Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 55 of 295
Found at i:16298069 original size:18 final size:18
Alignment explanation
Indices: 16298042--16298081 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16298032 CTTGATTATT
* *
16298042 AAAAATTAAAAATTAAAA
1 AAAAACTAAAAACTAAAA
*
16298060 AAAAACTAAAACCTAAAA
1 AAAAACTAAAAACTAAAA
16298078 AAAA
1 AAAA
16298082 TTTAAAAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAACTAAAAACTAAAA
Found at i:16310110 original size:18 final size:18
Alignment explanation
Indices: 16310089--16310372 Score: 146
Period size: 18 Copynumber: 15.3 Consensus size: 18
16310079 GAACAATTAT
16310089 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
16310107 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
16310125 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
16310143 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
16310169 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
16310187 TTATTCAGTAA-AATTAG
1 TTATTCAGTAACAGTCAG
* * *
16310204 ATATTCAGTAACAATTAAG
1 TTATTCAGTAAC-AGTCAG
*
16310223 TTATTCCGTAACAGTCA-
1 TTATTCAGTAACAGTCAG
* *
16310240 TTCATTCAGTGACAATCAAG
1 TT-ATTCAGTAACAGTC-AG
* *
16310260 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
16310278 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
16310296 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* *
16310314 ATATCCAGTAACAGTCAAG
1 TTATTCAGTAACAGTC-AG
* * *
16310333 -TATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
16310350 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
16310368 TTATT
1 TTATT
16310373 TTATACCTTT
Statistics
Matches: 199, Mismatches: 49, Indels: 36
0.70 0.17 0.13
Matches are distributed among these distances:
17 16 0.08
18 138 0.69
19 27 0.14
20 2 0.01
21 2 0.01
22 1 0.01
23 2 0.01
26 11 0.06
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:16310129 original size:36 final size:36
Alignment explanation
Indices: 16310080--16310372 Score: 182
Period size: 36 Copynumber: 7.9 Consensus size: 36
16310070 TAACAATTAG
* * * *
16310080 AACAATTATTTATTCAGTAACAGTCAGTTATTCGGT
1 AACAATCAATTATTCAGTAACAATCAGTTATTCAGT
* * *
16310116 AACAATCAATTATTCAATAATAACCAGTTATTCAGT
1 AACAATCAATTATTCAGTAACAATCAGTTATTCAGT
* * * *
16310152 ATCGATCAATTGATCGGTTATCCAGTAACAGTCAATTATTCAGT
1 AACAATCAATT-A-----T-T-CAGTAACAATCAGTTATTCAGT
* * *
16310196 AA-AATTAGA-TATTCAGTAACAATTAAGTTATTCCGT
1 AACAATCA-ATTATTCAGTAACAA-TCAGTTATTCAGT
* *
16310232 AACAGTC-ATTCATTCAGTGACAATCAAGTTATTCAGT
1 AACAATCAATT-ATTCAGTAACAATC-AGTTATTCAGT
** * *
16310269 AATGATCAATTATTCAGTAATATTCAGTTATTCAGT
1 AACAATCAATTATTCAGTAACAATCAGTTATTCAGT
* * * * *
16310305 AACAGTCTAA-TATCCAGTAACAGTCAAG-TATCCGGT
1 AACAATC-AATTATTCAGTAACAATC-AGTTATTCAGT
* *
16310341 AACAGTCAATTATTCAGTAATAATCAGTTATT
1 AACAATCAATTATTCAGTAACAATCAGTTATT
16310373 TTATACCTTT
Statistics
Matches: 194, Mismatches: 44, Indels: 38
0.70 0.16 0.14
Matches are distributed among these distances:
35 13 0.07
36 108 0.56
37 44 0.23
38 3 0.02
42 2 0.01
43 5 0.03
44 19 0.10
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (36 bp):
AACAATCAATTATTCAGTAACAATCAGTTATTCAGT
Found at i:16310486 original size:6 final size:6
Alignment explanation
Indices: 16310477--16310507 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
16310467 CCGAAGCCGA
*
16310477 AACAGT AACAGT AACAGT AACAGT AGCAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
16310508 CGGTACACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:16310552 original size:53 final size:53
Alignment explanation
Indices: 16310489--16310666 Score: 293
Period size: 53 Copynumber: 3.4 Consensus size: 53
16310479 CAGTAACAGT
* *
16310489 AACAGTAACAGTAGCAGTACGGTACACAGAGTACCTCATCGGAACAAATTCGA
1 AACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
* *
16310542 AACAGTAACAGTAACAGTACGGTACACAGAGTGCCTCATCAGAACAAATCCGA
1 AACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
* * *
16310595 AACAGTAACAGTAATATTACGGTACACAGAGTACTTCATCGGAACAAATCCGA
1 AACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
16310648 AACAGTAACAGTAACAGTA
1 AACAGTAACAGTAACAGTA
16310667 ACAGTAACAA
Statistics
Matches: 114, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 114 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (53 bp):
AACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:16310659 original size:6 final size:6
Alignment explanation
Indices: 16310648--16310675 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
16310638 ACAAATCCGA
16310648 AACAGT AACAGT AACAGT AACAGT AACA
1 AACAGT AACAGT AACAGT AACAGT AACA
16310676 ATATCCGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.18, G:0.14, T:0.14
Consensus pattern (6 bp):
AACAGT
Found at i:16312283 original size:16 final size:16
Alignment explanation
Indices: 16312262--16312300 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
16312252 AATTTTCCCC
*
16312262 TTTTTCCTTCTTTCTT
1 TTTTTCCTTCCTTCTT
16312278 TTTTTCCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
16312294 TCTTTCC
1 TTTTTCC
16312301 CCTGCTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:16328789 original size:25 final size:24
Alignment explanation
Indices: 16328761--16328818 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
16328751 ATCATGAATT
* *
16328761 ATTAAATTTAGAGTA-GATTAATATA
1 ATTAAATGTAGAATATG-TTAA-ATA
*
16328786 ATTATATGTAGAATATGTTAAATA
1 ATTAAATGTAGAATATGTTAAATA
16328810 ATTAAATGT
1 ATTAAATGT
16328819 TTGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 11 0.39
25 16 0.57
26 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (24 bp):
ATTAAATGTAGAATATGTTAAATA
Found at i:16333881 original size:6 final size:7
Alignment explanation
Indices: 16333861--16333886 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16333851 TGGAGTTTGG
16333861 AATAAAA
1 AATAAAA
16333868 AATAAAA
1 AATAAAA
16333875 AATAAAA
1 AATAAAA
16333882 AATAA
1 AATAA
16333887 GAAGTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AATAAAA
Found at i:16334855 original size:23 final size:23
Alignment explanation
Indices: 16334829--16334882 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
16334819 GGGGTTAAAA
*
16334829 GCCATTGCTACATACCATATCGT
1 GCCATTACTACATACCATATCGT
16334852 GCCATTACTACATACCATATCGT
1 GCCATTACTACATACCATATCGT
16334875 GCCATTAC
1 GCCATTAC
16334883 GGCACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (23 bp):
GCCATTACTACATACCATATCGT
Found at i:16339466 original size:20 final size:21
Alignment explanation
Indices: 16339423--16339468 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
16339413 ACTGTTTTGT
16339423 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
16339443 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
16339462 TATGGGC
1 TATGGGC
16339469 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:16339568 original size:60 final size:62
Alignment explanation
Indices: 16339493--16339632 Score: 173
Period size: 60 Copynumber: 2.3 Consensus size: 62
16339483 CTCGACTTGT
*
16339493 AATAGGGC-TACGGCCCAGATTGATACTGACATGGGCT-AGGCCCAG-TATACTCTGATA-CTG
1 AATAGGGCTTA-GGCCCAGATTAATACTGACATGGGCTAAGGCCCAGTTA-ACTCTGATATCTG
* * * *
16339553 TA-AGGGGTTATGGCCCAGATTAATATTGATATGGGCTAAGGCCCAGTTAACTCTGATATCTG
1 AATAGGGCTTA-GGCCCAGATTAATACTGACATGGGCTAAGGCCCAGTTAACTCTGATATCTG
16339615 AATAGGGCTTAGGCCCAG
1 AATAGGGCTTAGGCCCAG
16339633 TAAAGCTTGA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
59 4 0.06
60 26 0.39
61 17 0.25
62 13 0.19
63 7 0.10
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (62 bp):
AATAGGGCTTAGGCCCAGATTAATACTGACATGGGCTAAGGCCCAGTTAACTCTGATATCTG
Found at i:16340412 original size:48 final size:48
Alignment explanation
Indices: 16340336--16340489 Score: 173
Period size: 48 Copynumber: 3.2 Consensus size: 48
16340326 TGGAGTGTTA
* * * *
16340336 CAATGTCAATACCATATCCCAAATATGGTCTTACATGGGACCACATAT
1 CAATGCCAATGCCATATCCCAAACATGGTCTTACATGGGATCACATAT
* * * ** *
16340384 CAATGCCAATGCCATATCCCAGACATGGTCTTACATAGAATCGTAGAT
1 CAATGCCAATGCCATATCCCAAACATGGTCTTACATGGGATCACATAT
* * *
16340432 CGATGCCAATGACATGTCCCAAACATGGTCTTACATGGGATCACATAT
1 CAATGCCAATGCCATATCCCAAACATGGTCTTACATGGGATCACATAT
* *
16340480 CGATGTCAAT
1 CAATGCCAAT
16340490 AGCCCAGCTA
Statistics
Matches: 86, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 86 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (48 bp):
CAATGCCAATGCCATATCCCAAACATGGTCTTACATGGGATCACATAT
Found at i:16343225 original size:23 final size:23
Alignment explanation
Indices: 16343195--16343240 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16343185 CACTTTGAAT
16343195 TAGAAAAATGCATGTGAAATCTA
1 TAGAAAAATGCATGTGAAATCTA
16343218 TAGAAAAATGCATGTGAAATCTA
1 TAGAAAAATGCATGTGAAATCTA
16343241 AGTTTTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (23 bp):
TAGAAAAATGCATGTGAAATCTA
Found at i:16348369 original size:6 final size:6
Alignment explanation
Indices: 16348361--16348399 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
