Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold440
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: 783396
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:491962 original size:2 final size:2
Alignment explanation
Indices: 491938--491983 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
491928 AATTTAAATT
* *
491938 TA TA -A TA TA TT TA TA T- TA AA 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 TA TA TA TA TA
491978 TA TA TA
1 TA TA TA
491984 AAATTTACCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:492126 original size:22 final size:22
Alignment explanation
Indices: 492101--492152 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
492091 CTGCTTCTGT
*
492101 ACTATATACTATGAGCTAATGA
1 ACTATATACTATGAACTAATGA
*
492123 ACTATATACTATGAACTAGTGA
1 ACTATATACTATGAACTAATGA
*
492145 AATATATA
1 ACTATATA
492153 TTTATTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
ACTATATACTATGAACTAATGA
Found at i:492170 original size:21 final size:21
Alignment explanation
Indices: 492144--492193 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 21
492134 TGAACTAGTG
492144 AAATATATATTTATTTATATC
1 AAATATATATTTATTTATATC
492165 -AA-ATATA--TATTTATATC
1 AAATATATATTTATTTATATC
492182 AAATATATATTT
1 AAATATATATTT
492194 TAACCAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 10 0.40
18 2 0.08
19 10 0.40
20 2 0.08
21 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATATATTTATTTATATC
Found at i:492189 original size:15 final size:17
Alignment explanation
Indices: 492150--492193 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
492140 AGTGAAATAT
*
492150 ATATTTATTTATATCAA
1 ATATATATTTATATCAA
492167 ATATATATTTATATCAA
1 ATATATATTTATATCAA
492184 ATATATATTT
1 ATATATATTT
492194 TAACCAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATTTATATCAA
Found at i:492201 original size:17 final size:17
Alignment explanation
Indices: 492150--492203 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
492140 AGTGAAATAT
* *
492150 ATATTTATTTATATCAA
1 ATATATATTTATACCAA
*
492167 ATATATATTTATATCAA
1 ATATATATTTATACCAA
492184 ATATATATTT-TAACCAA
1 ATATATATTTAT-ACCAA
492201 ATA
1 ATA
492204 ATACAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 1 0.03
17 33 0.97
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATATTTATACCAA
Found at i:492703 original size:15 final size:16
Alignment explanation
Indices: 492683--492715 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
492673 TTTTTAAAAA
492683 ATTAAATAT-ATTTAT
1 ATTAAATATAATTTAT
492698 ATTAAATATAATTTAT
1 ATTAAATATAATTTAT
492714 AT
1 AT
492716 GCGATATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTAAATATAATTTAT
Found at i:492990 original size:5 final size:5
Alignment explanation
Indices: 492980--493011 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
492970 ATATTTTCAT
492980 ATATA ATATA ATATA ATAT- ATAT- ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT
493012 TGATTATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
ATATA
Found at i:493405 original size:218 final size:218
Alignment explanation
Indices: 493022--493463 Score: 798
Period size: 218 Copynumber: 2.0 Consensus size: 218
493012 TGATTATGAA
*
493022 ATATAAAATTTTACAAATGAGATTAATATGTTATTTTATTAATTTATTTTATAAAATTTTTACAT
1 ATATATAATTTTACAAATGAGATTAATATGTTATTTTATTAATTTATTTTATAAAATTTTTACAT
* *
493087 TTTAATGTGGATATAAAAAACTATTATTCATATATGTATATATAATATATTTATTTTACATACTA
66 TTTAATATGGATATAAAAAACTATTATTCATATATGTATATATAATATATTTATTTTACACACTA
493152 ATAATGAAAAGAAAAACTCTGTTAATGAATTTGTAAATGAGACATATTTTTAGTGTATATT-AAA
131 ATAATGAAAAGAAAAACTCTGTTAATGAATTTGTAAATGAGACATATTTTTAGTGTATATTAAAA
493216 AAATAAAAATAATTAAATGATAT
196 AAATAAAAATAATTAAATGATAT
*
493239 ATATATAATTTTACAAATGAGATTAATATGTTATTTTATTAATTT-TTTTATAAAATTTTTATAT
1 ATATATAATTTTACAAATGAGATTAATATGTTATTTTATTAATTTATTTTATAAAATTTTTACAT
* *
493303 TTTAATATGGATATAAAAAATTATTATTCATATATGTATATATATAATATATTTATTTTACGCAC
66 TTTAATATGGATATAAAAAACTATTATTCATATATG--TATATATAATATATTTATTTTACACAC
493368 TAATAATGAAAAGAAAAACTCTGTTAATGAATTTGTAAATGAGACATATTTTTAGTGTATATTAA
129 TAATAATGAAAAGAAAAACTCTGTTAATGAATTTGTAAATGAGACATATTTTTAGTGTATATTAA
493433 AAAAATAAAAATAATTAAATGATAT
194 AAAAATAAAAATAATTAAATGATAT
493458 ATATAT
1 ATATAT
493464 CCAGCTGATG
Statistics
Matches: 216, Mismatches: 6, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
216 52 0.24
217 44 0.20
218 88 0.41
219 32 0.15
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (218 bp):
ATATATAATTTTACAAATGAGATTAATATGTTATTTTATTAATTTATTTTATAAAATTTTTACAT
TTTAATATGGATATAAAAAACTATTATTCATATATGTATATATAATATATTTATTTTACACACTA
ATAATGAAAAGAAAAACTCTGTTAATGAATTTGTAAATGAGACATATTTTTAGTGTATATTAAAA
AAATAAAAATAATTAAATGATAT
Found at i:495402 original size:16 final size:17
Alignment explanation
Indices: 495374--495405 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
495364 TAACGAACTC
495374 GAACTCGAAAATAATTA
1 GAACTCGAAAATAATTA
495391 GAACTC-AAAATAATT
1 GAACTCGAAAATAATT
495406 TAAATTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.25
Consensus pattern (17 bp):
GAACTCGAAAATAATTA
Found at i:495548 original size:22 final size:23
Alignment explanation
Indices: 495499--495548 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
495489 TCTAATGAAT
495499 TCAAAATCGATTAATCTTAATAC
1 TCAAAATCGATTAATCTTAATAC
*
495522 T--AAATCTGATTGA-CTTAA-AC
1 TCAAAATC-GATTAATCTTAATAC
495542 TCAAAAT
1 TCAAAAT
495549 AATAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
22 9 0.39
23 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (23 bp):
TCAAAATCGATTAATCTTAATAC
Found at i:503646 original size:21 final size:21
Alignment explanation
Indices: 503620--503662 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
503610 ACCACTGTAA
503620 ATAATTCCGTCCATCCAACCG
1 ATAATTCCGTCCATCCAACCG
503641 ATAATTCCGTCCATCCAACCG
1 ATAATTCCGTCCATCCAACCG
503662 A
1 A
503663 AAGGCAGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.37, G:0.09, T:0.23
Consensus pattern (21 bp):
ATAATTCCGTCCATCCAACCG
Found at i:506595 original size:20 final size:20
Alignment explanation
Indices: 506551--506613 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
506541 AATATAAAAA
* *
506551 TATAAAT-TTTAAAAAAACTT
1 TATAAATATATAAAATAA-TT
506571 T-TAAATATATAAAATAATT
1 TATAAATATATAAAATAATT
* *
506590 TATAAA-AAATTAAATATATT
1 TATAAATATATAAAATA-ATT
506610 TATA
1 TATA
506614 TTATATTTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TATAAATATATAAAATAATT
Found at i:511099 original size:2 final size:2
Alignment explanation
Indices: 511092--511118 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
511082 GGCTTGCTCT
511092 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 T
511119 TTAGGGGGGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:514792 original size:2 final size:2
Alignment explanation
Indices: 514785--514813 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
514775 ACAGCCTCCA
514785 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
514814 TATGTTAAGC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:517685 original size:23 final size:24
Alignment explanation
Indices: 517633--517687 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
517623 GGTGACTTGT
517633 TACATGAACCCTATTAAATATCTA
1 TACATGAACCCTATTAAATATCTA
* *
517657 TACATGTACCCTAATT-AAT-TTTA
1 TACATGAACCCT-ATTAAATATCTA
517680 TACATGAA
1 TACATGAA
517688 TTACATGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.37
