Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 87 of 362
Found at i:27637696 original size:20 final size:22
Alignment explanation
Indices: 27637671--27637712 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
27637661 GTAAAAGAAT
*
27637671 TTATATTTATA-ATAAA-ATAA
1 TTATATATATATATAAATATAA
27637691 TTATATATATATATAAATATAA
1 TTATATATATATATAAATATAA
27637713 GTTTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 5 0.26
22 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATATATATATATAAATATAA
Found at i:27637892 original size:19 final size:19
Alignment explanation
Indices: 27637870--27637929 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 19
27637860 TAAAACCTTT
27637870 AATAATAATATATAGATAA
1 AATAATAATATATAGATAA
27637889 AAT-AT-ATATAATAG-TATA
1 AATAATAATAT-ATAGATA-A
*
27637907 AA-AATAATATA-ATATAA
1 AATAATAATATATAGATAA
27637924 AATAAT
1 AATAAT
27637930 TATAATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
17 10 0.29
18 17 0.50
19 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AATAATAATATATAGATAA
Found at i:27637924 original size:16 final size:16
Alignment explanation
Indices: 27637873--27637939 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 16
27637863 AACCTTTAAT
*
27637873 AATAATATATAGATAAA
1 AATAATATA-ATATAAA
*
27637890 ATATATATAATAGTATAAA
1 A-ATA-AT-ATAATATAAA
27637909 AATAATATAATAT-AA
1 AATAATATAATATAAA
27637924 AATAATTATAATATAA
1 AATAA-TATAATATAA
27637940 TATGAAAGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
15 7 0.17
16 14 0.33
17 4 0.10
18 6 0.14
19 8 0.19
20 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AATAATATAATATAAA
Found at i:27637934 original size:35 final size:35
Alignment explanation
Indices: 27637873--27637990 Score: 111
Period size: 36 Copynumber: 3.3 Consensus size: 35
27637863 AACCTTTAAT
*
27637873 AATAATATATAGATAAAAT-ATATATAATAGTATAAA
1 AATAATATA-ATATAAAATAATATATAATA-TATAAA
27637909 AATAATATAATATAAAATAAT-TATAATATAATATGAA
1 AATAATATAATATAAAATAATATATAATAT-ATA--AA
* * *
27637946 AGT-ATAT-ATGTAAAAATAATATATAATATATATA
1 AATAATATAATAT-AAAATAATATATAATATATAAA
27637980 AATAAT-TAATA
1 AATAATATAATA
27637991 AATATATTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 17
0.75 0.07 0.19
Matches are distributed among these distances:
34 5 0.07
35 25 0.37
36 26 0.38
37 12 0.18
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (35 bp):
AATAATATAATATAAAATAATATATAATATATAAA
Found at i:27637973 original size:7 final size:7
Alignment explanation
Indices: 27637961--27638124 Score: 64
Period size: 7 Copynumber: 23.9 Consensus size: 7
27637951 ATATGTAAAA
27637961 ATAATAT
1 ATAATAT
27637968 ATAATAT
1 ATAATAT
*
27637975 AT-ATAA
1 ATAATAT
27637981 ATAAT-T
1 ATAATAT
27637987 AATAA-AT
1 -ATAATAT
*
27637994 ATATTAT
1 ATAATAT
*
27638001 ACAAGTA-
1 ATAA-TAT
*
27638008 AAAATAT
1 ATAATAT
27638015 AATAATAT
1 -ATAATAT
27638023 ATAA-AT
1 ATAATAT
*
27638029 AATAATGT
1 -ATAATAT
*
27638037 AAAATA-
1 ATAATAT
27638043 ATAATATTT
1 ATAATA--T
27638052 CATGAA-AT
1 -AT-AATAT
* *
27638060 GTAGTAT
1 ATAATAT
*
27638067 ATAATAA
1 ATAATAT
27638074 ATAATA-
1 ATAATAT
*
27638080 AT-ATAA
1 ATAATAT
27638086 ATAATAT
1 ATAATAT
27638093 ATAA-A-
1 ATAATAT
27638098 ATAATTAT
1 ATAA-TAT
27638106 ATAATAT
1 ATAATAT
27638113 AT-ATAT
1 ATAATAT
*
27638119 AAAATA
1 ATAATA
27638125 AGGTTAAAAA
Statistics
Matches: 118, Mismatches: 18, Indels: 42
0.66 0.10 0.24
Matches are distributed among these distances:
5 7 0.06
6 28 0.24
7 64 0.54
8 14 0.12
10 3 0.03
11 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:27638007 original size:58 final size:58
Alignment explanation
Indices: 27637910--27638114 Score: 185
Period size: 58 Copynumber: 3.5 Consensus size: 58
27637900 TAGTATAAAA
* *
27637910 ATAATATAATATAAAATAATT-ATAATATAATATGAAAGTATATATGTAAAAATAATAT
1 ATAATAT-ATATAAAATAATTAATAATATATTATGAAAGTATATATATAAAAATAATAT
* * * *
27637968 ATAATATATAT-AAATAATTAATAAATATATTAT-ACAAGTAAAAATATAATAATATATAA
1 ATAATATATATAAAATAATTAAT-AATATATTATGA-AAGTATATATATAAAAATA-ATAT
* *
27638027 ATAATA-ATGTAAAATAA-TAAT-AT-T-TCATGAAATGTAGTATATAATAAATAATAATAT
1 ATAATATATATAAAATAATTAATAATATATTATGAAA-GTA-TATAT-ATAAA-AATAATAT
27638084 A-AATAATATATAAAATAATTATATAATATAT
1 ATAAT-ATATATAAAATAATTA-ATAATATAT
27638115 ATATAAAATA
Statistics
Matches: 117, Mismatches: 13, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
54 5 0.04
55 5 0.04
56 16 0.14
57 16 0.14
58 52 0.44
59 17 0.15
60 2 0.02
61 2 0.02
62 1 0.01
63 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.37
Consensus pattern (58 bp):
ATAATATATATAAAATAATTAATAATATATTATGAAAGTATATATATAAAAATAATAT
Found at i:27638042 original size:24 final size:24
Alignment explanation
Indices: 27637873--27638121 Score: 130
Period size: 24 Copynumber: 10.5 Consensus size: 24
27637863 AACCTTTAAT
*
27637873 AATAATATATAGATAA-AATATATA
1 AATAATATATAAATAATAATATA-A
* *
27637897 TAATAGTATAAAAATAATATAATATAA
1 -AATAATATATAAAT-A-ATAATATAA
27637924 AATAAT-TAT-AAT-ATAATATGAA
1 AATAATATATAAATAATAATAT-AA
* * *
27637946 AGTATATATGTAAA-AATAATATAT
1 AATA-ATATATAAATAATAATATAA
27637970 AAT-ATATATAAATAATTAATA-AA
1 AATAATATATAAATAA-TAATATAA
* * * * *
27637993 TATATTATACAAGTAA-AA-ATAT
1 AATAATATATAAATAATAATATAA
*
27638015 AATAATATATAAATAATAATGTAA
1 AATAATATATAAATAATAATATAA
** * **
27638039 AATAATA-ATATTTCATGAA-ATGT
1 AATAATATATAAATAAT-AATATAA
*
27638062 AGT-ATATAATAAATAATAATAT-A
1 AATAATAT-ATAAATAATAATATAA
*
27638085 AATAATATATAAAATAATTATATAA
1 AATAATATAT-AAATAATAATATAA
*
27638110 TAT-ATATATAAA
1 AATAATATATAAA
27638122 ATAAGGTTAA
Statistics
Matches: 167, Mismatches: 36, Indels: 44
0.68 0.15 0.18
Matches are distributed among these distances:
21 8 0.05
22 31 0.19
23 27 0.16
24 62 0.37
25 25 0.15
26 6 0.04
27 2 0.01
28 6 0.04
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (24 bp):
AATAATATATAAATAATAATATAA
Found at i:27638087 original size:12 final size:12
Alignment explanation
Indices: 27638070--27638121 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
27638060 GTAGTATATA
27638070 ATAAATAATAAT
1 ATAAATAATAAT
27638082 ATAAATAAT-AT
1 ATAAATAATAAT
*
27638093 ATAAAATAATTAT
1 AT-AAATAATAAT
27638106 AT-AAT-ATATAT
1 ATAAATAATA-AT
27638117 ATAAA
1 ATAAA
27638122 ATAAGGTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 2 0.06
11 11 0.31
12 18 0.51
13 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAAATAATAAT
Found at i:27638096 original size:11 final size:11
Alignment explanation
Indices: 27637873--27638121 Score: 98
Period size: 11 Copynumber: 22.2 Consensus size: 11
27637863 AACCTTTAAT
27637873 AATAATATATA
1 AATAATATATA
* *
27637884 GATAAAATATA
1 AATAATATATA
*
27637895 TATAATAGTATA
1 AATAATA-TATA
27637907 AA-AATA-AT-
1 AATAATATATA
27637915 -ATAATATA-A
1 AATAATATATA
27637924 AATAAT-TATA
1 AATAATATATA
27637934 ATATAATATGA-A
1 A-ATAATAT-ATA
* *
27637946 AGTATATATGTA
1 AATA-ATATATA
27637958 AA-AATAATATA
1 AATAAT-ATATA
27637969 TAAT-ATATATA
1 -AATAATATATA
27637980 AATAAT-TAATA
1 AATAATAT-ATA
27637991 AAT-ATATTATA
1 AATAATA-TATA
*
27638002 CAAGTAA-AAATA
1 -AA-TAATATATA
27638014 TAATAATATATA
1 -AATAATATATA
*
27638026 AATAATAATGTAA
1 AATAAT-ATAT-A
*
27638039 AATAATAATATTT
1 AATAAT-ATA-TA
* *
27638052 CATGAA-ATGT-
1 AAT-AATATATA
*
27638062 AGT-ATATAATA
1 AATAATAT-ATA
27638073 AATAATAATATA
1 AATAAT-ATATA
27638085 AATAATATATAA
1 AATAATATAT-A
27638097 AATAAT-TATA
1 AATAATATATA
27638107 TAATATATATATA
1 -AATA-ATATATA
27638120 AA
1 AA
27638122 ATAAGGTTAA
Statistics
Matches: 182, Mismatches: 21, Indels: 69
0.67 0.08 0.25
Matches are distributed among these distances:
7 1 0.01
8 5 0.03
9 7 0.04
10 18 0.10
11 69 0.38
12 57 0.31
13 21 0.12
14 4 0.02
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (11 bp):
AATAATATATA
Found at i:27638114 original size:46 final size:45
Alignment explanation
Indices: 27637873--27638121 Score: 155
Period size: 46 Copynumber: 5.5 Consensus size: 45
27637863 AACCTTTAAT
* * *
27637873 AATAATATATAGATAAAATATATATAATAGTATAAA-AATA-AT--
1 AATAATATATA-ATAATATATAAATAATAATATAAATAATATATAA
* *
27637915 -ATAATATAAAATAAT-TAT-AAT-ATAATATGAAAGTATATATGTAAA
1 AATAATATATAATAATATATAAATAATAATAT-AAA-TA-ATATAT-AA
*
27637960 AATAATATATAAT-ATATATAAATAATTA-ATAAAT-ATATTATACA
1 AATAATATATAATAATATATAAATAATAATATAAATAATA-TATA-A
* * * **
27638004 AGTAAAAATATAATAATATATAAATAATAATGTAAAATAATAATATTT
1 AAT-AATATATAATAATATATAAATAATAATAT-AAATAAT-ATATAA
* * *
27638052 CATGAA-ATGTAGT-ATATAATAAATAATAATATAAATAATATATAA
1 AAT-AATATATAATAATAT-ATAAATAATAATATAAATAATATATAA
27638097 AATAATTATATAATATATATATAAA
1 AATAA-TATATAATA-ATATATAAA
27638122 ATAAGGTTAA
Statistics
Matches: 157, Mismatches: 25, Indels: 45
0.69 0.11 0.20
Matches are distributed among these distances:
37 6 0.04
38 5 0.03
39 3 0.02
40 5 0.03
41 12 0.08
42 1 0.01
43 4 0.03
44 7 0.04
45 18 0.11
46 47 0.30
47 29 0.18
48 14 0.09
49 5 0.03
50 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (45 bp):
AATAATATATAATAATATATAAATAATAATATAAATAATATATAA
Found at i:27638181 original size:45 final size:50
Alignment explanation
Indices: 27638064--27638185 Score: 113
Period size: 48 Copynumber: 2.6 Consensus size: 50
27638054 TGAAATGTAG
*
27638064 TATATA-ATAAATAATA-ATATAAATAATATATAAAATAATTATATAATA
1 TATATATATAAATAATAGAAATAAATAATATATAAAATAATTATATAATA
* * * *
27638112 TATATATA-AAATAA-GGTTAA-AAATAA-A-A-CAAATAA-TA-ATAATT
1 TATATATATAAATAATAG-AAATAAATAATATATAAAATAATTATATAATA
27638155 TATATATATAAATAATAGAAATAAAT-ATATA
1 TATATATATAAATAATAGAAATAAATAATATA
27638186 GGGTTAGATT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
43 13 0.22
44 11 0.19
45 12 0.20
46 2 0.03
47 1 0.02
48 18 0.31
49 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (50 bp):
TATATATATAAATAATAGAAATAAATAATATATAAAATAATTATATAATA