16348351 GAAAGAGATA
*
16348361 GGGAAA GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGG
1 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGG
16348400 GGCTTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:16369464 original size:17 final size:17
Alignment explanation
Indices: 16369442--16369475 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16369432 ATTTTTATTA
16369442 AATTTTTAATTAAATTT
1 AATTTTTAATTAAATTT
16369459 AATTTTTAATTAAATTT
1 AATTTTTAATTAAATTT
16369476 TACCACTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTTTAATTAAATTT
Found at i:16371484 original size:33 final size:34
Alignment explanation
Indices: 16371446--16371512 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
16371436 GGTCGGGGAG
16371446 GGGGAGAGAGAA-GGGGTGGGGAGATTTTTATTT
1 GGGGAGAGAGAAGGGGGTGGGGAGATTTTTATTT
16371479 GGGGAGAGAGAAGGGGGTGGGGAGATTTTTATTT
1 GGGGAGAGAGAAGGGGGTGGGGAGATTTTTATTT
16371513 TACTTAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 12 0.36
34 21 0.64
ACGTcount: A:0.24, C:0.00, G:0.49, T:0.27
Consensus pattern (34 bp):
GGGGAGAGAGAAGGGGGTGGGGAGATTTTTATTT
Found at i:16371607 original size:20 final size:19
Alignment explanation
Indices: 16371582--16371630 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
16371572 AAATTTTTAT
16371582 TTTATATATTTTAAAATTA
1 TTTATATATTTTAAAATTA
16371601 TTATATATATTTTAAAA-TA
1 TT-TATATATTTTAAAATTA
*
16371620 TTTATGTATTT
1 TTTATATATTT
16371631 ATGTATCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.29
19 6 0.21
20 14 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTATATATTTTAAAATTA
Found at i:16372024 original size:34 final size:34
Alignment explanation
Indices: 16371971--16372035 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
16371961 CATGTCTGTG
16371971 TTTCAAGTTATTACCCAATAAAAAGCTCCTAGTA
1 TTTCAAGTTATTACCCAATAAAAAGCTCCTAGTA
* *
16372005 TTTCAAGTTGTTACGCAATAAAAAGCTCCTA
1 TTTCAAGTTATTACCCAATAAAAAGCTCCTA
16372036 CTTGAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (34 bp):
TTTCAAGTTATTACCCAATAAAAAGCTCCTAGTA
Found at i:16375831 original size:55 final size:55
Alignment explanation
Indices: 16375747--16375865 Score: 220
Period size: 55 Copynumber: 2.2 Consensus size: 55
16375737 AAGGGTCTTT
16375747 CCTTAAATTCATTGTTGGAAAGAATGGAACACCTCTCCAATATTTACCACAGTGC
1 CCTTAAATTCATTGTTGGAAAGAATGGAACACCTCTCCAATATTTACCACAGTGC
*
16375802 CCTTAAATTCATTGTTGGAAGGAATGGAACACCTCTCCAATATTTACCACAGTGC
1 CCTTAAATTCATTGTTGGAAAGAATGGAACACCTCTCCAATATTTACCACAGTGC
*
16375857 CCTTCAATT
1 CCTTAAATT
16375866 TCCTCTCAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (55 bp):
CCTTAAATTCATTGTTGGAAAGAATGGAACACCTCTCCAATATTTACCACAGTGC
Found at i:16379572 original size:3 final size:3
Alignment explanation
Indices: 16379564--16379729 Score: 65
Period size: 3 Copynumber: 54.3 Consensus size: 3
16379554 ATTAGTTAAT
* * *
16379564 TTA TTA TTA TTC TTA TTAA TGTA -TA TTA TTA TTC TTA TTAA TGTA TTC
1 TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TT-A T-TA TTA
* * * * * * *
16379612 TTA TTA TT- GTA TTA TTG CTA TTA TTT TTA TTA TTA TCA CTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** **
16379659 TTA -TA TT- TCC TT- TCTA TGC TTA TGTA TTTA TTTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA T-TA TTA TTA T-TA -TTA -TTA TTA TTA TTA TTA
* *
16379704 TTT TGTA TTA TTA TTA CTA TTA TTA T
1 TTA T-TA TTA TTA TTA TTA TTA TTA T
16379730 ATCTCTATTT
Statistics
Matches: 119, Mismatches: 30, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
2 9 0.08
3 89 0.75
4 18 0.15
5 3 0.03
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:16379593 original size:22 final size:23
Alignment explanation
Indices: 16379564--16379647 Score: 100
Period size: 22 Copynumber: 3.7 Consensus size: 23
16379554 ATTAGTTAAT
16379564 TTATTATTATTCTTATTAATGTA
1 TTATTATTATTCTTATTAATGTA
16379587 -TATTATTATTCTTATTAATGTA
1 TTATTATTATTCTTATTAATGTA
* * *
16379609 TTCTTATTATT-GTATTATTGCTA
1 TTATTATTATTCTTATTAATG-TA
* *
16379632 TTATTTTTATTATTAT
1 TTATTATTATTCTTAT
16379648 CACTATTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
22 29 0.56
23 20 0.38
24 3 0.06
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (23 bp):
TTATTATTATTCTTATTAATGTA
Found at i:16379612 original size:14 final size:14
Alignment explanation
Indices: 16379571--16379624 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
16379561 AATTTATTAT
16379571 TATTCTTATTAATG
1 TATTCTTATTAATG
16379585 TA----TATT-AT-
1 TATTCTTATTAATG
16379593 TATTCTTATTAATG
1 TATTCTTATTAATG
*
16379607 TATTCTTATTATTG
1 TATTCTTATTAATG
16379621 TATT
1 TATT
16379625 ATTGCTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.12
12 4 0.12
13 2 0.06
14 19 0.58
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (14 bp):
TATTCTTATTAATG
Found at i:16380762 original size:26 final size:26
Alignment explanation
Indices: 16380725--16380808 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
16380715 TGATACAAAT
* *
16380725 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
16380751 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
16380777 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
16380803 TGATAA
1 TGATAA
16380809 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:16382475 original size:22 final size:22
Alignment explanation
Indices: 16382423--16382476 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
16382413 GACAGAGGAA
*
16382423 GTACTGAAAGTGGCTTGTCCAC
1 GTACTGAAGGTGGCTTGTCCAC
16382445 GTACTGAAGGTGGCTTGTCCAC
1 GTACTGAAGGTGGCTTGTCCAC
16382467 GTACTGAAGG
1 GTACTGAAGG
16382477 CTTTGCCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.26
Consensus pattern (22 bp):
GTACTGAAGGTGGCTTGTCCAC
Found at i:16387889 original size:26 final size:26
Alignment explanation
Indices: 16387853--16387934 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
16387843 ATACAAATTT
* *
16387853 ATAATAGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTTCATG
*
16387879 ATAATGGGTTAGGTAAATCTTTCATG
1 ATAATGGGTTAGGTAAATGTTTCATG
*
16387905 ATATTGGGTTAGGTAAATGTTTCATG
1 ATAATGGGTTAGGTAAATGTTTCATG
16387931 ATAA
1 ATAA
16387935 GAGTTTCATG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (26 bp):
ATAATGGGTTAGGTAAATGTTTCATG
Found at i:16401551 original size:17 final size:17
Alignment explanation
Indices: 16401517--16401571 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
16401507 TGACATATAT
*
16401517 ATATGA-CTAG-TTTCA
1 ATATGATCTAGCTTTAA
16401532 ATATGATCTAGCTTTAA
1 ATATGATCTAGCTTTAA
*
16401549 ATATGATCTAACTTTAA
1 ATATGATCTAGCTTTAA
16401566 ATATGA
1 ATATGA
16401572 ATGCTTGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.17
16 4 0.11
17 26 0.72
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (17 bp):
ATATGATCTAGCTTTAA
Found at i:16402629 original size:20 final size:20
Alignment explanation
Indices: 16402591--16402629 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16402581 CTGAATTAGT
* *
16402591 CCCATTTCGTCTGTTTTTGG
1 CCCATTTCGTCTCTCTTTGG
16402611 CCCATTTCGTCTCTCTTTG
1 CCCATTTCGTCTCTCTTTG
16402630 CTTTCCTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.31, G:0.15, T:0.49
Consensus pattern (20 bp):
CCCATTTCGTCTCTCTTTGG
Found at i:16403862 original size:17 final size:18
Alignment explanation
Indices: 16403834--16403867 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
16403824 AAATAGAAGA
16403834 TATTATTTTATTTTATTT
1 TATTATTTTATTTTATTT
16403852 TATTA-TTTATTTTATT
1 TATTATTTTATTTTATT
16403868 AATTTAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTATTTTATTTTATTT
Found at i:16409211 original size:10 final size:10
Alignment explanation
Indices: 16409196--16409225 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
16409186 GACCTACCCT
16409196 ACCCAATACA
1 ACCCAATACA
16409206 ACCCAAATACA
1 ACCC-AATACA
16409217 ACCCAATAC
1 ACCCAATAC
16409226 CCGATTGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (10 bp):
ACCCAATACA
Found at i:16410457 original size:8 final size:7
Alignment explanation
Indices: 16410427--16410485 Score: 52
Period size: 6 Copynumber: 8.6 Consensus size: 7
16410417 TTGCTAAATT
16410427 TATTAT-
1 TATTATA
16410433 TATTAT-
1 TATTATA
16410439 TATTATA
1 TATTATA
16410446 TATTAGTA
1 TATTA-TA
* *
16410454 TATTTTT
1 TATTATA
16410461 TATTATA
1 TATTATA
16410468 TATGTATA
1 TAT-TATA
*
16410476 T-GTATA
1 TATTATA
16410482 TATT
1 TATT
16410486 TTTATACATA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
6 17 0.40
7 15 0.35
8 11 0.26
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (7 bp):
TATTATA
Found at i:16410605 original size:19 final size:19
Alignment explanation
Indices: 16410578--16410618 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
16410568 CTATTATTAT
16410578 TATTATTATTAT-TAGTGTG
1 TATTATTATTATATA-TGTG
*
16410597 TATTTTTATTATATATGTG
1 TATTATTATTATATATGTG
16410616 TAT
1 TAT
16410619 GTATATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (19 bp):
TATTATTATTATATATGTG
Found at i:16410706 original size:142 final size:140
