Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 73 of 213
Found at i:19807277 original size:22 final size:20
Alignment explanation
Indices: 19807229--19807277 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
19807219 TTAGCATGCT
19807229 TGCAT-ACAGATATCATATA
1 TGCATAACAGATATCATATA
**
19807248 TGTTTAACAGAATAATCATATA
1 TGCATAACAG-AT-ATCATATA
19807270 TGCATAAC
1 TGCATAAC
19807278 GATGTCCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 4 0.17
21 2 0.09
22 14 0.61
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (20 bp):
TGCATAACAGATATCATATA
Found at i:19810019 original size:3 final size:3
Alignment explanation
Indices: 19810011--19810041 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
19810001 AGTGAATGGA
19810011 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
19810042 TTTGTGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:19810181 original size:22 final size:22
Alignment explanation
Indices: 19810156--19810207 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
19810146 TTTTATTTAT
*
19810156 TTTAAAGATT-TTTTTAAAAAAA
1 TTTAAA-ATTATTGTTAAAAAAA
* *
19810178 TTTACAATTATTGTTAAAAAAT
1 TTTAAAATTATTGTTAAAAAAA
19810200 TTTAAAAT
1 TTTAAAAT
19810208 GTCAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTAAAATTATTGTTAAAAAAA
Found at i:19812895 original size:17 final size:15
Alignment explanation
Indices: 19812881--19812942 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 15
19812871 ATTCAAAAGT
19812881 TATAAAAATTAAAAA
1 TATAAAAATTAAAAA
* *
19812896 -ATTAAAATTAAAAT
1 TATAAAAATTAAAAA
*
19812910 TAAAAAAATATAAAAA
1 TATAAAAAT-TAAAAA
*
19812926 GAATAAAAATTTAAAAA
1 -TATAAAAA-TTAAAAA
19812943 AATAGCATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
14 12 0.33
15 6 0.17
16 5 0.14
17 12 0.33
18 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
TATAAAAATTAAAAA
Found at i:19815499 original size:56 final size:56
Alignment explanation
Indices: 19815422--19815528 Score: 137
Period size: 55 Copynumber: 1.9 Consensus size: 56
19815412 TTCATTCTTT
* *
19815422 AAAATTTTAAAAATTTAAAAAAATTATAAAACTACTTTTAAAAATTAGAAATCACTAA
1 AAAATTTT-AAAATTTAAAAAAA-TATAAAAATACTTTTAAAAATTAAAAATCACTAA
* *
19815480 AAAATTTT-AAA-TTATAAAAAATATAAAAATATTTTTTAAAATTAAAAAT
1 AAAATTTTAAAATTTA-AAAAAATATAAAAATACTTTTAAAAATTAAAAAT
19815529 AATTAAATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
55 27 0.61
56 9 0.20
58 8 0.18
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.36
Consensus pattern (56 bp):
AAAATTTTAAAATTTAAAAAAATATAAAAATACTTTTAAAAATTAAAAATCACTAA
Found at i:19815526 original size:27 final size:26
Alignment explanation
Indices: 19815440--19815529 Score: 67
Period size: 28 Copynumber: 3.3 Consensus size: 26
19815430 AAAAATTTAA
* *
19815440 AAAAATTATAAAACTACTTTTAAAAATT
1 AAAAA-TATAAAAATA-TTTTTAAAATT
* *
19815468 AGAAATCACTAAAAA-A-TTTTAAATTATA
1 AAAAAT-A-TAAAAATATTTTTAAA--ATT
19815496 AAAAATATAAAAATATTTTTTAAAATT
1 AAAAATATAAAAATA-TTTTTAAAATT
19815523 AAAAATA
1 AAAAATA
19815530 ATTAAATGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
26 12 0.24
27 12 0.24
28 13 0.27
29 12 0.24
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (26 bp):
AAAAATATAAAAATATTTTTAAAATT
Found at i:19817909 original size:12 final size:13
Alignment explanation
Indices: 19817881--19817910 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19817871 TCTAGTCATA
19817881 TAATAAATTATTT
1 TAATAAATTATTT
19817894 TAATAAATTA-TT
1 TAATAAATTATTT
19817906 TAATA
1 TAATA
19817911 TTTCAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATAAATTATTT
Found at i:19820746 original size:20 final size:20
Alignment explanation
Indices: 19820698--19820746 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
19820688 AAATTTGAAT
*
19820698 CTATCGATACTTAACAAAAT
1 CTATCGATACTTAACAAAAA
*
19820718 CTATTGATACTTGAA-AAAAA
1 CTATCGATACTT-AACAAAAA
*
19820738 GTATCGATA
1 CTATCGATA
19820747 TAGGATCGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (20 bp):
CTATCGATACTTAACAAAAA
Found at i:19823741 original size:20 final size:19
Alignment explanation
Indices: 19823700--19823753 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
19823690 AACCCAATAG
*
19823700 GTATCGATAATTTTTTGTAA
1 GTATCGAT-ATTTTTTGAAA
19823720 GTATCGATACTTTTTAT-AAA
1 GTATCGATA-TTTTT-TGAAA
*
19823740 GTGTCGATATTTTT
1 GTATCGATATTTTT
19823754 GTATCGGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 6 0.20
20 23 0.77
21 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (19 bp):
GTATCGATATTTTTTGAAA
Found at i:19829857 original size:21 final size:20
Alignment explanation
Indices: 19829815--19829866 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
19829805 GATAAATTTG
*
19829815 AATCTATCGATACTGAACAA
1 AATCTATCGATACTGAAAAA
*
19829835 AATCTATTGATACTTGAAAAA
1 AATCTATCGATAC-TGAAAAA
*
19829856 AA-GTATCGATA
1 AATCTATCGATA
19829867 TAGGATCGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (20 bp):
AATCTATCGATACTGAAAAA
Found at i:19830756 original size:31 final size:31
Alignment explanation
Indices: 19830700--19830774 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
19830690 GATATATTAG
* * *
19830700 TTAAATTAAATT-AATTATTATATAATGTGA
1 TTAAATTAAATTAAAATATTACATAATGTAA
19830730 TTAAATTAAATTAAAATATTACATAATGTAA
1 TTAAATTAAATTAAAATATTACATAATGTAA
*
19830761 TTAAATTGAATTAA
1 TTAAATTAAATTAA
19830775 TAATGAGCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 12 0.30
31 28 0.70
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (31 bp):
TTAAATTAAATTAAAATATTACATAATGTAA
Found at i:19833091 original size:7 final size:7
Alignment explanation
Indices: 19833079--19833134 Score: 112
Period size: 7 Copynumber: 8.0 Consensus size: 7
19833069 TTTTCTTTCA
19833079 AAAAAAT
1 AAAAAAT
19833086 AAAAAAT
1 AAAAAAT
19833093 AAAAAAT
1 AAAAAAT
19833100 AAAAAAT
1 AAAAAAT
19833107 AAAAAAT
1 AAAAAAT
19833114 AAAAAAT
1 AAAAAAT
19833121 AAAAAAT
1 AAAAAAT
19833128 AAAAAAT
1 AAAAAAT
19833135 TAGAAATTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:19839621 original size:7 final size:7
Alignment explanation
Indices: 19839609--19839634 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19839599 ACCTTTAATG
19839609 AAAAGGC
1 AAAAGGC
19839616 AAAAGGC
1 AAAAGGC
19839623 AAAAGGC
1 AAAAGGC
19839630 AAAAG
1 AAAAG
19839635 CCCCCACTCC
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:0.62, C:0.12, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAAGGC
Found at i:19839898 original size:21 final size:21
Alignment explanation
Indices: 19839874--19839927 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
19839864 TATTACTGTT
19839874 TTCTTTTTATTTTTCTAAATA
1 TTCTTTTTATTTTTCTAAATA
19839895 TTCTTTTTATTTTTCTAAATA
1 TTCTTTTTATTTTTCTAAATA
19839916 TTCTTTTTATTT
1 TTCTTTTTATTT
19839928 ACCCCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (21 bp):
TTCTTTTTATTTTTCTAAATA
Found at i:19840512 original size:32 final size:32
Alignment explanation
Indices: 19840408--19840520 Score: 131
Period size: 32 Copynumber: 3.5 Consensus size: 32
19840398 CGCGCAGTTC
*
19840408 TGTGAAATGATAACAAATATCAACTTTCATTT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