24 14 0.52
25 3 0.11
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.36
Consensus pattern (24 bp):
TACATGAACCCTATTAAATATCTA
Found at i:522857 original size:6 final size:6
Alignment explanation
Indices: 522820--522910 Score: 71
Period size: 6 Copynumber: 15.0 Consensus size: 6
522810 CGATCGCGTA
* * * *
522820 TAAATT TAAAATTT TAATATT TAAA-- AAAATT TAAATT TAAATA AAAATA
1 TAAATT T-AAA-TT TAA-ATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
522869 T-AATT TAATTT TAATTT TAATATT TAAATT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT TAAATT
522911 ATTTTATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 3 0.04
5 4 0.06
6 44 0.63
7 15 0.21
8 4 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:522895 original size:19 final size:19
Alignment explanation
Indices: 522820--522907 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 19
522810 CGATCGCGTA
522820 TAAATTTAAAATTTTAATATT
1 TAAATTT-AAA-TTTAATATT
*
522841 TAAA--AAAATTTAA-ATT
1 TAAATTTAAATTTAATATT
** *
522857 TAAATAAAAATAT-A-ATT
1 TAAATTTAAATTTAATATT
* *
522874 TAATTTTAATTTTAATATT
1 TAAATTTAAATTTAATATT
522893 TAAATTTAAATTTAA
1 TAAATTTAAATTTAA
522908 ATTATTTTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
16 7 0.13
17 17 0.31
18 10 0.19
19 16 0.30
21 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAATTTAAATTTAATATT
Found at i:522925 original size:36 final size:36
Alignment explanation
Indices: 522849--522921 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
522839 TTTAAAAAAA
*
522849 TTTAA-ATTTAAATAAAAATATAATTTAATTTTAAT
1 TTTAATATTTAAATAAAAATATAAATTAATTTTAAT
** * *
522884 TTTAATATTTAAATTTAAATTTAAATT-ATTTTATT
1 TTTAATATTTAAATAAAAATATAAATTAATTTTAAT
522919 TTT
1 TTT
522922 TAATTATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 15 0.47
36 17 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
TTTAATATTTAAATAAAAATATAAATTAATTTTAAT
Found at i:524143 original size:23 final size:23
Alignment explanation
Indices: 524071--524143 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 23
524061 ATAACTTTAT
*
524071 ATATATATATTTTAAAAATATTATA
1 ATATA-ATATTTTAAAAATA-TAAA
524096 ATAT-ATATTTTAAAAAAATATAAA
1 ATATAATATTTT--AAAAATATAAA
*
524120 ATATAATATTTTAAATATATAAA
1 ATATAATATTTTAAAAATATAAA
524143 A
1 A
524144 AATTTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
23 18 0.42
24 7 0.16
25 18 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATAATATTTTAAAAATATAAA
Found at i:524145 original size:25 final size:25
Alignment explanation
Indices: 524071--524146 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
524061 ATAACTTTAT
*
524071 ATATATATATTTTAAAAATAT-TATA
1 ATATA-ATATTTTAAAAATATATAAA
*
524096 ATAT-ATATTTTAAAAAAATATAAA
1 ATATAATATTTTAAAAATATATAAA
* *
524120 ATATAATATTTTAAATATATAAAAA
1 ATATAATATTTTAAAAATATATAAA
524145 AT
1 AT
524147 TTTAAATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 14 0.32
24 7 0.16
25 23 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATAATATTTTAAAAATATATAAA
Found at i:524473 original size:2 final size:2
Alignment explanation
Indices: 524466--524498 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
524456 TTTCTTTGAC
524466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
524499 CTATTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:524852 original size:16 final size:16
Alignment explanation
Indices: 524815--524870 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
524805 TGAATTAATT
*
524815 TTAAATATTATAA-TAA
1 TTAAATATT-TAATTTA
524831 TATAAATATTTAATTTA
1 T-TAAATATTTAATTTA
*
524848 TTAAATATTTATTTTA
1 TTAAATATTTAATTTA
*
524864 TAAAATA
1 TTAAATA
524871 ATTATTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 24 0.69
17 11 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATATTTAATTTA
Found at i:524875 original size:16 final size:16
Alignment explanation
Indices: 524834--524908 Score: 77
Period size: 16 Copynumber: 4.9 Consensus size: 16
524824 ATAATAATAT
* *
524834 AAATATTTAATTTATT
1 AAATATTTATTTTATA
524850 AAATATTTATTTTATA
1 AAATATTTATTTTATA
*
524866 AAATAATTATTTT-T-
1 AAATATTTATTTTATA
*
524880 --ATTTTTATTTTATA
1 AAATATTTATTTTATA
*
524894 AAATAATTATTTTAT
1 AAATATTTATTTTAT
524909 TATAATTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
12 9 0.19
13 1 0.02
15 1 0.02
16 37 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAATATTTATTTTATA
Found at i:524898 original size:44 final size:43
Alignment explanation
Indices: 524839--524926 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
524829 AATATAAATA
* *
524839 TTTAATTTATTAAATATTTATTTTATAAAATAATTAT-TTTTATT
1 TTTAATTTATAAAATAATTATTTTAT--AATAATTATATTTTATT
* *
524883 TTTATTTTATAAAATAATTATTTTATTATAATTATATTTTATT
1 TTTAATTTATAAAATAATTATTTTATAATAATTATATTTTATT
524926 T
1 T
524927 AAGTGAACCG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
42 8 0.21
43 8 0.21
44 23 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (43 bp):
TTTAATTTATAAAATAATTATTTTATAATAATTATATTTTATT
Found at i:525308 original size:14 final size:15
Alignment explanation
Indices: 525287--525323 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
525277 AATAATAATA
525287 ATAATTTTAAAATTT
1 ATAATTTTAAAATTT
525302 A-AATTTTAAAATTT
1 ATAATTTTAAAATTT
525316 ATAATTTT
1 ATAATTTT
525324 TTAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATAATTTTAAAATTT
Found at i:525340 original size:15 final size:15
Alignment explanation
Indices: 525290--525340 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
525280 AATAATAATA
*
525290 ATTTTAAAATTTAA-
1 ATTTTAAAATTAAAT
525304 ATTTTAAAATTTATAAT
1 ATTTTAAAA-TTA-AAT
* *
525321 TTTTTAATATTAAAT
1 ATTTTAAAATTAAAT
525336 ATTTT
1 ATTTT
525341 TATACAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 9 0.30
15 9 0.30
16 5 0.17
17 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTAAAATTAAAT
Found at i:525738 original size:24 final size:24
Alignment explanation
Indices: 525704--525752 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
525694 AAAATAATTT
*
525704 TATTTTTATTTAAAAAATTAAAAA
1 TATTTTCATTTAAAAAATTAAAAA
* **
525728 TATTTTCATTTCAATGATTAAAAA
1 TATTTTCATTTAAAAAATTAAAAA
525752 T
1 T
525753 TCTTACATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTTTCATTTAAAAAATTAAAAA
Found at i:526333 original size:18 final size:18
Alignment explanation
Indices: 526324--526407 Score: 73
Period size: 18 Copynumber: 5.3 Consensus size: 18
526314 TTTAATTTTT
526324 ATTTTAAATTAAATTTAA
1 ATTTTAAATTAAATTTAA
*
526342 ATTTTAAATAAAATTT-A
1 ATTTTAAATTAAATTTAA
526359 A--TTAAATTAAA--TAA
1 ATTTTAAATTAAATTTAA
526373 ATTTT--ATT---TTTAA
1 ATTTTAAATTAAATTTAA
*
526386 TTTTTAAATTAAA-TTAA
1 ATTTTAAATTAAATTTAA
526403 ATTTT
1 ATTTT
526408 TTTACTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 21
0.68 0.05 0.27
Matches are distributed among these distances:
13 8 0.15
14 5 0.10
15 12 0.23
16 2 0.04
17 10 0.19
18 15 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTAAATTAAATTTAA
Found at i:529640 original size:27 final size:27
Alignment explanation
Indices: 529599--529658 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
529589 ATTATTAATA
529599 AATATTAAAAATAAT-TATAATATATTAT
1 AATA-TAAAAATAATATA-AATATATTAT
* *
529627 AATATAAAAGTAATATAAATATGTTAT
1 AATATAAAAATAATATAAATATATTAT
*
529654 TATAT
1 AATAT
529659 TAAATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
AATATAAAAATAATATAAATATATTAT
