Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 21 of 25
Found at i:3075798 original size:507 final size:506
Alignment explanation
Indices: 3074839--3075837 Score: 1724
Period size: 507 Copynumber: 2.0 Consensus size: 506
3074829 ATATATATAT
3074839 ATATATATATATATATAAACACACACATAGCAATGGAGTCGTGGGCCATGGGATTTTCTTCTATG
1 ATATATATATATATATAAACACACACATAGCAATGGAGTCGTGGGCCATGGGATTTTCTTCTATG
3074904 AAAGTGATTTATTTTCTCACTCACTTTTCCAAAACATTCTTATAAAAGGAAATAGTGAGGAAGGT
66 AAAGTGATTTATTTTCTCACTCACTTTTCCAAAACATTCTTATAAAAGGAAATAGTGAGGAAGGT
*
3074969 GAGTGAAAGAACATTTATTCTTTTTCAAGCACTTGTCATTTGTATTAGAAGAAATATTTAATAGA
131 GAGTGAAAGAACATTTATTCATTTTCAAGCACTTGTCATTTGTATTAGAAGAAATATTTAATAGA
* * *
3075034 AGTCTCAAACTAAAAATATTTTGTAATTCAATATTTAATTTAATTAATTTATGTAGTTATTTTTA
196 AGTCTCAAACTAAAAATATTTTATAATTCAATATGTAATTTAATTAATTTATATAGTTATTTTTA
* *
3075099 AAAAATAGTATTTAGTGAGTTTGAATTCAATTGTAAAAAAAAAAAATATTCTCGACAATTCTTTA
261 AAAAATAGTATTTAGTGAGTTTGAATTCAATTGT--AAAAAAAAAATATCCCCGACAATTCTTTA
3075164 TACTATAATTTTATAATTATGCTTAATTGGATTAAAAAAATTGATACATATAAAAAAAAAAACCT
324 TACTATAATTTTATAATTATGCTTAATTGGATTAAAAAAATTGATACATATAAAAAAAAAAACCT
*
3075229 TAGTTGCCAATATTGCAATTAAGAAGTAAGTCGTCAATGTTGTAAACCTATTAAATTTTTCCTTA
389 TAGTTGCCAATATTGCAATTAAGAAGTAAGTCGTCAATGTTGTAAACCTATTAAAATTTTCCTTA
3075294 ATCTAACTAAATACAATTG-A-ATTATAATATAAAAGTCCGGAAAAAGAATAC
454 ATCTAACTAAATACAATTGAAGATTATAATATAAAAGTCCGGAAAAAGAATAC
*
3075345 ATATATATATATATATAAACACACACATAGCAATGGAGTCGTGGGCCATGGGAATTTTCTTTTAT
1 ATATATATATATATATAAACACACACATAGCAATGGAGTCGTGGGCCATGGG-ATTTTCTTCTAT
*
3075410 GAAAGTGATTTATTTTCTCACTCACTTTTCCAAAACATTCTTATTAAAGGAAATAGTGAGGAAGG
65 GAAAGTGATTTATTTTCTCACTCACTTTTCCAAAACATTCTTATAAAAGGAAATAGTGAGGAAGG
3075475 TGAGTGAAAGAACATTTATTCATTTTCAAGCACTTGTCATTTGTATTAGAAGAAATATTTAATAG
130 TGAGTGAAAGAACATTTATTCATTTTCAAGCACTTGTCATTTGTATTAGAAGAAATATTTAATAG
* *
3075540 AAGTCTCAAACTAAAAATATTTTATAATTCAATGTGTAATTTAATTGATTTATATAGTTATTTTT
195 AAGTCTCAAACTAAAAATATTTTATAATTCAATATGTAATTTAATTAATTTATATAGTTATTTTT
* *
3075605 AAAAAAT-GATATTTAGTGAGTTTGAATTCAA-T-T-ATAAAAAAA-ATCCCCGATAATTCTTTA
260 AAAAAATAG-TATTTAGTGAGTTTGAATTCAATTGTAAAAAAAAAATATCCCCGACAATTCTTTA
*
3075665 TAGTATAATTTTATAATTATGCTTAATTGGATTAAAAAAATTGATACATATAGAAAAAAAAAAAA
324 TACTATAATTTTATAATTATGCTTAATTGGATTAAAAAAATTGATACATAT------AAAAAAAA
3075730 AAACCTTAGTTGCCAATATTGCAATTAAGAAGTAAGTCGTCAATGTTGTAAACCTATTAAAATTT
383 AAACCTTAGTTGCCAATATTGCAATTAAGAAGTAAGTCGTCAATGTTGTAAACCTATTAAAATTT
3075795 TCCTTAATCTAACTAAATACAATTGAAGGATTATAATATAAAA
448 TCCTTAATCTAACTAAATACAATTGAA-GATTATAATATAAAA
3075838 AAATTGTAAA
Statistics
Matches: 468, Mismatches: 14, Indels: 18
0.94 0.03 0.04
Matches are distributed among these distances:
501 65 0.14
502 8 0.02
505 1 0.00
506 54 0.12
507 325 0.69
508 1 0.00
510 14 0.03
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (506 bp):
ATATATATATATATATAAACACACACATAGCAATGGAGTCGTGGGCCATGGGATTTTCTTCTATG
AAAGTGATTTATTTTCTCACTCACTTTTCCAAAACATTCTTATAAAAGGAAATAGTGAGGAAGGT
GAGTGAAAGAACATTTATTCATTTTCAAGCACTTGTCATTTGTATTAGAAGAAATATTTAATAGA
AGTCTCAAACTAAAAATATTTTATAATTCAATATGTAATTTAATTAATTTATATAGTTATTTTTA
AAAAATAGTATTTAGTGAGTTTGAATTCAATTGTAAAAAAAAAATATCCCCGACAATTCTTTATA
CTATAATTTTATAATTATGCTTAATTGGATTAAAAAAATTGATACATATAAAAAAAAAAACCTTA
GTTGCCAATATTGCAATTAAGAAGTAAGTCGTCAATGTTGTAAACCTATTAAAATTTTCCTTAAT
CTAACTAAATACAATTGAAGATTATAATATAAAAGTCCGGAAAAAGAATAC
Found at i:3079454 original size:209 final size:209
Alignment explanation
Indices: 3079090--3079482 Score: 644
Period size: 209 Copynumber: 1.9 Consensus size: 209
3079080 CGTCTTAAAA
* * * * * *
3079090 TTTAATTTATATATATTACATGAACCAGCATATATGTGTTTTTAATATGAGATCTGACACCAACC
1 TTTAATTTATATATACTACATGAACCACCATATATATATTTCTAATATGAGATCCGACACCAACC
* * *
3079155 ACTCTTTTTTACTTTAAGTAAATATTTTGTGATTAATTTTTAATTTATTATAAATATTAATTATA
66 ACTCTTTTCTACTTTAAGTAAATATTTTATAATTAATTTTTAATTTATTATAAATATTAATTATA
*
3079220 TAATATATTTTATACATCGTATATTTAAATATAATAAATTATATAAATATATATTACATGTATAC
131 TAATATATTTTATACATCATATATTTAAATATAATAAATTATATAAATATATATTACATGTATAC
3079285 TACATGAATCAATT
196 TACATGAATCAATT
* * * *
3079299 TTTAATTTATATATACTACATGAATCACCCTGTATATATTTCTAATATGAGATCCGACACCAACT
1 TTTAATTTATATATACTACATGAACCACCATATATATATTTCTAATATGAGATCCGACACCAACC
3079364 ACTCTTTTCTACTTTTAAGTAAATATTTTATAATTAATTTTTAATTTATTATAAATATTAATTAT
66 ACTCTTTTCTAC-TTTAAGTAAATATTTTATAATTAATTTTTAATTTATTATAAATATTAATTAT
3079429 ATAATATA-TTTATACATCATATATTTAAATATAATAAATTATATAAATATATAT
130 ATAATATATTTTATACATCATATATTTAAATATAATAAATTATATAAATATATAT
3079483 ATTTAATATT
Statistics
Matches: 169, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
209 111 0.66
210 58 0.34
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (209 bp):
TTTAATTTATATATACTACATGAACCACCATATATATATTTCTAATATGAGATCCGACACCAACC
ACTCTTTTCTACTTTAAGTAAATATTTTATAATTAATTTTTAATTTATTATAAATATTAATTATA
TAATATATTTTATACATCATATATTTAAATATAATAAATTATATAAATATATATTACATGTATAC
TACATGAATCAATT
Found at i:3079482 original size:10 final size:10
Alignment explanation
Indices: 3079447--3079483 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
3079437 TTTATACATC
*
3079447 ATATATTTAA
1 ATATATATAA
3079457 ATATA-ATAA
1 ATATATATAA
3079466 AT-TATATAA
1 ATATATATAA
3079475 ATATATATA
1 ATATATATA
3079484 TTTAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
8 2 0.08
9 11 0.46
10 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATAA
Found at i:3079482 original size:22 final size:22
Alignment explanation
Indices: 3079423--3079483 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 22
3079413 TATAAATATT
*
3079423 AATTATAT-AATATAT-TTATA
1 AATTATATAAATATATATAATA
* * ** *
3079443 CATCATATATTTAAATATAATA
1 AATTATATAAATATATATAATA
3079465 AATTATATAAATATATATA
1 AATTATATAAATATATATA
3079484 TTTAATATTT
Statistics
Matches: 28, Mismatches: 11, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
20 6 0.21
21 4 0.14
22 18 0.64
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTATATAAATATATATAATA
Found at i:3079808 original size:14 final size:14
Alignment explanation
Indices: 3079775--3079808 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3079765 TAATGCATTC
*
3079775 ATATTAAAAATAAT
1 ATATTTAAAATAAT
3079789 ATATTTAAAATAAT
1 ATATTTAAAATAAT
3079803 ATATTT
1 ATATTT
3079809 TATTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATTTAAAATAAT
Found at i:3080225 original size:10 final size:10
Alignment explanation
Indices: 3080210--3080243 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3080200 AAGAAATCGA
3080210 AAATATTATT
1 AAATATTATT
3080220 AAATATT-TT
1 AAATATTATT
3080229 AAAATATTATT
1 -AAATATTATT
3080240 AAAT
1 AAAT
3080244 TCATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAATATTATT
Found at i:3080744 original size:20 final size:20
Alignment explanation
Indices: 3080694--3080747 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
3080684 AATAAATATT
*
3080694 TTAATTTTATA-AAAAATAA
1 TTAATTTTAAATAAAAATAA
* **
3080713 TTAACTAAAAATAAAAATAA
1 TTAATTTTAAATAAAAATAA
3080733 TTAATTTTAAATAAA
1 TTAATTTTAAATAAA
3080748 GATATATATA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAATTTTAAATAAAAATAA
Found at i:3081339 original size:11 final size:11
Alignment explanation
Indices: 3081323--3081353 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
3081313 TCATCTTTTA
3081323 ATTTATTAAAT
1 ATTTATTAAAT
3081334 ATTTATTAAAT
1 ATTTATTAAAT
3081345 ATTATATTA
1 ATT-TATTA
3081354 TTAAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTATTAAAT
Found at i:3081453 original size:3 final size:3
Alignment explanation
Indices: 3081447--3081489 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
3081437 GCTCAACAAC
*
3081447 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3081490 TTATTTACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3081788 original size:24 final size:25
