT
* *
1905914 TATTAAATA
1 TATTATATT
1905923 TATTATATT
1 TATTATATT
1905932 TAT
1 TAT
1905935 ATTATATCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 25 0.76
11 8 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TATTATATT
Found at i:1905917 original size:29 final size:29
Alignment explanation
Indices: 1905885--1905941 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1905875 TAATATATCA
* * *
1905885 TATTATATTTATTATATTAATTTTATATT
1 TATTAAATATATTATATTAATATTATATT
*
1905914 TATTAAATATATTATATTTATATTATAT
1 TATTAAATATATTATATTAATATTATAT
1905942 CTAAAGTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TATTAAATATATTATATTAATATTATATT
Found at i:1905924 original size:24 final size:26
Alignment explanation
Indices: 1905884--1905946 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
1905874 ATAATATATC
* *
1905884 ATATTATAT-TTATTATATTA-ATTTT
1 ATATTATATCTAAATATATTATA-TTT
1905909 ATATT-TAT-TAAATATATTATATTT
1 ATATTATATCTAAATATATTATATTT
1905933 ATATTATATCTAAA
1 ATATTATATCTAAA
1905947 GTTCTTGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 20 0.61
25 9 0.27
26 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATTATATCTAAATATATTATATTT
Found at i:1905937 original size:20 final size:20
Alignment explanation
Indices: 1905884--1905938 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1905874 ATAATATATC
*
1905884 ATATTATATTTATTATATTAAT
1 ATATTATATTTA-TAT-TAAAT
1905906 -T-TTATA-TT-TATTAAAT
1 ATATTATATTTATATTAAAT
1905922 ATATTATATTTATATTA
1 ATATTATATTTATATTA
1905939 TATCTAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 5 0.18
19 4 0.14
20 10 0.36
21 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTATATTTATATTAAAT
Found at i:1907137 original size:2 final size:2
Alignment explanation
Indices: 1907054--1907118 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
1907044 TTCGCCCTTA
*
1907054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1907096 AT AT TT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1907119 GTATGCTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1907957 original size:17 final size:16
Alignment explanation
Indices: 1907924--1907965 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
1907914 TTAAGCATTG
1907924 AATT-TATATTATAAA
1 AATTATATATTATAAA
1907939 AATTATATATTACTAAA
1 AATTATATATTA-TAAA
*
1907956 AATTAAATAT
1 AATTATATAT
1907966 CAAATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.17
16 7 0.29
17 13 0.54
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTATATATTATAAA
Found at i:1908045 original size:10 final size:10
Alignment explanation
Indices: 1908030--1908054 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1908020 TGTTAAAAAT
1908030 TATATTTAAA
1 TATATTTAAA
1908040 TATATTTAAA
1 TATATTTAAA
1908050 TATAT
1 TATAT
1908055 CATCTTTTTT
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):
TATATTTAAA
Found at i:1908290 original size:4 final size:4
Alignment explanation
Indices: 1908281--1908310 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1908271 AAAATGTATA
1908281 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
1908311 GGAGTCAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:1911507 original size:2 final size:2
Alignment explanation
Indices: 1911502--1911531 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1911492 GATACAAAAC
1911502 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1911532 TTCTTCTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1911828 original size:21 final size:22
Alignment explanation
Indices: 1911799--1911846 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
1911789 TAAAAATTCA
1911799 TTTTCTTTTCATATTTTTACTCT
1 TTTTCTTTTCATATTTTTACT-T
* *
1911822 TTTTTTTTTCATGTTTTTACTT
1 TTTTCTTTTCATATTTTTACTT
1911844 TTT
1 TTT
1911847 AACTCTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTCTTTTCATATTTTTACTT
Found at i:1912276 original size:182 final size:180
Alignment explanation
Indices: 1911811--1912347 Score: 956
Period size: 176 Copynumber: 3.0 Consensus size: 180
1911801 TTCTTTTCAT
* *
1911811 ATTTTTACTCTTTTTTTTTTCATGTTTTTACTTTTTAACTCTACTAAACACCCAAAAAACATTGA
1 ATTTTTACTCTTTTTTTTTTCATGTTTTTACTTTTTAACTCTACTAAACACCCAAAAAATACTGA
*
1911876 GAAAAATCTAAAACTTAACTTAAATGATTTATACTTTCATTTTTACAATAATTCATGCTTTTATT
66 GAAAAATCTAAAACTTAACTTAAATGATTTATACTATCATTTTTACAATAATTCATGCTTTTATT
*
1911941 ATTAAACGTATCATTCAATAAATTTAAAATTTAAATTTCAATATTCACAC
131 ATTAAACGTATCATTCAATAAATTTGAAATTTAAATTTCAATATTCACAC
*
1911991 ATTTTTA--C--ATTTTTTTCATGTTTTTACTTTTTAACTCTACTAAACACCCAAAAAATACTGA
1 ATTTTTACTCTTTTTTTTTTCATGTTTTTACTTTTTAACTCTACTAAACACCCAAAAAATACTGA
*
1912052 GAAAAATCTAAAACTTAACTTAAATGATTTATACTGTCATTTTTACAATAATTCATGCTTTTATT
66 GAAAAATCTAAAACTTAACTTAAATGATTTATACTATCATTTTTACAATAATTCATGCTTTTATT
1912117 ATTAAACGTATCATTCAATAAATTTGAAATTTAAATTTCAATATTCACAC
131 ATTAAACGTATCATTCAATAAATTTGAAATTTAAATTTCAATATTCACAC
1912167 ATTTTTACTCTCTTTTTTTTTTCATGTTTTTACTTTTTAACTCTACTAAACACCCAAAAAATACT
1 ATTTTTA--CTCTTTTTTTTTTCATGTTTTTACTTTTTAACTCTACTAAACACCCAAAAAATACT
* *
1912232 GAGAAAAATTTAAAAATTAACTTAAATGATTTATACTATCATTTTTACAATAATTCATGCTTTTA
64 GAGAAAAATCTAAAACTTAACTTAAATGATTTATACTATCATTTTTACAATAATTCATGCTTTTA
1912297 TTATTAAACGTATCATTCAATAAATTTGAAATTTAAATTTCAATATTCACA
129 TTATTAAACGTATCATTCAATAAATTTGAAATTTAAATTTCAATATTCACA
1912348 ATCTTTTTTA
Statistics
Matches: 342, Mismatches: 9, Indels: 10
0.95 0.02 0.03
Matches are distributed among these distances:
176 170 0.50
178 1 0.00
180 8 0.02
182 163 0.48
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.44
Consensus pattern (180 bp):
ATTTTTACTCTTTTTTTTTTCATGTTTTTACTTTTTAACTCTACTAAACACCCAAAAAATACTGA
GAAAAATCTAAAACTTAACTTAAATGATTTATACTATCATTTTTACAATAATTCATGCTTTTATT
