Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 23 of 27
Found at i:3197886 original size:27 final size:27
Alignment explanation
Indices: 3197848--3197900 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
3197838 TGCAGCCTTC
* * *
3197848 ACTATTTTAAATTGAATTTCATAATTT
1 ACTATTTCAAATTGAATATCAAAATTT
3197875 ACTATTTCAAATTGAATATCAAAATT
1 ACTATTTCAAATTGAATATCAAAATT
3197901 GGCGGCACAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (27 bp):
ACTATTTCAAATTGAATATCAAAATTT
Found at i:3197914 original size:12 final size:12
Alignment explanation
Indices: 3197899--3197930 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3197889 AATATCAAAA
*
3197899 TTGGCGGCACAG
1 TTGGCAGCACAG
3197911 TTGGCAGCACAG
1 TTGGCAGCACAG
3197923 TTGGCAGC
1 TTGGCAGC
3197931 CTTTGTTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (12 bp):
TTGGCAGCACAG
Found at i:3205500 original size:14 final size:13
Alignment explanation
Indices: 3205467--3205501 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3205457 TTATGGGAAT
*
3205467 AAGAAAGAAATAA
1 AAGAAAAAAATAA
3205480 AAGAAAAAAATAA
1 AAGAAAAAAATAA
3205493 AGAGAAAAA
1 A-AGAAAAA
3205502 TACCACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (13 bp):
AAGAAAAAAATAA
Found at i:3206474 original size:22 final size:20
Alignment explanation
Indices: 3206419--3206477 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
3206409 TATTATAAAA
3206419 TTTAAATATTTAATAAATAATT
1 TTTAAATATTT-A-AAATAATT
*
3206441 TTTAAATTTTTAAAATAATTT
1 TTTAAATATTTAAAATAA-TT
*
3206462 TTTATTATATTTAAAA
1 TTTA-AATATTTAAAA
3206478 ACTTAAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 6 0.19
21 7 0.22
22 19 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAAATATTTAAAATAATT
Found at i:3207512 original size:37 final size:37
Alignment explanation
Indices: 3207471--3207545 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
3207461 TAAAAATATG
* *
3207471 TAAAATTAATTTAATTTTATATTAATATAAATAAATC
1 TAAAACTAATTTAATTATATATTAATATAAATAAATC
3207508 TAAAACTAATTTAATTATATATTAATATAAATAAATC
1 TAAAACTAATTTAATTATATATTAATATAAATAAATC
3207545 T
1 T
3207546 CTTTTATGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (37 bp):
TAAAACTAATTTAATTATATATTAATATAAATAAATC
Found at i:3209438 original size:16 final size:18
Alignment explanation
Indices: 3209417--3209454 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
3209407 CACCGACTTA
3209417 AAAAAAATATT-T-TTTT
1 AAAAAAATATTATATTTT
*
3209433 AAAAAATTATTATATTTT
1 AAAAAAATATTATATTTT
3209451 AAAA
1 AAAA
3209455 GAAAAATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 1 0.05
18 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAAAAATATTATATTTT
Found at i:3217527 original size:12 final size:12
Alignment explanation
Indices: 3217510--3217534 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3217500 TTGCCACCTT
3217510 CATCTTTCTTGG
1 CATCTTTCTTGG
3217522 CATCTTTCTTGG
1 CATCTTTCTTGG
3217534 C
1 C
3217535 TCCTCCTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.28, G:0.16, T:0.48
Consensus pattern (12 bp):
CATCTTTCTTGG
Found at i:3218415 original size:20 final size:19
Alignment explanation
Indices: 3218401--3218437 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3218391 TTTTAAATTT
3218401 AATA-AAAATAATTTATTA
1 AATATAAAATAATTTATTA
3218419 AATATAAAATAATTT-TTA
1 AATATAAAATAATTTATTA
3218437 A
1 A
3218438 TTAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATAAAATAATTTATTA
Found at i:3218443 original size:21 final size:21
Alignment explanation
Indices: 3218390--3218444 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
3218380 TAATTATATT
3218390 TTTTTAAATTTAATA-AAAATAA
1 TTTTT-AA-TTAATATAAAATAA
3218412 --TTT-ATTAAATATAAAATAA
1 TTTTTAATT-AATATAAAATAA
3218431 TTTTTAATTAATAT
1 TTTTTAATTAATAT
3218445 TTATAAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
17 2 0.07
18 5 0.18
19 7 0.25
20 3 0.11
21 8 0.29
22 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTTAATTAATATAAAATAA
Found at i:3221533 original size:31 final size:30
Alignment explanation
Indices: 3221462--3221533 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 30
3221452 TGCTTGCTTT
* *
3221462 TACTTAATATATGGATTTGTAAAGTATTAGA
1 TACTAAATATATGGATTGGTAAAGTATTA-A
* *
3221493 TACTTAATATATGGATTCGGTTAAGTATT-A
1 TACTAAATATATGGATT-GGTAAAGTATTAA
3221523 TACATAAATAT
1 TAC-TAAATAT
3221534 GTTTCGGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 4 0.11
31 23 0.64
32 9 0.25
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.42
Consensus pattern (30 bp):
TACTAAATATATGGATTGGTAAAGTATTAA
Found at i:3223755 original size:15 final size:15
Alignment explanation
Indices: 3223735--3223774 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3223725 CGGTGGAAGC
3223735 GGGGGAGGAGAAGGA
1 GGGGGAGGAGAAGGA
**
3223750 GGGGGAGGAGGGGGA
1 GGGGGAGGAGAAGGA
3223765 GTGGGGAGGA
1 G-GGGGAGGA
3223775 ATTTAGAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.25, C:0.00, G:0.72, T:0.03
Consensus pattern (15 bp):
GGGGGAGGAGAAGGA
Found at i:3224870 original size:22 final size:23
Alignment explanation
Indices: 3224826--3224890 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
3224816 ATTTAAAATT
*
3224826 TAAATTTATTAAATATTATTTAAAA
1 TAAATTTA-T-AATATTAATTAAAA
*
3224851 T-AATTATATAA-ATTAATTAAAT
1 TAAATT-TATAATATTAATTAAAA
3224873 TAAATTTATAATATTAAT
1 TAAATTTATAATATTAAT
3224891 ATTATCATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
22 15 0.43
23 12 0.34
24 5 0.14
25 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAATTTATAATATTAATTAAAA
Found at i:3225245 original size:21 final size:21
Alignment explanation
Indices: 3225219--3225259 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3225209 TTATATGGTA
3225219 TTATTTATT-TATTTATTTTTC
1 TTATTT-TTATATTTATTTTTC
*
3225240 TTATTTTTATTTTTATTTTT
1 TTATTTTTATATTTATTTTT
3225260 ATTTTTTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (21 bp):
TTATTTTTATATTTATTTTTC
Found at i:3225251 original size:6 final size:6
Alignment explanation
Indices: 3225226--3225265 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
3225216 GTATTATTTA
3225226 TTTATT TATT-TT TCTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT T-TTATT T-TTATT TTTATT TTTATT TTTATT TTT
3225266 TACCTTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:3225857 original size:18 final size:17
Alignment explanation
Indices: 3225819--3225885 Score: 65
Period size: 16 Copynumber: 4.1 Consensus size: 17
3225809 GATATTATAA
3225819 TATATTTA-A-AATATTT
1 TATATTTATATAA-ATTT
3225835 TATATTTATATAAATTT
1 TATATTTATATAAATTT
3225852 TGATATATTA-AT-AA-TT
1 T-ATAT-TTATATAAATTT
3225868 TATA-TTATATAAATTT
1 TATATTTATATAAATTT
3225884 TA
1 TA
3225886 AAATATTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 5 0.11
16 15 0.34
17 8 0.18
18 8 0.18
19 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (17 bp):
TATATTTATATAAATTT
Found at i:3225858 original size:20 final size:18
Alignment explanation
Indices: 3225818--3225885 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
3225808 TGATATTATA
*
3225818 ATATATT-TAAAATATTTT
1 ATATATTATATAA-ATTTT
3225836 ATAT-TTATATAAATTTT
1 ATATATTATATAAATTTT
3225853 GATATATTA-AT-AA--TT
1 -ATATATTATATAAATTTT
3225868 -TATATTATATAAATTTT
1 ATATATTATATAAATTTT
3225885 A
1 A
3225886 AAATATTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 16
0.71 0.02 0.28
Matches are distributed among these distances:
13 7 0.17
14 2 0.05
15 4 0.10
17 11 0.27
18 14 0.34
