Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2409
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: 154369
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 1 of 2
Found at i:10853 original size:17 final size:17
Alignment explanation
Indices: 10814--10859 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
10804 TTTTATATTG
10814 TTTTAATAAAATATTTA
1 TTTTAATAAAATATTTA
*
10831 TATTT-ATAAATTATTTAA
1 T-TTTAATAAAATATTT-A
10849 TTTTAATAAAA
1 TTTTAATAAAA
10860 ATAACTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAATAAAATATTTA
Found at i:10955 original size:22 final size:22
Alignment explanation
Indices: 10909--10967 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
10899 ATTAAATAAG
10909 TTAAATTTAAATA-TTTTAATAT
1 TTAAA-TTAAATATTTTTAATAT
10931 TTAAATTAAATATTTTGTAAT-T
1 TTAAATTAAATATTTT-TAATAT
10953 TT-AATTAAA-ATTTTT
1 TTAAATTAAATATTTTT
10968 TATTATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
20 5 0.14
21 14 0.40
22 11 0.31
23 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAAATTAAATATTTTTAATAT
Found at i:11058 original size:156 final size:155
Alignment explanation
Indices: 10898--11191 Score: 475
Period size: 156 Copynumber: 1.9 Consensus size: 155
10888 AGTTCAAGTT
* *
10898 TATTAAATAAGT-TAAATTTAAATATTTTAATATTTAAATTAAATATTTTGTAATTTTAATTAAA
1 TATTAAATAA-TCTAAAATTAAATATTTTAATATTTAAATTAAATATTTTGTAAGTTTAATTAAA
10962 ATTTTTTATTATTAATATATAT-TTTTAAATTAATATTAAAAAAGTTAATTTAAATTCAAATTAA
65 ATTTTTTATTATTAATATATATATTTT-AATTAATATTAAAAAA-TTAATTTAAATTCAAATTAA
11026 AATATAACTAAGTTGTAATTAAGTAAGC
128 AATATAACTAAGTTGTAATTAAGTAAGC
** *
11054 TATTAAATAATCTAAAATTGTATATTTTAATATTTAAATTAAATATTTTGTAAGTTTAATTAAAT
1 TATTAAATAATCTAAAATTAAATATTTTAATATTTAAATTAAATATTTTGTAAGTTTAATTAAAA
* * *
11119 TTTTTTATTATTAATATATATATTTTAATTAGTATTAAAAAATTAATTTAAATTTAAATTTAAAT
66 TTTTTTATTATTAATATATATATTTTAATTAATATTAAAAAATTAATTTAAATTCAAATTAAAAT
11184 ATAACTAA
131 ATAACTAA
11192 ATTTAAAATT
Statistics
Matches: 128, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
155 30 0.23
156 94 0.73
157 4 0.03
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (155 bp):
TATTAAATAATCTAAAATTAAATATTTTAATATTTAAATTAAATATTTTGTAAGTTTAATTAAAA
TTTTTTATTATTAATATATATATTTTAATTAATATTAAAAAATTAATTTAAATTCAAATTAAAAT
ATAACTAAGTTGTAATTAAGTAAGC
Found at i:11399 original size:17 final size:17
Alignment explanation
Indices: 11377--11410 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11367 AATTTAAAAA
11377 TATTTAAATTTAAATTT
1 TATTTAAATTTAAATTT
*
11394 TATTTAAGTTTAAATTT
1 TATTTAAATTTAAATTT
11411 GGTTCAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TATTTAAATTTAAATTT
Found at i:11514 original size:24 final size:23
Alignment explanation
Indices: 11487--11552 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
11477 ATTAAAAATT
*
11487 TAAATATTTATAATTAAATTGAAA
1 TAAAAATTTATAATTAAATT-AAA
*
11511 TAAAAATTTATTTTATTAAA-TAAA
1 TAAAAATTTA--TAATTAAATTAAA
11535 TAAAAATTTA-AATTAAAT
1 TAAAAATTTATAATTAAAT
11553 AAAGCAGCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.17
24 22 0.61
25 1 0.03
26 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAAAATTTATAATTAAATTAAA
Found at i:14214 original size:21 final size:21
Alignment explanation
Indices: 14192--14251 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
14182 ATAAATAAAA
14192 TTAAAAAATTAATTTAATTAAT
1 TTAAAAAATT-ATTTAATTAAT
*
14214 TTAAATAAATTA-TTAAATAAT
1 TTAAA-AAATTATTTAATTAAT
*
14235 TTAAAAATTTTATTTAA
1 TTAAAAA-ATTATTTAA
14252 ATTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 10 0.30
23 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAAAAATTATTTAATTAAT
Found at i:14237 original size:30 final size:30
Alignment explanation
Indices: 14213--14270 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
14203 ATTTAATTAA
14213 TTTAAATAAATTATTAAATAATTTAAAAAT
1 TTTAAATAAATTATTAAATAATTTAAAAAT
**
14243 TTTATTTAAATTATTAAAT-ATTATAAAA
1 TTTAAATAAATTATTAAATAATT-TAAAA
14271 GTATATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TTTAAATAAATTATTAAATAATTTAAAAAT
Found at i:14525 original size:14 final size:15
Alignment explanation
Indices: 14506--14537 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
14496 GTTAAATATA
14506 TTTAATATTTA-AAT
1 TTTAATATTTATAAT
14520 TTTAATATTTATAAT
1 TTTAATATTTATAAT
14535 TTT
1 TTT
14538 TTATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATATTTATAAT
Found at i:15690 original size:11 final size:11
Alignment explanation
Indices: 15674--15710 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15664 AAAATTTTTA
15674 TATTTAAGTCT
1 TATTTAAGTCT
*
15685 TATTT-A-TTT
1 TATTTAAGTCT
15694 TATTTAAGTCT
1 TATTTAAGTCT
15705 TATTTA
1 TATTTA
15711 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 7 0.32
10 2 0.09
11 13 0.59
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (11 bp):
TATTTAAGTCT
Found at i:15699 original size:20 final size:20
Alignment explanation
Indices: 15674--15718 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
15664 AAAATTTTTA
15674 TATTTAAGTCTTATTTATTT
1 TATTTAAGTCTTATTTATTT
15694 TATTTAAGTCTTATTTATTT
1 TATTTAAGTCTTATTTATTT
15714 TATTT
1 TATTT
15719 TTTAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (20 bp):
TATTTAAGTCTTATTTATTT
Found at i:15752 original size:14 final size:14
Alignment explanation
Indices: 15735--15785 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
15725 ATTATATATT
15735 TATATAAATTTTAA
1 TATATAAATTTTAA
*
15749 TATATTAATAATTTATAT
1 TATA-T-A-AATTT-TAA
15767 TATATAAATTTTAA
1 TATATAAATTTTAA
15781 TATAT
1 TATAT
15786 TTATAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 11 0.35
15 6 0.19
16 2 0.06
17 6 0.19
18 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:15759 original size:18 final size:19
Alignment explanation
Indices: 15728--15809 Score: 81
Period size: 19 Copynumber: 4.6 Consensus size: 19
15718 TTTTAATATT
15728 ATATATTTATATAAATTTTA
1 ATATA-TTATATAAATTTTA
15748 ATATATTA-AT-AA--TT-
1 ATATATTATATAAATTTTA
15762 -TATATTATATAAATTTTA
1 ATATATTATATAAATTTTA
15780 ATATATT-TATAAATTATTA
1 ATATATTATATAAATT-TTA
*
15799 TTATATT-TATA
1 ATATATTATATA
15810 TTATTTTTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
13 7 0.13
14 2 0.04
15 4 0.07
17 4 0.07
18 10 0.19
19 22 0.41
20 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATTATATAAATTTTA
Found at i:15779 original size:16 final size:16
Alignment explanation
Indices: 15729--15861 Score: 63
Period size: 18 Copynumber: 7.6 Consensus size: 16
15719 TTTAATATTA
15729 TATATTTATATAAATTT
1 TATA-TTATATAAATTT
*
15746 TA-A-TATATTAATAATT
1 TATATTATA-TAA-ATTT
15762 TATATTATATAAATTT
1 TATATTATATAAATTT
*
15778 TAATATATTTATAAATTATTAT
1 T-ATAT-TATAT-AA--ATT-T
**
15800 TATATTTATATTATTTTT
1 TATA-TTATA-TAAATTT
* * *
15818 TATTTTATATTATTTT
1 TATATTATATAAATTT
*
15834 TATATTATATTATATTTT
1 TATATTATA-TA-AATTT
15852 TATATTATAT
1 TATATTATAT
15862 TCACGCTATT
Statistics
Matches: 91, Mismatches: 11, Indels: 28
0.70 0.08 0.22
Matches are distributed among these distances:
14 4 0.04
15 3 0.03
16 23 0.25
17 17 0.19
18 26 0.29
19 4 0.04
21 10 0.11
22 4 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATTATATAAATTT
Found at i:15811 original size:11 final size:11
Alignment explanation
Indices: 15749--15862 Score: 61
Period size: 11 Copynumber: 11.0 Consensus size: 11
15739 TAAATTTTAA
15749 TATATTAATAATT
1 TATATT-AT-ATT
*
15762 TATATTATATA
1 TATATTATATT
* * *
15773 AATTTTA-ATA
1 TATATTATATT
*
15783 TAT-TTATAAAT
1 TATATTAT-ATT
15794 TATTATTATATT
1 TA-TATTATATT
15806 TATA-T-TATT
1 TATATTATATT
15815 T-T-TTAT-TT
1 TATATTATATT
*
15823 TATATTATTTT
1 TATATTATATT
