Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 20 of 28
Found at i:2996609 original size:21 final size:22
Alignment explanation
Indices: 2996572--2996613 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2996562 ATTTTAAATA
2996572 AAAATATATAAATATAAATAAT
1 AAAATATATAAATATAAATAAT
*
2996594 AAAATAT-TATATATAAATAA
1 AAAATATATAAATATAAATAA
2996614 AAATGTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAATATATAAATATAAATAAT
Found at i:3000663 original size:2 final size:2
Alignment explanation
Indices: 3000645--3000684 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
3000635 TATAGAGCAA
*
3000645 AG AG AC AG AG CAG 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 AG AG AG AG AG A
3000685 AGCTGATGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.05, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3000949 original size:18 final size:17
Alignment explanation
Indices: 3000915--3000996 Score: 66
Period size: 17 Copynumber: 4.9 Consensus size: 17
3000905 TATTTAAAAT
3000915 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
3000932 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
3000949 A-TTTATA-TCATATAA
1 ATTTTATATTTATATAA
* *
3000964 TTTTTATATTT-TATTAT
1 ATTTTATATTTATA-TAA
3000981 ATTTTATATATTATAT
1 ATTTTATAT-TTATAT
3000997 CTTGTAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 4 0.08
16 11 0.22
17 18 0.35
18 9 0.18
19 5 0.10
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:3000954 original size:33 final size:32
Alignment explanation
Indices: 3000912--3000996 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 32
3000902 AAGTATTTAA
3000912 AATATTTTATATTTATATAAATTTTAATATATT
1 AATATTTTATATTTATAT-AATTTTAATATATT
* * * *
3000945 AATAATTTATA-TCATATAATTTTTATATTTT
1 AATATTTTATATTTATATAATTTTAATATATT
3000976 ATTATATTTTATATATTATAT
1 A--ATATTTTATAT-TTATAT
3000997 CTTGTAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
31 13 0.31
32 5 0.12
33 19 0.45
35 5 0.12
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (32 bp):
AATATTTTATATTTATATAATTTTAATATATT
Found at i:3001156 original size:28 final size:27
Alignment explanation
Indices: 3001089--3001177 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 27
3001079 TAATAATTTA
* *
3001089 TATATTTATATTATATTT-ATTTATTTT
1 TATATTTATATTAAATTTAAATT-TTTT
** *
3001116 TATATCAAAATTAAATTTTAAATTTTTT
1 TATATTTATATTAAA-TTTAAATTTTTT
*
3001144 TATATTTATATTAAATTAATAATTTATTT
1 TATATTTATATTAAATTTA-AATTT-TTT
3001173 TATAT
1 TATAT
3001178 AAATTTTAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 14 0.29
28 24 0.49
29 11 0.22
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (27 bp):
TATATTTATATTAAATTTAAATTTTTT
Found at i:3001177 original size:100 final size:95
Alignment explanation
Indices: 3001043--3001262 Score: 211
Period size: 95 Copynumber: 2.3 Consensus size: 95
3001033 AGTATTTTTA
* * *
3001043 TTTTATATTTTTA-T-AATTAATTATTTAAGATATATATAATAATTTATATATTTAT-ATTATAT
1 TTTTATATTTATATTAAATTAATAATTTAAGATATATA-AAT--TTTA-A-A-ATATGATTATAT
*
3001105 TTAT-TTATTTT-TATATCAAAATTA-AATTTTAAATTT
60 TTATATTATTTTCT-TAT-AAAATTATAA-TTTAAATAT
***
3001141 TTTTATATTTATATTAAATTAATAATTTATTTTATATAAATTTTAAAATATGATTATATTTATAT
1 TTTTATATTTATATTAAATTAATAATTTAAGATATATAAATTTTAAAATATGATTATATTTATAT
**
3001206 TATTTTCTTATATTATTATAATTTAAATAT
66 TATTTTCTTATAAAATTATAATTTAAATAT
3001236 TTTTATA-TTATATTTAAATTATATAAT
1 TTTTATATTTATA-TTAAATTA-ATAAT
3001263 ACTGATATTT
Statistics
Matches: 105, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
94 8 0.08
95 40 0.38
96 18 0.17
97 5 0.05
98 12 0.11
99 4 0.04
100 18 0.17
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (95 bp):
TTTTATATTTATATTAAATTAATAATTTAAGATATATAAATTTTAAAATATGATTATATTTATAT
TATTTTCTTATAAAATTATAATTTAAATAT
Found at i:3002694 original size:19 final size:19
Alignment explanation
Indices: 3002672--3002721 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
3002662 TTATAAAATA
3002672 TATAAAAATAATTTAATTT
1 TATAAAAATAATTTAATTT
*
3002691 TATATAAATATAA-ATAATTT
1 TATA-AAA-ATAATTTAATTT
3002711 T-T-AAAATAATT
1 TATAAAAATAATT
3002722 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.15
17 3 0.12
19 5 0.19
20 10 0.38
21 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAAAAATAATTTAATTT
Found at i:3002713 original size:21 final size:21
Alignment explanation
Indices: 3002670--3002711 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3002660 AATTATAAAA
*
3002670 TATATAAAAATAATTTAATTT
1 TATATAAAAATAATATAATTT
*
3002691 TATATAAATATAA-ATAATTT
1 TATATAAAAATAATATAATTT
3002711 T
1 T
3002712 TAAAATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATAAAAATAATATAATTT
Found at i:3002734 original size:24 final size:24
Alignment explanation
Indices: 3002705--3002759 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
3002695 TAAATATAAA
*
3002705 TAATTTTTAAAATAATTATATTTT
1 TAATTTTTAAAATAATTATATGTT
* **
3002729 TTATTTTTAAAATTTTTATATGTT
1 TAATTTTTAAAATAATTATATGTT
3002753 TAATTTT
1 TAATTTT
3002760 CACCGTATGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TAATTTTTAAAATAATTATATGTT
Found at i:3003062 original size:32 final size:31
Alignment explanation
Indices: 3003008--3003084 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
3002998 ATATTAAATA
*
3003008 ATAATAT-AATTA-TATATTTTAAAATGTAT
1 ATAATATAAATTATTATATATTAAAATGTAT
*
3003037 ATAATATAAATTATTAATATATTAAAATTTAT
1 ATAATATAAATTATT-ATATATTAAAATGTAT
*
3003069 ATAAATATAAAATATT
1 AT-AATATAAATTATT
3003085 TTAAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 7 0.17
30 5 0.12
31 1 0.02
32 16 0.39
33 12 0.29
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
ATAATATAAATTATTATATATTAAAATGTAT
Found at i:3003079 original size:17 final size:17
Alignment explanation
Indices: 3003027--3003081 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
3003017 TTATATATTT
*
3003027 TAAAATGTATAT-AATA
1 TAAAATTTATATAAATA
3003043 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
3003058 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
3003076 TAAAAT
1 TAAAAT
3003082 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 6 0.19
16 2 0.06
17 9 0.28
18 7 0.22
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:3004457 original size:108 final size:110
Alignment explanation
Indices: 3004303--3004511 Score: 343
Period size: 108 Copynumber: 1.9 Consensus size: 110
3004293 TTTACATAGG
* *
3004303 TTGGGTTGTAATATAATTTTTTTTCTTATTTAAATTCAAGTCTGTTGAG-TTTGAGCTAGTTTAA
1 TTGGGTTGTAATATAATTTTTTTTCCTATTTAAATTCAAGTCTGTTGAGCTTT-AACTAGTTTAA
3004367 AAGTTTATTTTACG-GTTAATATAATATTAAAAAAATATACATACA
65 AAGTTTATTTTACGAGTTAATATAATATTAAAAAAATATACATACA
* *
3004412 TTGGGTTGTAATATGA-TTTTTTTCCTATTTAAATTCAAGTTTGTTGAGCTTTAACTAGTTTAAA
1 TTGGGTTGTAATATAATTTTTTTTCCTATTTAAATTCAAGTCTGTTGAGCTTTAACTAGTTTAAA
*
3004476 AGTTTATTTTACGATTTAATATAATATTAAAAAAAT
66 AGTTTATTTTACGAGTTAATATAATATTAAAAAAAT
3004512 TTATATTAAT
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
108 54 0.58
109 39 0.42
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (110 bp):
TTGGGTTGTAATATAATTTTTTTTCCTATTTAAATTCAAGTCTGTTGAGCTTTAACTAGTTTAAA
AGTTTATTTTACGAGTTAATATAATATTAAAAAAATATACATACA