19 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (18 bp):
ATATATTATATAAATTTT
Found at i:3225872 original size:33 final size:32
Alignment explanation
Indices: 3225828--3225910 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 32
3225818 ATATATTTAA
* * *
3225828 AATATTTTATATTTATATAAATTTTGATATATT
1 AATAATTTATA-TTATATAAATTTTAAAATATT
3225861 AATAATTTATATTATATAAATTTTAAAATATT
1 AATAATTTATATTATATAAATTTTAAAATATT
*
3225893 TATATATTTATATTATAT
1 AATA-ATTTATATTATAT
3225911 TTATCTTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 22 0.49
33 23 0.51
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (32 bp):
AATAATTTATATTATATAAATTTTAAAATATT
Found at i:3231943 original size:3 final size:3
Alignment explanation
Indices: 3231937--3231969 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3231927 TTACATCATC
3231937 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3231970 TTCATATACC
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:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3232354 original size:23 final size:24
Alignment explanation
Indices: 3232299--3232354 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
3232289 TTCTTCAATT
3232299 TTTAAA-AT-TTTTTATATATTTA
1 TTTAAATATATTTTTATATATTTA
**
3232321 -AAAAATAATATTTTTATA-ATTTA
1 TTTAAAT-ATATTTTTATATATTTA
3232344 TTTAAATATAT
1 TTTAAATATAT
3232355 ATTAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
21 3 0.12
23 11 0.42
24 12 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAAATATATTTTTATATATTTA
Found at i:3234361 original size:11 final size:11
Alignment explanation
Indices: 3234345--3234378 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
3234335 TTGATTTGAG
3234345 TTTAATTAAAT
1 TTTAATTAAAT
3234356 TTTAATTAAAT
1 TTTAATTAAAT
*
3234367 TTTAATTTAAT
1 TTTAATTAAAT
3234378 T
1 T
3234379 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAATTAAAT
Found at i:3234615 original size:19 final size:19
Alignment explanation
Indices: 3234591--3234631 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
3234581 AGTTGTCATA
3234591 AAATTTATATTATGTTTTT
1 AAATTTATATTATGTTTTT
3234610 AAATTTATATTATGTTTTT
1 AAATTTATATTATGTTTTT
3234629 AAA
1 AAA
3234632 AGGTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
AAATTTATATTATGTTTTT
Found at i:3234827 original size:2 final size:2
Alignment explanation
Indices: 3234822--3234848 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3234812 ATATATATAT
3234822 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 A
3234849 TATTAAAATT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3237002 original size:34 final size:33
Alignment explanation
Indices: 3236959--3237032 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
3236949 AAAATTATTC
* *
3236959 ATATA-TTTATAT-TATTTTTATTTTTTTATCATA
1 ATATATTTTATATATATTTTAATTATTTT-T-ATA
3236992 ATATATTTTATATAATATTTTAATTATTTTTATA
1 ATATATTTTATAT-ATATTTTAATTATTTTTATA
3237026 ATATATT
1 ATATATT
3237033 CATATAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
33 5 0.14
34 17 0.47
35 1 0.03
36 13 0.36
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (33 bp):
ATATATTTTATATATATTTTAATTATTTTTATA
Found at i:3237027 original size:20 final size:22
Alignment explanation
Indices: 3236990--3237038 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
3236980 TTTTTTATCA
3236990 TAATATATTTTATATAATATTT
1 TAATATATTTTATATAATATTT
*
3237012 TAAT-TATTTT-TATAATATAT
1 TAATATATTTTATATAATATTT
*
3237032 TCATATA
1 TAATATA
3237039 ATATAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.50
21 8 0.33
22 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TAATATATTTTATATAATATTT
Found at i:3237611 original size:19 final size:19
Alignment explanation
Indices: 3237589--3237653 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
3237579 TAATAAAGTG
3237589 TTTAAATAAA-AATATTAAA
1 TTTAAA-AAATAATATTAAA
*
3237608 TTTAAAAAATAATTTTAAA
1 TTTAAAAAATAATATTAAA
* *
3237627 -TAAAAAAATAA-ATT-TA
1 TTTAAAAAATAATATTAAA
3237643 TTTAAAAAATA
1 TTTAAAAAATA
3237654 GATTGAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 1 0.03
17 11 0.28
18 13 0.33
19 14 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTAAAAAATAATATTAAA
Found at i:3237634 original size:18 final size:18
Alignment explanation
Indices: 3237611--3237674 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
3237601 TATTAAATTT
3237611 AAAAAATAATTTTAAATA
1 AAAAAATAATTTTAAATA
* **
3237629 AAAAAATAAATTTATTTAA
1 AAAAAATAATTTTAAAT-A
3237648 AAAATAGATTGAATTTTAAATA
1 AAAA-A-A-T-AATTTTAAATA
3237670 AAAAA
1 AAAAA
3237675 TTATAAGCTC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
18 14 0.40
19 5 0.14
20 1 0.03
21 2 0.06
22 6 0.17
23 7 0.20
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAAATAATTTTAAATA
Found at i:3237751 original size:20 final size:20
Alignment explanation
Indices: 3237728--3237773 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3237718 AAATTTATTC
3237728 TTTTAT-ACTATAATTATATA
1 TTTTATAACTATAATTATA-A
* *
3237748 TTTTATAATTATAGTTATAA
1 TTTTATAACTATAATTATAA
3237768 TTTTAT
1 TTTTAT
3237774 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTATAACTATAATTATAA
Found at i:3237913 original size:17 final size:16
Alignment explanation
Indices: 3237872--3237916 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3237862 AATTGAATTA
*
3237872 AAATATATTTAAAAAT
1 AAATAAATTTAAAAAT
*
3237888 AAA-AAATTTATAATAT
1 AAATAAATTTA-AAAAT
3237904 AAATAAATTTAAA
1 AAATAAATTTAAA
3237917 TTATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 6 0.24
16 12 0.48
17 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAAATTTAAAAAT
Found at i:3237914 original size:32 final size:30
Alignment explanation
Indices: 3237855--3237916 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
3237845 ATAAAAACTT
* *
3237855 AATAAAAAATTGAATTAAAATATATTTAAA
1 AATAAAAAATTGAAATAAAATAAATTTAAA
*
3237885 AATAAAAAATTTATAATATAAATAAATTTAAA
1 AATAAAAAATTGA-AATA-AAATAAATTTAAA
3237917 TTATTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 12 0.44
31 3 0.11
32 12 0.44
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (30 bp):
AATAAAAAATTGAAATAAAATAAATTTAAA
Found at i:3238656 original size:5 final size:6
Alignment explanation
Indices: 3238646--3238681 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3238636 ATACTCTGAA
3238646 AAAC-C AAAC-C AAAC-C AAACTC AAACTC AAACTC AAA
1 AAACTC AAACTC AAACTC AAACTC AAACTC AAACTC AAA
3238682 GTCAGCAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 14 0.47
6 16 0.53
ACGTcount: A:0.58, C:0.33, G:0.00, T:0.08
Consensus pattern (6 bp):
AAACTC
Found at i:3240423 original size:24 final size:26
Alignment explanation
Indices: 3240369--3240415 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
3240359 AACATATATA
3240369 AATA-TAATATATATATTAAATATTT
1 AATATTAATATATATATTAAATATTT
3240394 AATATTAAT-TATAT-TTAAATAT
1 AATATTAATATATATATTAAATAT
3240416 ATTGTATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 9 0.43
26 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AATATTAATATATATATTAAATATTT
Found at i:3245844 original size:18 final size:18
Alignment explanation
Indices: 3245823--3245890 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 18
3245813 ATATATAAAG
3245823 ATATAAATTTTTATATAT
1 ATATAAATTTTTATATAT
** *
3245841 ATATAAATTAAAATATAAAT
1 ATATAAATT--TTTATATAT
* *
3245861 ATATTAATATTTTATATTT
1 ATATAAAT-TTTTATATAT
3245880 ATTATAAATTT
1 A-TATAAATTT
3245891 GAATAATATA
