Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 15 of 18
Found at i:2653272 original size:13 final size:13
Alignment explanation
Indices: 2653254--2653278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2653244 TGAATAAAAA
2653254 TAATTAAATTAAT
1 TAATTAAATTAAT
2653267 TAATTAAATTAA
1 TAATTAAATTAA
2653279 ATTTTAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:2657248 original size:2 final size:2
Alignment explanation
Indices: 2657241--2657265 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2657231 TAGAGATTCC
2657241 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
2657266 GAGAGAGAGA
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:2657270 original size:2 final size:2
Alignment explanation
Indices: 2657265--2657293 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2657255 ATATATATAT
2657265 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2657294 ATTGTTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2659801 original size:2 final size:2
Alignment explanation
Indices: 2659794--2659833 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2659784 TTGATACAAT
2659794 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2659834 CTTGACTTAC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2670941 original size:2 final size:2
Alignment explanation
Indices: 2670934--2670963 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2670924 TATGATTTTC
2670934 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
2670964 TTCAAGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2671020 original size:2 final size:2
Alignment explanation
Indices: 2671013--2671049 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2671003 GTTATATGAT
2671013 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 T
2671050 TTCTCCTCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2672704 original size:2 final size:2
Alignment explanation
Indices: 2672697--2672731 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2672687 TATTATTTAA
2672697 AT 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 AT A
2672732 ATTTTGATGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2672827 original size:3 final size:3
Alignment explanation
Indices: 2672812--2672854 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
2672802 CCTTCCCCAG
* *
2672812 CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTT TTT CTCT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT
2672855 GAACATTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
CTT
Found at i:2683486 original size:21 final size:20
Alignment explanation
Indices: 2683437--2683489 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
2683427 TATCAAAATT
*
2683437 TTATAAAAA-AA-ATTATAC
1 TTATAAAAATAATATTATAA
*
2683455 TT-TAAATATAATATTATAA
1 TTATAAAAATAATATTATAA
2683474 TATATAAAAATAATAT
1 T-TATAAAAATAATAT
2683490 AATCACAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 7 0.25
20 1 0.04
21 11 0.39
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTATAAAAATAATATTATAA
Found at i:2684986 original size:16 final size:15
Alignment explanation
Indices: 2684965--2685031 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 15
2684955 ATAATCGTGT
2684965 ATTTTATTATATAATA
1 ATTTTA-TATATAATA
* *
2684981 ATTTTATTTAAAAT-
1 ATTTTATATATAATA
*
2684995 ATTTTATATTTATATA
1 ATTTTATATATA-ATA
2685011 TATTTTGATATATTAATA
1 -ATTTT-ATATA-TAATA
2685029 ATT
1 ATT
2685032 CATATTATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 9 0.22
15 8 0.20
16 6 0.15
17 8 0.20
18 7 0.17
19 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (15 bp):
ATTTTATATATAATA
Found at i:2686360 original size:2 final size:2
Alignment explanation
Indices: 2686353--2686387 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2686343 AATGACAAAT
*
2686353 TA TA TA TA TT 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 T
2686388 TTGGAGCGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2687935 original size:20 final size:18
Alignment explanation
Indices: 2687881--2687940 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 18
2687871 AAATATTTAA
2687881 AAAT-TAATTTTATAAA-
1 AAATATAATTTTATAAAT
*
2687897 AAAT-TAATTTTATATAT
1 AAATATAATTTTATAAAT
2687914 AAATATAGATTTTAATAAAT
1 AAATATA-ATTTT-ATAAAT
2687934 AAATATA
1 AAATATA
2687941 TTAAAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.39
17 4 0.11
18 2 0.05
19 5 0.13
20 12 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATATAATTTTATAAAT
Found at i:2688854 original size:5 final size:5
Alignment explanation
Indices: 2688844--2688899 Score: 58
Period size: 6 Copynumber: 10.0 Consensus size: 5
2688834 AAATTATAAT
2688844 ATTTA ATTTA ATTTA ATTTAA ATATTA ATATTA TATTTA ATTTTA ATTTTA
1 ATTTA ATTTA ATTTA ATTT-A AT-TTA AT-TTA -ATTTA A-TTTA A-TTTA
2688895 ATTTA
1 ATTTA
2688900 TGAATTAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
5 19 0.40
6 24 0.51
7 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:2688864 original size:29 final size:31
Alignment explanation
Indices: 2688830--2688897 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
2688820 TCAAAAATCG
2688830 ATTTAAATTA-TAATATT-TAATTTAA-TTTA
1 ATTTAAATTATTAATATTAT-ATTTAATTTTA
2688859 ATTTAAA-TATTAATATTATATTTAATTTTA
1 ATTTAAATTATTAATATTATATTTAATTTTA
*
2688889 ATTTTAATT
1 ATTTAAATT
2688898 TATGAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 2 0.06
29 20 0.59
30 11 0.32
31 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTTAAATTATTAATATTATATTTAATTTTA
Found at i:2688897 original size:6 final size:6
Alignment explanation
Indices: 2688830--2688898 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
2688820 TCAAAAATCG
* * * * *
2688830 ATTTAA ATTATA ATATTTA A-TTTA A-TTTA ATTTAA ATATTA ATATT-
1 ATTTTA ATTTTA AT-TTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
2688876 ATATTTA ATTTTA ATTTTA ATTT
1 AT-TTTA ATTTTA ATTTTA ATTT
2688899 ATGAATTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
5 12 0.23
6 34 0.65
7 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
ATTTTA
Found at i:2688907 original size:24 final size:23
Alignment explanation
Indices: 2688830--2688900 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
2688820 TCAAAAATCG
*
2688830 ATTTAAATTATAATATTTAATTTA-
1 ATTT-AATTTTAAT-TTTAATTTAT
* *
2688854 ATTTAATTTAAATATTAATATTAT
1 ATTTAATTTTAATTTTAAT-TTAT
2688878 ATTTAATTTTAATTTTAATTTAT
1 ATTTAATTTTAATTTTAATTTAT
2688901 GAATTAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.12