Found at i:27640239 original size:205 final size:205
Alignment explanation
Indices: 27639718--27640670 Score: 1465
Period size: 205 Copynumber: 4.6 Consensus size: 205
27639708 CTACTTTTTT
* * *
27639718 GATTTGTTTTCTGACAGTACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
* *
27639783 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* * * * * *
27639848 CTGCTTCAGTCTAATCATCTGAAGGTTAGATATGCTATGTGTCTGCCCTCCGTCGAATATGGAGA
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAA-GTGGAGA
** ** *
27639913 CGCCAAACTTT
195 TACCGGACTTC
* * * *
27639924 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAAGCGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
* * * * *
27639989 AAACCAAATCAGCTATGTCTTCGATTTGTTTCTTGTAATCACAAGGATACCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* * *
27640054 GTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTTTTCCCTCCGTCGAAGTGGAGAT
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
27640119 ACCGGACTTC
196 ACCGGACTTC
* * * *
27640129 GATTTTTTCTCTGTCAATATAGAGATGCCAAATCATCTTAGATTTGCTTCAACGCAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
27640194 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* *
27640259 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTTGAAGTAGAGAT
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
*
27640324 GCCGGACTTC
196 ACCGGACTTC
* *
27640334 GATTTGTTCTCTGACAATACAGAGGTGCCAAATCATCTTAGATTTGCTTCAACGCAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
* *
27640399 AAGCCAAATCATCTATGTCTTCGATATGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* *
27640464 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGCGTCTGTCCTCCGTCGAAGTGGAGAT
131 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
*
27640529 ACCGGACTTT
196 ACCGGACTTC
* * * * *
27640539 GATTTGTTTTCTGACAATACAGAGATGTCAAATCATTTTAGATTTGCTTTAACATAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
*
27640604 AAGCCAAATCAGCTATGTCTTCAATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
27640669 CT
131 CT
27640671 TGCTTCAGCC
Statistics
Matches: 683, Mismatches: 64, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
205 513 0.75
206 170 0.25
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (205 bp):
GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
ACCGGACTTC
Found at i:27648899 original size:40 final size:40
Alignment explanation
Indices: 27648843--27649035 Score: 300
Period size: 40 Copynumber: 4.8 Consensus size: 40
27648833 TTATTTGACG
* *
27648843 TGGAATTGTATTCGGGCTTAAAGACCCGCAGACTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* *
27648883 TGGAATCGTATCCGGGCTTAAAGACCCGCAGGCTTCGTAC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
27648923 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
27648963 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* * *
27649003 TGGAA-TGACATCCGGG-TTAAAAACCTGCAGGCT
1 TGGAATTG-TATCCGGGCTTAAAGACCCGCAGGCT
27649036 GTGCTAGATA
Statistics
Matches: 143, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 17 0.12
40 126 0.88
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
Found at i:27652642 original size:46 final size:46
Alignment explanation
Indices: 27652592--27652764 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
27652582 TGGTTGAGCA
27652592 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
27652638 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* * *
27652683 CATTCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
27652731 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
27652765 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 59 0.56
47 28 0.26
48 4 0.04
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:27652753 original size:93 final size:93
Alignment explanation
Indices: 27652589--27652759 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
27652579 GGATGGTTGA
*
27652589 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
27652654 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
27652682 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
27652747 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
27652760 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:27653026 original size:19 final size:20
Alignment explanation
Indices: 27652989--27653026 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
27652979 ATAAGGTGGT
27652989 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
27653009 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
27653027 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:27658882 original size:18 final size:19
Alignment explanation
Indices: 27658834--27658892 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 19
27658824 ACAATATATA
* *
27658834 ATATATAATAACAAAAATT
1 ATATATAAGAATAAAAATT
* *
27658853 -TATAAAAGAATAATAATT
1 ATATATAAGAATAAAAATT
*
27658871 ATATATAA-AATAAAAAAT
1 ATATATAAGAATAAAAATT
27658889 ATAT
1 ATAT
27658893 TGGTTTAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
ATATATAAGAATAAAAATT
Found at i:27658969 original size:21 final size:21
Alignment explanation
Indices: 27658945--27659001 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
27658935 AATTTATATT
*
27658945 TATA-ATAAAATAA-TTATAA
1 TATATATAAAATAAGTTAGAA
27658964 TATATATAAATATAAGTTTAGAA
1 TATATATAAA-ATAAG-TTAGAA
27658987 TA-ATATAAAATAAGT
1 TATATATAAAATAAGT
27659002 AATTAATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 4 0.12
20 6 0.18
21 9 0.27
22 7 0.21
23 7 0.21
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
TATATATAAAATAAGTTAGAA
Found at i:27659158 original size:13 final size:13
Alignment explanation
Indices: 27659133--27659313 Score: 96
Period size: 11 Copynumber: 15.1 Consensus size: 13
27659123 AGTTAAAACC
27659133 TATAATAATAATA
1 TATAATAATAATA
27659146 TATAGATAA-AATA
1 TATA-ATAATAATA
*
27659159 TATAATAGT-ATA
1 TATAATAATAATA
*
27659171 -AAAATAAT-ATAA
1 TATAATAATAAT-A
27659183 TATAA-AATAAT-
1 TATAATAATAATA
27659194 TATAAT-ATAATA
1 TATAATAATAATA
27659206 TGA-AAGT-AT-ATA
1 T-ATAA-TAATAATA
* *
27659218 TGTAAAAATAATA
1 TATAATAATAATA
27659231 TATAAT-AT-ATA
1 TATAATAATAATA
*
27659242 TA-AATAAT-TTA
1 TATAATAATAATA
*
27659253 TA-AAT-ATATTA
1 TATAATAATAATA
*
27659264 TACAAGTAA-AA-A
1 TATAA-TAATAATA
27659276 TATAATAAT-ATA
1 TATAATAATAATA
*
27659288 TA-AATAATAATG
1 TATAATAATAATA
*
27659300 TAAAATAATAATA
1 TATAATAATAATA
27659313 T
1 T
27659314 TTCGTGAAAA
Statistics
Matches: 134, Mismatches: 13, Indels: 42
0.71 0.07 0.22
Matches are distributed among these distances:
10 5 0.04
11 47 0.35
12 37 0.28
13 40 0.30
14 5 0.04
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.36
Consensus pattern (13 bp):
TATAATAATAATA
Found at i:27659177 original size:23 final size:24
Alignment explanation
Indices: 27659137--27659191 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
27659127 AAAACCTATA
* *
27659137 ATAATAATATATAGATAAAAT-AT
1 ATAATAATATAAAAATAAAATAAT
* *
27659160 ATAATAGTATAAAAATAATATAAT
1 ATAATAATATAAAAATAAAATAAT
27659184 ATAA-AATA
1 ATAATAATA
27659192 ATTATAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAATAATATAAAAATAAAATAAT
Found at i:27659179 original size:14 final size:15
Alignment explanation
Indices: 27659133--27659203 Score: 70
Period size: 16 Copynumber: 4.3 Consensus size: 15
27659123 AGTTAAAACC
27659133 TATAATAATAATATATA
1 TATAA-AATAATATA-A
* *
27659150 GATAAAATATATAATAG
1 TATAAAATA-AT-ATAA
27659167 TATAAAAATAATATAA
1 TAT-AAAATAATATAA
27659183 TATAAAATAATTATAA
1 TATAAAATAA-TATAA
27659199 TATAA
1 TATAA
27659204 TATGAAAGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
15 7 0.15
16 20 0.43
17 10 0.22
18 9 0.20
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
TATAAAATAATATAA
Found at i:27659193 original size:55 final size:53
Alignment explanation
Indices: 27659134--27659298 Score: 130
Period size: 55 Copynumber: 3.2 Consensus size: 53
27659124 GTTAAAACCT
*
27659134 ATAATAATAATATATAGAT-AAAATATATAATAGTATAAA-AATAATATAATATAAA
1 ATAATAATAATATA-AGATGAAAATATAT-AT-GTAAAAATAAT-ATATAATATAAA
* * * *
27659189 ATAATTATAATATAATATGAAAGTATATATGTAAAAATAATATATAATAT-AT
1 ATAATAATAATATAAGATGAAAATATATATGTAAAAATAATATATAATATAAA
* * * * *
27659241 ATAAATAAT-TTATAA-AT-ATATTATACAAGTAAAAAT-ATA-ATAATATATAA
1 AT-AATAATAATATAAGATGAAAATATATATGTAAAAATAATATATAATATA-AA
27659291 ATAATAAT
1 ATAATAAT
27659299 GTAAAATAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
48 7 0.08
49 9 0.10
50 18 0.19
51 2 0.02
52 8 0.09
53 20 0.22
54 8 0.09
55 21 0.23
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.36
Consensus pattern (53 bp):
ATAATAATAATATAAGATGAAAATATATATGTAAAAATAATATATAATATAAA
Found at i:27659313 original size:35 final size:35
Alignment explanation
Indices: 27659137--27659396 Score: 123
Period size: 35 Copynumber: 7.3 Consensus size: 35
27659127 AAAACCTATA
*
27659137 ATAATAATATATAGATAA-AATATATAATAGTATAA-
1 ATAATAATATATAAATAATAATATATAATA--ATAAT
27659172 A-AATAATATAATATAA-AATAAT-TATAAT-ATAAT
1 ATAATAATAT-ATA-AATAATAATATATAATAATAAT
*
27659205 ATGAAAGTATATATGTAAA-AATAATATATAAT-AT-AT
1 AT--AA-TA-ATATATAAATAATAATATATAATAATAAT
* * * *
27659241 ATAAATAATTTATAAAT-ATATTATACAAGTAAAAAT
1 AT-AATAATATATAAATAATAATATATAA-TAATAAT
* *
27659277 ATAATAATATATAAATAATAATGTAAAATAATAAT
1 ATAATAATATATAAATAATAATATATAATAATAAT
** * *
27659312 ATTTCGTGAA-A-AGT-AATATATAATAAATAAAAATAAT
1 A--TAAT-AATATA-TAAATA-ATAATATATAATAATAAT
* *
27659349 ATAGATAATATATAATAAAATAATTATATAAAATATAAT
1 ATA-ATAATATATAA-ATAATAA-TATATAATA-ATAAT
*
27659388 ATAAAAATA
1 ATAATAATA
27659397 AGGTTAAAAA
Statistics
Matches: 175, Mismatches: 23, Indels: 51
0.70 0.09 0.20
Matches are distributed among these distances:
32 4 0.02
33 17 0.10
34 11 0.06
35 39 0.22
36 38 0.22
37 37 0.21
38 21 0.12
39 8 0.05
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (35 bp):