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
18 9 0.24
19 8 0.22
20 19 0.51
21 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATAAATTTTTATATAT
Found at i:3247132 original size:26 final size:24
Alignment explanation
Indices: 3247081--3247139 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
3247071 GAAAACAATA
*
3247081 AAAAAGAAAAAAACATCGTATACTG
1 AAAAA-AAAAAAACATCATATACTG
*
3247106 AAAAAAAAAAAACAATACATATGCTG
1 AAAAAAAAAAAAC-AT-CATATACTG
*
3247132 AGAAAAAA
1 AAAAAAAA
3247140 GGGCATGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 8 0.28
25 7 0.24
26 14 0.48
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (24 bp):
AAAAAAAAAAAACATCATATACTG
Found at i:3247964 original size:13 final size:13
Alignment explanation
Indices: 3247946--3248036 Score: 68
Period size: 13 Copynumber: 7.0 Consensus size: 13
3247936 TTTTTTATAA
*
3247946 AATATTTATGTTT
1 AATATTTATATTT
3247959 AATATTTATATTT
1 AATATTTATATTT
3247972 -A-ATTTATAATTT
1 AATATTTAT-ATTT
3247984 AATATTTATA--T
1 AATATTTATATTT
*
3247995 AAGA-TTATAACTTTAT
1 AATATTTAT-A--TT-T
3248011 ATATATTTATATTT
1 A-ATATTTATATTT
3248025 AATATTTA-ATTT
1 AATATTTATATTT
3248037 TAAATATAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 23
0.71 0.03 0.26
Matches are distributed among these distances:
10 4 0.06
11 11 0.17
12 9 0.14
13 21 0.33
14 8 0.12
15 2 0.03
16 2 0.03
17 3 0.05
18 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:3247986 original size:5 final size:6
Alignment explanation
Indices: 3247947--3248036 Score: 57
Period size: 6 Copynumber: 15.0 Consensus size: 6
3247937 TTTTTATAAA
* *
3247947 ATATTT ATGTTT AATATTT ATATTT A-ATTT ATAATTT AATATTT ATA-TA
1 ATATTT ATATTT -ATATTT ATATTT ATATTT AT-ATTT -ATATTT ATATTT
*
3247996 AGA-TT ATAACTTT ATA--T ATATTT ATATTT AATATTT A-ATTT
1 ATATTT AT-A-TTT ATATTT ATATTT ATATTT -ATATTT ATATTT
3248037 TAAATATAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
4 4 0.06
5 14 0.21
6 24 0.35
7 20 0.29
8 6 0.09
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (6 bp):
ATATTT
Found at i:3248804 original size:13 final size:13
Alignment explanation
Indices: 3248786--3248824 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3248776 GATATTTTAT
*
3248786 TTTTTAAAAAATA
1 TTTTTATAAAATA
*
3248799 TTTTTATATAATA
1 TTTTTATAAAATA
*
3248812 TTTATATAAAATA
1 TTTTTATAAAATA
3248825 CGTATTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTTTATAAAATA
Found at i:3248850 original size:13 final size:13
Alignment explanation
Indices: 3248793--3248850 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
3248783 TATTTTTTAA
*
3248793 AAAATATTTTTAT
1 AAAATATTTATAT
*
3248806 ATAATATTTATAT
1 AAAATATTTATAT
**
3248819 AAAATACGTAT-T
1 AAAATATTTATAT
*
3248831 CAAATATTTATAT
1 AAAATATTTATAT
3248844 AAAATAT
1 AAAATAT
3248851 AATTTTTAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 9 0.26
13 26 0.74
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (13 bp):
AAAATATTTATAT
Found at i:3249075 original size:2 final size:2
Alignment explanation
Indices: 3249068--3249094 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3249058 TCTTTTAGTG
3249068 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 A
3249095 AAATTTAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3249292 original size:18 final size:19
Alignment explanation
Indices: 3249269--3249307 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3249259 GATTATTTTA
*
3249269 TTTAAAT-TTAATATAAAT
1 TTTAAATATAAATATAAAT
*
3249287 TTTAAATATAAATATATAT
1 TTTAAATATAAATATAAAT
3249306 TT
1 TT
3249308 AAAGAAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAAATATAAATATAAAT
Found at i:3249302 original size:19 final size:18
Alignment explanation
Indices: 3249269--3249332 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
3249259 GATTATTTTA
*
3249269 TTTAAATTTAATATAAAT
1 TTTAAATTAAATATAAAT
*
3249287 TTTAAATATAAATATATA-
1 TTTAAAT-TAAATATAAAT
* **
3249305 TTTAAA-GAAAT-TCGAT
1 TTTAAATTAAATATAAAT
3249321 TTTAAATTAAAT
1 TTTAAATTAAAT
3249333 TTTTAGTGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
15 2 0.05
16 10 0.27
17 4 0.11
18 13 0.35
19 8 0.22
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (18 bp):
TTTAAATTAAATATAAAT
Found at i:3249463 original size:16 final size:17
Alignment explanation
Indices: 3249442--3249473 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3249432 TATTCAATTT
3249442 AATTTAAA-ATAAAATA
1 AATTTAAATATAAAATA
3249458 AATTTAAATATAAAAT
1 AATTTAAATATAAAAT
3249474 TTTAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTTAAATATAAAATA
Found at i:3249499 original size:22 final size:20
Alignment explanation
Indices: 3249471--3249528 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 20
3249461 TTAAATATAA
3249471 AATTTTAATTAATAATTAAATT
1 AATTTTAATTAAT--TTAAATT
3249493 AATTTTAAATTAATTTAAATT
1 AATTTT-AATTAATTTAAATT
3249514 ATATTTTAA-TAATTT
1 A-ATTTTAATTAATTT
3249529 TTATTAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.18
21 10 0.29
22 11 0.32
23 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTTAATTAATTTAAATT
Found at i:3249500 original size:11 final size:11
Alignment explanation
Indices: 3249471--3249522 Score: 63
Period size: 10 Copynumber: 4.7 Consensus size: 11
3249461 TTAAATATAA
3249471 AATTTT-AATT
1 AATTTTAAATT
*
3249481 AATAATTAAATT
1 AAT-TTTAAATT
3249493 AATTTTAAATT
1 AATTTTAAATT
3249504 AA-TTTAAATT
1 AATTTTAAATT
3249514 ATATTTTAA
1 A-ATTTTAA
3249523 TAATTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 12 0.33
11 12 0.33
12 12 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTTAAATT
Found at i:3251581 original size:14 final size:14
Alignment explanation
Indices: 3251562--3251595 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3251552 TATTTAAATA
3251562 TATTATATCATATT
1 TATTATATCATATT
*
3251576 TATTATATTATATT
1 TATTATATCATATT
*
3251590 TTTTAT
1 TATTAT
3251596 TAAATATAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATATCATATT
Found at i:3251596 original size:17 final size:18
Alignment explanation
Indices: 3251550--3251597 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3251540 CATTATTAAT
*
3251550 TATATTTAAATATATTATA
1 TATATTT-ATTATATTATA
3251569 TCATATTTATTATATTATA
1 T-ATATTTATTATATTATA
*
3251588 T-TTTTTATTA
1 TATATTTATTA
3251598 AATATAGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 8 0.31
19 12 0.46
20 6 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATTTATTATATTATA
Found at i:3257382 original size:6 final size:6
Alignment explanation
Indices: 3257371--3257398 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3257361 ACTAGTCAGT
3257371 CAGCCC CAGCCC CAGCCC CAGCCC CAGC
1 CAGCCC CAGCCC CAGCCC CAGCCC CAGC
3257399 TGCTCCAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.64, G:0.18, T:0.00
Consensus pattern (6 bp):
CAGCCC
Found at i:3258839 original size:2 final size:2
Alignment explanation
Indices: 3258832--3258866 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3258822 TCTTTGCCCT
3258832 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3258867 GACAAAAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3260360 original size:1 final size:1
Alignment explanation
Indices: 3260354--3260378 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3260344 TGAGAGCTCT
3260354 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
3260379 TCTTAAGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3263078 original size:18 final size:18