Found at i:3004519 original size:15 final size:18
Alignment explanation
Indices: 3004499--3004539 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
3004489 ATTTAATATA
3004499 ATATTAA-A-AAA-ATTT
1 ATATTAATATAAATATTT
3004514 ATATTAATATAAATATTT
1 ATATTAATATAAATATTT
3004532 ATAATTAA
1 AT-ATTAA
3004540 CTTTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
16 1 0.05
17 3 0.14
18 6 0.27
19 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTAATATAAATATTT
Found at i:3005764 original size:2 final size:2
Alignment explanation
Indices: 3005757--3005785 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3005747 GGAGAATACA
3005757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3005786 ATTTGTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3006088 original size:12 final size:14
Alignment explanation
Indices: 3006061--3006099 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3006051 TAAAATTTTT
3006061 TATTTTTTATATAA
1 TATTTTTTATATAA
3006075 TATTTTTTA-A-AA
1 TATTTTTTATATAA
3006087 TAATTTTTTATAT
1 T-ATTTTTTATAT
3006100 GTTAAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 9 0.41
14 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTTTTTATATAA
Found at i:3006597 original size:15 final size:15
Alignment explanation
Indices: 3006577--3006607 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3006567 TATAAAATTA
3006577 ATTTAATTTATTTTT
1 ATTTAATTTATTTTT
3006592 ATTTAATTTATTTTT
1 ATTTAATTTATTTTT
3006607 A
1 A
3006608 CATGTATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTAATTTATTTTT
Found at i:3010278 original size:21 final size:21
Alignment explanation
Indices: 3010254--3010293 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3010244 CGTGACCCTT
*
3010254 TTTTTA-AATTTAATTTTTTTA
1 TTTTTATAA-TTAATATTTTTA
3010275 TTTTTATAATTAATATTTT
1 TTTTTATAATTAATATTTT
3010294 AAATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTATAATTAATATTTTTA
Found at i:3010345 original size:20 final size:19
Alignment explanation
Indices: 3010314--3010368 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
3010304 ATAATAAAAT
3010314 AAAAAA-TAAATTTTATAA
1 AAAAAATTAAATTTTATAA
3010332 AAATAAATTAAATTAATT-TAA
1 AAA-AAATTAAATT--TTATAA
3010353 AAAAAATTAAATTTTA
1 AAAAAATTAAATTTTA
3010369 AAATTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
18 5 0.16
19 3 0.09
20 16 0.50
21 6 0.19
22 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAAATTAAATTTTATAA
Found at i:3013050 original size:44 final size:44
Alignment explanation
Indices: 3012987--3013074 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
3012977 GAGATCCAGA
*
3012987 ATCTTAACCTTAGCAACTCTTCCCTCCATTCTCACACCGCAAAC
1 ATCTTAACCTTAGCAACTCTTCCCTCCATTCTCACACCCCAAAC
3013031 ATCTTAACCTTAGCAACTCTTCCCTCCATTCTCACACCCCAAAC
1 ATCTTAACCTTAGCAACTCTTCCCTCCATTCTCACACCCCAAAC
3013075 TCTGTTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.27, C:0.42, G:0.03, T:0.27
Consensus pattern (44 bp):
ATCTTAACCTTAGCAACTCTTCCCTCCATTCTCACACCCCAAAC
Found at i:3013474 original size:20 final size:20
Alignment explanation
Indices: 3013410--3013486 Score: 56
Period size: 20 Copynumber: 4.0 Consensus size: 20
3013400 ATTTAACATC
3013410 ATATAAATATATTAAAA-TTT
1 ATATAAATAT-TTAAAATTTT
* *
3013430 ATAT-AATA--T-GAATTAT
1 ATATAAATATTTAAAATTTT
* *
3013446 ACATTAATATTTAAAATTTT
1 ATATAAATATTTAAAATTTT
* *
3013466 ATATAAATATATAATATTTT
1 ATATAAATATTTAAAATTTT
3013486 A
1 A
3013487 AACATAATTA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
15 2 0.05
16 6 0.14
17 4 0.09
19 5 0.12
20 26 0.60
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (20 bp):
ATATAAATATTTAAAATTTT
Found at i:3018095 original size:3 final size:3
Alignment explanation
Indices: 3018087--3018121 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
3018077 GGGTTAATGA
3018087 TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
3018122 TTTAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3018702 original size:11 final size:12
Alignment explanation
Indices: 3018680--3018720 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
3018670 ATTACAAAAA
3018680 AAAAATTATATT
1 AAAAATTATATT
3018692 AAAAATT-TATT
1 AAAAATTATATT
*
3018703 AAAATATAATA-T
1 AAAA-ATTATATT
3018715 AAAAAT
1 AAAAAT
3018721 ATTAATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 10 0.38
12 14 0.54
13 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAAAATTATATT
Found at i:3020127 original size:17 final size:18
Alignment explanation
Indices: 3020101--3020152 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
3020091 AAATTGTAGT
3020101 TAAATA-TAAAA-AATTA
1 TAAATATTAAAATAATTA
3020117 TAAATATTAAAATTAATTA
1 TAAATATTAAAA-TAATTA
*
3020136 T-AATTTTAAAATAATTA
1 TAAATATTAAAATAATTA
3020153 CATTAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 6 0.19
17 11 0.34
18 9 0.28
19 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATATTAAAATAATTA
Found at i:3024368 original size:30 final size:31
Alignment explanation
Indices: 3024321--3024380 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
3024311 TAAATATGAA
3024321 ATAAATGTATAAATATATCAAAATATATAAT
1 ATAAATGTATAAATATATCAAAATATATAAT
* * *
3024352 ATAAAT-TATTAATATATTAAAATTTATAA
1 ATAAATGTATAAATATATCAAAATATATAA
3024381 AAATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (31 bp):
ATAAATGTATAAATATATCAAAATATATAAT
Found at i:3024392 original size:47 final size:48
Alignment explanation
Indices: 3024291--3024436 Score: 126
Period size: 47 Copynumber: 3.1 Consensus size: 48
3024281 ATGACAAAAA
* * * *
3024291 AAAATAATTA-AAATAT-TTTATAAATATGAAATAAATGTATAAATATATC
1 AAAAT-ATTATAAATATAATTAT-AATAT-ATATAAATATATAAAAATATC
*
3024340 AAAATA-TAT-AATATAAATTATTAATATAT-TAAAATTTATAAAAATAT-
1 AAAATATTATAAATAT-AATTA-TAATATATAT-AAATATATAAAAATATC
* *
3024387 AAAATATTTTAAATATAATTATAATATATATAAATATAT-AAATTATC
1 AAAATATTATAAATATAATTATAATATATATAAATATATAAAAATATC
3024434 AAA
1 AAA
3024437 TGTGCTTTTC
Statistics
Matches: 81, Mismatches: 7, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
46 6 0.07
47 32 0.40
48 24 0.30
49 18 0.22
50 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (48 bp):
AAAATATTATAAATATAATTATAATATATATAAATATATAAAAATATC
Found at i:3027064 original size:15 final size:15
Alignment explanation
Indices: 3027022--3027067 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
3027012 ATTTATATTT
3027022 AAATATAAAAATT--
1 AAATATAAAAATTAA
***
3027035 AAATATAATTTTTAA
1 AAATATAAAAATTAA
3027050 AAATATAAAAATTAA
1 AAATATAAAAATTAA
3027065 AAA
1 AAA
3027068 ATTAAATATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.40
15 15 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATAAAAATTAA
Found at i:3027100 original size:16 final size:15
Alignment explanation
Indices: 3027068--3027106 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3027058 AAATTAAAAA
*
3027068 ATTAAATATATTTAT
1 ATTAAATAAATTTAT
3027083 ATTAAATAAATATTAT
1 ATTAAATAAAT-TTAT
*
3027099 ATTTAATA
1 ATTAAATA
3027107 TTTAATTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAAATAAATTTAT
Found at i:3027461 original size:15 final size:15
Alignment explanation
Indices: 3027437--3027470 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3027427 AAGTACTGGG