ATAATAATATATAAATAATAATATATAATAATAAT
Found at i:27659391 original size:25 final size:24
Alignment explanation
Indices: 27659136--27659393 Score: 99
Period size: 24 Copynumber: 11.1 Consensus size: 24
27659126 TAAAACCTAT
* *
27659136 AATAATAATATATAGATAAAATATAT
1 AATAAT-ATATATA-ATATAATATAA
* *
27659162 AATAGTATAAAAATAATATAATATAA
1 AATA--ATATATATAATATAATATAA
27659188 AAT-A-AT-TATAATATAATATGAA
1 AATAATATATATAATATAATAT-AA
* *
27659210 AGT-ATATATGTAA-A-AATA-ATA
1 AATAATATATATAATATAATATA-A
* *
27659231 TATAATATATATAA-ATAATTTATA
1 AATAATATATATAATATAATATA-A
* * *
27659255 AAT-ATATTATACAAGTA-AAAATAT
1 AATAATA-TATATAA-TATAATATAA
*
27659279 AATAATATATA-AATAATAATGTAA
1 AATAATATATATAAT-ATAATATAA
**
27659303 AATAATA-ATAT--T-TCGTGA-AA
1 AATAATATATATAATATAAT-ATAA
*
27659323 AGT-A-ATATATAATA-AATA-AA
1 AATAATATATATAATATAATATAA
*
27659343 AATAATATAGATAATAT-ATAATAA
1 AATAATATATATAATATAAT-ATAA
*
27659367 AATAATTATATAAAATATAATATAA
1 AATAA-TATATATAATATAATATAA
27659392 AA
1 AA
27659394 ATAAGGTTAA
Statistics
Matches: 174, Mismatches: 30, Indels: 57
0.67 0.11 0.22
Matches are distributed among these distances:
18 1 0.01
19 5 0.03
20 12 0.07
21 17 0.10
22 33 0.19
23 17 0.10
24 40 0.23
25 23 0.13
26 19 0.11
27 5 0.03
28 2 0.01
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (24 bp):
AATAATATATATAATATAATATAA
Found at i:27659397 original size:18 final size:19
Alignment explanation
Indices: 27659158--27659397 Score: 68
Period size: 19 Copynumber: 11.7 Consensus size: 19
27659148 TAGATAAAAT
*
27659158 ATATAATAGTATAAAA-ATA
1 ATATAATA-AATAAAATATA
27659177 ATATAATATAA-AATAATTATA
1 ATATAATA-AATAA-AA-TATA
*
27659198 ATATAAT--ATGAAAGTATA
1 ATATAATAAAT-AAAATATA
* *
27659216 TATGTAA-AAATAATATATA
1 -ATATAATAAATAAAATATA
**
27659235 ATATATATAAATAATTTATAA
1 ATATA-ATAAATAAAATAT-A
27659256 ATATATTATACAAGTAAAAATATA
1 ATATA--ATA-AA-T-AAAATATA
*
27659280 ATAATATATAAATAATAATGTA
1 AT-ATA-ATAAATAA-AATATA
*
27659302 AAATAATAATATTTCGTGAAAAGTA-A
1 ATATAATAA-A-----T-AAAA-TATA
27659328 TATATAATAAATAAAA-ATA
1 -ATATAATAAATAAAATATA
*
27659347 ATATAGATAATATATAATA-A
1 ATATA-ATAA-ATAAAATATA
*
27659367 A-ATAATTATATAAAATATA
1 ATATAA-TAAATAAAATATA
27659386 ATATAA-AAATAA
1 ATATAATAAATAA
27659398 GGTTAAAAAT
Statistics
Matches: 170, Mismatches: 18, Indels: 67
0.67 0.07 0.26
Matches are distributed among these distances:
18 30 0.18
19 36 0.21
20 33 0.19
21 24 0.14
22 11 0.06
23 4 0.02
24 8 0.05
25 8 0.05
26 5 0.03
27 11 0.06
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (19 bp):
ATATAATAAATAAAATATA
Found at i:27659409 original size:99 final size:99
Alignment explanation
Indices: 27659221--27659409 Score: 222
Period size: 99 Copynumber: 1.9 Consensus size: 99
27659211 GTATATATGT
* * * * * *
27659221 AAAAATAATATATAATATATATAAATAATTTATAAATATATTATACAAGTAAAAATATAATAATA
1 AAAAATAATATATAATAAATAAAAATAATATAGAAATATATAATACAAATAAAAATATAATAATA
* *
27659286 TATAAATAATAATGTAAAATAATAATATTTCGTG
66 TATAAAAAATAAGGTAAAATAATAATATTTCGTG
* **
27659320 AAAAGTAATATATAATAAATAAAAATAATATAGATAATATATAATA-AAATAATTATATAA-AAT
1 AAAAATAATATATAATAAATAAAAATAATATAGA-AATATATAATACAAATAAAAATATAATAAT
*
27659383 ATAATATAAAAATAAGGTTAAA-AATAA
65 AT-ATA-AAAAATAAGGTAAAATAATAA
27659410 AACAAATAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
98 5 0.07
99 48 0.64
100 22 0.29
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (99 bp):
AAAAATAATATATAATAAATAAAAATAATATAGAAATATATAATACAAATAAAAATATAATAATA
TATAAAAAATAAGGTAAAATAATAATATTTCGTG
Found at i:27659441 original size:22 final size:22
Alignment explanation
Indices: 27659415--27659459 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
27659405 AATAAAACAA
**
27659415 ATAATAATAAAATTTTATATAT
1 ATAATAATAAAATTAAATATAT
*
27659437 ATAATAATAGAATTAAATATAT
1 ATAATAATAAAATTAAATATAT
27659459 A
1 A
27659460 GGGTTAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAATAATAAAATTAAATATAT
Found at i:27663851 original size:52 final size:51
Alignment explanation
Indices: 27663792--27663993 Score: 246
Period size: 50 Copynumber: 3.9 Consensus size: 51
27663782 TAAAAAACAT
* * *
27663792 ATTTTTTTGAGGGTGGAGGGGGAGAGATGGGTAGCACCAGTAT-AAAAAATTAGA
1 ATTTTTTT--GGGTGGAGGGAGAGAGATAGGTGGCACCAGTATAAAAAAATT--A
* * *
27663846 ATTTTTTTGGGTGGAGAGAGAGAGATGGGTGGCACTAGTATAAAAAAATT-
1 ATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTATAAAAAAATTA
* * * *
27663896 ATTTTTTTTGGTGAAGGGAGAGAGATAGGTGTCTCCAGTATAAAAAAATTA
1 ATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTATAAAAAAATTA
* *
27663947 CTTTTTTTGGGTGGAGGGAGAGAGATAGGCGGCACCAGTATAAAAAA
1 ATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTATAAAAAA
27663994 GTAATATTAT
Statistics
Matches: 129, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
50 43 0.33
51 41 0.32
52 29 0.22
53 8 0.06
54 8 0.06
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (51 bp):
ATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTATAAAAAAATTA
Found at i:27663943 original size:51 final size:50
Alignment explanation
Indices: 27663782--27663993 Score: 248
Period size: 51 Copynumber: 4.1 Consensus size: 50
27663772 TGATGTGTTT
* * *
27663782 TAAAAAACA-TATTTTTTTGAGGGTGGAGGGGGAGAGATGGGTAGCACCAGTA
1 TAAAAAA-ATTATTTTTTT--GGGTGGAGGGAGAGAGATAGGTGGCACCAGTA
* * *
27663834 T-AAAAAATTAGAATTTTTTTGGGTGGAGAGAGAGAGATGGGTGGCACTAGTA
1 TAAAAAAATT---ATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTA
* * * *
27663886 TAAAAAAATTATTTTTTTTGGTGAAGGGAGAGAGATAGGTGTCTCCAGTA
1 TAAAAAAATTATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTA
*
27663936 TAAAAAAATTACTTTTTTTGGGTGGAGGGAGAGAGATAGGCGGCACCAGTA
1 TAAAAAAATTA-TTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTA
27663987 TAAAAAA
1 TAAAAAA
27663994 GTAATATTAT
Statistics
Matches: 138, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
50 45 0.33
51 47 0.34
52 30 0.22
53 8 0.06
54 8 0.06
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (50 bp):
TAAAAAAATTATTTTTTTGGGTGGAGGGAGAGAGATAGGTGGCACCAGTA
Found at i:27664018 original size:51 final size:47
Alignment explanation
Indices: 27663813--27664023 Score: 165
Period size: 51 Copynumber: 4.1 Consensus size: 47
27663803 GGTGGAGGGG
* *
27663813 GAGAGATGGGTAGCACCAGTAT-AAAAAATTAGAATTTTTTTGGGTGG-AGAGA
1 GAGAGATAGGTGGCACCAGTATAAAAAAATT---ATTTTTTT---TGGAAG-GA
* *
27663865 GAGAGATGGGTGGCACTAGTATAAAAAAATTATTTTTTTTGGTGAAGGGA
1 GAGAGATAGGTGGCACCAGTATAAAAAAATTATTTTTTTT-G-GAA-GGA
* * *
27663915 GAGAGATAGGTGTCTCCAGTATAAAAAAATTACTTTTTTTGGGTGGAGGGA
1 GAGAGATAGGTGGCACCAGTATAAAAAAATTA-TTTTTTT---TGGAAGGA
* *
27663966 GAGAGATAGGCGGCACCAGTATAAAAAAGTAATATTATTTTATTGGAAGGA
1 GAGAGATAGGTGGCACCAGTATAAAAAA--ATTATT-TTTT-TTGGAAGGA
27664017 GAGAGAT
1 GAGAGAT
27664024 GGGCAACATC
Statistics
Matches: 134, Mismatches: 12, Indels: 27
0.77 0.07 0.16
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 1 0.01
50 39 0.29
51 50 0.37
52 24 0.18
53 16 0.12
54 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.29, T:0.28
Consensus pattern (47 bp):
GAGAGATAGGTGGCACCAGTATAAAAAAATTATTTTTTTTGGAAGGA
Found at i:27666243 original size:44 final size:44
Alignment explanation
Indices: 27666178--27666265 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
27666168 ACTCGGTCTA
27666178 CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
1 CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
*
27666222 CACTTAACCTTTTCACGTAAAATGAATTTTCTTCATCTAATTAG
1 CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
27666266 TCATCTATGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.41
Consensus pattern (44 bp):
CACTTAACCTTTTCACCTAAAATGAATTTTCTTCATCTAATTAG
Found at i:27672245 original size:39 final size:39
Alignment explanation
Indices: 27672188--27672263 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
27672178 TGCAGAACAT
*
27672188 ATATTAATGATGTGCAAACTATGACATAATTAAAGACTC
1 ATATTAATGATGTGCAAACTATGACATAAGTAAAGACTC
*
27672227 ATATTAATGATGTTCAAACTATGACATAAGTAAAGAC
1 ATATTAATGATGTGCAAACTATGACATAAGTAAAGAC
27672264 AAACTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (39 bp):
ATATTAATGATGTGCAAACTATGACATAAGTAAAGACTC
Found at i:27672279 original size:9 final size:9
Alignment explanation
Indices: 27672265--27672290 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
27672255 AGTAAAGACA
27672265 AACTAAAAT
1 AACTAAAAT
27672274 AACTAAAAT
1 AACTAAAAT
27672283 AACTAAAA
1 AACTAAAA
27672291 ATAAATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AACTAAAAT
Found at i:27673929 original size:31 final size:32
Alignment explanation
Indices: 27673882--27673945 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
27673872 CTTTTTGTTC
* *
27673882 TCTTTCGTTCTCTTTTTCTTTTTGT-TTTCTT
1 TCTTTCATTCTCTTTTTCTTTTTATATTTCTT
*
27673913 TCTTTCATTCTTTTTTTCTTTTTATATTTCTT
1 TCTTTCATTCTCTTTTTCTTTTTATATTTCTT
27673945 T
1 T
27673946 TTCTTTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (32 bp):
TCTTTCATTCTCTTTTTCTTTTTATATTTCTT
Found at i:27674762 original size:16 final size:15
Alignment explanation
Indices: 27674739--27674768 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
27674729 TCAACAATCT
27674739 ATAAAACAGAGAAAC
1 ATAAAACAGAGAAAC
27674754 ATAACAACAGAGAAA
1 ATAA-AACAGAGAAA
27674769 ACTTTTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.13, G:0.13, T:0.07
Consensus pattern (15 bp):
ATAAAACAGAGAAAC
Found at i:27675493 original size:37 final size:37
Alignment explanation
Indices: 27675434--27675505 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
27675424 TTTAGCTCGA
*
27675434 ATAATCCCCACACGTAGTCATCGGGTCTTACCCGGGC
1 ATAATCCCCACACGTAGCCATCGGGTCTTACCCGGGC
* *
27675471 ATAATCTCCACATGTAGCCATCGGGTCTTACCCGG
1 ATAATCCCCACACGTAGCCATCGGGTCTTACCCGG
27675506 AATATATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.24
