Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 33 of 52
Found at i:5681091 original size:2 final size:2
Alignment explanation
Indices: 5681086--5681115 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5681076 AATACTATTA
5681086 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
5681116 AATGCTCCAC
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:5681730 original size:2 final size:2
Alignment explanation
Indices: 5681718--5681779 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
5681708 AATTGGATCC
*
5681718 AT AT GT AT AT AT 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 AT AT AT AT AT AT
5681760 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
5681780 TTTTATTTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5682039 original size:18 final size:18
Alignment explanation
Indices: 5682002--5682039 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5681992 TGTTAATATT
*
5682002 TTAAAATTAAATTTAAAA
1 TTAAAATTAAATATAAAA
5682020 TTAAAA-TAAATATAATAA
1 TTAAAATTAAATATAA-AA
5682038 TT
1 TT
5682040 TATTAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAATTAAATATAAAA
Found at i:5682154 original size:17 final size:18
Alignment explanation
Indices: 5682132--5682173 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
5682122 CAAGTCAATG
5682132 AATTTAATAAAT-AATTT
1 AATTTAATAAATAAATTT
5682149 AATTT-ATAAATAAATTT
1 AATTTAATAAATAAATTT
*
5682166 ATTTTAAT
1 AATTTAAT
5682174 GCTCAATGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 14 0.64
18 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTAATAAATAAATTT
Found at i:5683344 original size:2 final size:2
Alignment explanation
Indices: 5683332--5683362 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5683322 GATCATGGTG
*
5683332 AT AT AT CT 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
5683363 AATTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5683425 original size:15 final size:15
Alignment explanation
Indices: 5683405--5683435 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5683395 CATCCAATTC
*
5683405 ATACAATCATTGTTA
1 ATACAAGCATTGTTA
5683420 ATACAAGCATTGTTA
1 ATACAAGCATTGTTA
5683435 A
1 A
5683436 AAAAAGATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (15 bp):
ATACAAGCATTGTTA
Found at i:5685112 original size:19 final size:19
Alignment explanation
Indices: 5685088--5685125 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5685078 AATATAATAA
*
5685088 TTATAA-TTATAGTTACTTT
1 TTATAACTTAAAG-TACTTT
5685107 TTATAACTTAAAGTACTTT
1 TTATAACTTAAAGTACTTT
5685126 ATGACACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATAACTTAAAGTACTTT
Found at i:5686810 original size:25 final size:25
Alignment explanation
Indices: 5686752--5686810 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
5686742 TTAAATTAAA
5686752 TAAAAATAATATATTAAATATAATTTT
1 TAAAAAT--TATATTAAATATAATTTT
* *
5686779 TTAAAATTATATTTAA-ATAATTTT
1 TAAAAATTATATTAAATATAATTTT
5686803 TAATAAAT
1 TAA-AAAT
5686811 ACTTATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 10 0.36
25 12 0.43
27 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TAAAAATTATATTAAATATAATTTT
Found at i:5687791 original size:20 final size:21
Alignment explanation
Indices: 5687745--5687798 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5687735 TAAAATTTAC
* *
5687745 TTTAAAATAAAAATGTCATCT
1 TTTAAATTAAAAATATCATCT
* *
5687766 TATAAATTAAAAATATTAT-T
1 TTTAAATTAAAAATATCATCT
5687786 TTTAAATTAAAAA
1 TTTAAATTAAAAA
5687799 ATACGAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (21 bp):
TTTAAATTAAAAATATCATCT
Found at i:5690441 original size:2 final size:2
Alignment explanation
Indices: 5690434--5690467 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5690424 TCTCCTTTTA
5690434 AT AT 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 AT AT
5690468 TTGCCAGATG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5691837 original size:3 final size:3
Alignment explanation
Indices: 5691829--5691874 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5691819 ATAAAACACA
5691829 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5691875 TAAATTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5696158 original size:21 final size:20
Alignment explanation
Indices: 5696095--5696159 Score: 53
Period size: 22 Copynumber: 3.1 Consensus size: 20
5696085 CAATCCGATT
5696095 TATTTTTTAA-TTATATAATAAA
1 TATTTTTTAATTTAT-TAAT--A
* *
5696117 TAATTTTT-ATTTGTTATATA
1 TATTTTTTAATTTATTA-ATA
5696137 TATTTTTTAATTTATGTAATA
1 TATTTTTTAATTTAT-TAATA
5696158 TA
1 TA
5696160 AATATTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
20 8 0.23
21 13 0.37
22 14 0.40
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TATTTTTTAATTTATTAATA
Found at i:5696691 original size:28 final size:29
Alignment explanation
Indices: 5696653--5696729 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 29
5696643 TACAAATTCA
*
5696653 TATTTAAATATAAAATATATATTATATG-
1 TATTTATATATAAAATATATATTATATGC
* *
5696681 TATTTATATAT-ATATATA-ATTTTATGCC
1 TATTTATATATAAAATATATATTATATG-C
*
5696709 TCATTAATATATAAAATATAT
1 T-ATTTATATATAAAATATAT
5696730 TTAAATATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 7 0.18
27 6 0.15
28 11 0.28
29 9 0.23
30 6 0.15
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (29 bp):
TATTTATATATAAAATATATATTATATGC
Found at i:5696763 original size:2 final size:2
Alignment explanation
Indices: 5696758--5696784 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5696748 TATTTGTGGA
5696758 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
5696785 ATGTTATCAT
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:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:5702692 original size:57 final size:57
Alignment explanation
Indices: 5702603--5702711 Score: 200
Period size: 57 Copynumber: 1.9 Consensus size: 57
5702593 CCGACATCTT
**
5702603 GTGCTGCTTTAGCATTTGGACTATTTTGTTTCTGAGCAAAAGAGTCATTTTCCTGTA
1 GTGCTGCTTTAGCATTTGGACTATTTCATTTCTGAGCAAAAGAGTCATTTTCCTGTA
5702660 GTGCTGCTTTAGCATTTGGACTATTTCATTTCTGAGCAAAAGAGTCATTTTC
1 GTGCTGCTTTAGCATTTGGACTATTTCATTTCTGAGCAAAAGAGTCATTTTC
5702712 AAGTAGTGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (57 bp):
GTGCTGCTTTAGCATTTGGACTATTTCATTTCTGAGCAAAAGAGTCATTTTCCTGTA
Found at i:5704525 original size:15 final size:17
Alignment explanation
Indices: 5704491--5704528 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
5704481 TTTTATTTTT
5704491 TTATATATAATAATTGA
1 TTATATATAATAATTGA
*
5704508 TTATA-ATAAT-ATTTA
1 TTATATATAATAATTGA
5704523 TTATAT
1 TTATAT
5704529 TTAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 5 0.26
17 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTATATATAATAATTGA
Found at i:5704548 original size:21 final size:23
Alignment explanation
Indices: 5704522--5704586 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 23
5704512 AATAATATTT
5704522 ATTAT-ATTTAAAATTATA-ATA
1 ATTATAATTTAAAATTATATATA
*
5704543 ATTATAATATAAAATATATGTATATA
1 ATTATAATTTAAAAT-TA--TATATA
*
5704569 ATTATAATTTAAATTTAT
1 ATTATAATTTAAAATTAT
5704587 TATTAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 5 0.14
22 8 0.22
23 3 0.08
25 4 0.11
26 16 0.44
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTATAATTTAAAATTATATATA
Found at i:5705106 original size:27 final size:27
Alignment explanation
Indices: 5705032--5705132 Score: 89
Period size: 32 Copynumber: 3.5 Consensus size: 27
5705022 TATTACGAGG
*
5705032 ATATAAATATATAATTTTATTAAAATTA
1 ATATAAATATATAA-TATATTAAAATTA
*
5705060 ATATAATATTAATTATTAATATATTAAAATTT
1 ATATAA-A-T-A-TA-TAATATATTAAAATTA
*
5705092 ATATAAATATATAATAT-TTTAAATGTA
1 ATATAAATATATAATATATTAAAAT-TA
5705119 AT-TATAATATATAA
1 ATATA-AATATATAA
5705133 AAAATATGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
26 8 0.13
27 18 0.29
28 8 0.13
29 2 0.03
30 2 0.03
31 2 0.03
32 19 0.31
33 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
ATATAAATATATAATATATTAAAATTA
Found at i:5706740 original size:28 final size:27