23 14 0.35
24 21 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTAATTTTAATTTTAATTTAT
Found at i:2693277 original size:14 final size:14
Alignment explanation
Indices: 2693261--2693309 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
2693251 TTTAAAATAT
*
2693261 TATATAAATTTTAT
1 TATATAAATTTTAA
2693275 TAT-TAATAATTTATAA
1 TATAT-A-AATTT-TAA
2693291 TATATAAATTTTAA
1 TATATAAATTTTAA
2693305 TATAT
1 TATAT
2693310 TTATATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 1 0.03
14 12 0.40
15 10 0.33
16 6 0.20
17 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:2693297 original size:30 final size:33
Alignment explanation
Indices: 2693261--2693328 Score: 97
Period size: 30 Copynumber: 2.2 Consensus size: 33
2693251 TTTAAAATAT
2693261 TATATAAATTTT-AT-TATTAATA-ATTTATAA
1 TATATAAATTTTAATATATTAATATATTTATAA
* *
2693291 TATATAAATTTTAATATATTTATATATTTATAT
1 TATATAAATTTTAATATATTAATATATTTATAA
2693324 TATAT
1 TATAT
2693329 TTATTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 12 0.36
31 2 0.06
32 7 0.21
33 12 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TATATAAATTTTAATATATTAATATATTTATAA
Found at i:2693328 original size:5 final size:5
Alignment explanation
Indices: 2693305--2693359 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
2693295 TAAATTTTAA
2693305 TATAT T-TA- TATATT TATAT TATAT T-TAT T-T-T TATAT TATAT TATAT
1 TATAT TATAT TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT
2693351 TATAAT TAT
1 TAT-AT TAT
2693360 TTTTTATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.07
4 10 0.23
5 22 0.50
6 9 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TATAT
Found at i:2693335 original size:33 final size:32
Alignment explanation
Indices: 2693257--2693359 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 32
2693247 TTTATTTAAA
*
2693257 ATATTATATAAATTTTAT-TATTAATA-ATTT
1 ATATTATATAAATTTTATATATTTATATATTT
*
2693287 ATAATATATAAATTTTAATATATTTATATATTT
1 ATATTATATAAATTTT-ATATATTTATATATTT
**
2693320 ATATTATATTTATTTT-TATA-TTATATTATATT
1 ATATTATATAAATTTTATATATTTATA-TAT-TT
2693352 ATAATTAT
1 AT-ATTAT
2693360 TTTTTATTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
30 20 0.32
31 9 0.15
32 11 0.18
33 22 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
ATATTATATAAATTTTATATATTTATATATTT
Found at i:2693337 original size:17 final size:18
Alignment explanation
Indices: 2693305--2693353 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
2693295 TAAATTTTAA
2693305 TATATTTATATATTTATAT
1 TATATTTAT-TATTTATAT
2693324 TATATTTATT-TTTATAT
1 TATATTTATTATTTATAT
2693341 TATATTATATTAT
1 TATATT-TATTAT
2693354 AATTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.46
18 5 0.18
19 10 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATATTTATTATTTATAT
Found at i:2693346 original size:22 final size:23
Alignment explanation
Indices: 2693307--2693351 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2693297 AATTTTAATA
2693307 TATTTATATATTTATATTATATT
1 TATTTATATATTTATATTATATT
*
2693330 TATTTTTATA-TTATATTATATT
1 TATTTATATATTTATATTATATT
2693352 ATAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTATATATTTATATTATATT
Found at i:2693354 original size:27 final size:26
Alignment explanation
Indices: 2693309--2693367 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
2693299 TTTTAATATA
*
2693309 TTTATA-TATTTATATTATATTTATT
1 TTTATATTATTTATATTATAATTATT
2693334 TTTATATTATATTATATTATAATTATT
1 TTTATATTAT-TTATATTATAATTATT
2693361 TTT-TATT
1 TTTATATT
2693368 TAAAATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 6 0.19
26 7 0.23
27 18 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTATATTATTTATATTATAATTATT
Found at i:2694451 original size:3 final size:3
Alignment explanation
Indices: 2694443--2694467 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2694433 TGACAGCCTA
2694443 AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC A
2694468 GCCACAGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2695133 original size:31 final size:31
Alignment explanation
Indices: 2695097--2695155 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2695087 AAACGCTGCG
* *
2695097 AGAGGATTTGTGGAATTTTATTTTATTTCAT
1 AGAGGATGTGTAGAATTTTATTTTATTTCAT
2695128 AGAGGATGTGTAGAATTTTATTTTATTT
1 AGAGGATGTGTAGAATTTTATTTTATTT
2695156 TATCATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (31 bp):
AGAGGATGTGTAGAATTTTATTTTATTTCAT
Found at i:2698089 original size:2 final size:2
Alignment explanation
Indices: 2698082--2698107 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2698072 AATGATTTGG
2698082 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
2698108 TGGATCTTTT
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:2698729 original size:38 final size:39
Alignment explanation
Indices: 2698687--2698766 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 39
2698677 TATTTGATAC
*
2698687 ATACAAAAATAATATGATAAATATAAGATA-ATATATTT
1 ATACAAAAATAATATGATAAATATAAGATATATATATAT
* * * * *
2698725 ATACATAATTAATATGATACATTTAATATATATATATAT
1 ATACAAAAATAATATGATAAATATAAGATATATATATAT
2698764 ATA
1 ATA
2698767 ATGTATTCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
38 25 0.71
39 10 0.29
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (39 bp):
ATACAAAAATAATATGATAAATATAAGATATATATATAT
Found at i:2700751 original size:6 final size:6
Alignment explanation
Indices: 2700742--2700780 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
2700732 AGAGGAAAGT
2700742 GAAGGA GAAGGA GAAGGA GAAGGA G-AGGA G-AGG- GAAGGA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
2700781 ATGAAGAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 1 0.03
5 11 0.35
6 19 0.61
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:2703475 original size:2 final size:2
Alignment explanation
Indices: 2703468--2703511 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2703458 TACCGATGAC
*
2703468 AT AT AT AT AT AT AT TT 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
2703510 AT
1 AT
2703512 GAGAAGTGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2711793 original size:20 final size:21
Alignment explanation
Indices: 2711770--2711808 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2711760 TTATTATTAT
2711770 TATT-TTATGTGT-TTTTGTAA
1 TATTCTTA-GTGTATTTTGTAA
2711790 TATTCTTAGTGTATTTTGT
1 TATTCTTAGTGTATTTTGT
2711809 TGTTAGCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (21 bp):
TATTCTTAGTGTATTTTGTAA