Consensus pattern (37 bp):
ATAATCCCCACACGTAGCCATCGGGTCTTACCCGGGC
Found at i:27675699 original size:48 final size:48
Alignment explanation
Indices: 27675639--27675744 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
27675629 CGGCCACAAT
* *
27675639 ATATACACATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
27675687 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
* *
27675735 ACATATATAT
1 ATATACATAT
27675745 ATTTATCTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (48 bp):
ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
Found at i:27680276 original size:39 final size:39
Alignment explanation
Indices: 27680218--27680294 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
27680208 ATGTAGAACA
27680218 CATATTAATGATGTGCAAACTATGACATAATTAAAGACT
1 CATATTAATGATGTGCAAACTATGACATAATTAAAGACT
*
27680257 CATATTAATGATGTTCAAACTATGACATAATTAAAGAC
1 CATATTAATGATGTGCAAACTATGACATAATTAAAGAC
27680295 ACAAAGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (39 bp):
CATATTAATGATGTGCAAACTATGACATAATTAAAGACT
Found at i:27682976 original size:40 final size:40
Alignment explanation
Indices: 27682921--27683098 Score: 231
Period size: 40 Copynumber: 4.5 Consensus size: 40
27682911 CGGATGATAA
* *
27682921 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
*
27682961 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-T
*
27683001 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATT
*
27683042 -CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAAT-T
*
27683081 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
27683099 TACTTGGTTT
Statistics
Matches: 124, Mismatches: 8, Indels: 13
0.86 0.06 0.09
Matches are distributed among these distances:
38 1 0.01
39 20 0.16
40 101 0.81
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
Found at i:27683056 original size:80 final size:80
Alignment explanation
Indices: 27682921--27683098 Score: 263
Period size: 80 Copynumber: 2.2 Consensus size: 80
27682911 CGGATGATAA
* *
27682921 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAATCCGGGCTAAGCCCCGAAGGCATTTG
*
27682986 TGCGAGTTA-CTATAT
66 AGCGAG-TAGCTATAT
* *
27683001 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAT-CGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTA-AATCCGGGCTAAGCCCCGAAGGCATTT
27683065 GAGCGAGTAGCTATAT
65 GAGCGAGTAGCTATAT
*
27683081 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
27683099 TACTTGGTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
79 17 0.19
80 71 0.79
81 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAATCCGGGCTAAGCCCCGAAGGCATTTG
AGCGAGTAGCTATAT
Found at i:27685676 original size:14 final size:14
Alignment explanation
Indices: 27685657--27685683 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27685647 CTGGTTTTAG
27685657 ATATTCCCTTCGGA
1 ATATTCCCTTCGGA
27685671 ATATTCCCTTCGG
1 ATATTCCCTTCGG
27685684 CAAGAATGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.37
Consensus pattern (14 bp):
ATATTCCCTTCGGA
Found at i:27693951 original size:29 final size:28
Alignment explanation
Indices: 27693894--27693979 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 28
27693884 TACCTGTATT
* *
27693894 TGGCCCATTAAGCCCAATCATATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
*
27693922 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCC-AATCACATTCATA
* *
27693951 TGGCCCGTTAGGCCCAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
27693979 T
1 T
27693980 TCATGCTCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
28 26 0.51
29 25 0.49
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTCATA
Found at i:27695298 original size:16 final size:16
Alignment explanation
Indices: 27695274--27695305 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27695264 AAATTCGGGA
27695274 TTTCAGGATTTTTGGG
1 TTTCAGGATTTTTGGG
*
27695290 TTTCGGGATTTTTGGG
1 TTTCAGGATTTTTGGG
27695306 GCGTTACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.34, T:0.50
Consensus pattern (16 bp):
TTTCAGGATTTTTGGG
Found at i:27703187 original size:30 final size:30
Alignment explanation
Indices: 27703130--27703188 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
27703120 TTTTTAGGCC
**
27703130 TAAGGGTAAAATCATAATTTTTGCAAAGTT
1 TAAGGGTAAAATCATAATTTTACCAAAGTT
*
27703160 TAAGGGTAAAA-CGATCATTTTACCAAAGT
1 TAAGGGTAAAATC-ATAATTTTACCAAAGT
27703189 ATGAGTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (30 bp):
TAAGGGTAAAATCATAATTTTACCAAAGTT
Found at i:27707317 original size:24 final size:24
Alignment explanation
Indices: 27707289--27707349 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
27707279 AACCGTATTT
* * *
27707289 GCACACATAGTGCTA-ATTACACTC
1 GCACACATAGTGCCATAGTAAAC-C
*
27707313 GCACACATAGTCCCATAGTAAACC
1 GCACACATAGTGCCATAGTAAACC
27707337 GCACACATAGTGC
1 GCACACATAGTGC
27707350 ATTGGATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.34, C:0.31, G:0.15, T:0.20
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTAAACC
Found at i:27709766 original size:5 final size:5
Alignment explanation
Indices: 27709756--27709820 Score: 55
Period size: 5 Copynumber: 13.6 Consensus size: 5
27709746 CACCATAATC
* * * *
27709756 ATTTA ATTTA ATATA ATTCA A-TTA A-TTC ATTAA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
* *
27709804 ATATA ATTCA A-TTA ATT
1 ATTTA ATTTA ATTTA ATT
27709821 CATTAAATTT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
4 9 0.20
5 37 0.80
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.51
Consensus pattern (5 bp):
ATTTA
Found at i:27709804 original size:38 final size:38
Alignment explanation
Indices: 27709756--27709832 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
27709746 CACCATAATC
27709756 ATTTAATTTAATATAATTCAATTAATTCATTAAATTTA
1 ATTTAATTTAATATAATTCAATTAATTCATTAAATTTA
27709794 ATTTAATTTAATATAATTCAATTAATTCATTAAATTTA
1 ATTTAATTTAATATAATTCAATTAATTCATTAAATTTA
27709832 A
1 A
27709833 CTTTCAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.49
Consensus pattern (38 bp):
ATTTAATTTAATATAATTCAATTAATTCATTAAATTTA
Found at i:27710152 original size:30 final size:30
Alignment explanation
Indices: 27710118--27710178 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
27710108 TCCTTAACTC
27710118 AAACTTTTGCAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
27710148 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
27710178 A
1 A
27710179 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:27723218 original size:49 final size:49
Alignment explanation
Indices: 27723159--27723256 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
27723149 TTCAAGACCA
*
27723159 CAAATCCGATCCGAAAATAAAATTTATTTTTATTTTAATACATGGTCCT
1 CAAATCCGATCCGAAAATAAAATTTATTTTTATTTTAATACAGGGTCCT
*
27723208 CAAATTCGATCCGAAAATAAAATTTATTTTTATTTTAATACAGGGTCCT
1 CAAATCCGATCCGAAAATAAAATTTATTTTTATTTTAATACAGGGTCCT
27723257 TAATATGTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (49 bp):
CAAATCCGATCCGAAAATAAAATTTATTTTTATTTTAATACAGGGTCCT
Found at i:27727029 original size:40 final size:40
Alignment explanation
Indices: 27726935--27727079 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
27726925 TACTCGAATG
*
27726935 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
27726976 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
27727016 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
27727056 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
27727080 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:27735063 original size:40 final size:40
Alignment explanation
Indices: 27734969--27735113 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
27734959 TACTCGAATG
*
27734969 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
27735010 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
27735050 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
27735090 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
27735114 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:27739586 original size:28 final size:26
Alignment explanation
Indices: 27739525--27739594 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 26
27739515 ATATGAATTG
27739525 CACAATTAATAACATGGAGATAGTAA
1 CACAATTAATAACATGGAGATAGTAA
** * *
27739551 CATGATTAAAATAACATGGAGGTAGTCA
1 CACAATT--AATAACATGGAGATAGTAA
27739579 CACAATTAATAACATG
1 CACAATTAATAACATG
27739595 TATTCTGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 14 0.39
28 22 0.61
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (26 bp):
CACAATTAATAACATGGAGATAGTAA
Found at i:27741142 original size:29 final size:29
Alignment explanation
Indices: 27741055--27741146 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 29
27741045 TACCTGTATC
* * *
27741055 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* * * *
27741083 TGACCCATCAGGCCCAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
*
27741112 TGGCCCATTAGGCCCAAATCACATTTGTA
1 TGGCCCATTAGGCCCAAATCACATTTATA
27741141 TGGCCC
1 TGGCCC
27741147 GTTACACCCA
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
28 12 0.24
29 39 0.76
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:27741156 original size:29 final size:29
Alignment explanation
Indices: 27741055--27741169 Score: 74
Period size: 29 Copynumber: 4.0 Consensus size: 29
27741045 TACCTGTATC
* *
27741055 TGGCCCATTA-AGCCC-AATCATATTCATA
1 TGGCCCATTACA-CCCAAATCACATTTATA
* * ** * *
27741083 TGACCCATCAGGCCCAAATCACCTGTATA
1 TGGCCCATTACACCCAAATCACATTTATA
** *
27741112 TGGCCCATTAGGCCCAAATCACATTTGTA
1 TGGCCCATTACACCCAAATCACATTTATA
* * *
27741141 TGGCCCGTTACACCC-AGTCACATTCATA
1 TGGCCCATTACACCCAAATCACATTTATA
27741169 T
1 T
27741170 TCATGCTCAC
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
28 22 0.33
29 45 0.67