15834 TATATTATA-T
1 TATATTATATT
15844 TATA-T-T-TT
1 TATATTATATT
15852 TATATTATATT
1 TATATTATATT
15863 CACGCTATTT
Statistics
Matches: 80, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
8 11 0.14
9 12 0.15
10 16 0.20
11 24 0.30
12 7 0.09
13 10 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTATATT
Found at i:15814 original size:17 final size:16
Alignment explanation
Indices: 15704--15862 Score: 78
Period size: 17 Copynumber: 9.4 Consensus size: 16
15694 TATTTAAGTC
15704 TTAT-TTATTTTAT-T
1 TTATATTATTTTATAT
* * *
15718 TTTTAATATTATATAT
1 TTATATTATTTTATAT
*
15734 TTATATAAATTTTAATAT
1 TTATAT-TATTTT-ATAT
*
15752 ATTA-A-TAATTTATAT
1 -TTATATTATTTTATAT
*
15767 TATATAAATT-TTAATATAT
1 T-TAT--ATTATT-TTATAT
15786 TTATAAATTATTATTATAT
1 TTAT--ATTATT-TTATAT
*
15805 TTATATTATTTTTTATT
1 TTATATTATTTTATA-T
15822 TTATATTATTTT-TAT
1 TTATATTATTTTATAT
*
15837 ATTATATTATATTTTTAT
1 -TTATATTAT-TTTATAT
15855 ATTATATT
1 -TTATATT
15863 CACGCTATTT
Statistics
Matches: 116, Mismatches: 13, Indels: 28
0.74 0.08 0.18
Matches are distributed among these distances:
14 4 0.03
15 14 0.12
16 24 0.21
17 26 0.22
18 26 0.22
19 22 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATATTATTTTATAT
Found at i:15815 original size:28 final size:29
Alignment explanation
Indices: 15783--15862 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
15773 AATTTTAATA
15783 TATTTATAAATTAT-TATTATATTTATAT
1 TATTTATAAATTATATATTATATTTATAT
** * *
15811 TATTT-TTTATTTTATATTATTTTTATAT
1 TATTTATAAATTATATATTATATTTATAT
* *
15839 TATATTAT-ATTTTTATATTATATT
1 TAT-TTATAAATTATATATTATATT
15863 CACGCTATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
27 5 0.12
28 21 0.50
29 15 0.36
30 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (29 bp):
TATTTATAAATTATATATTATATTTATAT
Found at i:15834 original size:18 final size:16
Alignment explanation
Indices: 15760--15862 Score: 89
Period size: 18 Copynumber: 5.8 Consensus size: 16
15750 ATATTAATAA
*
15760 TTTATATTATATAAATT
1 TTTATATTATAT-TATT
15777 TTAATATATTTATAAATTATT
1 TT--TATA-TTAT--ATTATT
*
15798 ATTATATTTATATTATTT
1 TTTATA-TTATATTA-TT
*
15816 TTTATTTTATATTATT
1 TTTATATTATATTATT
15832 TTTATATTATATTATATT
1 TTTATATTATA-T-TATT
15850 TTTATATTATATT
1 TTTATATTATATT
15863 CACGCTATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
16 13 0.18
17 16 0.22
18 21 0.29
19 13 0.18
20 4 0.05
21 4 0.05
22 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATATTATATTATT
Found at i:15837 original size:34 final size:34
Alignment explanation
Indices: 15761--15862 Score: 109
Period size: 34 Copynumber: 2.9 Consensus size: 34
15751 TATTAATAAT
*
15761 TTATATTATA-TAAATTTTAATATATTTATAAATTATTA
1 TTATATTATATTATATTTT--TAT-TTTAT--ATTATTA
*
15799 TTATATTTATATTAT-TTTTTATTTTATATTATTT
1 TTATA-TTATATTATATTTTTATTTTATATTATTA
*
15833 TTATATTATATTATATTTTTATATTATATT
1 TTATATTATATTATATTTTTATTTTATATT
15863 CACGCTATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
33 9 0.16
34 25 0.43
36 5 0.09
37 3 0.05
38 5 0.09
39 9 0.16
40 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (34 bp):
TTATATTATATTATATTTTTATTTTATATTATTA
Found at i:16132 original size:16 final size:15
Alignment explanation
Indices: 16109--16255 Score: 66
Period size: 16 Copynumber: 8.9 Consensus size: 15
16099 AATATTGGAC
*
16109 ATATATAATTATAAA
1 ATATATAAATATAAA
16124 ATATAATAAATATAATATA
1 ATAT-ATAAATAT-A-A-A
16143 AGTATATAAATATTTTAAA
1 A-TATATAAATA---TAAA
*
16162 ATTTATATAATATAAA
1 ATATATA-AATATAAA
*
16178 TTAT-TAATATATTAAA
1 ATATATAA-ATA-TAAA
*
16194 TTTTATATAAATATAAA
1 --ATATATAAATATAAA
* *
16211 ATATTTTAAAT-TATA
1 ATA-TATAAATATAAA
*
16226 AT-TATAATATAATTAA
1 ATATATAA-AT-ATAAA
16242 ATATATAAATATAA
1 ATATATAAATATAA
16256 TAAAATAAAT
Statistics
Matches: 102, Mismatches: 11, Indels: 38
0.68 0.07 0.25
Matches are distributed among these distances:
13 4 0.04
14 3 0.03
15 19 0.19
16 29 0.28
17 10 0.10
18 13 0.13
19 18 0.18
20 4 0.04
21 1 0.01
22 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.44
Consensus pattern (15 bp):
ATATATAAATATAAA
Found at i:16148 original size:11 final size:9
Alignment explanation
Indices: 16122--16269 Score: 56
Period size: 9 Copynumber: 15.4 Consensus size: 9
16112 TATAATTATA
16122 AAATATAAT
1 AAATATAAT
16131 AAATATAAT
1 AAATATAAT
16140 ATAAGTAT-AT
1 A-AA-TATAAT
**
16150 AAATATTTT
1 AAATATAAT
*
16159 AAA-ATTTAT
1 AAATA-TAAT
16168 ATAATATAAATT
1 A-AATAT-AA-T
*
16180 ATTAATATATT
1 A--AATATAAT
*
16191 AAATTTTATAT
1 AAA-TATA-AT
16202 AAATAT-A-
1 AAATATAAT
**
16209 AAATATTTT
1 AAATATAAT
16218 AAATTATAATT
1 AAA-TATAA-T
16229 ATAATATAATT
1 A-AATATAA-T
16240 AAATAT-AT
1 AAATATAAT
16248 AAATATAAT
1 AAATATAAT
16257 AAA-ATAAAT
1 AAATAT-AAT
16266 AAAT
1 AAAT
16270 TATTAGATCT
Statistics
Matches: 110, Mismatches: 10, Indels: 37
0.70 0.06 0.24
Matches are distributed among these distances:
7 6 0.05
8 14 0.13
9 37 0.34
10 21 0.19
11 21 0.19
12 5 0.05
13 6 0.05
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
AAATATAAT
Found at i:16175 original size:33 final size:32
Alignment explanation
Indices: 16133--16261 Score: 109
Period size: 32 Copynumber: 3.9 Consensus size: 32
16123 AATATAATAA
* *
16133 ATATAATATAAGTATATAAATATTTTAAAATTT
1 ATATAATATAAAT-TATAAATATATTAAAATTT
* *
16166 ATATAATATAAATTATTAATATATTAAATTTT
1 ATATAATATAAATTATAAATATATTAAAATTT
* ** * *
16198 ATATAAATATAAAATAT-TTTAAATTATAATTAT
1 ATAT-AATATAAATTATAAATATATTAAAATT-T
*
16231 AATATAAT-TAAATATATAAATATAATAAAAT
1 -ATATAATATAAAT-TATAAATATATTAAAAT
16262 AAATAAATTA
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
32 33 0.44
33 30 0.40
34 12 0.16
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
ATATAATATAAATTATAAATATATTAAAATTT
Found at i:16187 original size:18 final size:17
Alignment explanation
Indices: 16166--16261 Score: 69
Period size: 16 Copynumber: 5.7 Consensus size: 17
16156 TTTAAAATTT
16166 ATATAATATAAATTATTA
1 ATATAAT-TAAATTATTA
16184 ATAT-ATTAAATT-TT-
1 ATATAATTAAATTATTA
*
16198 ATATAAATATAAAATATT-
1 ATAT-AAT-TAAATTATTA
*
16216 TTA-AATTATAATTA-TA
1 ATATAATTA-AATTATTA
*
16232 ATATAATTAAATATATAA
1 ATATAATTAAAT-TATTA
*
16250 ATATAATAAAAT
1 ATATAATTAAAT
16262 AAATAAATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 4 0.06
15 5 0.08
16 20 0.32
17 14 0.22
18 20 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTAAATTATTA
Found at i:16201 original size:27 final size:27
Alignment explanation
Indices: 16110--16222 Score: 91
Period size: 27 Copynumber: 4.0 Consensus size: 27
16100 ATATTGGACA
* * *
16110 TATATAATTATAAAATATAATAAATAT
1 TATATAAATATAAAATATATTAAATTT
* * * *
16137 AATATAAGTATATAAATATTTTAAAATT
1 TATATAAATATA-AAATATATTAAATTT
*
16165 TATATAATATAAATTATTAATATATTAAATTT
1 TATATAA-AT--A-TA-AAATATATTAAATTT
*
16197 TATATAAATATAAAATATTTTAAATT
1 TATATAAATATAAAATATATTAAATT
16223 ATAATTATAA
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
27 22 0.32
28 19 0.28
29 2 0.03
31 3 0.04
32 22 0.32
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (27 bp):
TATATAAATATAAAATATATTAAATTT
Found at i:16202 original size:60 final size:59
Alignment explanation
Indices: 16109--16262 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 59
16099 AATATTGGAC
*
16109 ATATATAATTATAAAATATAATAAATATAATATAAGTATATAAATATTTTAAAATT-T-A-TATA
1 ATATA-AATTAT--AATAT-ATAAATATAATATAAATATA-AAATATTTT-AAATTATAATTATA
* *
16171 ATATAAATTATTAATATATTAAATTTTATATAAATATAAAATATTTTAAATTATAATTATA
1 ATATAAATTA-TAATATA-TAAATATAATATAAATATAAAATATTTTAAATTATAATTATA
16232 ATAT-AATTA-AATATATAAATATAATA-AAATA
1 ATATAAATTATAATATATAAATATAATATAAATA
16263 AATAAATTAT
Statistics
Matches: 82, Mismatches: 5, Indels: 16
0.80 0.05 0.16