Found at i:2713375 original size:27 final size:27
Alignment explanation
Indices: 2713325--2713376 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2713315 ATTAATATTT
**
2713325 ATATTTTATAATTAAATTTAAATAAAA
1 ATATTTTATAATTAAATGAAAATAAAA
2713352 ATATTTTAT-ATTAAATGAATAATAA
1 ATATTTTATAATTAAATGAA-AATAA
2713377 CTTTAATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
ATATTTTATAATTAAATGAAAATAAAA
Found at i:2714622 original size:2 final size:2
Alignment explanation
Indices: 2714579--2714603 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2714569 CTCTCTACTG
2714579 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2714604 GTGCTTCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2715336 original size:2 final size:2
Alignment explanation
Indices: 2715319--2715356 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2715309 TTGTAAAAAC
*
2715319 TA TA T- TA TA TA AA 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
2715357 TAAGTTGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2715712 original size:10 final size:9
Alignment explanation
Indices: 2715686--2715744 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
2715676 ATACGGGTTA
2715686 AATATTTAT
1 AATATTTAT
*
2715695 AAAATTTAT
1 AATATTTAT
2715704 AATATTT-T
1 AATATTTAT
2715712 AAT-TTTA-
1 AATATTTAT
* *
2715719 AATTTTTTT
1 AATATTTAT
2715728 AAT-TTATAT
1 AATATT-TAT
2715737 AATATTTA
1 AATATTTA
2715745 AATTTATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 6 0.15
8 9 0.22
9 24 0.59
10 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTAT
Found at i:2715750 original size:17 final size:17
Alignment explanation
Indices: 2715701--2715761 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
2715691 TTATAAAATT
*
2715701 TATAATATTTTAATTT-
1 TATAATATTTAAATTTA
* *
2715717 TA-AATTTTTTTAATTTA
1 TATAA-TATTTAAATTTA
2715734 TATAATATTTAAATTTA
1 TATAATATTTAAATTTA
* *
2715751 TTTATTATTTA
1 TATAATATTTA
2715762 CTGTTTGAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
15 2 0.05
16 12 0.32
17 21 0.57
18 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATAATATTTAAATTTA
Found at i:2719227 original size:29 final size:30
Alignment explanation
Indices: 2719184--2719265 Score: 132
Period size: 29 Copynumber: 2.8 Consensus size: 30
2719174 TATTTTTATC
2719184 ATATTTAAATAAATTTTTAATATTTAATTT
1 ATATTTAAATAAATTTTTAATATTTAATTT
*
2719214 ATATTTAAAT-AATTTTTAACATTTAATTT
1 ATATTTAAATAAATTTTTAATATTTAATTT
*
2719243 ATA-TTAAATAAACTTTTAATATT
1 ATATTTAAATAAATTTTTAATATT
2719266 ATTTTTTTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
28 6 0.12
29 32 0.67
30 10 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (30 bp):
ATATTTAAATAAATTTTTAATATTTAATTT
Found at i:2720881 original size:8 final size:8
Alignment explanation
Indices: 2720868--2720956 Score: 60
Period size: 8 Copynumber: 10.8 Consensus size: 8
2720858 ACAATAATTA
2720868 ATATATTT
1 ATATATTT
2720876 ATATATTCTTT
1 ATATA---TTT
*
2720887 AAATAATTT
1 ATAT-ATTT
2720896 ATATTATATT
1 ATA-TAT-TT
*
2720906 A-ATTTTT
1 ATATATTT
*
2720913 ACATATTT
1 ATATATTT
2720921 ATATATTT
1 ATATATTT
2720929 ATAT-TTT
1 ATATATTT
2720936 ATTATATTT
1 A-TATATTT
2720945 A-A-ATTT
1 ATATATTT
2720951 ATATAT
1 ATATAT
2720957 AAAATTACAT
Statistics
Matches: 65, Mismatches: 5, Indels: 22
0.71 0.05 0.24
Matches are distributed among these distances:
6 5 0.08
7 9 0.14
8 28 0.43
9 12 0.18
10 4 0.06
11 6 0.09
12 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
ATATATTT
Found at i:2720899 original size:28 final size:28
Alignment explanation
Indices: 2720854--2720932 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
2720844 GGGTTATTTC
*
2720854 TTTTACAATAATTAATATATTTATAT-AT
1 TTTTA-AATAATTTATATATTTATATAAT
*
2720882 TCTTTAAATAATTTATAT-TATAT-TAAT
1 T-TTTAAATAATTTATATATTTATATAAT
*
2720909 TTTTACAT-ATTTATATATTTATAT
1 TTTTAAATAATTTATATATTTATAT
2720933 TTTATTATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
25 8 0.19
26 11 0.26
27 8 0.19
28 12 0.28
29 4 0.09
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTAAATAATTTATATATTTATATAAT
Found at i:2721141 original size:14 final size:14
Alignment explanation
Indices: 2721114--2721142 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2721104 AATAAATTAA
2721114 TAAATATTTATTTT
1 TAAATATTTATTTT
2721128 TAAA-ATTTATTTT
1 TAAATATTTATTTT
2721141 TA
1 TA
2721143 TATTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TAAATATTTATTTT
Found at i:2727244 original size:3 final size:3
Alignment explanation
Indices: 2727238--2727262 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2727228 TTGTTGGGAG
2727238 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
2727263 AACTGGAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:2727912 original size:2 final size:2
Alignment explanation
Indices: 2727905--2727934 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2727895 CAATTTTCAA
2727905 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2727935 CAAGTGCCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2729911 original size:20 final size:22
Alignment explanation
Indices: 2729881--2729921 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2729871 AATTAGGTTG
2729881 AATTATTATTT-ATTTAATAAA
1 AATTATTATTTAATTTAATAAA
2729902 AATT-TTATTTAATTTAATAA
1 AATTATTATTTAATTTAATAA
2729922 TATAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTATTATTTAATTTAATAAA
Found at i:2731485 original size:13 final size:13
Alignment explanation
Indices: 2731467--2731491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2731457 AATTTTAAAT
2731467 ATAATATAAAAAC
1 ATAATATAAAAAC
2731480 ATAATATAAAAA
1 ATAATATAAAAA
2731492 TAATATGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAATATAAAAAC
Found at i:2736559 original size:17 final size:17
Alignment explanation
Indices: 2736515--2736564 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
2736505 ATATTACTAT
*
2736515 AATAAT-TTAATCATGAA
1 AATAATCTT-ATCATTAA
* *
2736532 AATAATTTTATTATTAA
1 AATAATCTTATCATTAA
2736549 AATAATCTTATCATTA
1 AATAATCTTATCATTA
2736565 GAGATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 26 0.93
18 2 0.07
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (17 bp):
AATAATCTTATCATTAA
Found at i:2744828 original size:14 final size:14
Alignment explanation
Indices: 2744809--2744891 Score: 59
Period size: 14 Copynumber: 6.2 Consensus size: 14
2744799 TAATAAAAAA
2744809 TTTTAT-ATTAATAT
1 TTTTATAATTAA-AT
2744823 TTTTATAATTAAA-
1 TTTTATAATTAAAT