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (29 bp):
TGGCCCATTACACCCAAATCACATTTATA
Found at i:27746455 original size:47 final size:47
Alignment explanation
Indices: 27746386--27746557 Score: 159
Period size: 49 Copynumber: 3.6 Consensus size: 47
27746376 GGTATAATGC
* *
27746386 CGATGTCATGTCCCAGACATGGTCTTACACTGGCTTATCCATCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATCAATCAAGT
*
27746433 CGATGCCATGTCCCAGACATGGTCTTACACTGAC-TATCGAAATCGAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATC--AATC-AAGT
* ** * * ** *
27746482 CGACGCCATGTCCCAGATGTGTTCTTACACTAGCTCTCAT-ATATCCCTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-T-ATCA-AT-CAAGT
*
27746532 CGATGCCATGTCCTAGACATGGTCTT
1 CGATGCCATGTCCCAGACATGGTCTT
27746558 GCATTGATAC
Statistics
Matches: 100, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
46 4 0.04
47 32 0.32
48 3 0.03
49 33 0.33
50 24 0.24
51 2 0.02
52 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATCAATCAAGT
Found at i:27748498 original size:101 final size:101
Alignment explanation
Indices: 27748388--27748582 Score: 250
Period size: 101 Copynumber: 1.9 Consensus size: 101
27748378 TTACATTAGT
* * * *
27748388 AGTGCCATAACCTAGTTAT-AGT-TTTATCATCAGAATGCCATAGCCCAGCCATGGTCTTGCATA
1 AGTGCCATAACCCAGTTATGA-TCTTT-TCATCAAAATGCCATAGCCCAACCATGGTCTTACATA
** * *
27748451 TAATTATTGTCATGGTCCAACCATGGTCTTATGTTCAA
64 TAAACACTGCCATGGTCCAACCATGGTCTTATGTTCAA
* * * *
27748489 AGTGGCATAACCCAGTTATGATCTTTTCATTAAAATGCCATAGCCCAACTATGGTCTTACATGTA
1 AGTGCCATAACCCAGTTATGATCTTTTCATCAAAATGCCATAGCCCAACCATGGTCTTACATATA
27748554 AACACTGCCATGGTCCAACCATGGTCTTA
66 AACACTGCCATGGTCCAACCATGGTCTTA
27748583 CCTATCAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
101 76 0.95
102 4 0.05
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (101 bp):
AGTGCCATAACCCAGTTATGATCTTTTCATCAAAATGCCATAGCCCAACCATGGTCTTACATATA
AACACTGCCATGGTCCAACCATGGTCTTATGTTCAA
Found at i:27748958 original size:124 final size:124
Alignment explanation
Indices: 27748733--27748985 Score: 418
Period size: 124 Copynumber: 2.0 Consensus size: 124
27748723 AAAGTTTAAC
* *
27748733 CATATGAACTTACCTGGGGTAGATTGTGGAAGTTGTAGTAATTCAGGGACTATTCGACTAATCTC
1 CATATGAACTTACCTGGGGTAGATTGTGAAAATTGTAGTAATTCAGGGACTATTCGACTAATCTC
*
27748798 CCTTTTTCTCGTTGGTCTACGAGCTCTTGATTTAAAATGTAAAATTTTTCATTAATTAG
66 CCTTTTTCTCGTTGGTCTACGAGCTCTTGATCTAAAATGTAAAATTTTTCATTAATTAG
*
27748857 CATATGAACTTACCTGGGGTAGATTGTGAAAATTGTAGTAATTCAGGGACTATTC-AGCTAATTT
1 CATATGAACTTACCTGGGGTAGATTGTGAAAATTGTAGTAATTCAGGGACTATTCGA-CTAATCT
* * * *
27748921 CCCTTTTTCTTGTTGGTTTACGGGCTCTTGATCTAAAATGTAAAATTTTTCATTCATTAG
65 CCCTTTTTCTCGTTGGTCTACGAGCTCTTGATCTAAAATGTAAAATTTTTCATTAATTAG
27748981 CATAT
1 CATAT
27748986 ATTTCAATTT
Statistics
Matches: 120, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
123 1 0.01
124 119 0.99
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (124 bp):
CATATGAACTTACCTGGGGTAGATTGTGAAAATTGTAGTAATTCAGGGACTATTCGACTAATCTC
CCTTTTTCTCGTTGGTCTACGAGCTCTTGATCTAAAATGTAAAATTTTTCATTAATTAG
Found at i:27752795 original size:29 final size:29
Alignment explanation
Indices: 27752740--27752797 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
27752730 TCTCGACATA
* * *
27752740 TACTGGGCCGAAGCCTTTCGTTTAACGGT
1 TACTAGGCCGAAGCCTTACGTTAAACGGT
27752769 TACTAGGCCGAAGCCTTAC-TGTAAACGGT
1 TACTAGGCCGAAGCCTTACGT-TAAACGGT
27752798 ATGACCCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (29 bp):
TACTAGGCCGAAGCCTTACGTTAAACGGT
Found at i:27753032 original size:25 final size:25
Alignment explanation
Indices: 27753004--27753073 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
27752994 CTATTTTAAT
27753004 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
27753029 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
27753054 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
27753074 AGCACTTCCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:27753320 original size:27 final size:27
Alignment explanation
Indices: 27753299--27753524 Score: 326
Period size: 27 Copynumber: 8.3 Consensus size: 27
27753289 AAAGGTTATC
* *
27753299 TCAGTAATTCTACCTTACAAGGGTATT
1 TCAGTAATTCTACCCTACAGGGGTATT
* *
27753326 TTAGTAATTCTACCCTACAGGGGTAGT
1 TCAGTAATTCTACCCTACAGGGGTATT
27753353 TCAGTAATTCTACCCTACAGGGGTATT
1 TCAGTAATTCTACCCTACAGGGGTATT
* *
27753380 TCAGTAATTCTACCTTACTATGGGTATT
1 TCAGTAATTCTACCCTAC-AGGGGTATT
* *
27753408 CCGGTAATTCTACCCTACAGGGGTATT
1 TCAGTAATTCTACCCTACAGGGGTATT
*
27753435 TCAATAATTCTACCCTACAGGGGTATT
1 TCAGTAATTCTACCCTACAGGGGTATT
*
27753462 TCAGTAATTCTACCCTATAGGGGTATT
1 TCAGTAATTCTACCCTACAGGGGTATT
* *
27753489 TCAGTAATTCTACCCTACAAGAGTATT
1 TCAGTAATTCTACCCTACAGGGGTATT
*
27753516 TCAATAATT
1 TCAGTAATT
27753525 TTGTCAATTG
Statistics
Matches: 177, Mismatches: 21, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
27 154 0.87
28 23 0.13
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (27 bp):
TCAGTAATTCTACCCTACAGGGGTATT
Found at i:27753493 original size:109 final size:109
Alignment explanation
Indices: 27753302--27753502 Score: 348
Period size: 109 Copynumber: 1.8 Consensus size: 109
27753292 GGTTATCTCA
* * *
27753302 GTAATTCTACCTTACAAGGGTATTTTAGTAATTCTACCCTACAGGGGTAGTTCAGTAATTCTACC
1 GTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTAGTTCAGTAATTCTACC
27753367 CTACAGGGGTATTTCAGTAATTCTACCTTACTATGGGTATTCCG
66 CTACAGGGGTATTTCAGTAATTCTACCTTACTATGGGTATTCCG
* *
27753411 GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAATTCTACC
1 GTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTAGTTCAGTAATTCTACC
*
27753476 CTATAGGGGTATTTCAGTAATTCTACC
66 CTACAGGGGTATTTCAGTAATTCTACC
27753503 CTACAAGAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 86 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35
Consensus pattern (109 bp):
GTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTAGTTCAGTAATTCTACC
CTACAGGGGTATTTCAGTAATTCTACCTTACTATGGGTATTCCG
Found at i:27753629 original size:81 final size:77
Alignment explanation
Indices: 27753511--27753741 Score: 187
Period size: 81 Copynumber: 2.8 Consensus size: 77
27753501 CCCTACAAGA
* * ***
27753511 GTATTTCAATAATTTTGTC-AATTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTACTTTGGT
1 GTATTTCAGTAATTTTG-CAAACTGAGGGTATTTCGGTAATT-T-TAAA-CGAGGGTA-TTTGGT
27753575 AATTTTACAAATCGA-GG
61 AATTTTACAAA-CGAGGG
*
27753592 GTATTTCAGTAATTTTGCAAACTGAGGGTATTTCGGTAATTTTACAAACTGAGGCTATTTCGGTA
1 GTATTTCAGTAATTTTGCAAACTGAGGGTATTTCGGTAATTTT--AAAC-GAGGGTATTT-GGTA
*
27753657 ATTTTACAAACTAGGG
62 ATTTTACAAACGAGGG
** ** ** * *
27753673 GTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTATAAACTAGGGGTATTTTGGTA
1 GTATTTCAGTAATTTTGCAAACTGAGGGTATTTCGGTAA-TTT-TAAACGA-GGGTA-TTTGGTA
27753738 ATTT
62 ATTT
27753742 GGTAAACTAA
Statistics
Matches: 124, Mismatches: 16, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
79 1 0.01
80 9 0.07
81 107 0.86
82 6 0.05
83 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (77 bp):
GTATTTCAGTAATTTTGCAAACTGAGGGTATTTCGGTAATTTTAAACGAGGGTATTTGGTAATTT
TACAAACGAGGG
Found at i:27753651 original size:54 final size:54
Alignment explanation
Indices: 27753563--27753741 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 54
27753553 TGTAAATCGA
* * *
27753563 GGGTACTTTGGTAATTTTACAAA-TCGAGGGTATTTCAGTAATTTTGCAAACT-G
1 GGGTATTTTGGTAATTTTACAAACT-GAGGGTATTTCGGTAATTTTACAAACTAG
* *
27753616 AGGGTATTTCGGTAATTTTACAAACTGAGGCTATTTCGGTAATTTTACAAACTAG
1 -GGGTATTTTGGTAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAACTAG
* ** * *
27753671 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTATAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAACTAG
27753725 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
27753742 GGTAAACTAA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
54 109 0.98
55 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAACTAG
Found at i:27753747 original size:27 final size:27
Alignment explanation
Indices: 27753563--27753750 Score: 184
Period size: 27 Copynumber: 7.0 Consensus size: 27
27753553 TGTAAATCGA
* * *
27753563 GGGTACTTTGGTAATTTTACAAA-TCG
1 GGGTATTTTGGTAATTTTATAAACTAG
** **
27753589 AGGGTATTTCAGTAATTTTGCAAACT-G
1 -GGGTATTTTGGTAATTTTATAAACTAG
* *
27753616 AGGGTATTTCGGTAATTTTACAAACT-G
1 -GGGTATTTTGGTAATTTTATAAACTAG
* * *
27753643 AGGCTATTTCGGTAATTTTACAAACTAG
1 -GGGTATTTTGGTAATTTTATAAACTAG
* *
27753671 GGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTATAAACTAG
27753698 GGGTATTTTGGTAATTTTATAAACTAG
1 GGGTATTTTGGTAATTTTATAAACTAG
**
27753725 GGGTATTTTGGTAATTTGGTAAACTA
1 GGGTATTTTGGTAATTTTATAAACTA
27753751 AAGTATTCTA
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
27 141 0.99
28 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACTAG
Found at i:27760292 original size:16 final size:16
Alignment explanation
Indices: 27760273--27760303 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27760263 CTTCTTCACT
27760273 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
27760289 TACTTACTTACTTAA
1 TACTCACTTACTTAA
27760304 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:27760309 original size:20 final size:20
Alignment explanation
Indices: 27760270--27760309 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
27760260 AAACTTCTTC
* *
27760270 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
27760290 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
27760310 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:27760626 original size:53 final size:54
Alignment explanation
Indices: 27760534--27760749 Score: 231
Period size: 55 Copynumber: 4.0 Consensus size: 54
27760524 TATGTGGTAT
* * * * * *
27760534 CCTTTTGAAACTAACCATTGCCATGTCTCGACATTGTCTTACATGGTATCCTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
* * * *