Alignment explanation
Indices: 3081754--3081819 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
3081744 ATACAATTAA
3081754 TTAATATTAAATTTATTATTAT-ATT
1 TTAAT-TTAAATTTATTATTATCATT
3081779 TTAATTTAAAATTT-TT-TTATCATT
1 TTAATTT-AAATTTATTATTATCATT
*
3081803 ATAATTT-AATTTCATTA
1 TTAATTTAAATTT-ATTA
3081820 ATTTGTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 5 0.14
23 4 0.11
24 15 0.43
25 11 0.31
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAATTTAAATTTATTATTATCATT
Found at i:3082250 original size:20 final size:20
Alignment explanation
Indices: 3082225--3082264 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3082215 TAATTTAATT
3082225 ATAAAAATATAAAAA-TATTA
1 ATAAAAATA-AAAAATTATTA
3082245 ATAAAAATAAAAAATTATTA
1 ATAAAAATAAAAAATTATTA
3082265 TTTTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAAAATAAAAAATTATTA
Found at i:3082310 original size:6 final size:6
Alignment explanation
Indices: 3082299--3082323 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3082289 CGATTTGAAC
3082299 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
3082324 TTTAAATTCG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:3082777 original size:18 final size:18
Alignment explanation
Indices: 3082751--3082786 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3082741 TATTCTTTTT
*
3082751 TTTTGTAAAATTTAAAAA
1 TTTTATAAAATTTAAAAA
3082769 TTTTATAAAATTTAAAAA
1 TTTTATAAAATTTAAAAA
3082787 CGTATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTTATAAAATTTAAAAA
Found at i:3082990 original size:15 final size:14
Alignment explanation
Indices: 3082970--3083023 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
3082960 TGATCTCAAA
3082970 ATTTAATTTATATTT
1 ATTTAATTT-TATTT
3082985 ATTTAATTTT-TTAT
1 ATTTAATTTTATT-T
*
3082999 AATTTAATTTTATAT
1 -ATTTAATTTTATTT
*
3083014 ATTAAATTTT
1 ATTTAATTTT
3083024 TAGACAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 2 0.06
14 11 0.32
15 20 0.59
16 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTAATTTTATTT
Found at i:3083920 original size:24 final size:24
Alignment explanation
Indices: 3083867--3083921 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
3083857 ATTATTATTT
* *
3083867 AAATAA-TAAAAATATTTATATAT
1 AAATAATTAAAAATATTAATATAA
** *
3083890 ATTTAATTATAAATATTAATATAA
1 AAATAATTAAAAATATTAATATAA
3083914 AAATAATT
1 AAATAATT
3083922 TTTATATTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATAATTAAAAATATTAATATAA
Found at i:3084242 original size:21 final size:22
Alignment explanation
Indices: 3084218--3084259 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3084208 CTATATTATA
*
3084218 ATTTTTTAAAATTTAA-AATTT
1 ATTTTTTAAAAATTAATAATTT
3084239 ATTTTTTAAAAATTAATAATT
1 ATTTTTTAAAAATTAATAATT
3084260 GATAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTTAAAAATTAATAATTT
Found at i:3084713 original size:3 final size:3
Alignment explanation
Indices: 3084705--3084751 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
3084695 AACATAATCT
*
3084705 ATA ATA ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3084752 TAGACAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3084997 original size:29 final size:30
Alignment explanation
Indices: 3084965--3085023 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
3084955 ATAAACAAGA
* *
3084965 TTAATAATTTTTTTTATATTTTATT-TATT
1 TTAATAATTTTTTTAATATTTAATTATATT
*
3084994 TTAATTATTTTTTTAATATTTAATTATATT
1 TTAATAATTTTTTTAATATTTAATTATATT
3085024 ATGTCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (30 bp):
TTAATAATTTTTTTAATATTTAATTATATT
Found at i:3085005 original size:19 final size:20
Alignment explanation
Indices: 3084978--3085023 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3084968 ATAATTTTTT
*
3084978 TTATATTTTATTTAT-TTTAA
1 TTATATTTT-TTAATATTTAA
3084998 TTAT-TTTTTTAATATTTAA
1 TTATATTTTTTAATATTTAA
3085017 TTATATT
1 TTATATT
3085024 ATGTCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATATTTTTTAATATTTAA
Found at i:3085134 original size:4 final size:4
Alignment explanation
Indices: 3085127--3085167 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
3085117 AAGAAAGAGG
*
3085127 ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATTT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
3085168 GGTGTGTGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
4 31 0.94
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
ATGT
Found at i:3085153 original size:18 final size:18
Alignment explanation
Indices: 3085130--3085166 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3085120 AAAGAGGATG
3085130 TATGTATGTATGTATGTA
1 TATGTATGTATGTATGTA
*
3085148 TATGTATGTATTTATGTA
1 TATGTATGTATGTATGTA
3085166 T
1 T
3085167 GGGTGTGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (18 bp):
TATGTATGTATGTATGTA
Found at i:3090258 original size:20 final size:19
Alignment explanation
Indices: 3090217--3090275 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
3090207 ATATAATTAT
*
3090217 ATTATTAAATTTAATAATAAA
1 ATTATTAAATAT-ATAA-AAA
*
3090238 TTTATTAAATATATAAAAA
1 ATTATTAAATATATAAAAA
*
3090257 ATTATAAAATTATATAAAA
1 ATTATTAAA-TATATAAAA
3090276 TTAATTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 10 0.30
20 13 0.39
21 10 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTATTAAATATATAAAAA
Found at i:3090276 original size:18 final size:19
Alignment explanation
Indices: 3090233--3090278 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3090223 AAATTTAATA
* *
3090233 ATAAATTTATTAAATATAT
1 ATAAAATTATAAAATATAT
*
3090252 AAAAAATTATAAAAT-TAT
1 ATAAAATTATAAAATATAT
3090270 ATAAAATTA
1 ATAAAATTA
3090279 ATTTAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAAATTATAAAATATAT
Found at i:3090477 original size:10 final size:10
Alignment explanation
Indices: 3090448--3090483 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
3090438 TTTAGCAATG
3090448 TTATTAAATA
1 TTATTAAATA
*
3090458 TTATT-GATA
1 TTATTAAATA
3090467 TTATTAAATA
1 TTATTAAATA
3090477 TTATTAA
1 TTATTAA
3090484 TGTGATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (10 bp):
TTATTAAATA
Found at i:3092144 original size:15 final size:16
Alignment explanation
Indices: 3092126--3092161 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3092116 CTATATATTA
*
3092126 TATATATTATA-AATT
1 TATATATTACATAATT
3092141 TATATATTACATAATT
1 TATATATTACATAATT
3092157 TATAT
1 TATAT
3092162 TATATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTACATAATT
Found at i:3092173 original size:17 final size:16
Alignment explanation
Indices: 3092123--3092184 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
3092113 CTTCTATATA
*
3092123 TTATATATATTATAAAT
1 TTATATATA-TAAAAAT
*
3092140 TTATATAT-TACATAAT
1 TTATATATATA-AAAAT
3092156 TTATATTATATAAAAAT
1 TTATA-TATATAAAAAT
*
3092173 TAATCATATATA
1 TTAT-ATATATA
3092185 GTATAAACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 2 0.05
16 8 0.22
17 24 0.65
18 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATATATATAAAAAT
Found at i:3094137 original size:19 final size:18
Alignment explanation
Indices: 3094111--3094146 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3094101 AATAATTAAA
*
3094111 AAATTAAATTAAAATTAT
1 AAATTAAAATAAAATTAT
3094129 AAATATAAAATAAAATTA
1 AAAT-TAAAATAAAATTA
3094147 AAAGTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTAAAATAAAATTAT
Found at i:3095199 original size:2 final size:2
Alignment explanation
Indices: 3095192--3095227 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3095182 TCTCTGCCGA
3095192 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
3095228 GACTATGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3095506 original size:2 final size:2