*
3027437 TGGTCGCCTCAAGTA
1 TGGTCCCCTCAAGTA
*
3027452 TGGTCCCCTCAAGTC
1 TGGTCCCCTCAAGTA
3027467 TGGT
1 TGGT
3027471 GTGAACTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.29, G:0.26, T:0.29
Consensus pattern (15 bp):
TGGTCCCCTCAAGTA
Found at i:3031995 original size:2 final size:2
Alignment explanation
Indices: 3031988--3032020 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3031978 TCCAACATAG
3031988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3032021 ATTGGCTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3032851 original size:14 final size:14
Alignment explanation
Indices: 3032832--3032862 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3032822 TTAATACTTG
3032832 TATAATTATTCTAA
1 TATAATTATTCTAA
*
3032846 TATAATTATTTTAA
1 TATAATTATTCTAA
3032860 TAT
1 TAT
3032863 TTTAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TATAATTATTCTAA
Found at i:3033290 original size:38 final size:38
Alignment explanation
Indices: 3033237--3033369 Score: 158
Period size: 38 Copynumber: 3.5 Consensus size: 38
3033227 AGTTGAAGGT
* * *
3033237 TAGAAAATTTAATTTGAAATTGGCTGGCGGCTGACGGC
1 TAGAGAATTCAATTTGAAATTGGCCGGCGGCTGACGGC
**
3033275 TAGAGAATTCAATTTGAAATTGGCCGGCGGCTGACGAT
1 TAGAGAATTCAATTTGAAATTGGCCGGCGGCTGACGGC
* * * **
3033313 TAGAGAATTCAATTTGGAATTGACCGGTGGCTGGTGGC
1 TAGAGAATTCAATTTGAAATTGGCCGGCGGCTGACGGC
*
3033351 TAGAGAATTCCAAATTGAA
1 TAGAGAATT-CAATTTGAA
3033370 CTCTCTTTGA
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 73 0.91
39 7 0.09
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.28
Consensus pattern (38 bp):
TAGAGAATTCAATTTGAAATTGGCCGGCGGCTGACGGC
Found at i:3037904 original size:38 final size:38
Alignment explanation
Indices: 3037861--3037976 Score: 169
Period size: 38 Copynumber: 3.1 Consensus size: 38
3037851 TTGAATTAGT
* * *
3037861 TGACGGTTAGAGAATTCAATTTGAAATTGGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGGAATTGGCTGGTGGC
*
3037899 TGACGGCTAGAGAATTCAATTTGGAATTGGCCGGTGGC
1 TGACGGCTAGAGAATTCAATTTGGAATTGGCTGGTGGC
** *
3037937 TGACAACTAGAGAATTCGATTTGGAATTGGCTGGTGGC
1 TGACGGCTAGAGAATTCAATTTGGAATTGGCTGGTGGC
3037975 TG
1 TG
3037977 GTGGCTGGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 70 1.00
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (38 bp):
TGACGGCTAGAGAATTCAATTTGGAATTGGCTGGTGGC
Found at i:3037976 original size:7 final size:7
Alignment explanation
Indices: 3037964--3037989 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3037954 GATTTGGAAT
3037964 TGGCTGG
1 TGGCTGG
3037971 TGGCTGG
1 TGGCTGG
3037978 TGGCTGG
1 TGGCTGG
3037985 TGGCT
1 TGGCT
3037990 AGAGAATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.54, T:0.31
Consensus pattern (7 bp):
TGGCTGG
Found at i:3040102 original size:17 final size:17
Alignment explanation
Indices: 3040077--3040153 Score: 56
Period size: 17 Copynumber: 4.8 Consensus size: 17
3040067 TTAAGTTGGA
* *
3040077 TTTATATTATTTTGAAT
1 TTTAAATTATTTTAAAT
3040094 TTTAAATTATTTTAAAT
1 TTTAAATTATTTTAAAT
** *
3040111 TGGATAA-T-TTTT--AG
1 TTTA-AATTATTTTAAAT
3040125 TTTAAATTATTTTAAA-
1 TTTAAATTATTTTAAAT
*
3040141 TTTAAATAATTTT
1 TTTAAATTATTTT
3040154 GTTATTAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
13 2 0.04
14 4 0.09
15 4 0.09
16 16 0.34
17 19 0.40
18 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTAAATTATTTTAAAT
Found at i:3040136 original size:16 final size:16
Alignment explanation
Indices: 3040094--3040153 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
3040084 TATTTTGAAT
*
3040094 TTTAAATTATTTTAAA
1 TTTAAATAATTTTAAA
** * *
3040110 -TTGGATAATTTTTAG
1 TTTAAATAATTTTAAA
*
3040125 TTTAAATTATTTTAAA
1 TTTAAATAATTTTAAA
3040141 TTTAAATAATTTT
1 TTTAAATAATTTT
3040154 GTTATTAAAT
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
15 10 0.31
16 22 0.69
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTAAATAATTTTAAA
Found at i:3040162 original size:32 final size:30
Alignment explanation
Indices: 3040095--3040166 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
3040085 ATTTTGAATT
**
3040095 TTAAATTATTTTAAATTGGATAATTTTTAG
1 TTAAATTATTTTAAATTAAATAATTTTTAG
3040125 TTTAAATTATTTTAAATTTAAATAATTTTGTTA-
1 -TTAAATTATTTTAAA-TTAAATAA-TTT-TTAG
3040158 TTAAATTAT
1 TTAAATTAT
3040167 ATGATTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 15 0.42
32 15 0.42
33 3 0.08
34 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (30 bp):
TTAAATTATTTTAAATTAAATAATTTTTAG
Found at i:3040603 original size:3 final size:3
Alignment explanation
Indices: 3040595--3040621 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3040585 TGTAGTTAGT
3040595 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
3040622 ATCTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3042541 original size:26 final size:26
Alignment explanation
Indices: 3042507--3042565 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
3042497 TATTGTTTAA
* **
3042507 ATAATTATTTTTATATAAATTTAATT
1 ATAAATATTTTTATATAAAAATAATT
3042533 ATAAATA--TTTATATAAAAATAATT
1 ATAAATATTTTTATATAAAAATAATT
*
3042557 TTAAATATT
1 ATAAATATT
3042566 CTTTTAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 21 0.78
26 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATAAATATTTTTATATAAAAATAATT
Found at i:3042543 original size:24 final size:24
Alignment explanation
Indices: 3042516--3042565 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3042506 AATAATTATT
**
3042516 TTTATATAAATTTAATTATAAATA
1 TTTATATAAAAATAATTATAAATA
*
3042540 TTTATATAAAAATAATTTTAAATA
1 TTTATATAAAAATAATTATAAATA
3042564 TT
1 TT
3042566 CTTTTAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTATATAAAAATAATTATAAATA
Found at i:3042573 original size:24 final size:25
Alignment explanation
Indices: 3042528--3042579 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
3042518 TATATAAATT
3042528 TAATTATAAATATTTATATAAA-AA
1 TAATTATAAATATTTATATAAACAA
* *
3042552 TAATTTTAAATATTCT-TTTAAACAA
1 TAATTATAAATATT-TATATAAACAA
3042577 TAA
1 TAA
3042580 AATGAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATTATAAATATTTATATAAACAA
Found at i:3047077 original size:2 final size:2
Alignment explanation
Indices: 3047070--3047109 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3047060 AAAGGTGTTC
3047070 AT AT 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
3047110 CAATAATCAA
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):
AT
Found at i:3048689 original size:2 final size:2
Alignment explanation
Indices: 3048682--3048714 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3048672 AATGGAGGTG
3048682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3048715 TATGAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3049427 original size:62 final size:62
Alignment explanation
Indices: 3049323--3049445 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 62
3049313 ATACTTCATT
*
3049323 ATTAAATACAAAGTTATATGTATTTATTTTTTAAAATATTTAATAAAATAATATAATCTGATTC
1 ATTAAATACAAAGTTATA-GTATTTATTTTTTAAAATATTTAATAAAATAATA-AATATGATTC
*
3049387 ATTAAATACAAAGTTATA-TATTTA-TTTTTAAAATTTTTTAATAAAATAATAAATATGAT
1 ATTAAATACAAAGTTATAGTATTTATTTTTTAAAA-TATTTAATAAAATAATAAATATGAT