Alignment explanation
Indices: 5706698--5706752 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5706688 CTCAATTACT
* *
5706698 ATTTAAATAATTAAAATAATTTTTTAAA
1 ATTTAAATAAAT-AAATAAATTTTTAAA
*
5706726 ATTTTAATAAATAAATAAATTTTTAAA
1 ATTTAAATAAATAAATAAATTTTTAAA
5706753 TTAAATGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
ATTTAAATAAATAAATAAATTTTTAAA
Found at i:5709196 original size:19 final size:16
Alignment explanation
Indices: 5709166--5709213 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 16
5709156 ATATTATTAT
5709166 TTATTTAATATTAATAA
1 TTATTTAATATTAA-AA
5709183 TATATTTAAATATTTAAAA
1 T-TATTT-AATA-TTAAAA
5709202 TTATTTTAATAT
1 TTA-TTTAATAT
5709214 AAATTGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.07
18 11 0.41
19 10 0.37
20 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTTAATATTAAAA
Found at i:5710326 original size:26 final size:27
Alignment explanation
Indices: 5710274--5710326 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
5710264 GTAAACGGAG
* * *
5710274 ATTTTATAATTTTTTTTAAGTACATAT
1 ATTTTATAATTTATATTAAATACATAT
*
5710301 ATTTTAT-ATTTATATTAAATATATAT
1 ATTTTATAATTTATATTAAATACATAT
5710327 TTAAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
ATTTTATAATTTATATTAAATACATAT
Found at i:5710327 original size:17 final size:18
Alignment explanation
Indices: 5710305--5710373 Score: 76
Period size: 18 Copynumber: 4.1 Consensus size: 18
5710295 ACATATATTT
*
5710305 TATATTTATAT-TAAATA
1 TATATTTAAATATAAATA
5710322 TATATTTAAATATAAATA
1 TATATTTAAATATAAATA
*
5710340 TA-A---AAATATAATTA
1 TATATTTAAATATAAATA
*
5710354 TATATATAAATATAAATA
1 TATATTTAAATATAAATA
5710372 TA
1 TA
5710374 AAAAAATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
17 11 0.25
18 20 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATTTAAATATAAATA
Found at i:5710339 original size:6 final size:6
Alignment explanation
Indices: 5710316--5710386 Score: 67
Period size: 6 Copynumber: 12.0 Consensus size: 6
5710306 ATATTTATAT
* * * *
5710316 TAAATA TATATT TAAATA TAAATA TAAAAATA TAATTA TATATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA T--AAATA TAAATA TAAATA TAAATA
5710366 TAAATA TAAA-A -AAAT- TAAATA
1 TAAATA TAAATA TAAATA TAAATA
5710387 AATTCATATT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
4 3 0.06
5 5 0.10
6 38 0.73
8 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TAAATA
Found at i:5710346 original size:26 final size:26
Alignment explanation
Indices: 5710317--5710369 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
5710307 TATTTATATT
5710317 AAATATATATT-TAAATATAAATATAA
1 AAATATA-ATTATAAATATAAATATAA
*
5710343 AAATATAATTATATATATAAATATAA
1 AAATATAATTATAAATATAAATATAA
5710369 A
1 A
5710370 TATAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATATAATTATAAATATAAATATAA
Found at i:5711071 original size:19 final size:19
Alignment explanation
Indices: 5711049--5711086 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5711039 TATAAATATT
*
5711049 TATTTATAT-TAATATATAA
1 TATTTAAATATAAT-TATAA
5711068 TATTTAAATATAATTATAA
1 TATTTAAATATAATTATAA
5711087 AATTAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTAAATATAATTATAA
Found at i:5711083 original size:24 final size:24
Alignment explanation
Indices: 5711026--5711079 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
5711016 GTATAAAAAA
*
5711026 TAAAT-TATTATTATATAAATATT
1 TAAATATATTAATATATAAATATT
**
5711049 TATTTATATTAATATAT-AATATT
1 TAAATATATTAATATATAAATATT
5711072 TAAATATA
1 TAAATATA
5711080 ATTATAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAATATATTAATATATAAATATT
Found at i:5711328 original size:11 final size:11
Alignment explanation
Indices: 5711312--5711378 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
5711302 TATTAATTTA
5711312 TATATTTATAT
1 TATATTTATAT
*
5711323 TATATTTATTT
1 TATATTTATAT
*
5711334 TAATTTTTATAT
1 T-ATATTTATAT
* *
5711346 TTTAATTATAT
1 TATATTTATAT
* *
5711357 TAAATTT-TTT
1 TATATTTATAT
5711367 ATATATTTATAT
1 -TATATTTATAT
5711379 AATTTTTTAT
Statistics
Matches: 41, Mismatches: 12, Indels: 5
0.71 0.21 0.09
Matches are distributed among these distances:
10 2 0.05
11 28 0.68
12 11 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTTATAT
Found at i:5711333 original size:23 final size:22
Alignment explanation
Indices: 5711302--5711384 Score: 55
Period size: 23 Copynumber: 3.7 Consensus size: 22
5711292 TAATTAAATC
*
5711302 TATTAATTTATATATTTATATTA
1 TATTTATTTATAT-TTTATATTA
*
5711325 TATTTATTT-TAATTTTTATATTT
1 TATTTATTTAT-A-TTTTATATTA
* * *
5711348 TAATTATATTAAATTTTTTA-TA
1 TATTTAT-TTATATTTTATATTA
*
5711370 TATTTATATA-ATTTT
1 TATTTATTTATATTTT
5711385 TTATAAATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
20 5 0.10
21 2 0.04
22 8 0.17
23 29 0.60
24 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTTATTTATATTTTATATTA
Found at i:5711344 original size:29 final size:29
Alignment explanation
Indices: 5711304--5711378 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
5711294 ATTAAATCTA
* *
5711304 TTAATTTATATATTTATATTATATTTATT
1 TTAATTTATATATTTATATTATATTAAAT
*
5711333 TTAATTTTTATATTT-TAATTATATTAAAT
1 TTAATTTATATATTTAT-ATTATATTAAAT
5711362 TT--TTTATATATTTATAT
1 TTAATTTATATATTTATAT
5711379 AATTTTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 12 0.30
28 2 0.05
29 26 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TTAATTTATATATTTATATTATATTAAAT
Found at i:5711365 original size:25 final size:23
Alignment explanation
Indices: 5711307--5711375 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
5711297 AAATCTATTA
* * * *
5711307 ATTTATATATTTATATTATATTT
1 ATTTAAATTTTTATATTTTAATT
*
5711330 ATTTTAATTTTTATATTTTAATT
1 ATTTAAATTTTTATATTTTAATT
5711353 ATATTAAATTTTTTATATATTTA
1 AT-TTAAA-TTTTTATAT-TTTA
5711376 TATAATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 20 0.54
24 4 0.11
25 9 0.24
26 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTAAATTTTTATATTTTAATT
Found at i:5711384 original size:20 final size:20
Alignment explanation
Indices: 5711359--5711419 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
5711349 AATTATATTA
5711359 AATTTTTTATATATTTATAT
1 AATTTTTTATATATTTATAT
*
5711379 AATTTTTTATA-AATTA-AT
1 AATTTTTTATATATTTATAT
5711397 AATATTTATTATATATTT-TAT
1 AAT-TTT-TTATATATTTATAT
5711418 AA
1 AA
5711420 ATTAATGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 5 0.14
19 7 0.20
20 16 0.46
21 7 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AATTTTTTATATATTTATAT
Found at i:5711389 original size:34 final size:32
Alignment explanation
Indices: 5711304--5711389 Score: 81
Period size: 34 Copynumber: 2.7 Consensus size: 32
5711294 ATTAAATCTA
*
5711304 TTAATTTATATA---TTTATATTATATTTATT
1 TTAATTTATATATTTTTTATATTAAATTTATT
*
5711333 TTAATTTTTATATTTTAATTATATTAAATTT-TT
1 TTAATTTATATATTTT--TTATATTAAATTTATT
5711366 TATATATTTATATAATTTTTTATA
1 T-TA-ATTTATAT-ATTTTTTATA
5711390 AATTAATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
29 11 0.24
32 1 0.02
33 3 0.07
34 19 0.41
35 7 0.15
36 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (32 bp):
TTAATTTATATATTTTTTATATTAAATTTATT
Found at i:5711403 original size:29 final size:29
Alignment explanation
Indices: 5711367--5711435 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
5711357 TAAATTTTTT
*
5711367 ATATATTTATATA-ATTTTTTATAAATTA
1 ATATATTTATATATATATTTTATAAATTA
5711395 ATAATATTTAT-TATATATTTTATAAATTA
1 AT-ATATTTATATATATATTTTATAAATTA
*
5711424 ATGTATTTATAT
1 ATATATTTATAT
5711436 TACTCTCATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 11 0.31
29 25 0.69
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (29 bp):
ATATATTTATATATATATTTTATAAATTA
Found at i:5711808 original size:28 final size:28
Alignment explanation
Indices: 5711775--5711857 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
5711765 GTTCATATTT
5711775 TATTTTTTAATTTAATTTTAAAAATATA
1 TATTTTTTAATTTAATTTTAAAAATATA
* ** * *
5711803 TGTTTTAAAATTTAATTTTTAATAATTTAA
1 TATTTTTTAATTTAA-TTTTAAAAATAT-A
5711833 TATTTTTTAA-TT-ATTTT-AAAATATA