* *
19840440 TATGAAAT-AGTAACAAAT-TACAACTTCAATTT
1 TGTGAAATGA-TAACAAATAT-CAACTTTAATTT
*
19840472 TGTGAAATGATAACAAATATCAACTTTAATGT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
* * *
19840504 GGTTAAATGATGACAAA
1 TGTGAAATGATAACAAA
19840521 ATTACTCTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.03
32 64 0.94
33 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.34
Consensus pattern (32 bp):
TGTGAAATGATAACAAATATCAACTTTAATTT
Found at i:19843309 original size:12 final size:12
Alignment explanation
Indices: 19843294--19843323 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19843284 AGTATAACCT
19843294 TATATATATATG
1 TATATATATATG
*
19843306 TATATATATATT
1 TATATATATATG
19843318 TATATA
1 TATATA
19843324 AAGGTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
TATATATATATG
Found at i:19844307 original size:43 final size:42
Alignment explanation
Indices: 19844244--19844363 Score: 154
Period size: 43 Copynumber: 2.8 Consensus size: 42
19844234 AGGACTCCGA
19844244 TATGTGTTTTCATGTAAGACCACGTCTGGGACGTCAGCATCGAC
1 TATGTGTTTTCATGTAAGACCACGTCTGGGACGT-AGCATCG-C
* *
19844288 T-TGTGTTTTCATGTAAGACC-CTGTCTGGGACAGTTGCATCGG
1 TATGTGTTTTCATGTAAGACCAC-GTCTGGGAC-GTAGCATCGC
* *
19844330 TATGTGATTACATGTAAGACCACGTCTGGGACGT
1 TATGTGTTTTCATGTAAGACCACGTCTGGGACGT
19844364 TGGCATTGTA
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
42 4 0.06
43 60 0.88
44 4 0.06
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (42 bp):
TATGTGTTTTCATGTAAGACCACGTCTGGGACGTAGCATCGC
Found at i:19845048 original size:15 final size:15
Alignment explanation
Indices: 19845016--19845064 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
19845006 TACTTTAATC
19845016 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
19845031 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
* *
19845046 ATGGTAATGTATATAT
1 ATGGTTA-GTATTTAT
19845062 ATG
1 ATG
19845065 TGCATGGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 9 0.30
15 11 0.37
16 10 0.33
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:19845365 original size:23 final size:23
Alignment explanation
Indices: 19845339--19845459 Score: 81
Period size: 23 Copynumber: 5.2 Consensus size: 23
19845329 AATGGAGTTC
19845339 AATTATATATGTGTATGCTGTCA
1 AATTATATATGTGTATGCTGTCA
* *
19845362 AATT-T-TGATGTACAG-ATGCAGTCC
1 AATTATAT-ATGT---GTATGCTGTCA
19845386 AATTATATATGTGTATGCTGTCA
1 AATTATATATGTGTATGCTGTCA
* ** *
19845409 AATT-T-TGATGTATAAATGGAGTCC
1 AATTATAT-ATGTGT--ATGCTGTCA
*
19845433 AATTATATATGTATATGCTGTCA
1 AATTATATATGTGTATGCTGTCA
19845456 AATT
1 AATT
19845460 TTGATGTACA
Statistics
Matches: 75, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
21 2 0.03
22 12 0.16
23 25 0.33
24 21 0.28
25 13 0.17
26 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.40
Consensus pattern (23 bp):
AATTATATATGTGTATGCTGTCA
Found at i:19845372 original size:47 final size:47
Alignment explanation
Indices: 19845300--19845556 Score: 356
Period size: 47 Copynumber: 5.5 Consensus size: 47
19845290 GAGTAAATGA
* * *
19845300 ATGTATATGCTATCAAATTTTGATGTATAAATGGAGTTCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATAT
* * *
19845347 ATGTGTATGCTGTCAAATTTTGATGTACAGATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATAT
* *
19845394 ATGTGTATGCTGTCAAATTTTGATGTATAAATGGAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATAT
* * * *
19845441 ATGTATATGCTGTCAAATTTTGATGTACAAATACAATCCAATTATTT
1 ATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATAT
19845488 ATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAAATT-T-T
1 ATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCC-AATTATAT
* *
19845534 GTATATATGCTGTCCAAATTTTG
1 ATGTATATGCTGT-CAAATTTTG
19845557 GTGTGAAAAT
Statistics
Matches: 188, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
46 12 0.06
47 172 0.91
48 4 0.02
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (47 bp):
ATGTATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATAT
Found at i:19845584 original size:46 final size:46
Alignment explanation
Indices: 19845303--19845610 Score: 199
Period size: 47 Copynumber: 6.6 Consensus size: 46
19845293 TAAATGAATG
* * * *
19845303 TATATGCTATCAAATTTTGATGTATAAATGGAGTTC-AATTAT-ATA
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAAATT-TGGTA
* * * *
19845348 TGTGTATGCTGTCAAATTTTGATGTACAGATGCAGTCC-AATTAT-ATA
1 --TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAAATT-TGGTA
* * *
19845395 TGTGTATGCTGTCAAATTTTGATGTATAAATGGAGTCC-AATTAT-ATA
1 --TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAAATT-TGGTA
* * * * *
19845442 TGTATATGCTGTCAAATTTTGATGTACAAATACAATCCAATTATTT-ATG
1 --TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAA--ATTTGGTA
*
19845491 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAAATTTTGTA
1 TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAAATTTGGTA
* * *
19845537 TATATGCTGTCCAAATTTTGGTGTGA-AAATGCTA-T-CTAGTTTGGTA
1 TATATGCTGT-CAAATTTTGATGT-ATAAATGC-AGTCCAAATTTGGTA
19845583 TATAAATGCTGTTCAAA--TTGATGTATAA
1 TAT--ATGCTG-TCAAATTTTGATGTATAA
19845611 TAATTGTCCA
Statistics
Matches: 225, Mismatches: 25, Indels: 23
0.82 0.09 0.08
Matches are distributed among these distances:
45 5 0.02
46 30 0.13
47 170 0.76
48 13 0.06
49 4 0.02
50 3 0.01
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.41
Consensus pattern (46 bp):
TATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAAATTTGGTA
Found at i:19845592 original size:94 final size:94
Alignment explanation
Indices: 19845306--19845610 Score: 316
Period size: 94 Copynumber: 3.3 Consensus size: 94
19845296 ATGAATGTAT
* * * * *
19845306 ATGCTATCAAATTTTGATGTATAAATGGAGTTCAATTATATATGTGTATGCTGTCAAATTTTGAT
1 ATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATATATGCTGTCAAATTTTGAT
* * * * * **
19845371 GTACAGATGCAGTCCAATTATATATGTGT
66 GTACAAATACAATCCAATTATGTATATAA
* *
19845400 ATGCTGTCAAATTTTGATGTATAAATGGAGTCCAATTATATATGTATATGCTGTCAAATTTTGAT
1 ATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATATATGCTGTCAAATTTTGAT
* * *
19845465 GTACAAATACAATCCAATTATTTATGTAT
66 GTACAAATACAATCCAATTATGTATATAA
*
19845494 ATGCTGTCAAATTTTGATGTATAAATGCAGTCCAAATT-T-TGTATATATGCTGTCCAAATTTTG
1 ATGCTGTCAAATTTTGATGTATAAATGCAGTCC-AATTATATATATATATGCTGT-CAAATTTTG
* * * * *
19845557 GTGTGA-AAATGCTATCTAGTT-TGGTATATAA
64 ATGT-ACAAATACAATCCAATTAT-GTATATAA
19845588 ATGCTGTTCAAA--TTGATGTATAA
1 ATGCTG-TCAAATTTTGATGTATAA
19845611 TAATTGTCCA
Statistics
Matches: 187, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
93 24 0.13
94 153 0.82
95 10 0.05
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (94 bp):
ATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATATATATGCTGTCAAATTTTGAT
GTACAAATACAATCCAATTATGTATATAA
Found at i:19853981 original size:19 final size:19
Alignment explanation
Indices: 19853957--19854009 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
19853947 TTTTAACAAG
*
19853957 TTTA-TTTAATATTACAATT
1 TTTACTTTAATAATA-AATT
*
19853976 TTTATTTTAATAATAAATT
1 TTTACTTTAATAATAAATT
*
19853995 TTAACTTTAATAATA
1 TTTACTTTAATAATA
19854010 GTTTTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTACTTTAATAATAAATT
Found at i:19854094 original size:24 final size:25
Alignment explanation
Indices: 19854042--19854094 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
19854032 CTTACTCTAT
*
19854042 TAAAT-AATATATTTAATATTTTAG
1 TAAATAAATATATTTAATAATTTAG
19854066 T-AATAAATATATATT-ATAATTTA-
1 TAAATAAATATAT-TTAATAATTTAG
19854089 TAAATA
1 TAAATA
19854095 TTTAGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.16
24 19 0.76
25 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TAAATAAATATATTTAATAATTTAG
Found at i:19854129 original size:23 final size:22
Alignment explanation
Indices: 19854103--19854156 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
19854093 TATTTAGTAA
*
19854103 AATATTTTATAGTATAAAATATG
1 AATATTTTATAATAT-AAATATG
*
19854126 AATATATTAATAATATAAATATG
1 AATAT-TTTATAATATAAATATG
*
19854149 AGTATTTT
1 AATATTTT
19854157 TTTAAATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.08
23 16 0.62
24 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
AATATTTTATAATATAAATATG
Found at i:19854893 original size:17 final size:18
Alignment explanation
Indices: 19854867--19854910 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
19854857 ATTAAATCTA
*
19854867 TATAATATATTAT-TTAT
1 TATAAAATATTATCTTAT
19854884 TATAAAATATTATCTTAT
1 TATAAAATATTATCTTAT
19854902 TATAAAATA
1 TATAAAATA
19854911 AATTTTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAAATATTATCTTAT
Found at i:19863405 original size:43 final size:43
Alignment explanation
Indices: 19863358--19863439 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
19863348 ATCATATAAC
* *
19863358 GATGCCACTGTCCCAGATAG-GGTCTTACACG-TAAACACAGGTT
1 GATGCCAATGTCCCAAAT-GTGGTCTTACACGAT-AACACAGGTT
19863401 GATGCCAATGTCCCAAATGTGGTCTTACACGATAACACA
1 GATGCCAATGTCCCAAATGTGGTCTTACACGATAACACA
19863440 TAACAGAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 1 0.03
43 33 0.94
44 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (43 bp):
GATGCCAATGTCCCAAATGTGGTCTTACACGATAACACAGGTT
Found at i:19866037 original size:40 final size:40
Alignment explanation
Indices: 19865962--19866040 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
19865952 TACGTGGCAA
* * *
19865962 CAAAACGCGCTTACGTGGACGCGCTTTGTTTCCACGTAGG
1 CAAAACGCGCTGACGTGGACGCGCTTTGCTGCCACGTAGG
* **
19866002 CAAAGCGCGCTGACGTGGACGCTTTTTGCTGCCACGTAG
1 CAAAACGCGCTGACGTGGACGCGCTTTGCTGCCACGTAG
19866041 CGCGCCCCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (40 bp):
CAAAACGCGCTGACGTGGACGCGCTTTGCTGCCACGTAGG
Found at i:19866105 original size:22 final size:21
Alignment explanation
Indices: 19866076--19866121 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
19866066 TTCCTCCAAC
**
19866076 GTTAGGTTTTGGGTTTTTAGG
1 GTTAGGTTTAAGGTTTTTAGG
19866097 GTTAGGGTTTAAGGTTTTTAGG
1 GTTA-GGTTTAAGGTTTTTAGG
19866119 GTT
1 GTT
19866122 TTAGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (21 bp):
GTTAGGTTTAAGGTTTTTAGG
Found at i:19866362 original size:27 final size:27
Alignment explanation
Indices: 19866324--19866412 Score: 127
Period size: 27 Copynumber: 3.5 Consensus size: 27
19866314 TAATTAAGGC
19866324 TTTTTAAGTTAAGGAATACAGTTAGGG
1 TTTTTAAGTTAAGGAATACAGTTAGGG
*
19866351 TTTTTAAGTTAAGTAATACAGTTAGGG
1 TTTTTAAGTTAAGGAATACAGTTAGGG
19866378 TTTTTAAGTTAAGG------GTTAGGG
1 TTTTTAAGTTAAGGAATACAGTTAGGG
19866399 TTTTTAAGTTAAGG
1 TTTTTAAGTTAAGG
19866413 GTTAGGGTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
21 21 0.35
27 39 0.65
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (27 bp):
TTTTTAAGTTAAGGAATACAGTTAGGG
Found at i:19866397 original size:21 final size:21
Alignment explanation
Indices: 19866371--19866615 Score: 337
Period size: 21 Copynumber: 11.5 Consensus size: 21
19866361 AAGTAATACA
19866371 GTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
19866392 GTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
*
19866413 GTTAGGGTATTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
*
19866434 GTTTAAGGTTTTTAAGTTAAGG
1 G-TTAGGGTTTTTAAGTTAAGG
* * *
19866456 GTTAAGGTTTTTAGGTTAAGA
1 GTTAGGGTTTTTAAGTTAAGG
*
19866477 GTTAGGGTATTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
19866498 GCTTAGGGTTTTTAAGTTAAGG
1 G-TTAGGGTTTTTAAGTTAAGG
19866520 GTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
* * *
19866541 ATTTAGGGTTTTTAACTTAAGA
1 -GTTAGGGTTTTTAAGTTAAGG
* * *
19866563 GTTTGGGTTTATAACTTAAGG
1 GTTAGGGTTTTTAAGTTAAGG
19866584 GTTTAGGGTTTTTAAGTTAAGG
1 G-TTAGGGTTTTTAAGTTAAGG
*
19866606 GTTAGAGTTT
1 GTTAGGGTTT
19866616 AGGGTTAGGG
Statistics
Matches: 199, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
21 124 0.62
22 75 0.38
ACGTcount: A:0.26, C:0.01, G:0.30, T:0.43
Consensus pattern (21 bp):
GTTAGGGTTTTTAAGTTAAGG
Found at i:19866465 original size:64 final size:64
Alignment explanation
Indices: 19866372--19866610 Score: 354
Period size: 64 Copynumber: 3.7 Consensus size: 64
19866362 AGTAATACAG
19866372 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTATTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTATTTAAGTTAAGGGT
* * * * *
19866436 TTAAGGTTTTTAAGTTAAGGGTTAAGGTTTTTAGGTTAAGAGTTAGGGTATTTAAGTTAAGGGC
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTATTTAAGTTAAGGGT
* * * *
19866500 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGATTTAGGGTTTTTAACTTAAGAGT
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG-GTTAGGGTATTTAAGTTAAGGGT
* *
19866565 TT-GGGTTTATAACTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAG
1 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTAG
19866611 AGTTTAGGGT
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
64 116 0.74
65 40 0.26
ACGTcount: A:0.26, C:0.01, G:0.30, T:0.43
Consensus pattern (64 bp):
TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTATTTAAGTTAAGGGT
Found at i:19866616 original size:43 final size:42
Alignment explanation
Indices: 19866371--19866615 Score: 337
Period size: 43 Copynumber: 5.7 Consensus size: 42
19866361 AAGTAATACA
19866371 GTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
* *
19866413 GTTAGGGTATTTAAGTTAAGGGTTTAAGGTTTTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGG
* * * *
19866456 GTTAAGGTTTTTAGGTTAAGAGTTAGGGTATTTAAGTTAAGG
1 GTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
19866498 GCTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
1 G-TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
* * * * * *
19866541 ATTTAGGGTTTTTAACTTAAGAGTTTGGGTTTATAACTTAAGG
1 -GTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
*
19866584 GTTTAGGGTTTTTAAGTTAAGGGTTAGAGTTT
1 G-TTAGGGTTTTTAAGTTAAGGGTTAGGGTTT
19866616 AGGGTTAGGG
Statistics
Matches: 176, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
42 40 0.23
43 136 0.77
ACGTcount: A:0.26, C:0.01, G:0.30, T:0.43
Consensus pattern (42 bp):
GTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
Found at i:19868999 original size:51 final size:51
Alignment explanation
Indices: 19868944--19869041 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
19868934 AAATAATTAA
19868944 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAAATT
* * *
