Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold287
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: 796744
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
File 4 of 5
Found at i:476638 original size:27 final size:24
Alignment explanation
Indices: 476608--476673 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 24
476598 TGTATTTATG
476608 TTATATTTATATTATTTTTATATCATA
1 TTATATTTATATTATTTTT-TA--ATA
476635 TTATATTT-TAATTATTTTTTAATA
1 TTATATTTAT-ATTATTTTTTAATA
*
476659 TTATATTTATGTTAT
1 TTATATTTATATTAT
476674 GTTTCAGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 15 0.42
25 1 0.03
26 3 0.08
27 17 0.47
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
TTATATTTATATTATTTTTTAATA
Found at i:476664 original size:29 final size:27
Alignment explanation
Indices: 476603--476699 Score: 78
Period size: 27 Copynumber: 3.6 Consensus size: 27
476593 ATTTGTGTAT
*
476603 TTATGTTATATTTATATTATTTTTATA
1 TTATATTATATTTATATTATTTTTATA
*
476630 TCATATTATATTT-TAATTATTTTT-TA
1 TTATATTATATTTAT-ATTATTTTTATA
* *
476656 --ATATTATATTTATGTTATGTTTCAGT-
1 TTATATTATATTTATATTAT-TTTTA-TA
*
476682 TTATTTTATATTTTATAT
1 TTATATTATA-TTTATAT
476700 AAATTTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
24 15 0.27
25 4 0.07
26 3 0.05
27 21 0.38
28 7 0.12
29 6 0.11
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
TTATATTATATTTATATTATTTTTATA
Found at i:476777 original size:15 final size:16
Alignment explanation
Indices: 476756--476796 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
476746 ATTTTTAAAT
476756 AAATTTTATTAATT-A
1 AAATTTTATTAATTAA
*
476771 TAATTTTATTTAATTAA
1 AAATTTTA-TTAATTAA
476788 AAATTTTAT
1 AAATTTTAT
476797 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATTTTATTAATTAA
Found at i:477750 original size:3 final size:3
Alignment explanation
Indices: 477742--477782 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
477732 TTAATCTCTC
477742 TAT TAT TAT TACT CTAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T -TAT TAT TAT TAT TAT TAT TAT TAT TAT
477783 ACAAATTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 32 0.89
4 2 0.06
5 2 0.06
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:477758 original size:14 final size:14
Alignment explanation
Indices: 477739--477778 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
477729 AGATTAATCT
477739 CTCTATTATTATTA
1 CTCTATTATTATTA
477753 CTCTATTATTATTA
1 CTCTATTATTATTA
477767 -T-TATTATTATTA
1 CTCTATTATTATTA
477779 TTATACAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 11 0.42
13 1 0.04
14 14 0.54
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (14 bp):
CTCTATTATTATTA
Found at i:478812 original size:11 final size:11
Alignment explanation
Indices: 478791--478829 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
478781 GCCCATACAT
478791 TTTTTTCTCTTA
1 TTTTTT-TCTTA
*
478803 TTTTTTTCTTT
1 TTTTTTTCTTA
478814 TTTTTTTCTTA
1 TTTTTTTCTTA
478825 TTTTT
1 TTTTT
478830 CTTTACTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTCTTA
Found at i:479369 original size:22 final size:22
Alignment explanation
Indices: 479333--479389 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
479323 AATATAAATT
479333 AAATAATTAAAAAATAAC-ATATAA
1 AAATAATT--AAAAT-ACGATATAA
479357 AAATAATTAAAATACGATATAA
1 AAATAATTAAAATACGATATAA
479379 AAA-AATATAAA
1 AAATAAT-TAAA
479390 TATATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.16
22 18 0.58
24 8 0.26
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (22 bp):
AAATAATTAAAATACGATATAA
Found at i:480344 original size:5 final size:5
Alignment explanation
Indices: 480329--480405 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
480319 GATAAATTAG
** ** * *
480329 ATTTAA ATTTA ATTTA ATTTA AAATA AAATA TTTTA ATTATA AATTA ATTTA
1 ATTT-A ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATT-TA ATTTA ATTTA
480381 ATTTA ATTTA ATTTA TTATTTA ATT
1 ATTTA ATTTA ATTTA --ATTTA ATT
480406 ATAAAATATA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
5 47 0.78
6 8 0.13
7 5 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTTA
Found at i:480854 original size:17 final size:17
Alignment explanation
Indices: 480832--480867 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
480822 TTTATTTATT
480832 TTAAATAAAAAATTTAA
1 TTAAATAAAAAATTTAA
**
480849 TTAAATAATTAATTTAA
1 TTAAATAAAAAATTTAA
480866 TT
1 TT
480868 GATTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAAAAAATTTAA
Found at i:481210 original size:16 final size:15
Alignment explanation
Indices: 481189--481250 Score: 56
Period size: 15 Copynumber: 4.0 Consensus size: 15
481179 TAAAGATATT
481189 ATATATATAAATTTTA
1 ATATATATAAA-TTTA
481205 ATATAT-TGATAATTT-
1 ATATATAT-A-AATTTA
481220 ATATTATATAAATTTA
1 ATA-TATATAAATTTA
* *
481236 ATATTTTTAAATTTA
1 ATATATATAAATTTA
481251 TTTTTAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
15 19 0.49
16 17 0.44
17 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATATATATAAATTTA
Found at i:481227 original size:18 final size:19
Alignment explanation
Indices: 481184--481229 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
481174 ATTATTAAAG
481184 ATATTATATATATAAATTT
1 ATATTATATATATAAATTT
*
481203 -TAATATAT-TGAT-AATTT
1 ATATTATATAT-ATAAATTT
481220 ATATTATATA
1 ATATTATATA
481230 AATTTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATATTATATATATAAATTT
Found at i:481254 original size:12 final size:12
Alignment explanation
Indices: 481237--481277 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
481227 ATAAATTTAA
481237 TATTTTTAAATT
1 TATTTTTAAATT
481249 TATTTTTAAA-T
1 TATTTTTAAATT
*
481260 TATGTTTTATATT
1 TAT-TTTTAAATT
481273 TATTT
1 TATTT
481278 ATTTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 4 0.15
12 18 0.69
13 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (12 bp):
TATTTTTAAATT
Found at i:482135 original size:73 final size:73
Alignment explanation
Indices: 482061--482202 Score: 180
Period size: 73 Copynumber: 1.9 Consensus size: 73
482051 GTGTAAGTTT
* * *
482061 AATTTATTTTTTAATTTGATTATATGA-GTTTAGATT-TTCTTAAAATATGATATATTTTCATTT
1 AATTTA-TTTTTAAGTTGATTATA-GAGGTATAAATTATT-TTAAAATATGATATATTTTCATTT
482124 ATAAAAATTTA
63 ATAAAAATTTA
** * *
482135 AATTTATTTTTAAGTTGATTATAGAGGTATAAATTATTTTAAGGTATGATTTATTTTTATTTATA
1 AATTTATTTTTAAGTTGATTATAGAGGTATAAATTATTTTAAAATATGATATATTTTCATTTATA
482200 AAA
66 AAA
482203 TTAGTTTCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
72 2 0.03
73 49 0.83
74 8 0.14
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (73 bp):
AATTTATTTTTAAGTTGATTATAGAGGTATAAATTATTTTAAAATATGATATATTTTCATTTATA
AAAATTTA
Found at i:482468 original size:71 final size:72
Alignment explanation
Indices: 482308--483941 Score: 484
Period size: 74 Copynumber: 22.2 Consensus size: 72
482298 ATCTTTAGGC
* * * *
482308 ATGATTATACGA-ATT-AAATTATTAAGGTATAATTTATTTTTATTTGTGAAAGTTTAAATTTGT
1 ATGATTATACGAGTTTAAAATT-TTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTAT
*
482371 ATTTTGGT
65 TTTTTGGT
* * * * * *
482379 TTGATTATAGGAGTTTAAAATTTTAAGATATTATCTA-TTTT-TTTGTAAAATTTTAAAGTTATT
1 ATGATTATACGAGTTTAAAATTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATT
482442 TTTTAGGT
66 TTTT-GGT
* * * *
482450 ATGATTATATGAGTTTAAATTTTTTAA-AGTATGATTTATTTTTATTTGTAAAGGTTTAAATTT-
1 ATGATTATACGAGTTTAAA-ATTTTAAGA-TATAATTTATTTTTATTTGTAAAAGTTTAAATTTA
*
482513 GTTTTT-GT
64 TTTTTTGGT
* * * *
482521 TTGATTATACAAGTTTAAATTTTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTATATTTAT
1 ATGATTATACGAGTTTAAA-ATTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTAT
*
482586 TTTTTGAT
65 TTTTTGGT
* * * * *
482594 -TGATTATAGGAG-TTAAAATTTTTTTAAGGTATGATTTATTTTTACTTGTCAAATTAGTTT-GA
1 ATGATTATACGAGTTTAAAA---TTTTAAGATATAATTTATTTTTATTTGT-AAA--AGTTTAAA
*
482656 TTT-TTATTTTGAT
60 TTTATT-TTTTGGT
* * * * * ** *
482669 -TGCATTAGTGC-ATTTTTATTGAAATATT-AG--GTAATTCATATTTTAAATG-AAAATATTGT
1 ATG-ATTA-TACGA-GTTTA---AAATTTTAAGATATAATTTAT-TTTTATTTGTAAAA-GTT-T
* *
482728 TATTTGTAAAAATGTTTTTGGGT
57 AAATT-T----AT-TTTTT-GGT
* * * *
482751 ATAATTATACGAATTT-AAATTATTAAGATATAATTAATTTTTATTTGTAGAAGTTTAAATTTAT
1 ATGATTATACGAGTTTAAAATT-TTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTAT
*
482815 ATTTTGGT
65 TTTTTGGT
* * * * * * * *
482823 TTGATTATAAGAATCTAAATTTTTAAGGTATTA-TT-TTTTTA-TTG---AAGTTGT---TATAT
1 ATGATTATACGAGTTTAAAATTTTAAGATATAATTTATTTTTATTTGTAAAAGTT-TAAATTTAT
482879 TTTTTGGGT
65 TTTTT-GGT
* * * * * *
482888 ATGATTATATGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTGTGAAAGTTTATATTTAT
1 ATGATTATACGAGTTTAAA-ATTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTAT
*
482953 TTTTTGAT
65 TTTTTGGT
* * * * *
482961 TTGATTATACAAGTTTAAAATTTTTTAAGATATGATTT-TTTCTTATTTATAAAAATTTAAATTT
1 ATGATTATACGAGTTTAAAA--TTTTAAGATATAATTTATTT-TTATTTGTAAAAGTTTAAATTT
483025 ATTTTTTGAGT
63 ATTTTTTG-GT
* * * * * *
483036 -TGATTATAAGAG-TTAAAATTTTTTTAAAGGTA-GATATATTTTTATTTATAAGATTAGTTT-G
1 ATGATTATACGAGTTTAAAA---TTTT-AAGATATAATTTATTTTTATTTGTAA-A--AGTTTAA
*
483097 ATTT-TTATTTTGAT
59 ATTTATT-TTTTGGT
* * * * * ** ** *
483111 -TGCATTAGT--GTATTTTTGTAGAAATATT-AG--GTGATTCATATTTTAAATAAAAATATTTT
1 ATG-ATTA-TACG-A--GTT-TA-AAATTTTAAGATATAATTTAT-TTTTATTTGTAAA-A-GTT
* * *
483170 TTATTTGTAAAAAGTGTTTTGGGTT
56 TAAATT-T----A-T-TTTTTGG-T
* * *
483195 AT-ATTATAGGAGTTT-AAATTATTAAGATATAATTTATTTTTATTCGTAAAAGTTTAAATTTGT
1 ATGATTATACGAGTTTAAAATT-TTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTAT
*
483258 ATTTTGGT
65 TTTTTGGT
* * * * ** *
483266 TTGATTATAGGAG-TTAAATTTTTAAG--AT--GTTATTTTT-TTTGTAAAAAATTAGATTTATT
1 ATGATTATACGAGTTTAAAATTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATT
* *
483325 TATGGGT
66 TTTTGGT
* * ** * * * *
483332 ATGATTACATGAGTTTTAATTTTTTTAAGGTATGACTTAGTTTTATTTGTAAAAGTTTAAATTTA
1 ATGATTATACGAG-TTTAA-AATTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTA
483397 TTTTTAT--T
64 TTTTT-TGGT
** * **
483405 -TGATTATACGAGTTTAATTTTTTTAAGATGTGGTTTATTTTTATTTGTAAAAGTTTAAATTTAA
1 ATGATTATACGAGTTTAA-AATTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTT-A
*
483469 TTTTTGGGT
64 TTTTTTGGT
* * * *
483478 -TGATTATATGAGTATAAATTATTTT-AGGTATAATTTATTTTTATTTGTAAGATTAGTTT-TAT
1 ATGATTATACGAGTTTAAA--ATTTTAAGATATAATTTATTTTTATTTGTAA-A--AGTTTAAAT
*
483540 TT-TTATTTTGAT
61 TTATT-TTTTGGT
* * *** ** * **
483552 -TGAAT-TA-GTGTATTTTTATTGAAATATTAGGTAATTGGTA-TTTTAAATG-AAAA-TATATA
1 ATGATTATACGAGT-TTAAAATTTTAAGA-TA--TAATT--TATTTTTATTTGTAAAAGT-T-TA
** *
483611 TTTTTTATAAAAGTGTTTTAGAAT
58 -AATTTAT-----T-TTTT-G-GT
* * * * * *
483635 ATGATTATACAAGTTTAAATTTTTTAAAGA-ATAGTTTATTTTTATTTTTAAAA-TTTTAATTTG
1 ATGATTATACGAGTTTAAA-ATTTT-AAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTA
**
483698 TTTTTTAATT
64 TTTTTT-GGT
* * * ** *
483708 TTG-TTATATGAGTTTAAAATTTTAA-AGTATTATTTATTTTTATTTGTAAAAGTTTATGTTTGT
1 ATGATTATACGAGTTTAAAATTTTAAGA-TATAATTTATTTTTATTTGTAAAAGTTTAAATTTAT
*
483771 TTTTTAAGT
65 TTTTT-GGT
* ** ** * * *
483780 ATAATGGTACGAGTTTTAATTTTTTAA-AGTATGATTTATTTATATTTGTAAAAATTTAAATTTA
1 ATGATTATACGAG-TTTAAAATTTTAAGA-TATAATTTATTTTTATTTGTAAAAGTTTAAATTTA
483844 TTTTTTGGT
64 TTTTTTGGT
* * ** * *
483853 TTGATTATACGAGTTTAAATTTTTTTAAGGCATGATTTGTTTTTATTTGTAAAAGTTTAAATTTA
1 ATGATTATACGAGTTTAAA--ATTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTA
483918 TTTTTTAGGT
64 TTTTTT-GGT
*
483928 -TGATTATAGGAGTT
1 ATGATTATACGAGTT
483942 AATTTTTTTA
Statistics
Matches: 1178, Mismatches: 235, Indels: 297
0.69 0.14 0.17
Matches are distributed among these distances:
64 8 0.01
65 18 0.02
66 49 0.04
67 11 0.01
68 10 0.01
69 17 0.01
70 29 0.02
71 183 0.16
72 149 0.13
73 151 0.13
74 255 0.22
75 65 0.06
76 58 0.05
77 15 0.01
78 17 0.01
79 15 0.01
80 19 0.02
81 44 0.04
82 23 0.02
83 22 0.02
84 7 0.01
85 6 0.01
86 4 0.00
87 3 0.00
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (72 bp):
ATGATTATACGAGTTTAAAATTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATT
TTTTGGT
Found at i:483000 original size:138 final size:136
Alignment explanation
Indices: 482742--483001 Score: 326
Period size: 138 Copynumber: 1.9 Consensus size: 136
482732 TGTAAAAATG
482742 TTTTTGGGTATAATTATACGAATTTAAATTATTAAGATATAATTAATTTTTATTTGTAGAAGTTT
1 TTTTTGGGTATAATTATACGAATTTAAATTATTAAGATATAATTAATTTTTATTTGTAGAAGTTT
* * *
482807 AAATTTATATTTTGGTTTGATTATAAGAATCTAAATTTTTAAGGTATTATTTTTTTATTGAAGTT
66 AAATTTATATTTTGATTTGATTATAAGAATCTAAATTTTTAAGATATGA-TTTTTTATTGAAGTT
482872 GTTATAT
130 GTTATAT
* * * * * * *
482879 TTTTTGGGTATGATTATATGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTGT-GAAAGT
1 TTTTTGGGTATAATTATACGAATTTAAA-TTATTAAGATATAATTAATTTTTATTTGTAG-AAGT
* * * *
482943 TTATATTTATTTTTTGATTTGATTATACA-AGTTTAAAATTTTTTAAGATATGATTTTTT
64 TTAAATTTATATTTTGATTTGATTATA-AGAATCT-AAA-TTTTTAAGATATGATTTTTT
483002 CTTATTTATA
Statistics
Matches: 104, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
137 26 0.25
138 56 0.54
139 10 0.10
140 12 0.12
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (136 bp):
TTTTTGGGTATAATTATACGAATTTAAATTATTAAGATATAATTAATTTTTATTTGTAGAAGTTT
AAATTTATATTTTGATTTGATTATAAGAATCTAAATTTTTAAGATATGATTTTTTATTGAAGTTG
TTATAT
Found at i:483166 original size:442 final size:443
Alignment explanation
Indices: 481992--484054 Score: 2339
Period size: 442 Copynumber: 4.7 Consensus size: 443
481982 ATTTATAAAA
* * * * * * * * **
481992 ATATTTTTT-TGTATGAATATTTGAATTTAAATTTTATAAAATATAATTTATTCTTATTTGTGTA
1 ATATTTTTTAGGTATGATTATATGAGTTTAAATTTTTTAAAGTATGATTTATTTTTATTTGTAAA
* * * * * *
482056 AGTTT-AATTTATTTTTTAATTTGATTATATGAGTTTAGATTTTCTTAAAATATGATATATTTTC
66 AGTTTAAATTTATTTTTTGATTTGATTATACGAGTTTAAATTTT-TTAAGATATGATTTATTTTT
* * * * *
482120 ATTTATAAAAATTTAAATTTA-TTTTTAAGTTGATTAT-AGAGGTATAAATTATTTTAAGGTATG
130 ATTTGTAAAAGTTTAAATTTATTTTTTGAGTTGATTATAAGAGTTA-AAATTTTTTTAAGGTATG
* * *
482183 ATTTATTTTTATTTATAAAATTAGTTTCATTTTTATTTTAATTGCATTAGTATATTTTTGTTGAA
194 ATTTATTTTTATTTATAAAATTAGTTTGATTTTTATTTTGATTGCATTAGTGTATTTTTGTTGAA
** * * * * * *
482248 ATATTAGGTAATTCATATTTTAAACAAAAATATTTTTTATTTGCAAAAATATCTTTAGGCATGAT
259 ATATTAGGTAATTCATATTTTAAATGAAAATATTTTTTATTTGTAAAAATGTTTTTGGGTATAAT
*
482313 TATACGAA-TTAAATTATTAAGGTATAATTTATTTTTATTTGT-GAAAGTTTAAATTTGTATTTT
324 TATACGAATTTAAATTATTAAGATATAATTTATTTTTATTTGTAG-AAGTTTAAATTTGTATTTT
482376 GGTTTGATTATAGGAGTTTAAAATTTTAAGATATTATCTATTTTTTTGTAAAATT-TT
388 GGTTTGATTATAGGAGTTTAAAATTTTAAGATATTAT-TATTTTTTTG-AAAATTGTT
482433 AAAGTTATTTTTTAGGTATGATTATATGAGTTTAAATTTTTTAAAGTATGATTTATTTTTATTTG
1 --A--TATTTTTTAGGTATGATTATATGAGTTTAAATTTTTTAAAGTATGATTTATTTTTATTTG
* * * *
482498 TAAAGGTTTAAATTT-GTTTTTG-TTTGATTATACAAGTTTAAATTTTTTAAGATATAATTTATT
62 TAAAAGTTTAAATTTATTTTTTGATTTGATTATACGAGTTTAAATTTTTTAAGATATGATTTATT
* *
482561 TTTATTTGTAAAAGTTTATATTTATTTTTTGA-TTGATTATAGGAGTTAAAATTTTTTTAAGGTA
127 TTTATTTGTAAAAGTTTAAATTTATTTTTTGAGTTGATTATAAGAGTTAAAATTTTTTTAAGGTA
* * * * *
482625 TGATTTATTTTTACTTGTCAAATTAGTTTGATTTTTATTTTGATTGCATTAGTGCATTTTTATTG
192 TGATTTATTTTTATTTATAAAATTAGTTTGATTTTTATTTTGATTGCATTAGTGTATTTTTGTTG
*
482690 AAATATTAGGTAATTCATATTTTAAATGAAAATA-TTGTTATTTGTAAAAATGTTTTTGGGTATA
257 AAATATTAGGTAATTCATATTTTAAATGAAAATATTTTTTATTTGTAAAAATGTTTTTGGGTATA
* *
482754 ATTATACGAATTTAAATTATTAAGATATAATTAATTTTTATTTGTAGAAGTTTAAATTTATATTT
322 ATTATACGAATTTAAATTATTAAGATATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTATTT
* * * * * *
482819 TGGTTTGATTATAAGAATCTAAATTTTTAAGGTATTATT-TTTTTATTG-AAGTTGTT
387 TGGTTTGATTATAGGAGTTTAAAATTTTAAGATATTATTATTTTT-TTGAAAATTGTT
* * *
482875 ATATTTTTTGGGTATGATTATATGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTGTGAA
1 ATATTTTTTAGGTATGATTATATGAGTTTAAATTTTTTAAAGTATGATTTATTTTTATTTGTAAA
* *
482940 AGTTTATATTTATTTTTTGATTTGATTATACAAGTTTAAAATTTTTTAAGATATGATTT-TTTCT
66 AGTTTAAATTTATTTTTTGATTTGATTATACGAGTTT-AAATTTTTTAAGATATGATTTATTT-T
* *
483004 TATTTATAAAAATTTAAATTTATTTTTTGAGTTGATTATAAGAGTTAAAATTTTTTTAAAGGTA-
129 TATTTGTAAAAGTTTAAATTTATTTTTTGAGTTGATTATAAGAGTTAAAATTTTTTT-AAGGTAT
* * *
483068 GATATATTTTTATTTATAAGATTAGTTTGATTTTTATTTTGATTGCATTAGTGTATTTTTGTAGA
193 GATTTATTTTTATTTATAAAATTAGTTTGATTTTTATTTTGATTGCATTAGTGTATTTTTGTTGA
* *
483133 AATATTAGGTGATTCATATTTTAAATAAAAATATTTTTTATTTGTAAAAA-GTGTTTTGGGT-TA
258 AATATTAGGTAATTCATATTTTAAATGAAAATATTTTTTATTTGTAAAAATGT-TTTTGGGTATA
* * * *
483196 TATTATAGGAGTTTAAATTATTAAGATATAATTTATTTTTATTCGTAAAAGTTTAAATTTGTATT
322 -ATTATACGAATTTAAATTATTAAGATATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTATT
* * *
483261 TTGGTTTGATTATAGGAG-TTAAATTTTTAAGATGTTATT-TTTTTTGTAAAAAATTAGATT
386 TTGGTTTGATTATAGGAGTTTAAAATTTTAAGATATTATTATTTTTT-T-GAAAATT-G-TT
* * * * * * *
483321 -TA-TTTATGGGTATGATTACATGAGTTTTAATTTTTTTAAGGTATGACTTAGTTTTATTTGTAA
1 ATATTTTTTAGGTATGATTATATGAG-TTTAAATTTTTTAAAGTATGATTTATTTTTATTTGTAA
* * *
483384 AAGTTTAAATTTA-TTTTT-ATTTGATTATACGAGTTTAATTTTTTTAAGATGTGGTTTATTTTT
65 AAGTTTAAATTTATTTTTTGATTTGATTATACGAGTTTAAATTTTTTAAGATATGATTTATTTTT
* * * * *
483447 ATTTGTAAAAGTTTAAATTTAATTTTTGGGTTGATTATATGAG-TATAAATTATTTT-AGGTATA
130 ATTTGTAAAAGTTTAAATTTATTTTTTGAGTTGATTATAAGAGTTA-AAATTTTTTTAAGGTATG
* * * * *
483510 ATTTATTTTTATTTGTAAGATTAGTTTTATTTTTATTTTGATTGAATTAGTGTATTTTTATTGAA
194 ATTTATTTTTATTTATAAAATTAGTTTGATTTTTATTTTGATTGCATTAGTGTATTTTTGTTGAA
** * * * * ** *
483575 ATATTAGGTAATTGGTATTTTAAATGAAAATATATATTT-TTTATAAAAGTGTTTTAGAATATGA
259 ATATTAGGTAATTCATATTTTAAATGAAAATAT-TTTTTATTTGTAAAAATGTTTTTGGGTATAA
* * * * * *
483639 TTATAC-AAGTTTAAATTTTTTAAAGA-ATAGTTTATTTTTATTTTTA-AAATTTTAATTTGTTT
323 TTATACGAA-TTTAAA-TTATT-AAGATATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTAT
** *
483701 TTTAATTTTG-TTATATGAGTTTAAAATTTTAA-AGTATTATTTATTTTTATTTGTAAAAGTTTA
385 TTT-GGTTTGATTATAGGAGTTTAAAATTTTAAGA-TATTA-TTA-TTTT-TTTG-AAAA---T-
483764 TGTT
440 TGTT
* * * ** * * *
483768 -TGTTTTTTAAGTATAATGGTACGAGTTTTAATTTTTTAAAGTATGATTTATTTATATTTGTAAA
1 ATATTTTTTAGGTATGATTATATGAGTTTAAATTTTTTAAAGTATGATTTATTTTTATTTGTAAA
* * ** *
483832 AATTTAAATTTATTTTTTGGTTTGATTATACGAGTTTAAATTTTTTTAAGGCATGATTTGTTTTT
66 AGTTTAAATTTATTTTTTGATTTGATTATACGAGTTTAAA-TTTTTTAAGATATGATTTATTTTT
* *
483897 ATTTGTAAAAGTTTAAATTTATTTTTT-AGGTTGATTATAGGAGTT--AATTTTTTTAAAAGT-T
130 ATTTGTAAAAGTTTAAATTTATTTTTTGA-GTTGATTATAAGAGTTAAAATTTTTTT-AAGGTAT
* * * *
483958 AGATGTATTTTTATATATAAAATCAG-TTGATTTTTATTTTGATTGCATTAGTATATTTTTGTTG
193 -GATTTATTTTTATTTATAAAATTAGTTTGATTTTTATTTTGATTGCATTAGTGTATTTTTGTTG
484022 AAATATTAGGTAATT-ACTATTTTAAATGAAAAT
257 AAATATTAGGTAATTCA-TATTTTAAATGAAAAT
484055 GTAAATTATT
Statistics
Matches: 1387, Mismatches: 177, Indels: 106
0.83 0.11 0.06
Matches are distributed among these distances:
438 70 0.05
439 6 0.00
440 27 0.02
441 193 0.14
442 262 0.19
443 167 0.12
444 257 0.19
445 99 0.07
446 58 0.04
447 52 0.04
448 29 0.02
449 86 0.06
450 80 0.06
451 1 0.00
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.53
Consensus pattern (443 bp):
ATATTTTTTAGGTATGATTATATGAGTTTAAATTTTTTAAAGTATGATTTATTTTTATTTGTAAA
AGTTTAAATTTATTTTTTGATTTGATTATACGAGTTTAAATTTTTTAAGATATGATTTATTTTTA
TTTGTAAAAGTTTAAATTTATTTTTTGAGTTGATTATAAGAGTTAAAATTTTTTTAAGGTATGAT
TTATTTTTATTTATAAAATTAGTTTGATTTTTATTTTGATTGCATTAGTGTATTTTTGTTGAAAT
ATTAGGTAATTCATATTTTAAATGAAAATATTTTTTATTTGTAAAAATGTTTTTGGGTATAATTA
TACGAATTTAAATTATTAAGATATAATTTATTTTTATTTGTAGAAGTTTAAATTTGTATTTTGGT
TTGATTATAGGAGTTTAAAATTTTAAGATATTATTATTTTTTTGAAAATTGTT
Found at i:483378 original size:140 final size:143
Alignment explanation
Indices: 483204--483527 Score: 358
Period size: 140 Copynumber: 2.3 Consensus size: 143
483194 TATATTATAG
* * * * * * *
483204 GAGTTTAAATTA-TTAAGATATAATTTATTTTTATTCGTAAAAGTTTAAATTTGTATTTTGGTTT
1 GAGTATAAATTATTTTAGGTATAACTTAGTTTTATTTGTAAAAGTTTAAA-TT-TATTTTGATTT
* *
483268 GATTATAGGAG-TTAA-ATTTTTAAGA-T-G-TTATTTTT-TTTGTAAAAAATTAGATTT-ATTT
64 GATTATACGAGTTTAATATTTTTAAGAGTGGTTTATTTTTATTTGTAAAAAATTAAATTTAATTT
483326 ATGGGTATGATTACAT
129 ATGGGT-TGATTACAT
* * * * *
483342 GAGTTTTAATTTTTTTAAGGTATGACTTAGTTTTATTTGTAAAAGTTTAAATTTATTTTTATTTG
1 GAGTATAAATTATTTT-AGGTATAACTTAGTTTTATTTGTAAAAGTTTAAATTTATTTTGATTTG
* **
483407 ATTATACGAGTTTAATTTTTTTAAGATGTGGTTTATTTTTATTTGTAAAAGTTTAAATTTAATTT
65 ATTATACGAGTTTAATATTTTTAAGA-GTGGTTTATTTTTATTTGTAAAAAATTAAATTTAATTT
* *
483472 TTGGGTTGATTATAT
129 ATGGGTTGATTACAT
* *
483487 GAGTATAAATTATTTTAGGTATAATTTATTTTTATTTGTAA
1 GAGTATAAATTATTTTAGGTATAACTTAGTTTTATTTGTAA
483528 GATTAGTTTT
Statistics
Matches: 153, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
138 29 0.19
139 8 0.05
140 38 0.25
142 1 0.01
143 1 0.01
144 30 0.20
145 37 0.24
146 9 0.06
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.53
Consensus pattern (143 bp):
GAGTATAAATTATTTTAGGTATAACTTAGTTTTATTTGTAAAAGTTTAAATTTATTTTGATTTGA
TTATACGAGTTTAATATTTTTAAGAGTGGTTTATTTTTATTTGTAAAAAATTAAATTTAATTTAT
GGGTTGATTACAT
Found at i:483818 original size:145 final size:147
Alignment explanation
Indices: 483646--483911 Score: 351
Period size: 145 Copynumber: 1.8 Consensus size: 147
483636 TGATTATACA
* * * * *
483646 AGTTTAAATTTTTTAAAGAATAGTTTATTTTTATTT-TTAAAATTTTAATTTGTTTTTTAATTTT
1 AGTTTAAATTTTTTAAAGAATAGTTTATTTATATTTGTAAAAATTTAAATTTATTTTTT-AGTTT
* * *
483710 G-TTATATGAGTTTAAA-ATTTTAAAGTATTATTTATTTTTATTTGTAAAAGTTTATGTTTGTTT
65 GATTATACGAGTTTAAATATTTTAAAGCATGATTTATTTTTATTTGTAAAAGTTTATGTTTGTTT
483773 TTTAAGTATAATGGTACG
130 TTTAAGTATAATGGTACG
* * *
483791 AGTTTTAATTTTTTAAAGTAT-GATTTATTTATATTTGTAAAAATTTAAATTTATTTTTTGGTTT
1 AGTTTAAATTTTTTAAAGAATAG-TTTATTTATATTTGTAAAAATTTAAATTTATTTTTTAGTTT