1 TATTTTTTAATTTAATTTTAAAAATATA
5711858 AATAACTTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
25 1 0.02
26 5 0.12
27 4 0.09
28 13 0.30
29 12 0.28
30 8 0.19
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (28 bp):
TATTTTTTAATTTAATTTTAAAAATATA
Found at i:5711822 original size:14 final size:15
Alignment explanation
Indices: 5711783--5711838 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
5711773 TTTATTTTTT
*
5711783 AATTTAAT-TTTAAA
1 AATTTAATATTTTAA
* *
5711797 AATAT-ATGTTTTAA
1 AATTTAATATTTTAA
5711811 AATTTAAT-TTTTAA
1 AATTTAATATTTTAA
5711825 TAATTTAATATTTT
1 -AATTTAATATTTT
5711839 TTAATTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 2 0.06
14 19 0.54
15 10 0.29
16 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
AATTTAATATTTTAA
Found at i:5711844 original size:15 final size:15
Alignment explanation
Indices: 5711782--5711838 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
5711772 TTTTATTTTT
5711782 TAATTTAA-TTTTAA
1 TAATTTAATTTTTAA
* *
5711796 AAATAT-ATGTTTTAA
1 TAATTTAAT-TTTTAA
5711811 -AATTTAATTTTTAA
1 TAATTTAATTTTTAA
5711825 TAATTTAATATTTT
1 TAATTTAAT-TTTT
5711839 TTAATTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 1 0.03
14 14 0.40
15 16 0.46
16 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TAATTTAATTTTTAA
Found at i:5711888 original size:16 final size:16
Alignment explanation
Indices: 5711869--5711915 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
5711859 ATAACTTAAC
5711869 ATATTTTATAATATTT
1 ATATTTTATAATATTT
*
5711885 ATATTATA-ATATATTT
1 ATATTTTATA-ATATTT
5711901 ATTATTTATATAATA
1 A-TATTT-TATAATA
5711916 AAAATTACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.04
16 14 0.56
17 4 0.16
18 5 0.20
19 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTTTATAATATTT
Found at i:5712289 original size:17 final size:19
Alignment explanation
Indices: 5712264--5712305 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
5712254 AGATCGTTTA
*
5712264 TTATTTTAAA-AA-TATTT
1 TTATATTAAATAATTATTT
5712281 TTATATTAAATTAATTATTT
1 TTATATTAAA-TAATTATTT
5712301 TTATA
1 TTATA
5712306 AAATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATTAAATAATTATTT
Found at i:5712311 original size:18 final size:19
Alignment explanation
Indices: 5712276--5712312 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5712266 ATTTTAAAAA
5712276 TATTTTTATATTAAATTAAT
1 TATTTTTATA-TAAATTAAT
5712296 TATTTTTATA-AAATTAA
1 TATTTTTATATAAATTAA
5712313 AAATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTTATATAAATTAAT
Found at i:5714970 original size:24 final size:24
Alignment explanation
Indices: 5714920--5714970 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
5714910 TTATCTAAAT
*
5714920 TTTCTTTTTATTTAAAAAATTATC
1 TTTCTTTTTATTTAAAAAATTAAC
5714944 TTTCTTTTTATTTGAAAAAA-TAAC
1 TTTCTTTTTATTT-AAAAAATTAAC
5714968 TTT
1 TTT
5714971 ATACTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTCTTTTTATTTAAAAAATTAAC
Found at i:5715680 original size:31 final size:31
Alignment explanation
Indices: 5715643--5715765 Score: 114
Period size: 31 Copynumber: 4.0 Consensus size: 31
5715633 TCATTATTTG
5715643 ATATAAATATAATTTTAATAATTTATTTTTA
1 ATATAAATATAATTTTAATAATTTATTTTTA
*
5715674 ATATAAATATAATTTT--T--TGTTA-TTTGA
1 ATATAAATATAATTTTAATAAT-TTATTTTTA
* *
5715701 TTA-AAATATAATTTTATTTATATTTTATTATTTA
1 ATATAAATATAATTTTA---ATAATTTATT-TTTA
*
5715735 ATATAAATAATAATTTTAATTATTTATTTTT
1 ATATAAAT-ATAATTTTAATAATTTATTTTT
5715766 TAAATATATA
Statistics
Matches: 74, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
26 12 0.16
27 7 0.09
28 3 0.04
29 1 0.01
31 17 0.23
32 6 0.08
33 10 0.14
34 5 0.07
35 4 0.05
36 9 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
ATATAAATATAATTTTAATAATTTATTTTTA
Found at i:5715699 original size:57 final size:60
Alignment explanation
Indices: 5715636--5715751 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 60
5715626 ATATATTTCA
5715636 TTATTTGA-TATAAATATAATTTTA-ATAATTTATT-TTTAATATAAAT-ATAATTTTTTG
1 TTATTTGATTA-AAATATAATTTTATATAATTTATTATTTAATATAAATAATAATTTTTTG
*
5715693 TTATTTGATTAAAATATAATTTTATTTATATTTTATTATTTAATATAAATAATAATTTT
1 TTATTTGATTAAAATATAATTTTA--TATAATTTATTATTTAATATAAATAATAATTTT
5715752 AATTATTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
57 21 0.40
58 2 0.04
60 9 0.17
61 12 0.23
62 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (60 bp):
TTATTTGATTAAAATATAATTTTATATAATTTATTATTTAATATAAATAATAATTTTTTG
Found at i:5717122 original size:9 final size:8
Alignment explanation
Indices: 5717110--5717233 Score: 66
Period size: 7 Copynumber: 15.6 Consensus size: 8
5717100 ACTTCAAGAC
*
5717110 AAAAGTAT
1 AAAAATAT
5717118 AAAAATTAT
1 AAAAA-TAT
5717127 AAAAAT-T
1 AAAAATAT
*
5717134 AAAAAAAT
1 AAAAATAT
5717142 AAAAATTAT
1 AAAAA-TAT
*
5717151 AAAAATCT
1 AAAAATAT
5717159 ATAAAAT-T
1 A-AAAATAT
*
5717167 TAAAATA-
1 AAAAATAT
**
5717174 AATTATA-
1 AAAAATAT
5717181 AAAAAT-T
1 AAAAATAT
5717188 CAAAAATTAT
1 -AAAAA-TAT
5717198 AAAAA-ATT
1 AAAAATA-T
5717206 ATAAAAT-T
1 A-AAAATAT
5717214 AAAAAT-T
1 AAAAATAT
*
5717221 AAAAAAAT
1 AAAAATAT
5717229 AAAAA
1 AAAAA
5717234 ATTAGATTAA
Statistics
Matches: 92, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
7 31 0.34
8 30 0.33
9 30 0.33
10 1 0.01
ACGTcount: A:0.70, C:0.02, G:0.01, T:0.27
Consensus pattern (8 bp):
AAAAATAT
Found at i:5717194 original size:71 final size:69
Alignment explanation
Indices: 5717118--5717283 Score: 183
Period size: 71 Copynumber: 2.3 Consensus size: 69
5717108 ACAAAAGTAT
* *
5717118 AAAAATTATAAAAATTAAAAAAATAAAAATTATAAAAATCTATAAAATTTA-A-AATAAATTATA
1 AAAAATTATAAAAATTAAAAAAATAAAAATTA-AAAAA-ATA-AAAAATTAGATAA-AAATTATA
*
5717181 AAAAATTC
62 AAAAATTA
* * *
5717189 AAAAATTATAAAAAATTATAAAATTAAAAATTAAAAAAATAAAAAATTAGATTAAAAATTATAAT
1 AAAAATTAT-AAAAATTAAAAAAATAAAAATTAAAAAAATAAAAAATTAGA-TAAAAATTATAAA
*
5717254 AGATTA
64 AAATTA
*
5717260 AAAAATTATAAAAATAAGAAAAAA
1 AAAAATTATAAAAATTA-AAAAAA
5717284 ATCTATTAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
69 7 0.09
70 10 0.12
71 40 0.50
72 23 0.29
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (69 bp):
AAAAATTATAAAAATTAAAAAAATAAAAATTAAAAAAATAAAAAATTAGATAAAAATTATAAAAA
ATTA
Found at i:5717249 original size:7 final size:7
Alignment explanation
Indices: 5717126--5717225 Score: 58
Period size: 8 Copynumber: 12.9 Consensus size: 7
5717116 ATAAAAATTA
5717126 TAAAAAT
1 TAAAAAT
*
5717133 TAAAAAAA
1 T-AAAAAT
5717141 TAAAAATT
1 TAAAAA-T
5717149 ATAAAAAT
1 -TAAAAAT
5717157 CTATAAAAT
1 -TA-AAAAT
*
5717166 TTAAAA-
1 TAAAAAT
*
5717172 TAAATTAT
1 TAAA-AAT
*
5717180 AAAAAAT
1 TAAAAAT
5717187 TCAAAAATT
1 T-AAAAA-T
5717196 ATAAAAAAT
1 -T-AAAAAT
5717205 TATAAAAT
1 TA-AAAAT
5717213 TAAAAAT
1 TAAAAAT
5717220 TAAAAA
1 TAAAAA
5717226 AATAAAAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
6 3 0.04
7 25 0.34
8 26 0.36
9 13 0.18
10 6 0.08
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (7 bp):
TAAAAAT
Found at i:5717262 original size:30 final size:28
Alignment explanation
Indices: 5717126--5717267 Score: 80
Period size: 30 Copynumber: 4.9 Consensus size: 28
5717116 ATAAAAATTA
5717126 TAAAAATTAAAAAAAT-AAAAATT--A-
1 TAAAAATTAAAAAAATAAAAAATTAGAT
**
5717150 TAAAAATCTATAAAATTTAAAATAAATT--AT
1 TAAAAAT-TA-AAAAAAT-AAA-AAATTAGAT
* * *
5717180 AAAAAATTCAAAAATTATAAAAAATTATAAAAT
1 TAAAAATT-AAAAA-AATAAAAAA-T-T-AGAT
5717213 TAAAAATTAAAAAAATAAAAAATTAGAT
1 TAAAAATTAAAAAAATAAAAAATTAGAT
* *
5717241 TAAAAATTATAATAGATTAAAAAATTA
1 TAAAAATTA-AA-AAAATAAAAAATTA
5717268 TAAAAATAAG
Statistics
Matches: 94, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
24 7 0.07
25 2 0.02
26 5 0.05
28 17 0.18
29 18 0.19
30 23 0.24
31 8 0.09
32 5 0.05
33 9 0.10
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (28 bp):
TAAAAATTAAAAAAATAAAAAATTAGAT
Found at i:5717273 original size:46 final size:42
Alignment explanation
Indices: 5717110--5717281 Score: 170
Period size: 43 Copynumber: 3.9 Consensus size: 42
5717100 ACTTCAAGAC
*
5717110 AAAAGTATAAAAATTATAAAAATTAAAAAAAT-AAAAATTA-TA