Alignment explanation
Indices: 16410427--16410718 Score: 333
Period size: 142 Copynumber: 2.1 Consensus size: 140
16410417 TTGCTAAATT
16410427 TATTATTATTATTATTATATATTAGTATATTTTTTATTATATATGTATATGTATATATTTTTATA
1 TATTATTATTATTATTATATATTAGTATATTTTTTATTATATATGTATATGTATATATTTTTATA
* * * * *
16410492 CATAGTATTATTTTTTTATTACTTTATTTTAATATTTTTTTATACTACATTTGCTTTTCGTATTT
66 CATAGTATTATTTCTTTATTACTTTATTTT-ATATTATATTATACTA-ATTTGCATTTCATATTT
*
16410557 TAATATTATTGC
129 TAATATTATTAC
* * *
16410569 TATTATTATTATTATTAT-TATTAGTGTGTATTTTTATTATATATGTGTATGTATATGTATATGT
1 TATTATTATTATTATTATATATTAGTATAT-TTTTTATTATATATGTATATGTATA--TAT-T-T
* * * *
16410633 TTATATATAGTATTA-TTCTTTATTACTTTATTTT-TATTATATT-TGCT-TTTTGGATTTCAAT
61 TTATACATAGTATTATTTCTTTATTACTTTATTTTATATTATATTATACTAATTTGCATTTC-AT
* *
16410694 ATTATTACTATTATTAT
125 ATT-TTAATATTATTAC
16410711 TATTATTA
1 TATTATTA
16410719 GTGTATATTT
Statistics
Matches: 128, Mismatches: 15, Indels: 14
0.82 0.10 0.09
Matches are distributed among these distances:
140 8 0.06
141 13 0.10
142 63 0.49
143 7 0.05
144 3 0.02
145 19 0.15
146 15 0.12
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (140 bp):
TATTATTATTATTATTATATATTAGTATATTTTTTATTATATATGTATATGTATATATTTTTATA
CATAGTATTATTTCTTTATTACTTTATTTTATATTATATTATACTAATTTGCATTTCATATTTTA
ATATTATTAC
Found at i:16410875 original size:3 final size:3
Alignment explanation
Indices: 16410861--16411081 Score: 51
Period size: 3 Copynumber: 72.3 Consensus size: 3
16410851 TTAATTTAAC
* * * * * *
16410861 TTA TTAA TTA TTA TTA TCA TTA TCA CTA TTG TTA TTA CT- TTA CTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
16410906 TCGTA ATA TAA TATA TTA TTA ATA TTA CTT- TTA TT- TTCA TTA TTA
1 T--TA TTA TTA T-TA TTA TTA TTA TTA -TTA TTA TTA TT-A TTA TTA
* * * * ** *
16410951 TTA TTA TTA CTA TTA TTCT TTA TTG TCA TGG TTA TT- TTA TTTA TTT
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * * * * * * * *
16410997 TTA -TA GCTA TTA TTT TTT TTA TCA CTA ATA TTA CTA CTG TTA -TA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
16411041 TTTA TTA TTA TTA CTT- TTA TTA TAA TTA CTA TTA TTA TTA T
1 -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16411082 AGTTTTTCTT
Statistics
Matches: 153, Mismatches: 47, Indels: 36
0.65 0.20 0.15
Matches are distributed among these distances:
2 13 0.08
3 118 0.77
4 20 0.13
5 2 0.01
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:16411061 original size:15 final size:15
Alignment explanation
Indices: 16411041--16411081 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
16411031 TACTGTTATA
16411041 TTTATTATTATTACT
1 TTTATTATTATTACT
*
16411056 TTTATTATAATTACT
1 TTTATTATTATTACT
*
16411071 ATTATTATTAT
1 TTTATTATTAT
16411082 AGTTTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATTATTATTACT
Found at i:16423357 original size:18 final size:18
Alignment explanation
Indices: 16423336--16423370 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16423326 TTATTATTAG
* *
16423336 TGTATATTTTTTTATATA
1 TGTATATGTATTTATATA
16423354 TGTATATGTATTTATAT
1 TGTATATGTATTTATAT
16423371 TTATACATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.63
Consensus pattern (18 bp):
TGTATATGTATTTATATA
Found at i:16423417 original size:116 final size:124
Alignment explanation
Indices: 16423188--16423461 Score: 339
Period size: 116 Copynumber: 2.2 Consensus size: 124
16423178 AATTTATTAT
* *
16423188 TATTATTATTATATATTAGTATATTTTTTTTATTATATATGTATATGTATATATTTTTATACATA
1 TATTATTATTAT-TATTAGTATATTATTTTTATTATATATGTATATGTATATATATTTATACATA
*
16423253 GTATTATTTTTTTATTACTTTATTTTAATGTTTTTATTATACTACATTTGCTTTTCGTATTTCAA
65 G--TTATTTTTTTA-TAC-TTACTTTAA-GTTTTTATTATACTACATTTGCTTTTCGTATTTCAA
* *
16423318 TATTATTATTATTATTAGTGTA-TATTTTT-TTATATATGTATATGTATTTATATTTATACATAG
1 TATTATTATTATTATTAGTATATTATTTTTATTATATATGTATATGTATATATATTTATACATAG
* * *
16423381 -TA-TTTTTTA-A-TTACTTT-A-TTTTTATTATACTACATTTGTTTTTTGTATTTTAA
66 TTATTTTTTTATACTTACTTTAAGTTTTTATTATACTACATTTGCTTTTCGTATTTCAA
* *
16423434 TATTATTACTATTATTATTATTATTATT
1 TATTATTATTATTATTAGTA-TATTATT
16423462 AATATTAGTG
Statistics
Matches: 131, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
116 49 0.37
117 2 0.02
118 5 0.04
119 6 0.05
121 1 0.01
123 7 0.05
124 2 0.02
127 32 0.24
128 6 0.05
129 9 0.07
130 12 0.09
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (124 bp):
TATTATTATTATTATTAGTATATTATTTTTATTATATATGTATATGTATATATATTTATACATAG
TTATTTTTTTATACTTACTTTAAGTTTTTATTATACTACATTTGCTTTTCGTATTTCAA
Found at i:16423449 original size:3 final size:3
Alignment explanation
Indices: 16423434--16423468 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
16423424 TGTATTTTAA
* *
16423434 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16423469 GTGTGTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:16423542 original size:15 final size:15
Alignment explanation
Indices: 16423507--16423552 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
16423497 TATATGTATA
*
16423507 TATTTATATATACTAT
1 TATTTTTAT-TACTAT
16423523 TATTTTTTATTACT-T
1 TA-TTTTTATTACTAT
16423538 TATTTTTATTA-TAT
1 TATTTTTATTACTAT
16423552 T
1 T
16423553 TGCTTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 1 0.04
14 11 0.41
15 3 0.11
16 6 0.22
17 6 0.22
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTATTACTAT
Found at i:16423613 original size:135 final size:138
Alignment explanation
Indices: 16423318--16423640 Score: 441
Period size: 135 Copynumber: 2.4 Consensus size: 138
16423308 CGTATTTCAA
* *
16423318 TATTATTATTATTATTAGTGTATATTTTT-TTATATATGTATATG--TAT-T-TATATTTATACA
1 TATTATTATTAATATTAGTGTATATTTTTATTATATATGCATATGTATATGTATATATTTATACA
* * * *
16423378 TAGTATTTTTTAATTACTTTATTTTTATTATACTACATTTGTTTTTTGTATTTTAATATTATTAC
66 TACTATTTTTTAATTACTTTATTTTTATTATACTA-ATTTGCTTTTTGAATTTCAATATTATTAC
16423443 TATTATTAT
130 TATTATTAT
* ** *
16423452 TATTATTATTAATATTAGTGTGTATTTTTATTATATATGTGTATGTATATGTATATATTTATATA
1 TATTATTATTAATATTAGTGTATATTTTTATTATATATGCATATGTATATGTATATATTTATACA
*
16423517 TACTATTATTTTTTATTACTTTATTTTTA-T-TA-T-ATTTGCTTTTTGAATTTCAATATTATT-
66 TACTA-T-TTTTTAATTACTTTATTTTTATTATACTAATTTGCTTTTTGAATTTCAATATTATTA
16423577 CTATTATTAT
129 CTATTATTAT
*
16423587 TATTATTATTAATATTAGTGTATATTTTTATTATATATGCATATATATATGTAT
1 TATTATTATTAATATTAGTGTATATTTTTATTATATATGCATATGTATATGTAT
16423641 TTATATAGTA
Statistics
Matches: 169, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
134 27 0.16
135 74 0.44
136 24 0.14
137 3 0.02
138 2 0.01
139 17 0.10
140 2 0.01
141 20 0.12
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.60
Consensus pattern (138 bp):
TATTATTATTAATATTAGTGTATATTTTTATTATATATGCATATGTATATGTATATATTTATACA
TACTATTTTTTAATTACTTTATTTTTATTATACTAATTTGCTTTTTGAATTTCAATATTATTACT
ATTATTAT
Found at i:16423902 original size:18 final size:18
Alignment explanation
Indices: 16423879--16423913 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16423869 ATTATGTTTA
*
16423879 TTTTTATAACTATTATTT
1 TTTTTATAACTAATATTT
*
16423897 TTTTTATCACTAATATT
1 TTTTTATAACTAATATT
16423914 ACTACTGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTATAACTAATATTT
Found at i:16423946 original size:15 final size:15
Alignment explanation
Indices: 16423926--16423966 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
16423916 TACTGTTATA
*
16423926 TTTATTATTATTTCT
1 TTTATTATTATTACT
*
16423941 TTTATTATAATTACT
1 TTTATTATTATTACT
*
16423956 ATTATTATTAT
1 TTTATTATTAT
16423967 AGCTTTTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATTATTATTACT
Found at i:16423953 original size:21 final size:21
Alignment explanation
Indices: 16423882--16423958 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
16423872 ATGTTTATTT
* *
16423882 TTATAACTATTATTTTTTTTA
1 TTATAATTATTATTTCTTTTA
* * *
16423903 TCACTAA-TATTACTACTGTTATA
1 TTA-TAATTATTATTTCT-TT-TA
16423926 TT-T-ATTATTATTTCTTTTA
1 TTATAATTATTATTTCTTTTA
*
16423945 TTATAATTACTATT
1 TTATAATTATTATT
16423959 ATTATTATAG
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
19 4 0.10
20 4 0.10
21 26 0.62
22 5 0.12
23 3 0.07
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.60
Consensus pattern (21 bp):
TTATAATTATTATTTCTTTTA
Found at i:16426339 original size:9 final size:9
Alignment explanation
Indices: 16426325--16426354 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16426315 CCAACTCCTA
16426325 TTTTTTTTC
1 TTTTTTTTC
16426334 TTTTTTTTC
1 TTTTTTTTC
*
16426343 TTCTTTTTC
1 TTTTTTTTC
16426352 TTT
1 TTT
16426355 GAAACACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:16439665 original size:44 final size:44
Alignment explanation
Indices: 16439602--16439708 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
16439592 ACGGCGAATC
*
16439602 TTATCTCTCTGAAA-TTGCAGTGGAGCAGACTGAAGATACCAATA
1 TTATCTCTCT-AAAGTTGCAGCGGAGCAGACTGAAGATACCAATA
* * * * *
16439646 TTATCTCTCTAAAGTTGCAGCGGAGTAGAGTGAAGCTACTAATC
1 TTATCTCTCTAAAGTTGCAGCGGAGCAGACTGAAGATACCAATA
* *
16439690 CTATCTCCCTAAAGTTGCA
1 TTATCTCTCTAAAGTTGCA