3049446 ACATCAATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
61 16 0.29
62 22 0.39
64 18 0.32
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (62 bp):
ATTAAATACAAAGTTATAGTATTTATTTTTTAAAATATTTAATAAAATAATAAATATGATTC
Found at i:3050109 original size:16 final size:15
Alignment explanation
Indices: 3050082--3050163 Score: 50
Period size: 16 Copynumber: 5.4 Consensus size: 15
3050072 AAATATATTT
3050082 TAAAA-TTT-ATATA
1 TAAAATTTTAATATA
3050095 TAAAATTATTAATATA
1 TAAAATT-TTAATATA
*
3050111 CT-AAATTTATATAAATA
1 -TAAAATTT-TA-ATATA
3050128 TAATATATTTTAA-ATA
1 TAA-A-ATTTTAATATA
3050144 T--AATTTTAATATAA
1 TAAAATTTTAATAT-A
3050158 TAAAAT
1 TAAAAT
3050164 ATAAAATAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 23
0.70 0.01 0.29
Matches are distributed among these distances:
12 7 0.13
13 8 0.15
14 3 0.05
15 3 0.05
16 20 0.36
17 7 0.13
18 3 0.05
19 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATTTTAATATA
Found at i:3050133 original size:11 final size:11
Alignment explanation
Indices: 3050119--3050177 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
3050109 TACTAAATTT
3050119 ATATAA-ATATA
1 ATATAATATA-A
* *
3050130 ATATATTTTAA
1 ATATAATATAA
* *
3050141 ATATAATTTTA
1 ATATAATATAA
3050152 ATATAATA-AA
1 ATATAATATAA
*
3050162 ATATAAAATAA
1 ATATAATATAA
3050173 ATATA
1 ATATA
3050178 TAAATAATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 8 0.21
11 29 0.74
12 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATAATATAA
Found at i:3050325 original size:2 final size:2
Alignment explanation
Indices: 3050307--3050352 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
3050297 GTTTTTCATG
* *
3050307 AT AT AC AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3050348 AT AT A
1 AT AT A
3050353 GATTGGGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3052344 original size:18 final size:18
Alignment explanation
Indices: 3052300--3052351 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
3052290 TTTTTATTTG
* *
3052300 ATATATAATAAAATATAA
1 ATATATAAAAAAATTTAA
* * *
3052318 CTTTTTAAAAAAATTTAA
1 ATATATAAAAAAATTTAA
3052336 ATATATAAAAAAATTT
1 ATATATAAAAAAATTT
3052352 TAAAAAATTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATATAAAAAAATTTAA
Found at i:3053242 original size:21 final size:21
Alignment explanation
Indices: 3053218--3053262 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3053208 GACAAGTAAT
3053218 AATTATATCTAAAAA-TATAAA
1 AATTAT-TCTAAAAATTATAAA
* *
3053239 AATTATTTTAAAAATTTTAAA
1 AATTATTCTAAAAATTATAAA
3053260 AAT
1 AAT
3053263 AATTTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTATTCTAAAAATTATAAA
Found at i:3053252 original size:20 final size:21
Alignment explanation
Indices: 3053227--3053267 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3053217 TAATTATATC
*
3053227 TAAAAA-TATAAAAATTATTT
1 TAAAAATTATAAAAATAATTT
*
3053247 TAAAAATTTTAAAAATAATTT
1 TAAAAATTATAAAAATAATTT
3053268 ACTTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAATTATAAAAATAATTT
Found at i:3057124 original size:13 final size:14
Alignment explanation
Indices: 3057106--3057136 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3057096 ATCGAAACTA
3057106 TTTTTTTTCTT-TT
1 TTTTTTTTCTTCTT
3057119 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
3057133 TTTT
1 TTTT
3057137 CTTGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Found at i:3057125 original size:16 final size:16
Alignment explanation
Indices: 3057106--3057136 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3057096 ATCGAAACTA
3057106 TTTTTT-TTCTTTTTT
1 TTTTTTCTTCTTTTTT
3057121 TTTTTTCTTCTTTTTT
1 TTTTTTCTTCTTTTTT
3057137 CTTGATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTTCTTCTTTTTT
Found at i:3058346 original size:18 final size:20
Alignment explanation
Indices: 3058323--3058367 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
3058313 TAATTATCAC
* *
3058323 ATAATA-AAATATATAAA-T
1 ATAATATAAATACACAAATT
3058341 ATAATATAAATACACAAATT
1 ATAATATAAATACACAAATT
3058361 ATAATAT
1 ATAATAT
3058368 CCATCGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 9 0.39
20 8 0.35
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATATAAATACACAAATT
Found at i:3058618 original size:17 final size:17
Alignment explanation
Indices: 3058585--3058624 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3058575 AATTATTCAA
3058585 AATTTTAATTTTAATTT
1 AATTTTAATTTTAATTT
*
3058602 AGATTTT-ATTTTTATTT
1 A-ATTTTAATTTTAATTT
3058619 AATTTT
1 AATTTT
3058625 TTTGATTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 11 0.52
18 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
AATTTTAATTTTAATTT
Found at i:3058858 original size:11 final size:11
Alignment explanation
Indices: 3058824--3058869 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
3058814 ATAATTTTAA
3058824 TTAATTTAATT
1 TTAATTTAATT
3058835 TTATATATT--TT
1 TTA-AT-TTAATT
3058846 TTAATTTAATT
1 TTAATTTAATT
3058857 TTAATTTAATT
1 TTAATTTAATT
3058868 TT
1 TT
3058870 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.06
10 2 0.06
11 23 0.74
12 2 0.06
13 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTAATTTAATT
Found at i:3058893 original size:33 final size:33
Alignment explanation
Indices: 3058795--3058886 Score: 86
Period size: 33 Copynumber: 2.8 Consensus size: 33
3058785 TTAATCAAAA
* *
3058795 TAATTTAAATTTATAAA--ATATAATTTTAA--T
1 TAATTTAATTTTATAAATTTTATAA-TTTAATTT
* *
3058825 TAATTTAATTTTATATATTTTTTAATTTAATTT
1 TAATTTAATTTTATAAATTTTATAATTTAATTT
3058858 TAATTTAATTTT-TAAAATTTTATATATTT
1 TAATTTAATTTTAT-AAATTTTATA-ATTT
3058887 TTTTTAAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
30 15 0.30
31 5 0.10
32 5 0.10
33 21 0.42
34 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TAATTTAATTTTATAAATTTTATAATTTAATTT
Found at i:3059033 original size:15 final size:15
Alignment explanation
Indices: 3058998--3059048 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
3058988 CTTTTACTCC
*
3058998 TTTTTAAATTTTTTTA
1 TTTTTAAA-TATTTTA
*
3059014 ATTTTAAATATTTTA
1 TTTTTAAATATTTTA
*
3059029 TTTTT-AATCTTTTA
1 TTTTTAAATATTTTA
3059043 TTTTTA
1 TTTTTA
3059049 TTTTATCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 13 0.43
15 10 0.33
16 7 0.23
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTAAATATTTTA
Found at i:3059098 original size:12 final size:12
Alignment explanation
Indices: 3059076--3059117 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
3059066 TTTAACATAA
3059076 ATATAATTTTATT
1 ATAT-ATTTTATT
3059089 ATATATTTTATT
1 ATATATTTTATT
* *
3059101 ATTTATTATA-T
1 ATATATTTTATT
3059112 ATATAT
1 ATATAT
3059118 CTATATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 6 0.23
12 16 0.62
13 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATATTTTATT
Found at i:3059241 original size:18 final size:18
Alignment explanation
Indices: 3059209--3059247 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3059199 TATAATTTCA
*
3059209 TTATTATATTAATTAGTT
1 TTATTATAATAATTAGTT
* *
3059227 TTATTATAATCATTATTT
1 TTATTATAATAATTAGTT
3059245 TTA
1 TTA
3059248 ATTTTATCCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATTATAATAATTAGTT
Found at i:3061525 original size:32 final size:32
Alignment explanation
Indices: 3061484--3061579 Score: 192
Period size: 32 Copynumber: 3.0 Consensus size: 32
3061474 CGTGGAAGTG
3061484 CCTAATTTCTACCAGATATATATATATATATA
1 CCTAATTTCTACCAGATATATATATATATATA
3061516 CCTAATTTCTACCAGATATATATATATATATA
1 CCTAATTTCTACCAGATATATATATATATATA
3061548 CCTAATTTCTACCAGATATATATATATATATA
1 CCTAATTTCTACCAGATATATATATATATATA
3061580 TATATATAGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.41
Consensus pattern (32 bp):
CCTAATTTCTACCAGATATATATATATATATA
Found at i:3061599 original size:2 final size:2
Alignment explanation
Indices: 3061563--3061587 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3061553 TTTCTACCAG
3061563 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3061588 GGTCATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3061793 original size:14 final size:14
Alignment explanation
Indices: 3061745--3061795 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3061735 TTATTATTTA
3061745 TTATATTATTAA-AT
1 TTATA-TATTAATAT
* * *
3061759 TTTTAAAATAATAT
1 TTATATATTAATAT
*
3061773 TTTTATATTAATAT
1 TTATATATTAATAT
3061787 TTATATATT
1 TTATATATT
3061796 TTATAATTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
13 4 0.13
14 26 0.87
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATATTAATAT
Found at i:3065949 original size:16 final size:16
Alignment explanation
Indices: 3065928--3066017 Score: 52
Period size: 16 Copynumber: 5.9 Consensus size: 16
3065918 TCCGATTTAA
3065928 TAAATTTAATTTATAT
1 TAAATTTAATTTATAT
* *
3065944 TAAATTAAATTTAAAT
1 TAAATTTAATTTATAT
*
3065960 AAAATATT--TTTA-ATT
1 TAAAT-TTAATTTATA-T
3065975 TAAATTTAA---ATA-
1 TAAATTTAATTTATAT
* *
3065987 TAAATTTTATTAATTAT
1 TAAATTTAATTTA-TAT
3066004 T-AATTTAATTTATA
1 TAAATTTAATTTATA
3066018 AATAAATCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 21
0.66 0.09 0.25
Matches are distributed among these distances:
12 8 0.14
13 1 0.02
14 4 0.07
15 12 0.21
16 29 0.52
17 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATTTAATTTATAT
Found at i:3065977 original size:26 final size:27
Alignment explanation
Indices: 3065935--3066020 Score: 95
Period size: 26 Copynumber: 3.1 Consensus size: 27
3065925 TAATAAATTT
*
3065935 AATTTATATTAAATTAAATTTAAATA-A
1 AATTT-TATTAATTTAAATTTAAATATA
3065962 AATATTT-TTAATTTAAATTTAAATATA
1 AAT-TTTATTAATTTAAATTTAAATATA
* *
3065989 AATTTTATTAATTATTAATTTAATTTATA
1 AATTTTATTAATT-TAAATTTAA-ATATA
3066018 AAT
1 AAT
3066021 AAATCTAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
26 20 0.39
27 14 0.27
28 10 0.20
29 7 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTTTATTAATTTAAATTTAAATATA
Found at i:3066461 original size:23 final size:21
Alignment explanation
Indices: 3066426--3066467 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3066416 TATAAAATAG
3066426 ATTTTTTTTAATTAAATTAAT
1 ATTTTTTTTAATTAAATTAAT
*
3066447 ATTTTTATTTAAATTTAATTA
1 ATTTTT-TTT-AATTAAATTA
3066468 TAAAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 3 0.17
23 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTTTTAATTAAATTAAT
Found at i:3066509 original size:26 final size:26
Alignment explanation
Indices: 3066467--3066523 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
3066457 AAATTTAATT
3066467 ATAAAATATATAAATA-TTAATATAAAA
1 ATAAAATATATAAATATTTAA-AT-AAA
*
3066494 ATAAAAT-TTTAAATATTTAAATAAA
1 ATAAAATATATAAATATTTAAATAAA
3066519 ATAAA
1 ATAAA
3066524 TAATAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 8 0.29
26 9 0.32
27 11 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAAAATATATAAATATTTAAATAAA
Found at i:3069485 original size:2 final size:2
Alignment explanation
Indices: 3069478--3069511 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3069468 TAGAAAACCA
3069478 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
3069512 TTCGTATCAA
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:3070765 original size:17 final size:19
Alignment explanation
Indices: 3070743--3070784 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
3070733 ATGAATTAAT
3070743 TTATAATAAAAT-AAT-TA
1 TTATAATAAAATAAATATA
*
3070760 TTATAATAAATTAAATATA
1 TTATAATAAAATAAATATA
3070779 TTATAA
1 TTATAA
3070785 ATCTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
18 3 0.14
19 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATAATAAAATAAATATA
Found at i:3090382 original size:14 final size:14
Alignment explanation
Indices: 3090363--3090418 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
3090353 AAAAACATGT
3090363 TATAAATTATATAA
1 TATAAATTATATAA
3090377 TATAAATTAT-TAA
1 TATAAATTATATAA
*
3090390 T-T-TATTA-ATACA
1 TATAAATTATATA-A
*
3090402 TATAAAATATATAA
1 TATAAATTATATAA
3090416 TAT
1 TAT
3090419 TTTAAATATG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
11 6 0.18
12 3 0.09
13 5 0.15
14 17 0.50
15 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TATAAATTATATAA
Found at i:3090404 original size:25 final size:26
Alignment explanation
Indices: 3090368--3090416 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
3090358 CATGTTATAA
*
3090368 ATTATATAATATAAATTAT-TAATTT
1 ATTATATAATATAAAATATATAATTT
3090393 ATTA-ATACATATAAAATATATAAT
1 ATTATATA-ATATAAAATATATAAT
3090417 ATTTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTATATAATATAAAATATATAATTT
Found at i:3090857 original size:14 final size:15
Alignment explanation
Indices: 3090835--3090863 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3090825 TTATTCAGTT
3090835 ATTATTATTATATTA
1 ATTATTATTATATTA
3090850 ATTA-TATTATATTA
1 ATTATTATTATATTA
3090864 CACAAGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATTATTATATTA
Found at i:3091244 original size:40 final size:42
Alignment explanation
Indices: 3091200--3091306 Score: 113
Period size: 40 Copynumber: 2.7 Consensus size: 42
3091190 TTGAAATTTG
3091200 TTTTATTATTTAAAATAAT-ATTAAAATTTTAAA-AAAT-TAT
1 TTTTATTATTTAAAATAATAATT-AAATTTTAAATAAATATAT
* *
3091240 TTTTA-TA-TTAATATTTATAATTAAA-TTTAAATAAATATAT
1 TTTTATTATTTAA-AATAATAATTAAATTTTAAATAAATATAT
3091280 TTTTATT-TTT-AAATAATAATTTAAATT
1 TTTTATTATTTAAAATAATAA-TTAAATT
3091307 AAATTATAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
38 10 0.18
39 19 0.35
40 22 0.40
41 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (42 bp):
TTTTATTATTTAAAATAATAATTAAATTTTAAATAAATATAT
Found at i:3091299 original size:39 final size:38
Alignment explanation
Indices: 3091200--3091310 Score: 104
Period size: 39 Copynumber: 2.8 Consensus size: 38
3091190 TTGAAATTTG
3091200 TTTTATTATTTAAAATAAT-ATTAAAATTTTAAA-AAATTAT
1 TTTTATT-TTT-AAATAATAATT-AAA-TTTAAATAAATTAT
* *
3091240 TTTTA-TATTAATATTTATAATTAAATTTAAATAAATATAT
1 TTTTATTTTTAA-A-TAATAATTAAATTTAAATAAAT-TAT
3091280 TTTTATTTTTAAATAATAATTTAAA-TTAAAT
1 TTTTATTTTTAAATAATAA-TTAAATTTAAAT
3091311 TATAAAATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
37 2 0.03
38 9 0.15
39 22 0.37
40 22 0.37
41 5 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
TTTTATTTTTAAATAATAATTAAATTTAAATAAATTAT
Found at i:3091829 original size:21 final size:21
Alignment explanation