1 AAAATTAT-AAAATTA-AAAAATTAAAAAAATAAAAAATTATTA
* *
5717152 AAAATCTATAAAATTTAAAATAAATTATAAAAAATTCAAAAATTATAA
1 AAAAT-TATAAAA-TT-AAA-AAATTA-AAAAAA-TAAAAAATTATTA
5717200 AAAATTATAAAATT-AAAAATTAAAAAAATAAAAAATTAGATTA
1 AAAATTATAAAATTAAAAAATTAAAAAAATAAAAAATT--ATTA
*
5717243 AAAATTATAATAGATTAAAAAATTATAAAAATAAGAAAA
1 AAAATTATAA-A-ATTAAAAAATTAAAAAAATAA-AAAA
5717282 AAATCTATTA
Statistics
Matches: 111, Mismatches: 5, Indels: 23
0.80 0.04 0.17
Matches are distributed among these distances:
41 8 0.07
42 14 0.13
43 26 0.23
44 10 0.09
45 9 0.08
46 19 0.17
47 19 0.17
48 6 0.05
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (42 bp):
AAAATTATAAAATTAAAAAATTAAAAAAATAAAAAATTATTA
Found at i:5717274 original size:9 final size:9
Alignment explanation
Indices: 5717110--5717274 Score: 134
Period size: 9 Copynumber: 18.6 Consensus size: 9
5717100 ACTTCAAGAC
*
5717110 AAAAGTATA
1 AAAATTATA
5717119 AAAATTATA
1 AAAATTATA
5717128 AAAATTA-A
1 AAAATTATA
5717136 AAAA--ATA
1 AAAATTATA
5717143 AAAATTATA
1 AAAATTATA
5717152 AAAATCTATA
1 AAAAT-TATA
* *
5717162 AAATTTAAA
1 AAAATTATA
5717171 ATAAATTATAA
1 A-AAATTAT-A
*
5717182 AAAATT-CA
1 AAAATTATA
5717190 AAAATTATAA
1 AAAATTAT-A
5717200 AAAATTAT-
1 AAAATTATA
5717208 AAAA-T-TA
1 AAAATTATA
5717215 AAAATTA-A
1 AAAATTATA
*
5717223 AAAAATA-A
1 AAAATTATA
5717231 AAAATTAGATTA
1 AAAATT--A-TA
5717243 AAAATTATA
1 AAAATTATA
*
5717252 ATAGATTA-A
1 A-AAATTATA
5717261 AAAATTATA
1 AAAATTATA
5717270 AAAAT
1 AAAAT
5717275 AAGAAAAAAA
Statistics
Matches: 128, Mismatches: 11, Indels: 34
0.74 0.06 0.20
Matches are distributed among these distances:
6 2 0.02
7 10 0.08
8 35 0.27
9 38 0.30
10 34 0.27
11 2 0.02
12 7 0.05
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:5717339 original size:25 final size:24
Alignment explanation
Indices: 5717311--5717444 Score: 82
Period size: 25 Copynumber: 5.5 Consensus size: 24
5717301 AATTATAATT
5717311 TTTTTAATTTTAAACATTTTTATAA
1 TTTTTAATTTTAAA-ATTTTTATAA
*
5717336 TTTTTAATATTCT-GAATTTTT-T-A
1 TTTTTAAT-TT-TAAAATTTTTATAA
* *
5717359 TTTTATAA-TTTATATATTTTTAAAA
1 TTTT-TAATTTTA-AAATTTTTATAA
* * *
5717384 TTTATGAATTTTTAATTTTTTATAA
1 TTT-TTAATTTTAAAATTTTTATAA
*
5717409 TTTTATAGATTTTTATAATTTTT-T-A
1 TTTT-TA-A-TTTTAAAATTTTTATAA
5717434 TTTTTAATTTT
1 TTTTTAATTTT
5717445 TTATAAATTT
Statistics
Matches: 84, Mismatches: 13, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
21 1 0.01
22 6 0.07
23 12 0.14
24 7 0.08
25 38 0.45
26 9 0.11
27 11 0.13
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTTAATTTTAAAATTTTTATAA
Found at i:5717385 original size:17 final size:17
Alignment explanation
Indices: 5717359--5717398 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5717349 GAATTTTTTA
*
5717359 TTTTATAATTTAT-ATAT
1 TTTTAAAATTTATGA-AT
5717376 TTTTAAAATTTATGAAT
1 TTTTAAAATTTATGAAT
5717393 TTTTAA
1 TTTTAA
5717399 TTTTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTAAAATTTATGAAT
Found at i:5717397 original size:10 final size:9
Alignment explanation
Indices: 5717303--5717482 Score: 102
Period size: 9 Copynumber: 21.2 Consensus size: 9
5717293 ATTCAAAAAA
5717303 TTATAATTT
1 TTATAATTT
*
5717312 TTTTAA-TT
1 TTATAATTT
*
5717320 TTAAACATTT
1 TTATA-ATTT
5717330 TTATAA-TT
1 TTATAATTT
5717338 TT-TAATATT
1 TTATAAT-TT
* *
5717347 CT-GAATTT
1 TTATAATTT
5717355 TT-T-A-TT
1 TTATAATTT
5717361 TTATAATTT
1 TTATAATTT
*
5717370 ATAT-ATTT
1 TTATAATTT
*
5717378 TTA-AA-AT
1 TTATAATTT
5717385 TTATGAATTT
1 TTAT-AATTT
*
5717395 TTA-ATTTT
1 TTATAATTT
5717403 TTATAA-TT
1 TTATAATTT
5717411 TTATAGATTT
1 TTATA-ATTT
5717421 TTATAATTT
1 TTATAATTT
5717430 TT-T-ATTT
1 TTATAATTT
*
5717437 TTA-ATTTT
1 TTATAATTT
*
5717445 TTATAAATT
1 TTATAATTT
*
5717454 TTAAAATTT
1 TTATAATTT
* * *
5717463 ATAGATTTT
1 TTATAATTT
5717472 TTATAATTT
1 TTATAATTT
5717481 TT
1 TT
5717483 TGTTTTTATT
Statistics
Matches: 129, Mismatches: 25, Indels: 34
0.69 0.13 0.18
Matches are distributed among these distances:
6 4 0.03
7 15 0.12
8 41 0.32
9 52 0.40
10 17 0.13
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (9 bp):
TTATAATTT
Found at i:5717437 original size:42 final size:43
Alignment explanation
Indices: 5717328--5717456 Score: 144
Period size: 42 Copynumber: 3.1 Consensus size: 43
5717318 TTTTAAACAT
* * *
5717328 TTTTATA-ATTTTTAATA-TTCTGAATTTTT--TATTTTATAA
1 TTTTATAGATTTTTAAAATTTATGAATTTTTAATTTTTTATAA
*
5717367 -TTTATATATTTTTAAAATTTATGAATTTTTAATTTTTTATAA
1 TTTTATAGATTTTTAAAATTTATGAATTTTTAATTTTTTATAA
* **
5717409 TTTTATAGATTTTTATAATTT-TTTATTTTTAATTTTTTATAAA
1 TTTTATAGATTTTTAAAATTTATGAATTTTTAATTTTTTAT-AA
5717452 TTTTA
1 TTTTA
5717457 AAATTTATAG
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
38 6 0.08
39 9 0.12
40 11 0.14
42 26 0.34
43 25 0.32
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (43 bp):
TTTTATAGATTTTTAAAATTTATGAATTTTTAATTTTTTATAA
Found at i:5717438 original size:16 final size:16
Alignment explanation
Indices: 5717326--5717475 Score: 67
Period size: 16 Copynumber: 9.1 Consensus size: 16
5717316 AATTTTAAAC
*
5717326 ATTTTTATAATTTTTA
1 ATTTTTATAATTTTTT
* *
5717342 ATATTCT-GAATTTTTT
1 AT-TTTTATAATTTTTT
*
5717358 A-TTTTATAATTTATAT
1 ATTTTTATAATTT-TTT
* * *
5717374 ATTTTTAAAATTTATG
1 ATTTTTATAATTTTTT
*
5717390 AATTTT-TAATTTTTT
1 ATTTTTATAATTTTTT
5717405 ATAATTTTATAGATTTTTAT
1 AT--TTTTATA-ATTTTT-T
*
5717425 AATTTTT-T-ATTTTTA
1 -ATTTTTATAATTTTTT
* *
5717440 ATTTTTTATAAATTTTA
1 A-TTTTTATAATTTTTT
**
5717457 AAATTTATAGATTTTTT
1 ATTTTTATA-ATTTTTT
5717474 AT
1 AT
5717476 AATTTTTTGT
Statistics
Matches: 98, Mismatches: 22, Indels: 27
0.67 0.15 0.18
Matches are distributed among these distances:
14 4 0.04
15 17 0.17
16 31 0.32
17 30 0.31
18 3 0.03
19 10 0.10
20 1 0.01
21 2 0.02
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.64
Consensus pattern (16 bp):
ATTTTTATAATTTTTT
Found at i:5717439 original size:6 final size:7
Alignment explanation
Indices: 5717328--5717445 Score: 56
Period size: 8 Copynumber: 14.7 Consensus size: 7
5717318 TTTTAAACAT
5717328 TTTTATAA
1 TTTT-TAA
5717336 TTTTTAA
1 TTTTTAA
*
5717343 TATTCTGAA
1 T-TT-TTAA
*
5717352 TTTTTTA
1 TTTTTAA
5717359 TTTTATAA
1 TTTT-TAA
*
5717367 TTTATATA
1 TTTTTA-A
5717375 TTTTTAAAA
1 TTTTT--AA
*
5717384 TTTATGAA
1 TTT-TTAA
5717392 TTTTTAA
1 TTTTTAA
5717399 TTTTTTATAA
1 --TTTT-TAA
5717409 TTTTATAGA
1 TTTT-TA-A
5717418 TTTTTATAA
1 -TTTT-TAA
*
5717427 TTTTTTA
1 TTTTTAA
5717434 TTTTTAA
1 TTTTTAA
5717441 TTTTT
1 TTTTT
5717446 TATAAATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 25
0.72 0.08 0.20
Matches are distributed among these distances:
7 28 0.32
8 34 0.39
9 14 0.16
10 12 0.14
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.66
Consensus pattern (7 bp):
TTTTTAA
Found at i:5717473 original size:42 final size:44
Alignment explanation
Indices: 5717359--5717482 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 44
5717349 GAATTTTTTA
* * *
5717359 TTTTATAA-TTTATATATTTTTA-AA-ATTTATGAATTTTTAATT
1 TTTTATAATTTTATAAATTTATAGAATTTTTAT-AATTTTTAATT
* * *
5717401 TTTTATAATTTTATAGATTTTTATAATTTTT-T-ATTTTTAATT
1 TTTTATAATTTTATAAATTTATAGAATTTTTATAATTTTTAATT
*
5717443 TTTTATAAATTTTA-AAATTTATAGATTTTTTATAATTTTT
1 TTTTAT-AATTTTATAAATTTATAGAATTTTTATAATTTTT
5717483 TGTTTTTATT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 37 0.53
43 21 0.30
44 9 0.13
45 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (44 bp):
TTTTATAATTTTATAAATTTATAGAATTTTTATAATTTTTAATT
Found at i:5717483 original size:10 final size:10
Alignment explanation
Indices: 5717392--5717483 Score: 56
Period size: 10 Copynumber: 9.4 Consensus size: 10
5717382 AATTTATGAA
5717392 TTTT-TAATT
1 TTTTATAATT
5717401 TTTTATAA--
1 TTTTATAATT
5717409 TTTTATAGA-T
1 TTTTATA-ATT
5717419 TTTTATAATT
1 TTTTATAATT
5717429 TTTTATTTTTAATT
1 TTTTA----TAATT
*
5717443 TTTTATAA-A
1 TTTTATAATT
5717452 TTTTA-AA--
1 TTTTATAATT
*
5717459 ATTTATAGATT
1 TTTTATA-ATT
5717470 TTTTATAATT
1 TTTTATAATT
5717480 TTTT
1 TTTT
5717484 GTTTTTATTG
Statistics
Matches: 68, Mismatches: 3, Indels: 23
0.72 0.03 0.24