ATTAAACGTATCATTCAATAAATTTGAAATTTAAATTTCAATATTCACAC
Found at i:1915735 original size:53 final size:53
Alignment explanation
Indices: 1915654--1915757 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 53
1915644 AGAGTGATGC
*
1915654 TTCTTTCCACTGTTTTTGTGAAGCTTCTGGTTTAGTTTTTCTGGTTTTGAAAGT
1 TTCTTTCCACTGTTTTTGTGAAGCTTCTGGTTT-GGTTTTCTGGTTTTGAAAGT
*
1915708 TTCTTTTCACTG-TTTTGTGAAGCTTCTGGTTTGGTTTTCTGGTTTTGAAA
1 TTCTTTCCACTGTTTTTGTGAAGCTTCTGGTTTGGTTTTCTGGTTTTGAAA
1915758 ATAGGGTTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 17 0.35
53 20 0.42
54 11 0.23
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.54
Consensus pattern (53 bp):
TTCTTTCCACTGTTTTTGTGAAGCTTCTGGTTTGGTTTTCTGGTTTTGAAAGT
Found at i:1918758 original size:2 final size:2
Alignment explanation
Indices: 1918751--1918778 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1918741 CTGAAAAAGA
1918751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1918779 TAAAGTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1919401 original size:2 final size:2
Alignment explanation
Indices: 1919394--1919418 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1919384 TTATTTTAAG
1919394 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 A
1919419 ATTTTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1920986 original size:12 final size:12
Alignment explanation
Indices: 1920957--1920994 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1920947 AATTTGATAA
*
1920957 ATAAAATATTTT
1 ATAAAATTTTTT
1920969 -TAAAATTTTTT
1 ATAAAATTTTTT
*
1920980 ATAAAATTTTAT
1 ATAAAATTTTTT
1920992 ATA
1 ATA
1920995 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATAAAATTTTTT
Found at i:1923723 original size:18 final size:18
Alignment explanation
Indices: 1923700--1923741 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1923690 TTTTTCTGTT
*
1923700 AGTTCTGGGGCTGGCTGA
1 AGTTCTGGGACTGGCTGA
* *
1923718 AGTTCTGGGATTGGTTGA
1 AGTTCTGGGACTGGCTGA
1923736 AGTTCT
1 AGTTCT
1923742 ATTCTAGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.14, C:0.12, G:0.38, T:0.36
Consensus pattern (18 bp):
AGTTCTGGGACTGGCTGA
Found at i:1923966 original size:2 final size:2
Alignment explanation
Indices: 1923959--1923989 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1923949 AATTGTCCAA
1923959 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 A
1923990 CATGTCTATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1925496 original size:19 final size:18
Alignment explanation
Indices: 1925467--1925515 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1925457 CTAAAATATT
*
1925467 TATATATTTTTAATATAA
1 TATATAATTTTAATATAA
*
1925485 TAATATAATTTTAATTTAA
1 T-ATATAATTTTAATATAA
1925504 TATATATATTTT
1 TATATA-ATTTT
1925516 TTAATTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATAATTTTAATATAA
Found at i:1926979 original size:23 final size:25
Alignment explanation
Indices: 1926953--1927003 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
1926943 ATTAATTTAA
*
1926953 ATTCAAATTATGTTAAA-TT-AATT
1 ATTCAAATCATGTTAAATTTAAATT
*
1926976 ATTCAAATCATTTTAAATTTAAATT
1 ATTCAAATCATGTTAAATTTAAATT
1927001 ATT
1 ATT
1927004 ATGAATTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.62
24 2 0.08
25 7 0.29
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTCAAATCATGTTAAATTTAAATT
Found at i:1928146 original size:23 final size:22
Alignment explanation
Indices: 1928116--1928158 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1928106 TAAAAATGAT
1928116 ATAATAAATAAAATATTTAAAC
1 ATAATAAATAAAATATTTAAAC
* *
1928138 ATAATTAAATAATATTTTTAA
1 ATAA-TAAATAAAATATTTAA
1928159 TATATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATAAATAAAATATTTAAAC
Found at i:1928783 original size:21 final size:22
Alignment explanation
Indices: 1928748--1928789 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1928738 TAAACATAAT
1928748 ATTTTATAAATTTATAATTTAA
1 ATTTTATAAATTTATAATTTAA
*
1928770 ATTTTA-ATATTTATAATTTA
1 ATTTTATAAATTTATAATTTA
1928790 TTTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTATAAATTTATAATTTAA
Found at i:1928795 original size:21 final size:20
Alignment explanation
Indices: 1928747--1928796 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
1928737 ATAAACATAA
*
1928747 TATTTTATAAATTTATAATT
1 TATTTTTTAAATTTATAATT
**
1928767 TAAATTTTAATATTTATAATT
1 TATTTTTTAA-ATTTATAATT
1928788 TATTTTTTA
1 TATTTTTTA
1928797 TTTTCATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTTAAATTTATAATT
Found at i:1929544 original size:2 final size:2
Alignment explanation
Indices: 1929537--1929561 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1929527 TGATTGCCAC
1929537 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 T
1929562 GCATGTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1929888 original size:32 final size:30
Alignment explanation
Indices: 1929850--1929943 Score: 88
Period size: 32 Copynumber: 3.2 Consensus size: 30
1929840 TTTAAAAGTT
1929850 TATATATTATATAAATTTTAATATATTAATAA
1 TATATATTATATAAATTTT--TATATTAATAA
* *
1929882 TATATATTATA-AATATTTTTATATTTATAT
1 TATATATTATATAA-ATTTTTATATTAATAA
* * *
1929912 TTTAT-TTATATTAATTTTT-TATT-ATAT
1 TATATATTATATAAATTTTTATATTAATAA
1929939 TATAT
1 TATAT
1929944 TTTAATTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
27 8 0.15
28 4 0.07
29 11 0.20
30 14 0.25
31 2 0.04
32 16 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TATATATTATATAAATTTTTATATTAATAA
Found at i:1929906 original size:17 final size:18
Alignment explanation
Indices: 1929884--1929924 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1929874 ATTAATAATA
1929884 TATATTATAAATATT-TT
1 TATATTATAAATATTATT