Alignment explanation
Indices: 3263023--3263083 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
3263013 TTATAAATAT
3263023 ATAAATATTA-AAATTAAA
1 ATAAAT-TTATAAATTAAA
*
3263041 A-AATATTTTTAAATAATAAA
1 ATAA-ATTTATAAAT--TAAA
3263061 ATAAATTTATAAATTAAA
1 ATAAATTTATAAATTAAA
*
3263079 TTAAA
1 ATAAA
3263084 ATAAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
17 4 0.11
18 15 0.43
20 14 0.40
21 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATTTATAAATTAAA
Found at i:3264115 original size:26 final size:28
Alignment explanation
Indices: 3264053--3264115 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 28
3264043 AATAATTATT
**
3264053 TATTATAAGTTTGTTAATTAAATGATAGA
1 TATTATAA-TTTGTTAATTAAAAAATAGA
3264082 TATT-TAATTT-TTAATTAAAAAATA-A
1 TATTATAATTTGTTAATTAAAAAATAGA
*
3264107 TTTTATAAT
1 TATTATAAT
3264116 AATAATAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.13
26 16 0.53
27 3 0.10
28 3 0.10
29 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (28 bp):
TATTATAATTTGTTAATTAAAAAATAGA
Found at i:3264376 original size:22 final size:20
Alignment explanation
Indices: 3264351--3264402 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
3264341 TAAAGTTATT
3264351 TTTATTTTTAAATATATTTTAA
1 TTTATTTTTAAATA-A-TTTAA
*
3264373 TTTAATTTTAAATAATTTAA
1 TTTATTTTTAAATAATTTAA
*
3264393 TATATTTTTA
1 TTTATTTTTA
3264403 TTAAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 13 0.48
21 1 0.04
22 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTTTTAAATAATTTAA
Found at i:3264381 original size:28 final size:28
Alignment explanation
Indices: 3264329--3264382 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
3264319 AAATAAATAA
* *
3264329 TTTAAATTTATTTAAAGTTATTTTTATT
1 TTTAAATATATTTAAAGTTAATTTTATT
* *
3264357 TTTAAATATATTTTAATTTAATTTTA
1 TTTAAATATATTTAAAGTTAATTTTA
3264383 AATAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTAAATATATTTAAAGTTAATTTTATT
Found at i:3264901 original size:36 final size:36
Alignment explanation
Indices: 3264844--3264914 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
3264834 AATATATAAT
3264844 AAAATAATAATAAATATTTATAAAATTTTTAAAATA
1 AAAATAATAATAAATATTTATAAAATTTTTAAAATA
* * * *
3264880 AAAATTATATATAATTA-TTATAATATTTTTTAAAT
1 AAAATAATA-ATAAATATTTATAAAATTTTTAAAAT
3264915 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 24 0.80
37 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
AAAATAATAATAAATATTTATAAAATTTTTAAAATA
Found at i:3264904 original size:25 final size:24
Alignment explanation
Indices: 3264850--3264904 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
3264840 TAATAAAATA
* *
3264850 ATAATAAATATTTATAAAATTTTT
1 ATAATAAAAATTTATAAAATTATT
* *
3264874 AAAATAAAAATTATATATAATTATT
1 ATAATAAAAATT-TATAAAATTATT
3264899 ATAATA
1 ATAATA
3264905 TTTTTTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATAAAAATTTATAAAATTATT
Found at i:3265531 original size:24 final size:21
Alignment explanation
Indices: 3265498--3265555 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
3265488 AAATTAAATT
*
3265498 ATTTAAATTTATTTAATTATATA
1 ATTTAAATTTAATT-ATT-TATA
3265521 ATTTTAAATTTAATTATTTATA
1 A-TTTAAATTTAATTATTTATA
3265543 A-TTAAATTTAATT
1 ATTTAAATTTAATT
3265556 TTAACAAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 12 0.36
22 5 0.15
23 4 0.12
24 12 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTAAATTTAATTATTTATA
Found at i:3265674 original size:22 final size:22
Alignment explanation
Indices: 3265626--3265678 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
3265616 AAAATATTAA
* **
3265626 AATATTAATATTTAATTTATTTTT
1 AATA-TAA-ATTTAATTTAATAAT
3265650 AATATAAATTTAATTTAATAAT
1 AATATAAATTTAATTTAATAAT
3265672 AAT-TAAA
1 AATATAAA
3265679 AAAAATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 15 0.58
23 3 0.12
24 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATAAATTTAATTTAATAAT
Found at i:3273598 original size:21 final size:21
Alignment explanation
Indices: 3273572--3273613 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3273562 TCAACTGAGC
3273572 TTAACGGAAGTCTCGTCCTGT
1 TTAACGGAAGTCTCGTCCTGT
* *
3273593 TTAACGGTAGTCTTGTCCTGT
1 TTAACGGAAGTCTCGTCCTGT
3273614 GACACATCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (21 bp):
TTAACGGAAGTCTCGTCCTGT
Found at i:3277773 original size:20 final size:20
Alignment explanation
Indices: 3277748--3277789 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3277738 TTTCTTTGTT
*
3277748 TTTTTAAGTATTA-AGTTAAA
1 TTTTTAAGT-TTAGAATTAAA
3277768 TTTTTAAGTTTAGAATTAAA
1 TTTTTAAGTTTAGAATTAAA
3277788 TT
1 TT
3277790 ATTTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (20 bp):
TTTTTAAGTTTAGAATTAAA
Found at i:3278519 original size:33 final size:32
Alignment explanation
Indices: 3278481--3278558 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
3278471 AAAATATATA
3278481 ATATAATATAATATGAAT-ATATATTTA-AATTTT
1 ATATAATATAA-ATGAATAATAT-TTTATAA-TTT
* *
3278514 ATATAATATAAATTATTAATATTTTATAATTT
1 ATATAATATAAATGAATAATATTTTATAATTT
3278546 ATATAAATATAAA
1 ATAT-AATATAAA
3278559 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
32 15 0.38
33 25 0.62
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (32 bp):
ATATAATATAAATGAATAATATTTTATAATTT
Found at i:3278537 original size:25 final size:28
Alignment explanation
Indices: 3278486--3278541 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 28
3278476 ATATAATATA
3278486 ATATAATATGAATATATATTTAAATTTT
1 ATATAATATGAATATATATTTAAATTTT
3278514 ATATAATAT-AA-AT-TA-TTAATATTTT
1 ATATAATATGAATATATATTTAA-ATTTT
3278539 ATA
1 ATA
3278542 ATTTATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.15
25 10 0.37
26 2 0.07
27 2 0.07
28 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
ATATAATATGAATATATATTTAAATTTT
Found at i:3278609 original size:18 final size:20
Alignment explanation
Indices: 3278576--3278618 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
3278566 AAAAATAATT
3278576 ATAATATGATAATATATAAA
1 ATAATATGATAATATATAAA
3278596 ATAATAT-A-AATATATAAA
1 ATAATATGATAATATATAAA
3278614 A-AATA
1 ATAATA
3278619 CAAGAATTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 11 0.48
19 1 0.04
20 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAATATGATAATATATAAA
Found at i:3278612 original size:25 final size:25
Alignment explanation
Indices: 3278445--3278612 Score: 73
Period size: 27 Copynumber: 6.5 Consensus size: 25
3278435 GATACCATAT
*
3278445 TATAAA-ATTTAATTATATAAATATAA
1 TATAAATATATAA-TATATAAA-ATAA
3278471 -A-AAATATATAATATAATATAATATGAA
1 TATAAATATATAATAT-ATA-AA-AT-AA
* * * *
3278498 TAT--ATATTTAA-ATTTTATATAA
1 TATAAATATATAATATATAAAATAA
* * *
3278520 TATAAAT-TATTAATATTTTATAATTTA
1 TATAAATATA-TAATA-TATA-AAATAA
* *
3278547 TATAAATATAAAATATTTTAAAAATAA
1 TATAAATATATAATA-TAT-AAAATAA
3278574 T-TATAATATGATAATATATAAAATAA
1 TATA-AATAT-ATAATATATAAAATAA
3278600 TATAAATATATAA
1 TATAAATATATAA
3278613 AAAATACAAG
Statistics
Matches: 110, Mismatches: 15, Indels: 35
0.69 0.09 0.22
Matches are distributed among these distances:
22 5 0.05
23 3 0.03
24 12 0.11
25 15 0.14
26 25 0.23
27 41 0.37
28 9 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (25 bp):
TATAAATATATAATATATAAAATAA
Found at i:3278754 original size:20 final size:20
Alignment explanation
Indices: 3278729--3278766 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3278719 ACCAAAATAG
*
3278729 TTAAATTAAACTTTAAAAAT
1 TTAAATTAAACATTAAAAAT
*
3278749 TTAAATTTAACATTAAAA
