Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 32 of 33
Found at i:5492706 original size:20 final size:21
Alignment explanation
Indices: 5492636--5492728 Score: 56
Period size: 18 Copynumber: 4.6 Consensus size: 21
5492626 ATTAATTAAA
* *
5492636 ATATAATATA-ATATAAATATG
1 ATATAATATATA-ATAAAAATT
*
5492657 ATATAA-ATAT-ATAAATATTT
1 ATATAATATATAATAAA-AATT
* *
5492677 TTAAATATATATAATAAAAATT
1 ATATA-ATATATAATAAAAATT
*
5492699 AT-TAATATAT--TAAAATTT
1 ATATAATATATAATAAAAATT
5492717 ATATAA-ATATAA
1 ATATAATATATAA
5492729 ATTATTTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 17
0.68 0.11 0.21
Matches are distributed among these distances:
18 13 0.24
19 8 0.15
20 13 0.24
21 8 0.15
22 8 0.15
23 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (21 bp):
ATATAATATATAATAAAAATT
Found at i:5492770 original size:29 final size:31
Alignment explanation
Indices: 5492736--5492809 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
5492726 TAAATTATTT
*
5492736 TAAATATAAATATAA-TACA-ATAAAATAAA
1 TAAATATAAATATAATTACATAAAAAATAAA
*
5492765 TAAATATAACATA-AATTTCATAAAAAATAAA
1 TAAATATAA-ATATAATTACATAAAAAATAAA
*
5492796 AAAATA-AAATATAA
1 TAAATATAAATATAA
5492810 CCCATATGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 14 0.37
30 10 0.26
31 14 0.37
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (31 bp):
TAAATATAAATATAATTACATAAAAAATAAA
Found at i:5493177 original size:2 final size:2
Alignment explanation
Indices: 5493170--5493209 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5493160 AAGCGTTTAC
5493170 TA TA TA TA 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 TA
5493210 ATAGGATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5494340 original size:19 final size:22
Alignment explanation
Indices: 5494313--5494365 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
5494303 AAACTAAATA
*
5494313 TAAAAAAT-ATTTT-ATT-AAT
1 TAAATAATAATTTTAATTGAAT
5494332 TAAATAATAATTTTAATTGAAT
1 TAAATAATAATTTTAATTGAAT
*
5494354 CAAATAACTAAT
1 TAAATAA-TAAT
5494366 GAATATCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.25
20 5 0.18
21 3 0.11
22 9 0.32
23 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAATAATAATTTTAATTGAAT
Found at i:5496269 original size:2 final size:2
Alignment explanation
Indices: 5496262--5496290 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5496252 AGGAAAGGAA
5496262 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5496291 TGGAGATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5499283 original size:2 final size:2
Alignment explanation
Indices: 5499278--5499303 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5499268 GGGTTTTTTC
5499278 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
5499304 GTAAAGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5500141 original size:13 final size:13
Alignment explanation
Indices: 5500123--5500171 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
5500113 ATTTTATTTA
5500123 TATATAATATATT
1 TATATAATATATT
5500136 TATATAATA-ATT
1 TATATAATATATT
*
5500148 TA-A-AATTATATA
1 TATATAA-TATATT
*
5500160 AATATAATATAT
1 TATATAATATAT
5500172 AATTATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 2 0.07
11 3 0.10
12 8 0.27
13 15 0.50
14 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATAATATATT
Found at i:5500513 original size:2 final size:2
Alignment explanation
Indices: 5500506--5500530 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5500496 CCCTTTTAAT
5500506 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5500531 GATCCTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5500659 original size:2 final size:2
Alignment explanation
Indices: 5500652--5500677 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5500642 GTCACTAAAC
5500652 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
5500678 TATCAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5501946 original size:3 final size:3
Alignment explanation
Indices: 5501938--5501988 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
5501928 ATGAAGGAAT
5501938 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG
5501984 -AG AAG
1 AAG AAG
5501989 GATGGAGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5503145 original size:19 final size:19
Alignment explanation
Indices: 5503123--5503181 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
5503113 TTTTGTTTAC
5503123 TAAAAATTTATTTTAATAT
1 TAAAAATTTATTTTAATAT
*
5503142 TAAAAA--TATGTTAAATAT
1 TAAAAATTTAT-TTTAATAT
*
5503160 TAAAAATTTATTTTTATAT
1 TAAAAATTTATTTTAATAT
5503179 TAA
1 TAA
5503182 TAGTTTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.09
18 13 0.38
19 15 0.44
20 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TAAAAATTTATTTTAATAT
Found at i:5503146 original size:18 final size:18
Alignment explanation
Indices: 5503125--5503181 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
5503115 TTGTTTACTA
5503125 AAAATTTATTTTAATATT
1 AAAATTTATTTTAATATT
* *
5503143 AAAA-ATATGTTAAATATT
1 AAAATTTAT-TTTAATATT
*
5503161 AAAAATTTATTTTTATATT
1 -AAAATTTATTTTAATATT
5503180 AA
1 AA
5503182 TAGTTTATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 3 0.10
18 14 0.45
19 11 0.35
20 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AAAATTTATTTTAATATT
Found at i:5503188 original size:19 final size:20
Alignment explanation
Indices: 5503123--5503195 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 20
5503113 TTTTGTTTAC
*
5503123 TAAAAATTTAT-TTTAATAT
1 TAAAAATTTATATTTTATAT
* **
5503142 TAAAAA--TATGTTAAATAT
1 TAAAAATTTATATTTTATAT
5503160 TAAAAATTTAT-TTTTATAT
1 TAAAAATTTATATTTTATAT
* *
5503179 TAATAGTTTATATTTTA
1 TAAAAATTTATATTTTA
5503196 AAATTAAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.07
18 13 0.29
19 21 0.47
20 8 0.18
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (20 bp):
TAAAAATTTATATTTTATAT
Found at i:5503770 original size:20 final size:20
Alignment explanation
Indices: 5503731--5503770 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5503721 ATATATTTTT
*
5503731 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
5503751 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
5503771 TTTTGATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:5503785 original size:13 final size:15
Alignment explanation
Indices: 5503762--5503809 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
5503752 TATTATATAT
5503762 TTATATAAATTTTGA
1 TTATATAAATTTTGA
5503777 TTA-AT-AATTTAT-A
1 TTATATAAATTT-TGA
5503790 TTATATAAATTTTGA
1 TTATATAAATTTTGA
5503805 -TATAT
1 TTATAT
5503810 TTATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.31
14 11 0.38
15 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (15 bp):
TTATATAAATTTTGA
Found at i:5503842 original size:28 final size:28
Alignment explanation
Indices: 5503703--5503848 Score: 106
Period size: 28 Copynumber: 5.2 Consensus size: 28
5503693 AGAATTTGTG
* *
5503703 TATTTATATTATATTTT-TATA-TATTTT
1 TATTTATA-TATATTTTGAATATTATATT
**
5503730 TATATTATAATTATATTTAAAATATTATA--
1 TAT-TTAT-A-TATATTTTGAATATTATATT
* * *
5503759 TATTTATATAAATTTTGATTAATA-ATT
1 TATTTATATATATTTTGAATATTATATT
*
5503786 TATATTATATAAATTTTGATATATT-TATT
1 TAT-TTATATATATTTTGA-ATATTATATT
*
5503815 TATTTATATATATTTTTAATATTATATT
1 TATTTATATATATTTTGAATATTATATT
5503843 ATATTT
1 -TATTT
5503849 TGAGTTGTAT
Statistics
Matches: 96, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
25 1 0.01
26 11 0.11
27 12 0.12
28 40 0.42
29 26 0.27
30 3 0.03
31 3 0.03
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (28 bp):
TATTTATATATATTTTGAATATTATATT
Found at i:5503845 original size:19 final size:17
Alignment explanation
Indices: 5503804--5503849 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
5503794 ATAAATTTTG
*
5503804 ATATATTTATTTATTTAT
1 ATATATTT-TTAATTTAT
5503822 ATATATTTTTAATATTAT
1 ATATATTTTTAAT-TTAT