* * *
483855 GATTATACGAGTTTAAATTTTTTTAAGGCATGATTTGTTTTTATTTGTAAAAGTTTA
65 GATTATACGAGTTTAAA-TATTTTAAAGCATGATTTATTTTTATTTGTAAAAGTTTA
483912 AATTTATTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
144 1 0.01
145 35 0.34
146 33 0.32
148 33 0.32
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (147 bp):
AGTTTAAATTTTTTAAAGAATAGTTTATTTATATTTGTAAAAATTTAAATTTATTTTTTAGTTTG
ATTATACGAGTTTAAATATTTTAAAGCATGATTTATTTTTATTTGTAAAAGTTTATGTTTGTTTT
TTAAGTATAATGGTACG
Found at i:486954 original size:20 final size:20
Alignment explanation
Indices: 486929--486972 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
486919 TATATAATAA
*
486929 TTATATTATTT-TACTCATGT
1 TTATATCATTTGTA-TCATGT
*
486949 TTATATCATTTGTATCATTT
1 TTATATCATTTGTATCATGT
486969 TTAT
1 TTAT
486973 GATATGCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.61
Consensus pattern (20 bp):
TTATATCATTTGTATCATGT
Found at i:493555 original size:21 final size:20
Alignment explanation
Indices: 493528--493600 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 20
493518 ATTTGCCTGC
493528 ATGTATCGATACAAGATCAT
1 ATGTATCGATACAAGATCAT
*
493548 AGTGTATCGATACATGA--AT
1 A-TGTATCGATACAAGATCAT
493567 -TGCTATCGATACAAAGATCA-
1 ATG-TATCGATAC-AAGATCAT
493587 ATGTATCGATACAA
1 ATGTATCGATACAA
493601 TGTATCGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
17 2 0.04
18 9 0.20
19 7 0.16
20 10 0.22
21 17 0.38
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACAAGATCAT
Found at i:493603 original size:13 final size:13
Alignment explanation
Indices: 493585--493612 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
493575 ATACAAAGAT
493585 CAATGTATCGATA
1 CAATGTATCGATA
493598 CAATGTATCGATA
1 CAATGTATCGATA
493611 CA
1 CA
493613 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:493612 original size:33 final size:36
Alignment explanation
Indices: 493528--493612 Score: 106
Period size: 38 Copynumber: 2.4 Consensus size: 36
493518 ATTTGCCTGC
493528 ATGTATCGATAC-AAGATCATAGTGTATCGATACATGA
1 ATGTATCGATACAAAGATCATAGTGTATCGATACA--A
493565 ATTGCTATCGATACAAAGATCA-A-TGTATCGATAC-A
1 A-TG-TATCGATACAAAGATCATAGTGTATCGATACAA
493600 ATGTATCGATACA
1 ATGTATCGATACA
493613 TTTGAGTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
33 10 0.22
34 2 0.04
35 2 0.04
37 1 0.02
38 13 0.29
39 10 0.22
40 7 0.16
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (36 bp):
ATGTATCGATACAAAGATCATAGTGTATCGATACAA
Found at i:493704 original size:32 final size:32
Alignment explanation
Indices: 493663--493725 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
493653 GTAACTGTAC
*
493663 ATTGTATCGATACAAAACTTATGTATTGATAT
1 ATTGTATCGATACAAAACTTATGTATCGATAT
*
493695 ATTGTATCGATACAACACTTATGTATCGATA
1 ATTGTATCGATACAAAACTTATGTATCGATA
493726 CAAATCGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAT
Found at i:494208 original size:89 final size:87
Alignment explanation
Indices: 494036--494217 Score: 204
Period size: 89 Copynumber: 2.1 Consensus size: 87
494026 CTACAATAAT
* * * * *
494036 CAATCAACTTTTCTTTCTTTCTATCAAAAGGAATCCCATTCTCAAAAATAATCCATATATTATTC
1 CAATCAACTTTTCTTCCTTTCTACCAAAAAGAATCCCATTCTCAAAAATAATCCATATAATAGTC
*
494101 TGATCTTTGCAATCTGACATTTA
66 TAATCTTT-CAATCTGACATTTA
* * * * *
494124 CAATCAATCTTTTCTTCCTTTCTACCAAAAATAATTCGATTCTCAAAAATAATCTATGTAATAGT
1 CAATCAA-CTTTTCTTCCTTTCTACCAAAAAGAATCCCATTCTCAAAAATAATCCATATAATAGT
* *
494189 CTAATTCTTAT-AGTTTGACATTTA
65 CTAA-TCTT-TCAATCTGACATTTA
494213 CAATC
1 CAATC
494218 CATGCATTAG
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
88 7 0.09
89 66 0.85
90 4 0.05
91 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.40
Consensus pattern (87 bp):
CAATCAACTTTTCTTCCTTTCTACCAAAAAGAATCCCATTCTCAAAAATAATCCATATAATAGTC
TAATCTTTCAATCTGACATTTA
Found at i:494369 original size:39 final size:38
Alignment explanation
Indices: 494297--494440 Score: 128
Period size: 39 Copynumber: 3.7 Consensus size: 38
494287 AATCACATCT
* * * ** *
494297 ATTCCAAAAAAAATTTCATGCACTAATCTCATCTTTCAA
1 ATTCCAATAAAAATTT-ATGCATTAGTAACATCTTTCAG
*
494336 ATTCCAATAAAAATTTTATGTATTAGTAACATCTTTCAG
1 ATTCCAATAAAAA-TTTATGCATTAGTAACATCTTTCAG
* * * *
494375 ATTTCACTAAATAATTTATACATTACTAACATCTTTCAG
1 ATTCCAATAAA-AATTTATGCATTAGTAACATCTTTCAG
*
494414 A-TCCAAATAAAAAATCTATGCATTAGT
1 ATTCC-AAT-AAAAATTTATGCATTAGT
494441 CATATATTTT
Statistics
Matches: 84, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.02
39 74 0.88
40 8 0.10
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (38 bp):
ATTCCAATAAAAATTTATGCATTAGTAACATCTTTCAG
Found at i:495547 original size:11 final size:11
Alignment explanation
Indices: 495528--495562 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
495518 ACTTACAAGA
*
495528 ATTAGATTTAT
1 ATTATATTTAT
495539 ATTATATTTAT
1 ATTATATTTAT
495550 ATTAT-TTTAT
1 ATTATATTTAT
495560 ATT
1 ATT
495563 TGATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:495654 original size:14 final size:14
Alignment explanation
Indices: 495637--495670 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
495627 AAATTTAATA
*
495637 TTTTAATTTCGTAC
1 TTTTAAATTCGTAC
495651 TTTTAAAATTCGTAC
1 TTTT-AAATTCGTAC
495666 TTTTA
1 TTTTA
495671 TCTCAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTTAAATTCGTAC
Found at i:499999 original size:20 final size:20
Alignment explanation
Indices: 499955--500000 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
499945 AATTTTATTT
*
499955 AAAT-TTAATTATATAATAA
1 AAATATTAATTATAAAATAA
499974 AAATATTAA-TATAAAATAA
1 AAATATTAATTATAAAATAA
499993 AATATATT
1 AA-ATATT
500001 TTTAGTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATATTAATTATAAAATAA
Found at i:500198 original size:17 final size:18
Alignment explanation
Indices: 500170--500225 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 18
500160 TTATATTTAT
*
500170 TTATTTAATATTTAAAAA
1 TTATATAATATTTAAAAA
*
500188 TTATA-AATA-TTAAATA
1 TTATATAATATTTAAAAA
*
500204 TT-TATAAT-TTTAAAAT
1 TTATATAATATTTAAAAA
500220 TTATAT
1 TTATAT
500226 TTATATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 2 0.06
16 18 0.58
17 7 0.23
18 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATATAATATTTAAAAA
Found at i:500198 original size:24 final size:24
Alignment explanation
Indices: 500171--500228 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
500161 TATATTTATT
500171 TATTTAATATTTAAAAATTATAAA
1 TATTTAATATTTAAAAATTATAAA
* * *
500195 TATTAAATATTT-ATAATTTTAAA
1 TATTTAATATTTAAAAATTATAAA
500218 -ATTT-ATATTTA
1 TATTTAATATTTA
500229 TATAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 6 0.21
22 3 0.10
23 9 0.31
24 11 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTAATATTTAAAAATTATAAA
Found at i:501226 original size:18 final size:18
Alignment explanation
Indices: 501203--501238 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
501193 TTATATATAT
501203 AATTAATTTGTT-AAATAA
1 AATTAATTT-TTCAAATAA
501221 AATTAATTTTTCAAATAA
1 AATTAATTTTTCAAATAA
501239 TTTATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
AATTAATTTTTCAAATAA
Found at i:501806 original size:16 final size:15
Alignment explanation
Indices: 501779--501808 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
501769 ATGTTAACTT
501779 TATATTCTATTCTAC
1 TATATTCTATTCTAC
501794 TATATTGCTATTCTA
1 TATATT-CTATTCTA
501809 AGTGTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:502281 original size:16 final size:16
Alignment explanation
Indices: 502260--502313 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
502250 TATTAAATTA
* *
502260 GGGTTCGGGTTCTCTC
1 GGGTTCAGGTTCTTTC
502276 GGGTTCAGGTTCTTTC
1 GGGTTCAGGTTCTTTC
*
502292 GGATTCAGGTTCTTTC
1 GGGTTCAGGTTCTTTC
502308 GGGTTC
1 GGGTTC
502314 GAGCTTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.06, C:0.20, G:0.33, T:0.41
Consensus pattern (16 bp):
GGGTTCAGGTTCTTTC
Found at i:503979 original size:11 final size:11
Alignment explanation
Indices: 503965--503989 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
503955 AAAAAAATAC
503965 AAAAAAAGAAA
1 AAAAAAAGAAA
503976 AAAAAAAGAAA
1 AAAAAAAGAAA
503987 AAA
1 AAA
503990 GGGGGTGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:509339 original size:27 final size:27
Alignment explanation
Indices: 509299--510096 Score: 963
Period size: 27 Copynumber: 29.1 Consensus size: 27
509289 GTAGTGTAAT
*
509299 CTTTTAAGTTCACAACTCCGTGG-AACC
1 CTTTTAAGTCCACAACTCCGTGGCAA-C
*
509326 CTTTTAAGTCCACAACTCCATGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
*
509353 TTTTTAAGTCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
509380 CTTTTAAGTCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
* * * * * *
509407 CTTCTAAATTCTACAAGTCCATGGCAGCC
1 CTT-TTAAGTCCACAACTCCGTGGCA-AC
* * * *
509436 CTTTTTAACTCTACAACTTCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCAAC
*
509464 CTTTTAAGCCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
*
509491 CATTTAAGTCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
* * *
509518 CTTTTAAGTCCATAACTTCGTGGAAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
*
509545 CTTTAAAGTCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
*
509572 CTTTTAAAGTCCACAACTCCGTGGCAGCC
1 CTTTT-AAGTCCACAACTCCGTGGCA-AC
* *
509601 CTTTTTAAGTCCACAACTTCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCAAC
*
509629 CTTTTAAGCCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
509656 CTTTTAAGTCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
509683 CTTTTAAGTCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
* * *
509710 CTTCTAAAGTCCATAACTCCGTGGCACC
1 CTT-TTAAGTCCACAACTCCGTGGCAAC
*
509738 CTTTTAAGCCCACAACTCCGTGGCAA-
1 CTTTTAAGTCCACAACTCCGTGGCAAC
*
509764 CTATTTAAGTCCACAACTCCGTGGAAAC
1 CT-TTTAAGTCCACAACTCCGTGGCAAC
* *
509792 CTTTTAAGTCCACAACTCCATGGAAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
* *
509819 CTTTTAAGTCCACAACTCTGTGGTAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
* *
509846 CTTTTAAAGTCCATAACTCCGTGGCAGCC
1 CTTTT-AAGTCCACAACTCCGTGGCA-AC
* *
509875 CTTTTTAAATCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCAAC
* * *
509903 CTTTTCAGCCCACAACTGCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
* *
509930 CTTTTAAGTCCATAACTCCATGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
*** *
509957 CTTTTAAGTCCACAACTCCACAGTAAC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
* *
509984 CTTTTAAAGACCATAACTCCGTGGC-AC
1 CTTTT-AAGTCCACAACTCCGTGGCAAC
* *
510011 CTTTTTATGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCAAC
* *
510039 CTTTTAAGTCCACAACTCTGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
* * *
510066 CTTTTAAGTCCACAAGTCAGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCAAC
510093 CTTT
1 CTTT