Indices: 3091786--3091829 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3091776 TAAATTTAGG
* **
3091786 TTTAAGATAAAATTTGATTTT
1 TTTAAGATAAAATTTAAAATT
*
3091807 TTTAATATAAAATTTAAAATT
1 TTTAAGATAAAATTTAAAATT
3091828 TT
1 TT
3091830 ACATTACATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (21 bp):
TTTAAGATAAAATTTAAAATT
Found at i:3094471 original size:20 final size:20
Alignment explanation
Indices: 3094448--3094520 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
3094438 ACAATTCAAA
3094448 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
3094468 GTATCGATACATGAAAATG--AT
1 GTATCGATACATG---TTGCAAT
3094489 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3094509 GTATCGATACAT
1 GTATCGATACAT
3094521 AAAAAAGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
20 27 0.59
21 15 0.33
23 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3094492 original size:21 final size:21
Alignment explanation
Indices: 3094466--3094541 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
3094456 ACATGTTGCA
3094466 ATGTATCGATACATGAAAATG
1 ATGTATCGATACATGAAAATG
*
3094487 ATGTATCGATACATG---TTG
1 ATGTATCGATACATGAAAATG
* *
3094505 CAATGTATCGATACATAAAAAAG
1 --ATGTATCGATACATGAAAATG
3094528 ATGTATCGATACAT
1 ATGTATCGATACAT
3094542 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.04
20 14 0.30
21 29 0.63
23 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAATG
Found at i:3094499 original size:41 final size:41
Alignment explanation
Indices: 3094448--3094541 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3094438 ACAATTCAAA
* *
3094448 GTATCGATACATGTTGCAATGTATCGATACATGAAAATGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3094489 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3094530 GTATCGATACAT
1 GTATCGATACAT
3094542 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3094598 original size:13 final size:13
Alignment explanation
Indices: 3094580--3094605 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3094570 TACAGCAAGT
3094580 ATGTATCGATACA
1 ATGTATCGATACA
3094593 ATGTATCGATACA
1 ATGTATCGATACA
3094606 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3096852 original size:21 final size:21
Alignment explanation
Indices: 3096819--3096863 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3096809 TTGCAAGTTG
*
3096819 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3096841 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3096861 AAA
1 AAA
3096864 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3100786 original size:13 final size:13
Alignment explanation
Indices: 3100768--3100806 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3100758 ATATTTTTCT
3100768 TTGTATCGATACA
1 TTGTATCGATACA
3100781 TTGTATCGATACA
1 TTGTATCGATACA
*
3100794 CTGTATCGATACA
1 TTGTATCGATACA
3100807 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3103282 original size:20 final size:20
Alignment explanation
Indices: 3103259--3103331 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
3103249 ACAATTCAAA
3103259 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*
3103279 GTATCGATACATGAAAATG--AT
1 GTATCGATACATG---TTGCAAT
3103300 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3103320 GTATCGATACAT
1 GTATCGATACAT
3103332 AAAAAAGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
20 27 0.59
21 15 0.33
23 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3103303 original size:21 final size:21
Alignment explanation
Indices: 3103277--3103352 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
3103267 ACATGTTGCA
3103277 ATGTATCGATACATGAAAATG
1 ATGTATCGATACATGAAAATG
*
3103298 ATGTATCGATACATG---TTG
1 ATGTATCGATACATGAAAATG
* *
3103316 CAATGTATCGATACATAAAAAAG
1 --ATGTATCGATACATGAAAATG
3103339 ATGTATCGATACAT
1 ATGTATCGATACAT
3103353 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.04
20 14 0.30
21 29 0.63
23 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAATG
Found at i:3103310 original size:41 final size:41
Alignment explanation
Indices: 3103259--3103352 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3103249 ACAATTCAAA
* *
3103259 GTATCGATACATGTTGCAATGTATCGATACATGAAAATGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3103300 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3103341 GTATCGATACAT
1 GTATCGATACAT
3103353 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3103409 original size:13 final size:13
Alignment explanation
Indices: 3103391--3103416 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3103381 TACAGCAAGT
3103391 ATGTATCGATACA
1 ATGTATCGATACA
3103404 ATGTATCGATACA
1 ATGTATCGATACA
3103417 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3104773 original size:24 final size:25
Alignment explanation
Indices: 3104726--3104773 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3104716 TTTGATATTT
* **
3104726 AAAAAAATTAAAAATTATTTAAATG
1 AAAAAAACTAAAAATTATGAAAATG
3104751 AAAAAAACT-AAAATTATGAAAAT
1 AAAAAAACTAAAAATTATGAAAAT
3104774 TTGACTTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (25 bp):
AAAAAAACTAAAAATTATGAAAATG
Found at i:3105363 original size:21 final size:21
Alignment explanation
Indices: 3105308--3105363 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
3105298 ATGATAAATA
*
3105308 AATTTAATTTAAATTATTATTT
1 AATTTAA-TTAAAATATTATTT
*
3105330 AA-TAAATATAAAATA-TATTT
1 AATTTAAT-TAAAATATTATTT
3105350 GAATTTAATTAAAA
1 -AATTTAATTAAAA
3105364 ACCATATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 6 0.21
21 16 0.57
22 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AATTTAATTAAAATATTATTT
Found at i:3105511 original size:2 final size:2
Alignment explanation
Indices: 3105504--3105534 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3105494 TATCTTGTTT
*
3105504 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3105535 CTAATATGCA
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3108924 original size:21 final size:20
Alignment explanation
Indices: 3108864--3108926 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
3108854 ATTCATATTT
3108864 ATAA-TTAAATTAAATAAAA
1 ATAATTTAAATTAAATAAAA
** **
3108883 ATAATTTTTATTATTTAAAAA
1 ATAATTTAAATTAAAT-AAAA
*
3108904 ATAATTTAAATTAAATCAAA
1 ATAATTTAAATTAAATAAAA
3108924 ATA
1 ATA
3108927 TAAACAGTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 4 0.12
20 13 0.39
21 16 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATTTAAATTAAATAAAA
Found at i:3109600 original size:15 final size:16
Alignment explanation
Indices: 3109580--3109615 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3109570 TACTTTAATG
3109580 AAAATAAAAAAATA-A
1 AAAATAAAAAAATATA
*
3109595 AAAATAAATAAATATA
1 AAAATAAAAAAATATA
3109611 AAAAT
1 AAAAT
3109616 TGAAGAAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAAAAAAATATA
Found at i:3109833 original size:3 final size:3
Alignment explanation
Indices: 3109827--3109859 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3109817 ATGCAGATTG
3109827 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC
3109860 CGCCTCAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:3113245 original size:4 final size:5
Alignment explanation