*
2744836 -TTTA-AATAAAAT
1 TTTTATAATTAAAT
*
2744848 TTTTATTATTAAAT
1 TTTTATAATTAAAT
* * *
2744862 ATTTATTA-TAAAA
1 TTTTATAATTAAAT
* *
2744875 ATTTATATTTAAAT
1 TTTTATAATTAAAT
2744889 TTT
1 TTT
2744892 AAAGTTCGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 6 0.11
12 4 0.07
13 14 0.25
14 26 0.47
15 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTATAATTAAAT
Found at i:2744846 original size:40 final size:40
Alignment explanation
Indices: 2744804--2744879 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
2744794 AATATTAATA
2744804 AAAAATTTTA-TATT-AATATTT-TTATAATTAAATTTAAAT
1 AAAAATTTTATTATTAAATATTTATTATAA--AAATTTAAAT
*
2744843 AAAATTTTTATTATTAAATATTTATTATAAAAATTTA
1 AAAAATTTTATTATTAAATATTTATTATAAAAATTTA
2744880 TATTTAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
39 9 0.27
40 11 0.33
41 7 0.21
42 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
AAAAATTTTATTATTAAATATTTATTATAAAAATTTAAAT
Found at i:2747387 original size:20 final size:19
Alignment explanation
Indices: 2747337--2747397 Score: 79
Period size: 18 Copynumber: 3.2 Consensus size: 19
2747327 GCAAGATTAC
* *
2747337 ATAAATAAATATAATATAA
1 ATAAATAATTAAAATATAA
2747356 A-AAATAATTAAAATATAA
1 ATAAATAATTAAAATATAA
*
2747374 ATAAATATATTAAAATATAT
1 ATAAATA-ATTAAAATATAA
2747394 ATAA
1 ATAA
2747398 TAAAAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.43
19 6 0.16
20 15 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAATAATTAAAATATAA
Found at i:2747395 original size:12 final size:11
Alignment explanation
Indices: 2747343--2747392 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 11
2747333 TTACATAAAT
2747343 AAATATAATATA
1 AAATATAAT-TA
*
2747355 AAAAATAATTA
1 AAATATAATTA
*
2747366 AAATATAAAT-
1 AAATATAATTA
2747376 AAATAT-ATTA
1 AAATATAATTA
2747386 AAATATA
1 AAATATA
2747393 TATAATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 2 0.06
10 12 0.38
11 10 0.31
12 8 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATATAATTA
Found at i:2747395 original size:14 final size:14
Alignment explanation
Indices: 2747343--2747402 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
2747333 TTACATAAAT
2747343 AAATATAATATAA-A
1 AAATA-AATATAATA
* *
2747357 AAATAATTAAAATA
1 AAATAAATATAATA
*
2747371 TAAATAAATATATTA
1 -AAATAAATATAATA
*
2747386 AAATATATATAATA
1 AAATAAATATAATA
2747400 AAA
1 AAA
2747403 ATTATTAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 5 0.14
14 21 0.57
15 11 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATAAATATAATA
Found at i:2748308 original size:2 final size:2
Alignment explanation
Indices: 2748301--2748329 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2748291 AGATTGATGG
2748301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2748330 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2748334 original size:2 final size:2
Alignment explanation
Indices: 2748329--2748354 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2748319 TATATATATA
2748329 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
2748355 GCAAAAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2749126 original size:17 final size:16
Alignment explanation
Indices: 2749093--2749129 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
2749083 ATTATATTTT
*
2749093 TATATTTATATTTAAA
1 TATATTTAAATTTAAA
2749109 TATATTTAAATATTAAA
1 TATATTTAAAT-TTAAA
2749126 TATA
1 TATA
2749130 AATATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATTTAAATTTAAA
Found at i:2749133 original size:13 final size:14
Alignment explanation
Indices: 2749115--2749147 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2749105 TAAATATATT
*
2749115 TAAATA-TTAAATA
1 TAAATATTTAAAAA
2749128 TAAATATTTAAAAA
1 TAAATATTTAAAAA
2749142 TAAATA
1 TAAATA
2749148 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATATTTAAAAA
Found at i:2749153 original size:21 final size:20
Alignment explanation
Indices: 2749105--2749167 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
2749095 TATTTATATT
* *
2749105 TAAATATATTTAAATATTAAA
1 TAAAAATATTTAAA-AATAAA
*
2749126 TATAAATATTTAAAAATAAA
1 TAAAAATATTTAAAAATAAA
2749146 TAAAAA-A-TTAAAAAT-AA
1 TAAAAATATTTAAAAATAAA
2749163 TAAAA
1 TAAAA
2749168 CTTGATTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 1 0.03
20 10 0.26
21 12 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAAATATTTAAAAATAAA
Found at i:2752688 original size:2 final size:2
Alignment explanation
Indices: 2752675--2752718 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2752665 CAGCATCATG
*
2752675 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2752717 AT
1 AT
2752719 TGGGTTTATC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2759204 original size:17 final size:18
Alignment explanation
Indices: 2759184--2759222 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2759174 TAATTCAAAT
2759184 TAAAAAATTTAAATT-AA
1 TAAAAAATTTAAATTAAA
* *
2759201 TAAAAACTTTAATTTAAA
1 TAAAAAATTTAAATTAAA
2759219 TAAA
1 TAAA
2759223 TTAAATTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAAAATTTAAATTAAA
Found at i:2761242 original size:13 final size:13
Alignment explanation
Indices: 2761224--2761257 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2761214 ATAATTAGTG
2761224 GTAAACAAATAAA
1 GTAAACAAATAAA
2761237 GTAAACAAATAAA
1 GTAAACAAATAAA
2761250 -TAAA-AAAT
1 GTAAACAAAT
2761258 GCTTCACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 4 0.19
13 13 0.62
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (13 bp):
GTAAACAAATAAA
Found at i:2763870 original size:2 final size:2
Alignment explanation
Indices: 2763863--2763895 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2763853 TGGACACCAC
2763863 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
2763896 GTGGTCATAA
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:2765395 original size:4 final size:4
Alignment explanation
Indices: 2765386--2765410 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2765376 TAATAATAAT
2765386 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
2765411 TGCCAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:2765629 original size:15 final size:15
Alignment explanation
Indices: 2765611--2765641 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2765601 AAAAAGTTTC
*
2765611 AAAAAAGAAACAAAA
1 AAAAAAAAAACAAAA
2765626 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
2765641 A
1 A