Matches are distributed among these distances:
56 5 0.06
57 9 0.11
58 11 0.13
59 11 0.13
60 27 0.33
61 13 0.16
62 6 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (59 bp):
ATATAAATTATAATATATAAATATAATATAAATATAAAATATTTTAAATTATAATTATA
Found at i:16231 original size:23 final size:23
Alignment explanation
Indices: 16197--16255 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
16187 TATTAAATTT
*
16197 TATATAAATATAAAATATTTTAAA
1 TATATAAATATAAAATA-ATTAAA
* *
16221 T-TATAATTATAATATAATTAAA
1 TATATAAATATAAAATAATTAAA
16243 TATATAAATATAA
1 TATATAAATATAA
16256 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 6 0.20
23 23 0.77
24 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TATATAAATATAAAATAATTAAA
Found at i:16719 original size:30 final size:29
Alignment explanation
Indices: 16651--16719 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
16641 TTTAATAAAT
***
16651 TTAATTAAAGTTAAATTTTTATAAAATTT
1 TTAATTAAAGTTAAATTTTTATAAAAAAA
*
16680 TTATTTTAAA-TTAAGATTTTTATATAAAAAA
1 TTA-ATTAAAGTTAA-ATTTTTATA-AAAAAA
16711 TTAATTAAA
1 TTAATTAAA
16720 ATATATATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
29 7 0.22
30 19 0.59
31 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
TTAATTAAAGTTAAATTTTTATAAAAAAA
Found at i:16891 original size:22 final size:20
Alignment explanation
Indices: 16834--16891 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 20
16824 AGTATCTATT
16834 TTAATAACTTA-TATTATTTA
1 TTAATAA-TTATTATTATTTA
*
16854 TT-AT-ATTATTTTTTATTTA
1 TTAATAATTA-TTATTATTTA
16873 TTAATAATTTATTGATTAT
1 TTAATAA-TTATT-ATTAT
16892 AAAATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
17 3 0.10
18 1 0.03
19 12 0.40
20 4 0.13
21 3 0.10
22 7 0.23
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTAATAATTATTATTATTTA
Found at i:17774 original size:2 final size:2
Alignment explanation
Indices: 17767--17799 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17757 ACTAAACTCT
17767 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
17800 TTAACGAAGT
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:18112 original size:25 final size:27
Alignment explanation
Indices: 18083--18149 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
18073 TTAAAATTTT
18083 ATTAA-TATTAAAATT-TTAATTCTAA
1 ATTAAGTATTAAAATTATTAATTCTAA
* *
18108 TTTAAGTA-T-AAATTATTAATTTTAA
1 ATTAAGTATTAAAATTATTAATTCTAA
*
18133 ATTAAGTATAAAAATTA
1 ATTAAGTATTAAAATTA
18150 AAATTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 5 0.15
25 21 0.62
26 2 0.06
27 6 0.18
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (27 bp):
ATTAAGTATTAAAATTATTAATTCTAA
Found at i:18161 original size:25 final size:24
Alignment explanation
Indices: 18073--18162 Score: 69
Period size: 25 Copynumber: 3.7 Consensus size: 24
18063 ATTAATTTTT
18073 TTAAAATTTT-ATTAA-TATTAAAA
1 TTAAAATTTTAATTAAGTA-TAAAA
** *
18096 TTTTAATTCTAATTTAAGTAT-AAA
1 TTAAAATTTTAA-TTAAGTATAAAA
*
18120 TTATTAATTTTAAATTAAGTATAAAAA
1 TTA-AAATTTT-AATTAAGTAT-AAAA
*
18147 TTAAAATTTTTATTAA
1 TTAAAATTTTAATTAA
18163 TTTAAGTGAT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
23 7 0.13
24 6 0.11
25 24 0.45
26 10 0.19
27 6 0.11
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (24 bp):
TTAAAATTTTAATTAAGTATAAAA
Found at i:24241 original size:1 final size:1
Alignment explanation
Indices: 24235--24259 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
24225 TAGTTCATCT
24235 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
24260 AAACACCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:26120 original size:2 final size:2
Alignment explanation
Indices: 26109--26145 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
26099 TTAATACAAT
26109 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26146 AAATAAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:26273 original size:2 final size:2
Alignment explanation
Indices: 26266--26294 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26256 ACAAAGAATT
26266 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 T
26295 TTGAGAGCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27105 original size:2 final size:2
Alignment explanation
Indices: 27098--27129 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27088 ATGTTAAAAC
27098 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27130 AACTCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27394 original size:22 final size:22
Alignment explanation
Indices: 27369--27438 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 22
27359 TATAATTTAT
*
27369 ATATTTATATATTATCAATAAA
1 ATATTTATATATTATAAATAAA
*
27391 ATA-TT-T-TATTAAAAATAAA
1 ATATTTATATATTATAAATAAA
***
27410 ATTATTTATAT-TTATTTTTAAA
1 A-TATTTATATATTATAAATAAA
27432 ATATTTA
1 ATATTTA
27439 ATAAAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 12 0.32
20 3 0.08
21 10 0.26
22 12 0.32
23 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTATATATTATAAATAAA
Found at i:27487 original size:20 final size:21
Alignment explanation
Indices: 27464--27522 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
27454 TTAATTTATT
27464 TATTATTTATAACA-TAAATA
1 TATTATTTATAACATTAAATA
*
27484 TATTATTAAT-ACATTAAATA
1 TATTATTTATAACATTAAATA
*
27504 TACATTATTTATAAAATTA
1 T--ATTATTTATAACATTA
27523 TTAGTACTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 3 0.09
20 16 0.50
22 8 0.25
23 5 0.16
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTATTTATAACATTAAATA
Found at i:27801 original size:5 final size:5
Alignment explanation
Indices: 27791--27825 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
27781 AATTAATGCC
27791 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
27826 TTATAGTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:28764 original size:17 final size:18
Alignment explanation
Indices: 28731--28764 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28721 AAAAAAATAA
28731 AAATAAAAAATTTGATTT
1 AAATAAAAAATTTGATTT
*
28749 AAATATAAAA-TTGATT
1 AAATAAAAAATTTGATT
28765 ATACGTATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
AAATAAAAAATTTGATTT
Found at i:29914 original size:9 final size:9
Alignment explanation
Indices: 29900--29930 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
29890 ATGAATAAAT
29900 AAAAAAAAG
1 AAAAAAAAG
29909 AAAAAAAAG
1 AAAAAAAAG
29918 AAAAAAAAAG
1 -AAAAAAAAG
29928 AAA
1 AAA
29931 GAGTGGAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:29915 original size:10 final size:10
Alignment explanation
Indices: 29900--29930 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
29890 ATGAATAAAT
29900 AAAAAAAAG-
1 AAAAAAAAGA
29909 AAAAAAAAGA
1 AAAAAAAAGA
29919 AAAAAAAAGA
1 AAAAAAAAGA
29929 AA
1 AA
29931 GAGTGGAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:30596 original size:2 final size:2
Alignment explanation
Indices: 30589--30613 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30579 TTTATTACCA
30589 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
30614 GAAAACTTAA
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:31583 original size:22 final size:20
Alignment explanation
Indices: 31555--31608 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
31545 AAAATTCAAA
31555 TATAAATATAAAAATATAATTT
1 TATAAATATAAAAA-AT-ATTT
*
31577 TTTAAATATATAAAAATATTT
1 TATAAATATA-AAAAATATTT
*
31598 TATAAAAATAA
1 TATAAATATAA
31609 TTATATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 12 0.43
22 11 0.39
23 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATAAATATAAAAAATATTT
Found at i:31644 original size:23 final size:23
Alignment explanation