Found at i:529675 original size:33 final size:31
Alignment explanation
Indices: 529636--529723 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 31
529626 TAATATAAAA
* *
529636 GTAATATAAATATGTTATTATATTAAATTTTAT
1 GTAATATAAAT-TATTAATATATT-AATTTTAT
529669 GTAATATAAATTATTAATATATTAATTTTA-
1 GTAATATAAATTATTAATATATTAATTTTAT
*
529699 --AATAT-AATTATTATATATATAAATT
1 GTAATATAAATTATTA-ATATATTAATT
529724 ATAAACTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 8 0.16
28 15 0.29
31 7 0.14
32 10 0.20
33 11 0.22
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (31 bp):
GTAATATAAATTATTAATATATTAATTTTAT
Found at i:529680 original size:16 final size:17
Alignment explanation
Indices: 529636--529680 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
529626 TAATATAAAA
529636 GTAATATAAATATGTTAT
1 GTAATATAAAT-TGTTAT
529654 -T-ATATTAAATT-TTAT
1 GTAATA-TAAATTGTTAT
529669 GTAATATAAATT
1 GTAATATAAATT
529681 ATTAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
15 4 0.17
16 11 0.46
17 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (17 bp):
GTAATATAAATTGTTAT
Found at i:529688 original size:13 final size:14
Alignment explanation
Indices: 529665--529725 Score: 65
Period size: 13 Copynumber: 4.3 Consensus size: 14
529655 ATATTAAATT
529665 TTATGTAATATA-AA
1 TTAT-TAATATATAA
529679 TTATTAATATATTAA
1 TTATTAATATA-TAA
529694 TT-TTAA-ATATAA
1 TTATTAATATATAA
529706 TTATTATATATATAAA
1 TTATTA-ATATAT-AA
529722 TTAT
1 TTAT
529726 AAACTTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.12
13 13 0.32
14 9 0.22
15 8 0.20
16 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TTATTAATATATAA
Found at i:529695 original size:15 final size:15
Alignment explanation
Indices: 529672--529725 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
529662 ATTTTATGTA
529672 ATATAAATTATTAAT
1 ATATAAATTATTAAT
*
529687 ATATTAATT-TTAA-
1 ATATAAATTATTAAT
529700 ATAT-AATTATTATAT
1 ATATAAATTATTA-AT
529715 ATATAAATTAT
1 ATATAAATTAT
529726 AAACTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
12 4 0.12
13 7 0.21
14 5 0.15
15 12 0.35
16 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATAAATTATTAAT
Found at i:530237 original size:20 final size:18
Alignment explanation
Indices: 530196--530287 Score: 55
Period size: 20 Copynumber: 4.7 Consensus size: 18
530186 AAAAATAAAA
530196 ATATTTTTATAA-TAATATTT
1 ATATTTTTA-AATTAA-A-TT
530216 ATATATTTTATAATTAAATT
1 ATAT-TTTTA-AATTAAATT
*
530236 AT-TTTTTAAATTATTAAAT
1 ATATTTTTAAATTA--AATT
*
530255 A-ATAATTTAAATTAAATT
1 ATAT-TTTTAAATTAAATT
530273 ATATTAATTTAAATT
1 ATATT--TTTAAATT
530288 TTAAAAAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
17 5 0.08
18 9 0.15
19 8 0.14
20 25 0.42
21 9 0.15
22 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTTTTAAATTAAATT
Found at i:530298 original size:20 final size:20
Alignment explanation
Indices: 530240--530298 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
530230 TAAATTATTT
*
530240 TTTAAATTATTAAATAA-TAA
1 TTTAAATT-TTAAAAAATTAA
*
530260 TTTAAA--TTAAATTATATTAA
1 TTTAAATTTTAAA--AAATTAA
530280 TTTAAATTTTAAAAAATTA
1 TTTAAATTTTAAAAAATTA
530299 TGTGTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
17 5 0.16
19 1 0.03
20 20 0.65
22 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATTTTAAAAAATTAA
Found at i:530483 original size:16 final size:16
Alignment explanation
Indices: 530462--530519 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
530452 ATTTGATGTG
530462 AATTTTTAAAAATTAT
1 AATTTTTAAAAATTAT
*
530478 AATTTTTATTTAAATT-T
1 AATTTTTA--AAAATTAT
530495 AA-TTTTAAAAATATAT
1 AATTTTTAAAAAT-TAT
*
530511 AATTATTAA
1 AATTTTTAA
530520 TATATAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 4 0.12
15 1 0.03
16 16 0.47
17 8 0.24
18 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTTTAAAAATTAT
Found at i:531015 original size:18 final size:18
Alignment explanation
Indices: 530992--531029 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
530982 AAAATTAATT
530992 TAATTTTACATAT-ATTTA
1 TAATTTT-CATATAATTTA
*
531010 TAATTTTTATATAATTTA
1 TAATTTTCATATAATTTA
531028 TA
1 TA
531030 GTTATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATTTTCATATAATTTA
Found at i:531279 original size:20 final size:20
Alignment explanation
Indices: 531256--531317 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
531246 TCAATTTATT
531256 AAATTAAATAATTATATATA
1 AAATTAAATAATTATATATA
* *
531276 AAATTAATTAATTTTATAT-
1 AAATTAAATAATTATATATA
*
531295 TAATATAAATTAATATATATATA
1 AAAT-TAAA-TAAT-TATATATA
531318 TATATTTATG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
19 3 0.09
20 20 0.61
21 4 0.12
22 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTAAATAATTATATATA
Found at i:531307 original size:21 final size:22
Alignment explanation
Indices: 531267--531319 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
531257 AATTAAATAA
*
531267 TTATATATAAAATTAATTAATT
1 TTATATATAAAATAAATTAATT
*
531289 TTATAT-TAATATAAATTAATAT
1 TTATATATAAAATAAATTAAT-T
*
531311 ATATATATA
1 TTATATATA
531320 TATTTATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 12 0.46
22 12 0.46
23 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATATATAAAATAAATTAATT
Found at i:532008 original size:13 final size:13
Alignment explanation
Indices: 531990--532028 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
531980 AACAGATTAG
531990 ATTTATTTATATA
1 ATTTATTTATATA
532003 ATTTATTATATATTA
1 ATTTATT-TATA-TA
532018 A-TTATTTATAT
1 ATTTATTTATAT
532029 TATATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 11 0.46
14 9 0.38
15 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTATTTATATA
Found at i:532044 original size:19 final size:20
Alignment explanation
Indices: 532006--532049 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
531996 TTATATAATT
532006 TATTATATATTAATTATTTA
1 TATTATATATTAATTATTTA
*
532026 TATTATATA-TAATTTTTTA
1 TATTATATATTAATTATTTA
*
532045 AATTA
1 TATTA
532050 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTATATATTAATTATTTA
Found at i:532162 original size:21 final size:21
Alignment explanation
Indices: 532136--532176 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
532126 TTTTATTTTA
532136 AATTATTTTATAATATATATT
1 AATTATTTTATAATATATATT
*
532157 AATTATTTTATTATATATAT
1 AATTATTTTATAATATATAT
532177 ATATATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTATTTTATAATATATATT
Found at i:532199 original size:18 final size:18
Alignment explanation
Indices: 532138--532204 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
532128 TTATTTTAAA
532138 TTAT-TTTATAATATATAT
1 TTATATTTAT-ATATATAT
*
532156 TAATTATTTTATTATATATAT
1 TTA-TA-TTTA-TATATATAT
* *
532177 ATATATTTATATTTATAT
1 TTATATTTATATATATAT
*
532195 TTATAATTAT
1 TTATATTTAT
532205 TTCACGTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 18 0.46
19 5 0.13
20 2 0.05
21 13 0.33
22 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTTATATATATAT
Found at i:532204 original size:12 final size:12
Alignment explanation
Indices: 532128--532204 Score: 61
Period size: 12 Copynumber: 6.3 Consensus size: 12
532118 TAACTATATT
532128 TTAT-TTTA-AA
1 TTATATTTATAA
532138 TTAT-TTTATAA
1 TTATATTTATAA
* *
532149 TATATATTAATTA
1 T-TATATTTATAA
*
532162 TTTTATTATATATA
1 TTATATT-TATA-A
*
532176 TATATATTTATAT
1 T-TATATTTATAA
532189 TTATATTTATAA
1 TTATATTTATAA
532201 TTAT
1 TTAT
532205 TTCACGTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