* *
1929901 TATATT-TATATTTTATT
1 TATATTATAAATATTATT
1929918 TATATTA
1 TATATTA
1929925 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATTATAAATATTATT
Found at i:1929936 original size:16 final size:17
Alignment explanation
Indices: 1929899--1929946 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1929889 TATAAATATT
* *
1929899 TTTATATTTATATTTTA
1 TTTATATTAATTTTTTA
1929916 TTTATATTAATTTTTTA
1 TTTATATTAATTTTTTA
1929933 -TTATATTATATTTT
1 TTTATATTA-ATTTT
1929947 AATTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATATTAATTTTTTA
Found at i:1933475 original size:2 final size:2
Alignment explanation
Indices: 1933470--1933494 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1933460 TCTCTCTCTC
1933470 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 T
1933495 GTGTGTGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1933691 original size:2 final size:2
Alignment explanation
Indices: 1933684--1933713 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1933674 ACTCAAAACA
1933684 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1933714 TTTCATTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1938501 original size:16 final size:16
Alignment explanation
Indices: 1938480--1938545 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
1938470 ATAATTAATT
1938480 ATAATAAATAATATTA
1 ATAATAAATAATATTA
1938496 ATAATAAA-AAT-TATA
1 ATAATAAATAATAT-TA
*
1938511 ATTAT-AAT-ATATTA
1 ATAATAAATAATATTA
* *
1938525 ATCATAACATTATATT-
1 ATAATAA-ATAATATTA
1938541 ATAAT
1 ATAAT
1938546 CACTATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 11 0.27
15 11 0.27
16 14 0.34
17 5 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATAAATAATATTA
Found at i:1938552 original size:29 final size:29
Alignment explanation
Indices: 1938476--1938545 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
1938466 TATTATAATT
1938476 AATTATAA-TA-AATAATATTAATAATAAA
1 AATTATAATTATAAT-ATATTAATAATAAA
*
1938504 AATTATAATTATAATATATTAATCAT-AA
1 AATTATAATTATAATATATTAATAATAAA
*
1938532 CATTAT-ATTATAAT
1 AATTATAATTATAAT
1938546 CACTATTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 8 0.21
28 15 0.39
29 12 0.32
30 3 0.08
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
AATTATAATTATAATATATTAATAATAAA
Found at i:1939606 original size:19 final size:20
Alignment explanation
Indices: 1939556--1939607 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
1939546 TGACATGATA
*
1939556 TATTAATATTTTATTAATAT
1 TATTAATATTTTTTTAATAT
* *
1939576 T-TAAATAATTTTTTAATAT
1 TATTAATATTTTTTTAATAT
1939595 TATTAAT-TTTTTT
1 TATTAATATTTTTT
1939608 ATTTATTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTAATATTTTTTTAATAT
Found at i:1939613 original size:16 final size:17
Alignment explanation
Indices: 1939581--1939615 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1939571 AATATTTAAA
1939581 TAATTTTTTAATATTAT
1 TAATTTTTTAATATTAT
*
1939598 TAATTTTTTTAT-TTAT
1 TAATTTTTTAATATTAT
1939614 TA
1 TA
1939616 TAATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TAATTTTTTAATATTAT
Found at i:1939662 original size:29 final size:30
Alignment explanation
Indices: 1939611--1939669 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
1939601 TTTTTTTATT
1939611 TATTATAATTTTAAAAATATAAAAAATTAAA
1 TATTATAATTTTAAAAATAT-AAAAATTAAA
* *
1939642 TATTA-AA-TTTAATAATTTAAAAATTAAA
1 TATTATAATTTTAAAAATATAAAAATTAAA
1939670 ATACTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.38
29 9 0.35
30 2 0.08
31 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TATTATAATTTTAAAAATATAAAAATTAAA
Found at i:1940451 original size:28 final size:28
Alignment explanation
Indices: 1940388--1940452 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
1940378 CCACCTATTT
1940388 ATTTGTCAAAAATGATGATTATTTTGTG
1 ATTTGTCAAAAATGATGATTATTTTGTG
*
1940416 -TTTGTCAAAAATGATGATTTTCTTTG-G
1 ATTTGTCAAAAATGATGATTAT-TTTGTG
*
1940443 ATTTATCAAA
1 ATTTGTCAAA
1940453 TATGGAGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (28 bp):
ATTTGTCAAAAATGATGATTATTTTGTG
Found at i:1946728 original size:22 final size:23
Alignment explanation
Indices: 1946681--1946728 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1946671 TAATAAAAAA
* *
1946681 AAACTTCAAAATTAATTATGTAT
1 AAACTTCAAAAATAATTATCTAT
*
1946704 AAACTT-AAAAATAATTATCTTT
1 AAACTTCAAAAATAATTATCTAT
1946726 AAA
1 AAA
1946729 AAAACTCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (23 bp):
AAACTTCAAAAATAATTATCTAT
Found at i:1947343 original size:31 final size:29
Alignment explanation
Indices: 1947305--1947377 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 29
1947295 TGGAAGGAGG
* * *
1947305 GAAGAAAGTGAAGGAAATGAAAGGAAAAAGA
1 GAAGAAAGAGAAAGAAAAGAAA--AAAAAGA
1947336 GAAGAAAGAGAAAGAAAAGAAAAAAAAGA
1 GAAGAAAGAGAAAGAAAAGAAAAAAAAGA
1947365 -AAGGAAAG-GAAAG
1 GAA-GAAAGAGAAAG
1947378 GACAATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 7 0.18
29 12 0.32
31 19 0.50
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (29 bp):
GAAGAAAGAGAAAGAAAAGAAAAAAAAGA
Found at i:1947365 original size:18 final size:20
Alignment explanation
Indices: 1947330--1947372 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
1947320 AATGAAAGGA
*
1947330 AAAAGAGAAGAAAGAGAAAG
1 AAAAGAGAAGAAAAAGAAAG
1947350 AAAAGA-AA-AAAAAGAAAG
1 AAAAGAGAAGAAAAAGAAAG
*
1947368 GAAAG
1 AAAAG
1947373 GAAAGGACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.62
19 2 0.10
20 6 0.29
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAGAGAAGAAAAAGAAAG
Found at i:1947378 original size:10 final size:10
Alignment explanation
Indices: 1947315--1947379 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
1947305 GAAGAAAGTG