Alignment explanation
Indices: 3095499--3095555 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
3095489 TCTTATCTTT
* * *
3095499 TA TA TA TA CA TA TA TA TA -A TC T- TA TA -A TA TA TA TC T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3095537 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3095556 GTATCAATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
1 4 0.09
2 43 0.91
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3095530 original size:15 final size:16
Alignment explanation
Indices: 3095508--3095546 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
3095498 TTATATATAC
3095508 ATATATATAATCTTAT
1 ATATATATAATCTTAT
3095524 A-ATATAT-ATCTTAT
1 ATATATATAATCTTAT
3095538 ATATATATA
1 ATATATATA
3095547 TATATATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.38
15 12 0.57
16 1 0.05
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATATAATCTTAT
Found at i:3095549 original size:17 final size:15
Alignment explanation
Indices: 3095508--3095547 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
3095498 TTATATATAC
3095508 ATATATATA-ATCTT
1 ATATATATATATCTT
3095522 ATA-ATATATATCTT
1 ATATATATATATCTT
3095536 ATATATATATAT
1 ATATATATATAT
3095548 ATATATATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.21
14 11 0.46
15 8 0.33
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATATATCTT
Found at i:3097243 original size:20 final size:20
Alignment explanation
Indices: 3097218--3097262 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3097208 TATAAATTAA
3097218 AAATTATAATTT-TTTAAATT
1 AAATTA-AATTTATTTAAATT
*
3097238 AAATTAAATTTATTTTAATT
1 AAATTAAATTTATTTAAATT
*
3097258 TAATT
1 AAATT
3097263 TTTTATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATTAAATTTATTTAAATT
Found at i:3097389 original size:12 final size:12
Alignment explanation
Indices: 3097368--3097400 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3097358 TTTAATTTAA
3097368 ATAT-ATTTTTT
1 ATATAATTTTTT
3097379 ATATAATTTTTT
1 ATATAATTTTTT
*
3097391 ATTTAATTTT
1 ATATAATTTT
3097401 AATACCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATATAATTTTTT
Found at i:3100018 original size:14 final size:14
Alignment explanation
Indices: 3099973--3100025 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
3099963 TTTAATAATT
*
3099973 ATATAAATATAAAATA
1 ATATAAAT-TTAAA-A
3099989 ATATAATATTTAAAA
1 ATATAA-ATTTAAAA
* *
3100004 ATTTAAATTTTAAA
1 ATATAAATTTAAAA
3100018 ATATAAAT
1 ATATAAAT
3100026 ATAATATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 14 0.44
15 6 0.19
16 10 0.31
17 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAAATTTAAAA
Found at i:3100111 original size:19 final size:17
Alignment explanation
Indices: 3100069--3100127 Score: 68
Period size: 16 Copynumber: 3.4 Consensus size: 17
3100059 ATATTTTAAA
3100069 TATAATTTTATTATATT
1 TATAATTTTATTATATT
3100086 TAT-ATTTTATTATATT
1 TATAATTTTATTATATT
3100102 TATTAAATTTT-TATATATT
1 TA-T-AATTTTAT-TATATT
*
3100121 TAAAATT
1 TATAATT
3100128 ATTAAATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
16 15 0.41
17 8 0.22
18 1 0.03
19 13 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATAATTTTATTATATT
Found at i:3100111 original size:25 final size:26
Alignment explanation
Indices: 3100075--3100142 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
3100065 TAAATATAAT
* *
3100075 TTTATTATATTTATATTTTA-TTATA
1 TTTATTAAATTTATATTTTATTTAAA
* *
3100100 TTTATTAAATTTTTA-TATATTTAAA
1 TTTATTAAATTTATATTTTATTTAAA
* *
3100125 ATTATTAAATTTAAATTT
1 TTTATTAAATTTATATTT
3100143 AAATTTTTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
24 3 0.09
25 29 0.88
26 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTATTAAATTTATATTTTATTTAAA
Found at i:3100123 original size:16 final size:16
Alignment explanation
Indices: 3100074--3100142 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 16
3100064 TTAAATATAA
*
3100074 TTTTATTATATTTATATT
1 TTTTA-TATATTTA-AAT
*
3100092 TTATTATATTTATTAAAT
1 TT-TTATATAT-TTAAAT
3100110 TTTTATATATTTAAAAT
1 TTTTATATATTT-AAAT
*
3100127 TATTA-A-ATTTAAAT
1 TTTTATATATTTAAAT
3100141 TT
1 TT
3100143 AAATTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
14 5 0.12
15 4 0.09
16 3 0.07
17 15 0.35
18 10 0.23
19 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTATATATTTAAAT
Found at i:3100228 original size:17 final size:16
Alignment explanation
Indices: 3100196--3100262 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
3100186 ATTATTTATG
3100196 TTATATTTATATATAT
1 TTATATTTATATATAT
3100212 TTATATATTAT-TAATAT
1 TTATAT-TTATAT-ATAT
* *
3100229 TTATCA-TCATAGATAT
1 TTAT-ATTTATATATAT
*
3100245 TTATTATTT-TATTTAT
1 TTA-TATTTATATATAT
3100261 TT
1 TT
3100263 TTAAAATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
16 25 0.62
17 14 0.35
18 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (16 bp):
TTATATTTATATATAT
Found at i:3100737 original size:32 final size:29
Alignment explanation
Indices: 3100667--3100767 Score: 98
Period size: 32 Copynumber: 3.3 Consensus size: 29
3100657 TTAATTCAAA
*
3100667 AAATTTT-ATATTTATAATTT-TATATTAT
1 AAATTTTAATATTTAAAATTTATATA-TAT
**
3100695 AAATAATAATATTTAAAATTATATAATCATAT
1 AAATTTTAATATTTAAAATT-TAT-AT-ATAT
3100727 AAATTTTAATATATTAATAATTTATATTATAT
1 AAATTTTAATAT-TTAA-AATTTATA-TATAT
3100759 AAATTTTAA
1 AAATTTTAA
3100768 AATATTTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
28 5 0.08
29 11 0.18
30 1 0.02
31 1 0.02
32 29 0.48
33 9 0.15
34 4 0.07
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (29 bp):
AAATTTTAATATTTAAAATTTATATATAT
Found at i:3100746 original size:18 final size:19
Alignment explanation
Indices: 3100723--3100773 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 19
3100713 TTATATAATC
3100723 ATATAAATTTTAATATATT
1 ATATAAATTTTAATATATT
3100742 A-AT-AA--TT--TATATT
1 ATATAAATTTTAATATATT
*
3100755 ATATAAATTTTAAAATATT
1 ATATAAATTTTAATATATT
3100774 TTTATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 12
0.66 0.03 0.32
Matches are distributed among these distances:
13 7 0.28
14 2 0.08
15 4 0.16
17 4 0.16
18 2 0.08
19 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATAAATTTTAATATATT
Found at i:3100772 original size:14 final size:14
Alignment explanation
Indices: 3100667--3100772 Score: 54
Period size: 14 Copynumber: 7.0 Consensus size: 14
3100657 TTAATTCAAA
*
3100667 AAATTTT-ATATTT
1 AAATTTTAATATAT
3100680 ATAATTTT-ATATTAT
1 A-AATTTTAATA-TAT
** *
3100695 AAATAATAATATTT
1 AAATTTTAATATAT
3100709 AAAATTATATAATCATAT
1 -AAATT-T-TAAT-ATAT
3100727 AAATTTTAATATATT
1 AAATTTTAATATA-T
*
3100742 AATAATTTATATTATAT
1 -A-AATTT-TAATATAT
*
3100759 AAATTTTAAAATAT
1 AAATTTTAATATAT
3100773 TTTTATATTT
Statistics
Matches: 72, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
13 1 0.01
14 24 0.33
15 20 0.28
16 3 0.04
17 15 0.21
18 9 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATTTTAATATAT
Found at i:3100773 original size:32 final size:33
Alignment explanation
Indices: 3100723--3100790 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
3100713 TTATATAATC
*
3100723 ATATAAATTTTAATATATTAATA-ATTTATATT
1 ATATAAATTTTAAAATATTAATATATTTATATT
**
3100755 ATATAAATTTTAAAATATTTTTATATTTATATT
1 ATATAAATTTTAAAATATTAATATATTTATATT
3100788 ATA
1 ATA
3100791 ATTATCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 20 0.62
33 12 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
ATATAAATTTTAAAATATTAATATATTTATATT
Found at i:3100808 original size:24 final size:22
Alignment explanation
Indices: 3100780--3100826 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
3100770 TATTTTTATA
3100780 TTTATATTATAATTATCTTAATTT
1 TTTATATTATAATTAT-TT-ATTT
*
3100804 TTTATATTTTAATTATTTATTT