Indices: 31578--31650 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
31568 ATATAATTTT
* *
31578 TTAAATATATAAAAATATTTTATA
1 TTAAATATATATATA-ATTTTATA
*
31602 -AAAATA-AT-TAT-A-TTTATA
1 TTAAATATATATATAATTTTATA
31620 TTAAATATATATATAATTTTATA
1 TTAAATATATATATAATTTTATA
*
31643 TTTAATAT
1 TTAAATAT
31651 TCACTTACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
18 6 0.15
19 6 0.15
20 2 0.05
21 4 0.10
22 3 0.08
23 18 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAATATATATATAATTTTATA
Found at i:31864 original size:18 final size:17
Alignment explanation
Indices: 31815--31880 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
31805 AATTCAATTT
31815 TATTT-AATTTTTAAAAA
1 TATTTAAATTTTT-AAAA
** **
31832 TATTTTTATAATTAATAA
1 TATTTAAATTTTTAA-AA
31850 TATTTAAATTTTT-AAA
1 TATTTAAATTTTTAAAA
31866 TATTTAAAATTTTTA
1 TATTT-AAATTTTTA
31881 TGAATTAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 7 0.18
17 16 0.42
18 15 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTAAATTTTTAAAA
Found at i:31867 original size:16 final size:17
Alignment explanation
Indices: 31848--31880 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31838 TATAATTAAT
31848 AATATTT-AAATTTTTA
1 AATATTTAAAATTTTTA
31864 AATATTTAAAATTTTTA
1 AATATTTAAAATTTTTA
31881 TGAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATTTAAAATTTTTA
Found at i:32369 original size:14 final size:15
Alignment explanation
Indices: 32350--32382 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
32340 ATTTAAAAAT
32350 TATTTTTAT-ATTAA
1 TATTTTTATAATTAA
32364 TATTTTTATAATTAA
1 TATTTTTATAATTAA
32379 -ATTT
1 TATTT
32383 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTTTATAATTAA
Found at i:32866 original size:12 final size:12
Alignment explanation
Indices: 32851--32893 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
32841 AATTAAATTT
*
32851 AAATTTAAACTC
1 AAATTTAAACTA
*
32863 AAATTT-AACTT
1 AAATTTAAACTA
*
32874 ATATTTAAACTA
1 AAATTTAAACTA
32886 AAATTTAA
1 AAATTTAA
32894 GTTCAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTTAAACTA
Found at i:33041 original size:22 final size:21
Alignment explanation
Indices: 33014--33073 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
33004 TTGCTTATAT
33014 TTTTTATTTTTATTTTTAAAAA
1 TTTTTATTTTT-TTTTTAAAAA
* * *
33036 TTTTTAATTTTTTTTCAAAAT
1 TTTTTATTTTTTTTTTAAAAA
*
33057 TTTCTTCTTTTTTTTTT
1 TTT-TTATTTTTTTTTT
33074 TGTGATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTATTTTTTTTTTAAAAA
Found at i:34028 original size:21 final size:22
Alignment explanation
Indices: 34002--34045 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
33992 AATAATTTTT
34002 AAAATAAAATATAAATAT-TAA
1 AAAATAAAATATAAATATATAA
*
34023 AAAATATAATATAAATATATAA
1 AAAATAAAATATAAATATATAA
34045 A
1 A
34046 TTTAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAATAAAATATAAATATATAA
Found at i:34360 original size:19 final size:20
Alignment explanation
Indices: 34338--34379 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
34328 TAATTTTTAC
*
34338 TAATGATTTA-TCAATATAA
1 TAATGATTTATTCAATAAAA
**
34357 TAATTTTTTATTCAATAAAA
1 TAATGATTTATTCAATAAAA
34377 TAA
1 TAA
34380 AAAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
TAATGATTTATTCAATAAAA
Found at i:34504 original size:28 final size:29
Alignment explanation
Indices: 34473--34538 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
34463 ATCACATCAT
* *
34473 AAAAATAATTAAAATATAATATAACAT-G
1 AAAAATAATTAAAATATAATATAAAATAA
*
34501 AAAAATAACTAAAATATAATATAAAATAA
1 AAAAATAATTAAAATATAATATAAAATAA
34530 AAAAATAAT
1 AAAAATAAT
34539 ATGACCACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 25 0.76
29 8 0.24
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.26
Consensus pattern (29 bp):
AAAAATAATTAAAATATAATATAAAATAA
Found at i:35529 original size:13 final size:13
Alignment explanation
Indices: 35513--35537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35503 ATACACTAAA
35513 TAAAAATAAAAAT
1 TAAAAATAAAAAT
35526 TAAAAATAAAAA
1 TAAAAATAAAAA
35538 AATAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAATAAAAAT
Found at i:35544 original size:13 final size:13
Alignment explanation
Indices: 35510--35545 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
35500 TAAATACACT
35510 AAATAAAAATAAA
1 AAATAAAAATAAA
*
35523 AATTAAAAATAAAA
1 AAATAAAAAT-AAA
35537 AAATAAAAA
1 AAATAAAAA
35546 AATTAAGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:39262 original size:26 final size:24
Alignment explanation
Indices: 39215--39287 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
39205 TTATTATATT
* *
39215 TATATTTAA-TAATTAATATAAAAA
1 TATATATAATTAATTAA-ATATAAA
*
39239 TATATATAATTAATTAAATTTAAA
1 TATATATAATTAATTAAATATAAA
39263 TATA-AT-ATTAATTAAATAATAAA
1 TATATATAATTAATTAAAT-ATAAA
39286 TA
1 TA
39288 CACCAAACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
22 11 0.26
23 8 0.19
24 17 0.40
25 7 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATATAATTAATTAAATATAAA
Found at i:39272 original size:22 final size:24
Alignment explanation
Indices: 39236--39279 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
39226 ATTAATATAA
39236 AAATATATATAATTAATTAAATTT
1 AAATATATATAATTAATTAAATTT
39260 AAATATA-AT-ATTAATTAAAT
1 AAATATATATAATTAATTAAAT
39280 AATAAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
23 2 0.10
24 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATATATATAATTAATTAAATTT
Found at i:40335 original size:22 final size:22
Alignment explanation
Indices: 40303--40412 Score: 105
Period size: 24 Copynumber: 4.6 Consensus size: 22
40293 TTGCTATTTT
*
40303 TAAATATAATATTTAATATGATA
1 TAAATA-AATATTAAATATGATA
*
40326 TAACTAAATATTAAATATGATA
1 TAAATAAATATTAAATATGATA
40348 TAAATAAAATAATTAAAATATGATA
1 TAAAT-AAAT-ATT-AAATATGATA
*
40373 TAAATATATATTTTAAA-ATTGATA
1 TAAATA-A-ATATTAAATA-TGATA
40397 TAATATAAATTATTAA
1 TAA-ATAAA-TATTAA
40413 TGTATTAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
22 19 0.26
23 11 0.15
24 21 0.28
25 21 0.28
26 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (22 bp):
TAAATAAATATTAAATATGATA
Found at i:40412 original size:24 final size:24
Alignment explanation
Indices: 40317--40412 Score: 110
Period size: 25 Copynumber: 4.0 Consensus size: 24
40307 TATAATATTT
*
40317 AATATGATATAACTAAA-TATT-A
1 AATATGATATAAATAAATTATTAA
*
40339 AATATGATATAAATAAAATAATTAA
1 AATATGATATAAAT-AAATTATTAA
40364 AATATGATATAAATATATATT-TTAA
1 AATATGATATAAATA-A-ATTATTAA
40389 AAT-TGATATAATATAAATTATTAA
1 AATATGATATAA-ATAAATTATTAA
40413 TGTATTAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
22 13 0.20
23 6 0.09
24 17 0.27
25 26 0.41
26 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (24 bp):
AATATGATATAAATAAATTATTAA
Found at i:40439 original size:16 final size:15
Alignment explanation
Indices: 40388--40463 Score: 57
Period size: 16 Copynumber: 4.8 Consensus size: 15
40378 ATATATTTTA
40388 AAATTGATAT-AATAT
1 AAATT-ATATAAATAT
*
40403 AAATTAT-TAATGTATT
1 AAATTATATAA-ATA-T
40419 AAAATTGATATAAATAT
1 -AAATT-ATATAAATAT
*
40436 AAATTATTTTAAATAT
1 AAATTA-TATAAATAT
*
40452 AAATAATATAAA
1 AAATTATATAAA
40464 ATATTATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
13 1 0.02
14 3 0.06
15 13 0.27
16 19 0.39
17 6 0.12
18 4 0.08
19 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (15 bp):
AAATTATATAAATAT
Found at i:40469 original size:58 final size:57
Alignment explanation
Indices: 40359--40469 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 57
40349 AAATAAAATA
* *
40359 ATTAAAATATGATATAAATATATATTTTAAAATTGATATAATATAAATTATTAATGT
1 ATTAAAATATGATATAAATATATATTTTAAAATTGAAATAATATAAAATATTAATGT