510097 CAAAGCCCAC
Statistics
Matches: 668, Mismatches: 87, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
26 2 0.00
27 486 0.73
28 110 0.16
29 60 0.09
30 10 0.01
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.27
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCAAC
Found at i:509571 original size:165 final size:163
Alignment explanation
Indices: 509299--510096 Score: 949
Period size: 165 Copynumber: 4.9 Consensus size: 163
509289 GTAGTGTAAT
* * *
509299 CTTTTAAGTTCACAACTCCGTGG-AACCCTTTTAAGTCCACAACTCCATGGCAACTTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCAA-CCTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTC
* ** * * *
509363 CACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTCTAAATTCTACAAGTCCA
65 CACAACTCCGTGGCAACCTTTAAAGTCCACAACTCCGTGGCAACCTT-TAAAGCCCACAACTCCG
* * * *
509428 TGGCAGCCCTTTTTAACTCTACAACTTCGTGGCACC
129 TGGCA-CCCTTTTTAAGTCCACAACTCCGTGGCAAC
* *
509464 CTTTTAAGCCCACAACTCCGTGGCAACCATTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCC
* * * *
509529 ATAACTTCGTGGAAACCTTTAAAGTCCACAACTCCGTGGCAACCTTTTAAAGTCCACAACTCCGT
66 ACAACTCCGTGGCAACCTTTAAAGTCCACAACTCCGTGGCAACC-TTTAAAGCCCACAACTCCGT
* *
509594 GGCAGCCCTTTTTAAGTCCACAACTTCGTGGCACC
130 GGCA-CCCTTTTTAAGTCCACAACTCCGTGGCAAC
*
509629 CTTTTAAGCCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCC
* * *
509694 ACAACTCCGTGGCAACCTTCTAAAGTCCATAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGT
66 ACAACTCCGTGGCAACCTT-TAAAGTCCACAACTCCGTGGCAACCTTTAAAGCCCACAACTCCGT
* * *
509759 GGCA-ACTATTTAAGTCCACAACTCCGTGGAAAC
130 GGCACCCTTTTTAAGTCCACAACTCCGTGGCAAC
* * * *
509792 CTTTTAAGTCCACAACTCCATGGAAACCTTTTAAGTCCACAACTCTGTGGTAACCTTTTAAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTT-AAGTC
* * * ** *
509857 CATAACTCCGTGGCAGCCCTTTTTAAA-TCCACAACTCCGTGGCACCCTTTTCAGCCCACAACTG
65 CACAACTCCGTGGCA-ACC--TTTAAAGTCCACAACTCCGTGGCAACCTTTAAAGCCCACAACTC
* * *
509921 CGTGGCAACC-TTTTAAGTCCATAACTCCATGGCAAC
127 CGTGGCACCCTTTTTAAGTCCACAACTCCGTGGCAAC
*** * * * *
509957 CTTTTAAGTCCACAACTCCACAGTAACCTTTTAAAGACCATAACTCCGTGGC-ACCTTTTTATGT
1 CTTTTAAGTCCACAACTCCGTGGCAACCTTTT-AAGTCCACAACTCCGTGGCAACC-TTTTAAGT
* * * * * * * *
510021 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAAGTCAG
64 CCACAACTCCGTGGCAACCTTTAAAGTCCACAACTCCGTGGCAACCTTTAAAGCCCACAACTCCG
510086 TGGCACCCTTT
129 TGGCACCCTTT
510097 CAAAGCCCAC
Statistics
Matches: 560, Mismatches: 61, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
162 5 0.01
163 117 0.21
164 24 0.04
165 361 0.64
166 51 0.09
167 2 0.00
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.27
Consensus pattern (163 bp):
CTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCC
ACAACTCCGTGGCAACCTTTAAAGTCCACAACTCCGTGGCAACCTTTAAAGCCCACAACTCCGTG
GCACCCTTTTTAAGTCCACAACTCCGTGGCAAC
Found at i:509798 original size:274 final size:274
Alignment explanation
Indices: 509299--510138 Score: 1123
Period size: 274 Copynumber: 3.1 Consensus size: 274
509289 GTAGTGTAAT
* * * * *
509299 CTTTT-AAGTTCACAACTCCGTGG-AACCC-TTTTAAGTCCACAACTCCATGGCAACTTTTTAAG
1 CTTTTAAAGTCCACAACTCCGTGGCAGCCCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
* * * * *
509361 TCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTCTAAATTCTACAAGTC
66 CCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTT-TTAAGTCCACAACTC
* * * * * *
509426 CATGGCAGCCCTTTTTAACTCTACAACTTCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCAAC
130 CATGGCA-ACCTTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCAAC
* * * *
509491 CATTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCATAACTTCGTGGAAACCTTTAAAGTCC
194 TATTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCATGGAAACCTTTAAAGTCC
509556 ACAACTCCGTGGCAAC
259 ACAACTCCGTGGCAAC
*
509572 CTTTTAAAGTCCACAACTCCGTGGCAGCCCTTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAG
1 CTTTTAAAGTCCACAACTCCGTGGCAGCCCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
509637 CCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCC
66 CCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCC
* *
509702 GTGGCAACCTTCTAAAGTCCATAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCAACTA
131 ATGGCAACCTTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCAACTA
* *
509767 TTTAAGTCCACAACTCCGTGGAAACCTTTTAAGTCCACAACTCCATGGAAACCTTTTAAGTCCAC
196 TTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCATGGAAACCTTTAAAGTCCAC
* *
509832 AACTCTGTGGTAAC
261 AACTCCGTGGCAAC
* * *
509846 CTTTTAAAGTCCATAACTCCGTGGCAGCCCTTTTTAAATCCACAACTCCGTGGCACCCTTTTCAG
1 CTTTTAAAGTCCACAACTCCGTGGCAGCCCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
* * *
509911 CCCACAACTGCGTGGCAACCTTTTAAGTCCATAACTCCATGGCAACCTTTTAAGTCCACAACTCC
66 CCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCC
** * * * * * *
509976 ACAGTAACCTTTTAAAGACCATAACTCCGTGGCACCTTTTTATGTCCACAACTCCGTGGCACCCT
131 ATGGCAACCTTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCA-ACT
* * * * * *
510041 -TTTAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAAGT-CAGTGGCACCCTTTCAAAGCC
195 ATTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCA-TGGAAACCTTT-AAAGTC
* *
510104 CACAAGTCAGTGGCATACC
258 CACAACTCCGTGGCA-A-C
* *
510123 CTTTCAAAGCCCACAA
1 CTTTTAAAGTCCACAA
510139 GTCAGTAGCA
Statistics
Matches: 501, Mismatches: 58, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
273 7 0.01
274 362 0.72
275 39 0.08
276 79 0.16
277 14 0.03
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (274 bp):
CTTTTAAAGTCCACAACTCCGTGGCAGCCCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
CCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCC
ATGGCAACCTTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCAACTA
TTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCATGGAAACCTTTAAAGTCCAC
AACTCCGTGGCAAC
Found at i:510113 original size:28 final size:28
Alignment explanation
Indices: 510021--510814 Score: 626
Period size: 28 Copynumber: 27.2 Consensus size: 28
510011 CTTTTTATGT
* * * *
510021 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * * *
510048 CCACAACTCTGTGGCATCCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
510075 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
510103 CCACAAGTCAGTGGCATACCCTTTCAAAGC
1 CCACAAGTCAGTGGC--ACCCTTTCAAAGC
* *
510133 CCACAAGTCAGTAGCACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
510161 CCACAAGAT-AGTGGCATCTTTTCAAAGC
1 CCACAAG-TCAGTGGCACCCTTTCAAAGC
* *
510189 CCACAAGTCAGTGTCATCCTTTTCAAAAGC
1 CCACAAGTCAGTGGCA-CCCTTTC-AAAGC
* * **
510219 CCGCAAGTCTGTGGCATCTATTTCAAAGC
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
* * *
510248 CCACAAGTCTA-TGGCATTCTTTTGAAAGC
1 CCACAAGTC-AGTGGCA-CCCTTTCAAAGC
*
510277 CCATACAAGTCGGTGGCAACCCGTTTCAAAGC
1 CC--ACAAGTCAGTGGC-ACCC-TTTCAAAGC
* * * *
510309 CCACAAGTTAGTGGCATCATTTTAAAGCC
1 CCACAAGTCAGTGGCACCCTTTCAAAG-C
* *
510338 CACACAAGTCGGTGGCAACCTATTTGC-AAGCC
1 C-CACAAGTCAGTGGC-ACC-CTTT-CAAAG-C
* ** *
510370 CACACAAATTGGTGGCCACCCATTTGAAAGCC
1 C-CACAAGTCAGTGG-CACCC-TTTCAAAG-C
** *
510402 CACACAAGTTGGTGGCAACCCATTTGAAAGCC
1 C-CACAAGTCAGTGGC-ACCC-TTTCAAAG-C
** * *
510434 CACACAAGTTGGTGGTAACCCATTTTAAAGCC
1 C-CACAAGTCAGTGG-CACCC-TTTCAAAG-C
*
510466 CACACAAGTCGGTGGCAACCCATTTCAAAGC
1 C-CACAAGTCAGTGGC-ACCC-TTTCAAAGC
* * *
510497 TCACAAGTCAGTGGCATCCTTTTAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
510525 CCACAAGTCCGTGGCACCCTTTTAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * *
510553 CCACAAGTCAATGGCACCCTTCCAAGGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
510581 CCACAAGTTAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
510609 CCACAAGTCAATGGCATACCCTTTCAAAGC
1 CCACAAGTCAGTGGC--ACCCTTTCAAAGC
* *
510639 CCACAAGTCAGTGGTACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * * * *
510667 CCACTAGTTAATGGCATCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
510695 CCACAAGTCAGTGGCATCCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
*
510724 CCACAAGTCAGTGGCATCCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
* *
510753 CCATAAGTCAGTGGCATCCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
* * *
510782 CCATAAGTCAGTGGCATCCTTTTAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
510810 CCACA
1 CCACA
510815 CAAGTCGGTT
Statistics
Matches: 658, Mismatches: 82, Indels: 53
0.83 0.10 0.07
Matches are distributed among these distances:
27 45 0.07
28 228 0.35
29 127 0.19
30 113 0.17
31 16 0.02
32 128 0.19
33 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
CCACAAGTCAGTGGCACCCTTTCAAAGC
Found at i:510150 original size:58 final size:58
Alignment explanation
Indices: 510021--510814 Score: 615
Period size: 58 Copynumber: 13.6 Consensus size: 58
510011 CTTTTTATGT
* * * * * * * *
510021 CCACAACTCCGTGGCACCCTTT-TAAGTCCACAACTCTGTGGCAT--CCTTT-TAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC
510075 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC
* * *
510133 CCACAAGTCAGTAGCACCTTTTCAAAGCCCACAAGAT-AGTGGCAT--CTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG-TCAGTGGCATACCCTTTCAAAGC
* * * * **
510189 CCACAAGTCAGTGTCATCCTTTTCAAAAGCCCGCAAGTCTGTGGCAT-CTATTTCAAAGC
1 CCACAAGTCAGTGGCA-CCCTTTC-AAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC
* * * *
510248 CCACAAGTCTA-TGGCATTCTTTTGAAAGCCCATACAAGTCGGTGGCA-ACCCGTTTCAAAGC
1 CCACAAGTC-AGTGGCA-CCCTTTCAAAGCCC--ACAAGTCAGTGGCATACCC-TTTCAAAGC
* * * * * *
510309 CCACAAGTTAGTGGCATCATTTTAAAGCCCACACAAGTCGGTGGCA-ACCTATTTGC-AAGCC
1 CCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCATACC-CTTT-CAAAG-C
* ** * ** *
510370 CACACAAATTGGTGGCCACCCATTTGAAAGCCCACACAAGTTGGTGGCA-ACCCATTTGAAAGCC
1 C-CACAAGTCAGTGG-CACCC-TTTCAAAG-CC-CACAAGTCAGTGGCATACCC-TTTCAAAG-C
** * * *
510434 CACACAAGTTGGTGGTAACCCATTTTAAAGCCCACACAAGTCGGTGGCA-ACCCATTTCAAAGC
1 C-CACAAGTCAGTGG-CACCC-TTTCAAAG-CC-CACAAGTCAGTGGCATACCC-TTTCAAAGC
* * * * *
510497 TCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCCGTGGC--ACCCTTTTAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC
* * * *
510553 CCACAAGTCAATGGCACCCTTCCAAGGCCCACAAGTTAGTGGC--ACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC
* *
510609 CCACAAGTCAATGGCATACCCTTTCAAAGCCCACAAGTCAGTGG--TACCTTTTCAAAGC
1 CCACAAGTCAGTGGC--ACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC
* * * * * *
510667 CCACTAGTTAATGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAT-CCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC
* * *
510724 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCATAAGTCAGTGGCAT-CCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC
* * *
510782 CCATAAGTCAGTGGCATCCTTTTAAAGCCCACA
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACA
510815 CAAGTCGGTT
Statistics