1 TTTATATTATAATTATTTATTT
3100826 T
1 T
3100827 ATAGTTACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 2 0.09
24 15 0.68
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATATTATAATTATTTATTT
Found at i:3101276 original size:22 final size:22
Alignment explanation
Indices: 3101251--3101298 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3101241 AAATCATATT
*
3101251 TTAAAATAAAAAATTATAACTA
1 TTAAAATAAAAAATTAAAACTA
* * *
3101273 TTAAAATTAAAATTTAAAATTA
1 TTAAAATAAAAAATTAAAACTA
3101295 TTAA
1 TTAA
3101299 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAAATAAAAAATTAAAACTA
Found at i:3101788 original size:26 final size:25
Alignment explanation
Indices: 3101731--3101793 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
3101721 TTATTAAAAT
*
3101731 AAATTCAT-AAATATATCTTTTTAA
1 AAATTAATAAAATATATCTTTTTAA
* *
3101755 AATTTTAATAAAATATATTTTATTTAA
1 AA-ATTAATAAAATATATCTT-TTTAA
*
3101782 AAATTAAAAAAA
1 AAATTAATAAAA
3101794 ATTACTTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 2 0.06
25 4 0.13
26 18 0.58
27 7 0.23
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATTAATAAAATATATCTTTTTAA
Found at i:3103906 original size:15 final size:16
Alignment explanation
Indices: 3103882--3103918 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
3103872 TTTTATTATA
3103882 ATTATA-TTTAA-AAT
1 ATTATATTTTAATAAT
3103896 ATTATATTTTAATAAT
1 ATTATATTTTAATAAT
3103912 -TTATATT
1 ATTATATT
3103919 ATATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 12 0.57
16 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATATTTTAATAAT
Found at i:3103960 original size:9 final size:8
Alignment explanation
Indices: 3103948--3103990 Score: 50
Period size: 9 Copynumber: 4.9 Consensus size: 8
3103938 TATATCGGTA
3103948 TTATATTT
1 TTATATTT
3103956 ATTATATATT
1 -TTATAT-TT
3103966 TTATATTT
1 TTATATTT
3103974 TTATTATTTT
1 TTA-TA-TTT
3103984 TTATATT
1 TTATATT
3103991 ATATAATTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.23
9 16 0.52
10 8 0.26
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTATATTT
Found at i:3103969 original size:18 final size:18
Alignment explanation
Indices: 3103948--3103990 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3103938 TATATCGGTA
3103948 TTATATTTATTA-TATATT
1 TTATATTT-TTATTATATT
*
3103966 TTATATTTTTATTATTTT
1 TTATATTTTTATTATATT
3103984 TTATATT
1 TTATATT
3103991 ATATAATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATATTTTTATTATATT
Found at i:3104113 original size:35 final size:35
Alignment explanation
Indices: 3104067--3104142 Score: 152
Period size: 35 Copynumber: 2.2 Consensus size: 35
3104057 TAACACCTAG
3104067 CTAAATATTAGAATTGTTTATGAGCAGGTATCCAT
1 CTAAATATTAGAATTGTTTATGAGCAGGTATCCAT
3104102 CTAAATATTAGAATTGTTTATGAGCAGGTATCCAT
1 CTAAATATTAGAATTGTTTATGAGCAGGTATCCAT
3104137 CTAAAT
1 CTAAAT
3104143 CTCATGCCGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (35 bp):
CTAAATATTAGAATTGTTTATGAGCAGGTATCCAT
Found at i:3104303 original size:20 final size:20
Alignment explanation
Indices: 3104278--3104321 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3104268 TCGTTTTTAA
3104278 TTATA-TAATATATATTAATG
1 TTATATTAATATATATT-ATG
*
3104298 TTATATTTATATATATTATG
1 TTATATTAATATATATTATG
3104318 TTAT
1 TTAT
3104322 TTTTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
TTATATTAATATATATTATG
Found at i:3104326 original size:20 final size:21
Alignment explanation
Indices: 3104285--3104330 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
3104275 TAATTATATA
3104285 ATATATATTAATGTTATATTT
1 ATATATATTAATGTTATATTT
*
3104306 ATATATATT-ATGTTATTTTT
1 ATATATATTAATGTTATATTT
3104326 ATATA
1 ATATA
3104331 AAAATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
ATATATATTAATGTTATATTT
Found at i:3104450 original size:16 final size:15
Alignment explanation
Indices: 3104429--3104458 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3104419 AAAGAATAAA
3104429 TTTAAAAAATATATTT
1 TTTAAAAAAT-TATTT
3104445 TTTAAAAAATTATT
1 TTTAAAAAATTATT
3104459 ATGAGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAAAAATTATTT
Found at i:3104881 original size:18 final size:18
Alignment explanation
Indices: 3104858--3104892 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3104848 TGTTTTTAAG
3104858 TTAAAAATAT-TATATATT
1 TTAAAAA-ATGTATATATT
3104876 TTAAAAAATGTATATAT
1 TTAAAAAATGTATATAT
3104893 AATTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TTAAAAAATGTATATATT
Found at i:3107954 original size:33 final size:34
Alignment explanation
Indices: 3107907--3107973 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
3107897 AAAATGACAT
* *
3107907 TCACTTTAAGA-TTTTTTCATGTAGTTCTCTTAC
1 TCACTTTAAAATTTTTTTCAGGTAGTTCTCTTAC
3107940 TCACTTTAAAATTTTTTTCAGGTAGTTCTCTTAC
1 TCACTTTAAAATTTTTTTCAGGTAGTTCTCTTAC
3107974 ACCAGATTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 10 0.32
34 21 0.68
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (34 bp):
TCACTTTAAAATTTTTTTCAGGTAGTTCTCTTAC
Found at i:3112798 original size:24 final size:22
Alignment explanation
Indices: 3112755--3112816 Score: 54
Period size: 24 Copynumber: 2.7 Consensus size: 22
3112745 AATACATATG
*
3112755 AATAAAAATAATAATGAAAAGC
1 AATAAAAATAATAATAAAAAGC
*
3112777 AATAAAAATGTAATAGTAAAAAG-
1 AATAAAAA--TAATAATAAAAAGC
* *
3112800 AATGACAAACAATAATA
1 AAT-AAAAATAATAATA
3112817 TTAAAGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 14 0.44
23 3 0.09
24 15 0.47
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.19
Consensus pattern (22 bp):
AATAAAAATAATAATAAAAAGC
Found at i:3113418 original size:2 final size:2
Alignment explanation
Indices: 3113411--3113450 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3113401 TATGTCAAAA
3113411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3113451 GTACTACTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3115025 original size:41 final size:42
Alignment explanation
Indices: 3114968--3115050 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
3114958 ATGAATGAGA
* * * * *
3114968 GAGAGATGTATGCATTTTATAAATTACTTT-ATTCATGTATG
1 GAGAGATGAATACATTTAATAAATTAATTTGATTCATATATG
3115009 GAGAGATGAATACATTTAATAAATTAATTTGATTCATATATG
1 GAGAGATGAATACATTTAATAAATTAATTTGATTCATATATG
3115051 AAAGAAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 26 0.72
42 10 0.28
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (42 bp):
GAGAGATGAATACATTTAATAAATTAATTTGATTCATATATG
Found at i:3115062 original size:42 final size:41
Alignment explanation
Indices: 3114980--3115062 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
3114970 GAGATGTATG
* * * * *
3114980 CATTTTATAAATTACTTTATTCATGTATGGAGAGATGAATA
1 CATTTAATAAATTAATTTATTCATATATGAAGAGAAGAATA
3115021 CATTTAATAAATTAATTTGATTCATATATGAA-AGAAAGAATA
1 CATTTAATAAATTAATTT-ATTCATATATGAAGAG-AAGAATA
3115063 TTTATATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 18 0.51
42 17 0.49
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (41 bp):
CATTTAATAAATTAATTTATTCATATATGAAGAGAAGAATA
Found at i:3118771 original size:20 final size:18
Alignment explanation
Indices: 3118732--3118793 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 18
3118722 TATCATTGAT
3118732 TTTAATTTTACAATTATAATA
1 TTTAATTTTAC---TATAATA
3118753 TTTAATCTTATACTATAATA
1 TTTAAT-TT-TACTATAATA
*
3118773 ATTAATTTTACTATTAATA
1 TTTAATTTTACTA-TAATA
3118792 TT
1 TT
3118794 ATTTTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 5 0.14
19 8 0.22
20 12 0.33
21 6 0.17
22 2 0.06
23 3 0.08
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATTTTACTATAATA
Found at i:3118786 original size:18 final size:18
Alignment explanation
Indices: 3118746--3118800 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