40416 ATTAAAAT-TGATATAAATATAAATTATTTT-AAATAT-AAATAATATAAAATATTA
1 ATTAAAATATGATATAAATAT--A-TATTTTAAAAT-TGAAATAATATAAAATATTA
40470 TTTTATTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
56 12 0.25
57 8 0.17
58 21 0.44
59 7 0.15
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (57 bp):
ATTAAAATATGATATAAATATATATTTTAAAATTGAAATAATATAAAATATTAATGT
Found at i:40704 original size:21 final size:21
Alignment explanation
Indices: 40680--40719 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40670 TATTCTCATC
**
40680 ATTATAATTTTTAATTTTAAT
1 ATTATAATAATTAATTTTAAT
40701 ATTATAATAATTAATTTTA
1 ATTATAATAATTAATTTTA
40720 TAACTATCAT
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:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATAATAATTAATTTTAAT
Found at i:41145 original size:21 final size:21
Alignment explanation
Indices: 41111--41170 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
41101 AAATTAAATT
41111 TATTATCAAT-TTTAATTTTAGA
1 TATTAT-AATATTTAATTTTA-A
*
41133 -ATTATAATATTTAATTATAA
1 TATTATAATATTTAATTTTAA
*
41153 TATTATAATAATTAATTT
1 TATTATAATATTTAATTT
41171 CATCATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTATAATATTTAATTTTAA
Found at i:41150 original size:13 final size:14
Alignment explanation
Indices: 41111--41161 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
41101 AAATTAAATT
*
41111 TATTATCAATTTTAA
1 TATTAT-AATTATAA
* *
41126 TTTTAGAATTATAA
1 TATTATAATTATAA
41140 TATT-TAATTATAA
1 TATTATAATTATAA
41153 TATTATAAT
1 TATTATAAT
41162 AATTAATTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 12 0.40
14 14 0.47
15 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (14 bp):
TATTATAATTATAA
Found at i:42220 original size:6 final size:6
Alignment explanation
Indices: 42211--42252 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
42201 GAATCATCAA
* *
42211 CATCGT CATCGT CATCTT CATCTT CAT-GTT CATCGT CATCGT
1 CATCGT CATCGT CATCGT CATCGT CATCG-T CATCGT CATCGT
42253 AGAGTGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 31 0.97
7 1 0.03
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40
Consensus pattern (6 bp):
CATCGT
Found at i:45969 original size:31 final size:32
Alignment explanation
Indices: 45928--45989 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
45918 GACATAAAAA
*
45928 TATATCTTAAAATTTATAT-AATATAAATTAT
1 TATATATTAAAATTTATATAAATATAAATTAT
45959 TATATATTAAAATTTATATAAATATAAATTA
1 TATATATTAAAATTTATATAAATATAAATTA
45990 CTTTAAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (32 bp):
TATATATTAAAATTTATATAAATATAAATTAT
Found at i:46029 original size:18 final size:19
Alignment explanation
Indices: 46006--46045 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
45996 ATACTATTAT
*
46006 AATATAATA-AAATATATA
1 AATATAATATAAATACATA
46024 AATATAATATAAATACATA
1 AATATAATATAAATACATA
46043 AAT
1 AAT
46046 TACTAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AATATAATATAAATACATA
Found at i:46584 original size:122 final size:122
Alignment explanation
Indices: 46443--46667 Score: 310
Period size: 122 Copynumber: 1.8 Consensus size: 122
46433 TTAGTGGAGC
* * * *
46443 TATATGTATAAATTTAACAAGTAGACTACTAG-TTACCAATTTAAAGTGGAATTAGT-TGAACTA
1 TATATGCATAAATTTAACAAGTAAACTACT-GTTTACAAATTTAAAGTGAAATTAGTGT-AACTA
* *
46506 CTTAATAAAATTCATAAATTAAACTACTAATCACCAATTTCAACCCTTATCAGTGTAAA
64 CGTAATAAAATTCATAAATTAAACTACTAACCACCAATTTCAACCCTTATCAGTGTAAA
* *
46565 TATATGCATAAATTTAACAATTAAACTACTGTTTATAAATTTAAAGTGAAATTAGTGTAACTACG
1 TATATGCATAAATTTAACAAGTAAACTACTGTTTACAAATTTAAAGTGAAATTAGTGTAACTACG
* * * *
46630 TAATAAAATTCATCAATTAGATTATTAACCACCAATTT
66 TAATAAAATTCATAAATTAAACTACTAACCACCAATTT
46668 GACTTAAAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
121 1 0.01
122 87 0.98
123 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (122 bp):
TATATGCATAAATTTAACAAGTAAACTACTGTTTACAAATTTAAAGTGAAATTAGTGTAACTACG
TAATAAAATTCATAAATTAAACTACTAACCACCAATTTCAACCCTTATCAGTGTAAA
Found at i:46789 original size:69 final size:68
Alignment explanation
Indices: 46690--46819 Score: 161
Period size: 69 Copynumber: 1.9 Consensus size: 68
46680 GTGTAAATAC
* ** * * *
46690 ATATACAAATCATCGATTAAACTACCAATCATTAATTTAAAGTAGAATTAGTGTAACTATATATA
1 ATATACAAATCATCAATTAAACTACCAATCACCAATTTAAAATAAAATAAGTGTAACTATATATA
46755 TAT
66 TAT
** * *
46758 ATATACAAATTCATCAATTAGGCTACTAATCACCAATTTAAAATAAAATAAGTGTAATTATA
1 ATATACAAA-TCATCAATTAAACTACCAATCACCAATTTAAAATAAAATAAGTGTAACTATA
46820 AAATTCATCA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
68 9 0.18
69 42 0.82
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (68 bp):
ATATACAAATCATCAATTAAACTACCAATCACCAATTTAAAATAAAATAAGTGTAACTATATATA
TAT
Found at i:48755 original size:30 final size:28
Alignment explanation
Indices: 48705--48769 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 28
48695 AATGTATAAA
*
48705 TTTAT-ATTATTTTTATATATTTTATTAT
1 TTTATAATTATTTTTAAATATTTTA-TAT
48733 TTTATAATTATATTTTAAATATTTTATAT
1 TTTATAATTAT-TTTTAAATATTTTATAT
48762 TTATATAA
1 TT-TATAA
48770 ATTTTGATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 5 0.15
29 10 0.30
30 18 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTATAATTATTTTTAAATATTTTATAT
Found at i:48758 original size:22 final size:21
Alignment explanation
Indices: 48720--48767 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
48710 ATTATTTTTA
*
48720 TATATTTTATTATTTTATAAT
1 TATATTTTAATATTTTATAAT
*
48741 TATATTTTAAATATTTTATATT
1 TATATTTT-AATATTTTATAAT
48763 TATAT
1 TATAT
48768 AAATTTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATATTTTAATATTTTATAAT
Found at i:55566 original size:30 final size:30
Alignment explanation
Indices: 55511--55581 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
55501 ATATTGTAAT
* *
55511 AATAAATATTTAAAAATTAATTATATATAAA
1 AATAAATATTTAAAAAGTAAGTATAT-TAAA
* *
55542 TATAAAT-TTTAATAAGTAAGTATATTAAA
1 AATAAATATTTAAAAAGTAAGTATATTAAA
55571 AATAACATATT
1 AATAA-ATATT
55582 ATAATAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 8 0.24
30 17 0.52
31 8 0.24
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (30 bp):
AATAAATATTTAAAAAGTAAGTATATTAAA
Found at i:55585 original size:45 final size:43
Alignment explanation
Indices: 55496--55594 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 43
55486 AATTTGTAAT
* *
55496 ATATAATATTGTAATAATAAATATTTAAAAATTAATTATATATAA
1 ATATAA-ATTTTAATAATAAATATTTAAAAATTAAATATATAT-A
*
55541 ATATAAATTTTAATAAGTAAGTATATTAAAAA-TAACATAT-TATA
1 ATATAAATTTTAATAA-TAAATAT-TTAAAAATTAA-ATATATATA
*
55585 ATAAAAATTT
1 ATATAAATTT
55595 ACTTAAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
44 19 0.40
45 18 0.38
46 10 0.21
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (43 bp):
ATATAAATTTTAATAATAAATATTTAAAAATTAAATATATATA
Found at i:55745 original size:17 final size:16
Alignment explanation
Indices: 55723--55809 Score: 61
Period size: 16 Copynumber: 5.3 Consensus size: 16
55713 ACTCAAACTT
*
55723 AAAAAACCTTAAATTA
1 AAAAAAACTTAAATTA
* *
55739 AAAAAAAATTCAAACTA
1 AAAAAAACTT-AAATTA
*
55756 AAAAAAACTCAAA-TA
1 AAAAAAACTTAAATTA
* *
55771 TAAAAAATTTCAAACTTA
1 AAAAAAACTT-AAA-TTA
*
55789 AATAAAA-TTAAACTTA
1 AAAAAAACTTAAA-TTA
55805 AAAAA
1 AAAAA
55810 TATCATACTC
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
15 9 0.16
16 25 0.45
17 15 0.27
18 7 0.12
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAAACTTAAATTA
Found at i:55760 original size:32 final size:32
Alignment explanation
Indices: 55715--55809 Score: 102
Period size: 32 Copynumber: 2.9 Consensus size: 32
55705 GAATTCGAAC
55715 TCAAACTTAAAAAACCTTAAATTAAAAAAAAAT
1 TCAAACTTAAAAAA-CTTAAATTAAAAAAAAAT
* * * *