5503840 ATTATATTTT
1 A-TATATTTT
5503850 GAGTTGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 4 0.16
18 13 0.52
19 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATATTTTTAATTTAT
Found at i:5503845 original size:56 final size:56
Alignment explanation
Indices: 5503703--5503847 Score: 138
Period size: 56 Copynumber: 2.6 Consensus size: 56
5503693 AGAATTTGTG
*
5503703 TATTTATATTATATTTTTATATATT-T-TTATATTATAATTATATTTAAAATATTATA
1 TATTTATA-TATATTTTTA-ATATTATATTATATTATAATAATATTTAAAATATTATA
* * * * * * *
5503759 TATTTATATAAATTTTGATTAATA-ATTTATATTAT-ATAA-ATTTTGATATATTTATT
1 TATTTATATATATTTTTAATATTATA-TTATATTATAATAATA-TTTAAAATA-TTATA
5503815 TATTTATATATATTTTTAATATTATATTATATT
1 TATTTATATATATTTTTAATATTATATTATATT
5503848 TTGAGTTGTA
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
54 4 0.06
55 18 0.25
56 48 0.68
57 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (56 bp):
TATTTATATATATTTTTAATATTATATTATATTATAATAATATTTAAAATATTATA
Found at i:5506709 original size:29 final size:34
Alignment explanation
Indices: 5506646--5506728 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 34
5506636 TTAAATTTAA
5506646 TTATAAAATATAAAATATTAATATATTTAATATT
1 TTATAAAATATAAAATATTAATATATTTAATATT
*
5506680 TTATTAAA-ATAAAATA-T-ATAT-TTTAA-A-T
1 TTATAAAATATAAAATATTAATATATTTAATATT
* * *
5506708 TTATCAAATAAAAAATTTTAA
1 TTATAAAATATAAAATATTAA
5506729 ATAAATAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
28 8 0.19
29 7 0.17
30 6 0.14
31 5 0.12
32 1 0.02
33 8 0.19
34 7 0.17
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (34 bp):
TTATAAAATATAAAATATTAATATATTTAATATT
Found at i:5507011 original size:43 final size:43
Alignment explanation
Indices: 5506927--5507030 Score: 113
Period size: 43 Copynumber: 2.3 Consensus size: 43
5506917 GATATCTTTT
* *
5506927 AATATTAATTAATATATTATTTATAATTGTAATGTATTAAATATAA
1 AATATT-ATTAATATTTTATTTAT-ATTGTAATATATTAAATA-AA
* *
5506973 CA-ATTATTAATATTTTATATTAT-TTTTAATATATTAAATAAA
1 AATATTATTAATATTTTAT-TTATATTGTAATATATTAAATAAA
5507015 AATATTATTATATATT
1 AATATTATTA-ATATT
5507031 ATAATTTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
42 3 0.06
43 22 0.44
44 17 0.34
45 7 0.14
46 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (43 bp):
AATATTATTAATATTTTATTTATATTGTAATATATTAAATAAA
Found at i:5507038 original size:40 final size:41
Alignment explanation
Indices: 5506947--5507044 Score: 103
Period size: 43 Copynumber: 2.4 Consensus size: 41
5506937 AATATATTAT
* * * *
5506947 TTATAA-TTGTAATGTATTAAATATAACAATTATTAATATT
1 TTATAATTTTTAATATATTAAATATAAAAATTATTAATATA
5506987 TTATATTATTTTTAATATATTAAATA-AAAATATTATT-ATATA
1 TTATA--ATTTTTAATATATTAAATATAAAA-ATTATTAATATA
*
5507029 TTATAATTTTAAATAT
1 TTATAATTTTTAATAT
5507045 TGTGAGCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
40 15 0.31
42 13 0.27
43 21 0.43
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (41 bp):
TTATAATTTTTAATATATTAAATATAAAAATTATTAATATA
Found at i:5507182 original size:16 final size:14
Alignment explanation
Indices: 5507163--5507209 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
5507153 AATTTATTTT
5507163 TATATAAAATTTAA
1 TATATAAAATTTAA
*
5507177 CATATAAATAATTTAA
1 TATAT-AA-AATTTAA
5507193 T-TATAAAATTTTAA
1 TATATAAAA-TTTAA
5507207 TAT
1 TAT
5507210 TATTCATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 2 0.07
14 12 0.44
15 6 0.22
16 7 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAAATTTAA
Found at i:5507221 original size:8 final size:7
Alignment explanation
Indices: 5507210--5507279 Score: 58
Period size: 6 Copynumber: 10.1 Consensus size: 7
5507200 ATTTTAATAT
5507210 TATTCATA
1 TATT-ATA
5507218 TATTA-A
1 TATTATA
5507224 TATTATA
1 TATTATA
5507231 T-TTATA
1 TATTATA
*
5507237 TATTATT
1 TATTATA
*
5507244 TTTATATCA
1 TAT-TAT-A
5507253 TATTATA
1 TATTATA
5507260 T-TTATA
1 TATTATA
*
5507266 TAATATA
1 TATTATA
5507273 -ATTATA
1 TATTATA
5507279 T
1 T
5507280 TATATTTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
6 23 0.46
7 15 0.30
8 10 0.20
9 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (7 bp):
TATTATA
Found at i:5507228 original size:6 final size:5
Alignment explanation
Indices: 5507216--5507285 Score: 58
Period size: 5 Copynumber: 14.2 Consensus size: 5
5507206 ATATTATTCA
* *
5507216 TATAT TAATAT TATAT T-TA- TATAT TATTTT TATAT CATAT TATAT T-TA-
1 TATAT T-ATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT
*
5507264 TATAA TATAAT TATAT TATAT T
1 TATAT TAT-AT TATAT TATAT T
5507286 TAAAATAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
3 2 0.04
4 8 0.15
5 30 0.57
6 13 0.25
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:5507239 original size:13 final size:13
Alignment explanation
Indices: 5507210--5507287 Score: 63
Period size: 13 Copynumber: 5.8 Consensus size: 13
5507200 ATTTTAATAT
5507210 TATTCATATATTA-A
1 TATT-ATAT-TTATA
5507224 TATTATATTTATA
1 TATTATATTTATA
*
5507237 TATTATTTTTATATCA
1 TATTA-TATT-TAT-A
5507253 TATTATATTTATA
1 TATTATATTTATA
* *
5507266 TAATATA-AT-TA
1 TATTATATTTATA
5507277 TATTATATTTA
1 TATTATATTTA
5507288 AAATAATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
11 8 0.15
12 5 0.10
13 17 0.33
14 10 0.19
15 6 0.12
16 6 0.12
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATATTTATA
Found at i:5507248 original size:19 final size:19
Alignment explanation
Indices: 5507210--5507255 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
5507200 ATTTTAATAT
5507210 TATTCATATATTAATATTA
1 TATTCATATATTAATATTA
* * *
5507229 TATTTATATATTATTTTTA
1 TATTCATATATTAATATTA
5507248 TA-TCATAT
1 TATTCATAT
5507256 TATATTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTCATATATTAATATTA
Found at i:5507255 original size:16 final size:16
Alignment explanation
Indices: 5507216--5507271 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
5507206 ATATTATTCA
5507216 TATATTAATATTATA-T
1 TATA-TAATATTATATT
*
5507232 T-TAT-ATATTATTTT
1 TATATAATATTATATT
*
5507246 TATATCATATTATATT
1 TATATAATATTATATT
5507262 TATATAATAT
1 TATATAATAT
5507272 AATTATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 7 0.21
14 3 0.09
15 5 0.15
16 19 0.56
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATAATATTATATT
Found at i:5507256 original size:29 final size:29
Alignment explanation
Indices: 5507223--5507285 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
5507213 TCATATATTA
* **
5507223 ATATTATATTTATATATTATTTTTATATC
1 ATATTATATTTATATAATATAATTATATC
*
5507252 ATATTATATTTATATAATATAATTATATT
1 ATATTATATTTATATAATATAATTATATC
5507281 ATATT
1 ATATT
5507286 TAAAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
ATATTATATTTATATAATATAATTATATC
Found at i:5507283 original size:11 final size:12
Alignment explanation
Indices: 5507216--5507284 Score: 72
Period size: 11 Copynumber: 5.8 Consensus size: 12
5507206 ATATTATTCA
5507216 TATATTA-ATAT
1 TATATTATATAT
5507227 TATATTTATATAT
1 TATA-TTATATAT
*
5507240 TAT-TTTTATAT
1 TATATTATATAT
*
5507251 CATATTATAT-T
1 TATATTATATAT
*
5507262 TATATAATATAAT
1 TATATTATAT-AT
5507275 TATATTATAT
1 TATATTATAT
5507285 TTAAAATAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 22 0.47
12 8 0.17
13 17 0.36
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATTATATAT
Found at i:5507695 original size:17 final size:17
Alignment explanation
Indices: 5507675--5507708 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5507665 ATTAATAAAT
*
5507675 AAATAATAATATAATTA
1 AAATAAAAATATAATTA
5507692 AAATAAAAATATAATTA
1 AAATAAAAATATAATTA
5507709 CATCTTTAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATAAAAATATAATTA
Found at i:5507881 original size:2 final size:2
Alignment explanation
Indices: 5507874--5507907 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5507864 CATTCCTGTG
5507874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5507908 GGTGATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5509164 original size:12 final size:11