16439709 ATAGATCAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
43 3 0.06
44 51 0.94
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
TTATCTCTCTAAAGTTGCAGCGGAGCAGACTGAAGATACCAATA
Found at i:16439938 original size:85 final size:85
Alignment explanation
Indices: 16439783--16439938 Score: 199
Period size: 85 Copynumber: 1.8 Consensus size: 85
16439773 ATGACAATTC
* * * * *
16439783 TTATCTCCCTGAAGTTGCAGTGGGTCAGATTGAAGCCACAAGTTTTATCTATCTGAAGTTGTAGT
1 TTATCTCCCTGAAGTAGCAGTGGGTCAGATTGAAGCCACAAGTCTTATCTACCTGAAGTTGCAGC
16439848 AGAGCAGATCATAACAAACT
66 AGAGCAGATCATAACAAACT
** *
16439868 TTATCTCCCTGAAGTAGCAGTGGAG-CATG-TTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
1 TTATCTCCCTGAAGTAGCAGTGG-GTCA-GATTGAAGCCACAAGTCTTATCTACCTGAAGTTGCA
*
16439931 GCGGAGCA
64 GCAGAGCA
16439939 AACTAAAGAT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
85 58 0.97
86 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (85 bp):
TTATCTCCCTGAAGTAGCAGTGGGTCAGATTGAAGCCACAAGTCTTATCTACCTGAAGTTGCAGC
AGAGCAGATCATAACAAACT
Found at i:16440568 original size:24 final size:24
Alignment explanation
Indices: 16440523--16440568 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
16440513 ATAGATTTCG
**
16440523 AATACAAAAAAAAGAGTGAATCAA
1 AATACAAAAAAAAGAGCAAATCAA
* *
16440547 AATATAAAAAAAATAGCAAATC
1 AATACAAAAAAAAGAGCAAATC
16440569 GAAAGTTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.15
Consensus pattern (24 bp):
AATACAAAAAAAAGAGCAAATCAA
Found at i:16441388 original size:3 final size:3
Alignment explanation
Indices: 16441380--16441457 Score: 52
Period size: 3 Copynumber: 25.3 Consensus size: 3
16441370 ATTAGTTAAT
* *
16441380 TTA TTA TTAA TGTA -TA TTA TTA TTA TTC TTA TTAA TGTA TTC TTA TTA
1 TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA
* * * *
16441428 TT- GTA TTA TTG CTA TTA TTT TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16441458 CACATTATAA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
2 3 0.05
3 45 0.79
4 7 0.12
5 2 0.04
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:16441422 original size:14 final size:14
Alignment explanation
Indices: 16441383--16441434 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
16441373 AGTTAATTTA
*
16441383 TTATTAATGTA-TA
1 TTATTAATGTATTC
16441396 TTATT-AT-TATTC
1 TTATTAATGTATTC
16441408 TTATTAATGTATTC
1 TTATTAATGTATTC
*
16441422 TTATTATTGTATT
1 TTATTAATGTATT
16441435 ATTGCTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 2 0.06
12 8 0.24
13 7 0.21
14 17 0.50
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.62
Consensus pattern (14 bp):
TTATTAATGTATTC
Found at i:16441436 original size:25 final size:25
Alignment explanation
Indices: 16441381--16441437 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
16441371 TTAGTTAATT
*
16441381 TATTATTAATGTATATTATTATTAT
1 TATTATTAATGTATATTATTATTAG
* *
16441406 TCTTATTAATGTATTCTTATTATT-G
1 TATTATTAATGTA-TATTATTATTAG
16441431 TATTATT
1 TATTATT
16441438 GCTATTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (25 bp):
TATTATTAATGTATATTATTATTAG
Found at i:16441522 original size:15 final size:16
Alignment explanation
Indices: 16441491--16441527 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
16441481 CTATGCTTAT
*
16441491 TTATT-TATTTATTTA
1 TTATTATATTTATGTA
16441506 TTATTATATTT-TGTA
1 TTATTATATTTATGTA
16441521 TTATTAT
1 TTATTAT
16441528 TACTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTATTATATTTATGTA
Found at i:16443939 original size:39 final size:40
Alignment explanation
Indices: 16443896--16444063 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
16443886 CTCGTTCAAG
* * * *
16443896 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
16443935 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
16443975 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
16444015 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
16444055 TGCCTTCGG
1 TGCCTTCGG
16444064 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:16444047 original size:80 final size:80
Alignment explanation
Indices: 16443931--16444116 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
16443921 AGTAACTCAT
* * *
16443931 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
16443995 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
16444010 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
16444074 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
16444091 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
16444117 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:16444076 original size:40 final size:40
Alignment explanation
Indices: 16443933--16444116 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
16443923 TAACTCATAC
* *
16443933 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
16443973 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
16444013 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
16444053 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
16444094 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
16444117 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:16447241 original size:34 final size:34
Alignment explanation
Indices: 16447198--16447266 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
16447188 CCCTCACAAG
*
16447198 TATTATGAATATTCAATTCAGTACAATATGTCTC
1 TATTATGAATATTCAATTCAGTACAATATATCTC
16447232 TATTATGAATATTCAATTCAGTACAATATATCTC
1 TATTATGAATATTCAATTCAGTACAATATATCTC
16447266 T
1 T
16447267 TTAGGAGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.42
Consensus pattern (34 bp):
TATTATGAATATTCAATTCAGTACAATATATCTC
Found at i:16450846 original size:15 final size:15
Alignment explanation
Indices: 16450823--16450854 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16450813 AAAACAATCT
*
16450823 CTATGTTGAGAACAA
1 CTATATTGAGAACAA
16450838 CTATATTGAGAACAA
1 CTATATTGAGAACAA
16450853 CT
1 CT
16450855 CGTGTTTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (15 bp):
CTATATTGAGAACAA
Found at i:16451862 original size:28 final size:28
Alignment explanation
Indices: 16451802--16451862 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
16451792 TAAAATAATT
*
16451802 TTTTTTTTCATTTTTAAAAAGTTAAATA
1 TTTTTTTTCATTTTTAAAAAATTAAATA
*
16451830 CTTTTTTT-ATTTTTATAAAAATTGAAA-A
1 TTTTTTTTCATTTTTA-AAAAATT-AAATA
16451858 TTTTT
1 TTTTT
16451863 ATATAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 7 0.25
28 18 0.64
29 3 0.11
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTTTTTCATTTTTAAAAAATTAAATA
Found at i:16453023 original size:17 final size:19
Alignment explanation
Indices: 16452984--16453025 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
16452974 ATTTTTTACG
16452984 ATTTTTATAAAAATTTCTA
1 ATTTTTATAAAAATTTCTA
*
16453003 ATTTTTA-ATAAATTT-TA
1 ATTTTTATAAAAATTTCTA
16453020 ATTTTT
1 ATTTTT
16453026 TATATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 7 0.32
19 7 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTTATAAAAATTTCTA
Found at i:16453025 original size:18 final size:18
Alignment explanation
Indices: 16452984--16453027 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
16452974 ATTTTTTACG
16452984 ATTTTTATAAAAATTTCTA
1 ATTTTT-TAAAAATTTCTA
16453003 A-TTTTTAATAAATTT-TA
1 ATTTTTTAA-AAATTTCTA
16453020 ATTTTTTA
1 ATTTTTTA
16453028 TATTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.26
18 16 0.70
19 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTTAAAAATTTCTA
Found at i:16453033 original size:45 final size:45
Alignment explanation
Indices: 16452969--16453105 Score: 132
Period size: 46 Copynumber: 3.0 Consensus size: 45
16452959 TGTTACAATT
*
16452969 TTTTTATTTTTTACGATTTTTATAAAAATTTCTAATTTTTAATAAA
1 TTTTTATTTTTTA-TATTTTTATAAAAATTTCTAATTTTTAATAAA
* * * *
16453015 TTTTAATTTTTTATATTTTTATTAAAATTTAATAATTTTT-GTAAAA
1 TTTTTATTTTTTATATTTTTATAAAAATTT-CTAATTTTTAAT-AAA
* * ****
16453061 TTTATTATTTATTATTTTTTTATATTTTTTTCTAATTTTTAATAA
1 TTT-TTATTTTTTATATTTTTATAAAAATTTCTAATTTTTAATAA
16453106 GAGTAGGGGC
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
45 16 0.22
46 36 0.50
47 20 0.28
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (45 bp):
TTTTTATTTTTTATATTTTTATAAAAATTTCTAATTTTTAATAAA
Found at i:16453286 original size:90 final size:90
Alignment explanation
Indices: 16453107--16453330 Score: 235
Period size: 90 Copynumber: 2.5 Consensus size: 90
16453097 TTTTAATAAG
* *
16453107 AGTAGGGGCTTAATTGCTTTTTTGAAAAATTTTGAGAGTCTTTTTTATGCATTTTGAAAGTTCAA
1 AGTAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGAGCCTTTTTTATGCATTTTGAAAGTTCAA
* *
16453172 TTGTACCCAATTGAGTGAAAAAAAAA
66 -TGTACCCAATTAAATGAAAAAAAAA
16453198 AGTAGGGGCTTAATTG-TTTTTTGAAAAAGTTTGAG-GACCTTTTTGT-TGCATTTTGAAAGTTT
1 AGTAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGAG-CCTTTTT-TATGCATTTTGAAAG-TT
* * * * *
16453260 TAA-GTGCTCAATTAAATG-CAAGAAAA
63 CAATGTACCCAATTAAATGAAAAAAAAA
* * * * *
16453286 AGGAGAGACTTAATTACTTTTTTAAAAAAAGTTTGAGAG-CTTTTT