55748 TCAAACTAAAAAAAACTCAAA-TATAAAAAATT
1 TCAAACT-TAAAAAACTTAAATTAAAAAAAAAT
*
55780 TCAAACTTAAATAAAATTAAACTTAAAAAA
1 TCAAACTTAAA-AAACTTAAA-TTAAAAAA
55810 TATCATACTC
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
31 3 0.06
32 23 0.46
33 12 0.24
34 12 0.24
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (32 bp):
TCAAACTTAAAAAACTTAAATTAAAAAAAAAT
Found at i:55849 original size:16 final size:16
Alignment explanation
Indices: 55825--55863 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
55815 TACTCAAACT
*
55825 AAATAAATTTAAATTTA
1 AAAT-AATTTAAATATA
55842 AAATAATTTAAATATA
1 AAATAATTTAAATATA
55858 AAATAA
1 AAATAA
55864 CACAATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATTTAAATATA
Found at i:56747 original size:28 final size:29
Alignment explanation
Indices: 56716--56770 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
56706 TGTATTCATG
*
56716 TTATTTTTTTTTATTATA-TTATTTTTAA
1 TTATTTTTTTATATTATATTTATTTTTAA
56744 TTATTTTTTTATATTATATTTATTTTT
1 TTATTTTTTTATATTATATTTATTTTT
56771 TATAATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (29 bp):
TTATTTTTTTATATTATATTTATTTTTAA
Found at i:56755 original size:18 final size:19
Alignment explanation
Indices: 56741--56780 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
56731 ATATTATTTT
56741 TAATTATTTTTTTATATTA
1 TAATTATTTTTTTATATTA
*
56760 TATTTA-TTTTTTATAATTA
1 TAATTATTTTTTTAT-ATTA
56779 TA
1 TA
56781 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TAATTATTTTTTTATATTA
Found at i:56773 original size:13 final size:14
Alignment explanation
Indices: 56716--56785 Score: 63
Period size: 15 Copynumber: 4.9 Consensus size: 14
56706 TGTATTCATG
56716 TTATTT-TTTTTTA
1 TTATTTATTTTTTA
*
56729 TTATATTATTTTTAA
1 TTAT-TTATTTTTTA
*
56744 TTATTT-TTTTATA
1 TTATTTATTTTTTA
56757 TTATATTTATTTTTTA
1 -T-TATTTATTTTTTA
*
56773 TAATTATATTTTT
1 TTATT-TATTTTT
56786 AAAATTACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
13 9 0.20
14 8 0.17
15 23 0.50
16 6 0.13
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTATTTTTTA
Found at i:60766 original size:2 final size:2
Alignment explanation
Indices: 60755--60784 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
60745 CATTTTATTT
60755 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60785 GCAATCTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61033 original size:16 final size:17
Alignment explanation
Indices: 60989--61034 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
60979 AATTATAAAA
**
60989 AATA-AATTAAAAACAT
1 AATATAATTAAAATGAT
61005 AATATAATT-AAATGAT
1 AATATAATTAAAATGAT
61021 AAT-TAATTAAAATG
1 AATATAATTAAAATG
61035 TGCCTCACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 5 0.19
16 17 0.65
17 4 0.15
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AATATAATTAAAATGAT
Found at i:61831 original size:12 final size:13
Alignment explanation
Indices: 61809--61840 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
61799 TTAATATAAA
61809 ATAAATGATAATT
1 ATAAATGATAATT
61822 ATAAAT-ATAATT
1 ATAAATGATAATT
61834 -TAAATGA
1 ATAAATGA
61841 ATTAAATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 7 0.39
13 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (13 bp):
ATAAATGATAATT
Found at i:62200 original size:10 final size:10
Alignment explanation
Indices: 62179--62270 Score: 57
Period size: 10 Copynumber: 9.0 Consensus size: 10
62169 ATGTTAATAT
*
62179 AAATATAATA
1 AAATATATTA
*
62189 AAATTTATT-
1 AAATATATTA
62198 AAATATATTA
1 AAATATATTA
*
62208 AAATAT-TAA
1 AAATATATTA
62217 ATAATA-ATATA
1 A-AATATAT-TA
*
62228 ATATATATT-
1 AAATATATTA
62237 AAATATATTA
1 AAATATATTA
*
62247 TATTAATCATATTT
1 -A--AAT-ATATTA
62261 AAATATATTA
1 AAATATATTA
62271 TTTTATATTT
Statistics
Matches: 63, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
9 19 0.30
10 27 0.43
11 8 0.13
13 4 0.06
14 5 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (10 bp):
AAATATATTA
Found at i:62202 original size:19 final size:18
Alignment explanation
Indices: 62178--62243 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 18
62168 TATGTTAATA
62178 TAAATATAATAAAATTTAT
1 TAAATATAATAAAA-TTAT
*
62197 TAAATATATTAAAA-TAT
1 TAAATATAATAAAATTAT
62214 TAAATAATAATATAATATATAT
1 TAAAT-ATAATA-AA-AT-TAT
62236 TAAATATA
1 TAAATATA
62244 TTATATTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 8 0.20
18 5 0.12
19 15 0.38
20 1 0.03
21 3 0.08
22 8 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATATAATAAAATTAT
Found at i:62241 original size:39 final size:35
Alignment explanation
Indices: 62174--62246 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 35
62164 TAATTATGTT
*
62174 AATATAAATATAATAAAATTTATTAAATATATTAA
1 AATATAAATATAATAAAATATATTAAATATATTAA
62209 AATATTAAATAATAATATAATATATATTAAATATATTA
1 AATA-TAAAT-ATAATA-AA-ATATATTAAATATATTA
62247 TATTAATCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 4 0.12
36 5 0.15
37 6 0.18
38 2 0.06
39 16 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
AATATAAATATAATAAAATATATTAAATATATTAA
Found at i:62244 original size:9 final size:9
Alignment explanation
Indices: 62178--62312 Score: 70
Period size: 9 Copynumber: 15.2 Consensus size: 9
62168 TATGTTAATA
62178 TAAATATAAT
1 TAAATAT-AT
* *
62188 AAAATTTAT
1 TAAATATAT
62197 TAAATATAT
1 TAAATATAT
62206 TAAA-ATAT
1 TAAATATAT
62214 TAAATAATAAT
1 TAAAT-AT-AT
62225 ATAATATATAT
1 -TAA-ATATAT
62236 TAAATATAT
1 TAAATATAT
* *
62245 TATAT-TAA
1 TAAATATAT
*
62253 T-CATAT-T
1 TAAATATAT
62260 TAAATATAT
1 TAAATATAT
62269 T--AT-T-T
1 TAAATATAT
* *
62274 TATATTTAT
1 TAAATATAT
* *
62283 TATATTATTT
1 TA-AATATAT
*
62293 TAAATTTAT
1 TAAATATAT
62302 TAAATATAT
1 TAAATATAT
62311 TA
1 TA
62313 TATTTATATA
Statistics
Matches: 95, Mismatches: 17, Indels: 27
0.68 0.12 0.19
Matches are distributed among these distances:
5 2 0.02
6 1 0.01
7 7 0.07
8 17 0.18
9 42 0.44
10 15 0.16
11 4 0.04
12 5 0.05
13 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (9 bp):
TAAATATAT
Found at i:62286 original size:19 final size:19
Alignment explanation
Indices: 62231--62328 Score: 85
Period size: 19 Copynumber: 5.3 Consensus size: 19
62221 TAATATAATA
* *
62231 TATATTAAATATATTATAT
1 TATATTATATTTATTATAT
* *
62250 TA-ATCATATTTAAATATAT
1 TATATTATATTT-ATTATAT
*
62269 TATTTTATATTTATTATAT
1 TATATTATATTTATTATAT
* * *
62288 TATTTTAAATTTATTA-AA
1 TATATTATATTTATTATAT
62306 TATATTATATTTA-TATAT
1 TATATTATATTTATTATAT
*
62324 CATAT
1 TATAT
62329 CCAAAATTAT
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
17 2 0.03
18 23 0.37
19 31 0.49
20 7 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTTATTATAT
Found at i:62287 original size:43 final size:43
Alignment explanation
Indices: 62201--62321 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 43
62191 ATTTATTAAA
* *
62201 TATATTAAA-ATATTAAATAATAATATAATATATATTAAATATAT
1 TATATTAAATATATTAAAT-ATATTAT-ATTTATATTAAATATAT
* *
62245 TATATT-AATCATATTTAAATATATTAT-TTTATATTTATTATAT
1 TATATTAAAT-ATA-TTAAATATATTATATTTATATTAAATATAT
* *
62288 TATTTTAAATTTATTAAATATATTATATTTATAT
1 TATATTAAATATATTAAATATATTATATTTATAT
62322 ATCATATCCA
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
42 13 0.20
43 29 0.44
44 9 0.14
45 9 0.14
46 6 0.09
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (43 bp):
TATATTAAATATATTAAATATATTATATTTATATTAAATATAT
Found at i:68016 original size:15 final size:16
Alignment explanation
Indices: 67984--68030 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
67974 TTTTTTATAA
67984 AAAATATTTAATAAATT
1 AAAAT-TTTAATAAATT
*
68001 AAAATTTTAA-ATATT
1 AAAATTTTAATAAATT
68016 AAATATTTATAATAA
1 AAA-ATTT-TAATAA