19868995 AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGA
19869042 GAAAATAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAAATT
Found at i:19892736 original size:80 final size:79
Alignment explanation
Indices: 19892651--19892822 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
19892641 GGACTAAGAT
*
19892651 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
19892715 AAACCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
19892731 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
19892796 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
19892810 CCGAAGGCATTTG
1 CCGAAGGCATTTG
19892823 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:19892802 original size:39 final size:39
Alignment explanation
Indices: 19892598--19892820 Score: 200
Period size: 40 Copynumber: 5.6 Consensus size: 39
19892588 TTGAATGCTG
* * * * *
19892598 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
19892638 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
19892677 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* * *
19892718 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
19892758 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
19892797 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
19892821 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
39 40 0.26
40 101 0.65
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:19892840 original size:79 final size:80
Alignment explanation
Indices: 19892678--19892855 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
19892668 AGATACAAAT
* * * *
19892678 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAACCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
19892743 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
19892758 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
19892822 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
19892837 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
19892856 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:19898517 original size:45 final size:46
Alignment explanation
Indices: 19898466--19898615 Score: 135
Period size: 45 Copynumber: 3.3 Consensus size: 46
19898456 GAAAAGCAGC
19898466 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAA-GAAAGT
1 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAGT
* *** ** *** * * *
19898511 AGATCTTGTCTTCATGTACCAG-CATGAAGTAGATCAAAGGTAA-C
1 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAGT
*
19898555 AAATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAAAGT
1 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGG--AAAGT
*
19898603 AGATCTTGTCTTC
1 AGATCTTGCCTTC
19898616 ATGTACTGGC
Statistics
Matches: 73, Mismatches: 27, Indels: 7
0.68 0.25 0.07
Matches are distributed among these distances:
44 27 0.37
45 33 0.45
47 2 0.03
48 11 0.15
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (46 bp):
AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAGT
Found at i:19898575 original size:89 final size:91
Alignment explanation
Indices: 19898468--19898641 Score: 298
Period size: 92 Copynumber: 1.9 Consensus size: 91
19898458 AAAGCAGCAG
19898468 ATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAA-G-AAAGTAGATCTTGTCTTCATGTACC
1 ATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAAGTAGATCTTGTCTTCATGTACC
19898531 AGCATGAAGTAGATCAAAGGTAACAA
66 AGCATGAAGTAGATCAAAGGTAACAA
19898557 ATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAAAGTAGATCTTGTCTTCATGTAC
1 ATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGG-AAAAGTAGATCTTGTCTTCATGTAC
** *
19898622 TGGCGTGAAGTAGATCAAAG
65 CAGCATGAAGTAGATCAAAG
19898642 ACATCAGGTC
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
89 37 0.47
90 1 0.01
92 41 0.52
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (91 bp):
ATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGGAAAAGTAGATCTTGTCTTCATGTACC
AGCATGAAGTAGATCAAAGGTAACAA
Found at i:19904285 original size:19 final size:19
Alignment explanation
Indices: 19904230--19904287 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
19904220 TGGCATCGGA
* *
19904230 GTGCATCTTGACGTACAAG
1 GTGCATCTTGGCGCACAAG
* * *
19904249 ATGCATACCTGGCACACAAG
1 GTGCAT-CTTGGCGCACAAG
19904269 GTGCATCTTGGCGCACAAG
1 GTGCATCTTGGCGCACAAG
19904288 CGTATATCTA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (19 bp):
GTGCATCTTGGCGCACAAG
Found at i:19904646 original size:243 final size:243
Alignment explanation
Indices: 19904218--19904693 Score: 702
Period size: 243 Copynumber: 2.0 Consensus size: 243
19904208 TATTAACTTG
* * * * * * *
19904218 ACTGGCATCGGAGTGCATCTTGACGTACAAGATGCATACCTGGCACACAAGGTGCATCTTGGCGC
1 ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGACACACAAGGTACAGCTTGGCGC
* * *
19904283 ACAAGCGTATATCTAGTACATGAAATGCATCCTGGCGTATAAACACATAATCCCGTACTTAATCC
66 ACAAGCGTATATCTAGCACATGAAATGCATCCTGGCGTATAAACACATAATCCCATACTCAATCC
* *
19904348 AATCCTATGGCATGCCAACCATATCCAACTCAATTCCACTAGTTAATAGGGTATCAAATTTCAAT
131 AATCCTATGACATGCCAACCATATCCAACTCAATCCCACTAGTTAATAGGGTATCAAATTTCAAT
*
19904413 TCCATTTAGAATATAATACACATATCAATTTTTCAATCAACACACCAA
196 TCCATTTAGAATATAATACACATATCAAATTTTCAATCAACACACCAA
* *
19904461 ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGATACACAAGGTACAGCTTGGTGC
1 ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGACACACAAGGTACAGCTTGGCGC
* * * * *
19904526 ATAAGTGTATATCTAGCACATGAAATGCATCCTGGGGTATAAGCGCATAATCCCATACTCAATCC
66 ACAAGCGTATATCTAGCACATGAAATGCATCCTGGCGTATAAACACATAATCCCATACTCAATCC
** *
19904591 AATCCTATGACATGCCAATTATATCCAACTCAA-CCCGACTAGTTAATAGGGTATCAAATTTTAA
131 AATCCTATGACATGCCAACCATATCCAACTCAATCCC-ACTAGTTAATAGGGTATCAAATTTCAA
** *
19904655 TTCTGTTTAGAGTATAATACACATATCAAATTTTCAATC
195 TTCCATTTAGAATATAATACACATATCAAATTTTCAATC
19904694 CTATACACTA
Statistics
Matches: 206, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
242 2 0.01
243 204 0.99
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (243 bp):
ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGACACACAAGGTACAGCTTGGCGC
ACAAGCGTATATCTAGCACATGAAATGCATCCTGGCGTATAAACACATAATCCCATACTCAATCC
AATCCTATGACATGCCAACCATATCCAACTCAATCCCACTAGTTAATAGGGTATCAAATTTCAAT
TCCATTTAGAATATAATACACATATCAAATTTTCAATCAACACACCAA
Found at i:19905650 original size:20 final size:20
Alignment explanation
Indices: 19905627--19905666 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19905617 TTAATTAACA
*
19905627 TAATTAACCTTACTTTAATT
1 TAATAAACCTTACTTTAATT
*
19905647 TAATAAACCTTATTTTAATT
1 TAATAAACCTTACTTTAATT
19905667 AAGTTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAACCTTACTTTAATT
Found at i:19906191 original size:23 final size:23
Alignment explanation
Indices: 19906165--19906210 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
19906155 AAGTTGATGG
19906165 AACTTGATTGTATGGGAAATATA
1 AACTTGATTGTATGGGAAATATA
19906188 AACTTGATTGTATGGGAAATATA
1 AACTTGATTGTATGGGAAATATA
19906211 TGCAAATCCT
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:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (23 bp):
AACTTGATTGTATGGGAAATATA
Found at i:19912298 original size:118 final size:118
Alignment explanation