1 AGTAGGGGCTTAATTGCTTTTTT-GAAAAAGTTTGAGAGCCTTTTT
16453331 ACATCCCTAA
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
88 18 0.16
89 24 0.21
90 49 0.43
91 22 0.19
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (90 bp):
AGTAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGAGCCTTTTTTATGCATTTTGAAAGTTCAA
TGTACCCAATTAAATGAAAAAAAAA
Found at i:16463797 original size:24 final size:24
Alignment explanation
Indices: 16463767--16463812 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
16463757 TTTAATTTTC
16463767 AAAATTTTAAAAAAATAAAAATAA
1 AAAATTTTAAAAAAATAAAAATAA
*
16463791 AAAATTTTCAAAAAATAAAAAT
1 AAAATTTTAAAAAAATAAAAAT
16463813 TGCATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAATTTTAAAAAAATAAAAATAA
Found at i:16463865 original size:29 final size:30
Alignment explanation
Indices: 16463809--16463928 Score: 131
Period size: 30 Copynumber: 4.1 Consensus size: 30
16463799 CAAAAAATAA
*
16463809 AAATTGCATTTTTACCCTTAAACTTTTCCT
1 AAATTGCATTTTAACCCTTAAACTTTTCCT
* *
16463839 AAATTTCATTTTAACCCTTAAAC-TTTCTTT
1 AAATTGCATTTTAACCCTTAAACTTTTC-CT
* * * * *
16463869 AAATTTCACTTAAACCCCTAAACTTTTCTT
1 AAATTGCATTTTAACCCTTAAACTTTTCCT
16463899 AAATTGCATTTTAACCC-TAAA-TTTT-CT
1 AAATTGCATTTTAACCCTTAAACTTTTCCT
16463926 AAA
1 AAA
16463929 AATTACATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.05
28 4 0.05
29 8 0.10
30 58 0.74
31 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.44
Consensus pattern (30 bp):
AAATTGCATTTTAACCCTTAAACTTTTCCT
Found at i:16464170 original size:15 final size:16
Alignment explanation
Indices: 16464152--16464190 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
16464142 AAAAGAGCAA
16464152 AAAAAAAATTT-CAGC
1 AAAAAAAATTTCCAGC
*
16464167 AAAAAAATTTTCCAGC
1 AAAAAAAATTTCCAGC
16464183 AAAAAAAA
1 AAAAAAAA
16464191 AAACAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.64, C:0.13, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAAAAATTTCCAGC
Found at i:16464170 original size:16 final size:17
Alignment explanation
Indices: 16464151--16464191 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
16464141 AAAAAGAGCA
16464151 AAAAAAAAATTT-CAGC
1 AAAAAAAAATTTCCAGC
*
16464167 -AAAAAAATTTTCCAGC
1 AAAAAAAAATTTCCAGC
16464183 AAAAAAAAA
1 AAAAAAAAA
16464192 AACAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 10 0.48
16 4 0.19
17 7 0.33
ACGTcount: A:0.66, C:0.12, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAAAAAATTTCCAGC
Found at i:16464996 original size:19 final size:19
Alignment explanation
Indices: 16464974--16465010 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
16464964 AACTATATTA
16464974 TGTACATAT-ATATATTTTT
1 TGTACATATCAT-TATTTTT
16464993 TGTACATATCATTATTTT
1 TGTACATATCATTATTTT
16465011 ATATTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (19 bp):
TGTACATATCATTATTTTT
Found at i:16486270 original size:73 final size:73
Alignment explanation
Indices: 16486127--16486263 Score: 184
Period size: 73 Copynumber: 1.9 Consensus size: 73
16486117 ATTTCTGTTC
* * * * * **
16486127 CAAAGATCAACTCATATTACGAGAGGTGAGTTAAGCCTCGGGGCACGCTGTGGTTTTTTCAATTA
1 CAAAAATCAACTCATACTACGAGAGGTGAGTTAAGCCTCAGGACACGCTGAGGTAATTTCAATTA
16486192 CTGTTTGT
66 CTGTTTGT
* * *
16486200 CAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATT
1 CAAAAATCAACTCATACTACGAGAGGTGAGTTAAGCCTCAGGACACGCTGAGGTAATTTCAATT
16486264 TTTGTTTTCT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 54 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (73 bp):
CAAAAATCAACTCATACTACGAGAGGTGAGTTAAGCCTCAGGACACGCTGAGGTAATTTCAATTA
CTGTTTGT
Found at i:16486332 original size:88 final size:89
Alignment explanation
Indices: 16486193--16486354 Score: 256
Period size: 88 Copynumber: 1.8 Consensus size: 89
16486183 TTTCAATTAC
* * *
16486193 TGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATT
1 TGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGAT-ATT
16486258 -TCAATTTTTGTTTTCTCCAATTTA
65 GTCAATTTTTGTTTTCTCCAATTTA
* *
16486282 TGTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGATATTG
1 TGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGATATTG
16486346 TCAATTTTT
66 TCAATTTTT
16486355 TATGTTTCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
87 3 0.04
88 59 0.88
89 5 0.07
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (89 bp):
TGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGATATTG
TCAATTTTTGTTTTCTCCAATTTA
Found at i:16486398 original size:162 final size:159
Alignment explanation
Indices: 16486127--16486526 Score: 536
Period size: 162 Copynumber: 2.5 Consensus size: 159
16486117 ATTTCTGTTC
* * * * * *
16486127 CAAAGATCAACTCATATTACGAGAGGTGAGTTAAGCCTCGGGGCACGCTGTGGTTTTTTCAATTA
1 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTA
*
16486192 CTGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAAT
66 -TGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
* *
16486257 TTCAATTTTTGTTTTCTCCAATTTATGT-TTT
130 TTCAATTTCTGTTTT-T-CAATTTATGTCCTT
* * *
16486288 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGATATTGTCAATT-
1 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTA
* *
16486352 TTTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
66 TGTT-TG--TCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
* *
16486417 TTTTCAATTTCTGTTTTTCAATTTCTGTCCTT
128 ATTTCAATTTCTGTTTTTCAATTTATGTCCTT
* *
16486449 CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCAATT
1 C-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATT
16486514 GATGATTTG-CAAA
65 -ATG-TTTGTCAAA
16486527 TTTTGTTTTC
Statistics
Matches: 209, Mismatches: 22, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
159 3 0.01
160 11 0.05
161 63 0.30
162 127 0.61
164 3 0.01
165 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (159 bp):
CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTA
TGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT
TCAATTTCTGTTTTTCAATTTATGTCCTT
Found at i:16486400 original size:74 final size:75
Alignment explanation
Indices: 16486278--16486426 Score: 255
Period size: 74 Copynumber: 2.0 Consensus size: 75
16486268 TTTTCTCCAA
*
16486278 TTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGATA
1 TTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGATA
16486343 TTGTCAATTT
66 TTGTCAATTT
* *
16486353 TTTATG-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
1 TTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGATA
*
16486417 TTTTCAATTT
66 TTGTCAATTT
16486427 CTGTTTTTCA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
74 64 0.91
75 6 0.09
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (75 bp):
TTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGATA
TTGTCAATTT
Found at i:16486436 original size:14 final size:14
Alignment explanation
Indices: 16486417--16486444 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16486407 CGCTGAGGTA
16486417 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
16486431 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
16486445 CCTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:16486500 original size:88 final size:85
Alignment explanation
Indices: 16486359--16486665 Score: 352
Period size: 87 Copynumber: 3.6 Consensus size: 85
16486349 ATTTTTTATG
* *
16486359 TTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
1 TTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCA
16486423 ATTTCTGTTTTTCAATTTCTGT
66 ATTTCTG-TTTTCAATTT-TGT
* *
16486445 CCTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTC
1 -TTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTC
** *
16486510 AATTGATGATTTGCAAATTTTGT
65 AATTTCTG-TTTTC-AATTTTGT
** * * *
16486533 TTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGACTCG-CGTGCTGCGTTATTT
1 TTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCC-T--CAGGACATGCTGAGGTATTT
* *
16486597 TTAATTTCTGTTTT-AATGTATGT
63 TCAATTTCTGTTTTCAAT-TTTGT
* * *
16486620 TTTTAAAGAGTCAACTCATATTGCGAGAAGTGAGTTGAG-CTCAGGA
1 TTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGA
16486666 TCACACACCA
Statistics
Matches: 190, Mismatches: 23, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
83 2 0.01
85 1 0.01
86 4 0.02
87 82 0.43
88 75 0.39
89 24 0.13
90 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (85 bp):
TTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCA
ATTTCTGTTTTCAATTTTGT
Found at i:16487660 original size:17 final size:19
Alignment explanation
Indices: 16487626--16487664 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
16487616 TCTTATCTTC
16487626 TTTATTATTTACTCTTATT
1 TTTATTATTTACTCTTATT
*
16487645 TTTATT-TTTA-TTTTATT
1 TTTATTATTTACTCTTATT
16487662 TTT
1 TTT
16487665 TCCCCTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTATTATTTACTCTTATT
Found at i:16487848 original size:11 final size:11
Alignment explanation
Indices: 16487832--16487866 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
16487822 CCCTTCCCCC
16487832 CTCCCTTCTCT
1 CTCCCTTCTCT
16487843 CTCCCTTCTCT
1 CTCCCTTCTCT