*
1947315 AAGGAAATGA
1 AAGGAAAAGA
1947325 AAGGAAAAAGA
1 AAGG-AAAAGA
1947336 GAA-GAAAGAGA
1 -AAGGAAA-AGA
1947347 AA-GAAAAGA
1 AAGGAAAAGA
*
1947356 AA-AAAAAGA
1 AAGGAAAAGA
*
1947365 AAGGAAAGGA
1 AAGGAAAAGA
1947375 AAGGA
1 AAGGA
1947380 CAATATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
9 13 0.28
10 23 0.49
11 9 0.19
12 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (10 bp):
AAGGAAAAGA
Found at i:1947566 original size:21 final size:21
Alignment explanation
Indices: 1947531--1947586 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1947521 TATTATGTTA
*
1947531 TATTTTAATTATTTTTTAAAAT
1 TATTTTTA-TATTTTTTAAAAT
* *
1947553 TATTTTTATATTTTTTTAATT
1 TATTTTTATATTTTTTAAAAT
1947574 TA-TTTTATATTTT
1 TATTTTTATATTTT
1947587 GTATAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 11 0.35
21 13 0.42
22 7 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTTTATATTTTTTAAAAT
Found at i:1947573 original size:20 final size:21
Alignment explanation
Indices: 1947531--1947598 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1947521 TATTATGTTA
1947531 TATTTTAATTATTTTTTAAAA-T
1 TATTTT-A-TATTTTTTAAAATT
*
1947553 TATTTTTATATTTTTT-TAATT
1 TA-TTTTATATTTTTTAAAATT
* *
1947574 TATTTTATATTTTGTATAATT
1 TATTTTATATTTTTTAAAATT
1947595 TATT
1 TATT
1947599 ATAATTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 14 0.34
21 20 0.49
22 3 0.07
23 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (21 bp):
TATTTTATATTTTTTAAAATT
Found at i:1947580 original size:10 final size:10
Alignment explanation
Indices: 1947531--1947630 Score: 55
Period size: 10 Copynumber: 9.5 Consensus size: 10
1947521 TATTATGTTA
1947531 TATTTTAATT
1 TATTTTAATT
* *
1947541 ATTTTTTAAAAT
1 -TATTTT-AATT
1947553 TATTTTTATATT
1 TA-TTTTA-ATT
1947565 T-TTTTAATT
1 TATTTTAATT
1947574 TATTTTATATT
1 TATTTTA-ATT
*
1947585 T-TGTATAATT
1 TAT-TTTAATT
*
1947595 TATTATAA-T
1 TATTTTAATT
1947604 TA-TTTAATTT
1 TATTTTAA-TT
1947614 TAATTTTAAATT
1 T-ATTTT-AATT
1947626 TATTT
1 TATTT
1947631 ATTTAAAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
8 4 0.06
9 7 0.10
10 22 0.31
11 20 0.28
12 16 0.23
13 2 0.03
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (10 bp):
TATTTTAATT
Found at i:1947593 original size:21 final size:20
Alignment explanation
Indices: 1947539--1947598 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1947529 TATATTTTAA
*
1947539 TTAT-TTTTTA-AAATTATTT
1 TTATATTTTTATAATTTA-TT
*
1947558 TTATATTTTTTTAATTTATT
1 TTATATTTTTATAATTTATT
1947578 TTATATTTTGTATAATTTATT
1 TTATATTTT-TATAATTTATT
1947599 ATAATTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.11
20 16 0.46
21 15 0.43
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TTATATTTTTATAATTTATT
Found at i:1948105 original size:2 final size:2
Alignment explanation
Indices: 1948098--1948138 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1948088 CTTTTCCTTC
1948098 TA TA TA TA TA 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 TA TA TA TA TA T
1948139 TAGTGCCGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1949373 original size:2 final size:2
Alignment explanation
Indices: 1949366--1949398 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1949356 AAATTAATAC
1949366 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 A
1949399 ACTACTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1949544 original size:2 final size:2
Alignment explanation
Indices: 1949537--1949580 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1949527 AACCTAGTGT
*
1949537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1949579 TA
1 TA
1949581 CATACGAGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1950005 original size:2 final size:2
Alignment explanation
Indices: 1949998--1950026 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1949988 GCAACTGCAA
1949998 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 A
1950027 AAATAGCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1952513 original size:17 final size:17
Alignment explanation
Indices: 1952491--1952524 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1952481 ATTATAATTT
1952491 TTTTTAAATAACAAATC
1 TTTTTAAATAACAAATC
1952508 TTTTTAAATAACAAATC
1 TTTTTAAATAACAAATC
1952525 ATTAAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTTTAAATAACAAATC
Found at i:1952824 original size:21 final size:20
Alignment explanation
Indices: 1952799--1952874 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 20
1952789 AATAATAAGT
1952799 ATTATTTAAATTTAATTATAA
1 ATTATTTAAATTTAA-TATAA
*
1952820 ATTATATAAATATTAATATAA
1 ATTATTTAAAT-TTAATATAA
* *
1952841 ATT-TTTAATATTTTATAAAA
1 ATTATTTAA-ATTTAATATAA
* *
1952861 ATGATTCAAATTTA
1 ATTATTTAAATTTA
1952875 TGATCTGAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 17 0.38
21 24 0.53
22 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
ATTATTTAAATTTAATATAA
Found at i:1952834 original size:32 final size:33
Alignment explanation
Indices: 1952776--1952844 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 33
1952766 TTAAATTATT
* * *
1952776 ATTTACTTAATAAAATAATAAGTATT-ATTTAA
1 ATTTAATTAATAAAATAATAAATATTAATATAA
*
1952808 ATTTAATT-ATAAATTATATAAATATTAATATAA
1 ATTTAATTAATAAAATA-ATAAATATTAATATAA
1952841 ATTT
1 ATTT
1952845 TTAATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 7 0.23
32 15 0.48
33 9 0.29
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (33 bp):
ATTTAATTAATAAAATAATAAATATTAATATAA
Found at i:1954601 original size:9 final size:10
Alignment explanation
Indices: 1954584--1954618 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1954574 ATTAAATATG
1954584 AAATATATAA
1 AAATATATAA
1954594 AAAT-TATAAA
1 AAATATAT-AA