3118736 ATTTTACAAT
*
3118746 TATAATATTTAATCTTATAC
1 TATAATAATTAAT-TT-TAC
3118766 TATAATAATTAATTTTAC
1 TATAATAATTAATTTTAC
*
3118784 TATTAAT-ATTATTTTTA
1 TA-TAATAATTAATTTTA
3118801 ATTTTACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 14 0.44
19 6 0.19
20 12 0.38
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TATAATAATTAATTTTAC
Found at i:3119492 original size:16 final size:16
Alignment explanation
Indices: 3119480--3119548 Score: 86
Period size: 15 Copynumber: 4.2 Consensus size: 16
3119470 GTATAAATTT
3119480 ATTTAAATATAAAATA
1 ATTTAAATATAAAATA
*
3119496 ATTTGAAT-TAAAATA
1 ATTTAAATATAAAATA
*
3119511 ATTTAAATTTAAAATAA
1 ATTTAAATATAAAAT-A
*
3119528 ATTTAAATTAAAAAATA
1 ATTTAAA-TATAAAATA
3119545 ATTT
1 ATTT
3119549 GATTTTAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
15 14 0.30
16 13 0.28
17 13 0.28
18 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
ATTTAAATATAAAATA
Found at i:3119518 original size:31 final size:32
Alignment explanation
Indices: 3119480--3119540 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
3119470 GTATAAATTT
*
3119480 ATTTAAATATAAAAT-AATTTGAATTAAAATA
1 ATTTAAATATAAAATAAATTTAAATTAAAATA
*
3119511 ATTTAAATTTAAAATAAATTTAAATTAAAA
1 ATTTAAATATAAAATAAATTTAAATTAAAA
3119541 AATAATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (32 bp):
ATTTAAATATAAAATAAATTTAAATTAAAATA
Found at i:3119590 original size:18 final size:16
Alignment explanation
Indices: 3119567--3119614 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 16
3119557 GTAATATAAA
3119567 AAAATTAAATCAATTT
1 AAAATTAAATCAATTT
*
3119583 AATTAATTAAATTAATTT
1 AA--AATTAAATCAATTT
*
3119601 AAATTTAAATCAAT
1 AAAATTAAATCAAT
3119615 GACTTAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.44
18 15 0.56
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATTAAATCAATTT
Found at i:3119800 original size:16 final size:15
Alignment explanation
Indices: 3119762--3119811 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 15
3119752 TTAATATTTT
3119762 AATTATTTATTAA-A
1 AATTATTTATTAATA
3119776 AATTA--TATTAATA
1 AATTATTTATTAATA
*
3119789 AATTATTTTATTAATT
1 AATTA-TTTATTAATA
3119805 AATTATT
1 AATTATT
3119812 AATATTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
14 5 0.16
15 2 0.06
16 12 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTATTTATTAATA
Found at i:3120189 original size:17 final size:17
Alignment explanation
Indices: 3120167--3120199 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3120157 TATTTTATTA
3120167 ATATTTAAAATAATTTT
1 ATATTTAAAATAATTTT
*
3120184 ATATTTTAAATAATTT
1 ATATTTAAAATAATTT
3120200 AATAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTAAAATAATTTT
Found at i:3120208 original size:17 final size:17
Alignment explanation
Indices: 3120164--3120208 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3120154 ATATATTTTA
3120164 TTAAT-ATTTAAAATAAT
1 TTAATAATTT-AAATAAT
* *
3120181 TTTATATTTTAAATAAT
1 TTAATAATTTAAATAAT
3120198 TTAATAATTTA
1 TTAATAATTTA
3120209 TATTATGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATAATTTAAATAAT
Found at i:3120231 original size:29 final size:28
Alignment explanation
Indices: 3120199--3120270 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 28
3120189 TTAAATAATT
*
3120199 TAATAATTTATATTATGTTAT-TTGTATTA
1 TAAT-ATTTATATTATATTATATTGTA-TA
* *
3120228 TAAT-TTTATATTTTATTATATTTTATA
1 TAATATTTATATTATATTATATTGTATA
3120255 TAATATTT-TAATTATA
1 TAATATTTAT-ATTATA
3120271 ATTTCCTACT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
27 20 0.56
28 12 0.33
29 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (28 bp):
TAATATTTATATTATATTATATTGTATA
Found at i:3120246 original size:27 final size:26
Alignment explanation
Indices: 3120141--3120254 Score: 74
Period size: 27 Copynumber: 4.3 Consensus size: 26
3120131 TATTTGTATG
3120141 TATTATATATTTCATATATTTTATTAATATT
1 TATTATA-ATTT--TATATTTTATT-AT-TT
** * *
3120172 TAAAATAATTTTATATTTTAAATAATT
1 TATTATAATTTTATATTTT-ATTATTT
* *
3120199 TA--ATAA-TTTATATTATGTTATTT
1 TATTATAATTTTATATTTTATTATTT
*
3120222 GTATTATAATTTTATATTTTATTATAT
1 -TATTATAATTTTATATTTTATTATTT
3120249 T-TTATA
1 TATTATA
3120255 TAATATTTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
23 4 0.06
24 11 0.16
25 9 0.13
26 5 0.07
27 18 0.27
28 9 0.13
29 2 0.03
30 4 0.06
31 5 0.07
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTATAATTTTATATTTTATTATTT
Found at i:3120250 original size:17 final size:17
Alignment explanation
Indices: 3120176--3120255 Score: 74
Period size: 17 Copynumber: 4.7 Consensus size: 17
3120166 AATATTTAAA
*
3120176 ATAATTTTATATTTTAA
1 ATAATTTTATATTTTAT
* *
3120193 ATAATTTAATAATTTAT
1 ATAATTTTATATTTTAT
* * *
3120210 ATTATGTTAT-TTGTATT
1 ATAATTTTATATTTTA-T
3120227 ATAATTTTATATTTTAT
1 ATAATTTTATATTTTAT
3120244 -TATATTTTATAT
1 ATA-ATTTTATAT
3120256 AATATTTTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
16 5 0.10
17 40 0.82
18 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
ATAATTTTATATTTTAT
Found at i:3120261 original size:17 final size:18
Alignment explanation
Indices: 3120223--3120267 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
3120213 ATGTTATTTG
**
3120223 TATTATAATTTTATATTT
1 TATTATAATTTTATATAA
3120241 TATTAT-ATTTTATATAA
1 TATTATAATTTTATATAA
*
3120258 TATTTTAATT
1 TATTATAATT
3120268 ATAATTTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTATAATTTTATATAA
Found at i:3120274 original size:12 final size:11
Alignment explanation
Indices: 3120233--3120270 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
3120223 TATTATAATT
3120233 TTATATTTT-A
1 TTATATTTTAA
3120243 TTATATTTTATA
1 TTATATTTTA-A
*
3120255 TAATATTTTAA
1 TTATATTTTAA
3120266 TTATA
1 TTATA
3120271 ATTTCCTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.38
11 5 0.21
12 10 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:3126499 original size:17 final size:17
Alignment explanation
Indices: 3126479--3126517 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
3126469 AGCTTCCATT
3126479 AAAAAAAAAT-TGGATTGA
1 AAAAAAAAATGT-G-TTGA
3126497 AAAAAAAAATGTGTTGA
1 AAAAAAAAATGTGTTGA
3126514 AAAA
1 AAAA
3126518 TATAGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 11 0.55
19 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (17 bp):
AAAAAAAAATGTGTTGA
Found at i:3129712 original size:32 final size:32
Alignment explanation
Indices: 3129634--3129715 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 32
3129624 TTATATTTAA
3129634 AATATTATATATTTATATAAATTCAGATACGAT
1 AATATTATATA-TTATATAAATTCAGATACGAT
* **
3129667 AATAATT-TTTATTATATAAATTTTTGATACG-T
1 AAT-ATTATATATTATATAAA-TTCAGATACGAT
*
3129699 TATATTATATATTATAT
1 AATATTATATATTATAT
3129716 TTTAATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
31 3 0.07
32 21 0.51
33 14 0.34
34 3 0.07
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (32 bp):
AATATTATATATTATATAAATTCAGATACGAT
Found at i:3130851 original size:13 final size:13
Alignment explanation
Indices: 3130829--3130872 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
3130819 AAAATTTAAG
3130829 TTTTATTATGTTAT
1 TTTTA-TATGTTAT
3130843 TTTTATATGTTAT
1 TTTTATATGTTAT
* *
3130856 TCTTATATATTAT
1 TTTTATATGTTAT
3130869 TTTT
1 TTTT
3130873 TAAAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (13 bp):
TTTTATATGTTAT
Found at i:3134994 original size:19 final size:17
Alignment explanation
Indices: 3134959--3135001 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 17
3134949 TTTTTAACAT
3134959 TTTATAAAAAAAAAATAG
1 TTTA-AAAAAAAAAATAG
3134977 TTTAAAAAAATAATAATAG
1 TTTAAAAAAA-AA-AATAG
3134996 TATTAA
1 T-TTAA
3135002 TAATTTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
18 6 0.27
19 6 0.27
20 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