Matches are distributed among these distances:
7 4 0.06
8 10 0.15
9 12 0.18
10 26 0.38
11 6 0.09
14 10 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:5717524 original size:51 final size:51
Alignment explanation
Indices: 5717401--5717506 Score: 130
Period size: 51 Copynumber: 2.1 Consensus size: 51
5717391 ATTTTTAATT
* *
5717401 TTTTATAATTTTATAG-ATTTTTATAATTTTTTATTTTTAATTTTTTATAAA
1 TTTTA-AAATTTATAGAATTTTTATAATTTTTTATTTTTAATTTGTTATAAA
* *
5717452 TTTTAAAATTTATAGATTTTTTATAATTTTTTGTTTTT-A-TTGTTA-AAA
1 TTTTAAAATTTATAGAATTTTTATAATTTTTTATTTTTAATTTGTTATAAA
5717500 TCTTTAA
1 T-TTTAA
5717507 TAGTTTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
48 4 0.08
49 10 0.20
50 10 0.20
51 25 0.51
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (51 bp):
TTTTAAAATTTATAGAATTTTTATAATTTTTTATTTTTAATTTGTTATAAA
Found at i:5718057 original size:14 final size:14
Alignment explanation
Indices: 5718038--5718064 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5718028 AAATTAAAAA
5718038 TTAATATTTTTATT
1 TTAATATTTTTATT
5718052 TTAATATTTTTAT
1 TTAATATTTTTAT
5718065 ACAATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTAATATTTTTATT
Found at i:5718586 original size:22 final size:20
Alignment explanation
Indices: 5718560--5718609 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
5718550 TATTTGAAAT
**
5718560 TTTAAATTTATTTATTATTTA
1 TTTAAATTTATAAATTA-TTA
5718581 TATTAAATTTATAAATTATTA
1 T-TTAAATTTATAAATTATTA
5718602 TTTAAATT
1 TTTAAATT
5718610 CAAATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 5 0.19
22 14 0.54
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAAATTTATAAATTATTA
Found at i:5718773 original size:13 final size:14
Alignment explanation
Indices: 5718747--5718790 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
5718737 ATTATGTACA
5718747 TAAATAATATAAATT
1 TAAAT-ATATAAATT
5718762 TAAATA-ATAAATT
1 TAAATATATAAATT
* *
5718775 AAAATATTTAAATT
1 TAAATATATAAATT
5718789 TA
1 TA
5718791 TTATTCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 12 0.48
14 8 0.32
15 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATATATAAATT
Found at i:5719215 original size:15 final size:15
Alignment explanation
Indices: 5719174--5719227 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
5719164 TTTTTCTATT
*
5719174 TATATTTAATATTAA
1 TATATTTAATATAAA
*
5719189 -ATATTAAATATAAA
1 TATATTTAATATAAA
*
5719203 TATATTTATTATAAA
1 TATATTTAATATAAA
*
5719218 TATTTTTAAT
1 TATATTTAAT
5719228 TTTTATTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATTTAATATAAA
Found at i:5719220 original size:13 final size:13
Alignment explanation
Indices: 5719175--5719222 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
5719165 TTTTCTATTT
5719175 ATATTTAATATTAA
1 ATATTTAATA-TAA
*
5719189 ATATTAAATATAAA
1 ATATTTAATAT-AA
*
5719203 TATATTTATTATAA
1 -ATATTTAATATAA
5719217 ATATTT
1 ATATTT
5719223 TTAATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 7 0.24
14 13 0.45
15 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATTTAATATAA
Found at i:5719236 original size:41 final size:36
Alignment explanation
Indices: 5719190--5719280 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 36
5719180 TAATATTAAA
*
5719190 TATTAAATATAAATATATTTATTATAAATATTTTTAATTTT
1 TATT-AATATAAATATATTT-TTA-AAATA-TTAT-ATTTT
*
5719231 TATTAATATATA-ATATTTTTAAAATATTATATTTT
1 TATTAATATAAATATATTTTTAAAATATTATATTTT
*
5719266 TATTCATATAAATAT
1 TATTAATATAAATAT
5719281 TTATAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
35 15 0.33
36 5 0.11
37 5 0.11
38 3 0.07
39 6 0.13
40 7 0.16
41 4 0.09
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (36 bp):
TATTAATATAAATATATTTTTAAAATATTATATTTT
Found at i:5719257 original size:16 final size:16
Alignment explanation
Indices: 5719233--5719324 Score: 55
Period size: 16 Copynumber: 5.7 Consensus size: 16
5719223 TTAATTTTTA
*
5719233 TTAATATATAATATTT
1 TTAAAATATAATATTT
*
5719249 TTAAAATATTATATTT
1 TTAAAATATAATATTT
**
5719265 TTATTCATATAAATATTT
1 TTA-AAATAT-AATATTT
*
5719283 ATAAAATA-AA-A-TT
1 TTAAAATATAATATTT
* * *
5719296 TAAAAATACAAACATTTT
1 TTAAAATA-TAATA-TTT
5719314 TTAAAATATAA
1 TTAAAATATAA
5719325 AAAAATAATC
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
13 8 0.14
14 1 0.02
15 4 0.07
16 18 0.32
17 9 0.16
18 17 0.30
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAAATATAATATTT
Found at i:5722613 original size:2 final size:2
Alignment explanation
Indices: 5722606--5722633 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5722596 ATATTCATAC
5722606 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
5722634 GTATTCCAAC
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:5724077 original size:25 final size:24
Alignment explanation
Indices: 5723978--5724082 Score: 65
Period size: 25 Copynumber: 4.2 Consensus size: 24
5723968 TATTAATTAC
5723978 TTTATTTATTTTAAAA-ATATATAA
1 TTTATTTATTTTAAAATATATA-AA
*
5724002 TTT-TATATTTTATAAATA-ATTAAAA
1 TTTATTTATTTTA-AAATATA-T-AAA
** * * *
5724027 TTAATAAATATATTAACATGTA-AAA
1 TT--TATTTATTTTAAAATATATAAA
5724052 TTTATTTAATTTTAAAATATATAAA
1 TTTATTT-ATTTTAAAATATATAAA
5724077 TTTATT
1 TTTATT
5724083 ATAAAATTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
23 11 0.18
24 17 0.28
25 20 0.33
26 1 0.02
27 4 0.07
28 8 0.13
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (24 bp):
TTTATTTATTTTAAAATATATAAA
Found at i:5724096 original size:18 final size:18
Alignment explanation
Indices: 5724047--5724104 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
5724037 TATTAACATG
*
5724047 TAAAATTT--ATTTAATTT
1 TAAAATTTAAATTT-ATTA
5724064 TAAAATATATAAATTTATTA
1 TAAAAT-T-TAAATTTATTA
*
5724084 TAAAATTTAAATTTATGA
1 TAAAATTTAAATTTATTA
5724102 TAA
1 TAA
5724105 TAAAAAGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 6 0.17
18 14 0.40
19 2 0.06
20 9 0.26
21 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TAAAATTTAAATTTATTA
Found at i:5724873 original size:26 final size:25
Alignment explanation
Indices: 5724817--5724873 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
5724807 AATAATATTA
* * *
5724817 ATATAAAAATATTTTTTAATATTTT
1 ATATAAAAATATTTTTAAAAAATTT
*
5724842 A-ATAAAATTATTATTTAAAAAATTT
1 ATATAAAAATATT-TTTAAAAAATTT
5724867 ATATAAA
1 ATATAAA
5724874 TATAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 10 0.38
25 11 0.42
26 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATAAAAATATTTTTAAAAAATTT
Found at i:5725143 original size:19 final size:19
Alignment explanation
Indices: 5725107--5725144 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5725097 AATTATGTTT
*
5725107 TAAATATTTTATATTTATA
1 TAAATATTTTATAGTTATA
5725126 TAAAT-TTTTATACGTTATA
1 TAAATATTTTATA-GTTATA
5725145 ATTTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
TAAATATTTTATAGTTATA
Found at i:5725233 original size:19 final size:20
Alignment explanation
Indices: 5725188--5725247 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
5725178 TTTTATGTAA
*
5725188 TTATATATAA-AAATAATAT
1 TTATATATAACTAATAATAT
*
5725207 TT-TATATAACTAA-AATGT
1 TTATATATAACTAATAATAT
* *
5725225 TTATATATAACTGATAAAAT
1 TTATATATAACTAATAATAT
5725245 TTA
1 TTA
5725248 CATGTGATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
18 13 0.39
19 14 0.42
20 6 0.18
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (20 bp):
TTATATATAACTAATAATAT
Found at i:5725349 original size:19 final size:20
Alignment explanation
Indices: 5725311--5725349 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5725301 ACTAGTAATG
*
5725311 GTAATATTTATATGTCATTA
1 GTAATATTTATATGTAATTA
5725331 GTAATATTT-TATGTAATTA
1 GTAATATTTATATGTAATTA
5725350 TATGTAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (20 bp):
GTAATATTTATATGTAATTA
Found at i:5728176 original size:21 final size:21
Alignment explanation
Indices: 5728152--5728191 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5728142 GAGAAGCCTC
5728152 TATTTATAGTTGAATCCTCCT
1 TATTTATAGTTGAATCCTCCT
5728173 TATTTATAGTTGAATCCTC
1 TATTTATAGTTGAATCCTC