Alignment explanation
Indices: 5509106--5509194 Score: 50
Period size: 10 Copynumber: 8.5 Consensus size: 11
5509096 GCCATTTGTC
5509106 TATA-ATAAAT
1 TATATATAAAT
5509116 TATATA-AAA-
1 TATATATAAAT
*
5509125 AAT-TATAAAT
1 TATATATAAAT
5509135 T-TATATAAAT
1 TATATATAAAT
*
5509145 TTTAATATAAA-
1 TAT-ATATAAAT
*
5509156 TATATAT-ATT
1 TATATATAAAT
**
5509166 TATAT-TATTTT
1 TATATATA-AAT
5509177 TATATTATAAAT
1 TATA-TATAAAT
5509189 TATATA
1 TATATA
5509195 AAAAATTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 21
0.69 0.08 0.24
Matches are distributed among these distances:
8 2 0.03
9 8 0.13
10 24 0.39
11 12 0.20
12 13 0.21
13 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TATATATAAAT
Found at i:5509169 original size:30 final size:31
Alignment explanation
Indices: 5509115--5509194 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 31
5509105 CTATAATAAA
* * *
5509115 TTATATAAAAAATTATAAATTTATATAAATT
1 TTATATTATAAATTATATATTTATATAAATT
* *
5509146 TTA-A-TATAAATATATATATTTATATTATTT
1 TTATATTATAAAT-TATATATTTATATAAATT
5509176 TTATATTATAAATTATATA
1 TTATATTATAAATTATATA
5509195 AAAAATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
29 5 0.12
30 19 0.46
31 10 0.24
32 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTATATTATAAATTATATATTTATATAAATT
Found at i:5509527 original size:15 final size:16
Alignment explanation
Indices: 5509504--5509533 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5509494 TTATTATTTT
5509504 TAAATATATATTAAAA
1 TAAATATATATTAAAA
5509520 TAAA-ATATATTAAA
1 TAAATATATATTAAA
5509534 TTATTATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATATATATTAAAA
Found at i:5509665 original size:42 final size:44
Alignment explanation
Indices: 5509582--5509665 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 44
5509572 TTATATTTCA
* *
5509582 TTTATATTATAAAATTATTAATCAAATTGATATGATTAATATTT
1 TTTATATTATAAAATTATTAATAAAATTCATATGATTAATATTT
* *
5509626 TTTAT-TTATTAATTTATTAA-AAAATTCATAT-ATATAATAT
1 TTTATATTATAAAATTATTAATAAAATTCATATGAT-TAATAT
5509666 ATATACCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 2 0.06
42 15 0.43
43 13 0.37
44 5 0.14
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (44 bp):
TTTATATTATAAAATTATTAATAAAATTCATATGATTAATATTT
Found at i:5509924 original size:32 final size:34
Alignment explanation
Indices: 5509862--5509930 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
5509852 ATATTATAAT
*
5509862 TATATTTATAATATTATATAATATAAAAATTTTAA
1 TATATTAATAATATTATAT-ATATAAAAATTTTAA
*
5509897 TATATTAATAAT-TTATAT-TATATAAATTTTAA
1 TATATTAATAATATTATATATATAAAAATTTTAA
5509929 TA
1 TA
5509931 AATATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 15 0.47
34 6 0.19
35 11 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATATTAATAATATTATATATATAAAAATTTTAA
Found at i:5509927 original size:16 final size:17
Alignment explanation
Indices: 5509861--5509943 Score: 56
Period size: 16 Copynumber: 5.3 Consensus size: 17
5509851 TATATTATAA
5509861 TTATATT-TATAATATT
1 TTATATTATATAATATT
* * *
5509877 ATATAATATA-AAAATT
1 TTATATTATATAATATT
*
5509893 TTA-A-TATATTAATAAT
1 TTATATTATA-TAATATT
5509909 TTATATTATATAA-ATT
1 TTATATTATATAATATT
*
5509925 TTA-A-TAAAT-ATATT
1 TTATATTATATAATATT
5509939 TTATA
1 TTATA
5509944 AAATATTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
13 1 0.02
14 14 0.27
15 3 0.06
16 24 0.46
17 6 0.12
18 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATATTATATAATATT
Found at i:5509952 original size:25 final size:25
Alignment explanation
Indices: 5509895--5509954 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
5509885 TAAAAATTTT
*
5509895 AATATATTAATAATTTATATTATATA
1 AATAT-TTAATAATATATATTATATA
*
5509921 AAT-TTTAATAA-ATATATTTTATAA
1 AATATTTAATAATATATATTATAT-A
5509945 AATATTTAAT
1 AATATTTAAT
5509955 TAATTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 9 0.30
24 11 0.37
25 7 0.23
26 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATATTTAATAATATATATTATATA
Found at i:5515331 original size:2 final size:2
Alignment explanation
Indices: 5515324--5515351 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5515314 TACTGTTACA
5515324 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
5515352 CTATTTTGGG
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:5515639 original size:28 final size:26
Alignment explanation
Indices: 5515603--5515664 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
5515593 TATATTTAAA
*
5515603 ATATT-ATATAAATTT-TGATATGTTTAT
1 ATATTAATAT-AATTTGTAATAT-TTT-T
*
5515630 ATATTAATATTATTTGTAATATTTTT
1 ATATTAATATAATTTGTAATATTTTT
5515656 ATATTAATA
1 ATATTAATA
5515665 ACGTGTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 10 0.32
27 12 0.39
28 9 0.29
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (26 bp):
ATATTAATATAATTTGTAATATTTTT
Found at i:5515654 original size:36 final size:34
Alignment explanation
Indices: 5515556--5515659 Score: 79
Period size: 36 Copynumber: 2.9 Consensus size: 34
5515546 TGATAATTAG
*
5515556 TATATTAATATTATATTTATATTATTTTTTATGTTAT
1 TATATTAATATTAT-TTTA-A-TATTTTATATGTTAT
*
5515593 TATATTTAAAATATTA-TATAA-ATTTTGATATGTT-T
1 TATA-TT--AATATTATTTTAATATTTT-ATATGTTAT
5515628 ATATATTAATATTATTTGTAATATTTTTATAT
1 -TATATTAATATTATTT-TAATA-TTTTATAT
5515660 TAATAACGTG
Statistics
Matches: 55, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
33 7 0.13
34 1 0.02
35 11 0.20
36 15 0.27
37 9 0.16
38 5 0.09
40 7 0.13
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (34 bp):
TATATTAATATTATTTTAATATTTTATATGTTAT
Found at i:5518135 original size:17 final size:18
Alignment explanation
Indices: 5518108--5518147 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
5518098 TTCGATCTTT
5518108 AATTTTATTTAAAAATTA
1 AATTTTATTTAAAAATTA
*
5518126 AATTTT-TTTAAAATTTA
1 AATTTTATTTAAAAATTA
5518143 AATTT
1 AATTT
5518148 AACATCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTTTATTTAAAAATTA
Found at i:5519660 original size:3 final size:3
Alignment explanation
Indices: 5519654--5519689 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5519644 ATACTACTAC
5519654 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5519690 GGCATTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5526999 original size:28 final size:28
Alignment explanation
Indices: 5526924--5526999 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 28
5526914 GTTTGAATTG
* *
5526924 AATA-TAATTTTAATAAATAAAAATATTTT
1 AATATTAA-TTTAA-AAATAAAAATATATA
* **
5526953 TAT-TTAAATTTAATTATAAAAATATATA
1 AATATT-AATTTAAAAATAAAAATATATA
5526981 AATATTAATTTAAAAATAA
1 AATATTAATTTAAAAATAA
5527000 TATTTTAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
28 24 0.67
29 10 0.28
30 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AATATTAATTTAAAAATAAAAATATATA
Found at i:5527002 original size:23 final size:22
Alignment explanation
Indices: 5526957--5526998 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5526947 TATTTTTATT
5526957 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
5526979 TAAATATTAATT-TAAAAATA
1 TAAAT-TTAATTATAAAAATA
5526999 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:5527664 original size:2 final size:2
Alignment explanation
Indices: 5527657--5527686 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5527647 GACCCTTTCA
5527657 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5527687 ACTCACTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5527940 original size:14 final size:15
Alignment explanation
Indices: 5527921--5527949 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5527911 AAATTTTAAA
5527921 TTTTAAT-ATATTAT
1 TTTTAATAATATTAT
5527935 TTTTAATAATATTAT
1 TTTTAATAATATTAT
5527950 GATGAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAATAATATTAT
Found at i:5528182 original size:28 final size:31