10 8 0.15
11 3 0.06
12 22 0.42
13 9 0.17
14 6 0.11
15 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATTTATAA
Found at i:532274 original size:2 final size:2
Alignment explanation
Indices: 532267--532300 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
532257 CATCTCTTAA
532267 AG AG 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 AG AG
532301 TTAAGAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:537568 original size:5 final size:5
Alignment explanation
Indices: 537560--537584 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
537550 ATCTGACATC
537560 ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT
537585 GTTGGAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:539891 original size:43 final size:45
Alignment explanation
Indices: 539808--539905 Score: 119
Period size: 43 Copynumber: 2.2 Consensus size: 45
539798 AATTTGACTA
*** *
539808 ATTAATTTTATCTCACTCATCTTCATTCATTGTGTATAATATAGTAT
1 ATTAATTTTATCTCA--CATCTTCATTCATTAAATATAATATAATAT
*
539855 ATTAATTTTATCTCA-AT-TTCATTCATTAAATTTAATATAATAT
1 ATTAATTTTATCTCACATCTTCATTCATTAAATATAATATAATAT
539898 ATTAATTT
1 ATTAATTT
539906 CATTAATTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 29 0.63
44 2 0.04
47 15 0.33
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.51
Consensus pattern (45 bp):
ATTAATTTTATCTCACATCTTCATTCATTAAATATAATATAATAT
Found at i:539960 original size:73 final size:73
Alignment explanation
Indices: 539877--540023 Score: 267
Period size: 73 Copynumber: 2.0 Consensus size: 73
539867 TCAATTTCAT
*
539877 TCATTAAATTTAATATAATATATTAATTTCATTAATTACTTTTTAAATTATATTTTAATTCTTTT
1 TCATTAAATTTAATATAATATATTAATTTCATTAATTACTTTTTAAATTACATTTTAATTCTTTT
539942 TAGTAGAA
66 TAGTAGAA
* *
539950 TCATTGAATTTAATATAATATATTAATTTCATTAATTACTTTTTAAATTACATTTTAATTTTTTT
1 TCATTAAATTTAATATAATATATTAATTTCATTAATTACTTTTTAAATTACATTTTAATTCTTTT
540015 TAGTAGAA
66 TAGTAGAA
540023 T
1 T
540024 TTGAATGGTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.54
Consensus pattern (73 bp):
TCATTAAATTTAATATAATATATTAATTTCATTAATTACTTTTTAAATTACATTTTAATTCTTTT
TAGTAGAA
Found at i:540853 original size:90 final size:90
Alignment explanation
Indices: 540749--540915 Score: 244
Period size: 90 Copynumber: 1.9 Consensus size: 90
540739 GAACGAACAT
* ** *
540749 AAATTTAAAATTCTTACTAAACATGAATCAATACATGAACAAATTTAAAAATAAATAAACAAATA
1 AAATTTAAAATTCTTAATAAACATGAATCAATACACAAACAAATTTAAAAATAAACAAACAAATA
540814 CGTATAAAAATCTAAATACAAATTA
66 CGTATAAAAATCTAAATACAAATTA
* * * **
540839 AAATTTTAAATTCTTAATAAACATGAATCAGTACACAAATAAATTTAAAAATAAACAAATGAATA
1 AAATTTAAAATTCTTAATAAACATGAATCAATACACAAACAAATTTAAAAATAAACAAACAAATA
*
540904 TGTATAAAAATC
66 CGTATAAAAATC
540916 CGTTGACCCT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 67 1.00
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (90 bp):
AAATTTAAAATTCTTAATAAACATGAATCAATACACAAACAAATTTAAAAATAAACAAACAAATA
CGTATAAAAATCTAAATACAAATTA
Found at i:541495 original size:15 final size:15
Alignment explanation
Indices: 541472--541507 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
541462 GATCTGTTTG
* *
541472 TTATGAATTTGAATA
1 TTATAAATTTAAATA
541487 TTATAAATTTAAATA
1 TTATAAATTTAAATA
541502 TTATAA
1 TTATAA
541508 TTATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
TTATAAATTTAAATA
Found at i:542144 original size:2 final size:2
Alignment explanation
Indices: 542133--542169 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
542123 ATTTTTTGAC
*
542133 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
542170 ATTGAAAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:542843 original size:2 final size:2
Alignment explanation
Indices: 542838--542869 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
542828 AAATCATTTA
542838 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
542870 TTGCACTTAC
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):
AT
Found at i:543329 original size:4 final size:4
Alignment explanation
Indices: 543306--543352 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
543296 AACATATTCA
* * * *
543306 TATG TATA TATA TATA TATG TATG TATG TATG TATG TAGG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
543353 ATGCTTTGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:544076 original size:228 final size:232
Alignment explanation
Indices: 543553--544126 Score: 628
Period size: 234 Copynumber: 2.5 Consensus size: 232
543543 GTGGCGATCG
* *
543553 CCGTTGTTTGTAGTTGGATATTTATCATCTTTAGCTCCAACATCGGCCTTTCGATCCAGCGGATG
1 CCGTTGTTTGCAGTTGGATATTTATCATCTTTAGCTCCAACATCGGCCTTTCGATCCAGCTGATG
* * ** * * *
543618 AGTACTTGCCTGGCCACTTAAGATAAGAGCACGCTCCTTCTCCACGGTTAGCCGCTTTCCGTTGG
66 AGTACTTGCCTGACCACTTAAGATAACAGCACGCTCCTTCTCCACGGCCACCCGCTTTCCATTAG
* * * *
543683 CGTCCAGGGTGCGCTTCTTGTAATCCTTTGGATGAACAGTACGCGAACGAGAAGCAGGCCAAGGT
131 CGTCCAGGGTGCGCTTCTTGTAATCCTTTGAACGAACAG-ACACGAACGAGAAGCAGGCCAAGGA
* * *
543748 TTCGTAATTTTTATATAATAAAGGTGGCGTTGATCATCA
195 TTCCTAATGTTTATATAATAAAGGTGGCGCTGATCA-CA
* * * * * *
543787 CCCTTGTTTGCGGTTGAATATTTATCATCTTTAGCTCCAACCTCGGCCTTTCGGTCCAGCTGACG
1 CCGTTGTTTGCAGTTGGATATTTATCATCTTTAGCTCCAACATCGGCCTTTCGATCCAGCTGATG
* * * * * *
543852 AGTACTTGCCTGATCACTTAAGATAACCGCACGCTCCTTCTCCTCTGCCACCCGTTTTTTTCTAT
66 AGTACTTGCCTGACCACTTAAGATAACAGCACGCTCCTTCTCCACGGCCACCCG---CTTTCCAT
* * *
543917 TAGCTTCCATGGTGCGCTTGTTGTAATCCTTTGAACGAACAG-CACG-A-G-GAA-CAGGCCAAG
128 TAGCGTCCAGGGTGCGCTTCTTGTAATCCTTTGAACGAACAGACACGAACGAGAAGCAGGCCAAG
* *
543977 GATTCCT-ATCGTTTATA-AATTTACGGTGGCGCTGATC-C-
193 GATTCCTAAT-GTTTATATAA-TAAAGGTGGCGCTGATCACA
* * * *
544015 CTGTTGTTTGCAGTTGGATGTTTATGATCTTTAGCTCCAACATCGGCCTTTCGACCCAGCTGATG
1 CCGTTGTTTGCAGTTGGATATTTATCATCTTTAGCTCCAACATCGGCCTTTCGATCCAGCTGATG
* * * * *
544080 AGCAGTTGCCTGACCACTTAGGATAAGTA-CACGCTCTTTCTCCACGG
66 AGTACTTGCCTGACCACTTAAGATAA-CAGCACGCTCCTTCTCCACGG
544127 TGCGCTTGTC
Statistics
Matches: 282, Mismatches: 52, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
228 92 0.33
229 1 0.00
230 4 0.01
231 34 0.12
232 3 0.01
233 1 0.00
234 103 0.37
235 3 0.01
237 41 0.15
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (232 bp):
CCGTTGTTTGCAGTTGGATATTTATCATCTTTAGCTCCAACATCGGCCTTTCGATCCAGCTGATG
AGTACTTGCCTGACCACTTAAGATAACAGCACGCTCCTTCTCCACGGCCACCCGCTTTCCATTAG
CGTCCAGGGTGCGCTTCTTGTAATCCTTTGAACGAACAGACACGAACGAGAAGCAGGCCAAGGAT
TCCTAATGTTTATATAATAAAGGTGGCGCTGATCACA
Found at i:550202 original size:21 final size:21
Alignment explanation
Indices: 550150--550290 Score: 82
Period size: 21 Copynumber: 6.7 Consensus size: 21
550140 TAAAAGTAAT
550150 AAATTATTTAAATTT-ATTTAA
1 AAATTA-TTAAATTTAATTTAA
550171 AAATT-TTAAATTTAATTTAA
1 AAATTATTAAATTTAATTTAA
** *
550191 TCATTATTAAATTAAATTTAA
1 AAATTATTAAATTTAATTTAA
*
550212 ATAATT-TATAATTTTAA-TTAGA
1 A-AATTAT-TAAATTTAATTTA-A
** *
550234 ATTTTTATTTTTAA-TTAATATTAA
1 A-AATTA--TTAAATTTAAT-TTAA
550258 AAATT-TTAAATTTAAATTT--
1 AAATTATTAAATTT-AATTTAA
550277 AAATTATTAAATTT
1 AAATTATTAAATTT
550291 TAAACTAAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 27
0.69 0.10 0.20
Matches are distributed among these distances:
19 13 0.14
20 21 0.23
21 27 0.29
22 18 0.19
23 6 0.06
24 4 0.04
25 4 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (21 bp):
AAATTATTAAATTTAATTTAA
Found at i:550271 original size:6 final size:6
Alignment explanation
Indices: 550262--550376 Score: 57
Period size: 6 Copynumber: 19.3 Consensus size: 6