1 TTAAATTAAACATTAAAA
3278767 TATGACTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAATTAAACATTAAAAAT
Found at i:3281918 original size:2 final size:2
Alignment explanation
Indices: 3281911--3281947 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3281901 CAATTGAAAC
3281911 TA TA TA TA -A TA TA -A 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
3281948 TACATAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3292467 original size:14 final size:14
Alignment explanation
Indices: 3292450--3292483 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3292440 TAATGTATAA
*
3292450 AATATAGATTTATT
1 AATATAGATATATT
*
3292464 AATATATATATATT
1 AATATAGATATATT
3292478 AATATA
1 AATATA
3292484 ATCATTGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
AATATAGATATATT
Found at i:3293002 original size:6 final size:6
Alignment explanation
Indices: 3292991--3293020 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3292981 AAAATTGACA
3292991 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
3293021 TAGGTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:3293341 original size:7 final size:7
Alignment explanation
Indices: 3293296--3293353 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
3293286 AAGTAATAAT
3293296 TTTTATA
1 TTTTATA
3293303 TAATTTATA
1 T--TTTATA
*
3293312 TTTATTTA
1 TTT-TATA
3293320 TTTT-TA
1 TTTTATA
*
3293326 TAATTATA
1 T-TTTATA
3293334 TTTTATA
1 TTTTATA
3293341 TTTTATA
1 TTTTATA
3293348 TTTTAT
1 TTTTAT
3293354 TTATTTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 3 0.07
7 24 0.56
8 9 0.21
9 7 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTATA
Found at i:3293420 original size:17 final size:19
Alignment explanation
Indices: 3293390--3293443 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
3293380 ATAAATATAG
3293390 TATTAAAATTAATAATAAATT-
1 TATTAAAA-TAATAAT--ATTA
*
3293411 TATTAAAATATTAATATTA
1 TATTAAAATAATAATATTA
3293430 TATTAAAATCAATA
1 TATTAAAAT-AATA
3293444 CGTATCGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 3 0.10
19 9 0.31
20 9 0.31
21 8 0.28
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTAAAATAATAATATTA
Found at i:3301095 original size:20 final size:21
Alignment explanation
Indices: 3301044--3301096 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
3301034 TTTATGTATA
3301044 TTCTGCAAATTTTTTTCATCGG
1 TTCT-CAAATTTTTTTCATCGG
*
3301066 TTC-CACAATTTTTTTCATC-T
1 TTCTCA-AATTTTTTTCATCGG
3301086 TTCTCAAATTT
1 TTCTCAAATTT
3301097 AAAATTTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 10 0.36
21 15 0.54
22 3 0.11
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (21 bp):
TTCTCAAATTTTTTTCATCGG
Found at i:3301194 original size:16 final size:16
Alignment explanation
Indices: 3301173--3301217 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
3301163 TTAATTTTAA
3301173 AATTTTTTATTATTTT
1 AATTTTTTATTATTTT
*
3301189 AATTTTTAATT-TTTT
1 AATTTTTTATTATTTT
*
3301204 -A-TTATTATTATTTT
1 AATTTTTTATTATTTT
3301218 TTTTCATAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 6 0.24
14 5 0.20
15 4 0.16
16 10 0.40
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
AATTTTTTATTATTTT
Found at i:3301203 original size:23 final size:24
Alignment explanation
Indices: 3301162--3301219 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
3301152 TTGATGTTTA
*
3301162 ATTAATTTTAAAATTTTTTATTATT
1 ATTAATTTT-TAATTTTTTATTATT
3301187 -TTAATTTTTAATTTTTTATTATT
1 ATTAATTTTTAATTTTTTATTATT
*
3301210 ATTATTTTTT
1 ATTAATTTTT
3301220 TTCATAGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 14 0.47
24 16 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
ATTAATTTTTAATTTTTTATTATT
Found at i:3302798 original size:153 final size:156
Alignment explanation
Indices: 3302507--3302824 Score: 502
Period size: 153 Copynumber: 2.1 Consensus size: 156
3302497 TATTTTATTC
*
3302507 AAAAA-ATATTTGAATTCATTAAATGCAAACCTAATATATATAAAAAAGGCTTTTTTAAAAATAA
1 AAAAATATATTTGAATTCATTAAATGCAAACCTAATATATATAAAAAAGGATTTTTTAAAAATAA
* *
3302571 AATTACCAAATAATTTTCAAATAAACACGTAATGTCATCTTTAAATAAGTTAATTAAACAGAGGC
66 AATTACCAAATAATTTTCAAATAAACACATAATGTCATCTTCAAATAAGTTAATTAAACAGAGGC
*
3302636 CGATATTATAAATAAATTAAGAATTT
131 CGAGATTATAAATAAATTAAGAATTT
* * *
3302662 AAAAATATATTTGAATTCTTTAAATGTAAACCTAATATATATATAAAA-GATTTTTTAAAAATAA
1 AAAAATATATTTGAATTCATTAAATGCAAACCTAATATATATAAAAAAGGATTTTTTAAAAATAA
* * *
3302726 AATTACCAAAT-A-TTTCAAATAAACACATAATGTCATCTTCAAATATGTTAATTAGATAG-GGA
66 AATTACCAAATAATTTTCAAATAAACACATAATGTCATCTTCAAATAAGTTAATTAAACAGAGG-
3302788 CCGAGATTATAAATAAATTAAGAATTT
130 CCGAGATTATAAATAAATTAAGAATTT
3302815 AAAAATATAT
1 AAAAATATAT
3302825 ATAGTTTATT
Statistics
Matches: 151, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
152 2 0.01
153 78 0.52
154 1 0.01
155 31 0.21
156 39 0.26
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.34
Consensus pattern (156 bp):
AAAAATATATTTGAATTCATTAAATGCAAACCTAATATATATAAAAAAGGATTTTTTAAAAATAA
AATTACCAAATAATTTTCAAATAAACACATAATGTCATCTTCAAATAAGTTAATTAAACAGAGGC
CGAGATTATAAATAAATTAAGAATTT
Found at i:3304145 original size:31 final size:29
Alignment explanation
Indices: 3304105--3304167 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3304095 ATTTAAATTA
* *
3304105 ATTTAATTTAATTTATTATTATAATAAAAAT
1 ATTTAATTTAA--AATTAATATAATAAAAAT
* *
3304136 ATTTTATTTAAAATTAATATAATTAAAAT
1 ATTTAATTTAAAATTAATATAATAAAAAT
3304165 ATT
1 ATT
3304168 AACGTCGACG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 18 0.64
31 10 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTAATTTAAAATTAATATAATAAAAAT
Found at i:3304983 original size:7 final size:7
Alignment explanation
Indices: 3304971--3305000 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
3304961 TAATTAAATT
3304971 AAATTTA
1 AAATTTA
3304978 AAATTTA
1 AAATTTA
3304985 AAATTTA
1 AAATTTA
3304992 AAATATTA
1 AAAT-TTA
3305000 A
1 A
3305001 TCTTTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:3305048 original size:59 final size:58
Alignment explanation
Indices: 3304994--3305117 Score: 107
Period size: 58 Copynumber: 2.1 Consensus size: 58
3304984 AAAATTTAAA
* * *
3304994 ATATTAATC-TTTTTATATAAAAAAATTACAT-A-TATTAAAATTCAAATATTAAATTGATTA
1 ATATTAATCATTTTT-T-TAAAAAAACTACATAATTATTAAAATT-AAAT-TTAAATTTA-AA
*
3305054 A-A-T-ATCATTTTTTTAAAAAAACTACATAAATTATTTAAATTAAATCTTAAATTTAAA
1 ATATTAATCATTTTTTTAAAAAAACTACAT-AATTATTAAAATTAAAT-TTAAATTTAAA
3305111 ATATTAA
1 ATATTAA
3305118 ATTTTTAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
56 13 0.25
57 6 0.12
58 20 0.38
59 11 0.21
60 2 0.04
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.43
Consensus pattern (58 bp):
ATATTAATCATTTTTTTAAAAAAACTACATAATTATTAAAATTAAATTTAAATTTAAA
Found at i:3305122 original size:58 final size:58
Alignment explanation
Indices: 3304968--3305124 Score: 137
Period size: 59 Copynumber: 2.7 Consensus size: 58
3304958 AATTAATTAA
* * * *
3304968 ATTAAATTTAAAAT-TTAAAATTTAAAATATTAATCTTTTTATATAAAAAAATTACATAT
1 ATTAAAATTCAAATATT-AAATTTAAAATATTAA-ATTTTTATATAAAAAAACTACATAT
* *
3305027 ATTAAAATTCAAATATTAAATTGATTAAATA-T-CATTTTT-T-TAAAAAAACTACATAAATT
1 ATTAAAATTCAAATATTAAATT--TAAAATATTAAATTTTTATATAAAAAAACTACAT--A-T
* *
3305086 ATTTAAATT-AAATCTTAAATTTAAAATATTAAATTTTTA
1 ATTAAAATTCAAATATTAAATTTAAAATATTAAATTTTTA
3305125 ATTACGATGC
Statistics
Matches: 79, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
56 19 0.24
57 2 0.03
58 23 0.29
59 26 0.33
60 3 0.04
61 6 0.08