1954604 AAATATATAA
1 AAATATATAA
1954614 AAATA
1 AAATA
1954619 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATATATAA
Found at i:1955106 original size:14 final size:13
Alignment explanation
Indices: 1955089--1955123 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1955079 TAAATTATAA
1955089 ATAATTAATTTTAC
1 ATAATTAATTTT-C
*
1955103 ATAATTAATTTTT
1 ATAATTAATTTTC
1955116 ATAATTAA
1 ATAATTAA
1955124 CAAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (13 bp):
ATAATTAATTTTC
Found at i:1955202 original size:22 final size:23
Alignment explanation
Indices: 1955172--1955217 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1955162 TAAAATATAA
*
1955172 TATT-TTTTTCTTTTTTTATTTT
1 TATTGTTTTCCTTTTTTTATTTT
*
1955194 TATTGTTTTCCTTTTTTTTTTTT
1 TATTGTTTTCCTTTTTTTATTTT
1955217 T
1 T
1955218 CTCTTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.85
Consensus pattern (23 bp):
TATTGTTTTCCTTTTTTTATTTT
Found at i:1955224 original size:22 final size:23
Alignment explanation
Indices: 1955172--1955224 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
1955162 TAAAATATAA
*
1955172 TATT-TTTTTCTTTTTTTATTTT
1 TATTCTTTTCCTTTTTTTATTTT
*
1955194 TATTGTTTTCCTTTTTTT-TTTT
1 TATTCTTTTCCTTTTTTTATTTT
1955216 T-TCTCTTTT
1 TAT-TCTTTT
1955225 AACTTTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 14 0.52
23 12 0.44
ACGTcount: A:0.06, C:0.09, G:0.02, T:0.83
Consensus pattern (23 bp):
TATTCTTTTCCTTTTTTTATTTT
Found at i:1957717 original size:22 final size:21
Alignment explanation
Indices: 1957692--1957740 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1957682 TAATATTTTT
* *
1957692 TTAAAAAATTATCTACTTATTC
1 TTAAAAAATAAT-AACTTATTC
*
1957714 TTAAAAACTAATAACTTATTC
1 TTAAAAAATAATAACTTATTC
1957735 TTAAAA
1 TTAAAA
1957741 CTATCCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAAAATAATAACTTATTC
Found at i:1959865 original size:8 final size:8
Alignment explanation
Indices: 1959848--1959897 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
1959838 AGATAAAAAG
1959848 TATT-TTT
1 TATTATTT
1959855 TATTATTT
1 TATTATTT
1959863 TATT-TTGT
1 TATTATT-T
1959871 TATTATTT
1 TATTATTT
*
1959879 TTTTATTT
1 TATTATTT
*
1959887 TTTTAATTT
1 TATT-ATTT
1959896 TA
1 TA
1959898 CTTTTGTAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
7 6 0.16
8 24 0.65
9 7 0.19
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (8 bp):
TATTATTT
Found at i:1959875 original size:16 final size:15
Alignment explanation
Indices: 1959848--1959902 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
1959838 AGATAAAAAG
1959848 TATTTTTTATTATTT
1 TATTTTTTATTATTT
1959863 TATTTTGTTATTATTT
1 TATTTT-TTATTATTT
* *
1959879 TTTTATTTTTTTAATTT
1 TATT-TTTTATT-ATTT
1959896 TACTTTT
1 TA-TTTT
1959903 GTAACTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.18
16 16 0.48
17 9 0.27
18 2 0.06
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (15 bp):
TATTTTTTATTATTT
Found at i:1961171 original size:29 final size:30
Alignment explanation
Indices: 1961138--1961199 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1961128 ACGGGCTGCT
*
1961138 TGCTGGAAGC-GGTCCGTGATCGTGGATGC
1 TGCTGGAAGCTAGTCCGTGATCGTGGATGC
***
1961167 TGCTGGAAGCTAGTTTTTGATCGTGGATGC
1 TGCTGGAAGCTAGTCCGTGATCGTGGATGC
1961197 TGC
1 TGC
1961200 CTTTTCGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.15, C:0.18, G:0.37, T:0.31
Consensus pattern (30 bp):
TGCTGGAAGCTAGTCCGTGATCGTGGATGC
Found at i:1961194 original size:124 final size:124
Alignment explanation
Indices: 1960981--1961214 Score: 324
Period size: 124 Copynumber: 1.9 Consensus size: 124
1960971 AGCTGGGGTA
* * * * **
1960981 GATGCGGAAAGCTGCTGGAGCTTACGGGCTGCTTGTTGAAAGTTGTCCGTGACCATAGATGCTAC
1 GATGCAGAAAGCTGCTGGACCGTACGGGCTGCTTGCTGAAAGCGGTCCGTGACCATAGATGCTAC
* *
1961046 TGGAAGCTAGTTTTTTATCATGGATGCTGTCTTTTAGTTGCTGCCCGTGAGTTGGGATG
66 TGGAAGCTAGTTTTTGATCATGGATGCTGCCTTTTAGTTGCTGCCCGTGAGTTGGGATG
* * * * * *
1961105 GATGCAGAAAGTTGCTGGACCGTACGGGCTGCTTGCTGGAAGCGGTCCGTGATCGTGGATGCTGC
1 GATGCAGAAAGCTGCTGGACCGTACGGGCTGCTTGCTGAAAGCGGTCCGTGACCATAGATGCTAC
* *
1961170 TGGAAGCTAGTTTTTGATCGTGGATGCTGCCTTTTCGTTGCTGCC
66 TGGAAGCTAGTTTTTGATCATGGATGCTGCCTTTTAGTTGCTGCC
1961215 GTACTTGTTC
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
124 94 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.32
Consensus pattern (124 bp):
GATGCAGAAAGCTGCTGGACCGTACGGGCTGCTTGCTGAAAGCGGTCCGTGACCATAGATGCTAC
TGGAAGCTAGTTTTTGATCATGGATGCTGCCTTTTAGTTGCTGCCCGTGAGTTGGGATG
Found at i:1961318 original size:41 final size:41
Alignment explanation
Indices: 1961255--1961335 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
1961245 TAGAAGCCGT
*
1961255 TTTTTTTTTGAACTCCCCTGCTGCTAGAAGCTGGTTTCTTC
1 TTTTTTTTTGAACCCCCCTGCTGCTAGAAGCTGGTTTCTTC
*
1961296 TTTTTTTTTG-ACCCCCCTTGCTGCTGGAAGCTGGTTTCTT
1 TTTTTTTTTGAACCCCCC-TGCTGCTAGAAGCTGGTTTCTT
1961336 TTTATCGTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 6 0.16
41 31 0.84
ACGTcount: A:0.10, C:0.25, G:0.19, T:0.47
Consensus pattern (41 bp):
TTTTTTTTTGAACCCCCCTGCTGCTAGAAGCTGGTTTCTTC
Found at i:1961717 original size:25 final size:25
Alignment explanation
Indices: 1961687--1961852 Score: 185
Period size: 25 Copynumber: 6.6 Consensus size: 25
1961677 GTGCATGAAA
*
1961687 TGAAATACATGAAATGAAAATTATG
1 TGAAATGCATGAAATGAAAATTATG
* * ** *
1961712 TGAAATACATG-CATGGAATGTTACG
1 TGAAATGCATGAAAT-GAAAATTATG
*
1961737 TAAAATGCATGAAATGAAAATTATG
1 TGAAATGCATGAAATGAAAATTATG
* *
1961762 TGAAATGCATG-CATGAAATTTTATG
1 TGAAATGCATGAAATGAAA-ATTATG
1961787 TGAAATGCATGAAATGAAAATTATG
1 TGAAATGCATGAAATGAAAATTATG
* *
1961812 TGAAATGCATG-CATGAAATGTTATG
1 TGAAATGCATGAAATGAAA-ATTATG
1961837 TGAAATGCATGAAATG
1 TGAAATGCATGAAATG