27760588 CCTTATG-AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CATTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATC-CTTG
* * *
27760641 CCTTATAGTAACTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTG
1 CCTTAT-GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
* * *
27760696 CCTTA-GAAACCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTTTCCTT
1 CCTTATGAAA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
27760750 AAACTCTAAT
Statistics
Matches: 135, Mismatches: 21, Indels: 11
0.81 0.13 0.07
Matches are distributed among these distances:
52 1 0.01
53 45 0.33
54 14 0.10
55 74 0.55
56 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
Found at i:27760743 original size:55 final size:54
Alignment explanation
Indices: 27760495--27760749 Score: 224
Period size: 55 Copynumber: 4.8 Consensus size: 54
27760485 ACACGGGTAC
* * * **
27760495 CTTACC-ATTTCCATGACTTGTCATGGTCTTATGTGGTATCCTT---TT-GAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* * * *
27760544 CTAACC-ATTGCCATGTCTCGACATTGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA
* * * * *
27760597 CTCACCAA-TGCCATGCCTTGGCATGGTCTTACATGGGA-CATTTGCCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATC-CTTGCC-T-TAGAAA
* *
27760652 CTTATCAA-TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* * *
27760705 CCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTTTCCTT
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT
27760750 AAACTCTAAT
Statistics
Matches: 166, Mismatches: 27, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
49 35 0.21
52 3 0.02
53 42 0.25
54 12 0.07
55 73 0.44
56 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
Found at i:27767896 original size:16 final size:16
Alignment explanation
Indices: 27767877--27767907 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27767867 CTTCTTCACT
27767877 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
27767893 TACTTACTTACTTAA
1 TACTCACTTACTTAA
27767908 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:27767913 original size:20 final size:20
Alignment explanation
Indices: 27767874--27767913 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
27767864 AAACTTCTTC
* *
27767874 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
27767894 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
27767914 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:27768283 original size:108 final size:110
Alignment explanation
Indices: 27768147--27768347 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 110
27768137 ATCCTTTTGA
*
27768147 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTACCCTTGCCTTATG-AA-CTTACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTACCCTTGCCTTA-GAAACCTTACCAA
27768210 -TGCCATGCCTTGGCATGGTCTTACATGGGACATTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACATTTGCCTTATAGT
* * *
27768255 AACTTATCAATGCCATTTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTACCCTTGCCTTAGAAACCTTACCAAT
*
27768320 TTCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
27768348 TATCCTTAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 8 0.09
110 27 0.32
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTACCCTTGCCTTAGAAACCTTACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACATTTGCCTTATAGT
Found at i:27768348 original size:55 final size:54
Alignment explanation
Indices: 27768100--27768354 Score: 269
Period size: 55 Copynumber: 4.8 Consensus size: 54
27768090 ACACAGGTAC
* * *
27768100 CTTACC-ATTGCCATGACTTGTCATGATCTTACATGGTATCCTT---TT-GAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* *
27768149 CTTACC-ATTGCCATGTCTTGACATGGTCTTACATGGTACCCTTGCCTTATG-AA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA
* * * *
27768202 CTTACCAA-TGCCATGCCTTGGCATGGTCTTACATGGGA-CATTTGCCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATC-CTTGCC-T-TAGAAA
* **
27768257 CTTATCAA-TGCCATTTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* *
27768310 CCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT
27768355 AAACCCTAAT
Statistics
Matches: 173, Mismatches: 20, Indels: 20
0.81 0.09 0.09
Matches are distributed among these distances:
49 39 0.23
52 3 0.02
53 45 0.26
54 12 0.07
55 73 0.42
56 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.36
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
Found at i:27782796 original size:15 final size:15
Alignment explanation
Indices: 27782778--27782820 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
27782768 TCTGAGACAG
27782778 AGAAATCCAAGATAA
1 AGAAATCCAAGATAA
**
27782793 AGAAACTCCCAAGATTC
1 AGAAA-T-CCAAGATAA
27782810 AGAAATCCAAG
1 AGAAATCCAAG
27782821 TTACAATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 12 0.50
ACGTcount: A:0.51, C:0.21, G:0.14, T:0.14
Consensus pattern (15 bp):
AGAAATCCAAGATAA
Found at i:27789420 original size:20 final size:21
Alignment explanation
Indices: 27789395--27789436 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
27789385 TCTTTGAAAC
27789395 AAGGC-ACACGCTCGTGTGGA
1 AAGGCAACACGCTCGTGTGGA
27789415 AAGGCAACACGCTCGTGTGGA
1 AAGGCAACACGCTCGTGTGGA
27789436 A
1 A
27789437 TTAATTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.29, C:0.24, G:0.33, T:0.14
Consensus pattern (21 bp):
AAGGCAACACGCTCGTGTGGA
Found at i:27791407 original size:45 final size:45
Alignment explanation
Indices: 27791287--27791409 Score: 185
Period size: 45 Copynumber: 2.7 Consensus size: 45
27791277 CATCCATTAT
* *
27791287 GAACTTGGACCAACTCCACAAGCTTGGA-TGCTTCACATATACCAC
1 GAACTTGGACCAACTCAACAAGCTTGGATTTC-TCACATATACCAC
* * *
27791332 GAACTTGGACCAACTCAACAAGTTTAGATTTCTCACATATATCAC
1 GAACTTGGACCAACTCAACAAGCTTGGATTTCTCACATATACCAC
27791377 GAACTTGGACCAACTCAACAAGCTTGGATTTCT
1 GAACTTGGACCAACTCAACAAGCTTGGATTTCT
27791410 TAATTCCTAG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
45 68 0.97
46 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.26
Consensus pattern (45 bp):
GAACTTGGACCAACTCAACAAGCTTGGATTTCTCACATATACCAC
Found at i:27802337 original size:43 final size:43
Alignment explanation
Indices: 27802290--27802382 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 43
27802280 CTAGATAGCA
* *
27802290 TCTTACACAAAATCA-TATAACAATGCCAATGTCCCAGACATTG
1 TCTTACACAAAATCACAAT-ACAATGCCAATGTCCCAGACATGG
*
27802333 TCTTACACATAATCACAATACAATGCCAATGTCCCAGACATGG
1 TCTTACACAAAATCACAATACAATGCCAATGTCCCAGACATGG
27802376 TCTTACA
1 TCTTACA
27802383 TGTAACCACA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 44 0.96
44 2 0.04
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.26
Consensus pattern (43 bp):
TCTTACACAAAATCACAATACAATGCCAATGTCCCAGACATGG
Found at i:27804634 original size:15 final size:15
Alignment explanation
Indices: 27804614--27804645 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
27804604 CATTTCACTA
27804614 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
27804629 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
27804644 TT
1 TT
27804646 TGCATGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:27810535 original size:106 final size:107
Alignment explanation
Indices: 27810410--27810625 Score: 380
Period size: 106 Copynumber: 2.0 Consensus size: 107
27810400 GCATGCTCAT
* * * *
27810410 TTTTATTTTGAGAGTAAACCAAAATATCATCTATAAATACCATCACAAACTTGTCCAAGTACGGG
1 TTTTATTTCGAGAGTAAACCAAAATATCATCTATAAATACCATCACAAACCTGTCCAAATACAGG
27810475 CTGAAAATTTTGTTCATCAAATCCATAAACACTGCAGGTG-A
66 CTGAAAATTTTGTTCATCAAATCCATAAACACTGCAGGTGCA
27810516 TTTTATTTCGAGAGTAAACCAAAATATCATCTATAAATACCATCACAAACCTGTCCAAATACAGG
1 TTTTATTTCGAGAGTAAACCAAAATATCATCTATAAATACCATCACAAACCTGTCCAAATACAGG
*
27810581 CTGAAAATTTTGTTCATCAAATCCATAAACACTGTAGGTGCA
66 CTGAAAATTTTGTTCATCAAATCCATAAACACTGCAGGTGCA
27810623 TTT
1 TTT
27810626 GTCAAGTCGA
Statistics
Matches: 104, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
106 100 0.96
107 4 0.04
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (107 bp):
TTTTATTTCGAGAGTAAACCAAAATATCATCTATAAATACCATCACAAACCTGTCCAAATACAGG
CTGAAAATTTTGTTCATCAAATCCATAAACACTGCAGGTGCA
Found at i:27815440 original size:45 final size:45
Alignment explanation
Indices: 27815376--27815463 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
27815366 AAACATGTGC
*
27815376 CACATACATCATGAACTCAGACCACAACTCAATGAGTTTAGATGT
1 CACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGATGT
*
27815421 CACATATATCATGAACTCAGACCACAACTCAATGAGTTCAGAT
1 CACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGAT
27815464 CACATAGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (45 bp):
CACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGATGT
Found at i:27815461 original size:21 final size:21
Alignment explanation
Indices: 27815392--27815467 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
27815382 CATCATGAAC
27815392 TCAGACCACAACTCAATGAGT
1 TCAGACCACAACTCAATGAGT
* * * **
27815413 TTAGATGTCACATATATC-ATGAAC
1 TCAGA--CCACA-A-CTCAATGAGT
27815437 TCAGACCACAACTCAATGAGT
1 TCAGACCACAACTCAATGAGT
*
27815458 TCAGATCACA
1 TCAGACCACA
27815468 TAGTTCCTAG
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
20 2 0.05
21 18 0.46
22 4 0.10
23 4 0.10
24 9 0.23
25 2 0.05
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (21 bp):
TCAGACCACAACTCAATGAGT
Found at i:27818686 original size:31 final size:29
Alignment explanation
Indices: 27818651--27818708 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
27818641 ACTAGTATTT
*
27818651 TATTAATTTAATATTAAAGTGATTATCTTAA
1 TATTAAATTAA-ATTAAA-TGATTATCTTAA
* *
27818682 TATTAAATTAAATTTAATGTTTATCTT
1 TATTAAATTAAATTAAATGATTATCTT
27818709 GTAGATAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 5 0.21
31 10 0.42
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAA
Found at i:27818769 original size:11 final size:12
Alignment explanation
Indices: 27818734--27818766 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27818724 ATTATTTTAA
27818734 TAATATTTAATAC
1 TAATATTTAAT-C
27818747 TAA-ATTTAATC
1 TAATATTTAATC
27818758 TAATATTTA
1 TAATATTTA
27818767 TCTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 12 0.63
13 3 0.16
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATATTTAATC
Found at i:27822492 original size:31 final size:32
Alignment explanation
Indices: 27822457--27822522 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
27822447 TTTTATAGCT
* *
27822457 AAATTTGGCCATCAATCTTTT-AAAAAGAGTC
1 AAATTTGACCATCAACCTTTTGAAAAAGAGTC
**
27822488 AAATTTGACCATTGACCTTTTGAAAAAGAGTC
1 AAATTTGACCATCAACCTTTTGAAAAAGAGTC
27822520 AAA
1 AAA
27822523 ATGATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (32 bp):
AAATTTGACCATCAACCTTTTGAAAAAGAGTC
Found at i:27823374 original size:23 final size:23
Alignment explanation
Indices: 27823348--27823396 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
27823338 ATTATTTGTA
27823348 AATATGTT-TAAACATATTCATTT
1 AATAT-TTGTAAACATATTCATTT
* *
27823371 AATATTTGTAAATATATTTATTT
1 AATATTTGTAAACATATTCATTT
27823394 AAT
1 AAT
27823397 TTCATGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (23 bp):
AATATTTGTAAACATATTCATTT
Found at i:27823687 original size:16 final size:18
Alignment explanation
Indices: 27823666--27823702 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
27823656 TTTATAATAC
27823666 TTTT-TATATTATGTAAT
1 TTTTATATATTATGTAAT
27823683 TTTTATATATTATGTAAT
1 TTTTATATATTATGTAAT
27823701 TT
1 TT
27823703 ATAACACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTATATATTATGTAAT
Found at i:27823815 original size:23 final size:23
Alignment explanation
Indices: 27823789--27823833 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
27823779 TGATGATAAA
27823789 AAAATTCAATAAATA-TAAAATAT
1 AAAATT-AATAAATATTAAAATAT
*
27823812 AAAATTATTAAATATTAAAATA
1 AAAATTAATAAATATTAAAATA
27823834 ATATCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATTAATAAATATTAAAATAT
Found at i:27828744 original size:27 final size:27
Alignment explanation
Indices: 27828714--27828945 Score: 313
Period size: 27 Copynumber: 8.6 Consensus size: 27
27828704 ATATTGAGTC
* * * *
27828714 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
27828741 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27828768 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
27828796 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
27828823 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
27828850 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27828877 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27828904 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27828931 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
27828946 GTACAATTTA
Statistics
Matches: 184, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
27 160 0.87
28 24 0.13
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:27843306 original size:39 final size:39
Alignment explanation
Indices: 27843245--27843408 Score: 265
Period size: 39 Copynumber: 4.2 Consensus size: 39
27843235 GAAATGTGTA
27843245 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * *
27843284 TGGAAATATATCTGGGCCAAAGACCCGCAGGCTTCGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
27843323 TGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* *
27843362 TGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
27843401 TGGTAATA
1 TGGAAATA
27843409 AAATTTCGGG
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 115 1.00
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (39 bp):
TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
Found at i:27862991 original size:43 final size:42
Alignment explanation
Indices: 27862944--27863024 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
27862934 CTTATATGGG
*
27862944 ATCTCAAATCGATGCCAATAGCCCAGCTATGGTCTTACACAAA
1 ATCTCAAATCGATGCC-ATAGCCCAGATATGGTCTTACACAAA
* * *
27862987 ATCTCATATCGATGCCATATCCTAGATATGGTCTTACA
1 ATCTCAAATCGATGCCATAGCCCAGATATGGTCTTACA
27863025 TGTAAACTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 19 0.56
43 15 0.44
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (42 bp):
ATCTCAAATCGATGCCATAGCCCAGATATGGTCTTACACAAA
Found at i:27867987 original size:27 final size:27
Alignment explanation
Indices: 27867955--27868059 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 27
27867945 AGGAAGTGTC
* *
27867955 CTGGTGGTTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
27867982 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* *
27868009 CTAGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* * *
27868036 CTTGTGACTCTGTCAC-ATTATCTG
1 CTGGTGGCTCTGCCACAATTATCTG
27868060 TTGTGGCAGC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 10 0.14
27 57 0.83
28 2 0.03
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:27869464 original size:24 final size:24
Alignment explanation
Indices: 27869437--27869495 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
27869427 ATGTTTAAGT
27869437 GAGCTATATTACGAAGCTCATAAA
1 GAGCTATATTACGAAGCTCATAAA
* * *
27869461 GAGCCTATATCAGGATGCTCATAAA
1 GAG-CTATATTACGAAGCTCATAAA
* *
27869486 AAGCTGTATT
1 GAGCTATATT
27869496 TGTGTCTGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
GAGCTATATTACGAAGCTCATAAA
Found at i:27873523 original size:21 final size:21
Alignment explanation
Indices: 27873494--27873538 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
27873484 TATAAACTAT
* *
27873494 ATTTCTTAATTAGTTTTTTAAA
1 ATTTCTTAATGA-TTTTTCAAA
27873516 ATTT-TTAATGATTTTTCAAA
1 ATTTCTTAATGATTTTTCAAA
27873536 ATT
1 ATT
27873539 AGAATAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 6 0.29
22 4 0.19
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTTCTTAATGATTTTTCAAA
Found at i:27878843 original size:21 final size:21
Alignment explanation
Indices: 27878819--27878858 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27878809 ATTTAACATC
*
27878819 AATTTAATCCATTTCACACTT
1 AATTTAATCCAATTCACACTT
*
27878840 AATTTAATTCAATTCACAC
1 AATTTAATCCAATTCACAC
27878859 CCTAAGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTAATCCAATTCACACTT
Found at i:27879772 original size:39 final size:39
Alignment explanation
Indices: 27879718--27879795 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
27879708 CACTGAAAAC
27879718 GGGCTATTACATTTTCCAATGCAAATTCAAACAATTAAT
1 GGGCTATTACATTTTCCAATGCAAATTCAAACAATTAAT
27879757 GGGCTATTACATTTTCCAATGCAAATTCAAACAATTAAT
1 GGGCTATTACATTTTCCAATGCAAATTCAAACAATTAAT
27879796 CAATCTTCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (39 bp):
GGGCTATTACATTTTCCAATGCAAATTCAAACAATTAAT
Found at i:27881244 original size:25 final size:25
Alignment explanation
Indices: 27881216--27881274 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
27881206 CAGCTCGTAT
27881216 GAGCTTACCGTTATTCAGCTCAGAG
1 GAGCTTACCGTTATTCAGCTCAGAG
* *
27881241 GAGCTTACTGTTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCAGAG
*
27881266 GAACTTACC
1 GAGCTTACC
27881275 TTTTACAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCAGAG
Found at i:27883283 original size:22 final size:22
Alignment explanation
Indices: 27883253--27883296 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
27883243 AAAATAAATC
*
27883253 AAAAGTAATTAAAATTTAATAT
1 AAAAGTAATTAAAATTAAATAT
*
27883275 AAAATTAATTAAAATTAAATAT
1 AAAAGTAATTAAAATTAAATAT
27883297 GTTAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAAGTAATTAAAATTAAATAT
Found at i:27883289 original size:10 final size:10
Alignment explanation
Indices: 27883243--27883292 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
27883233 AAATCTGTCG
* *
27883243 AAAATAAATC
1 AAAATTAATT
*
27883253 AAAAGTAATT
1 AAAATTAATT
27883263 AAAATTTAATAT
1 AAAA-TTAAT-T
27883275 AAAATTAATT
1 AAAATTAATT
27883285 AAAATTAA
1 AAAATTAA
27883293 ATATGTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 20 0.59
11 9 0.26
12 5 0.15
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAATTAATT
Found at i:27888412 original size:16 final size:16
Alignment explanation
Indices: 27888391--27888421 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27888381 AATTAATTTA
*
27888391 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
27888407 AATTAAATAATTTTC
1 AATTAAATAATTTTC
27888422 TCAGCCCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:27898738 original size:17 final size:18
Alignment explanation
Indices: 27898712--27898745 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27898702 TTTTTGTTTA
27898712 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
27898729 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
27898746 ATATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:27901823 original size:9 final size:9
Alignment explanation
Indices: 27901809--27901842 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
27901799 ATTTTATAAT
27901809 TAATTTTGG
1 TAATTTTGG
27901818 TAATTTTGG
1 TAATTTTGG
27901827 TTAATTTTGAG
1 -TAATTTTG-G
27901838 TAATT
1 TAATT
27901843 ATACTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 13 0.57
11 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (9 bp):
TAATTTTGG
Found at i:27901850 original size:20 final size:19
Alignment explanation
Indices: 27901802--27901850 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
27901792 TTAGTTAATT
27901802 TTATAATTAATTTTGGTAA
1 TTATAATTAATTTTGGTAA
* **
27901821 TTTTGGTTAATTTTGAGTAA
1 TTATAATTAATTTTG-GTAA
*
27901841 TTATACTTAA
1 TTATAATTAA
27901851 ATTATAATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (19 bp):
TTATAATTAATTTTGGTAA