550252 TATTAAAAAT
* *
550262 TTTAAA TTTAAA TTTAAA TTATTAAA TTTTAAA CTAAAA TATT--A TTTAAA
1 TTTAAA TTTAAA TTTAAA -T-TTAAA -TTTAAA TTTAAA T-TTAAA TTTAAA
* * * *
550312 ---AAA TTTAAAA TTTTAT TTTAAA -TTAAA TTTAAA TTTTAAAA ATAAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA -TTT-AAA TTTAAA
550359 TTT-AA -TTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
550377 AATTTTTCAT
Statistics
Matches: 83, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 11 0.13
6 38 0.46
7 17 0.20
8 10 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:550275 original size:26 final size:25
Alignment explanation
Indices: 550246--550320 Score: 62
Period size: 26 Copynumber: 2.9 Consensus size: 25
550236 TTTTATTTTT
*
550246 AATTAATATTAAAAATTTTAAATTTA
1 AATTAATATTAAAAATTTTAAA-CTA
*
550272 AATTTAA-ATTATTAAATTTTAAACTA
1 AA-TTAATATTA-AAAATTTTAAACTA
* * *
550298 AAATATTATTTAAAAAATTTAAA
1 AATTAATA-TTAAAAATTTTAAA
550321 ATTTTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
25 2 0.05
26 20 0.51
27 17 0.44
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTAATATTAAAAATTTTAAACTA
Found at i:550288 original size:8 final size:7
Alignment explanation
Indices: 550258--550294 Score: 51
Period size: 6 Copynumber: 5.4 Consensus size: 7
550248 TTAATATTAA
550258 AAATTTT
1 AAATTTT
550265 AAA-TTT
1 AAATTTT
550271 AAA-TTT
1 AAATTTT
550277 AAATTATT
1 AAATT-TT
550285 AAATTTT
1 AAATTTT
550292 AAA
1 AAA
550295 CTAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.43
7 9 0.32
8 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
AAATTTT
Found at i:550299 original size:20 final size:20
Alignment explanation
Indices: 550258--550305 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
550248 TTAATATTAA
*
550258 AAATT-TTAAATTTAAATTT
1 AAATTATTAAATTTAAATCT
550277 AAATTATTAAATTTTAAA-CT
1 AAATTATTAAA-TTTAAATCT
*
550297 AAAATATTA
1 AAATTATTA
550306 TTTAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 14 0.56
21 6 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTATTAAATTTAAATCT
Found at i:550311 original size:53 final size:55
Alignment explanation
Indices: 550253--550368 Score: 139
Period size: 54 Copynumber: 2.1 Consensus size: 55
550243 TTTAATTAAT
* *
550253 ATTAAAAATTTTAAATTTAAATTTAAATT-A-TTAAATTTT-AAACTAAAATATTA
1 ATTAAAAATTTAAAATTTAAATTTAAATTAATTTAAATTTTAAAAATAAAAT-TTA
* * *
550306 TTTAAAAAATTTAAAATTTTATTTTAAATTAAATTTAAATTTTAAAAATAAAATTTA
1 ATT-AAAAATTTAAAATTTAAATTTAAATT-AATTTAAATTTTAAAAATAAAATTTA
550363 ATTAAA
1 ATTAAA
550369 TTTAAATTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
53 2 0.04
54 23 0.44
56 4 0.08
57 14 0.27
58 9 0.17
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (55 bp):
ATTAAAAATTTAAAATTTAAATTTAAATTAATTTAAATTTTAAAAATAAAATTTA
Found at i:550320 original size:21 final size:23
Alignment explanation
Indices: 550296--550344 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
550286 AATTTTAAAC
550296 TAAAATATTA-TTTAAA-AAATT
1 TAAAATATTATTTTAAATAAATT
*
550317 TAAAATTTTATTTTAAATTAAATT
1 TAAAATATTATTTTAAA-TAAATT
550341 TAAA
1 TAAA
550345 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 6 0.25
24 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAAATATTATTTTAAATAAATT
Found at i:550328 original size:24 final size:22
Alignment explanation
Indices: 550298--550349 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
550288 TTTTAAACTA
*
550298 AAATATTA-TTTAAA-AAATTT
1 AAATTTTATTTTAAATAAATTT
550318 AAAATTTTATTTTAAATTAAATTT
1 -AAATTTTATTTTAAA-TAAATTT
550342 AAATTTTA
1 AAATTTTA
550350 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 7 0.26
22 6 0.22
23 8 0.30
24 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATTTTATTTTAAATAAATTT
Found at i:550370 original size:54 final size:57
Alignment explanation
Indices: 550243--550374 Score: 146
Period size: 57 Copynumber: 2.3 Consensus size: 57
550233 AATTTTTATT
* *
550243 TTTAATTAATATTAAAAATTTTAAATTTAAATTTAAATTATTAAATTTTAAACTAAAA
1 TTTAATTAA-ATTTAAAATTTTAAATTTAAATTTAAATTATTAAATTTTAAAATAAAA
* *
550301 TATTATTTAAAAAATTTAAAATTTT-ATTTTAAA-TTAAA-T-TTAAATTTTAAAAATAAAA
1 T-TTAATT---AAATTTAAAATTTTAAATTTAAATTTAAATTATTAAATTTT-AAAATAAAA
550359 TTTAATTAAATTTAAA
1 TTTAATTAAATTTAAA
550375 TTAATTTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
54 9 0.14
57 14 0.22
58 11 0.17
59 10 0.16
60 7 0.11
61 11 0.17
62 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (57 bp):
TTTAATTAAATTTAAAATTTTAAATTTAAATTTAAATTATTAAATTTTAAAATAAAA
Found at i:551689 original size:2 final size:2
Alignment explanation
Indices: 551682--551707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
551672 TACTTGCCCT
551682 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
551708 AGTAAGCATC
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:552373 original size:10 final size:10
Alignment explanation
Indices: 552347--552434 Score: 58
Period size: 10 Copynumber: 8.5 Consensus size: 10
552337 ATATGCATAT
552347 AATATAA-AA
1 AATATAATAA
552356 AATA-AATAA
1 AATATAATAA
552365 AATATAATATA
1 AATATAATA-A
552376 AATATATATTTTAA
1 AATATA-A---TAA
*
552390 AATTTAATAA
1 AATATAATAA
*
552400 AATA-ATTTAA
1 AATATA-ATAA
*
552410 AAT-TAATTAT
1 AATATAA-TAA
552420 AATATAATAA
1 AATATAATAA
552430 AATAT
1 AATAT
552435 GAGAATATGA
Statistics
Matches: 62, Mismatches: 6, Indels: 21
0.70 0.07 0.24
Matches are distributed among these distances:
8 2 0.03
9 11 0.18
10 29 0.47
11 10 0.16
12 1 0.02
13 1 0.02
14 6 0.10
15 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AATATAATAA
Found at i:552378 original size:11 final size:12
Alignment explanation
Indices: 552343--552426 Score: 62
Period size: 12 Copynumber: 6.9 Consensus size: 12
552333 TTTTATATGC
552343 ATATAATATAAA
1 ATATAATATAAA
*
552355 AAATAA-ATAAA
1 ATATAATATAAA
552366 ATATAATATAAA
1 ATATAATATAAA
* *
552378 TATATATTTTAAA
1 -ATATAATATAAA
* *
552391 ATTTAATAAAATA
1 ATATAATATAA-A
* * *
552404 ATTTAAAATTAA
1 ATATAATATAAA
*
552416 TTATAATATAA
1 ATATAATATAA
552427 TAAAATATGA
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
11 10 0.19
12 25 0.46
13 19 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:558425 original size:16 final size:13
Alignment explanation
Indices: 558408--558446 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
558398 ACATAAACAT
558408 ACATAC-GAATCC
1 ACATACAGAATCC
558420 ACATACAGAATCC
1 ACATACAGAATCC
*
558433 ACATACGGAATCC
1 ACATACAGAATCC
558446 A
1 A
558447 GACAAGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 6 0.24
13 19 0.76
ACGTcount: A:0.44, C:0.31, G:0.10, T:0.15
Consensus pattern (13 bp):
ACATACAGAATCC
Found at i:561002 original size:2 final size:2
Alignment explanation
Indices: 560986--561024 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
560976 CCCATCAATT
* *
560986 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
561025 TTCCTCAAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:562945 original size:12 final size:12
Alignment explanation
Indices: 562928--562967 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
562918 GCAGTCAGTT
*
562928 GATGACGATGAG
1 GATGACGACGAG
*
562940 GATGACGACGAC
1 GATGACGACGAG
*
562952 GACGACGACGAG
1 GATGACGACGAG
562964 GATG
1 GATG
562968 CTGAAGACGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.40, T:0.10
Consensus pattern (12 bp):
GATGACGACGAG
Found at i:562951 original size:3 final size:3
Alignment explanation
Indices: 562943--563020 Score: 59