Indices: 19912090--19912317 Score: 350
Period size: 118 Copynumber: 1.9 Consensus size: 118
19912080 GAAATACTAT
* * * *
19912090 CGAGCCATACCTACTGAATCTACTGAAATGTATGTGTTATTGAGCCATACCTAATGATTTACTGA
1 CGAGCCATACCTACTGAATCTACTGAAATGTATGCGCTATCGAGCCATACCTAATAATTTACTGA
* *
19912155 AATGTATGCGCTATTGAGCCATACCTACTGATTCTAATGAAAGTATGCTTTAG
66 AATGTATGCGCTATCGAGCCATACCTACCGATTCTAATGAAAGTATGCTTTAG
* *
19912208 CGAGCCATACCTACTGAATTTACTGAAATGTATGCGCTATCGAGCCATACCTACTAATTCTACTG
1 CGAGCCATACCTACTGAATCTACTGAAATGTATGCGCTATCGAGCCATACCTAATAATT-TACTG
* *
19912273 AAA-GTATGCTCTATCGAGCCATACCTACCGATTCTATTGAAAGTA
65 AAATGTATGCGCTATCGAGCCATACCTACCGATTCTAATGAAAGTA
19912318 GCTCAAACGA
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 91 0.92
119 8 0.08
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (118 bp):
CGAGCCATACCTACTGAATCTACTGAAATGTATGCGCTATCGAGCCATACCTAATAATTTACTGA
AATGTATGCGCTATCGAGCCATACCTACCGATTCTAATGAAAGTATGCTTTAG
Found at i:19912300 original size:79 final size:78
Alignment explanation
Indices: 19912086--19912314 Score: 318
Period size: 79 Copynumber: 2.9 Consensus size: 78
19912076 AGTTGAAATA
* *
19912086 CTATCGAGCCATACCTACTGAA-TCTACTGAAATGTATG-TGTTATTGAGCCATACCTAATGATT
1 CTATCGAGCCATACCTACT-AATTCTACTGAAA-GTATGCT-TTATCGAGCCATACCTACTGATT
19912149 TACTGAAATGTATGCG
63 TACTGAAATGTATGCG
* * * *
19912165 CTATTGAGCCATACCTACTGATTCTAATGAAAGTATGCTTTAGCGAGCCATACCTACTGAATTTA
1 CTATCGAGCCATACCTACTAATTCTACTGAAAGTATGCTTTATCGAGCCATACCTACTG-ATTTA
19912230 CTGAAATGTATGCG
65 CTGAAATGTATGCG
* *
19912244 CTATCGAGCCATACCTACTAATTCTACTGAAAGTATGCTCTATCGAGCCATACCTACCGATTCTA
1 CTATCGAGCCATACCTACTAATTCTACTGAAAGTATGCTTTATCGAGCCATACCTACTGATT-TA
*
19912309 TTGAAA
65 CTGAAA
19912315 GTAGCTCAAA
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
78 26 0.20
79 107 0.80
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (78 bp):
CTATCGAGCCATACCTACTAATTCTACTGAAAGTATGCTTTATCGAGCCATACCTACTGATTTAC
TGAAATGTATGCG
Found at i:19912315 original size:39 final size:40
Alignment explanation
Indices: 19912086--19912321 Score: 288
Period size: 39 Copynumber: 6.0 Consensus size: 40
19912076 AGTTGAAATA
*
19912086 CTATCGAGCCATACCTACTGAATCTACTGAAATGTATG-T
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
* * * *
19912125 GTTATTGAGCCATACCTAATGATT-TACTGAAATGTATGCG
1 -CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
* *
19912165 CTATTGAGCCATACCTACTGATTCTAATGAAA-GTATGCT
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
* * *
19912204 TTAGCGAGCCATACCTACTGAATT-TACTGAAATGTATGCG
1 CTATCGAGCCATACCTACTG-ATTCTACTGAAATGTATGCT
*
19912244 CTATCGAGCCATACCTACTAATTCTACTGAAA-GTATGCT
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
* *
19912283 CTATCGAGCCATACCTACCGATTCTATTGAAA-GTA-GCT
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
19912321 C
1 C
19912322 AAACGAGCAT
Statistics
Matches: 170, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
38 4 0.02
39 106 0.62
40 60 0.35
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (40 bp):
CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
Found at i:19914264 original size:24 final size:24
Alignment explanation
Indices: 19914232--19914287 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
19914222 GCAAACAGTT
19914232 ATTAAACACTATTTATTTGCTTTC
1 ATTAAACACTATTTATTTGCTTTC
* * *
19914256 ATTAAACACTATTTGTTTTCTTTT
1 ATTAAACACTATTTATTTGCTTTC
*
19914280 AGTAAACA
1 ATTAAACA
19914288 TTTAAGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.48
Consensus pattern (24 bp):
ATTAAACACTATTTATTTGCTTTC
Found at i:19918976 original size:19 final size:18
Alignment explanation
Indices: 19918952--19918995 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
19918942 TAATGATTAC
19918952 TTAAATTAATTATATAAAA
1 TTAAATTAATTAT-TAAAA
**
19918971 TTAAATTTTTTATTAAAA
1 TTAAATTAATTATTAAAA
19918989 -TAAATTA
1 TTAAATTA
19918996 TATAAATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 5 0.23
19 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATTAATTATTAAAA
Found at i:19919878 original size:24 final size:24
Alignment explanation
Indices: 19919850--19919897 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
19919840 AAGGTCAGTA
19919850 ATTCATATTTCTCTCTCTCTCTCT
1 ATTCATATTTCTCTCTCTCTCTCT
19919874 ATTCATATTTCTCTCTCTCTCTCT
1 ATTCATATTTCTCTCTCTCTCTCT
19919898 CTTTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTCATATTTCTCTCTCTCTCTCT
Found at i:19925683 original size:67 final size:67
Alignment explanation
Indices: 19925575--19925709 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
19925565 TATCTATATC
19925575 AAACCCAAATAGGGATGATAATAGAGCCTGGATATTACCAAACCTATCATCCTTCCACAGTTAAT
1 AAACCCAAATAGGGATGATAATAGAGCCTGGATATTACCAAACCTATCATCCTTCCACAGTTAAT
19925640 GG
66 GG
19925642 AAACCCAAATAGGGATGATAATAGAGCCTGGATATTACCAAACCTATCATCCTTCCACAGTTAAT
1 AAACCCAAATAGGGATGATAATAGAGCCTGGATATTACCAAACCTATCATCCTTCCACAGTTAAT
19925707 GG
66 GG
19925709 A
1 A
19925710 TTTTGTTGTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (67 bp):
AAACCCAAATAGGGATGATAATAGAGCCTGGATATTACCAAACCTATCATCCTTCCACAGTTAAT
GG
Found at i:19930374 original size:17 final size:18
Alignment explanation
Indices: 19930343--19930376 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19930333 AATTTAACTT
19930343 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
19930361 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
19930377 TTATAAACAA
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):
TAATTAAATTATTTAAAA
Found at i:19930572 original size:20 final size:20
Alignment explanation
Indices: 19930547--19930606 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
19930537 CCGAACCCCG
*
19930547 AGATTTAAGGTTTGGGTTTA
1 AGATTTAAGGTTTGGGTTCA
* *
19930567 AGATTTAAGATTTTGGGATCA
1 AGATTTAAG-GTTTGGGTTCA
*
19930588 AAATTTAAGGTTTAGGGTT
1 AGATTTAAGGTTT-GGGTT
19930607 ACGAATTATG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 12 0.38
21 20 0.62
ACGTcount: A:0.30, C:0.02, G:0.27, T:0.42
Consensus pattern (20 bp):
AGATTTAAGGTTTGGGTTCA
Found at i:19933390 original size:3 final size:3
Alignment explanation
Indices: 19933375--19933419 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
19933365 TAATTCTCTC
*
19933375 TTA TTA ATA 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
19933420 AGTGTAGAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:19936066 original size:20 final size:18
Alignment explanation
Indices: 19936016--19936067 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
19936006 CTTGTAGATA
19936016 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
19936033 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
19936053 AATATTAAATTAATA
1 AATATTAAATTAATA
19936068 AACTACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:19943236 original size:16 final size:16
Alignment explanation
Indices: 19943215--19943248 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19943205 CTATGCATGA
* *
19943215 AAAATATAAAAGTCAG
1 AAAATACAAAAGACAG
19943231 AAAATACAAAAGACAG
1 AAAATACAAAAGACAG
19943247 AA
1 AA
19943249 TCGTGAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.09, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:19949161 original size:25 final size:25