Found at i:27904323 original size:58 final size:58
Alignment explanation
Indices: 27904230--27904352 Score: 146
Period size: 58 Copynumber: 2.1 Consensus size: 58
27904220 TTCTTGTTTT
* *
27904230 CATTTCCATTTT--TTTTAAAGAAAACCATATTCATTTCCT-AATGATTCC-ATTTTCTC
1 CATTT-CATTTTCATTTTAAAGAAAACCATAATCATTTCCTGAACGATTCCTA-TTTCTC
* * *
27904286 CAATTTCATTTTCATTTTGAAGTAAACCATAATCATTTCCTGAACGTTTCCTATTTCTC
1 C-ATTTCATTTTCATTTTAAAGAAAACCATAATCATTTCCTGAACGATTCCTATTTCTC
27904345 CATTTCAT
1 CATTTCAT
27904353 CAATTCTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
56 7 0.12
57 4 0.07
58 31 0.54
59 14 0.25
60 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.46
Consensus pattern (58 bp):
CATTTCATTTTCATTTTAAAGAAAACCATAATCATTTCCTGAACGATTCCTATTTCTC
Found at i:27906243 original size:20 final size:20
Alignment explanation
Indices: 27906218--27906258 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
27906208 AGCATTGTAA
* *
27906218 TGAGGCACTGAAGTGCAAAC
1 TGAGGCACTAAAGTGAAAAC
27906238 TGAGGCACTAAAGTGAAAAC
1 TGAGGCACTAAAGTGAAAAC
27906258 T
1 T
27906259 CATACAAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (20 bp):
TGAGGCACTAAAGTGAAAAC
Found at i:27913585 original size:15 final size:15
Alignment explanation
Indices: 27913565--27913596 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27913555 TTAACTACAT
27913565 TTTCACAATCTATAG
1 TTTCACAATCTATAG
*
27913580 TTTCACAGTCTATAG
1 TTTCACAATCTATAG
27913595 TT
1 TT
27913597 CCAGTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (15 bp):
TTTCACAATCTATAG
Found at i:27914327 original size:21 final size:21
Alignment explanation
Indices: 27914288--27914327 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
27914278 GTCTTATGCC
*
27914288 ACAGTCCATAAAAATAATAAG
1 ACAGTCCATAAAAACAATAAG
27914309 ACAGTCC-TAAAATACAATA
1 ACAGTCCATAAAA-ACAATA
27914328 TAATAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.20
Consensus pattern (21 bp):
ACAGTCCATAAAAACAATAAG
Found at i:27929142 original size:71 final size:67
Alignment explanation
Indices: 27929065--27929206 Score: 194
Period size: 67 Copynumber: 2.1 Consensus size: 67
27929055 TCACCAGATA
* * * *
27929065 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACTAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
27929130 GGCTGC
62 GGCTGC
* *
27929136 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
27929201 GC
66 GC
27929203 CAGA
1 CAGA
27929207 ACGCTTCCTC
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
67 40 0.62
71 25 0.38
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.19
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:27929184 original size:27 final size:26
Alignment explanation
Indices: 27929136--27929187 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
27929126 GCGAGGCTGC
*
27929136 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
27929162 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
27929188 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:27942151 original size:45 final size:45
Alignment explanation
Indices: 27942066--27942151 Score: 100
Period size: 45 Copynumber: 1.9 Consensus size: 45
27942056 TATACGCCTA
** * *
27942066 AAATGAGTAAGACCATAGCTGAAAGATATTATGGCTTCATGATAT
1 AAATGAGTAAGACCATAGCTGAAAGATACCACGGCATCATGATAT
* * * *
27942111 AAATGTGTAAGACCCTGGCTGAAAGATGCCACGGCATCATG
1 AAATGAGTAAGACCATAGCTGAAAGATACCACGGCATCATG
27942152 GTAAATATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTGAAAGATACCACGGCATCATGATAT
Found at i:27942419 original size:27 final size:28
Alignment explanation
Indices: 27942388--27942448 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
27942378 TGGCATCAAA
*
27942388 GATAGTCT-GACGGGA-TGTTAAACATGG
1 GATAGTCTCGACGAGACT-TTAAACATGG
27942415 GATAGT-TCGACGAGACTTTAAACATGG
1 GATAGTCTCGACGAGACTTTAAACATGG
27942442 GATAGTC
1 GATAGTC
27942449 CAATAGGACG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.03
27 28 0.93
28 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (28 bp):
GATAGTCTCGACGAGACTTTAAACATGG
Found at i:27942462 original size:27 final size:27
Alignment explanation
Indices: 27942404--27942465 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
27942394 CTGACGGGAT
* * *
27942404 GTTAAACATGGGATAGTTCGACGAGAC
1 GTTAAACATGGGATAGTCCAAAGAGAC
*
27942431 TTTAAACATGGGATAGTCCAATAG-GAC
1 GTTAAACATGGGATAGTCCAA-AGAGAC
27942458 GTTAAACA
1 GTTAAACA
27942466 CACGGCAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (27 bp):
GTTAAACATGGGATAGTCCAAAGAGAC
Found at i:27945178 original size:12 final size:12
Alignment explanation
Indices: 27945161--27945185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27945151 TCTGAAGTCG
27945161 TAATATTATTTT
1 TAATATTATTTT
27945173 TAATATTATTTT
1 TAATATTATTTT
27945185 T
1 T
27945186 GGTGTTTACA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATATTATTTT
Found at i:27945800 original size:28 final size:29
Alignment explanation
Indices: 27945769--27945828 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
27945759 AAAGTGATTT
*
27945769 TTGAAAAAAATGTCAATT-AGGGATTAAA
1 TTGAAAAAAATGTAAATTGAGGGATTAAA
* * *
27945797 TTGAGAAAAGTGTAAATTGAGGGGTTAAA
1 TTGAAAAAAATGTAAATTGAGGGATTAAA
27945826 TTG
1 TTG
27945829 TGAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.43, C:0.02, G:0.25, T:0.30
Consensus pattern (29 bp):
TTGAAAAAAATGTAAATTGAGGGATTAAA
Found at i:27945824 original size:29 final size:28
Alignment explanation
Indices: 27945769--27945833 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 28
27945759 AAAGTGATTT
* *
27945769 TTGAAAAAAATGTCAATTAGGGATTAAA
1 TTGAGAAAAATGTAAATTAGGGATTAAA
* *
27945797 TTGAGAAAAGTGTAAATTGAGGGGTTAAA
1 TTGAGAAAAATGTAAATT-AGGGATTAAA
*
27945826 TTGTGAAA
1 TTGAGAAA
27945834 TAAATGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.29
Consensus pattern (28 bp):
TTGAGAAAAATGTAAATTAGGGATTAAA
Found at i:27950234 original size:29 final size:29
Alignment explanation
Indices: 27950192--27950265 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 29
27950182 TAGAACGAGG
27950192 TATGGACATT-ATGAAT-TCTTAGTTATGTCTT
1 TATGGAC-TTAATGAATCTCTTA--TA-GTCTT
27950223 T-TGGAC-TAATGAATGCTCTTATAGTCTT
1 TATGGACTTAATGAAT-CTCTTATAGTCTT
27950251 TATGGACTTAATGAA
1 TATGGACTTAATGAA
27950266 CCCTATTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
28 7 0.18
29 13 0.34
30 12 0.32
31 6 0.16
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (29 bp):
TATGGACTTAATGAATCTCTTATAGTCTT
Found at i:27954800 original size:46 final size:46
Alignment explanation
Indices: 27954750--27954925 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
27954740 TGGTTGAGCA
27954750 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27954796 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
27954841 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27954889 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
27954926 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:27954906 original size:93 final size:93
Alignment explanation
Indices: 27954747--27954918 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
27954737 GGATGGTTGA
* *
27954747 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27954812 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
27954840 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27954905 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
27954919 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:27962063 original size:46 final size:46
Alignment explanation
Indices: 27962013--27962188 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
27962003 TGGTTGAGCA
27962013 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27962059 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
27962104 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-A
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27962151 ACTCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
27962189 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 62 0.56
47 29 0.26
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:27962169 original size:93 final size:93
Alignment explanation
Indices: 27962010--27962181 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
27962000 GGATGGTTGA
**
27962010 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAACTCCGAACTCGTTGAGT
27962075 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
27962103 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAACT-CGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AAACTCCGAACTCGTTGAG
27962167 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
27962182 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
93 72 0.96
94 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAACTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:27973737 original size:28 final size:29
Alignment explanation
Indices: 27973706--27973765 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
27973696 AAAGTGATTT
*
27973706 TTGACAAAAATGTCAATT-AGGGATTAAA
1 TTGACAAAAATGTAAATTGAGGGATTAAA
* * *
27973734 TTGAGAAAAGTGTAAATTGAGGGGTTAAA
1 TTGACAAAAATGTAAATTGAGGGATTAAA
27973763 TTG
1 TTG
27973766 TGAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (29 bp):
TTGACAAAAATGTAAATTGAGGGATTAAA
Found at i:27973765 original size:29 final size:28
Alignment explanation
Indices: 27973706--27973770 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 28
27973696 AAAGTGATTT
* *
27973706 TTGACAAAAATGTCAATTAGGGATTAAA
1 TTGAGAAAAATGTAAATTAGGGATTAAA
* *
27973734 TTGAGAAAAGTGTAAATTGAGGGGTTAAA
1 TTGAGAAAAATGTAAATT-AGGGATTAAA
*
27973763 TTGTGAAA
1 TTGAGAAA
27973771 TAAATGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.43, C:0.03, G:0.25, T:0.29
Consensus pattern (28 bp):
TTGAGAAAAATGTAAATTAGGGATTAAA
Done.