Period size: 3 Copynumber: 26.0 Consensus size: 3
562933 CGATGAGGAT
* * * *
562943 GAC GAC GAC GAC GAC GAC GAG GAT G-C TGAA GAC GAC GAT GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC -GAC GAC GAC GAC GAC GAC
* * * * *
562988 GGC GAA GGC GAT GAC AAC GAC GAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
563021 AGCGATGACG
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.33, C:0.26, G:0.36, T:0.05
Consensus pattern (3 bp):
GAC
Found at i:562964 original size:24 final size:24
Alignment explanation
Indices: 562931--562986 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
562921 GTCAGTTGAT
* *
562931 GACGATGAGGATGAC-GACGACGAC
1 GACGACGAGGATG-CTGAAGACGAC
562955 GACGACGAGGATGCTGAAGACGAC
1 GACGACGAGGATGCTGAAGACGAC
*
562979 GATGACGA
1 GACGACGA
562987 CGGCGAAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.34, C:0.20, G:0.38, T:0.09
Consensus pattern (24 bp):
GACGACGAGGATGCTGAAGACGAC
Found at i:563007 original size:27 final size:27
Alignment explanation
Indices: 562940--563029 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
562930 TGACGATGAG
* *
562940 GATGACGACGACGACGACGACGAGGATGC
1 GATGACAACGACGACGACGACGA-CA-GC
* * * *
562969 TGAAGACGACGATGACGACGGCGA-AGGC
1 -GATGACAACGACGACGACGACGACA-GC
562997 GATGACAACGACGACGACGACGACAGC
1 GATGACAACGACGACGACGACGACAGC
563024 GATGAC
1 GATGAC
563030 GATGAGAAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 27 0.53
28 4 0.08
30 20 0.39
ACGTcount: A:0.33, C:0.24, G:0.36, T:0.07
Consensus pattern (27 bp):
GATGACAACGACGACGACGACGACAGC
Found at i:567115 original size:3 final size:3
Alignment explanation
Indices: 567098--567138 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
567088 TACCCTCTTT
567098 ATA AT- ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
567139 GTAAAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:567222 original size:29 final size:30
Alignment explanation
Indices: 567190--567246 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
567180 TTAATTTAAA
567190 TTTATTTATTTCA-ATTA-TTATTTTTATAT
1 TTTATTTATTT-ATATTATTTATTTTTATAT
567219 TTTATTTATTTATATTATTTATTTTTAT
1 TTTATTTATTTATATTATTTATTTTTAT
567247 TTGTGTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 1 0.04
29 15 0.58
30 10 0.38
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTATTTATTTATATTATTTATTTTTATAT
Found at i:567247 original size:13 final size:13
Alignment explanation
Indices: 567191--567247 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
567181 TAATTTAAAT
567191 TTATTTATTTCAATTA
1 TTATTTATTT--A-TA
*
567207 TTATTT-TTATATT
1 TTATTTATT-TATA
567220 TTATTTATTTATA
1 TTATTTATTTATA
*
567233 TTATTTATTTTTA
1 TTATTTATTTATA
567246 TT
1 TT
567248 TGTGTGTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
13 24 0.67
14 3 0.08
15 2 0.06
16 7 0.19
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTATTTATA
Found at i:572150 original size:19 final size:19
Alignment explanation
Indices: 572126--572180 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
572116 GAAAATAATT
572126 TAGAATGGAATGGAATAGG
1 TAGAATGGAATGGAATAGG
*
572145 TAGAATGGAATTGAATAGG
1 TAGAATGGAATGGAATAGG
*
572164 TGGAATGGAATGGAATA
1 TAGAATGGAATGGAATA
572181 AAAATTTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.24
Consensus pattern (19 bp):
TAGAATGGAATGGAATAGG
Found at i:577619 original size:52 final size:52
Alignment explanation
Indices: 577471--577599 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
577461 CGAAATATGA
* *
577471 AAATTTGCCAGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
* * * *
577523 AAATTTACCTGTATGTATCAATATATTTCATAGTGTATCGATACATCTGGAC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
577575 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
577600 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
Found at i:577709 original size:19 final size:19
Alignment explanation
Indices: 577685--577734 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
577675 AGCGATACAT
577685 TGTATCGATACAAAACCTA
1 TGTATCGATACAAAACCTA
* **
577704 TGTATCGATACAACATTTA
1 TGTATCGATACAAAACCTA
577723 TGTATCGATACA
1 TGTATCGATACA
577735 TTGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACCTA
Found at i:577741 original size:13 final size:13
Alignment explanation
Indices: 577723--577747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
577713 ACAACATTTA
577723 TGTATCGATACAT
1 TGTATCGATACAT
577736 TGTATCGATACA
1 TGTATCGATACA
577748 AATCGTTGAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:579686 original size:3 final size:3
Alignment explanation
Indices: 579678--579711 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
579668 AAGAAAAACA
*
579678 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
579712 GAGTATTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:579807 original size:15 final size:15
Alignment explanation
Indices: 579787--579825 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
579777 TTGATCATCT
579787 AAATTATTATTAAAA
1 AAATTATTATTAAAA
*
579802 AAATTAAATATTAAAA
1 AAATT-ATTATTAAAA
*
579818 AATTTATT
1 AAATTATT
579826 TTATATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTATTATTAAAA
Found at i:583840 original size:35 final size:35
Alignment explanation
Indices: 583787--583858 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
583777 TATCTGTATG
* * *
583787 AACTGTTTGTCTATGTATGTTAAGTATTCTACAGA
1 AACTGTTTGTCGACGTATGTTAAGTATTCCACAGA
*
583822 AACTGTTTGTCGCCGTATGTTAAGTATTCCACAGA
1 AACTGTTTGTCGACGTATGTTAAGTATTCCACAGA
583857 AA
1 AA
583859 GGAGCCATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (35 bp):
AACTGTTTGTCGACGTATGTTAAGTATTCCACAGA
Found at i:584601 original size:3 final size:3
Alignment explanation
Indices: 584593--584633 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
584583 ACCTTGAAAA
584593 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
584634 ATTATTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:584612 original size:88 final size:88
Alignment explanation
Indices: 584433--584614 Score: 278
Period size: 88 Copynumber: 2.1 Consensus size: 88
584423 ACTACAGTTG
* * *
584433 TCTTTTATTAAATTTTAGATGTCAAACCAATCAAGAGCAACTTCATTCTATGCTTTTGGTCTTAC
1 TCTTCTATTAAATTTTAGATGTCAAACCAATCAAGACCAACTACATTCTATGCTTTTGGTCTTAC
* *
584498 CTCGAAAGTTTTTCTTTCTTTTT
66 CTCGAAAATTCTTCTTTCTTTTT
584521 TCTTCTATTAAATTTTAGATGTCAAACCAATCAAGACCAACTACATTCTATGC-TTTGGTCTTAC
1 TCTTCTATTAAATTTTAGATGTCAAACCAATCAAGACCAACTACATTCTATGCTTTTGGTCTTAC
*
584585 CTTGAAAATTCTTC-TTCTTCTTCT
66 CTCGAAAATTCTTCTTTCTT-TT-T
584609 TCTTCT
1 TCTTCT
584615 TCTTCTTCTT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
86 5 0.06
87 24 0.28
88 57 0.66
ACGTcount: A:0.25, C:0.21, G:0.09, T:0.45
Consensus pattern (88 bp):
TCTTCTATTAAATTTTAGATGTCAAACCAATCAAGACCAACTACATTCTATGCTTTTGGTCTTAC
CTCGAAAATTCTTCTTTCTTTTT
Found at i:584638 original size:3 final size:3
Alignment explanation
Indices: 584632--584658 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
584622 CTTCTTCTTC
584632 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
584659 CTACTCTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:588753 original size:13 final size:13
Alignment explanation
Indices: 588735--588760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
588725 TTGGTTTTGG
588735 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
588748 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