Indices: 3113223--3113264 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
3113213 ACTAAAAAAA
* *
3113223 TTAAT TTAAT TTAAT TTAA- TTAAT TTGA- TTAAT TTAAA TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
3113265 ATTTTGATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 7 0.22
5 25 0.78
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
TTAAT
Found at i:3113245 original size:9 final size:9
Alignment explanation
Indices: 3113221--3113264 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
3113211 TAACTAAAAA
3113221 AATTAATTT
1 AATTAATTT
3113230 AATTTAATTT
1 AA-TTAATTT
3113240 AATTAATTT
1 AATTAATTT
*
3113249 GATTAATTT
1 AATTAATTT
3113258 AAATTAA
1 -AATTAA
3113265 ATTTTGATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 17 0.55
10 14 0.45
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (9 bp):
AATTAATTT
Found at i:3113272 original size:21 final size:19
Alignment explanation
Indices: 3113220--3113264 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3113210 TTAACTAAAA
*
3113220 AAATTAATTTAATTTAATTT
1 AAATTAATTTGA-TTAATTT
3113240 -AATTAATTTGATTAATTT
1 AAATTAATTTGATTAATTT
3113258 AAATTAA
1 AAATTAA
3113265 ATTTTGATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
AAATTAATTTGATTAATTT
Found at i:3113454 original size:28 final size:27
Alignment explanation
Indices: 3113422--3113481 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
3113412 GATTATTTCG
* *
3113422 ATTTTAAAATT-GATATTGATTGAGATCA
1 ATTTTAAAATTAAAT-TTGATT-AAATCA
*
3113450 ATTTTAATATTAAATTTGATTAAATCA
1 ATTTTAAAATTAAATTTGATTAAATCA
3113477 ATTTT
1 ATTTT
3113482 CGATTTAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 10 0.36
28 16 0.57
29 2 0.07
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (27 bp):
ATTTTAAAATTAAATTTGATTAAATCA
Found at i:3113616 original size:34 final size:34
Alignment explanation
Indices: 3113573--3113644 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
3113563 AGGGAAAGTA
*
3113573 AGAATCAATAATCCTTGTCCAATATGCCGATTAG
1 AGAATCAATAACCCTTGTCCAATATGCCGATTAG
3113607 AGAATCAATAACCCTTGTCCAATATGCCGATTAG
1 AGAATCAATAACCCTTGTCCAATATGCCGATTAG
3113641 -GAAT
1 AGAAT
3113645 TTCAAACGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 4 0.11
34 33 0.89
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (34 bp):
AGAATCAATAACCCTTGTCCAATATGCCGATTAG
Found at i:3115220 original size:2 final size:2
Alignment explanation
Indices: 3115215--3115248 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3115205 CTCTTTACAG
3115215 AT AT AT A- AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3115249 TTGTTCTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3115235 original size:15 final size:13
Alignment explanation
Indices: 3115215--3115248 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3115205 CTCTTTACAG
3115215 ATATATA-ATAT-
1 ATATATATATATA
3115226 ATATATATATATA
1 ATATATATATATA
3115239 ATATATATAT
1 ATATATATAT
3115249 TTGTTCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.33
12 4 0.19
13 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATATATATA
Found at i:3115237 original size:17 final size:17
Alignment explanation
Indices: 3115215--3115248 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3115205 CTCTTTACAG
3115215 ATATATAATATATATAT
1 ATATATAATATATATAT
3115232 ATATATAATATATATAT
1 ATATATAATATATATAT
3115249 TTGTTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATAATATATATAT
Found at i:3117125 original size:14 final size:16
Alignment explanation
Indices: 3117108--3117184 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 16
3117098 ATAATAATTT
3117108 TTATTTAAAT-T-TAA
1 TTATTTAAATATATAA
3117122 TTATTTAAATATATAA
1 TTATTTAAATATATAA
*
3117138 TTA-TTAATATAAAATAA
1 TTATTTAA-AT-ATATAA
*
3117155 TT-TTT-AATATTTAA
1 TTATTTAAATATATAA
*
3117169 TATTTTTAAATA-ATAA
1 T-TATTTAAATATATAA
3117185 AATAAATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
14 15 0.29
15 8 0.16
16 15 0.29
17 13 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTTAAATATATAA
Found at i:3117156 original size:33 final size:32
Alignment explanation
Indices: 3117093--3117169 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 32
3117083 AAGATTTTTG
* * *
3117093 TTTAAATA-ATAATTTTTATTTAAATTTAATT
1 TTTAAATATATAATTTTAATATAAATATAATT
3117124 ATTTAAATATATAATTATTAATATAAA-ATAATT
1 -TTTAAATATATAATT-TTAATATAAATATAATT
*
3117157 TTT-AATATTTAAT
1 TTTAAATATATAAT
3117170 ATTTTTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
31 9 0.23
32 11 0.28
33 11 0.28
34 8 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TTTAAATATATAATTTTAATATAAATATAATT
Found at i:3117170 original size:17 final size:17
Alignment explanation
Indices: 3117100--3117194 Score: 63
Period size: 17 Copynumber: 5.5 Consensus size: 17
3117090 TTGTTTAAAT
*
3117100 AATAATTTTT-ATTTAA
1 AATAATTTTTAATATAA
*
3117116 ATTTAATTATTTAA-AT-A
1 A-ATAATT-TTTAATATAA
* *
3117133 TATAATTATTAATATAA
1 AATAATTTTTAATATAA
**
3117150 AATAATTTTTAATATTT
1 AATAATTTTTAATATAA
3117167 AAT-ATTTTTAAATAATAA
1 AATAATTTTT-AAT-ATAA
3117185 AATAAATTTT
1 AAT-AATTTT
3117195 CGAACTTGAT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
15 4 0.07
16 14 0.24
17 26 0.44
18 9 0.15
19 1 0.02
20 5 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATAATTTTTAATATAA
Found at i:3117671 original size:2 final size:2
Alignment explanation
Indices: 3117664--3117702 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3117654 ACGGTGCATT
3117664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3117703 GTATTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3119742 original size:23 final size:20
Alignment explanation
Indices: 3119715--3119765 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 20
3119705 ATAATATATT
3119715 TAATTATAAATATTCATATTAAA
1 TAATTATAAATATT--T-TTAAA
* *
3119738 TAATTTTTAATATTTTTAAA
1 TAATTATAAATATTTTTAAA
3119758 TAATTATA
1 TAATTATA
3119766 TAAATCTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 11 0.46
21 1 0.04
23 12 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTATAAATATTTTTAAA
Found at i:3121196 original size:2 final size:2
Alignment explanation
Indices: 3121189--3121214 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3121179 AAGCGTGAAC
3121189 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
3121215 TAATTTATAG
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:3121888 original size:3 final size:3
Alignment explanation
Indices: 3121882--3121910 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3121872 TTCTTTCTTG
3121882 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3121911 GCTACTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3122079 original size:106 final size:106
Alignment explanation
Indices: 3121894--3122101 Score: 371
Period size: 106 Copynumber: 2.0 Consensus size: 106
3121884 ATTATTATTA
* *
3121894 TTATTATTATTATTATTGCTACTTTTTCGACTTTAACTCCTCAAATTCTGTGATGAGTTTTGTAT
1 TTATTATTATTATTACTACTACTTTTTCGACTTTAACTCCTCAAATTCTGTGATGAGTTTTGTAT
*
3121959 AGTCTTAATTTCTTATTGAATACAATGAACAAGTGTAATGT
66 AGTCTTAATTTCTTAATGAATACAATGAACAAGTGTAATGT
*
3122000 TTATTATTATTATTACTACTACTTTTTCGAGTTTAACTCCTCAAATTCTGTGATGAGTTTTGTAT