Alignment explanation
Indices: 5528136--5528194 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 31
5528126 GCCATTATAC
5528136 AATTACAAGATATGGATATAATA-AGAAATAA
1 AATTACAAGATATGGATATAATATA-AAATAA
5528167 AATTA-AA-ATAT-GATATAATATAAAATAA
1 AATTACAAGATATGGATATAATATAAAATAA
5528195 TAATATAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 15 0.56
29 5 0.19
30 2 0.07
31 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (31 bp):
AATTACAAGATATGGATATAATATAAAATAA
Found at i:5528192 original size:17 final size:17
Alignment explanation
Indices: 5528179--5528301 Score: 74
Period size: 17 Copynumber: 6.9 Consensus size: 17
5528169 TTAAAATATG
*
5528179 ATATAATATAAAATAATA
1 ATATAATATAATATAA-A
5528197 ATATAGATATAATATGAAA
1 ATATA-ATATAATAT-AAA
*
5528216 ATATAA-AT-GTATTAAA
1 ATATAATATAATA-TAAA
*
5528232 AT-TTATATAATATAAA
1 ATATAATATAATATAAA
* *
5528248 TTATTAATATATTA-AAA
1 ATA-TAATATAATATAAA
*
5528265 ATATATATATAATACTTTAA
1 ATATA-ATATAATA--TAAA
*
5528285 ATATGATTATAATATAA
1 ATAT-AATATAATATAA
5528302 TAAATATATA
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
15 2 0.02
16 16 0.20
17 17 0.21
18 16 0.20
19 14 0.17
20 15 0.19
21 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (17 bp):
ATATAATATAATATAAA
Found at i:5528210 original size:24 final size:22
Alignment explanation
Indices: 5528163--5528223 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 22
5528153 ATAATAAGAA
5528163 ATAAAATTAAAATATGATATAAT
1 ATAAAA-TAAAATATGATATAAT
5528186 ATAAAATAATAATATAGATATAAT
1 ATAAAATAA-AATAT-GATATAAT
5528210 ATGAAAATATAAAT
1 AT-AAAATA-AAAT
5528224 GTATTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
22 3 0.09
23 11 0.32
24 10 0.29
25 9 0.26
26 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
ATAAAATAAAATATGATATAAT
Found at i:5528219 original size:13 final size:12
Alignment explanation
Indices: 5528179--5528221 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
5528169 TTAAAATATG
5528179 ATATAATATAAA
1 ATATAATATAAA
*
5528191 ATAATAATAT-AG
1 AT-ATAATATAAA
5528203 ATATAATATGAAA
1 ATATAATAT-AAA
5528216 ATATAA
1 ATATAA
5528222 ATGTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 7 0.27
12 5 0.19
13 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:5528243 original size:33 final size:35
Alignment explanation
Indices: 5528196--5528278 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 35
5528186 ATAAAATAAT
* *
5528196 AATATAGATATAATATGAAAATATAAATGTATT-AA
1 AATATATATATAATAT-AAAATATAAATATATTAAA
* *
5528231 AAT-T-TATATAATATAAATTATTAATATATTAAA
1 AATATATATATAATATAAAATATAAATATATTAAA
5528264 AATATATATATAATA
1 AATATATATATAATA
5528279 CTTTAAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 13 0.32
33 14 0.34
34 2 0.05
35 12 0.29
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (35 bp):
AATATATATATAATATAAAATATAAATATATTAAA
Found at i:5528278 original size:11 final size:11
Alignment explanation
Indices: 5528174--5528311 Score: 51
Period size: 11 Copynumber: 12.5 Consensus size: 11
5528164 TAAAATTAAA
5528174 ATATGATATAAT
1 ATAT-ATATAAT
*
5528186 ATAAAATAATAAT
1 AT-ATAT-ATAAT
*
5528199 ATAGATATAAT
1 ATATATATAAT
*
5528210 ATGAAAATATAA-
1 AT--ATATATAAT
* *
5528222 ATGTAT-TAAA
1 ATATATATAAT
*
5528232 ATTTATATAAT
1 ATATATATAAT
*
5528243 ATAAATTATTAAT
1 ATATA-TA-TAAT
*
5528256 ATAT-TAAAAAT
1 ATATAT-ATAAT
5528267 ATATATATAAT
1 ATATATATAAT
5528278 ACT-T-TA-AAT
1 A-TATATATAAT
5528287 ATGAT-TATAAT
1 AT-ATATATAAT
5528298 ATA-ATA-AAT
1 ATATATATAAT
5528307 ATATA
1 ATATA
5528312 AATTATTAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 34
0.68 0.08 0.24
Matches are distributed among these distances:
8 1 0.01
9 13 0.13
10 16 0.16
11 32 0.33
12 14 0.14
13 22 0.22
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.40
Consensus pattern (11 bp):
ATATATATAAT
Found at i:5528284 original size:22 final size:25
Alignment explanation
Indices: 5528259--5528303 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5528249 TATTAATATA
5528259 TTAAAAAT-A-TAT-ATATAATACT
1 TTAAAAATGATTATAATATAATACT
*
5528281 TTAAATATGATTATAATATAATA
1 TTAAAAATGATTATAATATAATA
5528304 AATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 3 0.16
25 8 0.42
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
TTAAAAATGATTATAATATAATACT
Found at i:5528288 original size:20 final size:20
Alignment explanation
Indices: 5528263--5528311 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5528253 AATATATTAA
*
5528263 AAATATATATATAATACT-TT
1 AAATATATATATAATA-TAAT
5528283 AAATATGAT-TATAATATAAT
1 AAATAT-ATATATAATATAAT
5528303 AAATATATA
1 AAATATATA
5528312 AATTATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 3 0.12
20 20 0.80
21 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATATATATATAATATAAT
Found at i:5528733 original size:15 final size:15
Alignment explanation
Indices: 5528709--5528746 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
5528699 TTTTAATTTT
5528709 TTATAT-AATATAAA
1 TTATATAAATATAAA
*
5528723 TTATATAAATATATA
1 TTATATAAATATAAA
5528738 TTATA-AAAT
1 TTATATAAAT
5528747 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTATATAAATATAAA
Found at i:5529054 original size:16 final size:16
Alignment explanation
Indices: 5529033--5529067 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5529023 AAATTATAAT
*
5529033 AAAATTTTAAAATTTA
1 AAAATTTAAAAATTTA
5529049 AAAATTTAAAAATTTA
1 AAAATTTAAAAATTTA
5529065 AAA
1 AAA
5529068 TAAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATTTAAAAATTTA
Found at i:5529075 original size:26 final size:25
Alignment explanation
Indices: 5529046--5529140 Score: 72
Period size: 26 Copynumber: 3.7 Consensus size: 25
5529036 ATTTTAAAAT
5529046 TTAAAAATTTAAAAATTTAAAATAAA
1 TTAAAAATTTAAAAA-TTAAAATAAA
*
5529072 TTAATTAAA--TAAAAAATATAAATAAA
1 TTAA--AAATTTAAAAATTA-AAATAAA
* *
5529098 TT-AAAATATAAAAA-TAAATTAAA
1 TTAAAAATTTAAAAATTAAAATAAA
*
5529121 TCTAAAAAATTAAAATATTA
1 T-TAAAAATTTAAAA-ATTA
5529141 TATTAAATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
23 10 0.18
24 3 0.05
25 18 0.32
26 20 0.36
27 2 0.04
28 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (25 bp):
TTAAAAATTTAAAAATTAAAATAAA
Found at i:5529081 original size:13 final size:14
Alignment explanation
Indices: 5529065--5529210 Score: 67
Period size: 13 Copynumber: 10.6 Consensus size: 14
5529055 TAAAAATTTA
5529065 AAATAAATTAAT-T
1 AAATAAATTAATAT
*
5529078 AAATAAA-AAATAT
1 AAATAAATTAATAT
5529091 AAATAAATTAAAATAT
1 AAATAAATT--AATAT
*
5529107 AAAAATAAATTAAATCT
1 --AAATAAATT-AATAT
*
5529124 AAA-AAATTAAAAT
1 AAATAAATTAATAT
* *
5529137 -ATTATATTAAATAT
1 AAATAAATT-AATAT
* * *
5529151 AATTATATAAATAT
1 AAATAAATTAATAT
5529165 AAAT--ATTAAATAT
1 AAATAAATT-AATAT
*
5529178 TAA-AAATTAATA-
1 AAATAAATTAATAT
* *
5529190 AAATAAA-AAATAA
1 AAATAAATTAATAT
5529203 AAATAAAT
1 AAATAAAT
5529211 ATCTAAAGAT
Statistics
Matches: 104, Mismatches: 14, Indels: 29
0.71 0.10 0.20
Matches are distributed among these distances:
12 12 0.12
13 43 0.41
14 20 0.19
15 10 0.10
16 5 0.05
17 5 0.05
18 9 0.09
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATAAATTAATAT
Found at i:5529102 original size:18 final size:18
Alignment explanation
Indices: 5529042--5529210 Score: 68
Period size: 18 Copynumber: 9.2 Consensus size: 18
5529032 TAAAATTTTA
* *
5529042 AAATTTAAAAATTTAAA-
1 AAATTAAAAAATATAAAT
* *
5529059 AATTTAAAATAA-ATTAATT
1 AAATTAAAA-AATA-TAAAT
5529078 AAA-TAAAAAATATAAAT
1 AAATTAAAAAATATAAAT
* *
5529095 AAATTAAAATATAAAAAT
1 AAATTAAAAAATATAAAT
*
5529113 AAATT---AAATCTAAA-
1 AAATTAAAAAATATAAAT
5529127 AAATTAAAATATTATATTAAAT
1 AAATTAAAA-A--ATA-TAAAT
*
5529149 ATAATTATATAAATATAAATATT
1 A-AATTA-AAAAATAT-AA-A-T
*
5529172 AAATATTAAAAAT-T-AAT
1 AAAT-TAAAAAATATAAAT
* *
5529189 AAAATAAAAAATAAAAAT
1 AAATTAAAAAATATAAAT
5529207 AAAT
1 AAAT
5529211 ATCTAAAGAT
Statistics
Matches: 112, Mismatches: 19, Indels: 41