TTTAAAAAAAAAAATAG
Found at i:3135779 original size:25 final size:25
Alignment explanation
Indices: 3135733--3135780 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3135723 TGAAATTGAT
* *
3135733 TATAAAGTAAAAAATAATATAAATA
1 TATAAAATAAAAAATAACATAAATA
*
3135758 TATAAAATAAAAAATTACATAAA
1 TATAAAATAAAAAATAACATAAA
3135781 AATTCTCGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (25 bp):
TATAAAATAAAAAATAACATAAATA
Found at i:3136122 original size:27 final size:22
Alignment explanation
Indices: 3136067--3136110 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3136057 TAAAATTAAA
3136067 GTAAAAAGGTAAGATCCATAAT
1 GTAAAAAGGTAAGATCCATAAT
3136089 GTAAAAAGGTAAGATCCATAAT
1 GTAAAAAGGTAAGATCCATAAT
3136111 ATTTGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (22 bp):
GTAAAAAGGTAAGATCCATAAT
Found at i:3136177 original size:27 final size:24
Alignment explanation
Indices: 3136147--3136202 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
3136137 ATTTAATTTT
3136147 TATTAAAATGATAATGTAAATAATTAA
1 TATTAAAATGAT-A--TAAATAATTAA
* *
3136174 TATTAATATGATATAAATAATTTA
1 TATTAAAATGATATAAATAATTAA
3136198 TATTA
1 TATTA
3136203 TTTTAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 15 0.56
26 1 0.04
27 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (24 bp):
TATTAAAATGATATAAATAATTAA
Found at i:3136211 original size:24 final size:24
Alignment explanation
Indices: 3136157--3136213 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
3136147 TATTAAAATG
*
3136157 ATAATGTAAATAATTAATATTAAT
1 ATAATATAAATAATTAATATTAAT
* * *
3136181 ATGATATAAATAATTTATATTATT
1 ATAATATAAATAATTAATATTAAT
*
3136205 TTAATATAA
1 ATAATATAA
3136214 TTTTTTATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
ATAATATAAATAATTAATATTAAT
Found at i:3136665 original size:2 final size:2
Alignment explanation
Indices: 3136658--3136683 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3136648 TCGAAGAAGG
3136658 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
3136684 TGACAATGAT
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:3137191 original size:88 final size:89
Alignment explanation
Indices: 3137092--3137434 Score: 280
Period size: 89 Copynumber: 3.9 Consensus size: 89
3137082 GTTTCATATG
* * * *
3137092 AAAAAATTT-TATAGGCATTAATTGAATTTTTTTTTGTCATGTCAGAAA-AATTTGGTACTT-GC
1 AAAAAATTTAT-TAGGCATTAATT-AAATATTTTATGTCATGTCAGAAAGAATTTGATA-TTCGC
* * *
3137154 ATACAACTATCACATCTTTTGATTTTT
63 ATACAACTATCACATCTTTCGAGTTTC
* * * *
3137181 AAAAAATTTATTAGGTATTAGTTAAATATTTTATGTCGTGTCAGAAAGAATTTGATATTCGCATG
1 AAAAAATTTATTAGGCATTAATTAAATATTTTATGTCATGTCAGAAAGAATTTGATATTCGCATA
**
3137246 CATTTATCACATCTTTCGAGTTTC
66 CAACTATCACATCTTTCGAGTTTC
* * * * * * * * * *
3137270 AAAAAATTTATTAAGCATTAGTCAAATATTTTTTATTATGTCAGAAAGAATCTGATATCCGTATG
1 AAAAAATTTATTAGGCATTAATTAAATATTTTATGTCATGTCAGAAAGAATTTGATATTCGCATA
** * * * *
3137335 CTTCTGTCATATCTTTTGGGTTTC
66 CAACTATCACATCTTTCGAGTTTC
* * * * * * * * *
3137359 AAAAAATTTATTAGGTATTTACTAAATATTTTCTATCATGCCAGAAAGAATCT-ATATCCGTATA
1 AAAAAATTTATTAGGCATTAATTAAATATTTTATGTCATGTCAGAAAGAATTTGATATTCGCATA
*
3137423 CATCTATCACAT
66 CAACTATCACAT
3137435 ATTTTGGATT
Statistics
Matches: 209, Mismatches: 42, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
88 41 0.20
89 167 0.80
90 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.42
Consensus pattern (89 bp):
AAAAAATTTATTAGGCATTAATTAAATATTTTATGTCATGTCAGAAAGAATTTGATATTCGCATA
CAACTATCACATCTTTCGAGTTTC
Found at i:3137725 original size:7 final size:7
Alignment explanation
Indices: 3137712--3137825 Score: 100
Period size: 7 Copynumber: 16.6 Consensus size: 7
3137702 ATGCTATATA
3137712 ATATTAT
1 ATATTAT
*
3137719 ATGTTAT
1 ATATTAT
3137726 ATA-T-T
1 ATATTAT
3137731 ATA-TAT
1 ATATTAT
3137737 ATATTAT
1 ATATTAT
*
3137744 ATATGTAG
1 ATAT-TAT
3137752 ACTATATAT
1 A-TAT-TAT
3137761 ATTATTAT
1 A-TATTAT
3137769 ATATTAT
1 ATATTAT
3137776 ATATCTAT
1 ATAT-TAT
3137784 -TA-TAT
1 ATATTAT
3137789 ATATT-T
1 ATATTAT
3137795 ATATTA-
1 ATATTAT
3137801 ATATTAT
1 ATATTAT
3137808 ATA-TAT
1 ATATTAT
3137814 ATATATAT
1 ATAT-TAT
3137822 ATAT
1 ATAT
3137826 AATTGGGAAC
Statistics
Matches: 90, Mismatches: 6, Indels: 21
0.77 0.05 0.18
Matches are distributed among these distances:
5 8 0.09
6 25 0.28
7 31 0.34
8 17 0.19
9 9 0.10
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (7 bp):
ATATTAT
Found at i:3137728 original size:2 final size:2
Alignment explanation
Indices: 3137706--3137826 Score: 104
Period size: 2 Copynumber: 66.0 Consensus size: 2
3137696 TATTATATGC
*
3137706 TA TA TA -A TA T- TA TA TG T- TA TA TA T- TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3137743 TA TA TG TA GA CTA TA TA TA T- TA T- TA TA TA T- TA TA TA TC TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3137783 T- TA TA TA TA TT TA TA T- TA -A TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3137821 TA TA TA
1 TA TA TA
3137827 ATTGGGAACT
Statistics
Matches: 97, Mismatches: 9, Indels: 26
0.73 0.07 0.20
Matches are distributed among these distances:
1 12 0.12
2 84 0.87
3 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3137739 original size:11 final size:11
Alignment explanation
Indices: 3137723--3137825 Score: 126
Period size: 11 Copynumber: 9.6 Consensus size: 11
3137713 TATTATATGT
3137723 TATATATTATA
1 TATATATTATA
3137734 TATATATTATA
1 TATATATTATA
* *
3137745 TATGTA-GACTA
1 TATATATTA-TA
3137756 TATATATTAT-
1 TATATATTATA
3137766 TATATATTATA
1 TATATATTATA
*
3137777 TATCTATTATA
1 TATATATTATA
3137788 TATAT-TTATA
1 TATATATTATA
3137798 T-TAATATTATA
1 TAT-ATATTATA
3137809 TATATA-TATA
1 TATATATTATA
3137819 TATATAT
1 TATATAT
3137826 AATTGGGAAC
Statistics
Matches: 79, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
9 1 0.01
10 29 0.37
11 47 0.59
12 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TATATATTATA
Found at i:3137776 original size:17 final size:17
Alignment explanation
Indices: 3137696--3137825 Score: 107
Period size: 17 Copynumber: 8.0 Consensus size: 17
3137686 ATAAATAAAA
** *
3137696 TATTATATGCTATATAA
1 TATTATATATTATATAT
*
3137713 TATTATATGTTATATAT
1 TATTATATATTATATAT
3137730 TATATATATATTATATAT
1 TAT-TATATATTATATAT
* *
3137748 GTA-GA-CTA-TATATAT
1 -TATTATATATTATATAT
3137763 TATTATATATTATATAT
1 TATTATATATTATATAT
*
3137780 CTATTATATA-TATTTA-
1 -TATTATATATTATATAT
3137796 TATTA-ATATTATATA-
1 TATTATATATTATATAT
3137811 TA-TATATA-TATATAT
1 TATTATATATTATATAT
3137826 AATTGGGAAC
Statistics
Matches: 95, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
14 13 0.14
15 23 0.24
16 4 0.04
17 31 0.33
18 22 0.23
19 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTATATATTATATAT
Found at i:3137778 original size:43 final size:42
Alignment explanation
Indices: 3137706--3137826 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 42
3137696 TATTATATGC
*
3137706 TATATA-ATATT-ATA-TGTTATATATTATATATATATTATA
1 TATATAGATATTAATATTATTATATATTATATATATATTATA
* *
3137745 TATGTAGACTA-TATATATTATTATATATTATATATCTATTATA
1 TATATAGA-TATTA-ATATTATTATATATTATATATATATTATA
**
3137788 TATATTTATATTAATATTATATATATATATATATATATA
1 TATATAGATATTAATATTAT-TATATAT-TATATATATA
3137827 ATTGGGAACT
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 2 0.03
42 12 0.18
43 37 0.55
44 9 0.13
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (42 bp):
TATATAGATATTAATATTATTATATATTATATATATATTATA
Found at i:3144623 original size:2 final size:2
Alignment explanation
Indices: 3144616--3144645 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3144606 TTTGGTTATG
*
3144616 GA GA GA GA GA CA 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
3144646 ACCACCCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3145029 original size:2 final size:2