2765642 GCTTAGGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.90, C:0.06, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:2770532 original size:15 final size:14
Alignment explanation
Indices: 2770512--2770548 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2770502 TGACCTGTTA
*
2770512 ATATTAATATTTTTT
1 ATATTAATA-TTTGT
2770527 ATATTAATATTTGT
1 ATATTAATATTTGT
2770541 ATATTAAT
1 ATATTAAT
2770549 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
ATATTAATATTTGT
Found at i:2773286 original size:2 final size:2
Alignment explanation
Indices: 2773279--2773311 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2773269 TTTTACTACA
2773279 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
2773312 AAACAAAAGA
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:2776654 original size:2 final size:2
Alignment explanation
Indices: 2776647--2776675 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2776637 TTGTCTCCAA
2776647 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
2776676 GTTTAGTTGA
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:2785586 original size:21 final size:22
Alignment explanation
Indices: 2785549--2785601 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
2785539 ATAACTTTAT
*
2785549 TAAAAATAAATAAAATATATAA
1 TAAAAATAAATAAAATAAATAA
*
2785571 TAAAAATAAAT-TAATAAATAA
1 TAAAAATAAATAAAATAAATAA
*
2785592 TAAATATAAA
1 TAAAAATAAA
2785602 AATACGAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAAAATAAATAAAATAAATAA
Found at i:2790456 original size:19 final size:20
Alignment explanation
Indices: 2790407--2790456 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
2790397 ATTATAATTT
2790407 TTAAAAA-A-TATTTTTATA
1 TTAAAAATATTATTTTTATA
* * *
2790425 TTTAATATGTTATTTTTA-A
1 TTAAAAATATTATTTTTATA
2790444 TTAAAAATATTAT
1 TTAAAAATATTAT
2790457 ATTAATTATA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
18 5 0.21
19 11 0.46
20 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAAAAATATTATTTTTATA
Found at i:2790959 original size:17 final size:16
Alignment explanation
Indices: 2790911--2790955 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
2790901 AAAAAGAATT
2790911 TTATATAAATTTTAT-
1 TTATATAAATTTTATA
*
2790926 TAAT-TAAATATTTATA
1 TTATATAAAT-TTTATA
2790942 TTATATAAATTTTA
1 TTATATAAATTTTA
2790956 ATATATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.20
15 8 0.32
16 7 0.28
17 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATAAATTTTATA
Found at i:2796109 original size:2 final size:2
Alignment explanation
Indices: 2796102--2796127 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2796092 AATTAATAGC
2796102 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
2796128 AGACATGGAT
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):
TA
Found at i:2802606 original size:13 final size:13
Alignment explanation
Indices: 2802577--2802606 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2802567 GAATTATAAT
2802577 TTAAATTTTTTTA
1 TTAAATTTTTTTA
2802590 -TAAATTTTTTTA
1 TTAAATTTTTTTA
2802602 TTAAA
1 TTAAA
2802607 ATTGATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTAAATTTTTTTA
Found at i:2803530 original size:18 final size:18
Alignment explanation
Indices: 2803507--2803542 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2803497 ATTTTTACTC
2803507 AAAATTATTTTTAATTAT
1 AAAATTATTTTTAATTAT
2803525 AAAATTATTTTTAATTAT
1 AAAATTATTTTTAATTAT
2803543 TATTAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAAATTATTTTTAATTAT
Found at i:2808254 original size:2 final size:2
Alignment explanation
Indices: 2808247--2808277 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2808237 CAATTACTCC
2808247 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 T
2808278 TTTTTTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2810369 original size:2 final size:2
Alignment explanation
Indices: 2810362--2810398 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2810352 TTATTAACAA
2810362 AT AT 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 AT AT A
2810399 AACAAAGCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2811293 original size:12 final size:12
Alignment explanation
Indices: 2811271--2811304 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2811261 AAAATTTAAG
2811271 AAATG-ATAAAT
1 AAATGAATAAAT
2811282 AAATGAATAAAT
1 AAATGAATAAAT
*
2811294 AAATAAATAAA
1 AAATGAATAAA
2811305 AAGCTAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (12 bp):
AAATGAATAAAT
Found at i:2816337 original size:6 final size:6
Alignment explanation
Indices: 2816326--2816350 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2816316 AAAAATTTAA
2816326 AAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT A
2816351 TTTTAACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:2819416 original size:22 final size:22
Alignment explanation
Indices: 2819391--2819432 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2819381 AGAGTAAATC
2819391 TATTTAAAAATTAAGTTATTAT
1 TATTTAAAAATTAAGTTATTAT
* *
2819413 TATTTAAAAGTTGAGTTATT
1 TATTTAAAAATTAAGTTATT
2819433 CGTTTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
TATTTAAAAATTAAGTTATTAT
Found at i:2819576 original size:26 final size:24
Alignment explanation
Indices: 2819522--2819576 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
2819512 TAATAAAAAA
**
2819522 TAATATTAATTAAATTTAATATAT
1 TAATATTAATTAAAAATAATATAT
* *
2819546 GAATATTAATATAAAAAATAATATTT
1 TAATATTAAT-T-AAAAATAATATAT
2819572 TAATA
1 TAATA
2819577 ATATAATCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 9 0.38
25 1 0.04
26 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATATTAATTAAAAATAATATAT
Found at i:2820959 original size:11 final size:10
Alignment explanation
Indices: 2820928--2820960 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
2820918 TTCATGTGTC
2820928 TTAAAAATAT
1 TTAAAAATAT
2820938 TT-AAAATAT
1 TTAAAAATAT
2820947 TTAAAATATAT
1 TTAAAA-ATAT
2820958 TTA
1 TTA
2820961 TATAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 5 0.24
11 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:2821364 original size:2 final size:2
Alignment explanation
Indices: 2821357--2821386 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2821347 AAACCATTGC
2821357 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
2821387 TAAACCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2823995 original size:22 final size:22
Alignment explanation
Indices: 2823970--2824021 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