0.65 0.11 0.24
Matches are distributed among these distances:
14 5 0.04
15 6 0.05
16 7 0.06
17 21 0.19
18 36 0.32
19 3 0.03
20 3 0.03
21 10 0.09
22 10 0.09
23 9 0.08
24 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTAAAAAATATAAAT
Found at i:5529113 original size:8 final size:8
Alignment explanation
Indices: 5529041--5529207 Score: 50
Period size: 8 Copynumber: 20.8 Consensus size: 8
5529031 ATAAAATTTT
*
5529041 AAAATTTA
1 AAAATATA
*
5529049 AAAATTTA
1 AAAATATA
*
5529057 AAAATTTA
1 AAAATATA
*
5529065 AAATAAATTA
1 AAA-ATA-TA
5529075 ATTAAATA-A
1 A--AAATATA
5529084 AAAATATA
1 AAAATATA
*
5529092 AATAA-ATT
1 AA-AATATA
5529100 AAAATATA
1 AAAATATA
5529108 AAAATA-A
1 AAAATATA
*
5529115 ATTAAATCTA
1 A--AAATATA
5529125 AAAA-ATTA
1 AAAATA-TA
5529133 AAATATTATA
1 AAA-A-TATA
*
5529143 TTAAATAT-
1 -AAAATATA
*
5529151 -AATTATA
1 AAAATATA
*
5529158 TAAATATA
1 AAAATATA
*
5529166 AATAT-TA
1 AAAATATA
*
5529173 AATAT-TA
1 AAAATATA
5529180 AAAAT-TA
1 AAAATATA
5529187 ATAAA-ATA
1 A-AAATATA
5529195 AAAA-ATA
1 AAAATATA
5529202 AAAATA
1 AAAATA
5529208 AATATCTAAA
Statistics
Matches: 126, Mismatches: 13, Indels: 40
0.70 0.07 0.22
Matches are distributed among these distances:
6 5 0.04
7 35 0.28
8 58 0.46
9 13 0.10
10 8 0.06
11 5 0.04
12 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATATA
Found at i:5529135 original size:76 final size:72
Alignment explanation
Indices: 5529042--5529207 Score: 164
Period size: 76 Copynumber: 2.3 Consensus size: 72
5529032 TAAAATTTTA
* *
5529042 AAATTTAAAAATTTAAAAAT-TTAAAATAAAT-TAATTAAATAAAAAATATAAATAAATTAAA-A
1 AAATATAAAAAATTAAAAATATTAAAATAAATATAATT--AT-AAAAATATAAAT--ATTAAATA
5529104 TATAAAAATAAATT
61 T-TAAAAATAAA-T
* * * *
5529118 AAATCTAAAAAATT-AAAATATTATATTAAATATAATTATATAAATATAAATATTAAATATTAAA
1 AAATATAAAAAATTAAAAATATTAAAATAAATATAATTATAAAAATATAAATATTAAATATTAAA
*
5529182 AATTAAT
66 AATAAAT
5529189 AAA-ATAAAAAA-TAAAAATA
1 AAATATAAAAAATTAAAAATA
5529208 AATATCTAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
69 1 0.01
70 13 0.16
71 4 0.05
72 15 0.19
73 2 0.03
74 11 0.14
75 7 0.09
76 21 0.27
77 5 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (72 bp):
AAATATAAAAAATTAAAAATATTAAAATAAATATAATTATAAAAATATAAATATTAAATATTAAA
AATAAAT
Found at i:5529150 original size:7 final size:7
Alignment explanation
Indices: 5529140--5529187 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
5529130 TTAAAATATT
5529140 ATATTAA
1 ATATTAA
5529147 ATA-TAA
1 ATATTAA
*
5529153 TTATATAA
1 ATAT-TAA
5529161 ATA-TAA
1 ATATTAA
5529167 ATATTAA
1 ATATTAA
5529174 ATATTAA
1 ATATTAA
*
5529181 AAATTAA
1 ATATTAA
5529188 TAAAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
6 11 0.31
7 19 0.54
8 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATATTAA
Found at i:5529164 original size:6 final size:6
Alignment explanation
Indices: 5529085--5529212 Score: 67
Period size: 6 Copynumber: 22.0 Consensus size: 6
5529075 ATTAAATAAA
* * *
5529085 AAATAT AAATA- AATTA- AAATAT AAAAAT AAAT-T AAATCT AAA-A-
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
* *
5529128 AATTA- AAATAT -TATATT AAATAT AATTATAT AAATAT AAATATT AAATATT
1 AAATAT AAATAT AAATA-T AAATAT AA--ATAT AAATAT AAATA-T AAATA-T
* * * *
5529179 AAAAAT TAATA- AAATA- AAAAAT AAAAAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
5529213 CTAAAGATTT
Statistics
Matches: 97, Mismatches: 15, Indels: 20
0.73 0.11 0.15
Matches are distributed among these distances:
4 2 0.02
5 29 0.30
6 45 0.46
7 15 0.15
8 6 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATAT
Found at i:5529288 original size:13 final size:13
Alignment explanation
Indices: 5529224--5529296 Score: 52
Period size: 13 Copynumber: 6.0 Consensus size: 13
5529214 TAAAGATTTT
5529224 TTTATATT-ATAA
1 TTTATATTAATAA
5529236 TTT-TATTAA-AA
1 TTTATATTAATAA
*
5529247 CTT-T-TTAAT-A
1 TTTATATTAATAA
*
5529257 TTTATATAAAT-A
1 TTTATATTAATAA
*
5529269 TAATATATTAATAA
1 T-TTATATTAATAA
5529283 TTTATATTATATAA
1 TTTATATTA-ATAA
5529297 ATTAAAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
10 7 0.15
11 10 0.21
12 10 0.21
13 15 0.31
14 6 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTATATTAATAA
Found at i:5529294 original size:20 final size:18
Alignment explanation
Indices: 5529266--5529316 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
5529256 ATTTATATAA
*
5529266 ATATAATATATTAATAATTT
1 ATATTATATATTAA-AA-TT
5529286 ATATTATATAAATTAAAATT
1 ATATTATAT--ATTAAAATT
5529306 AT-TTATATATT
1 ATATTATATATT
5529317 TTATATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.11
19 6 0.21
20 12 0.43
21 2 0.07
22 5 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTATATATTAAAATT
Found at i:5529295 original size:31 final size:33
Alignment explanation
Indices: 5529258--5529327 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
5529248 TTTTTAATAT
*
5529258 TTATATAAA-TATAA-TATATTA-ATAATTTATA
1 TTATATAAATTAAAATTAT-TTATATAATTTATA
*
5529289 TTATATAAATTAAAATTATTTATATATTTTATA
1 TTATATAAATTAAAATTATTTATATAATTTATA
5529322 TTATAT
1 TTATAT
5529328 TTAATTTCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 9 0.26
32 7 0.21
33 18 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTATATAAATTAAAATTATTTATATAATTTATA
Found at i:5529325 original size:33 final size:31
Alignment explanation
Indices: 5529249--5529327 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 31
5529239 TATTAAAACT
*
5529249 TTTTAATATTTATATAAATATAATATATTAATA
1 TTTT-ATA-TTATATAAATAAAATATATTAATA
*
5529282 ATTTATATTATATAAATTAAAAT-TATTTATATA
1 TTTTATATTATATAAA-TAAAATATA-TTA-ATA
5529315 TTTTATATTATAT
1 TTTTATATTATAT
5529328 TTAATTTCGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 11 0.28
32 11 0.28
33 18 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TTTTATATTATATAAATAAAATATATTAATA
Found at i:5539280 original size:19 final size:19
Alignment explanation
Indices: 5539256--5539295 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5539246 TTAACTCTTA
*
5539256 AAATAATAATTT-TTTTCAT
1 AAATAAAAATTTATTTT-AT
5539275 AAATAAAAATTTATTTTAT
1 AAATAAAAATTTATTTTAT
5539294 AA
1 AA
5539296 GTTTTTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATAAAAATTTATTTTAT
Found at i:5539404 original size:19 final size:20
Alignment explanation
Indices: 5539380--5539425 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
5539370 TGTGTATGAT
*
5539380 AATTTTTTGATTTCA-TAAA
1 AATTTTTTAATTTCATTAAA
*
5539399 AATTTTTTAATTTTATTTAAA
1 AATTTTTTAATTTCA-TTAAA
5539420 AATTTT
1 AATTTT
5539426 AAAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 13 0.57
21 10 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
AATTTTTTAATTTCATTAAA
Found at i:5543835 original size:2 final size:2
Alignment explanation
Indices: 5543828--5543858 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5543818 TATTCAGAAA
5543828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5543859 AAGAGTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5552392 original size:20 final size:19
Alignment explanation
Indices: 5552360--5552411 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
5552350 TTTTAAATTA
*
5552360 ATTAAT-TTAATATTTATGAT
1 ATTAATATTAATA-TTA-AAT
5552380 ATTAATATT-ATATTAAAT
1 ATTAATATTAATATTAAAT
5552398 ATTAATATATAATA
1 ATTAATAT-TAATA
5552412 ATTTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.36
19 4 0.14
20 12 0.43
21 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATTAATATTAATATTAAAT
Found at i:5557857 original size:15 final size:16
Alignment explanation
Indices: 5557839--5557878 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
5557829 TTAAAAGTAA
5557839 TAAATATTATAATT-T
1 TAAATATTATAATTAT
*
5557854 TAAATTTTA-AATTAT
1 TAAATATTATAATTAT
5557869 TAAATATTAT
1 TAAATATTAT
5557879 TTTTTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATATTATAATTAT
Found at i:5559726 original size:13 final size:11