Alignment explanation
Indices: 3145022--3145048 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3145012 GTTTGTTAAG
3145022 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 T
3145049 GGATCTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3145978 original size:5 final size:5
Alignment explanation
Indices: 3145968--3145996 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3145958 AACAACAACG
3145968 CAAAT CAAAT CAAAT CAAAT CAAAT CAAA
1 CAAAT CAAAT CAAAT CAAAT CAAAT CAAA
3145997 AGTATTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (5 bp):
CAAAT
Found at i:3146499 original size:2 final size:2
Alignment explanation
Indices: 3146492--3146523 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3146482 CTGCTTCCTT
3146492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3146524 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3146529 original size:2 final size:2
Alignment explanation
Indices: 3146524--3146549 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3146514 TATATATATA
3146524 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
3146550 TGATAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3148643 original size:15 final size:15
Alignment explanation
Indices: 3148623--3148653 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3148613 TCTACATTAA
3148623 TTATAAGGTTAAGAT
1 TTATAAGGTTAAGAT
3148638 TTATAAGGTTAAGAT
1 TTATAAGGTTAAGAT
3148653 T
1 T
3148654 GTTTTTAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (15 bp):
TTATAAGGTTAAGAT
Found at i:3153242 original size:27 final size:27
Alignment explanation
Indices: 3153204--3153271 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
3153194 TTGAAAACGA
3153204 GGTTGGAGTGTCCCTTTAGAGGAATGG
1 GGTTGGAGTGTCCCTTTAGAGGAATGG
3153231 GGTTGGAGTGTCCCTTTAGAGGAATGG
1 GGTTGGAGTGTCCCTTTAGAGGAATGG
3153258 GGTTGGAGTGTCCC
1 GGTTGGAGTGTCCC
3153272 CGATGAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.16, C:0.13, G:0.41, T:0.29
Consensus pattern (27 bp):
GGTTGGAGTGTCCCTTTAGAGGAATGG
Found at i:3155500 original size:20 final size:20
Alignment explanation
Indices: 3155477--3155521 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3155467 AGATGTATTA
*
3155477 ATACAAAGATTAATGTATCG
1 ATACAAAGAATAATGTATCG
**
3155497 ATACATTGAATAATGTATCG
1 ATACAAAGAATAATGTATCG
3155517 ATACA
1 ATACA
3155522 TTTCCTTGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (20 bp):
ATACAAAGAATAATGTATCG
Found at i:3160537 original size:62 final size:63
Alignment explanation
Indices: 3160440--3160566 Score: 186
Period size: 62 Copynumber: 2.0 Consensus size: 63
3160430 GAATTTGAAC
* *
3160440 TAAAAGTGAGAAGTTTTTTTAGGAAAAATGATATGAATTAAGTGT-GGATATGTATAGAGGGA
1 TAAAAGTGAGAAGTTGTTTTAAGAAAAATGATATGAATTAAGTGTGGGATATGTATAGAGGGA
* *
3160502 TAAAAGTGAGAA-TTGTTTTAAGAAAGAATGATATGAATTAAGTGTGGGGGTGTGTATAGAGGGA
1 TAAAAGTGAGAAGTTGTTTTAAGAAA-AATGATATGAATTAAGTGT-GGGATATGTATAGAGGGA
3160566 T
1 T
3160567 TTGATGAGTG
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
61 11 0.19
62 31 0.53
64 16 0.28
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.31
Consensus pattern (63 bp):
TAAAAGTGAGAAGTTGTTTTAAGAAAAATGATATGAATTAAGTGTGGGATATGTATAGAGGGA
Found at i:3160668 original size:11 final size:11
Alignment explanation
Indices: 3160652--3160707 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
3160642 TTGATTTTTT
3160652 GAAAAAGAAAA
1 GAAAAAGAAAA
*
3160663 GAAAAA-AAATT
1 GAAAAAGAAA-A
3160674 GAAAAATGAAAA
1 GAAAAA-GAAAA
*
3160686 AAAAAAGAGAAA
1 GAAAAAGA-AAA
3160698 G-AAAAGAAAA
1 GAAAAAGAAAA
3160708 AAATTGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
10 6 0.16
11 20 0.54
12 8 0.22
13 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:3160697 original size:31 final size:31
Alignment explanation
Indices: 3160653--3160720 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
3160643 TGATTTTTTG
* ***
3160653 AAAAAGAAAAGAAAAAAAATTGAAAAA-TGA
1 AAAAAAAAAAGAAAAAAAAGAAAAAAATTGA
*
3160683 AAAAAAAAAGAGAAAGAAAAGAAAAAAATTGA
1 AAAAAAAAA-AGAAAAAAAAGAAAAAAATTGA
3160715 AAAAAA
1 AAAAAA
3160721 TTATATAAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 8 0.26
31 14 0.45
32 9 0.29
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.07
Consensus pattern (31 bp):
AAAAAAAAAAGAAAAAAAAGAAAAAAATTGA
Found at i:3160706 original size:29 final size:28
Alignment explanation
Indices: 3160651--3160708 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
3160641 TTTGATTTTT
*
3160651 TGAAAAAGAAAAGAAAAAAAATTGAAAAA
1 TGAAAAAAAAAAGAAAAAAAA-TGAAAAA
3160680 TGAAAAAAAAAAGAGAAAGAAAA-GAAAAA
1 TGAAAAAAAAAAGA-AAA-AAAATGAAAAA
3160709 AATTGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 19 0.73
30 3 0.12
31 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (28 bp):
TGAAAAAAAAAAGAAAAAAAATGAAAAA
Found at i:3165419 original size:16 final size:16
Alignment explanation
Indices: 3165398--3165438 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3165388 TTACTAAATG
*
3165398 TTTTAATATATTTATA
1 TTTTAATATAATTATA
*
3165414 TTTTAAAATAATTATA
1 TTTTAATATAATTATA
3165430 TATTTAATA
1 T-TTTAATA
3165439 AAAAATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAATATAATTATA
Found at i:3166092 original size:23 final size:23
Alignment explanation
Indices: 3166066--3166109 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3166056 AAAAAGTAAA
*
3166066 AAATATA-AAATTAAGTAATAATT
1 AAATATATAAA-TAAATAATAATT
3166089 AAATATATAAATAAATAATAA
1 AAATATATAAATAAATAATAA
3166110 ATTTAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
AAATATATAAATAAATAATAATT
Found at i:3169023 original size:26 final size:26
Alignment explanation
Indices: 3168985--3169062 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
3168975 CACATAGTTT
3168985 TGTATATAGCATCAGACCTAATTGGC
1 TGTATATAGCATCAGACCTAATTGGC
* * *
3169011 TGTATATAACATCGGACCTAGTTGGC
1 TGTATATAGCATCAGACCTAATTGGC
** *
3169037 TGTAGGTTGCATCAGACCTAATTGGC
1 TGTATATAGCATCAGACCTAATTGGC
3169063 CTCCAGTTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (26 bp):
TGTATATAGCATCAGACCTAATTGGC
Found at i:3169354 original size:34 final size:33
Alignment explanation
Indices: 3169308--3169371 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
3169298 ATATTTAAAT
3169308 TTTAAAATTTTAATATATATT-ATT-TTATATTTA
1 TTTAAAATTTTAAT-TA-ATTAATTATTATATTTA
3169341 TTTAAATATTTTAATTAATTAATTATTATAT
1 TTTAAA-ATTTTAATTAATTAATTATTATAT
3169372 AACTAGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 3 0.11
33 11 0.39
34 14 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
TTTAAAATTTTAATTAATTAATTATTATATTTA
Found at i:3169367 original size:17 final size:19
Alignment explanation
Indices: 3169316--3169372 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 19
3169306 ATTTTAAAAT
3169316 TTTAATATATATTATTTTATA
1 TTTAAT-TA-ATTATTTTATA
* *
3169337 TTTATTTAAATATTTTA-A
1 TTTAATTAATTATTTTATA
*
3169355 -TTAATTAATTATTATATA
1 TTTAATTAATTATTTTATA
3169373 ACTAGATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 8 0.27
20 2 0.07
21 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATTAATTATTTTATA
Found at i:3169922 original size:13 final size:13
Alignment explanation
Indices: 3169906--3169939 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3169896 TGACTTTAGA
3169906 AATTGAATCCATG
1 AATTGAATCCATG
* *
3169919 AATTGAAACTATG
1 AATTGAATCCATG
3169932 AATTGAAT
1 AATTGAAT
3169940 TGATATATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (13 bp):
AATTGAATCCATG
Found at i:3171042 original size:20 final size:21
Alignment explanation
Indices: 3171004--3171042 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3170994 TTTTAATTTT
* *
3171004 TTAATAATTTTTTACTTTAAA
1 TTAATAATTATTTAATTTAAA
3171025 TTAAT-ATTATTTAATTTA