2823960 CAGAGATATT
2823970 ACGTAAATTATATATCCATACA
1 ACGTAAATTATATATCCATACA
2823992 ACGTAAATTATATATCCATACA
1 ACGTAAATTATATATCCATACA
2824014 ACGTAAAT
1 ACGTAAAT
2824022 CAGATACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (22 bp):
ACGTAAATTATATATCCATACA
Found at i:2826458 original size:3 final size:3
Alignment explanation
Indices: 2826450--2826475 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2826440 TTGAGTGAGA
2826450 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
2826476 AGGAAAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:2826485 original size:5 final size:5
Alignment explanation
Indices: 2826475--2826514 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
2826465 GAGGAGGAGG
*
2826475 AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA GAGGA AAGGA
1 AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA
2826515 TGGGAATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
AAGGA
Found at i:2828697 original size:13 final size:13
Alignment explanation
Indices: 2828679--2828713 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
2828669 TATCAGCATC
2828679 TCTTTCAGAAGAT
1 TCTTTCAGAAGAT
2828692 TCTTTCAGAAGAT
1 TCTTTCAGAAGAT
2828705 TCTTTCAGA
1 TCTTTCAGA
2828714 TTCCTGCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (13 bp):
TCTTTCAGAAGAT
Found at i:2831167 original size:24 final size:24
Alignment explanation
Indices: 2831135--2831183 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2831125 GCAGTGATTG
*
2831135 ACAGTCAACTATTTCTGCTGGGGT
1 ACAGTCAACTATTTCTACTGGGGT
2831159 ACAGTCAACTATTTCTACTGGGGT
1 ACAGTCAACTATTTCTACTGGGGT
2831183 A
1 A
2831184 TTGCCACCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (24 bp):
ACAGTCAACTATTTCTACTGGGGT
Found at i:2841814 original size:31 final size:31
Alignment explanation
Indices: 2841779--2841873 Score: 91
Period size: 31 Copynumber: 3.4 Consensus size: 31
2841769 ATTGGATGAG
*
2841779 AATAAATATTTGAGAACTCATTTATTACAAT
1 AATAAAGATTTGAGAACTCATTTATTACAAT
* *
2841810 AATAAAGATTT-A-AA-T-A--GA-T-GAA-
1 AATAAAGATTTGAGAACTCATTTATTACAAT
*
2841832 AATAAATATTTGAGAACTCATTTATTACAAT
1 AATAAAGATTTGAGAACTCATTTATTACAAT
2841863 AATAAAGATTT
1 AATAAAGATTT
2841874 AAATGATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 18
0.66 0.10 0.25
Matches are distributed among these distances:
22 10 0.21
23 3 0.06
24 3 0.06
25 2 0.04
26 1 0.02
27 1 0.02
28 2 0.04
29 3 0.06
30 3 0.06
31 20 0.42
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.36
Consensus pattern (31 bp):
AATAAAGATTTGAGAACTCATTTATTACAAT
Found at i:2841836 original size:53 final size:53
Alignment explanation
Indices: 2841773--2841877 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
2841763 AGTTTAATTG
*
2841773 GATGAGAATAAATATTTGAGAACTCATTTATTACAATAATAAAGATTTAAATA
1 GATGAAAATAAATATTTGAGAACTCATTTATTACAATAATAAAGATTTAAATA
2841826 GATGAAAATAAATATTTGAGAACTCATTTATTACAATAATAAAGATTTAAAT
1 GATGAAAATAAATATTTGAGAACTCATTTATTACAATAATAAAGATTTAAAT
2841878 GATTTTTTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (53 bp):
GATGAAAATAAATATTTGAGAACTCATTTATTACAATAATAAAGATTTAAATA
Found at i:2841863 original size:28 final size:28
Alignment explanation
Indices: 2841779--2841864 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 28
2841769 ATTGGATGAG
2841779 AATAAATATTTGAGAACTCATTTATTAC
1 AATAAATATTTGAGAACTCATTTATTAC
* * * *
2841807 AATAATAAAGATTT-A-AA-T-A--GATGAA
1 ---AATAAATATTTGAGAACTCATTTATTAC
2841832 AATAAATATTTGAGAACTCATTTATTAC
1 AATAAATATTTGAGAACTCATTTATTAC
2841860 AATAA
1 AATAA
2841865 TAAAGATTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 15
0.64 0.12 0.23
Matches are distributed among these distances:
22 10 0.24
23 1 0.02
24 2 0.05
25 4 0.10
26 1 0.02
27 1 0.02
28 9 0.22
29 2 0.05
30 1 0.02
31 10 0.24
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (28 bp):
AATAAATATTTGAGAACTCATTTATTAC
Found at i:2842187 original size:28 final size:29
Alignment explanation
Indices: 2842120--2842190 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
2842110 AAAATTTGTA
* *
2842120 TATATATATATATATCATGTTTATATTAT
1 TATATATTTATATATCATATTTATATTAT
*
2842149 T-TTTATATTATA-ATCATATTTA-ATATAT
1 TATATAT-TTATATATCATATTTATAT-TAT
2842177 TATATATTTATATA
1 TATATATTTATATA
2842191 AATTTTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.06
28 22 0.65
29 10 0.29
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (29 bp):
TATATATTTATATATCATATTTATATTAT
Found at i:2842274 original size:12 final size:12
Alignment explanation
Indices: 2842245--2842286 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
2842235 TATATATTCG
2842245 TATTATAT-TTA
1 TATTATATCTTA
*
2842256 TATTTATGTCTTA
1 TA-TTATATCTTA
2842269 TATTATATCTTA
1 TATTATATCTTA
*
2842281 AATTAT
1 TATTAT
2842287 CAAATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 2 0.08
12 19 0.73
13 5 0.19
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (12 bp):
TATTATATCTTA
Found at i:2842746 original size:13 final size:11
Alignment explanation
Indices: 2842725--2842759 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
2842715 TTGAAAGATC
2842725 AAATAAATTTT
1 AAATAAATTTT
2842736 ATAATTAAATTTT
1 A-AA-TAAATTTT
2842749 AAATAAATTTT
1 AAATAAATTTT
2842760 TTATAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.41
12 4 0.18
13 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AAATAAATTTT
Found at i:2842765 original size:11 final size:11
Alignment explanation
Indices: 2842726--2842768 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
2842716 TGAAAGATCA
2842726 AATAAATTTTAT
1 AATAAATTTT-T
*
2842738 AATTAAATTTTA
1 AA-TAAATTTTT
2842750 AATAAATTTTT
1 AATAAATTTTT
*
2842761 TATAAATT
1 AATAAATT
2842769 CAAATCGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 15 0.56
12 4 0.15
13 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AATAAATTTTT
Found at i:2846442 original size:16 final size:14
Alignment explanation
Indices: 2846421--2846465 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2846411 ATACAATGAA
2846421 TTAATATTTGATAAAT
1 TTAATATTTG--AAAT
*
2846437 TTAATATTTGAATT
1 TTAATATTTGAAAT
*
2846451 TTAATATTTTAAAT
1 TTAATATTTGAAAT
2846465 T
1 T
2846466 AAGACTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 16 0.62
16 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (14 bp):
TTAATATTTGAAAT
Found at i:2852508 original size:15 final size:15
Alignment explanation
Indices: 2852490--2852519 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2852480 TTAAAAAATA