Alignment explanation
Indices: 5559695--5559740 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
5559685 TAAATATAAT
5559695 ATAATATAAAA
1 ATAATATAAAA
5559706 ATAATATAAAA
1 ATAATATAAAA
* * *
5559717 ATAATTTATAT
1 ATAATATAAAA
5559728 ATAATA-AAAA
1 ATAATATAAAA
5559738 ATA
1 ATA
5559741 TTAATATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
10 5 0.17
11 24 0.83
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:5559747 original size:20 final size:22
Alignment explanation
Indices: 5559706--5559749 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
5559696 TAATATAAAA
*
5559706 ATAATATAAAAATAATTTATAT
1 ATAATATAAAAATAATTAATAT
5559728 ATAATA-AAAAAT-ATTAATAT
1 ATAATATAAAAATAATTAATAT
5559748 AT
1 AT
5559750 TAAAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 6 0.29
22 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATATAAAAATAATTAATAT
Found at i:5559793 original size:30 final size:26
Alignment explanation
Indices: 5559736--5559794 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 26
5559726 ATATAATAAA
*
5559736 AAATATTAATATATTAAAATTTATAT
1 AAATATTAATATATTAAAAATTATAT
*
5559762 AAATATATAATATTTTAAATAAATTATTAT
1 AAATAT-TAATATATT-AA-AAATTA-TAT
5559792 AAA
1 AAA
5559795 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 6 0.22
27 8 0.30
28 2 0.07
29 5 0.19
30 6 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATATTAATATATTAAAAATTATAT
Found at i:5560329 original size:20 final size:20
Alignment explanation
Indices: 5560304--5560343 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5560294 ATTTAATTAT
5560304 TATTTTAATTACTA-TATTTA
1 TATTTTAATTA-TATTATTTA
5560324 TATTTTAATTATATTATTTA
1 TATTTTAATTATATTATTTA
5560344 AATATTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTAATTATATTATTTA
Found at i:5561203 original size:5 final size:5
Alignment explanation
Indices: 5561193--5561271 Score: 50
Period size: 5 Copynumber: 17.4 Consensus size: 5
5561183 TTTTTATAAT
* ** *
5561193 TTATA TTATA -TATA TTTTA AAATA TTA-A -TATA TTTGTA TTATA TT-T-
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA TTATA
5561239 TTATA TTATA TTA-A TTAT- TT-TA -TATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
5561272 TATACTATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
3 6 0.11
4 16 0.29
5 31 0.55
6 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:5561224 original size:27 final size:29
Alignment explanation
Indices: 5561194--5561266 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
5561184 TTTTATAATT
5561194 TATATTATATATATTTTA-A-AATATTAA
1 TATATTATATATATTTTATATAATATTAA
* *
5561221 TATATTTGTATTATATTTTTATATTATATTAA
1 TATA-TTATA-TATA-TTTTATATAATATTAA
*
5561253 T-TATTTTATATATT
1 TATATTATATATATT
5561267 ATATTTATAC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 4 0.11
28 6 0.16
29 8 0.21
30 9 0.24
31 3 0.08
32 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TATATTATATATATTTTATATAATATTAA
Found at i:5561225 original size:18 final size:19
Alignment explanation
Indices: 5561160--5561227 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 19
5561150 TTAAAGTAAT
*
5561160 ATATATTTATATAAATATAA
1 ATATATTT-TATAAATATTA
5561180 ATAT-TTTTATAATTTATATTA
1 ATATATTTTATAA---ATATTA
5561201 TATATATTTTA-AAATATTA
1 -ATATATTTTATAAATATTA
5561220 ATATATTT
1 ATATATTT
5561228 GTATTATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
18 13 0.31
19 9 0.21
20 4 0.10
21 5 0.12
22 6 0.14
23 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATATTTTATAAATATTA
Found at i:5561236 original size:19 final size:19
Alignment explanation
Indices: 5561193--5561281 Score: 64
Period size: 19 Copynumber: 4.9 Consensus size: 19
5561183 TTTTTATAAT
5561193 TTATATTATATATATTTTA
1 TTATATTATATATATTTTA
**
5561212 AAATATTA-ATATATTTGTA
1 TTATATTATATATATTT-TA
* *
5561231 TTATATT-TTTATATTATA
1 TTATATTATATATATTTTA
* *
5561249 TTA-ATTAT-TTTA-TATA
1 TTATATTATATATATTTTA
5561265 TTATATT-TATACTATTT
1 TTATATTATATA-TATTT
5561282 AATTTACATA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
16 8 0.15
17 10 0.19
18 16 0.30
19 20 0.37
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (19 bp):
TTATATTATATATATTTTA
Found at i:5561253 original size:32 final size:32
Alignment explanation
Indices: 5561192--5561285 Score: 88
Period size: 32 Copynumber: 2.9 Consensus size: 32
5561182 ATTTTTATAA
**
5561192 TTTATATTATATATATTT-TAAAATATTAATATAT
1 TTTATA-TAT-TATATTTATACTATATTAAT-TAT
* *
5561226 TTGTAT-TA-TATTTTTATATTATATTAATTAT
1 TT-TATATATTATATTTATACTATATTAATTAT
5561257 TTTATATATTATATTTATACTAT-TTAATT
1 TTTATATATTATATTTATACTATATTAATT
5561286 TACATAATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
30 3 0.06
31 19 0.37
32 22 0.43
33 2 0.04
34 2 0.04
35 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (32 bp):
TTTATATATTATATTTATACTATATTAATTAT
Found at i:5561287 original size:14 final size:13
Alignment explanation
Indices: 5561229--5561280 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
5561219 AATATATTTG
*
5561229 TATTATATTTTTA
1 TATTATATTTATA
5561242 TATTATA--T-TA
1 TATTATATTTATA
5561252 -ATTAT-TTTATA
1 TATTATATTTATA
5561263 TATTATATTTATA
1 TATTATATTTATA
5561276 CTATT
1 -TATT
5561281 TAATTTACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
9 5 0.15
10 3 0.09
11 3 0.09
12 5 0.15
13 13 0.39
14 4 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTATATTTATA
Found at i:5561538 original size:25 final size:27
Alignment explanation
Indices: 5561488--5561589 Score: 67
Period size: 25 Copynumber: 3.9 Consensus size: 27
5561478 AAAAATTATT
*
5561488 TTAATATATATTTTATTTAA-ATTTAATTA
1 TTAA-ATATAATTTA-TTAATA-TTAATTA
5561517 TTAAATAT-A-TTATTAATATTAA-TA
1 TTAAATATAATTTATTAATATTAATTA
* *
5561541 -TAAAAATAATTTTTTAATATT--TTA
1 TTAAATATAATTTATTAATATTAATTA
*
5561565 TTAAATAATAAATTTAATAAT-TTAA
1 TTAAAT-AT-AATTTATTAATATTAA
5561590 ATTAAAAGAG
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
23 6 0.10
24 5 0.09
25 22 0.38
26 8 0.14
27 9 0.16
28 4 0.07
29 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAAATATAATTTATTAATATTAATTA
Found at i:5562702 original size:24 final size:21
Alignment explanation
Indices: 5562671--5562758 Score: 60
Period size: 20 Copynumber: 4.1 Consensus size: 21
5562661 AATCTTGTCG
5562671 TAAATATAATAGTTTAATTTATT
1 TAAATATAATA-TTTAATTT-TT
*
5562694 T-AATCTATATAATTT--TTTTT
1 TAAATATA-AT-ATTTAATTTTT
5562714 TAAATATAATATTTAA--TTT
1 TAAATATAATATTTAATTTTT
*
5562733 TAAATTTTAATATTTCAAATTTTT
1 TAAA-TATAATATTT--AATTTTT
5562757 TA
1 TA
5562759 TTGTATTATA
Statistics
Matches: 52, Mismatches: 3, Indels: 19
0.70 0.04 0.26
Matches are distributed among these distances:
19 11 0.21
20 14 0.27
21 8 0.15
22 7 0.13
23 6 0.12
24 6 0.12
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (21 bp):
TAAATATAATATTTAATTTTT
Found at i:5562733 original size:20 final size:20
Alignment explanation
Indices: 5562671--5562747 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 20
5562661 AATCTTGTCG
5562671 TAAATATAATAGTTTAATTTAT
1 TAAATATAATA-TTTAATTT-T
* * *
5562693 TTAATCTATATAATTT-TTTTT
1 TAAATATA-AT-ATTTAATTTT
5562714 TAAATATAATATTTAA-TTT
1 TAAATATAATATTTAATTTT
*
5562733 TAAATTTTAATATTT
1 TAAA-TATAATATTT
5562748 CAAATTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
19 11 0.25
20 11 0.25
21 7 0.16
22 9 0.20
23 5 0.11
24 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (20 bp):
TAAATATAATATTTAATTTT
Found at i:5565681 original size:2 final size:2
Alignment explanation
Indices: 5565670--5565709 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5565660 TTTTTGTGTT
*
5565670 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5565710 CTTATCTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:5566247 original size:2 final size:2
Alignment explanation
Indices: 5566213--5566238 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5566203 ACAATGCTAC