Alignment explanation
Indices: 19949133--19949181 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
19949123 CTGTTTTTGA
* *
19949133 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATACTGAAACTACTATAGG
*
19949158 TAGTATATACTGAGACTACTATAG
1 TAGTATATACTGAAACTACTATAG
19949182 TTAGACTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:19956808 original size:14 final size:15
Alignment explanation
Indices: 19956782--19956811 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19956772 TTGGTATTAC
19956782 TTAATCTATTCATAT
1 TTAATCTATTCATAT
19956797 TTAATC-ATTCATAT
1 TTAATCTATTCATAT
19956811 T
1 T
19956812 ATTATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATCTATTCATAT
Found at i:19960761 original size:12 final size:12
Alignment explanation
Indices: 19960744--19960768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19960734 TATTCATGAA
19960744 TTTGTACATTCT
1 TTTGTACATTCT
19960756 TTTGTACATTCT
1 TTTGTACATTCT
19960768 T
1 T
19960769 CGGTACATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTGTACATTCT
Found at i:19961487 original size:6 final size:6
Alignment explanation
Indices: 19961478--19961510 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
19961468 ATTCAAAAAA
*
19961478 AAAATC AAAATC AAAATC AAAA-C AAAAAC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
19961511 AGAAGAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (6 bp):
AAAATC
Found at i:19961487 original size:12 final size:12
Alignment explanation
Indices: 19961470--19961511 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
19961460 CAGATCCAAT
19961470 TCAAAAAAAAAA
1 TCAAAAAAAAAA
**
19961482 TCAAAATCAAAA
1 TCAAAAAAAAAA
*
19961494 TCAAAACAAAAA
1 TCAAAAAAAAAA
19961506 -CAAAAA
1 TCAAAAA
19961512 GAAGAAAGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.76, C:0.14, G:0.00, T:0.10
Consensus pattern (12 bp):
TCAAAAAAAAAA
Found at i:19961559 original size:21 final size:21
Alignment explanation
Indices: 19961535--19961580 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
19961525 AATCAAAATC
* * *
19961535 AAAGTCAGAATGAAAATGAAA
1 AAAGACAGAAGGAAAAAGAAA
*
19961556 AAAGAGAGAAGGAAAAAGAAA
1 AAAGACAGAAGGAAAAAGAAA
19961577 AAAG
1 AAAG
19961581 GAAAAGGAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (21 bp):
AAAGACAGAAGGAAAAAGAAA
Found at i:19962647 original size:42 final size:42
Alignment explanation
Indices: 19962553--19962648 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
19962543 TTGATCAGGA
*
19962553 CATGAGGTGATTAGAGCAATTCAAATTCTAATCAGAGTGGGG
1 CATGAGGTGATCAGAGCAATTCAAATTCTAATCAGAGTGGGG
* * * * *
19962595 CATGAAGTGATCAGAGCAATTTAAATTTTGATCAGATTGGGG
1 CATGAGGTGATCAGAGCAATTCAAATTCTAATCAGAGTGGGG
*
19962637 CATGTGGTGATC
1 CATGAGGTGATC
19962649 TTGTTATACC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.29
Consensus pattern (42 bp):
CATGAGGTGATCAGAGCAATTCAAATTCTAATCAGAGTGGGG
Found at i:19964088 original size:88 final size:88
Alignment explanation
Indices: 19963723--19964345 Score: 734
Period size: 88 Copynumber: 7.2 Consensus size: 88
19963713 CAGATCAGTG
* * * * * *
19963723 AAGATAACAGATCTTGCCTTCTTGCATCGACAGTGAAGTAGATCGAAAGTA-A--AGCCTTGCCT
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCG-AAG-ACACCAGCCTTGCCT
* * * *
19963785 CCATCGGTTGTAGTGGAACGGGTTA
64 CCCTCGGTTGCAGTGGAGCAGGTTA
* * * *
19963810 AAGATAGCAGAT-TTGCCTTCTTGCATCGACAGCGAAACAGATCGAAAGTA-A--AGCCTTGCCT
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCG-AAG-ACACCAGCCTTGCCT
* *
19963871 CCATCGGTTGCAGTGGAGCTGGTTA
64 CCCTCGGTTGCAGTGGAGCAGGTTA
* * *
19963896 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAA-ACA-AAGCC-TGCC-CC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* *
19963957 CTCGATTGCAGTGGAGTAGGTTA
66 CTCGGTTGCAGTGGAGCAGGTTA
* * * *
19963980 AA-ATAGCAGATCTTGCCTTCCTGTGTAGACAGCGAAGCAGATCAAAGACACCGGCCTCGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
19964044 CTCGGTTGCAGTGGAGCAGGTTGA
66 CTCGGTTGCAGTGGAGCAGGTT-A
* *
19964068 AA-ATAGCAGATCTTGCCTTCCTACGTAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCT
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
**
19964132 CTCGGTTGCAGTGGAGTGGGTTA
66 CTCGGTTGCAGTGGAGCAGGTTA
* * *
19964155 AAGGTAGCAGATCTTGCCTTCCTACGTAGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * *
19964220 CTTGGTTGTAGTGGAGCGGGTTA
66 CTCGGTTGCAGTGGAGCAGGTTA
* * * *
19964243 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAACGAAGAAGATCGAAGACACAAGCCTCGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* *
19964308 ATCGGTTGCAGTGGAGCAGG-TG
66 CTCGGTTGCAGTGGAGCAGGTTA
19964330 AAGATAGCAGATCTTG
1 AAGATAGCAGATCTTG
19964346 TCTCCCTAAG
Statistics
Matches: 478, Mismatches: 49, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
83 40 0.08
84 27 0.06
85 8 0.02
86 89 0.19
87 82 0.17
88 232 0.49
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (88 bp):
AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
CTCGGTTGCAGTGGAGCAGGTTA
Found at i:19964129 original size:44 final size:43
Alignment explanation
Indices: 19963991--19964217 Score: 118
Period size: 44 Copynumber: 5.2 Consensus size: 43
19963981 AATAGCAGAT
* * *
19963991 CTTGCCTTCCTGTGTAGACAGCGAAGCAGATCAAAGACACCGGC
1 CTTGCCTTCCT-CGTAGACAGCGAAGCAGATCGAAGACACCAGC
* * * * * * * * * * *
19964035 CTCGCCTCCCTCGGTTG-CAGTGGAGCAGGTTGAAAATAGCAGAT
1 CTTGCCTTCCTC-GTAGACAGCGAAGCAGATCGAAGACACCAG-C
19964079 CTTGCCTTCCTACGTAGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCT-CGTAGACAGCGAAGCAGATCGAAGACACCAGC
* * * ** * ** ** * *
19964123 CTTGCC-TCTCTCGGTTG-CAGTGGAGTGGGTTAAAGGTAGCAGAT
1 CTTGCCTTC-CTC-GTAGACAGCGAAGCAGATCGAAGACACCAG-C
*
19964167 CTTGCCTTCCTACGTAGATAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCT-CGTAGACAGCGAAGCAGATCGAAGACACCAGC
19964211 CTTGCCT
1 CTTGCCT
19964218 CCCTTGGTTG
Statistics
Matches: 123, Mismatches: 50, Indels: 20
0.64 0.26 0.10
Matches are distributed among these distances:
43 34 0.28
44 53 0.43
45 36 0.29
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.22
Consensus pattern (43 bp):
CTTGCCTTCCTCGTAGACAGCGAAGCAGATCGAAGACACCAGC
Found at i:19966741 original size:14 final size:15
Alignment explanation
Indices: 19966715--19966744 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19966705 TTGGTATTAC
19966715 TTAATCTATTCATAT
1 TTAATCTATTCATAT
19966730 TTAATC-ATTCATAT
1 TTAATCTATTCATAT
19966744 T
1 T
19966745 ATTATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATCTATTCATAT
Found at i:19970687 original size:12 final size:12
Alignment explanation
Indices: 19970670--19970694 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19970660 TATTCATGAA
19970670 TTTGTACATTCT
1 TTTGTACATTCT
19970682 TTTGTACATTCT
1 TTTGTACATTCT
19970694 T
1 T
19970695 CGGTACATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTGTACATTCT
Found at i:19971439 original size:6 final size:6
Alignment explanation
Indices: 19971398--19971439 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
19971388 AGATCCAATT
* *
19971398 CAAAAA -AAAAA TCAAAAT CAAAAT CAAAAA CAAAAA CAAAAA