1 TTAATAATTATTTAATTTA
3171043 TAACATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAATAATTATTTAATTTAAA
Found at i:3171120 original size:23 final size:25
Alignment explanation
Indices: 3171071--3171146 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 25
3171061 AATTTTACTA
* *
3171071 TTAA-TATAAATAAAA-AATTATCAT
1 TTAATTATATATAAAATATTTAT-AT
3171095 TTAATTATA-ATAAAATATTTAT-T
1 TTAATTATATATAAAATATTTATAT
* *
3171118 TTAATTATATGTAAAATTTTTATAT
1 TTAATTATATATAAAATATTTATAT
3171143 TTAA
1 TTAA
3171147 AAATTTATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
23 10 0.22
24 21 0.47
25 14 0.31
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (25 bp):
TTAATTATATATAAAATATTTATAT
Found at i:3172975 original size:3 final size:3
Alignment explanation
Indices: 3172967--3173004 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3172957 ATGATAATGA
3172967 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3173005 GAATGAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3176593 original size:88 final size:89
Alignment explanation
Indices: 3176491--3176659 Score: 322
Period size: 89 Copynumber: 1.9 Consensus size: 89
3176481 TTAATTTTTG
*
3176491 GGCCAAAATTGTGCATAGAGCTGAATTATTTG-GCTTGTCTTCAAGTTTCTAATCTACCTTTAAT
1 GGCCAAAATTGTGCATAGAGCGGAATTATTTGTGCTTGTCTTCAAGTTTCTAATCTACCTTTAAT
3176555 CTCCAACCCGATTTATAAATCTTT
66 CTCCAACCCGATTTATAAATCTTT
3176579 GGCCAAAATTGTGCATAGAGCGGAATTATTTGTGCTTGTCTTCAAGTTTCTAATCTACCTTTAAT
1 GGCCAAAATTGTGCATAGAGCGGAATTATTTGTGCTTGTCTTCAAGTTTCTAATCTACCTTTAAT
3176644 CTCCAACCCGATTTAT
66 CTCCAACCCGATTTAT
3176660 CTAATAAACT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
88 31 0.39
89 48 0.61
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (89 bp):
GGCCAAAATTGTGCATAGAGCGGAATTATTTGTGCTTGTCTTCAAGTTTCTAATCTACCTTTAAT
CTCCAACCCGATTTATAAATCTTT
Found at i:3176778 original size:31 final size:31
Alignment explanation
Indices: 3176740--3176799 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
3176730 TTTGTCAGCA
3176740 ACATGTATGCCATATAAACTAATACCGAGCG
1 ACATGTATGCCATATAAACTAATACCGAGCG
3176771 ACATGTATGCCATATAAACTAATACCGAG
1 ACATGTATGCCATATAAACTAATACCGAG
3176800 TTGACCACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (31 bp):
ACATGTATGCCATATAAACTAATACCGAGCG
Found at i:3177978 original size:39 final size:39
Alignment explanation
Indices: 3177916--3177999 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
3177906 CATATAGCAT
3177916 CAAA-TATAAATTAATATTAAATTACATTTATTTAAGAA
1 CAAACTATAAATTAATATTAAATTACATTTATTTAAGAA
* * * *
3177954 CAAACTATTAATTCATATTGAATTACTTTTATTTAAGAA
1 CAAACTATAAATTAATATTAAATTACATTTATTTAAGAA
3177993 CAAACTA
1 CAAACTA
3178000 GAATTTGGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 4 0.10
39 37 0.90
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.39
Consensus pattern (39 bp):
CAAACTATAAATTAATATTAAATTACATTTATTTAAGAA
Found at i:3180189 original size:9 final size:9
Alignment explanation
Indices: 3180175--3180233 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
3180165 TTTAATTAGT
3180175 TTTTATTAA
1 TTTTATTAA
*
3180184 TTTTATTGA
1 TTTTATTAA
**
3180193 TTAAATTAA
1 TTTTATTAA
3180202 TTTTATATTAA
1 -TTT-TATTAA
*
3180213 TTTAATTAA
1 TTTTATTAA
3180222 -TTT-TTAA
1 TTTTATTAA
3180229 TTTTA
1 TTTTA
3180234 ACATATATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
7 4 0.11
8 5 0.13
9 19 0.50
10 5 0.13
11 5 0.13
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATTAA
Found at i:3180199 original size:28 final size:29
Alignment explanation
Indices: 3180156--3180215 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
3180146 AAAATCAGAT
* *
3180156 TTTTAATGATTTAATTAGTTTT-TATTAA
1 TTTTAATGATTAAATTAATTTTATATTAA
*
3180184 TTTTATTGATTAAATTAATTTTATATTAA
1 TTTTAATGATTAAATTAATTTTATATTAA
3180213 TTT
1 TTT
3180216 AATTAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (29 bp):
TTTTAATGATTAAATTAATTTTATATTAA
Found at i:3180213 original size:11 final size:10
Alignment explanation
Indices: 3180165--3180230 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
3180155 TTTTTAATGA
*
3180165 TTTAATTAGT
1 TTTAATTAAT
*
3180175 TTTTATTAAT
1 TTTAATTAAT
*
3180185 TTT-ATTGA-
1 TTTAATTAAT
*
3180193 TTAAATTAAT
1 TTTAATTAAT
3180203 TTTATATTAA-
1 TTTA-ATTAAT
3180213 TTTAATTAATT
1 TTTAATTAA-T
3180224 TTTAATT
1 TTTAATT
3180231 TTAACATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 2 0.04
9 13 0.29
10 18 0.40
11 12 0.27
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTAATTAAT
Found at i:3180217 original size:16 final size:18
Alignment explanation
Indices: 3180179--3180219 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
3180169 ATTAGTTTTT
3180179 ATTAATTTTATTGATTAA
1 ATTAATTTTATTGATTAA
3180197 ATTAATTTTA-T-ATTAA
1 ATTAATTTTATTGATTAA
*
3180213 TTTAATT
1 ATTAATT
3180220 AATTTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.50
17 1 0.05
18 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATTAATTTTATTGATTAA
Found at i:3180219 original size:20 final size:19
Alignment explanation
Indices: 3180179--3180227 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
3180169 ATTAGTTTTT
*
3180179 ATTAA-TTTTATTGATTAA
1 ATTAATTTTTATTAATTAA
*
3180197 ATTAATTTTATATTAATTTA
1 ATTAATTTT-TATTAATTAA
3180217 ATTAATTTTTA
1 ATTAATTTTTA
3180228 ATTTTAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 17 0.63
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTAATTTTTATTAATTAA
Found at i:3180872 original size:10 final size:10
Alignment explanation
Indices: 3180853--3180886 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3180843 TATTTAATAA
*
3180853 TTTATATATT
1 TTTAAATATT
*
3180863 TTTAATTATT
1 TTTAAATATT
3180873 TTTAAATATT
1 TTTAAATATT
3180883 TTTA
1 TTTA
3180887 TGTATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTAAATATT
Found at i:3180929 original size:28 final size:28
Alignment explanation
Indices: 3180841--3180930 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
3180831 TCCTACATAC
*
3180841 TATATTTAATAATTTATATATTTTTA-AT
1 TATATTTAA-AATTTATATTTTTTTATAT
* * * *
3180869 TATTTTTAAATATTTTTA-TGTATTATAAT
1 TATATTTAAA-ATTTATATTTTTTTAT-AT
3180898 TATATTTAAAATTTATATTTTTTTATAT
1 TATATTTAAAATTTATATTTTTTTATAT
3180926 TATAT
1 TATAT
3180931 ATATTTTGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
27 5 0.10
28 27 0.55
29 17 0.35
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (28 bp):
TATATTTAAAATTTATATTTTTTTATAT
Found at i:3181854 original size:18 final size:17
Alignment explanation
Indices: 3181818--3181862 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
3181808 TTGAGTATTG
*
3181818 AATAATTTTTTTATGTT
1 AATAATTTTTTAATGTT
*
3181835 AATACATTTTTTAATTTT
1 AATA-ATTTTTTAATGTT
*
3181853 AATTATTTTT
1 AATAATTTTT
3181863 AAAATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
AATAATTTTTTAATGTT
Found at i:3182333 original size:9 final size:8
Alignment explanation
Indices: 3182301--3182331 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
3182291 TTCAAGGTAA
3182301 AATTTTTT
1 AATTTTTT
3182309 AATTTTTT
1 AATTTTTT
*
3182317 AATTTTAT
1 AATTTTTT
3182325 AATTTTT
1 AATTTTT
3182332 ATGATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
AATTTTTT
Found at i:3184072 original size:26 final size:24
Alignment explanation
Indices: 3184043--3184102 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 24
3184033 GGTACAACTT
3184043 CAAGTGTTTGTCTTTGTTGAATTTGG
1 CAAGT-TTT-TCTTTGTTGAATTTGG
3184069 CAAGTTCTTTCTTTGTTGAATTTGG
1 CAAGTT-TTTCTTTGTTGAATTTGG
3184094 CAAGTTTTT
1 CAAGTTTTT
3184103 TCTTGTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 3 0.09
25 23 0.70
26 7 0.21
ACGTcount: A:0.17, C:0.10, G:0.22, T:0.52
Consensus pattern (24 bp):
CAAGTTTTTCTTTGTTGAATTTGG
Done.