5566213 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
5566239 GCATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5570654 original size:2 final size:2
Alignment explanation
Indices: 5570649--5570674 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5570639 CTGTGTGCAA
5570649 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
5570675 ACGAGAGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:5571598 original size:2 final size:2
Alignment explanation
Indices: 5571591--5571626 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5571581 AGTTTTTAAA
5571591 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
5571627 TCATAGTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5575066 original size:2 final size:2
Alignment explanation
Indices: 5575059--5575092 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5575049 TTTCACGATC
5575059 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5575093 ATAACTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5575653 original size:25 final size:25
Alignment explanation
Indices: 5575625--5575715 Score: 64
Period size: 25 Copynumber: 3.6 Consensus size: 25
5575615 TTTTAAATAA
5575625 TTATTTATTTAATAAAATATAATTT
1 TTATTTATTTAATAAAATATAATTT
* *
5575650 TTATTTAAATTTAAT--TATATAATAT
1 TTATTT--ATTTAATAAAATATAATTT
* * *
5575675 ATAATTATTAATATAAAATA-AATTT
1 TTATTTATTTA-ATAAAATATAATTT
*
5575700 TT-TTGTATTTTATAAA
1 TTATT-TATTTAATAAA
5575716 TAATAAAATA
Statistics
Matches: 49, Mismatches: 11, Indels: 13
0.67 0.15 0.18
Matches are distributed among these distances:
23 4 0.08
24 8 0.16
25 27 0.55
26 3 0.06
27 7 0.14
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
TTATTTATTTAATAAAATATAATTT
Found at i:5576385 original size:3 final size:3
Alignment explanation
Indices: 5576379--5576415 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
5576369 ACCCCCAAAG
*
5576379 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5576416 TAACTCGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5578653 original size:12 final size:12
Alignment explanation
Indices: 5578636--5578666 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5578626 GAGACAAAAG
5578636 TATTTTATTATT
1 TATTTTATTATT
5578648 TATTTTATTATT
1 TATTTTATTATT
*
5578660 TTTTTTA
1 TATTTTA
5578667 AAAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TATTTTATTATT
Found at i:5579129 original size:109 final size:103
Alignment explanation
Indices: 5578989--5579246 Score: 295
Period size: 103 Copynumber: 2.4 Consensus size: 103
5578979 TCTATTGGTA
* * * * *
5578989 CCTGAATACTATATAATT-ATTTGAAAAATAAATTATCTTATGTAAAAGGCGTTCGTACGTCACT
1 CCTGAAT-CTATATAATTAATGTAAAAAATAAATTATCTTATATAAAAAGCGTTCATACGTCA-T
*
5579053 TTATGAATTTAAACAATGA-CTAATTTTGGAGCCAATTTATTCATG
64 TTATGAATTTAAACAATAATCT-ATTTT-GAG---ATTT-TTCATG
* * *
5579098 CCTGAATCTATATAATTAATGTAAAAAATAAATTATTTTATATAAAAAGCGTTTATGCGTCATTT
1 CCTGAATCTATATAATTAATGTAAAAAATAAATTATCTTATATAAAAAGCGTTCATACGTCATTT
* * * *
5579163 ATGACTTTAGATAATAATCTATTTTGAGATTTTTGATG
66 ATGAATTTAAACAATAATCTATTTTGAGATTTTTCATG
* *
5579201 CCTAAATCTATGTAATTAATGTAAAAAATAAATTATCTTATATAAA
1 CCTGAATCTATATAATTAATGTAAAAAATAAATTATCTTATATAAA
5579247 GAGATAAGAT
Statistics
Matches: 131, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
103 48 0.37
104 4 0.03
107 3 0.02
108 31 0.24
109 45 0.34
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (103 bp):
CCTGAATCTATATAATTAATGTAAAAAATAAATTATCTTATATAAAAAGCGTTCATACGTCATTT
ATGAATTTAAACAATAATCTATTTTGAGATTTTTCATG
Found at i:5579545 original size:21 final size:19
Alignment explanation
Indices: 5579513--5579559 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
5579503 AACATTAACT
5579513 AATTATAAAAATATATAAACA
1 AATTA-AAAAATATATAAA-A
*
5579534 AATTAAATAAATATATTAAA
1 AATTAAA-AAATATATAAAA
5579554 AATTAA
1 AATTAA
5579560 TACAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTAAAAAATATATAAAA
Found at i:5581948 original size:13 final size:13
Alignment explanation
Indices: 5581911--5581954 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
5581901 ATATATATAT
*
5581911 ATATATATATTTA
1 ATATTTATATTTA
5581924 AGTATTTATATTTA
1 A-TATTTATATTTA
*
5581938 ATATTTGTATTTA
1 ATATTTATATTTA
5581951 ATAT
1 ATAT
5581955 AAAAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:5583809 original size:10 final size:10
Alignment explanation
Indices: 5583791--5583819 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5583781 AATTTTCAGC
5583791 AAAAA-AAAA
1 AAAAAGAAAA
5583800 AAAAAGAAAA
1 AAAAAGAAAA
5583810 AAAAAGAAAA
1 AAAAAGAAAA
5583820 CAGAAGCCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:5583813 original size:17 final size:17
Alignment explanation
Indices: 5583791--5583824 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5583781 AATTTTCAGC
5583791 AAAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAGAA
* *
5583808 AAAAAAAGAAAACAGAA
1 AAAAAAAAAAAAAAGAA
5583825 GCCGTAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAGAA
Found at i:5584494 original size:25 final size:26
Alignment explanation
Indices: 5584466--5584522 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
5584456 TATTAATCAA
*
5584466 TTAAAAATTATAA-AA-ATTATATATT
1 TTAAAAATAATAATAATATTAT-TATT
*
5584491 TTAATAATAATAATAATATTATTATT
1 TTAAAAATAATAATAATATTATTATT
5584517 TTAAAA
1 TTAAAA
5584523 TCTATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.41
26 11 0.41
27 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TTAAAAATAATAATAATATTATTATT
Found at i:5584751 original size:21 final size:21
Alignment explanation
Indices: 5584695--5584759 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 21
5584685 TATAATTATT
5584695 TTAAATTTTATATTTTTATTAA
1 TTAAA-TTTATATTTTTATTAA
*
5584717 TAATAATTTA-ATTTTTATTAA
1 TTA-AATTTATATTTTTATTAA
* *
5584738 TTAAATTAATA-TTTAATTAA
1 TTAAATTTATATTTTTATTAA
5584758 TT
1 TT
5584760 TATGACATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 15 0.41
21 14 0.38
22 6 0.16
23 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAAATTTATATTTTTATTAA
Found at i:5584791 original size:2 final size:2
Alignment explanation
Indices: 5584786--5584811 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5584776 TTATTTTTTA
5584786 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
5584812 TGATTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5585945 original size:18 final size:19
Alignment explanation
Indices: 5585922--5585960 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5585912 CAAAGAATGA
*
5585922 ATATTT-TTATATATATAT
1 ATATTTATTATATAAATAT
5585940 ATATTTGATTATATAAATAT
1 ATATTT-ATTATATAAATAT
5585960 A
1 A
5585961 ATATATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATATTTATTATATAAATAT
Found at i:5585968 original size:7 final size:7
Alignment explanation
Indices: 5585949--5586013 Score: 62
Period size: 7 Copynumber: 9.1 Consensus size: 7
5585939 TATATTTGAT
5585949 TATATAAA
1 TATA-AAA
*
5585957 TATAATA
1 TATAAAA
5585964 TATAAAA
1 TATAAAA
5585971 TTATTAAAA
1 -TA-TAAAA
5585980 TAT--AA
1 TATAAAA
*
5585985 TATAATA
1 TATAAAA
*
5585992 TAAAAAA
1 TATAAAA
5585999 TATAAAA
1 TATAAAA
5586006 TATAAAA
1 TATAAAA
5586013 T
1 T
5586014 TTATAAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
5 5 0.11
7 29 0.62
8 8 0.17
9 5 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
TATAAAA
Found at i:5585984 original size:16 final size:15
Alignment explanation
Indices: 5585957--5586051 Score: 72
Period size: 16 Copynumber: 6.3 Consensus size: 15
5585947 ATTATATAAA
*
5585957 TATAATATATAAAAT
1 TATAAAATATAAAAT
5585972 TATTAAAATAT--AA-
1 TA-TAAAATATAAAAT
* *
5585985 TATAATATA-AAAAA
1 TATAAAATATAAAAT
5585999 TATAAAATATAAAATT
1 TATAAAATATAAAA-T
* * *
5586015 TATAAATTATTAATT
1 TATAAAATATAAAAT
5586030 TAATATAAATATAAAAT
1 T-ATA-AAATATAAAAT
5586047 TATAA
1 TATAA
5586052 CATAAAATTA