*
2852490 TTAATTTATTCTTTT
1 TTAAATTATTCTTTT
2852505 TTAAATTATTCTTTT
1 TTAAATTATTCTTTT
2852520 AGATTAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTAAATTATTCTTTT
Found at i:2853045 original size:12 final size:12
Alignment explanation
Indices: 2853010--2853052 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
2853000 TGATTTATTT
2853010 TTAA-ATAAAAA
1 TTAATATAAAAA
2853021 -TAATATAATAAA
1 TTAATATAA-AAA
*
2853033 TTAATATCAAAA
1 TTAATATAAAAA
2853045 TTAATATA
1 TTAATATA
2853053 TATAACTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 3 0.11
11 4 0.15
12 13 0.48
13 7 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (12 bp):
TTAATATAAAAA
Found at i:2856197 original size:2 final size:2
Alignment explanation
Indices: 2856190--2856230 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2856180 TATCTCCCCC
*
2856190 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2856231 TGTTAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2856630 original size:19 final size:17
Alignment explanation
Indices: 2856603--2856641 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2856593 TCAATACATC
2856603 AAATATAAATTATTAAAAT
1 AAATATAAA-T-TTAAAAT
*
2856622 AAATTTAAATTTAAAAT
1 AAATATAAATTTAAAAT
2856639 AAA
1 AAA
2856642 ATATTATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 1 0.05
19 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAAATTTAAAAT
Found at i:2858370 original size:64 final size:64
Alignment explanation
Indices: 2858299--2858429 Score: 253
Period size: 64 Copynumber: 2.0 Consensus size: 64
2858289 TCGATAGTAA
2858299 ATTTTTTATACTCCTAATATTTGGTGCACTTGAAAGATCAACTGATCTCCTAAAAGAAAGAAAT
1 ATTTTTTATACTCCTAATATTTGGTGCACTTGAAAGATCAACTGATCTCCTAAAAGAAAGAAAT
*
2858363 ATTTTTTATACTCCTTATATTTGGTGCACTTGAAAGATCAACTGATCTCCTAAAAGAAAGAAAT
1 ATTTTTTATACTCCTAATATTTGGTGCACTTGAAAGATCAACTGATCTCCTAAAAGAAAGAAAT
2858427 ATT
1 ATT
2858430 GTAATTTCTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (64 bp):
ATTTTTTATACTCCTAATATTTGGTGCACTTGAAAGATCAACTGATCTCCTAAAAGAAAGAAAT
Found at i:2860880 original size:2 final size:2
Alignment explanation
Indices: 2860873--2860910 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2860863 TTGATTCAAC
2860873 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
2860911 CGGTTTAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2872567 original size:42 final size:43
Alignment explanation
Indices: 2872472--2872591 Score: 188
Period size: 42 Copynumber: 2.8 Consensus size: 43
2872462 TTCTTCTCTC
* *
2872472 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCCTGTCT
*
2872515 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCT-CCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCCTGTCT
* *
2872557 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
2872592 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 39 0.55
43 32 0.45
ACGTcount: A:0.08, C:0.47, G:0.03, T:0.42
Consensus pattern (43 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCCTGTCT
Found at i:2875187 original size:20 final size:20
Alignment explanation
Indices: 2875162--2875217 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2875152 ATAAAATTTT
2875162 TTAAATTTAAATTAATTTAA
1 TTAAATTTAAATTAATTTAA
* *
2875182 TTAAATTTAAATTATTTTTAT
1 TTAAATTTAAATTA-ATTTAA
*
2875203 TTAAATAT-AATTAAT
1 TTAAATTTAAATTAAT
2875218 AAAAATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 19 0.61
21 11 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAAATTTAAATTAATTTAA
Found at i:2879979 original size:4 final size:4
Alignment explanation
Indices: 2879970--2880004 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2879960 CCTTCTATCC
2879970 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2880005 TTAATAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2880288 original size:15 final size:17
Alignment explanation
Indices: 2880254--2880286 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2880244 GAATTATGAA
2880254 TATATAATTTTAATATT
1 TATATAATTTTAATATT
*
2880271 TATAT-ATTTTATTATT
1 TATATAATTTTAATATT
2880287 ATTTTTATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATAATTTTAATATT
Found at i:2881634 original size:2 final size:2
Alignment explanation
Indices: 2881627--2881651 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2881617 TTTGCTCTGA
2881627 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
2881652 GAGAGAGAGA
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:2883157 original size:2 final size:2
Alignment explanation
Indices: 2883150--2883179 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2883140 TGTGCACTCC
2883150 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2883180 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2883184 original size:2 final size:2
Alignment explanation
Indices: 2883179--2883204 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2883169 ACACACACAC
2883179 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
2883205 TTGTGTCCAA
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:2884093 original size:2 final size:2
Alignment explanation
Indices: 2884088--2884118 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2884078 AAAAAAAAAA
2884088 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2884119 AAATAATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2890157 original size:2 final size:2
Alignment explanation
Indices: 2890150--2890184 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2890140 TCATCACCAA
2890150 AT 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 AT A
2890185 AACAATTACG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2890340 original size:90 final size:90
Alignment explanation
Indices: 2890187--2890367 Score: 362
Period size: 90 Copynumber: 2.0 Consensus size: 90
2890177 TATATATAAA
2890187 CAATTACGACGGAACTGCAAAATTTTCTAACCAATCCGATTGAATATATATTGCCATAATAGCAT
1 CAATTACGACGGAACTGCAAAATTTTCTAACCAATCCGATTGAATATATATTGCCATAATAGCAT
2890252 ATGGGCCAGTGCCTCCACTGTCCGG
66 ATGGGCCAGTGCCTCCACTGTCCGG
2890277 CAATTACGACGGAACTGCAAAATTTTCTAACCAATCCGATTGAATATATATTGCCATAATAGCAT
1 CAATTACGACGGAACTGCAAAATTTTCTAACCAATCCGATTGAATATATATTGCCATAATAGCAT
2890342 ATGGGCCAGTGCCTCCACTGTCCGG
66 ATGGGCCAGTGCCTCCACTGTCCGG
2890367 C
1 C
2890368 TCAAGCGAGT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (90 bp):
CAATTACGACGGAACTGCAAAATTTTCTAACCAATCCGATTGAATATATATTGCCATAATAGCAT
ATGGGCCAGTGCCTCCACTGTCCGG
Found at i:2892231 original size:13 final size:13