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTAAAATTCAAATATTAAATTTAAAATATTAAATTTTTATATAAAAAAACTACATAT
Found at i:3305761 original size:19 final size:19
Alignment explanation
Indices: 3305715--3305762 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
3305705 ATGATTATAC
* *
3305715 AATA-AAAATATAATATAA
1 AATATAAAACATAAAATAA
* *
3305733 AATTTTAAACATAAAATAA
1 AATATAAAACATAAAATAA
3305752 AATATAAAACA
1 AATATAAAACA
3305763 ACATGAACAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (19 bp):
AATATAAAACATAAAATAA
Found at i:3305779 original size:23 final size:22
Alignment explanation
Indices: 3305740--3305782 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3305730 TAAAATTTTA
3305740 AACATAAAATAAAATATAAAAC
1 AACATAAAATAAAATATAAAAC
* *
3305762 AACATGAACATAACATATAAA
1 AACAT-AAAATAAAATATAAA
3305783 TATATCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.67, C:0.12, G:0.02, T:0.19
Consensus pattern (22 bp):
AACATAAAATAAAATATAAAAC
Found at i:3306565 original size:22 final size:23
Alignment explanation
Indices: 3306538--3306585 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3306528 AATGATAAAA
3306538 TAAAATTAT-AAA-TATTAAAATT
1 TAAAATT-TCAAATTATTAAAATT
*
3306560 TAAAATTTCAAATTATTAAATTT
1 TAAAATTTCAAATTATTAAAATT
3306583 TAA
1 TAA
3306586 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 1 0.04
22 10 0.43
23 12 0.52
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAATTTCAAATTATTAAAATT
Found at i:3307111 original size:18 final size:18
Alignment explanation
Indices: 3307088--3307126 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3307078 AGATTGTTTT
3307088 ACCAGAAGGTTTCTCTGC
1 ACCAGAAGGTTTCTCTGC
3307106 ACCAGAAGGTTTCTCTGC
1 ACCAGAAGGTTTCTCTGC
3307124 ACC
1 ACC
3307127 TAAATGGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (18 bp):
ACCAGAAGGTTTCTCTGC
Found at i:3310017 original size:36 final size:34
Alignment explanation
Indices: 3309945--3310016 Score: 83
Period size: 34 Copynumber: 2.0 Consensus size: 34
3309935 ATTTTTATTT
* *
3309945 AATTAATAAAAAATATTTTAAATTTAATTATAAA
1 AATTAACAAAAAATATTTTAAATTTAAATATAAA
3309979 AATTAACATAAAAAT-TTTTAATATCTTAAATAGTAAA
1 AATTAACA-AAAAATATTTTAA-AT-TTAAATA-TAAA
3310016 A
1 A
3310017 TAAAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 13 0.41
35 8 0.25
36 6 0.19
37 5 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (34 bp):
AATTAACAAAAAATATTTTAAATTTAAATATAAA
Found at i:3311054 original size:21 final size:21
Alignment explanation
Indices: 3311023--3311097 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
3311013 AATTATTATT
3311023 TTTAT-ATAATTTTAATAATA
1 TTTATAATAATTTTAATAATA
*
3311043 TTTATAATAATTTTAA-AA-G
1 TTTATAATAATTTTAATAATA
* * * *
3311062 TTTAGATATATTTTTGATAATT
1 TTTATA-ATAATTTTAATAATA
3311084 TTTATAATAATTTT
1 TTTATAATAATTTT
3311098 GATGCATCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.11
20 15 0.34
21 19 0.43
22 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTATAATAATTTTAATAATA
Found at i:3311099 original size:21 final size:21
Alignment explanation
Indices: 3311020--3311293 Score: 100
Period size: 20 Copynumber: 13.5 Consensus size: 21
3311010 TTAAATTATT
*
3311020 ATTTTTAT-ATAATTTTAATA
1 ATTTTTATAATAATTTTGATA
*
3311040 ATATTTATAATAATTTT-A-A
1 ATTTTTATAATAATTTTGATA
** * *
3311059 AAGTTTAGATATATTTTTGATA
1 ATTTTTATA-ATAATTTTGATA
*
3311081 ATTTTTATAATAATTTTGATGC
1 ATTTTTATAATAATTTTGAT-A
**
3311103 A-TCATAT-ATAATTTTGAT-
1 ATTTTTATAATAATTTTGATA
* * **
3311121 A-GTTTAGT-AT-TTTTTTTTA
1 ATTTTTA-TAATAATTTTGATA
* **
3311140 ATTTTGAGTAGCAATTTTTGATA
1 ATTTTTA-TAATAA-TTTTGATA
**
3311163 A-AATTATAATAATTTTAGATATA
1 ATTTTTATAATAATTTT-G--ATA
*
3311186 ATTTTGATAAT-ATTTATGATA
1 ATTTTTATAATAATTT-TGATA
3311207 A--TTT-TAATAATTTTGAT-
1 ATTTTTATAATAATTTTGATA
** **
3311224 A-TAAT-TAATAACCTTGATA
1 ATTTTTATAATAATTTTGATA
*
3311243 ATTTTTAAAATAAGTTTT-ATA
1 ATTTTTATAATAA-TTTTGATA
3311264 A-TTTTATAATAATTTTGATA
1 ATTTTTATAATAATTTTGATA
*
3311284 ATATTTATAA
1 ATTTTTATAA
3311294 CTCTATTTTC
Statistics
Matches: 185, Mismatches: 45, Indels: 47
0.67 0.16 0.17
Matches are distributed among these distances:
17 1 0.01
18 28 0.15
19 22 0.12
20 51 0.28
21 48 0.26
22 12 0.06
23 16 0.09
24 7 0.04
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (21 bp):
ATTTTTATAATAATTTTGATA
Found at i:3311186 original size:12 final size:11
Alignment explanation
Indices: 3311171--3311229 Score: 56
Period size: 9 Copynumber: 5.5 Consensus size: 11
3311161 TAAAATTATA
3311171 ATAATTTTAGAT
1 ATAATTTT-GAT
3311183 ATAATTTTG--
1 ATAATTTTGAT
3311192 ATAATATTT-AT
1 ATAAT-TTTGAT
3311203 GATAATTTT-A-
1 -ATAATTTTGAT
3311213 ATAATTTTGAT
1 ATAATTTTGAT
3311224 ATAATT
1 ATAATT
3311230 AATAACCTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
9 13 0.32
10 4 0.10
11 11 0.27
12 13 0.32
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.53
Consensus pattern (11 bp):
ATAATTTTGAT
Found at i:3311212 original size:11 final size:11
Alignment explanation
Indices: 3311152--3311229 Score: 51
Period size: 11 Copynumber: 7.4 Consensus size: 11
3311142 TTTGAGTAGC
3311152 AATTTT-TGAT
1 AATTTTATGAT
** *
3311162 AAAATTATAAT
1 AATTTTATGAT
3311173 AATTTTA-GAT
1 AATTTTATGAT
*
3311183 ATAATTT-TGAT
1 A-ATTTTATGAT
3311194 AATATTTATGAT
1 AAT-TTTATGAT
3311206 AATTTTA--AT
1 AATTTTATGAT
3311215 AATTTTGAT-AT
1 AATTTT-ATGAT
3311226 AATT
1 AATT
3311230 AATAACCTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
9 8 0.15
10 9 0.17
11 29 0.55
12 7 0.13
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.51
Consensus pattern (11 bp):
AATTTTATGAT
Found at i:3311289 original size:11 final size:11
Alignment explanation
Indices: 3311166--3311286 Score: 52
Period size: 9 Copynumber: 11.7 Consensus size: 11
3311156 TTTGATAAAA
3311166 TTATAATAATT
1 TTATAATAATT
*
3311177 TTAGATATAATT
1 TTATA-ATAATT
3311189 TTGATAAT-A-T
1 TT-ATAATAATT
*
3311199 TTATGATAA-T
1 TTATAATAATT
3311209 TT-TAATAATT
1 TTATAATAATT
3311219 TTGAT-ATAA--
1 TT-ATAATAATT
*
3311228 -T-TAATAACCT
1 TTATAATAA-TT
*
3311238 TGATAAT--TT
1 TTATAATAATT
* *
3311247 TTAAAATAAGT
1 TTATAATAATT
3311258 TT-T-ATAATT
1 TTATAATAATT
3311267 TTATAATAATT
1 TTATAATAATT
3311278 TTGATAATA
1 TT-ATAATA
3311287 TTTATAACTC
Statistics
Matches: 82, Mismatches: 11, Indels: 33
0.65 0.09 0.26
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
8 1 0.01
9 22 0.27
10 11 0.13
11 20 0.24
12 21 0.26
13 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (11 bp):
TTATAATAATT
Found at i:3311751 original size:10 final size:8
Alignment explanation
Indices: 3311730--3311755 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3311720 ATAAAATTTA
3311730 ATATATTC
1 ATATATTC
3311738 ATATATTC
1 ATATATTC
3311746 ATATATTC
1 ATATATTC
3311754 AT
1 AT
3311756 TTCATGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATATTC
Found at i:3318048 original size:21 final size:21
Alignment explanation
Indices: 3318024--3318065 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3318014 AAAAATTAAT
*
3318024 TAAAATATAATATAAAATATA
1 TAAAATATAAAATAAAATATA
* *
3318045 TAAATTATAAAATAAATTATA
1 TAAAATATAAAATAAAATATA
3318066 AATATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAATATAAAATAAAATATA
Found at i:3318172 original size:18 final size:19
Alignment explanation
Indices: 3318149--3318184 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3318139 CATTTATAAT
3318149 ATAATA-AAAAATATAAAC
1 ATAATATAAAAATATAAAC
*
3318167 ATAATATAAATATATAAA
1 ATAATATAAAAATATAAA