1961853 TATGCAATGA
Statistics
Matches: 117, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
24 14 0.12
25 92 0.79
26 11 0.09
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (25 bp):
TGAAATGCATGAAATGAAAATTATG
Found at i:1961749 original size:50 final size:50
Alignment explanation
Indices: 1961687--1961852 Score: 278
Period size: 50 Copynumber: 3.3 Consensus size: 50
1961677 GTGCATGAAA
* * * *
1961687 TGAAATACATGAAATGAAAATTATGTGAAATACATGCATGGAATGTTACG
1 TGAAATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATGTTATG
* *
1961737 TAAAATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATTTTATG
1 TGAAATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATGTTATG
1961787 TGAAATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATGTTATG
1 TGAAATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATGTTATG
1961837 TGAAATGCATGAAATG
1 TGAAATGCATGAAATG
1961853 TATGCAATGA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (50 bp):
TGAAATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATGTTATG
Found at i:1961796 original size:21 final size:21
Alignment explanation
Indices: 1961770--1961851 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 21
1961760 TGTGAAATGC
*
1961770 ATGCATGAAATTTTATGTGAA
1 ATGCATGAAATATTATGTGAA
1961791 ATGCATGAAATGAAAATTATGTGAAA
1 ATGCATGAAAT----ATTATGTG-AA
*
1961817 TGCATGCATGAAATGTTATGTGAA
1 ---ATGCATGAAATATTATGTGAA
1961841 ATGCATGAAAT
1 ATGCATGAAAT
1961852 GTATGCAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
21 22 0.43
24 2 0.04
25 14 0.27
26 2 0.04
29 11 0.22
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (21 bp):
ATGCATGAAATATTATGTGAA
Found at i:1962812 original size:12 final size:11
Alignment explanation
Indices: 1962795--1962840 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
1962785 AAGTATTATT
1962795 TAAATTTAATTA
1 TAAATTTAA-TA
1962807 TAAA-TT-ATA
1 TAAATTTAATA
1962816 TAAATATTAATA
1 TAAAT-TTAATA
1962828 TAAATTTTAATA
1 TAAA-TTTAATA
1962840 T
1 T
1962841 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 6 0.20
10 1 0.03
11 4 0.13
12 18 0.60
13 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAAATTTAATA
Found at i:1962813 original size:21 final size:21
Alignment explanation
Indices: 1962789--1962833 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1962779 AATAATAAGT
*
1962789 ATTATTTAAAT-TTAATTATAA
1 ATTATATAAATATTAA-TATAA
1962810 ATTATATAAATATTAATATAA
1 ATTATATAAATATTAATATAA
1962831 ATT
1 ATT
1962834 TTAATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATATAAATATTAATATAA
Found at i:1964588 original size:9 final size:10
Alignment explanation
Indices: 1964571--1964605 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1964561 ATTAAATATG
1964571 AAATATATAA
1 AAATATATAA
1964581 AAAT-TATAAA
1 AAATATAT-AA
1964591 AAATATATAA
1 AAATATATAA
1964601 AAATA
1 AAATA
1964606 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATATATAA
Found at i:1965098 original size:14 final size:13
Alignment explanation
Indices: 1965081--1965115 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1965071 TAAATTATAA
1965081 ATAATTAATTTTAC
1 ATAATTAATTTT-C
*
1965095 ATAATTAATTTTT
1 ATAATTAATTTTC
1965108 ATAATTAA
1 ATAATTAA
1965116 CAAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (13 bp):
ATAATTAATTTTC
Found at i:1965194 original size:22 final size:23
Alignment explanation
Indices: 1965164--1965209 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1965154 TAAAATATAA
*
1965164 TATT-TTTTTCTTTTTTTATTTT
1 TATTGTTTTCCTTTTTTTATTTT
*
1965186 TATTGTTTTCCTTTTTTTTTTTT
1 TATTGTTTTCCTTTTTTTATTTT
1965209 T
1 T
1965210 CTCTTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.85
Consensus pattern (23 bp):
TATTGTTTTCCTTTTTTTATTTT
Found at i:1965216 original size:22 final size:23
Alignment explanation
Indices: 1965164--1965216 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
1965154 TAAAATATAA
*
1965164 TATT-TTTTTCTTTTTTTATTTT
1 TATTCTTTTCCTTTTTTTATTTT
*
1965186 TATTGTTTTCCTTTTTTT-TTTT
1 TATTCTTTTCCTTTTTTTATTTT
1965208 T-TCTCTTTT
1 TAT-TCTTTT
1965217 AACTTTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 14 0.52
23 12 0.44
ACGTcount: A:0.06, C:0.09, G:0.02, T:0.83
Consensus pattern (23 bp):
TATTCTTTTCCTTTTTTTATTTT
Found at i:1967709 original size:22 final size:21
Alignment explanation
Indices: 1967684--1967732 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1967674 TAATATTTTT
* *
1967684 TTAAAAAATTATCTACTTATTC
1 TTAAAAAATAAT-AACTTATTC
*
1967706 TTAAAAACTAATAACTTATTC
1 TTAAAAAATAATAACTTATTC
1967727 TTAAAA
1 TTAAAA
1967733 CTATCCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAAAATAATAACTTATTC
Found at i:1968940 original size:17 final size:16
Alignment explanation
Indices: 1968918--1968953 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
1968908 CTTTTTTCTT
1968918 AAAAAAAAAATTTAACC
1 AAAAAAAAAA-TTAACC
1968935 AAAAAAAAAATTAACC
1 AAAAAAAAAATTAACC
1968951 AAA
1 AAA
1968954 CTTATTATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAAAAAAATTAACC
Found at i:1969375 original size:18 final size:18
Alignment explanation
Indices: 1969351--1969404 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
1969341 CTGTTTTAAG
1969351 AATATTAA-AA-ATTATTT
1 AATATTAATAATATT-TTT
1969368 ATATATTAATAATATTTTT
1 A-ATATTAATAATATTTTT
1969387 AATATTAAT-ATATTTTT
1 AATATTAATAATATTTTT
1969404 A
1 A
1969405 TTAAATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 10 0.29
18 15 0.44
19 6 0.18
20 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATATTAATAATATTTTT
Found at i:1969620 original size:8 final size:8
Alignment explanation
Indices: 1969609--1969646 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1969599 TATATAAAAT