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
12 6 0.10
13 4 0.06
14 10 0.16
15 9 0.15
16 24 0.39
17 9 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATAAAATATAAAAT
Found at i:5586691 original size:18 final size:18
Alignment explanation
Indices: 5586643--5586697 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
5586633 GTTCTATTTA
*
5586643 ATTATTTTTTTAATATAT
1 ATTATTTTTTTATTATAT
* *
5586661 ATTATTTTATTATTTTAT
1 ATTATTTTTTTATTATAT
5586679 -TTAATTTTTTTATTA-AT
1 ATT-ATTTTTTTATTATAT
5586696 AT
1 AT
5586698 AAAAAATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.13
18 26 0.87
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTATTTTTTTATTATAT
Found at i:5586812 original size:27 final size:25
Alignment explanation
Indices: 5586752--5586812 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 25
5586742 GTTTATTTTT
5586752 TATTTTTAATATAATAAATAAAAATA
1 TATTTTT-ATATAATAAATAAAAATA
* *
5586778 T-TAATTTATATAATAATTTAAAAAATA
1 TAT-TTTTATATAATAA-AT-AAAAATA
5586805 TATTTTTA
1 TATTTTTA
5586813 AAATATTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
25 10 0.36
26 5 0.18
27 12 0.43
28 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTTTTATATAATAAATAAAAATA
Found at i:5586817 original size:25 final size:27
Alignment explanation
Indices: 5586751--5586817 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 27
5586741 AGTTTATTTT
*
5586751 TTATTTTTAATATAATAAATAAAAATA
1 TTATTTTTAAAATAATAAATAAAAATA
* * **
5586778 TTAATTTATATAATAATTTA-AAAAATA
1 TT-ATTTTTAAAATAATAAATAAAAATA
5586805 -TATTTTTAAAATA
1 TTATTTTTAAAATA
5586818 TTTGTTAACA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
25 10 0.31
26 1 0.03
27 9 0.28
28 12 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TTATTTTTAAAATAATAAATAAAAATA
Found at i:5590909 original size:21 final size:21
Alignment explanation
Indices: 5590877--5590949 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
5590867 GTTTCTCCAC
5590877 TTAA-AATCAAAATATTATTTT
1 TTAAGAAT-AAAATATTATTTT
* **
5590898 TTAAGAATAAAAT-TCAAATT
1 TTAAGAATAAAATATTATTTT
* * *
5590918 TAAATTAATTAAATATTATTTT
1 TTAA-GAATAAAATATTATTTT
5590940 TTAAGAATAA
1 TTAAGAATAA
5590950 TTATATTAAT
Statistics
Matches: 37, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
20 7 0.19
21 20 0.54
22 10 0.27
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (21 bp):
TTAAGAATAAAATATTATTTT
Found at i:5591937 original size:25 final size:25
Alignment explanation
Indices: 5591909--5591961 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
5591899 TATTAATAGA
*
5591909 TTAAT-ATATGTATTATATTTTATAT
1 TTAATAATATATATTAT-TTTTATAT
*
5591934 TTAATAATTTATATTATTTTTATAT
1 TTAATAATATATATTATTTTTATAT
5591959 TTA
1 TTA
5591962 TAAAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTAATAATATATATTATTTTTATAT
Found at i:5591968 original size:26 final size:26
Alignment explanation
Indices: 5591919--5591973 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
5591909 TTAATATATG
* *
5591919 TATTATATTTTATATTTAATAATTTA
1 TATTATATTTTATATTTAAAAATTAA
5591945 TATTAT-TTTTATATTTATAAAATTAA
1 TATTATATTTTATATTTA-AAAATTAA
5591971 TAT
1 TAT
5591974 AAAAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTATATTTTATATTTAAAAATTAA
Found at i:5592417 original size:2 final size:2
Alignment explanation
Indices: 5592412--5592441 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5592402 ATGTGAATAA
5592412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5592442 TTAATTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5592527 original size:18 final size:18
Alignment explanation
Indices: 5592504--5592561 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
5592494 TGATTAATAT
5592504 AAAATAATTAAAATATAA
1 AAAATAATTAAAATATAA
* *
5592522 AAAATAAATAAATATATTA
1 AAAATAATTAAA-ATATAA
* * *
5592541 TAAATTATTAATATATTAA
1 AAAATAATTAAAATA-TAA
5592560 AA
1 AA
5592562 TTTATATAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATAATTAAAATATAA
Found at i:5592534 original size:17 final size:18
Alignment explanation
Indices: 5592504--5592537 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5592494 TGATTAATAT
*
5592504 AAAATAATTAAAATATAA
1 AAAATAAATAAAATATAA
5592522 AAAATAAAT-AAATATA
1 AAAATAAATAAAATATA
5592538 TTATAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAAATAAAATATAA
Found at i:5592560 original size:27 final size:28
Alignment explanation
Indices: 5592530--5592598 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
5592520 AAAAAATAAA
*
5592530 TAAATATATTATAAATTA-TTAATATAT
1 TAAATATATTATAAAATATTTAATATAT
*
5592557 TAAA-AT-TTATATAAATATTTAATATTT
1 TAAATATATTATA-AAATATTTAATATAT
5592584 TAAATATGATTATAA
1 TAAATAT-ATTATAA
5592599 TAAAAATTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
25 5 0.14
26 6 0.17
27 16 0.46
28 2 0.06
29 1 0.03
30 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
TAAATATATTATAAAATATTTAATATAT
Found at i:5592566 original size:18 final size:19
Alignment explanation
Indices: 5592532--5592598 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 19
5592522 AAAATAAATA
5592532 AATATATTATAAATTAT-T
1 AATATATTATAAATTATAT
5592550 AATATATTA-AAATTTATAT
1 AATATATTATAAA-TTATAT
*
5592569 AA-ATATT-TAATATTTTA-
1 AATATATTATAA-ATTATAT
5592586 AATATGATTATAA
1 AATAT-ATTATAA
5592599 TAAAAATTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
17 5 0.12
18 26 0.63
19 7 0.17
20 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (19 bp):
AATATATTATAAATTATAT
Found at i:5598400 original size:139 final size:139
Alignment explanation
Indices: 5598150--5598408 Score: 437
Period size: 139 Copynumber: 1.9 Consensus size: 139
5598140 AAGTGACATG
* *
5598150 AACATAACAATATCATAAACAAATTAACTGAAAGCAGTATTAAAATGAGTACAGACACAGTGTGT
1 AACATAACAATATCATAAACAAATTAACTGAAAGCAGTAGTAAAATGAGTACAGACACAGTATGT
* * * * *
5598215 GTGACCCACAAGAAAAAATGTTGAAAAGTTCAGTACTCTATATGCAGTTAAAACAGAGAACAGGT
66 CTAACCCACAAGAAAAAACGTTGAAAAGTACAGTACTCTATATGCAGTAAAAACAGAGAACAGGT
5598280 TCCCATCAA
131 TCCCATCAA
* *
5598289 AACATAACAATATCATAAACAAATTAACTGAAAGCAGTAGTAAAATGAGTATAGATACAGTATGT
1 AACATAACAATATCATAAACAAATTAACTGAAAGCAGTAGTAAAATGAGTACAGACACAGTATGT
5598354 CTAACCCACAAGAAAAAACGTTGAAAAGTACAGTACTCTATATGCAGTAAAAACA
66 CTAACCCACAAGAAAAAACGTTGAAAAGTACAGTACTCTATATGCAGTAAAAACA
5598409 AAAAAAAAAG
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
139 111 1.00
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (139 bp):
AACATAACAATATCATAAACAAATTAACTGAAAGCAGTAGTAAAATGAGTACAGACACAGTATGT
CTAACCCACAAGAAAAAACGTTGAAAAGTACAGTACTCTATATGCAGTAAAAACAGAGAACAGGT
TCCCATCAA
Found at i:5603397 original size:21 final size:21
Alignment explanation
Indices: 5603371--5603411 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5603361 ATTGTAATTA
*
5603371 AATAATTAACTTTAATAACAT
1 AATAATTAAATTTAATAACAT
5603392 AATAATTAAATTTAATAACA
1 AATAATTAAATTTAATAACA
5603412 CAAATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
AATAATTAAATTTAATAACAT
Found at i:5603425 original size:24 final size:21
Alignment explanation
Indices: 5603370--5603417 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
5603360 TATTGTAATT
*
5603370 AAATAATTAACTTTAATAACA
1 AAATAATTAAATTTAATAACA
*
5603391 TAATAATTAAATTTAATAACA
1 AAATAATTAAATTTAATAACA
5603412 CAAATA
1 -AAATA
5603418 TAATTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAATTAAATTTAATAACA
Found at i:5603697 original size:24 final size:23
Alignment explanation
Indices: 5603662--5603726 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 23
5603652 CTAGAATAAG
* *
5603662 ATCTATTATAATCATTAAAAATTT
1 ATCTATTTTAATC-TTAAAAATTC
5603686 ATCTATTTTAATCTCTAAAAATTC
1 ATCTATTTTAATCT-TAAAAATTC
5603710 ATCTATTTTAATCTTAA
1 ATCTATTTTAATCTTAA
5603727 GGATTTGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 4 0.11
24 34 0.89
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (23 bp):
ATCTATTTTAATCTTAAAAATTC
Done.