Matches: 633, Mismatches: 76, Indels: 59
0.82 0.10 0.08
Matches are distributed among these distances:
54 20 0.03
55 18 0.03
56 119 0.19
57 55 0.09
58 186 0.29
59 31 0.05
60 55 0.09
61 30 0.05
62 23 0.04
63 4 0.01
64 92 0.15
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (58 bp):
CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC
Found at i:510155 original size:247 final size:243
Alignment explanation
Indices: 509299--510166 Score: 913
Period size: 247 Copynumber: 3.5 Consensus size: 243
509289 GTAGTGTAAT
* * *
509299 CTTTTAAGTTCACAACTCCGTGG-AACCCTTTTAAGTCCACAACTCCA-TGGCA-ACTTTTTAAG
1 CTTTTAAGTCCACAACTCCGTGGCAA-CCTTTTAAGTCCACAACT-CAGTGGCACCCTTTTAAAG
* * ** ** * *
509361 TCCACAACTCCGTGGCAA-CCTTTTAAGTCCACAACTCCGTGGCAACCTTCTAAATTCTACAAGT
64 TCCACAACT-CGTGGCAACCCTTTAAAGCCCACAACTCCGTGGC-ACCTT-TTCAGCCCACAACT
* * * * * * * *
509425 CCATGGCAGCCCTTTTTAACTCTACAACTTCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCAA
126 CCGTGGCA-ACC-TTTTAAGTCCACAACTCCATGGCAACCTTTTAAGTCCACAACTCCGTGGCAA
* * * *
509490 CCATTTAAGTCCACAACTCCGTGGCAACC-TTTTAAGTCCATAACTTCGTGGAAAC
189 CCTTTTAAGACCACAACTCCGTGGC-ACCTTTTTAAGTCCACAACTCCGTGGAAAC
* * *
509545 CTTTAAAGTCCACAACTCCGTGGCAACCTTTTAAAGTCCACAACTCCGTGGCAGCCCTTTTTAAG
1 CTTTTAAGTCCACAACTCCGTGGCAACCTTTT-AAGTCCACAACTCAGTGGCA-CCCTTTTAAAG
* * *
509610 TCCACAACTTCGTGGC-ACCCTTTTAAGCCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTC
64 TCCACAAC-TCGTGGCAACCCTTTAAAGCCCACAACTCCGTGGC-ACCTTTTCAGCCCACAACTC
* * * *
509674 CGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTCTAAAGTCCATAACTCCGTGGCACCC
127 CGTGGCAACCTTTTAAGTCCACAACTCCATGGCAACCTT-TTAAGTCCACAACTCCGTGGCAACC
* * *
509739 TTTTAAGCCCACAACTCCGTGGCAACTATTTAAGTCCACAACTCCGTGGAAAC
191 TTTTAAGACCACAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGAAAC
* * * * *
509792 CTTTTAAGTCCACAACTCCATGGAAACCTTTTAAGTCCACAACTCTGTGGTAACCTTTTAAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCAGTGGCACCCTTTTAAAGTC
* * * *
509857 CATAACTCCGTGGCAGCCCTTTTTAAA-TCCACAACTCCGTGGCACCCTTTTCAGCCCACAACTG
66 CACAACT-CGTGGCAACCC--TTTAAAGCCCACAACTCCGTGGCA-CCTTTTCAGCCCACAACTC
* *** *
509921 CGTGGCAACCTTTTAAGTCCATAACTCCATGGCAACCTTTTAAGTCCACAACTCCACAGTAACCT
127 CGTGGCAACCTTTTAAGTCCACAACTCCATGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCT
* * * *
509986 TTTAAAGACCATAACTCCGTGGCACCTTTTTATGTCCACAACTCCGTGGCACC
192 TTT-AAGACCACAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGAAAC
* * * * *
510039 CTTTTAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCC
1 CTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCAGTGGCACCCTTTTAAAGTC
* * * *
510104 CACAAGTCAGTGGCATACCCTTTCAAAGCCCACAAGTCAGTAGCACCTTTTCAAAGCCCACAA
66 CACAACTC-GTGGCA-ACCCTTT-AAAGCCCACAACTCCGTGGCACCTTTTC--AGCCCACAA
510167 GATAGTGGCA
Statistics
Matches: 529, Mismatches: 72, Indels: 39
0.83 0.11 0.06
Matches are distributed among these distances:
244 1 0.00
245 22 0.04
246 103 0.19
247 301 0.57
248 39 0.07
249 62 0.12
250 1 0.00
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (243 bp):
CTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCAGTGGCACCCTTTTAAAGTC
CACAACTCGTGGCAACCCTTTAAAGCCCACAACTCCGTGGCACCTTTTCAGCCCACAACTCCGTG
GCAACCTTTTAAGTCCACAACTCCATGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTTA
AGACCACAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGAAAC
Found at i:510184 original size:86 final size:87
Alignment explanation
Indices: 510048--510814 Score: 653
Period size: 86 Copynumber: 8.7 Consensus size: 87
510038 CCTTTTAAGT
* * * * *
510048 CCACAACTCTGTGGCATCCTTTT--AAGTCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGT
510111 CAGTGGCATACCCTTTCAAAGC
66 CAGTGGCATACCCTTTCAAAGC
*
510133 CCACAAGTCAGTAGCA-CCTTTTCAAAGCCCACAAGAT-AGTGGCATCTTTTCAAAGCCCACAAG
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAG-TCAGTGGCATCTTTTCAAAGCCCACAAG
* *
510196 TCAGTGTCAT-CCTTTTCAAAAGC
65 TCAGTGGCATACCCTTTC-AAAGC
* * *
510219 CCGCAAGTCTGTGGCAT-CTATTTCAAAGCCCACAAGTCTA-TGGCATTCTTTTGAAAGCCCATA
1 CCACAAGTCAGTGGCATCCT-TTTCAAAGCCCACAAGTC-AGTGGCA-TCTTTTCAAAGCCC--A
*
510282 CAAGTCGGTGGCA-ACCCGTTTCAAAGC
61 CAAGTCAGTGGCATACCC-TTTCAAAGC
* * * *
510309 CCACAAGTTAGTGGCATCATTTT-AAAGCCCACACAAGTCGGTGGCAACCTATTTGC-AAGCCCA
1 CCACAAGTCAGTGGCATCCTTTTCAAAG-CC-CACAAGTCAGTGGC-ATCT-TTT-CAAAG-CC-
* ** * *
510372 CACAAATTGGTGGC-CACCCATTTGAAAGCC
59 CACAAGTCAGTGGCATACCC-TTTCAAAG-C
** * * * ** * *
510402 CACACAAGTTGGTGGCAACCCATTTGAAAGCCCACACAAGTTGGTGGTAACCCATTTT-AAAGCC
1 C-CACAAGTCAGTGGC-ATCCTTTTCAAAG-CC-CACAAGTCAGTGG-CA-TC-TTTTCAAAG-C
*
510466 CACACAAGTCGGTGGCA-ACCCATTTCAAAGC
58 C-CACAAGTCAGTGGCATACCC-TTTCAAAGC
* * *
510497 TCACAAGTCAGTGGCATCCTTTT-AAAGCCCACAAGTCCGTGGCACCCTTTT-AAAGCCCACAAG
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAG
* * *
510560 TCAATGGC--ACCCTTCCAAGGC
65 TCAGTGGCATACCCTTTCAAAGC
* * * *
510581 CCACAAGTTAGTGGCA-CCCTTTCAAAGCCCACAAGTCAATGGCATACCCTTTCAAAGCCCACAA
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCAT--CTTTTCAAAGCCCACAA
*
510645 GTCAGTGG--TACCTTTTCAAAGC
64 GTCAGTGGCATACCCTTTCAAAGC
* * *
510667 CCACTAGTTAATGGCAT-CTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAG
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAGCCCACAAG
*
510731 TCAGTGGCAT-CCTTTTCAAAGC
65 TCAGTGGCATACCCTTTCAAAGC
* *
510753 CCATAAGTCAGTGGCATCCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTT-AAAGCCCACA
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAGCCCACA
510815 CAAGTCGGTT
Statistics
Matches: 573, Mismatches: 68, Indels: 81
0.79 0.09 0.11
Matches are distributed among these distances:
83 5 0.01
84 46 0.08
85 52 0.09
86 179 0.31
87 58 0.10
88 22 0.04
89 8 0.01
90 49 0.09
91 21 0.04
92 33 0.06
93 10 0.02
94 26 0.05
95 6 0.01
96 52 0.09
97 5 0.01
98 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (87 bp):
CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGT
CAGTGGCATACCCTTTCAAAGC
Found at i:510374 original size:32 final size:32
Alignment explanation
Indices: 510268--510501 Score: 287
Period size: 32 Copynumber: 7.4 Consensus size: 32
510258 ATGGCATTCT
* * *
510268 TTTGAAAGCCCATACAAGTCGGTGGCAACCCG
1 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
* * *
510300 TTTCAAAG-CC-CACAAGTTAGTGGC-A-TCA
1 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
* * *
510328 TTTTAAAGCCCACACAAGTCGGTGGCAACCTA
1 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
* * *
510360 TTTGCAAGCCCACACAAATTGGTGGCCACCCA
1 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
510392 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
1 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
*
510424 TTTGAAAGCCCACACAAGTTGGTGGTAACCCA
1 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
* *
510456 TTTTAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
* *
510488 TTTCAAAGCTCACA
1 TTTGAAAGCCCACA
510502 AGTCAGTGGC
Statistics
Matches: 172, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
28 8 0.05
29 3 0.02
30 23 0.13
31 3 0.02
32 135 0.78
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (32 bp):
TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
Found at i:510856 original size:36 final size:35
Alignment explanation
Indices: 510801--510871 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
510791 AGTGGCATCC
* * *
510801 TTTTAAAGCCCACACAAGTCGGTTGCAACTCTTTT
1 TTTTAAAACCCACACAAGTCGATGGCAACTCTTTT
510836 TTTTCAAAACCCACACAAGTCGATGGCAACTCTTTT
1 TTTT-AAAACCCACACAAGTCGATGGCAACTCTTTT
510872 CAAAGCCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 4 0.12
36 28 0.88
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (35 bp):
TTTTAAAACCCACACAAGTCGATGGCAACTCTTTT
Found at i:511898 original size:20 final size:20
Alignment explanation
Indices: 511873--511927 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
511863 TTTTACCCAG
*
511873 ATGTATCGATACATTGAATA
1 ATGTATCGATACATCGAATA
511893 ATGTATCGATACATCGAATA
1 ATGTATCGATACATCGAATA
511913 ATGTATCGATACATC
1 ATGTATCGATACATC
511928 TAGATAAAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATCGAATA
Found at i:519817 original size:28 final size:25
Alignment explanation
Indices: 519786--519848 Score: 63
Period size: 28 Copynumber: 2.4 Consensus size: 25
519776 TTTTTACCCC
* *
519786 TTTTGATTTTTTACTTTTTAATATATA
1 TTTTTATTTTTTAATTTTT-ATA-ATA
* *
519813 TTTTTAATATTTTAATTTTTTTAATA
1 TTTTT-ATTTTTTAATTTTTATAATA
519839 TTTTTATTTT
1 TTTTTATTTT
519849 AATTTGTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 4 0.13
26 8 0.27
27 6 0.20
28 12 0.40
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTTTATTTTTTAATTTTTATAATA
Found at i:519822 original size:9 final size:9
Alignment explanation
Indices: 519810--519844 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
519800 TTTTTAATAT
519810 ATATTTTTA
1 ATATTTTTA
519819 ATA-TTTTA
1 ATATTTTTA
*
519827 ATTTTTTTA
1 ATATTTTTA
519836 ATATTTTTA
1 ATATTTTTA
519845 TTTTAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
ATATTTTTA
Found at i:519834 original size:30 final size:29
Alignment explanation
Indices: 519800--519892 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
519790 GATTTTTTAC
519800 TTTTTAATATATATTTTTAATATTTTAATT
1 TTTTTAATATATATTTTTAAT-TTTTAATT
* * *
519830 TTTTTAATATTTTTATTTTAATTTGT-A-T
1 TTTTTAATATATAT-TTTTAATTTTTAATT
* *
519858 TTTGTAA-A-ATATTTTTACTTTATTAATT
1 TTTTTAATATATATTTTTAATTT-TTAATT
519886 TTTTTAA
1 TTTTTAA
519893 ACATATTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
25 8 0.16
26 3 0.06
27 2 0.04
28 14 0.28
29 1 0.02
30 15 0.30
31 7 0.14
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (29 bp):
TTTTTAATATATATTTTTAATTTTTAATT
Found at i:519835 original size:17 final size:17
Alignment explanation
Indices: 519813--519848 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
519803 TTAATATATA
519813 TTTTTAATATTTTAATT
1 TTTTTAATATTTTAATT
*
519830 TTTTTAATATTTTTATT
1 TTTTTAATATTTTAATT
519847 TT
1 TT
519849 AATTTGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTAATATTTTAATT
Found at i:525310 original size:24 final size:24
Alignment explanation
Indices: 525283--525336 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
525273 GATTAGATTG
525283 ATAAATAAAAAAATTATCTCTT-A
1 ATAAATAAAAAAATTATCTCTTGA
* ** *
525306 TATAATTATGAAATTTATCTCTTGA
1 -ATAAATAAAAAAATTATCTCTTGA
525331 ATAAAT
1 ATAAAT
525337 GAAGAAAAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (24 bp):
ATAAATAAAAAAATTATCTCTTGA
Found at i:526952 original size:17 final size:18
Alignment explanation
Indices: 526932--526965 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
526922 ATGTGTAAAA
*
526932 TATATTAATAA-AATTTT
1 TATATAAATAATAATTTT
526949 TATATAAATAATAATTT
1 TATATAAATAATAATTT