*
1969609 TTTAAATA
1 TTTATATA
1969617 TTTATATA
1 TTTATATA
*
1969625 TATATATA
1 TTTATATA
1969633 TTTATATA
1 TTTATATA
1969641 -TTATAT
1 TTTATAT
1969647 TAAATACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TTTATATA
Found at i:1972460 original size:2 final size:2
Alignment explanation
Indices: 1972453--1972496 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1972443 ACTATTGTTT
1972453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1972494 TA T
1 TA T
1972497 TTTGTATTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1972715 original size:24 final size:27
Alignment explanation
Indices: 1972687--1972738 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1972677 AAAGTTCTTA
*
1972687 TTAAAAT-AAA-TTGA-TATTTTTTAT
1 TTAAAATAAAACTTGACTAATTTTTAT
1972711 TTAAAATAAAACTTGACTAATTTTTAT
1 TTAAAATAAAACTTGACTAATTTTTAT
1972738 T
1 T
1972739 AACAACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 3 0.12
26 4 0.17
27 10 0.42
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (27 bp):
TTAAAATAAAACTTGACTAATTTTTAT
Found at i:1972740 original size:26 final size:23
Alignment explanation
Indices: 1972684--1972740 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 23
1972674 ATTAAAGTTC
*
1972684 TTATTAAAATAAATTGATATTTT
1 TTATTAAAATAAATTGATAATTT
1972707 TTATTTAAAATAAAACTTGACTAATTT
1 TTA-TTAAAAT-AAA-TTGA-TAATTT
1972734 TTATTAA
1 TTATTAA
1972741 CAACTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.10
24 7 0.24
25 3 0.10
26 8 0.28
27 8 0.28
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
TTATTAAAATAAATTGATAATTT
Found at i:1973204 original size:12 final size:12
Alignment explanation
Indices: 1973164--1973227 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
1973154 ACAATTATAG
1973164 TAATTTTTGATA
1 TAATTTTTGATA
*
1973176 TGA-TTTT-A-A
1 TAATTTTTGATA
*
1973185 TAAGTTTTGATA
1 TAATTTTTGATA
** *
1973197 TAATTTTTTTTG
1 TAATTTTTGATA
1973209 TAATTTTTGATA
1 TAATTTTTGATA
*
1973221 TGATTTT
1 TAATTTT
1973228 ATTAACTTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
9 3 0.08
10 5 0.13
11 5 0.13
12 26 0.67
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (12 bp):
TAATTTTTGATA
Found at i:1973352 original size:21 final size:21
Alignment explanation
Indices: 1973294--1973353 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
1973284 GGTCTAAGCT
* * *
1973294 TTGATAATTTTTGAAATAATT
1 TTGATAATATTTGATATAATC
* ** *
1973315 TTTATAACGTTTAATATAATC
1 TTGATAATATTTGATATAATC
1973336 TTGATAATATTTGATATA
1 TTGATAATATTTGATATA
1973354 TTTAAGTAAT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.50
Consensus pattern (21 bp):
TTGATAATATTTGATATAATC
Found at i:1982756 original size:11 final size:11
Alignment explanation
Indices: 1982732--1982788 Score: 66
Period size: 10 Copynumber: 5.5 Consensus size: 11
1982722 TGAATATAGT
*
1982732 ATAAAAAAATA
1 ATAAAAATATA
*
1982743 ATATAAATATA
1 ATAAAAATATA
1982754 ATAAAAATAT-
1 ATAAAAATATA
*
1982764 ATAAAAAT-TT
1 ATAAAAATATA
1982774 ATAAAAATA-A
1 ATAAAAATATA
1982784 ATAAA
1 ATAAA
1982789 TAAAAAGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
9 1 0.03
10 21 0.52
11 18 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:1982793 original size:24 final size:23
Alignment explanation
Indices: 1982734--1982794 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
1982724 AATATAGTAT
*
1982734 AAAAAAAT-AATATAAA--TATA
1 AAAAAAATAAATAAAAATTTATA
* *
1982754 ATAAAAATATATAAAAATTTATA
1 AAAAAAATAAATAAAAATTTATA
1982777 AAAATAAATAAATAAAAA
1 AAAA-AAATAAATAAAAA
1982795 GTAAAAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 7 0.22
21 6 0.19
23 7 0.22
24 12 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAAAAATAAATAAAAATTTATA
Found at i:1982866 original size:22 final size:23
Alignment explanation
Indices: 1982832--1982874 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1982822 TTAAATTAAA
*
1982832 TAATATAATTCATAA-ATAAATT
1 TAATATAAATCATAATATAAATT
*
1982854 TAATCTAAATCATAATATAAA
1 TAATATAAATCATAATATAAA
1982875 CTTTTTCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (23 bp):
TAATATAAATCATAATATAAATT
Found at i:1983685 original size:20 final size:19
Alignment explanation
Indices: 1983640--1983689 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1983630 AATTTAAAAA
1983640 ATTT-TAATTTTATTTTAT
1 ATTTATAATTTTATTTTAT
*
1983658 ATTTATAATTTTATTTTTT
1 ATTTATAATTTTATTTTAT
*
1983677 TTTTGATAATTTT
1 ATTT-ATAATTTT
1983690 TCAACGTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 4 0.14
19 16 0.57
20 8 0.29
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
ATTTATAATTTTATTTTAT
Found at i:1984561 original size:2 final size:2
Alignment explanation
Indices: 1984556--1984614 Score: 64
Period size: 2 Copynumber: 29.0 Consensus size: 2
1984546 TTTTGATTTG
* * *
1984556 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AA AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1984598 CAA AT AT AT AT GT AT AT
1 -AT AT AT AT AT AT AT AT
1984615 CTGTAAATGT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
2 45 0.98
3 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1994120 original size:2 final size:2
Alignment explanation
Indices: 1994113--1994145 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1994103 CCTTTCCATT
1994113 TA 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 TA T
1994146 CTGCGTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1994341 original size:23 final size:23
Alignment explanation
Indices: 1994293--1994366 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 23
1994283 TTTAATAAAT
* *
1994293 ATAATGATAATTT-AATAAAATAAA
1 ATAAT-AT-ATTTAAATATAATTAA