16487854 CTTCCC-TCTCT
1 C-TCCCTTCTCT
16487865 CT
1 CT
16487867 TCTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:16488350 original size:3 final size:3
Alignment explanation
Indices: 16488342--16488387 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
16488332 TGTATTTCAA
*
16488342 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16488388 GTACATTAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:16500161 original size:27 final size:29
Alignment explanation
Indices: 16500131--16500190 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
16500121 TTTTTTACCT
* *
16500131 AAAAAAATAT-AAAAA-ATATTAATTATG
1 AAAAAAATATGAAAAATAAATTAATTACG
**
16500158 AAAAAGTTATGAAAAATAAATTAATTACG
1 AAAAAAATATGAAAAATAAATTAATTACG
16500187 AAAA
1 AAAA
16500191 TAGGCATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.30
28 5 0.19
29 14 0.52
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.27
Consensus pattern (29 bp):
AAAAAAATATGAAAAATAAATTAATTACG
Found at i:16500592 original size:18 final size:20
Alignment explanation
Indices: 16500559--16500595 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
16500549 TAGAAAAATC
16500559 TTATTATGTATAAATTATAA
1 TTATTATGTATAAATTATAA
16500579 TTATTA-GT-TAAATTATA
1 TTATTATGTATAAATTATA
16500596 GTTTCCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TTATTATGTATAAATTATAA
Found at i:16503274 original size:3 final size:3
Alignment explanation
Indices: 16503268--16503642 Score: 110
Period size: 3 Copynumber: 122.7 Consensus size: 3
16503258 AACAATGATG
* * * * * *
16503268 ATA ATA ATA ATA ATA AGTA ATA AAA ATG ACA ACA ATG ATA ACA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* ** * * *
16503314 ATA ATA ATA ATA ATA ATA ATA AGCA GCA AAA AAA AGTA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A-TA ATA ATA ATA
* * * * * * * *
16503361 ATA TTA ACA GTA ATG ATA ATG GTA ATA ATAA ATA ATA GTA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* * * * *
16503407 ATA ATA TTA GTA ATA ATA AT- ATA TTA A-A TTA GTTA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
* * * *
16503450 ATA ACGT- ATA AGTA A-A CAAA AAA ATA TATA ATA ATAA ATA AAA AGA
1 ATA A--TA ATA A-TA ATA -ATA ATA ATA -ATA ATA AT-A ATA ATA ATA
* * * * *
16503496 A-A GGTGA CA-A ATA TATA A-A ATA ATA GTA ACA GTA ATA A-G ATA A-A
1 ATA -AT-A -ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
16503540 TATA AT- ATA ATA A-A TATA AGA ATA ATA AGA ATA AAA ATA ATA ACA
1 -ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
16503585 CATTA CTA ATG ATA ATA ATA ATA ATA ATA TATA ATA ATA ACA ATA ATA
1 -A-TA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
16503633 A-A ATA ATA AT
1 ATA ATA ATA AT
16503643 CTTAAAATAG
Statistics
Matches: 272, Mismatches: 68, Indels: 64
0.67 0.17 0.16
Matches are distributed among these distances:
2 18 0.07
3 219 0.81
4 32 0.12
5 3 0.01
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:16503290 original size:40 final size:39
Alignment explanation
Indices: 16503246--16503329 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 39
16503236 AATATAACAA
* *
16503246 AATAAAAATGACAACAATGATGATAATAATAATAATAAGT
1 AATAAAAATGACAACAATGATAACAATAATAATAATAA-T
16503286 AATAAAAATGACAACAATGATAACAATAATAATAATAAT
1 AATAAAAATGACAACAATGATAACAATAATAATAATAAT
16503325 AATAA
1 AATAA
16503330 TAATAAGCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
39 6 0.14
40 36 0.86
ACGTcount: A:0.63, C:0.06, G:0.07, T:0.24
Consensus pattern (39 bp):
AATAAAAATGACAACAATGATAACAATAATAATAATAAT
Found at i:16503651 original size:22 final size:25
Alignment explanation
Indices: 16503515--16503642 Score: 81
Period size: 25 Copynumber: 5.2 Consensus size: 25
16503505 AATATATAAA
* *
16503515 ATAATAGTAACAGTAATAAGATAA-AT
1 ATAATAATAACAATAAT-A-ATAATAT
* *
16503541 ATAAT-ATAATAA-ATATAAGAATA-
1 ATAATAATAACAATA-ATAATAATAT
* * *
16503564 ATAAGAATAAAAATAATAACACAT-T
1 ATAATAATAACAATAATAATA-ATAT
* *
16503589 ACTAATGATAATAATAATAATAATAT
1 A-TAATAATAACAATAATAATAATAT
16503615 ATAATAATAACAATAATAA-AATA-
1 ATAATAATAACAATAATAATAATAT
16503638 ATAAT
1 ATAAT
16503643 CTTAAAATAG
Statistics
Matches: 81, Mismatches: 13, Indels: 19
0.72 0.12 0.17
Matches are distributed among these distances:
23 12 0.15
24 18 0.22
25 28 0.35
26 23 0.28
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (25 bp):
ATAATAATAACAATAATAATAATAT
Found at i:16512980 original size:50 final size:50
Alignment explanation
Indices: 16512905--16513081 Score: 257
Period size: 50 Copynumber: 3.5 Consensus size: 50
16512895 CCATGGAAAC
16512905 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
16512955 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
16513005 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGG-CAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATGA
* * * *
16513055 CAACTGAAAAGTGGTAGCTTCAGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
16513082 CTGATCAGTG
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
50 89 0.79
51 24 0.21
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:16513267 original size:31 final size:31
Alignment explanation
Indices: 16513059--16513260 Score: 305
Period size: 31 Copynumber: 6.5 Consensus size: 31
16513049 AAATGACAAC
16513059 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
16513090 TGAAAAGTGGTAGTTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
16513121 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
16513152 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* * *
16513183 TGAAAAGTGGTAGCTCCGGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* **
16513214 TGAAAAATGGTAGCACCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
16513245 TGAATAGTGGTAGCTT
1 TGAAAAGTGGTAGCTT
16513261 TGGCTACAAG
Statistics
Matches: 155, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 155 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
Found at i:16513278 original size:7 final size:7
Alignment explanation
Indices: 16513266--16513294 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
16513256 AGCTTTGGCT
16513266 ACAAGTG
1 ACAAGTG
16513273 ACAAGTG
1 ACAAGTG
16513280 ACAAGTG
1 ACAAGTG
16513287 ACAAGTG
1 ACAAGTG
16513294 A
1 A
16513295 TTTCTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.28, T:0.14
Consensus pattern (7 bp):
ACAAGTG
Found at i:16513367 original size:47 final size:48
Alignment explanation
Indices: 16513298--16513423 Score: 159
Period size: 47 Copynumber: 2.7 Consensus size: 48
16513288 CAAGTGATTT
* *
16513298 CTGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATG-CTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
* * *
16513345 CTGTATAAGACCATATCTGGGATATGACATCAGTGAGATATGTGATTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
* *
16513393 CGTGTA-AA-ACCATAGCTGGGCTATGGCATCA
1 C-TGTATAAGACCATATCTGGGATATGGCATCA
16513424 TTATGTAAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 60 0.87
48 5 0.07
49 4 0.06
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (48 bp):
CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
Found at i:16521191 original size:13 final size:13
Alignment explanation
Indices: 16521173--16521206 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
16521163 AGGGATACGG
16521173 CCGTGTGACACGC
1 CCGTGTGACACGC
16521186 CCGTGTGACACGC
1 CCGTGTGACACGC
16521199 CCGTGTGA
1 CCGTGTGA
16521207 GGAAGTCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.15, C:0.35, G:0.32, T:0.18
Consensus pattern (13 bp):
CCGTGTGACACGC
Found at i:16523027 original size:13 final size:13
Alignment explanation
Indices: 16523009--16523038 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
16522999 TTCCTGAAAC
16523009 TTTCACTCTACTT
1 TTTCACTCTACTT
16523022 TTTCACTCTACTT
1 TTTCACTCTACTT
16523035 TTTC
1 TTTC
16523039 TGTCACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.30, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTCACTCTACTT
Found at i:16530364 original size:14 final size:14
Alignment explanation
Indices: 16530347--16530379 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
16530337 AGGTCTGTAA
16530347 TCTTTGTTAATGCT
1 TCTTTGTTAATGCT
16530361 TCTTTGTTAATGCT
1 TCTTTGTTAATGCT
16530375 TCTTT
1 TCTTT
16530380 TATTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.61
Consensus pattern (14 bp):
TCTTTGTTAATGCT
Found at i:16530858 original size:24 final size:25
Alignment explanation
Indices: 16530831--16530879 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16530821 CTTTTTTTAT
*
16530831 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
16530855 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
16530880 AAAAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:16530962 original size:18 final size:17
Alignment explanation
Indices: 16530869--16530965 Score: 61
Period size: 18 Copynumber: 5.2 Consensus size: 17
16530859 TCAAATACAT
*
16530869 TTAAAACATAAAAAAATA
1 TTAAAA-ATAAAAAAAAA
16530887 TT-AAAATAAAAAAAAA
1 TTAAAAATAAAAAAAAA
*