526966 AAACTAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATAAATAATAATTTT
Found at i:527589 original size:19 final size:18
Alignment explanation
Indices: 527565--527628 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 18
527555 TAGCCAAACT
527565 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAA-A
527584 TGTATCGAT--AC---AA
1 TGTATCGATACACAAAAA
527597 TGTATCGATACACAAAAAA
1 TGTATCGATACAC-AAAAA
527616 TTGTATCGATACA
1 -TGTATCGATACA
527629 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 11 0.29
20 12 0.32
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (18 bp):
TGTATCGATACACAAAAA
Found at i:527601 original size:13 final size:13
Alignment explanation
Indices: 527583--527608 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
527573 TACACAAAAT
527583 ATGTATCGATACA
1 ATGTATCGATACA
527596 ATGTATCGATACA
1 ATGTATCGATACA
527609 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:527606 original size:32 final size:33
Alignment explanation
Indices: 527565--527628 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
527555 TAGCCAAACT
*
527565 TGTATCGATACACAAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
527597 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
527629 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:532628 original size:20 final size:20
Alignment explanation
Indices: 532600--532674 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
532590 TTTTACCTTG
532600 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
532620 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
532640 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
*
532660 ATGTATTGATACATT
1 ATGTATCGATACATT
532675 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:532671 original size:40 final size:39
Alignment explanation
Indices: 532600--532677 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
532590 TTTTACCTTG
* *
532600 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* * *
532640 ATGTATCGATATATTCTACAATGTATTGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
532678 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:533613 original size:22 final size:22
Alignment explanation
Indices: 533587--533641 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
533577 AGCCTTTGAC
533587 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
533609 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
533631 CATGCATTTTT
1 CATGCATTTTT
533642 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:533648 original size:20 final size:21
Alignment explanation
Indices: 533587--533648 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
533577 AGCCTTTGAC
**
533587 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
533609 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
533631 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
533649 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
22 28 0.74
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.58
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:537352 original size:13 final size:13
Alignment explanation
Indices: 537334--537371 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
537324 CATTTTTCTT
537334 TGTATCGATACAA
1 TGTATCGATACAA
*
537347 TGTATCGATACAC
1 TGTATCGATACAA
537360 TGTATCGATACA
1 TGTATCGATACA
537372 GGGAGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:537535 original size:20 final size:20
Alignment explanation
Indices: 537492--537537 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
537482 AAATCTTTTG
537492 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
537513 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
537533 CAAAA
1 CAAAA
537538 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:539033 original size:23 final size:21
Alignment explanation
Indices: 538991--539033 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
538981 GTTTAATGTT
**
538991 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
539012 TTTGCATTGTACTTTGAATTTT
1 TTTGC-TTG-ACTTTGAATTTT
539034 TAATCTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.60
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:539938 original size:19 final size:19
Alignment explanation
Indices: 539914--539977 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
539904 TAGCCAAACT
539914 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
539933 TGTATCGAT--AC--AATA
1 TGTATCGATACACAAAATA
*
539948 --TATCGATACACAAAAAA
1 TGTATCGATACACAAAATA
539965 TTGTATCGATACA
1 -TGTATCGATACA
539978 TTGGCTTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 7 0.19
15 6 0.16
17 5 0.14
19 9 0.24
20 10 0.27
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:539950 original size:17 final size:18
Alignment explanation
Indices: 539914--539975 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
539904 TAGCCAAACT
539914 TGTATCGATACACAAAATA
1 TGTATCGATA-ACAAAATA
539933 TGTATCGAT-AC--AATA
1 TGTATCGATAACAAAATA
*
539948 --TATCGATACACAAAAAA
1 TGTATCGATA-ACAAAATA
539965 TTGTATCGATA
1 -TGTATCGATA
539976 CATTGGCTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
13 7 0.20
15 6 0.17
17 5 0.14
19 9 0.26
20 8 0.23
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (18 bp):
TGTATCGATAACAAAATA
Found at i:539957 original size:32 final size:33
Alignment explanation
Indices: 539916--539977 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
539906 GCCAAACTTG
*
539916 TATCGATACACAAAATA-TGTATCGATACAATA
1 TATCGATACACAAAAAATTGTATCGATACAATA
539948 TATCGATACACAAAAAATTGTATCGATACA
1 TATCGATACACAAAAAATTGTATCGATACA
539978 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (33 bp):
TATCGATACACAAAAAATTGTATCGATACAATA
Found at i:540764 original size:21 final size:22
Alignment explanation
Indices: 540739--540785 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
540729 GATAGTTTAA
540739 TAAA-TTAATTAAATTAAATTT
1 TAAATTTAATTAAATTAAATTT
* *
540760 TAAATTTAATTAATTTAACTTT
1 TAAATTTAATTAAATTAAATTT
540782 TAAA
1 TAAA
540786 AATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAATTTAATTAAATTAAATTT
Found at i:550578 original size:2 final size:2
Alignment explanation
Indices: 550571--550595 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
550561 GAGCGCACGC
550571 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
550596 CATGTTAAAT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:552850 original size:52 final size:52
Alignment explanation
Indices: 552759--552861 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
552749 TTATGCCCTT
* * * * *
552759 AAAATCCTTTGCCGTTCCCTTTAATAGTTTCCAATTAAGAGAGATAGTACTC
1 AAAACCCTCTGCCCTTCCCTTTAAGAGTTTCCAAATAAGAGAGATAGTACTC
* * *
552811 AAAACCCTCTGCCCTTCCTTTTAAGAGTTTTCAAATAAGAGAGATGGTACT
1 AAAACCCTCTGCCCTTCCCTTTAAGAGTTTCCAAATAAGAGAGATAGTACT
552862 GTACTCTCTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (52 bp):
AAAACCCTCTGCCCTTCCCTTTAAGAGTTTCCAAATAAGAGAGATAGTACTC
Found at i:555050 original size:2 final size:2
Alignment explanation
Indices: 555043--555088 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
555033 AGGCTATTAT
*
555043 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CG CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
555085 CA CA
1 CA CA
555089 GACGCATTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.50, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:557422 original size:3 final size:3
Alignment explanation
Indices: 557414--557448 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
557404 ATTTTAAGTA
557414 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
557449 CTACTACTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:557585 original size:36 final size:35
Alignment explanation
Indices: 557510--557585 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
557500 GTTTTGTTAT
* * *
557510 TTTATATTTAATAATACTTAAATTTATTGATTTTT
1 TTTATATTTAAGAATACTTAAATTTAATGATTTTG
*
557545 TTTATATTTAAGAATCATTTAAATTTAAT-ATATTTG
1 TTTATATTTAAGAAT-ACTTAAATTTAATGAT-TTTG
557581 TTTAT
1 TTTAT
557586 TCTTCTTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 16 0.46
36 19 0.54
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.58
Consensus pattern (35 bp):
TTTATATTTAAGAATACTTAAATTTAATGATTTTG
Found at i:558588 original size:3 final size:3
Alignment explanation
Indices: 558580--558628 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
558570 ATAGAAAGGG
558580 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
558628 A
1 A
558629 AGATTATAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:560527 original size:4 final size:4
Alignment explanation
Indices: 560518--560553 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
560508 ACTGAAAACA
560518 TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC
560554 CAACTCAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:563973 original size:16 final size:16
Alignment explanation
Indices: 563949--563979 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
563939 CAGTTAAATT
563949 TTAAAATTTAAAATAA
1 TTAAAATTTAAAATAA
*
563965 TTAATATTTAAAATA
1 TTAAAATTTAAAATA
563980 TAAAGAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAAATTTAAAATAA
Found at i:566717 original size:90 final size:90
Alignment explanation
Indices: 566614--566832 Score: 393
Period size: 90 Copynumber: 2.4 Consensus size: 90
566604 CACTTCCATT
* *
566614 TACTTTTAATGCAATTTATTTATATTGTTGTTTCATTTTCTTGGAATCTAAGGAATAAACTTAAG
1 TACTTTTATTGCAATTTATTTATATTGTTGTTTCCTTTTCTTGGAATCTAAGGAATAAACTTAAG
566679 TTAAGATAGCAATATAGCTGTGCTG
66 TTAAGATAGCAATATAGCTGTGCTG
*
566704 TACTTTTATTGCAATTTATTTATATTGTTGTTTCCTTTTCTTGGAATCTAAGGAATAAACTTAGG
1 TACTTTTATTGCAATTTATTTATATTGTTGTTTCCTTTTCTTGGAATCTAAGGAATAAACTTAAG
* *
566769 TTAAGATAGCAATATGGCTTTGCTG
66 TTAAGATAGCAATATAGCTGTGCTG
566794 TACTTTTATTGCAATTTATTTATATTGTTGTTTCCTTTT
1 TACTTTTATTGCAATTTATTTATATTGTTGTTTCCTTTT
566833 TATTGCAATT
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 124 1.00
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.48
Consensus pattern (90 bp):
TACTTTTATTGCAATTTATTTATATTGTTGTTTCCTTTTCTTGGAATCTAAGGAATAAACTTAAG
TTAAGATAGCAATATAGCTGTGCTG
Found at i:566837 original size:33 final size:33
Alignment explanation
Indices: 566797--566865 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
566787 TTTGCTGTAC
566797 TTTTATTGCAATTTATTTATATTGTTGTTTCCT
1 TTTTATTGCAATTTATTTATATTGTTGTTTCCT
566830 TTTTATTGCAATTTATTTATATTGTTGTTTCCT
1 TTTTATTGCAATTTATTTATATTGTTGTTTCCT
566863 TTT
1 TTT
566866 CTTGGAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.65
Consensus pattern (33 bp):
TTTTATTGCAATTTATTTATATTGTTGTTTCCT
Found at i:567058 original size:80 final size:81