1 TTATTATTATTATTACTACTACTTTTTCGACTTTAACTCCTCAAATTCTGTGATGAGTTTTGTAT
*
3122065 GGTCTTAATTTCTTAATGAATACAATGAACAAGTGTA
66 AGTCTTAATTTCTTAATGAATACAATGAACAAGTGTA
3122102 GAGGCCGTTC
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 97 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (106 bp):
TTATTATTATTATTACTACTACTTTTTCGACTTTAACTCCTCAAATTCTGTGATGAGTTTTGTAT
AGTCTTAATTTCTTAATGAATACAATGAACAAGTGTAATGT
Found at i:3123330 original size:13 final size:13
Alignment explanation
Indices: 3123314--3123339 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3123304 TAAAAAAATG
3123314 TCATAAAACAAAA
1 TCATAAAACAAAA
3123327 TCATAAAACAAAA
1 TCATAAAACAAAA
3123340 GTTAAACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (13 bp):
TCATAAAACAAAA
Found at i:3124193 original size:13 final size:14
Alignment explanation
Indices: 3124175--3124207 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3124165 TTTAAAAAAA
3124175 TAATATT-TAATTT
1 TAATATTATAATTT
3124188 TAATATTATAATTT
1 TAATATTATAATTT
*
3124202 TTATAT
1 TAATAT
3124208 AAAAAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TAATATTATAATTT
Found at i:3124212 original size:38 final size:38
Alignment explanation
Indices: 3124139--3124223 Score: 91
Period size: 40 Copynumber: 2.1 Consensus size: 38
3124129 GTATATATAT
* *
3124139 ATATTTAATTAATTTATATAATTATTTTTAAAAAAATA
1 ATATTTAATTAATATATATAATTATTTATAAAAAAATA
*
3124177 ATATTTAATTTTAATAT-TATAATTTTTATATAAAAAAGATA
1 ATATTTAA--TTAATATATATAATTATT-TATAAAAAA-ATA
3124218 TATATT
1 -ATATT
3124224 ATTTAACTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
38 8 0.21
39 9 0.23
40 14 0.36
41 3 0.08
42 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (38 bp):
ATATTTAATTAATATATATAATTATTTATAAAAAAATA
Found at i:3124680 original size:2 final size:2
Alignment explanation
Indices: 3124673--3124700 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3124663 ATAAGCTAAT
3124673 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
3124701 CACACACCAA
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):
TA
Found at i:3126121 original size:25 final size:25
Alignment explanation
Indices: 3126091--3126140 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3126081 TGCATTTAAC
*
3126091 ATTATATTGAATT-AAAATTATTTAT
1 ATTATATTG-ATTAAAAATAATTTAT
3126116 ATTATATTGATTAAAAATAATTTAT
1 ATTATATTGATTAAAAATAATTTAT
3126141 TTTAATGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
ATTATATTGATTAAAAATAATTTAT
Found at i:3126186 original size:23 final size:23
Alignment explanation
Indices: 3126154--3126206 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
3126144 AATGTATTGA
* *
3126154 TAATATATTAATTTAT-TTAATTT
1 TAATAAATTAATTAATATT-ATTT
3126177 TAATAAATTAATTAATATTATTT
1 TAATAAATTAATTAATATTATTT
*
3126200 TATTAAA
1 TAATAAA
3126207 ATAAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATAAATTAATTAATATTATTT
Found at i:3126238 original size:20 final size:21
Alignment explanation
Indices: 3126209--3126248 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3126199 TTATTAAAAT
3126209 AAATATAAATATATTT-TATTA
1 AAATATAAAT-TATTTATATTA
3126230 AAATA-AAATTATTTATATT
1 AAATATAAATTATTTATATT
3126249 TATTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATATAAATTATTTATATTA
Found at i:3126930 original size:17 final size:17
Alignment explanation
Indices: 3126908--3126943 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3126898 TAATAAAAAT
3126908 ATAAAAATATTTATATA
1 ATAAAAATATTTATATA
*
3126925 ATAAAAATATTTATTTA
1 ATAAAAATATTTATATA
3126942 AT
1 AT
3126944 TTTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAAATATTTATATA
Found at i:3127006 original size:24 final size:24
Alignment explanation
Indices: 3126957--3127006 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
3126947 TTAATTTTAG
3126957 TTATAAAAATTAAAAATTTTACTTT
1 TTATAAAAA-TAAAAATTTTACTTT
3126982 TTATAAAAA-AATAAACTTTTA-TTT
1 TTATAAAAATAA-AAA-TTTTACTTT
3127006 T
1 T
3127007 ATTTGGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 2 0.09
24 7 0.30
25 14 0.61
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTATAAAAATAAAAATTTTACTTT
Found at i:3134079 original size:13 final size:14
Alignment explanation
Indices: 3134061--3134089 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3134051 ATTTTAAAAT
3134061 TTTAATT-AAATAA
1 TTTAATTCAAATAA
3134074 TTTAATTCAAATAA
1 TTTAATTCAAATAA
3134088 TT
1 TT
3134090 CAATCAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAATTCAAATAA
Found at i:3135487 original size:31 final size:32
Alignment explanation
Indices: 3135449--3135543 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 32
3135439 ATGCTTTATT
3135449 TTTATCCAATATTTTTAAAAATTATATTT-T-A
1 TTTATCCAATA-TTTTAAAAATTATATTTATCA
* *
3135480 TTTATCC-ATAGCTTTTAACAGTTATATTTATCA
1 TTTATCCAATA--TTTTAAAAATTATATTTATCA
*
3135513 TCTAT--AA-ATTTTAAAAATTATATTTATCA
1 TTTATCCAATATTTTAAAAATTATATTTATCA
3135542 TT
1 TT
3135544 AATAACCTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
29 20 0.38
30 3 0.06
31 23 0.43
32 2 0.04
33 5 0.09
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (32 bp):
TTTATCCAATATTTTAAAAATTATATTTATCA
Found at i:3135548 original size:29 final size:30
Alignment explanation
Indices: 3135461--3135558 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 30
3135451 TATCCAATAT
* * *
3135461 TTTTAAAAATTATATTTTATTTATCCATAGC-
1 TTTTAAAAATTATA-TTTA-TCATCTATAACA
* *
3135492 TTTTAACAGTTATATTTATCATCTATAA-A
1 TTTTAAAAATTATATTTATCATCTATAACA
*
3135521 TTTTAAAAATTATATTTATCAT-TAATAACC
1 TTTTAAAAATTATATTTATCATCT-ATAACA
3135551 TTTTAAAA
1 TTTTAAAA
3135559 GTTTATCTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
28 1 0.02
29 31 0.55
30 12 0.21
31 12 0.21
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (30 bp):
TTTTAAAAATTATATTTATCATCTATAACA
Found at i:3136044 original size:19 final size:20
Alignment explanation
Indices: 3136020--3136060 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3136010 AATTTGTGCA
* *
3136020 TTCAAATTTTTCAT-TTTTT
1 TTCAAATTATTAATATTTTT
3136039 TTCAAATTATTAATATTTTT
1 TTCAAATTATTAATATTTTT
3136059 TT
1 TT
3136061 TATTTTCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (20 bp):
TTCAAATTATTAATATTTTT
Found at i:3138339 original size:15 final size:15
Alignment explanation
Indices: 3138319--3138368 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
3138309 CAAGAGATTC
3138319 ATAAATCAAATCTAT
1 ATAAATCAAATCTAT
*
3138334 ATAAATTAAATCTAT
1 ATAAATCAAATCTAT
3138349 ATAAATCAAATCTAT
1 ATAAATCAAATCTAT
3138364 ATAAA
1 ATAAA
3138369 ACATAGCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAATCAAATCTAT
Found at i:3142292 original size:27 final size:28
Alignment explanation
Indices: 3142231--3142301 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
3142221 AAACAAGCCT
* * *
3142231 CCATATTTGACAAATACAAAGAAAACCG
1 CCATTTTTGACAAACACAAAGAAAACCA
*
3142259 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGAAAACCA
*
3142286 CTATTTTTGACAAACA
1 CCATTTTTGACAAACA
3142302 AATGGGTGGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 20 0.53
28 18 0.47
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAGAAAACCA
Done.