1994317 ATAATATATTTAAATATAATTAA
1 ATAATATATTTAAATATAATTAA
* * *
1994340 ATAAT-TAATAAAATATATTTAA
1 ATAATATATTTAAATATAATTAA
1994362 A-AATA
1 ATAATA
1994367 AATAATATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 3 0.07
22 19 0.44
23 16 0.37
24 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (23 bp):
ATAATATATTTAAATATAATTAA
Found at i:1994343 original size:28 final size:30
Alignment explanation
Indices: 1994305--1994367 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 30
1994295 AATGATAATT
*
1994305 TAATAAAATAA-AAT-AATATATTTAAATA
1 TAATAAAATAATAATAAATATATTTAAAAA
*
1994333 TAATTAAATAATTAATAAAATATATTTAAAAA
1 TAATAAAATAA-TAAT-AAATATATTTAAAAA
1994365 TAA
1 TAA
1994368 ATAATATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.34
30 3 0.10
32 16 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
TAATAAAATAATAATAAATATATTTAAAAA
Found at i:1994357 original size:24 final size:24
Alignment explanation
Indices: 1994330--1994390 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 24
1994320 ATATATTTAA
*
1994330 ATATAATTAAATAATTAATAAAAT-
1 ATAT-ATTAAATAATAAATAAAATC
*
1994354 ATAT-TTAAA-AATAAATAATATC
1 ATATATTAAATAATAAATAAAATC
*
1994376 ATATATTTAATAATA
1 ATATATTAAATAATA
1994391 TATTTTATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 10 0.32
22 9 0.29
23 4 0.13
24 8 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATATTAAATAATAAATAAAATC
Found at i:1994925 original size:3 final size:3
Alignment explanation
Indices: 1994906--1994941 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1994896 TCATGAACAA
* *
1994906 GAG GAG TAG GGG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1994942 AATGACTGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.67, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:1996963 original size:139 final size:139
Alignment explanation
Indices: 1996713--1996970 Score: 480
Period size: 139 Copynumber: 1.9 Consensus size: 139
1996703 CACCTGCCAA
* * *
1996713 AGTTCCATCTGTATGAAGCAAGTGCAGCAGTTACCATTCTAGATCACCATCCTAGGGAGTGGTCA
1 AGTTCCATCCGCATGAAGCAAGTCCAGCAGTTACCATTCTAGATCACCATCCTAGGGAGTGGTCA
1996778 GATTAAAATGTCATGGTTAGGTTTGATTAGGACTTGTTGTACATCTTAACCTTCTTTGTTGTTTA
66 GATTAAAATGTCATGGTTAGGTTTGATTAGGACTTGTTGTACATCTTAACCTTCTTTGTTGTTTA
1996843 TATATATAT
131 TATATATAT
1996852 AGTTCCATCCGCATGAAGCAAGTCCAGCAGTTACCATTCTAGATCACCATCCTAGGGAGTGGTCA
1 AGTTCCATCCGCATGAAGCAAGTCCAGCAGTTACCATTCTAGATCACCATCCTAGGGAGTGGTCA
*
1996917 GATTAAACTGTCATGGTTAGGTTTGATTAGGACTTGTTGTACATCTTAACCTTC
66 GATTAAAATGTCATGGTTAGGTTTGATTAGGACTTGTTGTACATCTTAACCTTC
1996971 CTTCTTGCCC
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 115 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (139 bp):
AGTTCCATCCGCATGAAGCAAGTCCAGCAGTTACCATTCTAGATCACCATCCTAGGGAGTGGTCA
GATTAAAATGTCATGGTTAGGTTTGATTAGGACTTGTTGTACATCTTAACCTTCTTTGTTGTTTA
TATATATAT
Found at i:2002722 original size:17 final size:17
Alignment explanation
Indices: 2002700--2002733 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2002690 CCCAAAGTCC
2002700 GGGTAACATAAGATTCT
1 GGGTAACATAAGATTCT
2002717 GGGTAACATAAGATTCT
1 GGGTAACATAAGATTCT
2002734 AGTTGCGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (17 bp):
GGGTAACATAAGATTCT
Found at i:2005559 original size:37 final size:37
Alignment explanation
Indices: 2005460--2005562 Score: 90
Period size: 37 Copynumber: 2.8 Consensus size: 37
2005450 AATTTTTTAA
* *
2005460 ATATAA-AAAATATAAAAATTAAA-TA-TATTCATATC
1 ATATAATAAAATATAAAAA-TAAATTATTTTTCAAATC
** * *
2005495 ATATACATATTCATAT-AAAAT-ATTTATTTTTGAAATC
1 ATATA-ATA-AAATATAAAAATAAATTATTTTTCAAATC
2005532 ATATAATAAAATATAAAAATAAATTATTTTT
1 ATATAATAAAATATAAAAATAAATTATTTTT
2005563 ACTCTTAATT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
35 10 0.19
36 12 0.23
37 26 0.50
38 4 0.08
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (37 bp):
ATATAATAAAATATAAAAATAAATTATTTTTCAAATC
Found at i:2006672 original size:2 final size:2
Alignment explanation
Indices: 2006665--2006710 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
2006655 CAATGATCTA
2006665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2006706 GT AT A
1 AT AT A
2006711 AAAGAGAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2007126 original size:20 final size:20
Alignment explanation
Indices: 2007101--2007143 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
2007091 CAATTAACTA
2007101 AATCAATAAA-AAGTTGATTT
1 AATCAATAAACAA-TTGATTT
2007121 AATCAATAAACAATTGATTT
1 AATCAATAAACAATTGATTT
2007141 AAT
1 AAT
2007144 TTATTTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (20 bp):
AATCAATAAACAATTGATTT
Found at i:2007679 original size:32 final size:34
Alignment explanation
Indices: 2007624--2007690 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
2007614 TAATATATTT
* * *
2007624 TTTATTAAAAAATAATTATAATA-TATTTTTAAA
1 TTTAGTAAAAAATAATTAAAATATTATTTTAAAA
2007657 TTTAGTAAAAAAT-ATTAAAATATTATTTTAAAA
1 TTTAGTAAAAAATAATTAAAATATTATTTTAAAA
2007690 T
1 T
2007691 AATAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (34 bp):
TTTAGTAAAAAATAATTAAAATATTATTTTAAAA
Found at i:2007702 original size:24 final size:24
Alignment explanation
Indices: 2007675--2007747 Score: 60
Period size: 29 Copynumber: 2.9 Consensus size: 24
2007665 AAAATATTAA
2007675 AATATTATTTTAAAATAATAATTT
1 AATATTATTTTAAAATAATAATTT
*
2007699 AATAATT-TTTAATAGTAATAATTAAATTT
1 AAT-ATTATTT--TA-AAATAA-T-AATTT
*
2007728 AATAATATTTTAAAA-AATAA
1 AATATTATTTTAAAATAATAA
2007748 AGAAATAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
23 2 0.05
24 7 0.18
25 5 0.13
26 4 0.10
27 7 0.18
28 3 0.08
29 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (24 bp):
AATATTATTTTAAAATAATAATTT
Done.