16530903 TAAAAAATAAGACTAAAATAA
1 TTAAAAATAA-A--AAAA-AA
* * *
16530924 TTCTTAAAATAATACATAAA
1 -T-TAAAAATAA-AAAAAAA
16530944 TTAAAAATAAAATAAAAA
1 TTAAAAATAAAA-AAAAA
16530962 TTAA
1 TTAA
16530966 TTATATTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
16 11 0.18
17 11 0.18
18 19 0.31
19 1 0.02
20 6 0.10
21 4 0.07
22 1 0.02
23 8 0.13
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (17 bp):
TTAAAAATAAAAAAAAA
Found at i:16532795 original size:14 final size:15
Alignment explanation
Indices: 16532776--16532810 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
16532766 TTTAATGTTC
16532776 AAAATTTCAAAAA-A
1 AAAATTTCAAAAATA
*
16532790 AAAATTTTAAAAATA
1 AAAATTTCAAAAATA
16532805 AAAATT
1 AAAATT
16532811 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTTCAAAAATA
Found at i:16532840 original size:30 final size:31
Alignment explanation
Indices: 16532806--16532907 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
16532796 TTAAAAATAA
*
16532806 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
16532836 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
16532866 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
16532896 AAATTTCATTTT
1 AAATTTCATTTT
16532908 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:16533284 original size:3 final size:3
Alignment explanation
Indices: 16533276--16533335 Score: 66
Period size: 3 Copynumber: 18.0 Consensus size: 3
16533266 GCTCGGTTTT
16533276 GAA GAA GAA GAA GAA GGAA GAA GAA GAA GAAA GAAA GAAA GAGA GAA
1 GAA GAA GAA GAA GAA -GAA GAA GAA GAA G-AA G-AA G-AA GA-A GAA
16533323 GAA GAAA GAA GAA
1 GAA G-AA GAA GAA
16533336 AAAAAAATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 33 0.62
4 20 0.38
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:16533304 original size:22 final size:23
Alignment explanation
Indices: 16533276--16533335 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 23
16533266 GCTCGGTTTT
*
16533276 GAAGAAGAAGAAGAAGGA-AGAA
1 GAAGAAGAAGAAGAAAGAGAGAA
16533298 GAAGAAGAAAGAAAGAAAGAGAGAA
1 GAAGAAG-AAG-AAGAAAGAGAGAA
16533323 GAAGAAAGAAGAA
1 GAAG-AAGAAGAA
16533336 AAAAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.21
23 3 0.09
24 9 0.27
25 11 0.33
26 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAGAAGAAGAAAGAGAGAA
Found at i:16533315 original size:8 final size:7
Alignment explanation
Indices: 16533276--16533336 Score: 67
Period size: 7 Copynumber: 9.0 Consensus size: 7
16533266 GCTCGGTTTT
16533276 GAAG-AA
1 GAAGAAA
16533282 GAAG-AA
1 GAAGAAA
*
16533288 GAAGGAA
1 GAAGAAA
16533295 GAAG-AA
1 GAAGAAA
16533301 GAAGAAA
1 GAAGAAA
16533308 GAAAGAAA
1 G-AAGAAA
16533316 G-AGAGAA
1 GAAGA-AA
16533323 GAAGAAA
1 GAAGAAA
16533330 GAAGAAA
1 GAAGAAA
16533337 AAAAAATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
6 19 0.38
7 21 0.42
8 10 0.20
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:16533322 original size:25 final size:24
Alignment explanation
Indices: 16533276--16533336 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 24
16533266 GCTCGGTTTT
*
16533276 GAAGAAG-AAG-AAGAAGGAAGAA
1 GAAGAAGAAAGAAAGAAAGAAGAA
16533298 GAAGAAGAAAGAAAGAAAG-AG-A
1 GAAGAAGAAAGAAAGAAAGAAGAA
16533320 GAAGAAGAAAG-AAGAAA
1 GAAGAAGAAAGAAAGAAA
16533337 AAAAAATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 6 0.17
22 19 0.53
23 5 0.14
24 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
GAAGAAGAAAGAAAGAAAGAAGAA
Found at i:16533416 original size:18 final size:18
Alignment explanation
Indices: 16533379--16533421 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
16533369 AACCGGGTAT
* * *
16533379 AACCCGACCCGATCCGGC
1 AACCCAACCCGACCCAGC
16533397 AACCCAACCCGACCCAGC
1 AACCCAACCCGACCCAGC
16533415 AAGCCCA
1 AA-CCCA
16533422 TTAGCCAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.30, C:0.51, G:0.16, T:0.02
Consensus pattern (18 bp):
AACCCAACCCGACCCAGC
Found at i:16533628 original size:23 final size:23
Alignment explanation
Indices: 16533602--16533679 Score: 97
Period size: 23 Copynumber: 3.3 Consensus size: 23
16533592 GCAGCCCAGC
*
16533602 AGAAAAAA-AAAGGAAGAAAAAGA
1 AGAAAAAAGAAA-AAAGAAAAAGA
16533625 AGAAAAAAGAAAAAAAGAAAAA-A
1 AGAAAAAAG-AAAAAAGAAAAAGA
16533648 AGAAAAAAGAAAAAAGAAAAAAGGA
1 AGAAAAAAGAAAAAAG-AAAAA-GA
16533673 AGAAAAA
1 AGAAAAA
16533680 GGGGGTTCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
22 7 0.14
23 23 0.47
24 8 0.16
25 11 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AGAAAAAAGAAAAAAGAAAAAGA
Found at i:16533636 original size:7 final size:7
Alignment explanation
Indices: 16533619--16533670 Score: 77
Period size: 7 Copynumber: 7.0 Consensus size: 7
16533609 AAAAGGAAGA
16533619 AAAAGAAG
1 AAAA-AAG
16533627 AAAAAAG
1 AAAAAAG
16533634 AAAAAAAG
1 -AAAAAAG
16533642 AAAAAAAG
1 -AAAAAAG
16533650 AAAAAAG
1 AAAAAAG
16533657 AAAAAAG
1 AAAAAAG
16533664 AAAAAAG
1 AAAAAAG
16533671 GAAGAAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
7 24 0.56
8 19 0.44
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:16533638 original size:8 final size:8
Alignment explanation
Indices: 16533615--16533680 Score: 84
Period size: 8 Copynumber: 8.4 Consensus size: 8
16533605 AAAAAAAAGG
16533615 AAGAAAAA
1 AAGAAAAA
16533623 GAAG-AAAA
1 -AAGAAAAA
16533631 AAGAAAAA
1 AAGAAAAA
16533639 AAGAAAAA
1 AAGAAAAA
16533647 AAG-AAAA
1 AAGAAAAA
16533654 AAG-AAAA
1 AAGAAAAA
16533661 AAGAAAAA
1 AAGAAAAA
*
16533669 AGGAAGAAA
1 AAGAA-AAA
16533678 AAG
1 AAG
16533681 GGGGTTCAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
7 17 0.33
8 27 0.52
9 8 0.15
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:16533638 original size:30 final size:30
Alignment explanation
Indices: 16533602--16533680 Score: 96
Period size: 26 Copynumber: 2.7 Consensus size: 30
16533592 GCAGCCCAGC
16533602 AGAAAAAAAAAGGAAGAAAAAGAAGAAAA-A
1 AGAAAAAAAAAGGAAGAAAAAGAA-AAAAGA
16533632 AG--AAAAAAA-GAA-AAAAAGAAAAAAGA
1 AGAAAAAAAAAGGAAGAAAAAGAAAAAAGA
*
16533658 AAAAAGAAAAAAGGAAGAAAAAG
1 AGAAA-AAAAAAGGAAGAAAAAG
16533681 GGGGTTCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
25 4 0.10
26 10 0.24
27 3 0.07
28 8 0.19
29 6 0.14
30 5 0.12
31 6 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (30 bp):
AGAAAAAAAAAGGAAGAAAAAGAAAAAAGA
Found at i:16534268 original size:19 final size:21
Alignment explanation
Indices: 16534229--16534269 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16534219 AATTTTGTGT
*
16534229 AAAAAATCCAGTGTTTTCAAA
1 AAAAAATCCAGTGTTTCCAAA
16534250 AAAAAATCCA-T-TTTCCAAA
1 AAAAAATCCAGTGTTTCCAAA
16534269 A
1 A
16534270 TTTTTAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAAATCCAGTGTTTCCAAA
Found at i:16534339 original size:18 final size:17
Alignment explanation
Indices: 16534265--16534425 Score: 141
Period size: 17 Copynumber: 9.4 Consensus size: 17
16534255 ATCCATTTTC
* *
16534265 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
16534283 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
16534301 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
16534317 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
16534334 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
16534352 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
16534369 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
16534387 C-AAAA-TTTCGATGTTT
1 CAAAAATTTTCG-TGTTT
**
16534403 TGAAAA-TTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
16534420 CAAAAA
1 CAAAAA
16534426 AAAATCTCGT
Statistics
Matches: 118, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
16 22 0.19
17 61 0.52
18 23 0.19
19 12 0.10
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:16534370 original size:35 final size:35
Alignment explanation
Indices: 16534286--16534424 Score: 155
Period size: 35 Copynumber: 4.1 Consensus size: 35
16534276 GTGTCTTCTA
16534286 AAAATTTTT-GTGTTTCAAAAATTTTC--GTTTTC
1 AAAATTTTTCGTGTTTCAAAAATTTTCGTGTTTTC
* *
16534318 AAAAATTTCCGTGTTTCAAAAATTTTCGTGTTTTC
1 AAAATTTTTCGTGTTTCAAAAATTTTCGTGTTTTC
* ** *
16534353 AAAATTTTTCGTATTTCAAAAATCCTCTTGTTTTC
1 AAAATTTTTCGTGTTTCAAAAATTTTCGTGTTTTC
**
16534388 AAAA--TTTCGATGTTTTGAAAA-TTTCGTGTTTTC
1 AAAATTTTTCG-TGTTTCAAAAATTTTCGTGTTTTC
16534421 AAAA
1 AAAA
16534425 AAAAATCTCG
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
32 7 0.08
33 35 0.39
34 8 0.09
35 39 0.44
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (35 bp):
AAAATTTTTCGTGTTTCAAAAATTTTCGTGTTTTC
Found at i:16534448 original size:37 final size:36
Alignment explanation
Indices: 16534405--16534517 Score: 106
Period size: 35 Copynumber: 3.1 Consensus size: 36
16534395 CGATGTTTTG
*
16534405 AAAATTTCGTGTTTTCAAAAAAAAATCTCGTGTTTC
1 AAAATTTCGTGTTTTCAAAAAAAAATATCGTGTTTC
* **
16534441 ATAAATTTTG-GTTTT-AAAAAAAAATATTATGTCTT-
1 A-AAATTTCGTGTTTTCAAAAAAAAATATCGTGT-TTC
*
16534476 AAAATTCTCGTGTTTTCAAAACAAGAAATTTTCGTGTTTC
1 AAAATT-TCGTGTTTTCAAAA-AA-AAA-TATCGTGTTTC
16534516 AA
1 AA
16534518 TCGGATCACG
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
34 5 0.08