1 CAAAAA CAAAAA -CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
19971440 GAAGAAAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 5 0.16
6 23 0.72
7 4 0.12
ACGTcount: A:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (6 bp):
CAAAAA
Found at i:19971513 original size:13 final size:15
Alignment explanation
Indices: 19971474--19971513 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
19971464 AAGTCAGAAT
*
19971474 GAAAATGAAAAAAGA
1 GAAAAGGAAAAAAGA
*
19971489 GAGAAGGAAAAAAGA
1 GAAAAGGAAAAAAGA
19971504 -AAAAGGAAAA
1 GAAAAGGAAAA
19971514 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (15 bp):
GAAAAGGAAAAAAGA
Found at i:19972577 original size:42 final size:42
Alignment explanation
Indices: 19972483--19972578 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
19972473 TTGATCAGGA
*
19972483 CATGAGGTGATTAGAGCAATTCAAATTCTAATCAGAGTGGGG
1 CATGAGGTGATCAGAGCAATTCAAATTCTAATCAGAGTGGGG
* * * * *
19972525 CATGAAGTGATCAGAGCAATTTAAATTTTGATCAGATTGGGG
1 CATGAGGTGATCAGAGCAATTCAAATTCTAATCAGAGTGGGG
*
19972567 CATGTGGTGATC
1 CATGAGGTGATC
19972579 TTGTTATACC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.29
Consensus pattern (42 bp):
CATGAGGTGATCAGAGCAATTCAAATTCTAATCAGAGTGGGG
Found at i:19974033 original size:88 final size:88
Alignment explanation
Indices: 19973671--19974298 Score: 736
Period size: 88 Copynumber: 7.2 Consensus size: 88
19973661 CAGATCAGTG
* * * * * *
19973671 AAGATAACAGATCTTGCCTTCTTGCATCGACAGTGAAGTAGATCGAAAGTA-A--AGCCTTGCCT
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATC-AAAG-ACACCAGCCTTGCCT
* * * *
19973733 CCATCGGTTGTAGTGGAACGGGTTA
64 CCCTCGGTTGCAGTGGAGCAGGTTA
* * * *
19973758 AAGATAGCAGATCTTGCCTTCTTGCATCGACAGCGAAACAGATCGAAAGTA-A--AGCCTTGCCT
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATC-AAAG-ACACCAGCCTTGCCT
* *
19973820 CCATCGGTTGCAGTGGAGCTGGTTA
64 CCCTCGGTTGCAGTGGAGCAGGTTA
* * *
19973845 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAA-ACA-AAGCCTTGCC-C
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATC-AAAGACACCAGCCTTGCCTC
* *
19973907 CCTCGATTGCAGTGGAGTAGGTTA
65 CCTCGGTTGCAGTGGAGCAGGTTA
* * * *
19973931 AAAATAGCAGATCTTGCCTTCCTGTGTAGACAGCGAAGCAGATCAAAGACACCGGCCTCGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
19973996 CTCGGTTGCAGTGGAGCAGGTTGA
66 CTCGGTTGCAGTGGAGCAGGTT-A
* * *
19974020 AA-ATAGCAGATCTTGCCTTCCTACGTAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCT
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
**
19974084 CTCGGTTGCAGTGGAGTGGGTTA
66 CTCGGTTGCAGTGGAGCAGGTTA
* * * *
19974107 AAGGTAGCAGATCTTGCCTTCCTACGTAGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
* * *
19974172 CTTGGTTGTAGTGGAGCGGGTTA
66 CTCGGTTGCAGTGGAGCAGGTTA
* * * * *
19974195 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAACGAAGAAGATCGAAGACACAAGCCTCGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
* *
19974260 ATCGGTTGCAGTGGAGCAGGTTG
66 CTCGGTTGCAGTGGAGCAGGTTA
19974283 AAGATAGCAGATCTTG
1 AAGATAGCAGATCTTG
19974299 TCTCCCTAAG
Statistics
Matches: 485, Mismatches: 49, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
85 4 0.01
86 65 0.13
87 144 0.30
88 269 0.55
89 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (88 bp):
AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
CTCGGTTGCAGTGGAGCAGGTTA
Found at i:19974081 original size:44 final size:43
Alignment explanation
Indices: 19973943--19974169 Score: 118
Period size: 44 Copynumber: 5.2 Consensus size: 43
19973933 AATAGCAGAT
* * *
19973943 CTTGCCTTCCTGTGTAGACAGCGAAGCAGATCAAAGACACCGGC
1 CTTGCCTTCCT-CGTAGACAGCGAAGCAGATCGAAGACACCAGC
* * * * * * * * * * *
19973987 CTCGCCTCCCTCGGTTG-CAGTGGAGCAGGTTGAAAATAGCAGAT
1 CTTGCCTTCCTC-GTAGACAGCGAAGCAGATCGAAGACACCAG-C
19974031 CTTGCCTTCCTACGTAGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCT-CGTAGACAGCGAAGCAGATCGAAGACACCAGC
* * * ** * ** ** * *
19974075 CTTGCC-TCTCTCGGTTG-CAGTGGAGTGGGTTAAAGGTAGCAGAT
1 CTTGCCTTC-CTC-GTAGACAGCGAAGCAGATCGAAGACACCAG-C
*
19974119 CTTGCCTTCCTACGTAGATAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCT-CGTAGACAGCGAAGCAGATCGAAGACACCAGC
19974163 CTTGCCT
1 CTTGCCT
19974170 CCCTTGGTTG
Statistics
Matches: 123, Mismatches: 50, Indels: 20
0.64 0.26 0.10
Matches are distributed among these distances:
43 34 0.28
44 53 0.43
45 36 0.29
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.22
Consensus pattern (43 bp):
CTTGCCTTCCTCGTAGACAGCGAAGCAGATCGAAGACACCAGC
Found at i:19981660 original size:52 final size:53
Alignment explanation
Indices: 19981558--19981663 Score: 205
Period size: 52 Copynumber: 2.0 Consensus size: 53
19981548 ATATGTATGG
19981558 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
19981611 TAGTTTTTGTGTATATCTCTTTC-TTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
19981663 T
1 T
19981664 TAGGAGATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.57
53 23 0.43
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.51
Consensus pattern (53 bp):
TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
Found at i:19986207 original size:51 final size:52
Alignment explanation
Indices: 19986113--19986213 Score: 186
Period size: 51 Copynumber: 1.9 Consensus size: 52
19986103 TGTATGGTAG
19986113 TTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGTTAGT
1 TTTTGTGTATATCTCTTTC-TTTTTAATTAGGAGATTAGATGCTAAAGTTAGT
19986166 TTTTGTGTATATCTCTTTC-TTTTAATTAGGAGATTAGATGCTAAAGTT
1 TTTTGTGTATATCTCTTTCTTTTTAATTAGGAGATTAGATGCTAAAGTT
19986214 TAGGAGATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 29 0.60
53 19 0.40
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (52 bp):
TTTTGTGTATATCTCTTTCTTTTTAATTAGGAGATTAGATGCTAAAGTTAGT
Found at i:19987250 original size:70 final size:70
Alignment explanation
Indices: 19987154--19987308 Score: 174
Period size: 70 Copynumber: 2.2 Consensus size: 70
19987144 TGATATTGTT
* * *
19987154 GGTTTATCTGACTAGTGCTGGACGCAAACCATTGTCGA-TTATCCGACTAGTGCA-AGACACACC
1 GGTTTATCTGACTAGTACTGGACGCAAAACATTATC-ATTTATCCGACTAGTGCAGAG-CACACC
*
19987217 TATCGTC
64 TATCATC
* * *
19987224 GGTTTATCTGACTAGTACTAGG-CGCAAAATATTATCATTTATCTGACTAGTGCAGAGCACACTT
1 GGTTTATCTGACTAGTACT-GGACGCAAAACATTATCATTTATCCGACTAGTGCAGAGCACACCT
19987288 ATCATC
65 ATCATC
*
19987294 AGTTTAT-TCGACTAG
1 GGTTTATCT-GACTAG
19987309 CGTTGAGTGC
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
69 2 0.03
70 67 0.92
71 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (70 bp):
GGTTTATCTGACTAGTACTGGACGCAAAACATTATCATTTATCCGACTAGTGCAGAGCACACCTA
TCATC
Found at i:19987300 original size:35 final size:35
Alignment explanation
Indices: 19987192--19987308 Score: 89
Period size: 35 Copynumber: 3.3 Consensus size: 35
19987182 CCATTGTCGA
* * * *
19987192 TTATCCGACTAGTGCA-AGACACACCTATCGTCGGT
1 TTATCTGACTAGTGCAGAG-CACACATATCATCAGT
* * * *
19987227 TTATCTGACTAGTACTAG-GCGCAAAATATTATCA-T
1 TTATCTGACTAGTGC-AGAGCAC-ACATATCATCAGT
*
19987262 TTATCTGACTAGTGCAGAGCACACTTATCATCAGT
1 TTATCTGACTAGTGCAGAGCACACATATCATCAGT
19987297 TTAT-TCGACTAG
1 TTATCT-GACTAG
19987309 CGTTGAGTGC
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
34 11 0.17
35 44 0.70
36 8 0.13
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (35 bp):