Alignment explanation
Indices: 2892215--2892241 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2892205 TTAACGATCG
2892215 TGATTAATAATAA
1 TGATTAATAATAA
2892228 TGATTAATAATAA
1 TGATTAATAATAA
2892241 T
1 T
2892242 AATCCCAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TGATTAATAATAA
Found at i:2892263 original size:19 final size:19
Alignment explanation
Indices: 2892241--2892320 Score: 99
Period size: 19 Copynumber: 4.2 Consensus size: 19
2892231 TTAATAATAA
2892241 TAATCCCAGAAATAATGAT
1 TAATCCCAGAAATAATGAT
*
2892260 TAATCCCAGTAATAATGAT
1 TAATCCCAGAAATAATGAT
***
2892279 TAATAATA-ATAATAATGAT
1 TAATCCCAGA-AATAATGAT
*
2892298 TAATCCCAGTAATAATGAT
1 TAATCCCAGAAATAATGAT
2892317 TAAT
1 TAAT
2892321 AATAATAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (19 bp):
TAATCCCAGAAATAATGAT
Found at i:2892302 original size:38 final size:38
Alignment explanation
Indices: 2892251--2892330 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
2892241 TAATCCCAGA
2892251 AATAATGATTAATCCCAGTAATAATGATTAATAATAAT
1 AATAATGATTAATCCCAGTAATAATGATTAATAATAAT
2892289 AATAATGATTAATCCCAGTAATAATGATTAATAATAAT
1 AATAATGATTAATCCCAGTAATAATGATTAATAATAAT
2892327 AATA
1 AATA
2892331 GGCTTGTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (38 bp):
AATAATGATTAATCCCAGTAATAATGATTAATAATAAT
Found at i:2892329 original size:19 final size:19
Alignment explanation
Indices: 2892269--2892330 Score: 88
Period size: 19 Copynumber: 3.3 Consensus size: 19
2892259 TTAATCCCAG
2892269 TAATAATGATTAATAATAA
1 TAATAATGATTAATAATAA
*** *
2892288 TAATAATGATTAATCCCAG
1 TAATAATGATTAATAATAA
2892307 TAATAATGATTAATAATAA
1 TAATAATGATTAATAATAA
2892326 TAATA
1 TAATA
2892331 GGCTTGTTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.35
Consensus pattern (19 bp):
TAATAATGATTAATAATAA
Found at i:2900075 original size:20 final size:21
Alignment explanation
Indices: 2900046--2900084 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2900036 TCTGATTTTG
*
2900046 TTTTATAAAATAAT-TTTATA
1 TTTTAAAAAATAATATTTATA
2900066 TTTTAAAAAATAATATTTA
1 TTTTAAAAAATAATATTTA
2900085 ATAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAAAAATAATATTTATA
Found at i:2900405 original size:25 final size:24
Alignment explanation
Indices: 2900377--2900453 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
2900367 TGAACACGAG
2900377 AAAATATCATATCAAGTACTTTAAA
1 AAAATATCATATCAAGTA-TTTAAA
2900402 AAAATA--A-A-CAGAGTATATTACGAA
1 AAAATATCATATCA-AGTAT-TTA--AA
2900426 AAAATATCATATCAAGTATTTAAA
1 AAAATATCATATCAAGTATTTAAA
2900450 AAAA
1 AAAA
2900454 ATAAGCAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
21 3 0.07
22 8 0.18
23 1 0.02
24 14 0.32
25 6 0.14
26 4 0.09
27 6 0.14
28 2 0.05
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.27
Consensus pattern (24 bp):
AAAATATCATATCAAGTATTTAAA
Found at i:2900430 original size:49 final size:49
Alignment explanation
Indices: 2900372--2900470 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
2900362 AAGATTGAAC
* *
2900372 ACGAGAAAATATCATATCAAGTACTTT-AAAAAAATAAACAGAGTATATT
1 ACGAAAAAATATCATATCAAGTA-TTTAAAAAAAATAAACAAAGTATATT
*
2900421 ACGAAAAAATATCATATCAAGTATTTAAAAAAAATAAGCAAAGTATATT
1 ACGAAAAAATATCATATCAAGTATTTAAAAAAAATAAACAAAGTATATT
2900470 A
1 A
2900471 ATCTCATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 3 0.07
49 43 0.93
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (49 bp):
ACGAAAAAATATCATATCAAGTATTTAAAAAAAATAAACAAAGTATATT
Found at i:2900454 original size:25 final size:25
Alignment explanation
Indices: 2900377--2900456 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
2900367 TGAACACGAG
2900377 AAAATATCATATCAAGTACTTT-AAA
1 AAAATATCATATCAAGTA-TTTAAAA
*
2900402 AAAATA--A-A-CAGAGTATATTACGAA
1 AAAATATCATATCA-AGTAT-TTA-AAA
2900426 AAAATATCATATCAAGTATTTAAAA
1 AAAATATCATATCAAGTATTTAAAA
2900451 AAAATA
1 AAAATA
2900457 AGCAAAGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
21 3 0.07
22 7 0.16
23 1 0.02
24 8 0.18
25 14 0.31
26 4 0.09
27 6 0.13
28 2 0.04
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (25 bp):
AAAATATCATATCAAGTATTTAAAA
Found at i:2900515 original size:22 final size:23
Alignment explanation
Indices: 2900490--2900534 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2900480 TAAATAAAAA
2900490 AAATTTAAATA-TATAAATGAAT
1 AAATTTAAATACTATAAATGAAT
2900512 AAATTTAAATACTTATAAATGAA
1 AAATTTAAATAC-TATAAATGAA
2900535 AATTAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
24 10 0.48
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (23 bp):
AAATTTAAATACTATAAATGAAT
Found at i:2900929 original size:2 final size:2
Alignment explanation
Indices: 2900922--2900946 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2900912 CCACTACCAT
2900922 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2900947 GCACGTGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2903182 original size:5 final size:6
Alignment explanation
Indices: 2903169--2903197 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2903159 TCTTAAGGTC
2903169 TATTTT TA-TTT TATTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT
2903198 GAGGTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:2904763 original size:32 final size:33
Alignment explanation
Indices: 2904720--2904791 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
2904710 AACAAATGTA
*
2904720 TATTTAGATAATTATA-CTTACAAATAGA-TATT
1 TATTTAAATAATTATATCTTACAAATA-ATTATT
*
2904752 TATTTAAATAATTATATTTTACAAATAATTATT
1 TATTTAAATAATTATATCTTACAAATAATTATT
2904785 TATTTAA
1 TATTTAA
2904792 TCATAAATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (33 bp):
TATTTAAATAATTATATCTTACAAATAATTATT
Found at i:2906587 original size:2 final size:2
Alignment explanation
Indices: 2906580--2906606 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2906570 ACAATTAATC
2906580 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
2906607 GGTCTTTGAT
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:2913647 original size:25 final size:25
Alignment explanation
Indices: 2913605--2913664 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
2913595 AAATATTTTA
* *
2913605 TTTAATATATTTATTTTACATATATT
1 TTTAAAAT-TTTATTTTACATAAATT
*
2913631 TTTAAAATTTTATTTTACTTAAATT
1 TTTAAAATTTTATTTTACATAAATT
2913656 TTTAAAATT
1 TTTAAAATT
2913665 CAATTGAGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 24 0.77
26 7 0.23
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTAAAATTTTATTTTACATAAATT
Done.