35 17 0.28
36 13 0.22
37 11 0.18
38 2 0.03
39 5 0.08
40 7 0.12
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (36 bp):
AAAATTTCGTGTTTTCAAAAAAAAATATCGTGTTTC
Found at i:16546730 original size:20 final size:20
Alignment explanation
Indices: 16546705--16546747 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
16546695 AGTAGGGAGA
16546705 AAGTATAATAAATAATACGC
1 AAGTATAATAAATAATACGC
16546725 AAGTATAATAAATAATACGC
1 AAGTATAATAAATAATACGC
16546745 AAG
1 AAG
16546748 AGAAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (20 bp):
AAGTATAATAAATAATACGC
Found at i:16548376 original size:32 final size:32
Alignment explanation
Indices: 16548340--16548409 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
16548330 GGGTTTTTTT
* *
16548340 TTTGTTATTTATTGTTTGAATGTGTTGA-ATTA
1 TTTGTTATTTATTATTTGAATGTGCTGAGA-TA
* *
16548372 TTTGTTATTTGTTATTTGATTGTGCTGAGATA
1 TTTGTTATTTATTATTTGAATGTGCTGAGATA
16548404 TTTGTT
1 TTTGTT
16548410 TTTTTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 32 0.97
33 1 0.03
ACGTcount: A:0.19, C:0.01, G:0.20, T:0.60
Consensus pattern (32 bp):
TTTGTTATTTATTATTTGAATGTGCTGAGATA
Found at i:16554986 original size:21 final size:20
Alignment explanation
Indices: 16554954--16555002 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
16554944 TTCTTCGAAT
*
16554954 TTGTTTACCTATTATTATTA
1 TTGTTTATCTATTATTATTA
16554974 TTCGTTTATCTATTATTATTA
1 TT-GTTTATCTATTATTATTA
16554995 TTGTTTAT
1 TTGTTTAT
16555003 ATTACAGGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.63
Consensus pattern (20 bp):
TTGTTTATCTATTATTATTA
Found at i:16566535 original size:13 final size:13
Alignment explanation
Indices: 16566517--16566542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16566507 AAGTAATCGT
16566517 ACACGGGCGTGTC
1 ACACGGGCGTGTC
16566530 ACACGGGCGTGTC
1 ACACGGGCGTGTC
16566543 CCTGCCGAGC
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:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
ACACGGGCGTGTC
Found at i:16570426 original size:51 final size:51
Alignment explanation
Indices: 16570359--16570468 Score: 175
Period size: 51 Copynumber: 2.2 Consensus size: 51
16570349 TCACATGTAT
* *
16570359 CACTTGTCACTAATCAGATAAGTGTAGCTAAAACTACTACTTATCACTTAC
1 CACTTGTCACTAATCAGATAAGTGTAACTAAAACTACCACTTATCACTTAC
* **
16570410 CACTTGTCACTAATCAGATAAGTGTAACTAAAGCTACCACTTATCACTTGT
1 CACTTGTCACTAATCAGATAAGTGTAACTAAAACTACCACTTATCACTTAC
16570461 CACTTGTC
1 CACTTGTC
16570469 GCTTGTCACT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.32
Consensus pattern (51 bp):
CACTTGTCACTAATCAGATAAGTGTAACTAAAACTACCACTTATCACTTAC
Found at i:16570463 original size:7 final size:7
Alignment explanation
Indices: 16570447--16570485 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
16570437 CTAAAGCTAC
*
16570447 CACTTAT
1 CACTTGT
16570454 CACTTGT
1 CACTTGT
16570461 CACTTGT
1 CACTTGT
*
16570468 CGCTTGT
1 CACTTGT
*
16570475 CACTTAT
1 CACTTGT
16570482 CACT
1 CACT
16570486 GCTCAGATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.18, C:0.31, G:0.10, T:0.41
Consensus pattern (7 bp):
CACTTGT
Found at i:16570474 original size:58 final size:61
Alignment explanation
Indices: 16570412--16570529 Score: 152
Period size: 65 Copynumber: 1.9 Consensus size: 61
16570402 TCACTTACCA
16570412 CTTGTCAC-TA-A-TCAGATAAGTGTAACTAAAGCTACCACTTATCACTTGTCACTTGTCG
1 CTTGTCACTTACACTCAGATAAGTGTAACTAAAGCTACCACTTATCACTTGTCACTTGTCG
* * *
16570470 CTTGTCACTTATCACTGCTCAGATAAGTGTAGCTGAGGCTACCACTTATCACTTGTCACT
1 CTTGTCACTTA-CA---CTCAGATAAGTGTAACTAAAGCTACCACTTATCACTTGTCACT
16570530 GATCAGAAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
58 8 0.16
59 2 0.04
61 1 0.02
65 39 0.78
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (61 bp):
CTTGTCACTTACACTCAGATAAGTGTAACTAAAGCTACCACTTATCACTTGTCACTTGTCG
Found at i:16573327 original size:12 final size:11
Alignment explanation
Indices: 16573310--16573336 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16573300 ATGTTTTTGC
16573310 AAAAAAAAAAG
1 AAAAAAAAAAG
16573321 AAAAAAAAAAG
1 AAAAAAAAAAG
16573332 AAAAA
1 AAAAA
16573337 GAAAGAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:16574309 original size:12 final size:12
Alignment explanation
Indices: 16574292--16574317 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16574282 AAAATAGGGC
16574292 TTTAGCGGCGTT
1 TTTAGCGGCGTT
16574304 TTTAGCGGCGTT
1 TTTAGCGGCGTT
16574316 TT
1 TT
16574318 ATCAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:16574451 original size:41 final size:41
Alignment explanation
Indices: 16574341--16574550 Score: 309
Period size: 41 Copynumber: 5.1 Consensus size: 41
16574331 GCAAAAATTA
* *
16574341 TAAAACACAGAGCAATAGCGGCG-TTTT-ATCAAAAACGCCGC
1 TAAAAGACAGAGCAATAGCGGCGCTTTTGGT--AAAACGCCGC
*
16574382 TAAAA-ACTGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAGACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* **
16574422 TAAAAGATAGAGCTTTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAGACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* *
16574463 TAAAAGACAGAGCAGTAGTGGCGCTTTTGGTAAAACGCCGC
1 TAAAAGACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
16574504 TAAAAGACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAGACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
16574545 TAAAAG
1 TAAAAG
16574551 TCATATAACT
Statistics
Matches: 154, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
40 31 0.20
41 122 0.79
42 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (41 bp):
TAAAAGACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
Found at i:16575195 original size:24 final size:24
Alignment explanation
Indices: 16575168--16575216 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
16575158 CGTATATTTA
*
16575168 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
16575192 TTAAAAGTCTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
16575216 T
1 T
16575217 GTTATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
TTAAAAGTCTATATAAAAATTAAT
Found at i:16575511 original size:7 final size:7
Alignment explanation
Indices: 16575501--16575549 Score: 80
Period size: 7 Copynumber: 6.9 Consensus size: 7
16575491 ATTTTAAGGT
16575501 TTATGGA
1 TTATGGA
16575508 TTATGGA
1 TTATGGA
16575515 TTATGGA
1 TTATGGA
16575522 TTATGGA
1 TTATGGA
*
16575529 TTATGGGT
1 TTAT-GGA
16575537 TTATGGA
1 TTATGGA
16575544 TTATGG
1 TTATGG
16575550 TTTACAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
7 33 0.85
8 6 0.15
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (7 bp):
TTATGGA
Found at i:16575551 original size:14 final size:14
Alignment explanation
Indices: 16575501--16575567 Score: 80
Period size: 14 Copynumber: 4.7 Consensus size: 14
16575491 ATTTTAAGGT
*
16575501 TTATGGATTATGGA
1 TTATGGTTTATGGA
*
16575515 TTATGGATTATGGA
1 TTATGGTTTATGGA
16575529 TTATGGGTTTATGGA
1 TTAT-GGTTTATGGA
** *
16575544 TTATGGTTTACAGT
1 TTATGGTTTATGGA
16575558 TTATGGTTTA
1 TTATGGTTTA
16575568 AGGGTTGGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
14 35 0.73
15 13 0.27
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.48
Consensus pattern (14 bp):
TTATGGTTTATGGA
Found at i:16575562 original size:36 final size:36
Alignment explanation
Indices: 16575494--16575573 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
16575484 AGTTACAATT
**
16575494 TTAA-GGTTTATGGATTATGGATTATGGATTATGGA
1 TTAAGGGTTTATGGATTATGGATTACAGATTATGGA
* * * *
16575529 TTATGGGTTTATGGATTATGGTTTACAGTTTATGGT
1 TTAAGGGTTTATGGATTATGGATTACAGATTATGGA
16575565 TTAAGGGTT
1 TTAAGGGTT
16575574 GGGGTTTAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 3 0.08
36 34 0.92
ACGTcount: A:0.24, C:0.01, G:0.29, T:0.46
Consensus pattern (36 bp):
TTAAGGGTTTATGGATTATGGATTACAGATTATGGA
Found at i:16575566 original size:7 final size:7
Alignment explanation
Indices: 16575493--16575567 Score: 69
Period size: 7 Copynumber: 10.6 Consensus size: 7
16575483 GAGTTACAAT
*
16575493 TTTAAGG
1 TTTATGG
16575500 TTTATGG
1 TTTATGG
*
16575507 ATTATGG
1 TTTATGG
*
16575514 ATTATGG
1 TTTATGG
*
16575521 ATTATGG
1 TTTATGG
*
16575528 ATTATGGG
1 TTTAT-GG
16575536 TTTATGG
1 TTTATGG
*
16575543 ATTATGG
1 TTTATGG
**
16575550 TTTACAG
1 TTTATGG
16575557 TTTATGG
1 TTTATGG
16575564 TTTA
1 TTTA
16575568 AGGGTTGGGG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
7 52 0.90
8 6 0.10
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.48
Consensus pattern (7 bp):
TTTATGG
Found at i:16575579 original size:28 final size:29
Alignment explanation
Indices: 16575548--16575608 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
16575538 TATGGATTAT
16575548 GGTTTACA-GTTTATGGT-TTAAGGGTT-GG
1 GGTTTA-AGGTTTA-GGTGTTAAGGGTTAGG
*
16575576 GGTTTAAGGTTTAGGTGTTAGGGGTTAGG
1 GGTTTAAGGTTTAGGTGTTAAGGGTTAGG
16575605 GGTT
1 GGTT
16575609 AGGGGTTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 4 0.14
28 19 0.66
29 6 0.21
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (29 bp):
GGTTTAAGGTTTAGGTGTTAAGGGTTAGG
Done.