Alignment explanation
Indices: 566955--567113 Score: 293
Period size: 80 Copynumber: 2.0 Consensus size: 81
566945 CACCATAGGC
*
566955 ATTTTACTGATAATGCATGAATTTTCAAACAAAAAGAATAATTTCTTAAATTTTTACGCGTTGGG
1 ATTTTACTGATAATGCATGAATTTTCAAACAAAAAGAATAATTTCTTAAATTTCTACGCGTTGGG
567020 AAAATGTTTAAGAGGT
66 AAAATGTTTAAGAGGT
*
567036 ATTTTACT-ATAATGCATGAATTTTCAAACGAAAAGAATAATTTCTTAAATTTCTACGCGTTGGG
1 ATTTTACTGATAATGCATGAATTTTCAAACAAAAAGAATAATTTCTTAAATTTCTACGCGTTGGG
567100 AAAATGTTTAAGAG
66 AAAATGTTTAAGAG
567114 ATTTTCTAAG
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
80 68 0.89
81 8 0.11
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (81 bp):
ATTTTACTGATAATGCATGAATTTTCAAACAAAAAGAATAATTTCTTAAATTTCTACGCGTTGGG
AAAATGTTTAAGAGGT
Found at i:568338 original size:18 final size:20
Alignment explanation
Indices: 568309--568357 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
568299 AGAACTAAAT
*
568309 TAAAAATAATTATATTTT-A
1 TAAAATTAATTATATTTTCA
568328 T-AAATTAATTATATTTTCA
1 TAAAATTAATTATATTTTCA
568347 TAAAATTAATT
1 TAAAATTAATT
568358 TAAATTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 15 0.56
19 3 0.11
20 9 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATTAATTATATTTTCA
Found at i:569770 original size:2 final size:2
Alignment explanation
Indices: 569763--569798 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
569753 TGGACTATGA
569763 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
569799 TCTCTTTTCT
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:574873 original size:16 final size:16
Alignment explanation
Indices: 574836--574876 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
574826 ACTACGTTAG
574836 TATTAATTTTCTAAATT
1 TATT-ATTTTCTAAATT
574853 TATTATTTT-TAAATT
1 TATTATTTTCTAAATT
574868 TAATTATTT
1 T-ATTATTT
574877 ATAATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.30
16 12 0.52
17 4 0.17
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTATTTTCTAAATT
Found at i:574891 original size:21 final size:22
Alignment explanation
Indices: 574850--574895 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
574840 AATTTTCTAA
*
574850 ATTTATTATTTTTAAATTTAATT
1 ATTTATAATTTTT-AATTTAATT
574873 ATTTATAATTTTT-ATTTAATT
1 ATTTATAATTTTTAATTTAATT
574894 AT
1 AT
574896 AAATATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
23 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTATAATTTTTAATTTAATT
Found at i:576926 original size:3 final size:3
Alignment explanation
Indices: 576920--576968 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
576910 CTAGTTGTTG
576920 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
576968 T
1 T
576969 AAAATTTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:584270 original size:86 final size:86
Alignment explanation
Indices: 584163--584332 Score: 286
Period size: 86 Copynumber: 2.0 Consensus size: 86
584153 GATCAAGATT
* * *
584163 TTATTACTTTCGATTTGGAATATAACTTAAGTTAAATAATCCAAGTTTGTGTATTCATTACTTAG
1 TTATTAATTTCAATATGGAATATAACTTAAGTTAAATAATCCAAGTTTGTGTATTCATTACTTAG
584228 ATCAACCTATCATTTTTATTA
66 ATCAACCTATCATTTTTATTA
* * *
584249 TTATTAATTTCAATATGGAATATAACTTAAGTTAAATAATCCAAGTTTGTGTGTTTATTGCTTAG
1 TTATTAATTTCAATATGGAATATAACTTAAGTTAAATAATCCAAGTTTGTGTATTCATTACTTAG
584314 ATCAACCTATCATTTTTAT
66 ATCAACCTATCATTTTTAT
584333 CATAAAGCTT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 78 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (86 bp):
TTATTAATTTCAATATGGAATATAACTTAAGTTAAATAATCCAAGTTTGTGTATTCATTACTTAG
ATCAACCTATCATTTTTATTA
Found at i:588809 original size:2 final size:2
Alignment explanation
Indices: 588792--588873 Score: 62
Period size: 2 Copynumber: 41.5 Consensus size: 2
588782 GGTATATTTG
* *
588792 TA TA TG TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA GA -A CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * ** *
588832 TA GA AA TA GGC TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
588874 GAAAAAATAT
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
1 3 0.05
2 60 0.95
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (2 bp):
TA
Found at i:593854 original size:18 final size:18
Alignment explanation
Indices: 593833--593888 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
593823 TATTAACTTC
* * *
593833 AAATTTTATTTTGTATTT
1 AAATTTTAATTTATATTA
*
593851 AAATTTAAATTTATATTA
1 AAATTTTAATTTATATTA
593869 AAATTTTTAATATTA-ATTA
1 AAA-TTTTAAT-TTATATTA
593888 A
1 A
593889 TAATAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 17 0.55
19 11 0.35
20 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
AAATTTTAATTTATATTA
Found at i:593967 original size:99 final size:94
Alignment explanation
Indices: 593851--594037 Score: 284
Period size: 99 Copynumber: 1.9 Consensus size: 94
593841 TTTTGTATTT
* * *
593851 AAATTTAAATTTATATTAAAATTTTTAATATTAATTAATAATAAAATATATATTAAAAATAAAAA
1 AAATTCAAATTTATATTAAAATTTTTAAAAATAATTAATAATAAAATATATATT----A-AAAAA
593916 AATTATTCAAACTTAACTCAAAATTACTCCAGCC
61 AATTATTCAAACTTAACTCAAAATTACTCCAGCC
593950 AAATTCAAATTTATATTAAAATTTTTAAAAATAATTAATAATAAAATATATATTAAAAAAAATTA
1 AAATTCAAATTTATATTAAAATTTTTAAAAATAATTAATAATAAAATATATATTAAAAAAAATTA
* *
594015 TTCAAGCTTACCTCAAAATTACT
66 TTCAAACTTAACTCAAAATTACT
594038 TTGAGCCAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
94 31 0.37
95 1 0.01
99 51 0.61
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.37
Consensus pattern (94 bp):
AAATTCAAATTTATATTAAAATTTTTAAAAATAATTAATAATAAAATATATATTAAAAAAAATTA
TTCAAACTTAACTCAAAATTACTCCAGCC
Found at i:596674 original size:5 final size:5
Alignment explanation
Indices: 596667--596707 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
596657 CCCCCCTTTT
* * *
596667 CCTTT CCTTT CCTTT CCTTC CCTTC CCTTC CCTTC CCTTC C
1 CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC C
596708 TCCATGAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (5 bp):
CCTTC
Found at i:596684 original size:15 final size:15
Alignment explanation
Indices: 596664--596707 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
596654 AAACCCCCCT
* *
596664 TTTCCTTTCCTTTCC
1 TTTCCTTCCCTTCCC
596679 TTTCCTTCCCTTCCC
1 TTTCCTTCCCTTCCC
*
596694 TTCCCTTCCCTTCC
1 TTTCCTTCCCTTCC
596708 TCCATGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTCCTTCCCTTCCC
Found at i:611047 original size:20 final size:20
Alignment explanation
Indices: 611022--611085 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
611012 GTTTGAAGCA
611022 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
611042 ATGTATCGAT---A--CA--
1 ATGTATCGATACAATTCATC
611055 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
611075 ATGTATCGATA
1 ATGTATCGATA
611086 TGCCATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.27
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 21 0.57
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:611060 original size:13 final size:13
Alignment explanation
Indices: 611020--611069 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
611010 CCGTTTGAAG
611020 CAATGTATCGATA
1 CAATGTATCGATA
611033 CAA--T-TC-AT-
1 CAATGTATCGATA
611041 C-ATGTATCGATA
1 CAATGTATCGATA
611053 CAATGTATCGATA
1 CAATGTATCGATA
611066 CAAT
1 CAAT
611070 TCATCATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.10
10 4 0.13
11 3 0.10
12 1 0.03
13 18 0.58
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:611062 original size:33 final size:34
Alignment explanation
Indices: 611018--611103 Score: 147
Period size: 33 Copynumber: 2.5 Consensus size: 34
611008 AGCCGTTTGA
611018 AGCAATGTATCGATACAATTCATCATGTATCGAT
1 AGCAATGTATCGATACAATTCATCATGTATCGAT
611052 A-CAATGTATCGATACAATTCATCATGTATCGAT
1 AGCAATGTATCGATACAATTCATCATGTATCGAT
*
611085 ATGCCATGTATCGATACAA
1 A-GCAATGTATCGATACAA
611104 ACAGTGGTAG
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 33 0.67
34 1 0.02
35 15 0.31
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (34 bp):
AGCAATGTATCGATACAATTCATCATGTATCGAT
Found at i:611182 original size:19 final size:19
Alignment explanation
Indices: 611136--611187 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
611126 CAGTTTCATA
**
611136 TATCGATACAATTGTGCATG
1 TATCGATACAA-TGAACATG
* *
611156 CATTGATACAATGAACATG
1 TATCGATACAATGAACATG
611175 TATCGATACAATG
1 TATCGATACAATG
611188 TATCGATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (19 bp):
TATCGATACAATGAACATG
Found at i:611190 original size:13 final size:13
Alignment explanation
Indices: 611172--611198 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
611162 TACAATGAAC
611172 ATGTATCGATACA
1 ATGTATCGATACA
611185 ATGTATCGATACA
1 ATGTATCGATACA
611198 A
1 A
611199 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:611209 original size:20 final size:20
Alignment explanation
Indices: 611184--611236 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
611174 GTATCGATAC
611184 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
611204 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
611224 AATGTATCGATAC
1 AATGTATCGATAC
611237 CTCTGGACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAAAGCAT
Found at i:612199 original size:33 final size:33
Alignment explanation
Indices: 612133--612199 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
612123 AAGTGCACTA
* * * *
612133 AAGTGCTCATCCATGCGTTGCTAGAGTGTAGTG
1 AAGTGCTCATCCATGCGATGCGAAAGTGAAGTG
* *
612166 AAGTGCTCATTCATGTGATGCGAAAGTGAAGTG
1 AAGTGCTCATCCATGCGATGCGAAAGTGAAGTG
612199 A
1 A
612200 TCAACTCTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (33 bp):
AAGTGCTCATCCATGCGATGCGAAAGTGAAGTG
Found at i:613549 original size:19 final size:21
Alignment explanation
Indices: 613504--613550 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
613494 AACGTTTTTG
613504 TTGATGATTTTGATGAAAAAA
1 TTGATGATTTTGATGAAAAAA
** *
613525 GAGATG-TTTTGATG-TAAAA
1 TTGATGATTTTGATGAAAAAA
613544 TTGATGA
1 TTGATGA
613551 AATTTTAAGA
Statistics
Matches: 20, Mismatches: 5, Indels: 3
0.71 0.18 0.11
Matches are distributed among these distances:
19 8 0.40
20 8 0.40
21 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (21 bp):
TTGATGATTTTGATGAAAAAA
Found at i:618367 original size:36 final size:34
Alignment explanation
Indices: 618283--618380 Score: 114
Period size: 36 Copynumber: 2.9 Consensus size: 34
618273 TCTTACAATA
618283 CTATC-TTTCAAGGCTAAGATAGAAA---TCTCC
1 CTATCTTTTCAAGGCTAAGATAGAAACTCTCTCC
* *
618313 TTATCTTTTCACGAGCTAAGATAGAAACTCTCTCC
1 CTATCTTTTCAAG-GCTAAGATAGAAACTCTCTCC
*
618348 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTC-AAGGCTAAGATAGAAACTCTC
618381 AATCACTTAG
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
30 4 0.07
31 6 0.11
32 13 0.23
35 9 0.16