588761 GGAATTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
TTTTGTTTTTGTT
Found at i:589761 original size:6 final size:6
Alignment explanation
Indices: 589750--589776 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
589740 AGGCAACATC
589750 CATCTT CATCTT CATCTT CATCTT CAT
1 CATCTT CATCTT CATCTT CATCTT CAT
589777 ATGCTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (6 bp):
CATCTT
Found at i:590341 original size:48 final size:48
Alignment explanation
Indices: 590289--590387 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
590279 CTCTCTCTCT
* * *
590289 CTCTCTCTCCACCATTCCATCACGTGCTTCACCTTCTCGTACGCTGTC
1 CTCTCTCTCCACCACTCAATCACGTGCTTCACCTTCTCGTACGCTATC
590337 CTCTCTCTCCACCACTCAATCACGTGCTTCACCTTCTCGTACGCTATC
1 CTCTCTCTCCACCACTCAATCACGTGCTTCACCTTCTCGTACGCTATC
590385 CTC
1 CTC
590388 ACAGGTGCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.14, C:0.44, G:0.09, T:0.32
Consensus pattern (48 bp):
CTCTCTCTCCACCACTCAATCACGTGCTTCACCTTCTCGTACGCTATC
Found at i:591668 original size:2 final size:2
Alignment explanation
Indices: 591661--591699 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
591651 TAATCCTCAA
591661 AT 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 AT A
591700 ATCAAAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:592074 original size:3 final size:3
Alignment explanation
Indices: 592066--592098 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
592056 GATATCTCCA
*
592066 ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
592099 TCGATCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:594513 original size:2 final size:2
Alignment explanation
Indices: 594508--594537 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
594498 AGGGAAACAA
594508 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
594538 TTGGATCCAT
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:594628 original size:2 final size:2
Alignment explanation
Indices: 594621--594658 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
594611 GGCTTGTGAC
594621 AG AG AG AG 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 AG AG AG AG
594659 CCGCAATAGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:595122 original size:30 final size:27
Alignment explanation
Indices: 595067--595122 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
595057 TTATTATTTT
*
595067 ATTATTATTGTTATAGTTAGTTAATTA
1 ATTATTATTGTTATAGTTAGCTAATTA
*
595094 ATTATTATTAGTTATTAGTCTTGCTAATT
1 ATTATTATT-GTTA-TAGT-TAGCTAATT
595123 CCTAGCTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.38
28 4 0.17
29 4 0.17
30 7 0.29
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (27 bp):
ATTATTATTGTTATAGTTAGCTAATTA
Found at i:597167 original size:3 final size:3
Alignment explanation
Indices: 597159--597195 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
597149 TCTTTTTCTT
* *
597159 TTA TTA TTA TTG CTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
597196 ATAAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:597586 original size:2 final size:2
Alignment explanation
Indices: 597579--597611 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
597569 TTTTAGTTAA
597579 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
597612 AACACATATA
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:598478 original size:2 final size:2
Alignment explanation
Indices: 598471--598495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
598461 GACGGTGTTC
598471 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
598496 TCTAATGGAT
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:603436 original size:24 final size:27
Alignment explanation
Indices: 603375--603430 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
603365 AAAGCCACCA
* * *
603375 TTTGTGTTTGTCAAAAATGGTGGTTAC
1 TTTGTATTTGTAAAAAATGGTGGATAC
603402 TTTGTATTTGTAAAAAATGGTGGAT-C
1 TTTGTATTTGTAAAAAATGGTGGATAC
603428 TTT
1 TTT
603431 TTTTGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.46
Consensus pattern (27 bp):
TTTGTATTTGTAAAAAATGGTGGATAC
Found at i:607451 original size:3 final size:3
Alignment explanation
Indices: 607443--607473 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
607433 AACTTTAGAC
607443 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
607474 TAATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:612726 original size:29 final size:28
Alignment explanation
Indices: 612686--612754 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
612676 ATAATTAAAA
612686 ATAAAAAATATTTAT-TTTTAAAATTTT
1 ATAAAAAATATTTATCTTTTAAAATTTT
*
612713 ATAAAACATATATTTATCTTTT--AATATT
1 ATAAAA-A-ATATTTATCTTTTAAAATTTT
612741 -TAAAAAATATTTAT
1 ATAAAAAATATTTAT
612755 TCACCTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
25 8 0.21
26 1 0.03
27 11 0.29
28 6 0.16
29 8 0.21
30 4 0.11
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (28 bp):
ATAAAAAATATTTATCTTTTAAAATTTT
Found at i:612827 original size:34 final size:33
Alignment explanation
Indices: 612764--612840 Score: 77
Period size: 34 Copynumber: 2.3 Consensus size: 33
612754 TTCACCTATT
* *
612764 TTAA-TTTAATTAAAAATATATTTATTTTTTAA
1 TTAATTTTAAATAAAAATATATATATTTTTTAA
* *
612796 GTTAATTTTAAATAAAAATTTA-ATATCTTTTTTA
1 -TTAATTTTAAATAAAAATATATATAT-TTTTTAA
612830 TTAATTATTAA
1 TTAATT-TTAA
612841 TTATTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 13 0.35
34 24 0.65
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (33 bp):
TTAATTTTAAATAAAAATATATATATTTTTTAA
Found at i:612876 original size:16 final size:17
Alignment explanation
Indices: 612856--612888 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
612846 ATTTTTTAAA
612856 ATTTTT-ATT-TAAAAT
1 ATTTTTAATTATAAAAT
612871 ATTTTTAATTATAAAAT
1 ATTTTTAATTATAAAAT
612888 A
1 A
612889 ATAAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTTAATTATAAAAT
Found at i:613048 original size:23 final size:23
Alignment explanation
Indices: 613003--613052 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
612993 AACTTTGAAA
* *
613003 TAAATTTATTAAAATATTTTTAT
1 TAAATTAATTAAAATATTATTAT
*
613026 GTAAATTAATT-AATTATTATTAT
1 -TAAATTAATTAAAATATTATTAT
613049 TAAA
1 TAAA
613053 AAATTTAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 10 0.43
24 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TAAATTAATTAAAATATTATTAT
Found at i:613299 original size:26 final size:26
Alignment explanation
Indices: 613251--613304 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
613241 ATCTTTAAAC
* * *
613251 TTTTTAAAATAATAATAATTAATTTA
1 TTTTTAAAATAAAAATAAGTAATATA
613277 TTTTT-AAATAAAAATAACGTAATATA
1 TTTTTAAAATAAAAATAA-GTAATATA
613303 TT
1 TT
613305 AATATCAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
TTTTTAAAATAAAAATAAGTAATATA
Found at i:617651 original size:32 final size:33
Alignment explanation
Indices: 617597--617666 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 33
617587 TAATGTAATG
617597 TATAAATGTATAAATATTTTAAAATTTATATAA
1 TATAAATGTATAAATATTTTAAAATTTATATAA
* *
617630 TATAAAT-TATTAATTTTTTAAAATTTATATAA
1 TATAAATGTATAAATATTTTAAAATTTATATAA
617662 -ATAAA
1 TATAAA
617667 AAATATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 5 0.14
32 23 0.66
33 7 0.20
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
TATAAATGTATAAATATTTTAAAATTTATATAA
Found at i:617688 original size:3 final size:3
Alignment explanation