5728192 ATTACATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
TATTTATAGTTGAATCCTCCT
Found at i:5731696 original size:62 final size:62
Alignment explanation
Indices: 5731612--5731728 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 62
5731602 AATTTTTAGT
* *
5731612 TTAATTATTATATAATTCTAATAGTAATTGACTGAA-AATTAATCTAAAATTATAACTCTAGC
1 TTAATTAATATATAATTCTAATAGTAATTAACT-AACAATTAATCTAAAATTATAACTCTAGC
* * * * * *
5731674 TTAATTAATATATATTTGTAATATTAATTAAGTAACCATTAATTTAAAATTATAA
1 TTAATTAATATATAATTCTAATAGTAATTAACTAACAATTAATCTAAAATTATAA
5731729 TTTACGTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
61 2 0.04
62 44 0.96
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (62 bp):
TTAATTAATATATAATTCTAATAGTAATTAACTAACAATTAATCTAAAATTATAACTCTAGC
Found at i:5731779 original size:7 final size:7
Alignment explanation
Indices: 5731744--5731823 Score: 56
Period size: 7 Copynumber: 10.9 Consensus size: 7
5731734 GTAAATACAA
5731744 ATAATAT
1 ATAATAT
*
5731751 ATGATAT
1 ATAATAT
*
5731758 CATTAATTTT
1 -A-TAA-TAT
5731768 ATAATAT
1 ATAATAT
5731775 ATAATAT
1 ATAATAT
5731782 ATAATAT
1 ATAATAT
5731789 AATAATA-
1 -ATAATAT
5731796 A-AATAT
1 ATAATAT
* *
5731802 ATTGACAT
1 A-TAATAT
5731810 ATAATAT
1 ATAATAT
5731817 AGTAATA
1 A-TAATA
5731824 AAAAGACAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
5 4 0.07
6 2 0.04
7 27 0.47
8 19 0.33
9 3 0.05
10 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:5733018 original size:32 final size:32
Alignment explanation
Indices: 5732958--5733045 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
5732948 ATGTGATACG
* * *
5732958 ATATAAAAAATAATATGAATAT-AATATAAAT
1 ATATTAAAAATTATATAAATATAAATATAAAT
5732989 ATATTAAAAATTATAT-AATATAAATTATAAAT
1 ATATTAAAAATTATATAAATATAAA-TATAAAT
* *
5733021 ATATTAAAATTTTTATAAATATAAA
1 ATATTAAAAATTATATAAATATAAA
5733046 ATATTTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.10
31 16 0.32
32 21 0.42
33 8 0.16
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (32 bp):
ATATTAAAAATTATATAAATATAAATATAAAT
Found at i:5733023 original size:13 final size:14
Alignment explanation
Indices: 5732976--5733023 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 14
5732966 AATAATATGA
5732976 ATATAATATAAA-T
1 ATATAATATAAATT
*
5732989 ATAT--TAAAAATT
1 ATATAATATAAATT
5733001 ATATAATATAAATT
1 ATATAATATAAATT
5733015 ATA-AATATA
1 ATATAATATA
5733024 TTAAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 10 0.33
14 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAATATAAATT
Found at i:5733028 original size:16 final size:16
Alignment explanation
Indices: 5732982--5733028 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 16
5732972 ATGAATATAA
5732982 TATAAATATATTAAAAAT
1 TATAAATATATT--AAAT
*
5733000 TATATA-ATA-TAAAT
1 TATAAATATATTAAAT
5733014 TATAAATATATTAAA
1 TATAAATATATTAAA
5733029 ATTTTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.36
15 3 0.12
16 5 0.20
17 3 0.12
18 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATAAATATATTAAAT
Found at i:5733058 original size:20 final size:19
Alignment explanation
Indices: 5733016--5733063 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 19
5733006 ATATAAATTA
*
5733016 TAAATATAT-TAAAATTTT
1 TAAATAAATATAAAATTTT
5733034 T--ATAAATATAAAATATTT
1 TAAATAAATATAAAAT-TTT
5733052 TAAATAAA-ATAA
1 TAAATAAATATAA
5733064 TGACATGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 5 0.20
17 6 0.24
18 5 0.20
19 4 0.16
20 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATAAATATAAAATTTT
Found at i:5733803 original size:22 final size:20
Alignment explanation
Indices: 5733778--5733822 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
5733768 GTAATAGTAG
5733778 AATTAATTAATGATATTAAAAA
1 AATTAATTAA--ATATTAAAAA
* *
5733800 AATTATTTAAATATTAATAA
1 AATTAATTAAATATTAAAAA
5733820 AAT
1 AAT
5733823 ATTTATGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
22 9 0.43
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATTAATTAAATATTAAAAA
Found at i:5733827 original size:19 final size:20
Alignment explanation
Indices: 5733790--5733827 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5733780 TTAATTAATG
5733790 ATATTAAAAAAATTATTTAA
1 ATATTAAAAAAATTATTTAA
*
5733810 ATATTAATAAAA-TATTTA
1 ATATTAAAAAAATTATTTA
5733828 TGTGTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATTAAAAAAATTATTTAA
Found at i:5734031 original size:23 final size:24
Alignment explanation
Indices: 5734002--5734052 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
5733992 TAGTGTAGTT
* *
5734002 TATTAATAATATA-TAAATTTATA
1 TATTAATAATATATTAAATATAAA
*
5734025 TATTAATAATTTATTAAATATAAA
1 TATTAATAATATATTAAATATAAA
5734049 TATT
1 TATT
5734053 TTAATGTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTAATAATATATTAAATATAAA
Found at i:5734073 original size:2 final size:2
Alignment explanation
Indices: 5734066--5734104 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5734056 ATGTTAGTAT
* *
5734066 TA TA TA TA TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5734105 TTGAGCCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5734785 original size:14 final size:16
Alignment explanation
Indices: 5734765--5734802 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
5734755 TATATATTAC
5734765 AAATATTAAAATT-TT
1 AAATATTAAAATTATT
*
5734780 -AATATTAAATTTATT
1 AAATATTAAAATTATT
5734795 AAATATTA
1 AAATATTA
5734803 TTTTAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.55
15 2 0.10
16 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTAAAATTATT
Found at i:5735712 original size:8 final size:9
Alignment explanation
Indices: 5735681--5735731 Score: 52
Period size: 8 Copynumber: 5.6 Consensus size: 9
5735671 ATATAATATT
5735681 TATATTTAA
1 TATATTTAA
*
5735690 GAT-TTTAA
1 TATATTTAA
5735698 TATATTTAA
1 TATATTTAA
5735707 TA-ATTTATA
1 TATATTTA-A
5735716 TTATATTTATA
1 -TATATTTA-A
5735727 TATAT
1 TATAT
5735732 ACAAATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
8 12 0.33
9 10 0.28
10 7 0.19
11 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
TATATTTAA
Found at i:5735713 original size:17 final size:19
Alignment explanation
Indices: 5735680--5735724 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
5735670 TATATAATAT
5735680 TTATATTTAAG-ATTT-TA
1 TTATATTTAAGAATTTATA
* *
5735697 ATATATTTAATAATTTATA
1 TTATATTTAAGAATTTATA
5735716 TTATATTTA
1 TTATATTTA
5735725 TATATATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 4 0.17
19 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATATTTAAGAATTTATA
Found at i:5737736 original size:17 final size:17
Alignment explanation
Indices: 5737700--5737741 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5737690 TATTTACTAT
*
5737700 AATTTAA-AAAATATAA
1 AATTTAATAAAATAAAA
*
5737716 AATTTAATAACATAAAA
1 AATTTAATAAAATAAAA
*
5737733 AATTAAATA
1 AATTTAATA
5737742 TTTTGCCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTTAATAAAATAAAA
Found at i:5737831 original size:14 final size:14
Alignment explanation
Indices: 5737814--5737842 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5737804 TATTTCTTGG
5737814 TTGACATTTTTTAA
1 TTGACATTTTTTAA
5737828 TTGACATTTTTTAA
1 TTGACATTTTTTAA
5737842 T
1 T
5737843 GGCCCACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TTGACATTTTTTAA
Found at i:5738867 original size:18 final size:18
Alignment explanation
Indices: 5738851--5738938 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 18
5738841 TTTAAATATG
5738851 ATATAATAATAAAATATTA
1 ATATAAT-ATAAAATATTA
*
5738870 ATATAATATAAAATAATTT
1 ATATAATATAAAAT-ATTA
* * *
5738889 ATAAAAATATAATATATAA
1 AT-ATAATATAAAATATTA
5738908 ATATAAATATATTAAA-ATTA
1 ATAT-AATATA--AAATATTA
5738928 ATA-AATATAAA
1 ATATAATATAAA
5738939 TTAATTTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.04
18 14 0.25
19 22 0.39
20 16 0.29
21 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATAATATAAAATATTA
Found at i:5738930 original size:14 final size:14
Alignment explanation
Indices: 5738866--5738952 Score: 63
Period size: 14 Copynumber: 6.1 Consensus size: 14