3318185 TTATTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAATATAAAAATATAAAC
Found at i:3327391 original size:2 final size:2
Alignment explanation
Indices: 3327378--3327416 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3327368 TTTGCAACAA
*
3327378 AT AT AT AC 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 AT AT AT A
3327417 GTAGTGCTCG
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:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3327820 original size:9 final size:9
Alignment explanation
Indices: 3327806--3327839 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
3327796 TATCATATCG
3327806 TATTATATT
1 TATTATATT
3327815 TATTATATT
1 TATTATATT
3327824 ATATTTATATT
1 -TA-TTATATT
3327835 TATTA
1 TATTA
3327840 AAAATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 12 0.52
10 4 0.17
11 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TATTATATT
Found at i:3328292 original size:2 final size:2
Alignment explanation
Indices: 3328285--3328329 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
3328275 ACATACATAC
*
3328285 AT AT AT AT AC 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
3328327 AT A
1 AT A
3328330 AAATGAGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3328296 original size:14 final size:14
Alignment explanation
Indices: 3328277--3328329 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
3328267 GCATACATAC
*
3328277 ATACATACATATAT
1 ATACATATATATAT
3328291 ATACATATATATAT
1 ATACATATATATAT
*
3328305 ATATATATATATAT
1 ATACATATATATAT
*
3328319 ATATATATATA
1 ATACATATATA
3328330 AAATGAGTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (14 bp):
ATACATATATATAT
Found at i:3328298 original size:8 final size:8
Alignment explanation
Indices: 3328262--3328325 Score: 56
Period size: 8 Copynumber: 7.8 Consensus size: 8
3328252 CCTTCTCCGC
*
3328262 TATATGCA
1 TATATACA
*
3328270 TACATACA
1 TATATACA
*
3328278 TACATACATA
1 TATATAC--A
3328288 TATATACA
1 TATATACA
*
3328296 TATATATA
1 TATATACA
*
3328304 TATATATA
1 TATATACA
*
3328312 TATATATA
1 TATATACA
3328320 TATATA
1 TATATA
3328326 TATAAAATGA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
8 43 0.86
10 7 0.14
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (8 bp):
TATATACA
Found at i:3328300 original size:12 final size:12
Alignment explanation
Indices: 3328262--3328329 Score: 73
Period size: 12 Copynumber: 5.5 Consensus size: 12
3328252 CCTTCTCCGC
* *
3328262 TATATGCATACA
1 TATATACATATA
*
3328274 TACATACATACATA
1 TATATACAT--ATA
3328288 TATATACATATA
1 TATATACATATA
*
3328300 TATATATATATA
1 TATATACATATA
*
3328312 TATATATATATA
1 TATATACATATA
3328324 TATATA
1 TATATA
3328330 AAATGAGTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
12 39 0.80
14 10 0.20
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (12 bp):
TATATACATATA
Found at i:3335464 original size:23 final size:23
Alignment explanation
Indices: 3335408--3335457 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
3335398 ATAAAGTAAG
* *
3335408 TAATAATTGTTTAAATTTATCAT
1 TAATAATTGATTAAATTAATCAT
3335431 TAATAATTGATTAAATTAATCAT
1 TAATAATTGATTAAATTAATCAT
3335454 TAAT
1 TAAT
3335458 CCTTGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
TAATAATTGATTAAATTAATCAT
Found at i:3336298 original size:31 final size:31
Alignment explanation
Indices: 3336249--3336309 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
3336239 TAAATTTTTT
* *
3336249 TAAAAATAATTAATTAATAAAAAATTTTAAA
1 TAAAAATAATTAAATAATAAAAAATATTAAA
* * *
3336280 TAAAATTATTTAAATAATATAAAATATTAA
1 TAAAAATAATTAAATAATAAAAAATATTAA
3336310 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAATAATTAAATAATAAAAAATATTAAA
Found at i:3338157 original size:47 final size:47
Alignment explanation
Indices: 3338106--3338215 Score: 132
Period size: 47 Copynumber: 2.3 Consensus size: 47
3338096 AATTATTAAT
* * *** *
3338106 TTAAATTTAAAAATTTATTTGATATTTAAATTT-TTTTAATAAATATA
1 TTAAATTTAAAAATATATTTAATAAAAAAATTTATTTTAA-AAATAAA
3338153 TTAAATTTAAAAATATATTTAATAAAAAAATTTATTTTAAAAATAAA
1 TTAAATTTAAAAATATATTTAATAAAAAAATTTATTTTAAAAATAAA
*
3338200 TTATATTTTAAAAATA
1 TTA-AATTTAAAAATA
3338216 AAATTTAACG
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 37 0.69
48 17 0.31
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (47 bp):
TTAAATTTAAAAATATATTTAATAAAAAAATTTATTTTAAAAATAAA
Found at i:3338168 original size:17 final size:17
Alignment explanation
Indices: 3338140--3338215 Score: 61
Period size: 18 Copynumber: 4.6 Consensus size: 17
3338130 TTTAAATTTT
3338140 TTTAATAAATATATTAAA
1 TTTAA-AAATATATTAAA
*
3338158 TTTAAAAATATATTTAA
1 TTTAAAAATATATTAAA
* *
3338175 --TAAAAA-A-ATTTAT
1 TTTAAAAATATATTAAA
* *
3338188 TTTAAAAATAAATTATAT
1 TTTAAAAATATATTA-AA
3338206 TTTAAAAATA
1 TTTAAAAATA
3338216 AAATTTAACG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 5 0.10
14 1 0.02
15 12 0.24
16 1 0.02
17 14 0.28
18 17 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAAAATATATTAAA
Found at i:3338176 original size:30 final size:30
Alignment explanation
Indices: 3338140--3338197 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3338130 TTTAAATTTT
* *
3338140 TTTAATAAATATATTAAATTTAAAAATATA
1 TTTAATAAAAAAATTAAATTTAAAAATATA
* *
3338170 TTTAATAAAAAAATTTATTTTAAAAATA
1 TTTAATAAAAAAATTAAATTTAAAAATA
3338198 AATTATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTAATAAAAAAATTAAATTTAAAAATATA
Found at i:3338182 original size:18 final size:15
Alignment explanation
Indices: 3338161--3338213 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 15
3338151 TATTAAATTT
3338161 AAAAATATATTTAATAA
1 AAAAATATATTT--TAA
*
3338178 AAAAATTTATTTTAAA
1 AAAAATATATTTT-AA
3338194 AATAAATTATATTTTAA
1 AA-AAA-TATATTTTAA
3338211 AAA
1 AAA
3338214 TAAAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 1 0.03
16 5 0.16
17 18 0.58
18 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAATATATTTTAA
Found at i:3338214 original size:18 final size:18
Alignment explanation
Indices: 3338165--3338217 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
3338155 AAATTTAAAA
*
3338165 ATATATTTAATAAAAAAATT
1 ATAT-TTTAA-AAATAAATT
3338185 -TATTTTAAAAATAAATT
1 ATATTTTAAAAATAAATT
3338202 ATATTTTAAAAATAAA
1 ATATTTTAAAAATAAA
3338218 ATTTAACGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 8 0.26
18 20 0.65
19 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTTTAAAAATAAATT
Found at i:3339369 original size:22 final size:22
Alignment explanation
Indices: 3339337--3339400 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
3339327 ATAAAAAATT
*
3339337 TTAAA-TT-AATTTAAATATAA
1 TTAAATTTAAATTTAAATAAAA
3339357 TTAAATTTAAATTTAAATAAAA
1 TTAAATTTAAATTTAAATAAAA
** *
3339379 TTATTTTTAAATCATAAATAAA
1 TTAAATTTAAAT-TTAAATAAA
3339401 TTCGAACCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 5 0.14
21 2 0.05
22 22 0.59
23 8 0.22
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAAATTTAAATTTAAATAAAA
Found at i:3339377 original size:16 final size:16
Alignment explanation
Indices: 3339336--3339377 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3339326 AATAAAAAAT
*
3339336 TTTAAATTAATTTAAA
1 TTTAAATAAATTTAAA
* *
3339352 TATAATTAAATTTAAA
1 TTTAAATAAATTTAAA
3339368 TTTAAATAAA
1 TTTAAATAAA
3339378 ATTATTTTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAATAAATTTAAA
Found at i:3342697 original size:17 final size:16
Alignment explanation
Indices: 3342668--3342706 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