Indices: 617680--617720 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
617670 TATTTTAAAT
*
617680 ATA ATA ATA ATA ATA ATA ATA ATA AT- GTA ATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
617721 AAAATATGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 31 0.91
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:620315 original size:7 final size:8
Alignment explanation
Indices: 620299--620330 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
620289 TCTATCTGTC
620299 TTCTTTTT
1 TTCTTTTT
620307 TTCTTTTT
1 TTCTTTTT
620315 TTCTTTTT
1 TTCTTTTT
620323 TTCCTTTT
1 TT-CTTTT
620331 AACAGAGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTCTTTTT
Found at i:621827 original size:17 final size:18
Alignment explanation
Indices: 621785--621828 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
621775 TAAAATATTT
621785 TAAATATA-ATTATAATA
1 TAAATATATATTATAATA
621802 T-AATA-ATATATATAATA
1 TAAATATATAT-TATAATA
621819 TAAATATATA
1 TAAATATATA
621829 AATTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 6 0.26
17 9 0.39
18 4 0.17
19 3 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATATATATTATAATA
Found at i:621836 original size:11 final size:12
Alignment explanation
Indices: 621771--621838 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
621761 TTAAAATTGA
*
621771 TATATAAAATAT
1 TATATATAATAT
* *
621783 TTTAAAT-ATAAT
1 TATATATAAT-AT
*
621795 TATAATATAATAA
1 TAT-ATATAATAT
621808 TATATATAATAT
1 TATATATAATAT
*
621820 AAATATATAA-AT
1 -TATATATAATAT
621832 TATATAT
1 TATATAT
621839 GAATCTAGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
11 8 0.19
12 18 0.42
13 15 0.35
14 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATATAATAT
Found at i:621836 original size:17 final size:17
Alignment explanation
Indices: 621770--621837 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 17
621760 ATTAAAATTG
* * *
621770 ATATATAAAATATTTTA
1 ATATATAAATTATATAA
621787 A-ATAT-AATTATAATATA
1 ATATATAAATTAT-ATA-A
* *
621804 ATAATATATATAATATAA
1 AT-ATATAAATTATATAA
621822 ATATATAAATTATATA
1 ATATATAAATTATATA
621838 TGAATCTAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
15 5 0.13
16 5 0.13
17 15 0.38
18 3 0.08
19 7 0.18
20 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATAAATTATATAA
Found at i:627700 original size:50 final size:50
Alignment explanation
Indices: 627637--627796 Score: 284
Period size: 50 Copynumber: 3.2 Consensus size: 50
627627 AGGTATTGCC
627637 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
* * *
627687 ATTATTGACTATTCTTCACCAAGCTTTGACAATCGAGAGAGGTGGTCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
*
627737 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
627787 ATTGTTGACT
1 ATTGTTGACT
627797 CTAAGCAACT
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 103 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTA
Found at i:628146 original size:50 final size:50
Alignment explanation
Indices: 628085--628294 Score: 321
Period size: 50 Copynumber: 4.2 Consensus size: 50
628075 AGGTGTTGCC
* *
628085 ATTGTTGACTATTCTTCACCAACCTTTGACACTCGAGAGAGATGGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGATGGTCGTA
* * * * **
628135 ATTGTTAACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTAATCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGATGGTCGTA
* *
628185 ATTGTTGACTATTCTTCACCAACTTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGATGGTCGTA
*
628235 ATTGTTGACTATTCTTCACCAAACTTTGACAATAGAGAGAGATGGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGATGGTCGTA
628285 ATTGTTGACT
1 ATTGTTGACT
628295 CTAAGCAACT
Statistics
Matches: 147, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 147 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGATGGTCGTA
Found at i:629742 original size:18 final size:18
Alignment explanation
Indices: 629719--629755 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
629709 GCTTAACAGT
629719 TGATGGTGATTAAAATGA
1 TGATGGTGATTAAAATGA
629737 TGATGGTGATTAAAATGA
1 TGATGGTGATTAAAATGA
629755 T
1 T
629756 TAGATTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.35
Consensus pattern (18 bp):
TGATGGTGATTAAAATGA
Found at i:640099 original size:2 final size:2
Alignment explanation
Indices: 640092--640126 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
640082 TTTGTAGAGG
640092 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
640127 AAAGTTGGAA
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:646588 original size:2 final size:2
Alignment explanation
Indices: 646581--646612 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
646571 AGATCATCAT
646581 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
646613 CCTTATGTCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:654472 original size:15 final size:15
Alignment explanation
Indices: 654452--654482 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
654442 GTGCAACATT
654452 AAGTATGGAGTATTA
1 AAGTATGGAGTATTA
654467 AAGTATGGAGTATTA
1 AAGTATGGAGTATTA
654482 A
1 A
654483 CATTATCAAA
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:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (15 bp):
AAGTATGGAGTATTA
Found at i:659103 original size:2 final size:2
Alignment explanation
Indices: 659096--659150 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
659086 ATGTACATTT
* *
659096 TA TA TA TA TG TA CA T- 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 TA TA TA TA TA
659137 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
659151 GGCATAAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:659108 original size:17 final size:17
Alignment explanation
Indices: 659086--659139 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
659076 TTCATACACA
*
659086 ATGTACATTTTATATAT
1 ATGTACATTATATATAT
659103 ATGTACATTATATATAT
1 ATGTACATTATATATAT
* *
659120 ATATATATATATATATAT
1 ATGTACAT-TATATATAT
659138 AT
1 AT
659140 ATATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 22 0.67
18 11 0.33
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (17 bp):
ATGTACATTATATATAT
Found at i:661666 original size:17 final size:17
Alignment explanation
Indices: 661644--661694 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
661634 GTGTTGCGAC
*
661644 TAGGGCTGGGGCTAGGT
1 TAGGGCTAGGGCTAGGT
*
661661 TAGGGCTAGGGCTAGGGC
1 TAGGGCTAGGGCTA-GGT
*
661679 TAGGGCTAGGGTTAGG
1 TAGGGCTAGGGCTAGG
661695 GCTAAGGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.16, C:0.12, G:0.51, T:0.22
Consensus pattern (17 bp):
TAGGGCTAGGGCTAGGT
Found at i:661670 original size:6 final size:6
Alignment explanation
Indices: 661643--661706 Score: 85
Period size: 6 Copynumber: 10.8 Consensus size: 6
661633 GGTGTTGCGA
* *
661643 CTAGGG CTGGGG CTA-GG TTAGGG CTAGGG CTAGGG CTAGGG CTAGGG
1 CTAGGG CTAGGG CTAGGG CTAGGG CTAGGG CTAGGG CTAGGG CTAGGG
* *
661690 TTAGGG CTAAGG CTAGG
1 CTAGGG CTAGGG CTAGG
661707 TGTGATTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
5 4 0.08
6 45 0.92
ACGTcount: A:0.17, C:0.14, G:0.48, T:0.20
Consensus pattern (6 bp):
CTAGGG
Found at i:662164 original size:21 final size:21
Alignment explanation
Indices: 662138--662179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
662128 TGACAGACTG
*
662138 GGCAAGTCTT-ATGGTAGCCTA
1 GGCAAGT-TTCATGGCAGCCTA
662159 GGCAAGTTTCATGGCAGCCTA
1 GGCAAGTTTCATGGCAGCCTA
662180 CATCGATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
GGCAAGTTTCATGGCAGCCTA
Done.