5738856 ATAATAAAAT
5738866 ATTAATATAATATAAA
1 ATTAATAT-AT-TAAA
* *
5738882 A-TAATTTATAAAA
1 ATTAATATATTAAA
5738895 ATATAATATA-TAAA
1 AT-TAATATATTAAA
*
5738909 TATAAATATATTAAA
1 -ATTAATATATTAAA
*
5738924 ATTAATA-AATATAA
1 ATTAATATATTA-AA
*
5738938 ATTAATTTATTAAA
1 ATTAATATATTAAA
5738952 A
1 A
5738953 ATTATAGATA
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
13 7 0.12
14 28 0.50
15 20 0.36
16 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTAATATATTAAA
Found at i:5738930 original size:28 final size:29
Alignment explanation
Indices: 5738872--5738969 Score: 98
Period size: 28 Copynumber: 3.4 Consensus size: 29
5738862 AAATATTAAT
*
5738872 ATAATATAAA-ATAATTTATAAAAATATA
1 ATAATATAAATATAATTTATTAAAATATA
*
5738900 AT-ATATAAATATAAATATATTAAAAT-TA
1 ATAATATAAATAT-AATTTATTAAAATATA
*
5738928 ATAAATATAAAT-TAATTTATTAAAA-ATT
1 AT-AATATAAATATAATTTATTAAAATATA
5738956 ATAGATATATAATA
1 ATA-ATATA-AATA
5738970 ATATAAACAC
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
27 8 0.14
28 27 0.47
29 15 0.26
30 8 0.14
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (29 bp):
ATAATATAAATATAATTTATTAAAATATA
Found at i:5738971 original size:28 final size:27
Alignment explanation
Indices: 5738871--5738971 Score: 84
Period size: 29 Copynumber: 3.6 Consensus size: 27
5738861 AAAATATTAA
*
5738871 TATAATATAAAATAATTTA-TAAAAA-
1 TATAATATATAATAATTTATTAAAAAT
*
5738896 TATAATATATAAATATAAATATATT-AAAAT
1 TATAATATAT--A-AT-AATTTATTAAAAAT
5738926 TAATAA-ATATAAATTAATTTATTAAAAAT
1 T-ATAATATAT-AA-TAATTTATTAAAAAT
5738955 TATAGATATATAATAAT
1 TATA-ATATATAATAAT
5738972 ATAAACACAA
Statistics
Matches: 62, Mismatches: 3, Indels: 19
0.74 0.04 0.23
Matches are distributed among these distances:
25 9 0.15
27 1 0.02
28 17 0.27
29 21 0.34
30 10 0.16
31 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (27 bp):
TATAATATATAATAATTTATTAAAAAT
Found at i:5747990 original size:35 final size:35
Alignment explanation
Indices: 5747940--5748009 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
5747930 TTCATTCCTT
*
5747940 TTGGCTCCTATATTTAGGTATTGTATATGGTGGGA
1 TTGGCTCCTAGATTTAGGTATTGTATATGGTGGGA
5747975 TTGGCTCCTAGATTTAGGTATTGTATATGGTGGGA
1 TTGGCTCCTAGATTTAGGTATTGTATATGGTGGGA
5748010 CTATTATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.09, G:0.30, T:0.41
Consensus pattern (35 bp):
TTGGCTCCTAGATTTAGGTATTGTATATGGTGGGA
Found at i:5751654 original size:16 final size:16
Alignment explanation
Indices: 5751633--5751665 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5751623 CTAGGAGAAT
5751633 ATATATATATATATAA
1 ATATATATATATATAA
*
5751649 ATATATTTATATATAA
1 ATATATATATATATAA
5751665 A
1 A
5751666 AGAAGGGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATATATATATATAA
Found at i:5752220 original size:17 final size:17
Alignment explanation
Indices: 5752198--5752236 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5752188 TAAGTTAATT
* *
5752198 TTTTTAAAATTATTATA
1 TTTTTAAAATAAATATA
*
5752215 TTTTTAATATAAATATA
1 TTTTTAAAATAAATATA
5752232 TTTTT
1 TTTTT
5752237 CAATTAGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTAAAATAAATATA
Found at i:5752262 original size:14 final size:16
Alignment explanation
Indices: 5752238--5752269 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5752228 TATATTTTTC
5752238 AATTAGATA-TTATAA
1 AATTAGATATTTATAA
5752253 AATT-GATATTTATAA
1 AATTAGATATTTATAA
5752268 AA
1 AA
5752270 ATATATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AATTAGATATTTATAA
Found at i:5752601 original size:13 final size:12
Alignment explanation
Indices: 5752583--5752626 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
5752573 TGTCAATACC
5752583 TTTTATAAATAA
1 TTTTATAAATAA
*
5752595 TTATTATAAATTAT
1 TT-TTATAAA-TAA
*
5752609 TTTTATAAGTAA
1 TTTTATAAATAA
5752621 TTTTAT
1 TTTTAT
5752627 TTAAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 10 0.37
13 13 0.48
14 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
TTTTATAAATAA
Found at i:5753299 original size:24 final size:24
Alignment explanation
Indices: 5753271--5753316 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5753261 CTTTTGAAAA
5753271 ATTCAATAACTCTATAATTTTTTT
1 ATTCAATAACTCTATAATTTTTTT
* *
5753295 ATTCAATAGCTTTATAATTTTT
1 ATTCAATAACTCTATAATTTTT
5753317 CAATAACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTCAATAACTCTATAATTTTTTT
Found at i:5753384 original size:20 final size:20
Alignment explanation
Indices: 5753355--5753411 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 20
5753345 ATATTAAATC
5753355 ATTT-TATATTTTTTATAAT
1 ATTTATATATTTTTTATAAT
* *
5753374 ATTTATATATTATTTGTAAT
1 ATTTATATATTTTTTATAAT
* * *
5753394 -CTCATACATTTTTTATAA
1 ATTTATATATTTTTTATAA
5753412 AAAACTTCTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTATATATTTTTTATAAT
Found at i:5754922 original size:21 final size:21
Alignment explanation
Indices: 5754873--5754920 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
5754863 AAGTAAATAA
5754873 TATATTTAAATTAAAATATAT
1 TATATTTAAATTAAAATATAT
5754894 TATATTTAAATTAAAATATAT
1 TATATTTAAATTAAAATATAT
5754915 TA-ATTT
1 TATATTT
5754921 TATGTGTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATTTAAATTAAAATATAT
Found at i:5755501 original size:86 final size:87
Alignment explanation
Indices: 5755404--5755573 Score: 261
Period size: 86 Copynumber: 2.0 Consensus size: 87
5755394 ATATGGACAA
* * *
5755404 TATTTTTAAATATATATTCATTTAAATTTAGATAAATTAATAAAATT-ATATTTAAATAGAAAAA
1 TATTTTTAAATATATATTAATTTAAATTTAAATAAATTAACAAAATTAATATTTAAATAGAAAAA
5755468 AATTATTAATTTTAAAGTTGAT
66 AATTATTAATTTTAAAGTTGAT
* *
5755490 TATTTTTAAATATCTATTAATTTAAATTTAAATAAATTAACAAAATTACATATTTAAATAGAAAG
1 TATTTTTAAATATATATTAATTTAAATTTAAATAAATTAACAAAATTA-ATATTTAAATAGAAAA
**
5755555 ATTTTATTAATTTTAAAGT
65 AAATTATTAATTTTAAAGT
5755574 AAATTAATAT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
86 43 0.57
88 32 0.43
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.45
Consensus pattern (87 bp):
TATTTTTAAATATATATTAATTTAAATTTAAATAAATTAACAAAATTAATATTTAAATAGAAAAA
AATTATTAATTTTAAAGTTGAT
Found at i:5755759 original size:16 final size:15
Alignment explanation
Indices: 5755740--5755774 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
5755730 ATAGAAGCAA
5755740 TTATTTATATATTAAT
1 TTATTTATATA-TAAT
*
5755756 TTATTTTTATATAAT
1 TTATTTATATATAAT
5755771 TTAT
1 TTAT
5755775 ATTTGTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTTATATATAAT
Found at i:5755772 original size:15 final size:15
Alignment explanation
Indices: 5755740--5755788 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
5755730 ATAGAAGCAA
*
5755740 TTATTTATATATTAAT
1 TTATTTTTATA-TAAT
5755756 TTATTTTTATATAAT
1 TTATTTTTATATAAT
* * *
5755771 TTATATTTGTTTAAT
1 TTATTTTTATATAAT
5755786 TTA
1 TTA
5755789 ATCATTGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 19 0.66
16 10 0.34
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATTTTTATATAAT
Found at i:5756281 original size:18 final size:19
Alignment explanation
Indices: 5756258--5756312 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
5756248 TAGTTTCTTT
5756258 AAGAATAAATATTTTTA-A
1 AAGAATAAATATTTTTAGA
*
5756276 AAGAATATATATCTATTTAGA
1 AAGAATAAATAT-T-TTTAGA
*
5756297 AAGATAAAAATATTTT
1 AAGA-ATAAATATTTT
5756313 ATTTTTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 11 0.37
19 1 0.03
20 6 0.20
21 6 0.20
22 6 0.20
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (19 bp):
AAGAATAAATATTTTTAGA
Found at i:5759003 original size:12 final size:12
Alignment explanation
Indices: 5758986--5759029 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
5758976 CTTAGATATA
5758986 ATAATTATAAAT
1 ATAATTATAAAT
5758998 ATAATTA-AAAT
1 ATAATTATAAAT
5759009 ATAATT-TAAA-
1 ATAATTATAAAT
5759019 ATAATATATAA
1 ATAAT-TATAA
5759030 TATTTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATTATAAAT
Found at i:5759010 original size:11 final size:11
Alignment explanation
Indices: 5758986--5759021 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 11