3342658 TTGTATCTGT
*
3342668 TTATATATCTTTACATA
1 TTAT-TATCTTTAAATA
3342685 TTATTATCTTTTAAATA
1 TTATTATC-TTTAAATA
3342702 TTATT
1 TTATT
3342707 TTATATTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTATCTTTAAATA
Found at i:3348471 original size:28 final size:27
Alignment explanation
Indices: 3348416--3348471 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
3348406 ACTATATATC
**
3348416 ATAAAAAATAATTAAAAATAATTTAAT
1 ATAAAAAATAATTAAAAATAATAAAAT
*
3348443 ATAAAAAATAATATAAACATAATAAAAT
1 ATAAAAAATAAT-TAAAAATAATAAAAT
3348471 A
1 A
3348472 AATATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (27 bp):
ATAAAAAATAATTAAAAATAATAAAAT
Found at i:3348472 original size:26 final size:27
Alignment explanation
Indices: 3348416--3348483 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
3348406 ACTATATATC
*
3348416 ATAAAAAATAAT-TAAAAATAATTTAAT
1 ATAAAAAATAATATAAAAATAA-TTAAA
*
3348443 ATAAAAAATAATATAAACATAA-TAAA
1 ATAAAAAATAATATAAAAATAATTAAA
* *
3348469 ATAAATATTAATATA
1 ATAAAAAATAATATA
3348484 TCAAATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 16 0.44
27 12 0.33
28 8 0.22
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (27 bp):
ATAAAAAATAATATAAAAATAATTAAA
Found at i:3348782 original size:6 final size:6
Alignment explanation
Indices: 3348771--3348797 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3348761 AAGCTCCCTA
3348771 TCTCCC TCTCCC TCTCCC TCTCCC TCT
1 TCTCCC TCTCCC TCTCCC TCTCCC TCT
3348798 TCCTTACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
TCTCCC
Found at i:3360425 original size:13 final size:14
Alignment explanation
Indices: 3360409--3360441 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
3360399 AGAAAAGTTT
3360409 AGAAAAAAAAA-AA
1 AGAAAAAAAAAGAA
3360422 AGAAAAAAAAAGAA
1 AGAAAAAAAAAGAA
3360436 AGAAAA
1 AGAAAA
3360442 GAACCCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAGAA
Found at i:3360428 original size:14 final size:14
Alignment explanation
Indices: 3360411--3360441 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3360401 AAAAGTTTAG
3360411 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
*
3360425 AAAAAAAAGAAAGA
1 AAAAAAAAAAAAGA
3360439 AAA
1 AAA
3360442 GAACCCAACT
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:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:3360818 original size:22 final size:21
Alignment explanation
Indices: 3360782--3360826 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3360772 TAATTACTTA
3360782 AATATATTTTAATTT-TTATGT
1 AATATATTTTAATTTATT-TGT
*
3360803 AATATATTTTTTATTTATTTGT
1 AATATA-TTTTAATTTATTTGT
3360825 AA
1 AA
3360827 AAAAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 13 0.62
23 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
AATATATTTTAATTTATTTGT
Found at i:3360849 original size:55 final size:56
Alignment explanation
Indices: 3360779--3360889 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 56
3360769 ACATAATTAC
3360779 TTAAATATATTTTAATTTTTATGTAATATATTTTTTATTTATTTGTAAAAAAATAA
1 TTAAATATATTTTAATTTTTATGTAATATATTTTTTATTTATTTGTAAAAAAATAA
3360835 TTAAA-ATATTTTAATTTTTATGTAATATATTTTTTATTTATTTGTAAAAAAATAA
1 TTAAATATATTTTAATTTTTATGTAATATATTTTTTATTTATTTGTAAAAAAATAA
3360890 AGAAGTAGAG
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 50 0.91
56 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (56 bp):
TTAAATATATTTTAATTTTTATGTAATATATTTTTTATTTATTTGTAAAAAAATAA
Found at i:3361201 original size:29 final size:31
Alignment explanation
Indices: 3361159--3361222 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
3361149 TCAATGAAAA
*
3361159 AATATTTTAATTTTTTTATTATT-AAATT-T
1 AATATTTTAATTTTTATATTATTAAAATTAT
*
3361188 AATATTTTAATTTTTATATTTTTAAAATTAT
1 AATATTTTAATTTTTATATTATTAAAATTAT
3361219 AATA
1 AATA
3361223 AATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 21 0.68
30 5 0.16
31 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
AATATTTTAATTTTTATATTATTAAAATTAT
Found at i:3361208 original size:21 final size:21
Alignment explanation
Indices: 3361164--3361208 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3361154 GAAAAAATAT
* *
3361164 TTTAATTTTTTTATTATTAAA
1 TTTAATATTTTAATTATTAAA
* *
3361185 TTTAATATTTTAATTTTTATA
1 TTTAATATTTTAATTATTAAA
3361206 TTT
1 TTT
3361209 TTAAAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTAATATTTTAATTATTAAA
Found at i:3361256 original size:11 final size:11
Alignment explanation
Indices: 3361240--3361265 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3361230 AATAATTAAT
3361240 ATTATTTAAAA
1 ATTATTTAAAA
3361251 ATTATTTAAAA
1 ATTATTTAAAA
3361262 ATTA
1 ATTA
3361266 AAAAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTATTTAAAA
Found at i:3361403 original size:24 final size:26
Alignment explanation
Indices: 3361346--3361427 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 26
3361336 CAAATTTATT
3361346 TTTAAATAAAATTTAAAATTTTAAGTA
1 TTTAAAT-AAATTTAAAATTTTAAGTA
* *
3361373 TAT-AATAAA-TTAATATTTTAA-TA
1 TTTAAATAAATTTAAAATTTTAAGTA
* *
3361396 TTTAAATAATTTTATAATATTATTAATTA
1 TTTAAATAAATTTA-AA-ATT-TTAAGTA
3361425 TTT
1 TTT
3361428 TTTATTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
23 4 0.09
24 16 0.36
25 6 0.14
26 4 0.09
27 5 0.11
28 4 0.09
29 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
TTTAAATAAATTTAAAATTTTAAGTA
Found at i:3361413 original size:19 final size:20
Alignment explanation
Indices: 3361378--3361416 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3361368 AAGTATATAA
3361378 TAAATTAATATTTTAATATT
1 TAAATTAATATTTTAATATT
3361398 TAAA-TAAT-TTTATAATATT
1 TAAATTAATATTT-TAATATT
3361417 ATTAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 11 0.61
20 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAATTAATATTTTAATATT
Found at i:3361445 original size:78 final size:71
Alignment explanation
Indices: 3361363--3361504 Score: 158
Period size: 71 Copynumber: 1.9 Consensus size: 71
3361353 AAAATTTAAA
** * * * *
3361363 ATTTTAAGTATATAATAAATTAATATTTTAATATTTAAATAATTTTATAATATTATTAATTATTT
1 ATTTTAAAAATATAA-AAATTAAAATATTAA-ATTT-AATAA-TATATAA-ATTA--AAATATTT
3361428 TTTATTTATTGTT
59 TTTATTTATTGTT
*
3361441 ATTTTAAAAATATAAATATTAAAATATTAAATTTAATAATATATAAATTAAAATATTTTTTATT
1 ATTTTAAAAATATAAAAATTAAAATATTAAATTTAATAATATATAAATTAAAATATTTTTTATT
3361505 ATAATAAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
71 13 0.23
73 4 0.07
74 6 0.11
75 5 0.09
76 4 0.07
77 12 0.21
78 13 0.23
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (71 bp):
ATTTTAAAAATATAAAAATTAAAATATTAAATTTAATAATATATAAATTAAAATATTTTTTATTT
ATTGTT
Found at i:3361462 original size:15 final size:15
Alignment explanation
Indices: 3361444--3361493 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
3361434 TATTGTTATT
3361444 TTAAAAATATAAATA
1 TTAAAAATATAAATA
3361459 TT-AAAATATTAAAT-
1 TTAAAAATA-TAAATA
*
3361473 TTAATAATATATAA-A
1 TTAAAAATATA-AATA
3361488 TTAAAA
1 TTAAAA
3361494 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAAAATATAAATA
Found at i:3361466 original size:14 final size:14
Alignment explanation
Indices: 3361447--3361496 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
3361437 TGTTATTTTA
3361447 AAAATATAAATATT
1 AAAATATAAATATT
3361461 AAAATATTAAAT-TT
1 AAAATA-TAAATATT
3361475 AATAATATATAA-ATT
1 AA-AATATA-AATATT
3361490 AAAATAT
1 AAAATAT
3361497 TTTTTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 17 0.53
15 15 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATATAAATATT
Done.