36 22 0.39
37 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (34 bp):
CTATCTTTTCAAGGCTAAGATAGAAACTCTCTCC
Found at i:618836 original size:20 final size:20
Alignment explanation
Indices: 618811--618848 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
618801 GTTAGGCTCA
618811 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
618831 ATGTATCGATACAATTCA
1 ATGTATCGATACAATTCA
618849 TTATATATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:618857 original size:20 final size:20
Alignment explanation
Indices: 618814--618860 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
618804 AGGCTCAATG
*
618814 TATCGATACAATTCACCATG
1 TATCGATACAATTCACCATA
**
618834 TATCGATACAATTCATTATA
1 TATCGATACAATTCACCATA
618854 TATCGAT
1 TATCGAT
618861 GTAATGTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (20 bp):
TATCGATACAATTCACCATA
Found at i:619109 original size:20 final size:21
Alignment explanation
Indices: 619084--619124 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
619074 GATACTTTGA
619084 ATTATTTTTA-CTTGAAAAAC
1 ATTATTTTTAGCTTGAAAAAC
619104 ATTATTTTTATGCTTGAAAAA
1 ATTATTTTTA-GCTTGAAAAA
619125 AATCTATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (21 bp):
ATTATTTTTAGCTTGAAAAAC
Found at i:620772 original size:32 final size:32
Alignment explanation
Indices: 620731--620799 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
620721 TATACTAAAG
620731 CAATGTATCGATAT-ATTAAAATTGTATCGATA
1 CAATGTATCGATATAATT-AAATTGTATCGATA
**
620763 CAATGTATCGATATAAATTTGATTGTATCGATA
1 CAATGTATCGATAT-AATTAAATTGTATCGATA
620796 CAAT
1 CAAT
620800 CTGAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (32 bp):
CAATGTATCGATATAATTAAATTGTATCGATA
Found at i:621906 original size:13 final size:13
Alignment explanation
Indices: 621885--621914 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
621875 ACAATTCTTC
*
621885 ATGTGTCGATACA
1 ATGTATCGATACA
621898 ATGTATCGATACA
1 ATGTATCGATACA
621911 ATGT
1 ATGT
621915 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:621906 original size:33 final size:33
Alignment explanation
Indices: 621864--621930 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
621854 CGTTGGGCAT
* *
621864 AATGTATCGATACAAT-TCTTCATGTGTCGATAC
1 AATGTATCGATACAATGTC-CCATGTATCGATAC
621897 AATGTATCGATACAATGTCCCATGTATCGATAC
1 AATGTATCGATACAATGTCCCATGTATCGATAC
621930 A
1 A
621931 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (33 bp):
AATGTATCGATACAATGTCCCATGTATCGATAC
Found at i:624807 original size:28 final size:29
Alignment explanation
Indices: 624766--624827 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 29
624756 AATAAATTAT
624766 CAAAAGTGCTACATGACATTTCATATGAC
1 CAAAAGTGCTACATGACATTTCATATGAC
624795 CAAAA-TGCTACATGACATTTCATATGAC
1 CAAAAGTGCTACATGACATTTCATATGAC
624823 CAAAA
1 CAAAA
624828 ATAATCATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (29 bp):
CAAAAGTGCTACATGACATTTCATATGAC
Found at i:625987 original size:16 final size:16
Alignment explanation
Indices: 625961--625997 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
625951 TTTTATCAAC
*
625961 ATTTCTTCTATTAAAA
1 ATTTTTTCTATTAAAA
*
625977 CTTTTTTCTATTAAAA
1 ATTTTTTCTATTAAAA
625993 ATTTT
1 ATTTT
625998 GAAAGCCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTTTCTATTAAAA
Found at i:628636 original size:24 final size:22
Alignment explanation
Indices: 628608--628653 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
628598 TTTCATCATT
628608 TAGTTTAGAGAGAGTTTTCTTTTC
1 TAGTTTAGAGA-A-TTTTCTTTTC
* *
628632 TAGTTTTGATAATTTTCTTTTC
1 TAGTTTAGAGAATTTTCTTTTC
628654 AAGAATTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 1 0.05
24 9 0.45
ACGTcount: A:0.20, C:0.09, G:0.15, T:0.57
Consensus pattern (22 bp):
TAGTTTAGAGAATTTTCTTTTC
Found at i:630076 original size:13 final size:13
Alignment explanation
Indices: 630058--630083 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
630048 CAATTTTTTG
630058 TGTATCGATACAT
1 TGTATCGATACAT
630071 TGTATCGATACAT
1 TGTATCGATACAT
630084 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:637957 original size:1 final size:1
Alignment explanation
Indices: 637947--638042 Score: 75
Period size: 1 Copynumber: 96.0 Consensus size: 1
637937 TGGCAATTGG
* * * ** * * * * **
637947 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAGAAAAAAACAAAACAAAAAAAAAAGG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
638012 AAAAAGAAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
638043 GTGAAGATTT
Statistics
Matches: 73, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:637986 original size:34 final size:34
Alignment explanation
Indices: 637948--638040 Score: 147
Period size: 34 Copynumber: 2.8 Consensus size: 34
637938 GGCAATTGGA
637948 AAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAG
1 AAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAG
637982 AAAAGAAAAAAACAAAACAAAAAAAAAAGGAAAAAG
1 AAAAGAAAAAAACAAAAC--AAAAAAAAGGAAAAAG
638018 -AAA-AAAAAAA-AAAACAAAAAAAA
1 AAAAGAAAAAAACAAAACAAAAAAAA
638041 AAGTGAAGAT
Statistics
Matches: 57, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
31 8 0.14
33 5 0.09
34 25 0.44
35 3 0.05
36 16 0.28
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (34 bp):
AAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAG
Found at i:638041 original size:34 final size:34
Alignment explanation
Indices: 637947--638042 Score: 131
Period size: 36 Copynumber: 2.7 Consensus size: 34
637937 TGGCAATTGG
*
637947 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGA
1 AAAAAAAAAAAAAC-AAA-AAAAAAAAGGAAAAAGA
637983 AAAGAAAAAAACAAA-ACAAAAAAAAAAGGAAAAAGA
1 AAA-AAAAAAA-AAACA-AAAAAAAAAAGGAAAAAGA
638019 AAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAACAAAAAAAAAA
638043 GTGAAGATTT
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
34 12 0.22
35 8 0.15
36 24 0.44
37 8 0.15
38 3 0.05
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAAAAACAAAAAAAAAAAGGAAAAAGA
Found at i:642733 original size:13 final size:13
Alignment explanation
Indices: 642715--642753 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
642705 ATAATCACCC
642715 TGTATCGATACAA
1 TGTATCGATACAA
642728 TGTATCGATACAA
1 TGTATCGATACAA
642741 TGTATCGATACAA
1 TGTATCGATACAA
642754 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:642764 original size:20 final size:20
Alignment explanation
Indices: 642739--642817 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
642729 GTATCGATAC
642739 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
**
642759 AATGTATCGATACATTGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
642784 AATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
642804 CATGTATCGATACA
1 AATGTATCGATACA
642818 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
20 31 0.63
25 18 0.37
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:644853 original size:15 final size:15
Alignment explanation
Indices: 644833--644863 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
644823 ATTTCGTTTG
*
644833 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
644848 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
644863 G
1 G
644864 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:646696 original size:21 final size:21
Alignment explanation
Indices: 646667--646711 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
646657 AAGTTTTCAT
646667 TTTTCTTAGCAAAC-TCATTA
1 TTTTCTTAGCAAACTTCATTA
* *
646687 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCAAACTTCATTA
646709 TTT
1 TTT
646712 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTTCTTAGCAAACTTCATTA
Found at i:648936 original size:13 final size:13
Alignment explanation
Indices: 648918--648943 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
648908 CAATTTTTTG
648918 TGTATCGATACAT
1 TGTATCGATACAT
648931 TGTATCGATACAT
1 TGTATCGATACAT
648944 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:650789 original size:20 final size:20
Alignment explanation
Indices: 650743--650795 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
650733 GTTGGACATA
*
650743 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTCTCC
*
650763 ATATATCGATACAATATC-CC
1 ATGTATCGATACAAT-TCTCC
*
650783 ATGTATCAATACA
1 ATGTATCGATACA
650796 TTTCACTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCTCC
Found at i:650864 original size:19 final size:20
Alignment explanation
Indices: 650824--650876 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
650814 CTGCCAGTTT
*
650824 CATGTATCAATACAATTGAG
1 CATGTATCGATACAATTGAG
650844 CATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
650863 CATGTATCGATACA
1 CATGTATCGATACA
650877 TTGTATCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:654201 original size:20 final size:20
Alignment explanation
Indices: 654178--654250 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
654168 ACAATTCAAA
654178 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
654198 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
654219 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
654239 GTATCGATACAT
1 GTATCGATACAT
654251 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:654222 original size:21 final size:21
Alignment explanation
Indices: 654196--654271 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
654186 ACATGTTGCA
654196 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
654217 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
654237 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
654258 TTGTATCGATACAT
1 ATGTATCGATACAT
654272 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:654229 original size:41 final size:41
Alignment explanation
Indices: 654178--654271 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
654168 ACAATTCAAA
*
654178 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
654219 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
654260 GTATCGATACAT
1 GTATCGATACAT
654272 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:654328 original size:13 final size:13
Alignment explanation
Indices: 654310--654335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
654300 TACATTAAGT
654310 ATGTATCGATACA
1 ATGTATCGATACA
654323 ATGTATCGATACA
1 ATGTATCGATACA
654336 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:658419 original size:15 final size:15
Alignment explanation
Indices: 658399--658429 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
658389 TAAAAATGTC
*
658399 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
658414 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
658429 C
1 C
658430 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Done.