68031 TTTTTTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 7 0.28
16 9 0.36
17 8 0.32
18 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTTTAATAAATT
Found at i:68695 original size:24 final size:25
Alignment explanation
Indices: 68648--68697 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
68638 TCTCTAATAA
68648 AATTTTATTATTATTTTTTAAATTT
1 AATTTTATTATTATTTTTTAAATTT
*
68673 AATTTTTTTA-TACTTTTTT-AATTT
1 AATTTTATTATTA-TTTTTTAAATTT
68697 A
1 A
68698 GTTAATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (25 bp):
AATTTTATTATTATTTTTTAAATTT
Found at i:69388 original size:2 final size:2
Alignment explanation
Indices: 69381--69408 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
69371 CTATCTATCC
69381 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
69409 GTACTTTGTT
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:71722 original size:31 final size:30
Alignment explanation
Indices: 71666--71727 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
71656 TGAAGATTAA
71666 AACTTTTATTGAAAGCATAACAATAATCTTG
1 AACTTTTATTGAAAGCATAACAATAAT-TTG
* *
71697 AACTTTTGTTGAAAGCGAT-ATAATAATTTG
1 AACTTTTATTGAAAGC-ATAACAATAATTTG
71727 A
1 A
71728 GCATTTGCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 22 0.79
32 2 0.07
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (30 bp):
AACTTTTATTGAAAGCATAACAATAATTTG
Found at i:71801 original size:81 final size:81
Alignment explanation
Indices: 71656--71997 Score: 286
Period size: 81 Copynumber: 4.3 Consensus size: 81
71646 GAATCTTTAT
* * ** * * ** * * *
71656 TGAAGATTAAAACTTTTATTGAAAG-CATAACAATAATCTTGAACTTTTGTTGAAAGCGATATAA
1 TGAAGGTTAAAACCTTTGCTGAAAGACATAATAATAGTCTCAAACTTTTGCTGAAGGCGAAATAA
*
71720 TAATTTGAGCATTTGC
66 TAATTTGAACATTTGC
* * * *
71736 TGAATGTTAAAATCTTTGCTGAAAGACATAATAATAGTTTCAAATTTTTGCTGAAGGCGAAATAA
1 TGAAGGTTAAAACCTTTGCTGAAAGACATAATAATAGTCTCAAACTTTTGCTGAAGGCGAAATAA
* *
71801 TAATTTGAATATTTGT
66 TAATTTGAACATTTGC
** *
71817 TGAAGGTTAAAACCTTTGCTGAAAGACATAATAATAGTCTCAAACTTTTGCTGAAGATGAGATAA
1 TGAAGGTTAAAACCTTTGCTGAAAGACATAATAATAGTCTCAAACTTTTGCTGAAGGCGAAATAA
**
71882 TAAAATGAAC-TTT--
66 TAATTTGAACATTTGC
* * * * * ** *
71895 TAAAAGGTTAAGAA--TTT-TTGAGAAGGCATAATAATAATCTTAAGTTTTTGCTGAAGGCGAGA
1 T-GAAGGTTAA-AACCTTTGCTGA-AAGACATAATAATAGTCTCAAACTTTTGCTGAAGGCGAAA
* *
71957 TAATAATCTGAA-TTTTGC
63 TAATAATTTGAACATTTGC
* *
71975 TGAAGGTTGAAGCCTTTGCTGAA
1 TGAAGGTTAAAACCTTTGCTGAA
71998 GGTATAACAG
Statistics
Matches: 209, Mismatches: 43, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
77 3 0.01
78 51 0.24
79 15 0.07
80 29 0.14
81 111 0.53
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (81 bp):
TGAAGGTTAAAACCTTTGCTGAAAGACATAATAATAGTCTCAAACTTTTGCTGAAGGCGAAATAA
TAATTTGAACATTTGC
Found at i:71952 original size:31 final size:29
Alignment explanation
Indices: 71916--71980 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
71906 GAATTTTTGA
*
71916 GAAGGC-ATAATAATAATCTTAAGTTTTTGCT
1 GAAGGCGA-AATAATAATCTGAA--TTTTGCT
*
71947 GAAGGCGAGATAATAATCTGAATTTTGCT
1 GAAGGCGAAATAATAATCTGAATTTTGCT
71976 GAAGG
1 GAAGG
71981 TTGAAGCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 12 0.39
31 18 0.58
32 1 0.03
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (29 bp):
GAAGGCGAAATAATAATCTGAATTTTGCT
Found at i:75448 original size:4 final size:4
Alignment explanation
Indices: 75439--75465 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
75429 TGTTTTAATT
75439 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
75466 GTTAGTTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:79671 original size:19 final size:19
Alignment explanation
Indices: 79647--79684 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
79637 ATAGCTAAAT
79647 GCATGCTTTATTATTATTA
1 GCATGCTTTATTATTATTA
79666 GCATGCTTTATTATTATTA
1 GCATGCTTTATTATTATTA
79685 TTATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (19 bp):
GCATGCTTTATTATTATTA
Found at i:79679 original size:3 final size:3
Alignment explanation
Indices: 79673--79701 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
79663 TTAGCATGCT
79673 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
79702 TTGTTGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:82170 original size:16 final size:16
Alignment explanation
Indices: 82059--82191 Score: 72
Period size: 15 Copynumber: 8.6 Consensus size: 16
82049 ATTTTAATTT
*
82059 ATTTAAATT-TTTTAT
1 ATTTAAATTATTTTAA
82074 ATTTAAATTAATTTATTTAA
1 ATTTAAATT-A--T-TTTAA
* *
82094 CATTTAAATT-TATCAA
1 -ATTTAAATTATTTTAA
82110 ATTT-AATTATTTTAA
1 ATTTAAATTATTTTAA
*
82125 TTTTAAA--ATTTT--
1 ATTTAAATTATTTTAA
* *
82137 A---AAATAATTTCAA
1 ATTTAAATTATTTTAA
82150 A-TTAAATTATTTTAA
1 ATTTAAATTATTTTAA
*
82165 ATTTAAATAATTTTAA
1 ATTTAAATTATTTTAA
82181 ATTTTAAATTA
1 A-TTTAAATTA
82192 ATTAATTTTG
Statistics
Matches: 90, Mismatches: 12, Indels: 30
0.68 0.09 0.23
Matches are distributed among these distances:
9 3 0.03
11 4 0.04
13 1 0.01
14 9 0.10
15 31 0.34
16 19 0.21
17 9 0.10
19 1 0.01
20 4 0.04
21 9 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:82196 original size:16 final size:17
Alignment explanation
Indices: 82130--82194 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 17
82120 TTTAATTTTA
*
82130 AAATTTTAAAATAATTT
1 AAATTTTAAATTAATTT
*
82147 CAAA--TTAAATTATTTT
1 -AAATTTTAAATTAATTT
82163 AAA-TTTAAA-TAATTTT
1 AAATTTTAAATTAA-TTT
82179 AAATTTTAAATTAATT
1 AAATTTTAAATTAATT
82195 AATTTTGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 5 0.12
16 21 0.52
17 8 0.20
18 6 0.15
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTTAAATTAATTT
Found at i:82208 original size:23 final size:23
Alignment explanation
Indices: 82158--82200 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
82148 AAATTAAATT
82158 ATTTTAAATTTAAATAATTTTAA
1 ATTTTAAATTTAAATAATTTTAA
*
82181 ATTTTAAA-TTAATTAATTTT
1 ATTTTAAATTTAAATAATTTT
82201 GATTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTAAATTTAAATAATTTTAA
Found at i:87904 original size:4 final size:4
Alignment explanation
Indices: 87895--87922 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
87885 GCACTAGTTA
87895 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
87923 CGTGAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:89531 original size:2 final size:2
Alignment explanation
Indices: 89524--89578 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
89514 AAACTCAACT
89524 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
89566 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
89579 CCAAAGACAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:93810 original size:26 final size:25
Alignment explanation
Indices: 93756--93810 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
93746 AAAATAATAA
*
93756 TTAATAAAAGTATTAATATTTATTT
1 TTAATAAAAGTATTAATATTTATTG
* *
93781 TTAATTAAAAGTCTATATTATTTA-TG
1 TTAA-TAAAAGTAT-TAATATTTATTG
93807 TTAA
1 TTAA
93811 ACTGGTAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.16
26 13 0.52
27 8 0.32
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (25 bp):
TTAATAAAAGTATTAATATTTATTG
Found at i:94015 original size:15 final size:15
Alignment explanation
Indices: 93995--94024 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
93985 TTTTAATTTA
93995 ATTTTTATAAAAATT
1 ATTTTTATAAAAATT
*
94010 ATTTTTTTAAAAATT
1 ATTTTTATAAAAATT
94025 TAACCTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTTATAAAAATT
Found at i:94905 original size:21 final size:21
Alignment explanation
Indices: 94871--94910 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
94861 AATTTAGTCA
* *
94871 TAAAAATTACTTAAAAATATT