5758976 CTTAGATATA
5758986 ATAATTATAAAT
1 ATAATTA-AAAT
5758998 ATAATTAAAAT
1 ATAATTAAAAT
5759009 ATAATTTAAAAT
1 ATAA-TTAAAAT
5759021 A
1 A
5759022 ATATATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATAATTAAAAT
Found at i:5759688 original size:7 final size:7
Alignment explanation
Indices: 5759641--5759668 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
5759631 TATTTAATAT
5759641 AATTTTA
1 AATTTTA
5759648 AATTTTA
1 AATTTTA
5759655 AATTTTA
1 AATTTTA
5759662 AATTTTA
1 AATTTTA
5759669 TTATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTTTA
Found at i:5759689 original size:14 final size:14
Alignment explanation
Indices: 5759643--5759692 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
5759633 TTTAATATAA
*
5759643 TTTTAAATTTTAAA
1 TTTTAAATTTTAAT
5759657 TTTTAAATTTT-AT
1 TTTTAAATTTTAAT
**
5759670 TATTTATTTTTTAAT
1 T-TTTAAATTTTAAT
5759685 TTTTAAAT
1 TTTTAAAT
5759693 AATATAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.83
15 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTAAATTTTAAT
Found at i:5760280 original size:18 final size:17
Alignment explanation
Indices: 5760250--5760325 Score: 65
Period size: 15 Copynumber: 4.8 Consensus size: 17
5760240 AAATAATTAA
5760250 AATA-AAATAAAAATAT
1 AATATAAATAAAAATAT
5760266 AATATAAATATAAAATAT
1 AATATAAATA-AAAATAT
*
5760284 TATAT-AATAAAAA-AT
1 AATATAAATAAAAATAT
* *
5760299 TAT-TAAAT--AATTAT
1 AATATAAATAAAAATAT
*
5760313 ATTATAAATAAAA
1 AATATAAATAAAA
5760326 TTATTGAGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
13 2 0.04
14 4 0.08
15 13 0.27
16 8 0.16
17 11 0.22
18 11 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATAAATAAAAATAT
Found at i:5760288 original size:23 final size:23
Alignment explanation
Indices: 5760262--5760344 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
5760252 TAAAATAAAA
5760262 ATATAATATAAATATAAAATATT
1 ATATAATATAAATATAAAATATT
* *
5760285 ATATAATAAAAAATTATTAAATAATT
1 ATATAAT-ATAAA-TATAAAAT-ATT
*
5760311 ATAT--TATAAATA-AAATTATT
1 ATATAATATAAATATAAAATATT
*
5760331 GAGATAATATAAAT
1 -ATATAATATAAAT
5760345 TTTATTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
20 3 0.06
21 6 0.12
22 2 0.04
23 18 0.38
24 5 0.10
25 7 0.15
26 7 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATAATATAAATATAAAATATT
Found at i:5760295 original size:15 final size:15
Alignment explanation
Indices: 5760275--5760349 Score: 55
Period size: 15 Copynumber: 4.8 Consensus size: 15
5760265 TAATATAAAT
5760275 ATAAAATATTATATA
1 ATAAAATATTATATA
*
5760290 ATAAAAAATTAT-TAA
1 ATAAAATATTATAT-A
*
5760305 ATAATTATATTATA-A
1 ATAA-AATATTATATA
*
5760320 ATAAAATTATTGAGATA
1 ATAAAA-TATT-ATATA
*
5760337 ATATAAATTTTAT
1 ATA-AAATATTAT
5760350 TTATTTATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
14 2 0.04
15 25 0.54
16 9 0.20
17 7 0.15
18 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
ATAAAATATTATATA
Found at i:5760305 original size:26 final size:28
Alignment explanation
Indices: 5760261--5760330 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
5760251 ATAAAATAAA
*
5760261 AATATAATATAAA-TATAAAAT-ATTATAT
1 AATA-AATA-AAATTATTAAATAATTATAT
5760289 AAT-AA-AAAATTATTAAATAATTATAT
1 AATAAATAAAATTATTAAATAATTATAT
*
5760315 TATAAATAAAATTATT
1 AATAAATAAAATTATT
5760331 GAGATAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
24 3 0.08
25 8 0.22
26 11 0.31
27 2 0.06
28 12 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AATAAATAAAATTATTAAATAATTATAT
Found at i:5760341 original size:28 final size:29
Alignment explanation
Indices: 5760275--5760341 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
5760265 TAATATAAAT
*
5760275 ATAAAATATTATATAATAAAAAATTATTAA
1 ATAATATATTATATAAT-AAAAATTATTAA
*
5760305 ATAATTATATTATA-AAT-AAAATTATTGAG
1 ATAA-TATATTATATAATAAAAATTATT-AA
5760334 ATAATATA
1 ATAATATA
5760342 AATTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 13 0.39
29 5 0.15
30 7 0.21
31 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
ATAATATATTATATAATAAAAATTATTAA
Found at i:5761001 original size:24 final size:24
Alignment explanation
Indices: 5760952--5761002 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5760942 AGAGAAAAAT
* *
5760952 TTTATATTTTAATAATTTATTTTA
1 TTTATATTTTAATAATTTAATATA
*
5760976 TTTATATTTTTAT-ATGTTAATATA
1 TTTATATTTTAATAAT-TTAATATA
5761000 TTT
1 TTT
5761003 TTGTTACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTATATTTTAATAATTTAATATA
Found at i:5761132 original size:29 final size:28
Alignment explanation
Indices: 5761026--5761134 Score: 80
Period size: 29 Copynumber: 3.9 Consensus size: 28
5761016 ATTATTTTTA
* * *
5761026 ATTTAAAAAATAT-TATAACTCTTT-AG
1 ATTTAAAAAATATATTTATCTTTTTAAG
* * *
5761052 ATTTAAAAATAATTTCATTTA-CTTCTTAAA
1 ATTT-AAAA-AATAT-ATTTATCTTTTTAAG
* * *
5761082 ATTTAAATAATATTTTTTTCTTTTTAAG
1 ATTTAAAAAATATATTTATCTTTTTAAG
5761110 ATTTAATAAAATATATTTATCTTTT
1 ATTTAA-AAAATATATTTATCTTTT
5761135 AAATTATTAT
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
26 4 0.06
27 7 0.11
28 21 0.34
29 22 0.35
30 8 0.13
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (28 bp):
ATTTAAAAAATATATTTATCTTTTTAAG
Found at i:5761135 original size:28 final size:27
Alignment explanation
Indices: 5761026--5761136 Score: 75
Period size: 28 Copynumber: 4.0 Consensus size: 27
5761016 ATTATTTTTA
* *
5761026 ATTTAAAAAATAT-TATAACTCTTT-AG
1 ATTTAAAAAATATATTTATCT-TTTAAG
* *
5761052 ATTTAAAAATAATTTCATTTA-CTTCTTAAA
1 ATTT-AAAA-AATAT-ATTTATCTT-TTAAG
* * *
5761082 ATTTAAATAATATTTTTTTCTTTTTAAG
1 ATTTAAAAAATATATTTATC-TTTTAAG
5761110 ATTTAATAAAATATATTTATCTTTTAA
1 ATTTAA-AAAATATATTTATCTTTTAA
5761137 ATTATTATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
26 4 0.06
27 7 0.11
28 26 0.40
29 20 0.31
30 8 0.12
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.50
Consensus pattern (27 bp):
ATTTAAAAAATATATTTATCTTTTAAG
Found at i:5761223 original size:16 final size:17
Alignment explanation
Indices: 5761202--5761243 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5761192 TTTATTTATT
5761202 TATTTTTTA-TACAAAA
1 TATTTTTTACTACAAAA
*
5761218 TATTTTTTACTATAAAA
1 TATTTTTTACTACAAAA
*
5761235 TTTTTTTTA
1 TATTTTTTA
5761244 ATTACTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTTTTACTACAAAA
Found at i:5761728 original size:21 final size:21
Alignment explanation
Indices: 5761704--5761744 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5761694 TTATTAATTA
5761704 TTTTTATTTTAAGTTTAAATG
1 TTTTTATTTTAAGTTTAAATG
**
5761725 TTTTTATTTTATTTTTAAAT
1 TTTTTATTTTAAGTTTAAAT
5761745 AATGTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTTATTTTAAGTTTAAATG
Found at i:5761846 original size:20 final size:21
Alignment explanation
Indices: 5761820--5761862 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
5761810 TTAAAATTTT
5761820 ATATTTTTA-TTTA-TTTTAA
1 ATATTTTTATTTTATTTTTAA
5761839 ATATTTTTATTTTATTTTTAA
1 ATATTTTTATTTTATTTTTAA
5761860 ATA
1 ATA
5761863 ATATATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.41
20 4 0.18
21 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATATTTTTATTTTATTTTTAA
Found at i:5761849 original size:25 final size:24
Alignment explanation
Indices: 5761809--5761855 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
5761799 GTAGAAAAAG
5761809 TTTAAAATTTTATATTTTTATTTAT
1 TTTAAAATTTTATA-TTTTATTTAT
5761834 TTTAAATATTTT-TATTTTATTT
1 TTTAAA-ATTTTATATTTTATTT
5761856 TTAAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTAAAATTTTATATTTTATTTAT
Found at i:5761871 original size:24 final size:23
Alignment explanation
Indices: 5761819--5761871 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 23
5761809 TTTAAAATTT
*
5761819 TATATTTTTATTTATTTTAAATA
1 TATATTTATATTTATTTTAAATA
5761842 T-T-TTTAT-TTTATTTTTAAATAA
1 TATATTTATATTTA-TTTTAAAT-A
5761864 TATATTTA
1 TATATTTA
5761872 AAATTATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 4 0.16
21 12 0.48
22 3 0.12
23 2 0.08
24 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATATTTATATTTATTTTAAATA
Done.