1 TAAAAAATAATTAAAAATATT
*
94892 TAAAAAATAATTAACAATA
1 TAAAAAATAATTAAAAATA
94911 ATATAAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAATAATTAAAAATATT
Found at i:95475 original size:23 final size:24
Alignment explanation
Indices: 95449--95501 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
95439 TTTTATAAAA
* *
95449 TTATATTATTATT-TAAATTAATT
1 TTATATTAATATTGTAAATAAATT
*
95472 TTAT-TTAATATTGTTAATAAATT
1 TTATATTAATATTGTAAATAAATT
*
95495 TTTTATT
1 TTATATT
95502 TATTTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 7 0.29
23 15 0.62
24 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATATTAATATTGTAAATAAATT
Found at i:95477 original size:15 final size:17
Alignment explanation
Indices: 95446--95479 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
95436 GTATTTTATA
95446 AAATTATATTATTATTT
1 AAATTATATTATTATTT
95463 AAATTA-ATT-TTATTT
1 AAATTATATTATTATTT
95478 AA
1 AA
95480 TATTGTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTATATTATTATTT
Found at i:95540 original size:29 final size:30
Alignment explanation
Indices: 95505--95564 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
95495 TTTTATTTAT
* *
95505 TTTAATTTTATATATATAAA-AATAAA-ATA
1 TTTAATTTAATA-ATAAAAAGAATAAATATA
95534 TTTAATTTAATAATAAAAAGAATAAATATA
1 TTTAATTTAATAATAAAAAGAATAAATATA
95564 T
1 T
95565 CTTTTAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 17 0.63
30 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
TTTAATTTAATAATAAAAAGAATAAATATA
Found at i:98069 original size:16 final size:17
Alignment explanation
Indices: 98048--98081 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
98038 TCTCTTTACA
98048 TTTATTTTTAT-TATTT
1 TTTATTTTTATATATTT
98064 TTTATTTTTATATATTT
1 TTTATTTTTATATATTT
98081 T
1 T
98082 AATATAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTTATATATTT
Found at i:99349 original size:16 final size:16
Alignment explanation
Indices: 99318--99360 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
99308 TTTAATATTT
* *
99318 ATAAAATTTTTAATTAA
1 ATAAAACTTATAATT-A
99335 ATAAAA-TTATAATTA
1 ATAAAACTTATAATTA
99350 ATAAAACTTAT
1 ATAAAACTTAT
99361 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAACTTATAATTA
Found at i:101900 original size:42 final size:42
Alignment explanation
Indices: 101839--101923 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
101829 CAAGATCAAG
* * * *
101839 AATGGGTTTAGATTTTGGAGATTCAAGTTTAGACACATGGTC
1 AATGGGTTCAAATTCTGGAGATTCAAGTTCAGACACATGGTC
* *
101881 AATGGGTTCAAATTCTGGAGATTCAGGTTCGGACACATGGTC
1 AATGGGTTCAAATTCTGGAGATTCAAGTTCAGACACATGGTC
101923 A
1 A
101924 GGTTTGGACA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (42 bp):
AATGGGTTCAAATTCTGGAGATTCAAGTTCAGACACATGGTC
Found at i:101926 original size:18 final size:18
Alignment explanation
Indices: 101903--101939 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
101893 TTCTGGAGAT
101903 TCAGGTTCGGACACATGG
1 TCAGGTTCGGACACATGG
*
101921 TCAGGTTTGGACACATGG
1 TCAGGTTCGGACACATGG
101939 T
1 T
101940 TCGGTGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (18 bp):
TCAGGTTCGGACACATGG
Found at i:103841 original size:31 final size:30
Alignment explanation
Indices: 103799--103915 Score: 108
Period size: 31 Copynumber: 3.8 Consensus size: 30
103789 CTATCAAACA
* *
103799 AAATCAATCAGCAATAAAGGCTGACTGAATG
1 AAATAAATCAGCAATAAAAGCTGACT-AATG
* **
103830 AAATAAATCAGCGATAAAAGCTGATCTAACA
1 AAATAAATCAGCAATAAAAGCTGA-CTAATG
* * * *
103861 AAATCAATCAGCATTGAAGGCTGACTAAGTG
1 AAATAAATCAGCAATAAAAGCTGACTAA-TG
* *
103892 AAATAAATTAGCGATAAAAGCTGA
1 AAATAAATCAGCAATAAAAGCTGA
103916 TTCAGTGAGA
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
30 4 0.06
31 60 0.91
32 2 0.03
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.21
Consensus pattern (30 bp):
AAATAAATCAGCAATAAAAGCTGACTAATG
Found at i:103894 original size:62 final size:62
Alignment explanation
Indices: 103795--103916 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 62
103785 CTAACTATCA
103795 AACAAAATCAATCAGCAATAAAGGCTGACTGAATGAAATAAATCAGCGATAAAAGCTGATCT
1 AACAAAATCAATCAGCAATAAAGGCTGACTGAATGAAATAAATCAGCGATAAAAGCTGATCT
* * *
103857 AACAAAATCAATCAGCATTGAAGGCTGACT-AAGTGAAATAAATTAGCGATAAAAGCTGAT
1 AACAAAATCAATCAGCAATAAAGGCTGACTGAA-TGAAATAAATCAGCGATAAAAGCTGAT
103917 TCAGTGAGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 2 0.04
62 54 0.96
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (62 bp):
AACAAAATCAATCAGCAATAAAGGCTGACTGAATGAAATAAATCAGCGATAAAAGCTGATCT
Found at i:103956 original size:23 final size:23
Alignment explanation
Indices: 103926--103979 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
103916 TTCAGTGAGA
103926 AAAAGAATCCCAGAATTTTTTTC
1 AAAAGAATCCCAGAATTTTTTTC
* * *
103949 AAAAGAATTCTAGAATTTTTTTT
1 AAAAGAATCCCAGAATTTTTTTC
*
103972 AGAAGAAT
1 AAAAGAAT
103980 ACGAACCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (23 bp):
AAAAGAATCCCAGAATTTTTTTC
Found at i:105772 original size:21 final size:21
Alignment explanation
Indices: 105746--105790 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
105736 AACATATAAT
*
105746 TTTTTTCACTTTATTTCTTTC
1 TTTTTTCACCTTATTTCTTTC
**
105767 TTTTTTTTCCTTATTTCTTTC
1 TTTTTTCACCTTATTTCTTTC
105788 TTT
1 TTT
105791 CTCCCTGTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTCACCTTATTTCTTTC
Found at i:108969 original size:13 final size:13
Alignment explanation
Indices: 108951--108977 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
108941 TACAAAGATT
108951 AATGTATCGATAC
1 AATGTATCGATAC
108964 AATGTATCGATAC
1 AATGTATCGATAC
108977 A
1 A
108978 TTGAATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:108974 original size:33 final size:33
Alignment explanation
Indices: 108932--108997 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
108922 AAATTCCCAG
* *
108932 ATGTATCGATACAAAGATTAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCAATACA
**
108965 ATGTATCGATACATTGAATAATGTATCAATACA
1 ATGTATCGATACAAAGAATAATGTATCAATACA
108998 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCAATACA
Found at i:109483 original size:2 final size:2
Alignment explanation
Indices: 109434--109467 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
109424 ATATTGTTCA
* *
109434 AT AT AA AT AT AA 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 AT AT
109468 GTTAGATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:109962 original size:2 final size:2
Alignment explanation
Indices: 109955--109981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
109945 CGTAAGATGG
109955 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
109982 TCGTTAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:110205 original size:19 final size:18
Alignment explanation
Indices: 110178--110228 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
110168 TTTTTACTTT
*
110178 AATTT-TTTTATTTTAAA
1 AATTTATTTTATTTGAAA
*
110195 AATTATATTTTAATTAGAAA
1 AATT-TATTTT-ATTTGAAA
110215 AATTTATTTTATTT
1 AATTTATTTTATTT
110229 ATTGTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 4 0.14
18 4 0.14
19 10 0.36
20 10 0.36
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
AATTTATTTTATTTGAAA
Found at i:110205 original size:20 final size:19
Alignment explanation
Indices: 110182--110228 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
110172 TACTTTAATT
*
110182 TTTTTATTTTAAAAATTATA
1 TTTTTATTTGAAAAATT-TA
* *
110202 TTTTAATTAGAAAAATTTA
1 TTTTTATTTGAAAAATTTA
110221 -TTTTATTT
1 TTTTTATTT
110229 ATTGTTAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 6 0.27
19 2 0.09
20 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTATTTGAAAAATTTA
Done.