TTATCTGACTAGTGCAGAGCACACATATCATCAGT
Found at i:19987719 original size:12 final size:12
Alignment explanation
Indices: 19987698--19987735 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
19987688 TTACGAGAAT
*
19987698 ATTGTGTACTAA
1 ATTGTATACTAA
19987710 ATTGTATACTAA
1 ATTGTATACTAA
*
19987722 ATTGTATATTAA
1 ATTGTATACTAA
19987734 AT
1 AT
19987736 AGAATCGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (12 bp):
ATTGTATACTAA
Found at i:19994416 original size:20 final size:18
Alignment explanation
Indices: 19994369--19994417 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
19994359 ATAGATAAAC
19994369 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
19994386 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
19994406 ATTAAATTAATA
1 ATTAAATTAATA
19994418 AAATATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:20004398 original size:33 final size:34
Alignment explanation
Indices: 20004334--20004408 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
20004324 AATATTGTTT
*
20004334 AATATAAATTAATTTTAATATTTTTCATTAAT-CA
1 AATATAAATTAATTTAAATATTTTT-ATTAATACA
*
20004368 ACTATAAA-TAATTTAAATAATTATTT-TTAATACA
1 AATATAAATTAATTTAAAT-ATT-TTTATTAATACA
20004402 AATATAA
1 AATATAA
20004409 TTTTATTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
33 14 0.40
34 18 0.51
35 3 0.09
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (34 bp):
AATATAAATTAATTTAAATATTTTTATTAATACA
Found at i:20006237 original size:2 final size:2
Alignment explanation
Indices: 20006230--20006259 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20006220 CATGTTATTC
20006230 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20006260 TTTAAACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:20007593 original size:14 final size:14
Alignment explanation
Indices: 20007574--20007601 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20007564 TTTTTTTAAT
20007574 GATACTATTCTAAC
1 GATACTATTCTAAC
20007588 GATACTATTCTAAC
1 GATACTATTCTAAC
20007602 ATGCAATTTG
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:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
GATACTATTCTAAC
Found at i:20008922 original size:62 final size:62
Alignment explanation
Indices: 20008778--20009011 Score: 342
Period size: 62 Copynumber: 3.7 Consensus size: 62
20008768 CAACATTACA
* * * *
20008778 ACATTAGAACACTAAAACTTGTAACAAAATTTGTAATATAAATTTTGTTTGTAATATAAATTAAA
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTG--T-T-ATATAAATTAAA
20008843 T
62 T
20008844 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* *
20008906 ACATTACAACATTAAAAATTGGAACAAACTTTGTAACATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* * * *
20008968 ACATTAGAGCATTAAAAATTAGAACAAACTTTGTAATATAAATT
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATT
20009012 AGGTACATTG
Statistics
Matches: 158, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
62 113 0.72
63 1 0.01
64 1 0.01
66 43 0.27
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (62 bp):
ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
Found at i:20021268 original size:21 final size:21
Alignment explanation
Indices: 20021219--20021273 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
20021209 ACCATTGTTT
** *
20021219 CTAATCTCACTACTACAGTAT
1 CTAATCTCACCGCTACAGTAG
* *
20021240 CCAGTCTCACCGCTACAGTAG
1 CTAATCTCACCGCTACAGTAG
20021261 CTAATCTCACCGC
1 CTAATCTCACCGC
20021274 CACCGTTGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.36, G:0.11, T:0.25
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAG
Found at i:20021437 original size:45 final size:45
Alignment explanation
Indices: 20021373--20021461 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
20021363 AATAGATACT
*
20021373 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
20021418 CGGTGGAATT-AGCATATAGCAACCACCTTACTAATCAATGATGT
1 CGGTGG-ATTCAGCACATAGCAACCACCTTACTAATCAATGATGT
20021462 TCAGTTCACA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 38 0.93
46 3 0.07
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (45 bp):
CGGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:20021543 original size:51 final size:51
Alignment explanation
Indices: 20021468--20021658 Score: 242
Period size: 51 Copynumber: 3.8 Consensus size: 51
20021458 ATGTTCAGTT
* * *
20021468 CACACAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTA
* * ** *
20021519 CACATAGTAGCTTGCACATAGTACTACACACGTGATCAAAACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTA
* * * *
20021570 CACATAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATTACCA-TCCGGTA
*
20021620 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
20021659 CACTTTCACT
Statistics
Matches: 118, Mismatches: 19, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 76 0.64
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTA
Found at i:20021678 original size:101 final size:101
Alignment explanation
Indices: 20021468--20021657 Score: 283
Period size: 101 Copynumber: 1.9 Consensus size: 101
20021458 ATGTTCAGTT
* * *
20021468 CACACAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACATAGTAGCTTG
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACATAGTAGCCTG
*
20021533 CACATAGTACTACACACGTGATCAAAACTATCCGGTA
65 CACATAGTACTACACACGTGACCAAAACTATCCGGTA
* * * *
20021570 CACATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCTGGTACACGTAGTAGCCTG
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACATAGTAGCCTG
20021634 CACATAGTACTACACACGTGACCA
65 CACATAGTACTACACACGTGACCA
20021658 TCACTTTCAC
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 4 0.05
101 40 0.51
102 35 0.44
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.23
Consensus pattern (101 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACATAGTAGCCTGC
ACATAGTACTACACACGTGACCAAAACTATCCGGTA
Found at i:20023530 original size:66 final size:62
Alignment explanation
Indices: 20023238--20023530 Score: 421
Period size: 62 Copynumber: 4.7 Consensus size: 62
20023228 CAATGTACCT
*
20023238 AATTTATATTACAAAGTTTGTTCCAA---TTAATGTTGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
* *
20023297 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTTTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
*
20023359 AATTTATATTACAAGGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
* * *
20023421 AACTTATATTATAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATTACAAAGA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATA-TA-ACA-A
* * * * *
20023486 AATTTTATATTATAAATTTTGTTACAAGTTTTAGTGTTTTAATGT
1 AA-TTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGT
20023531 TGTAATGTTG
Statistics
Matches: 214, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
59 26 0.12
62 144 0.67
63 2 0.01
64 2 0.01
65 3 0.01
66 37 0.17
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
Found at i:20024111 original size:18 final size:18
Alignment explanation
Indices: 20024090--20024143 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
20024080 GCTAGGGGTG
*
20024090 TGGCTCGAGCTTTGGCTC
1 TGGCTCGAGCTCTGGCTC
* * *
20024108 TGGCTTGGGCTCTGGTTC
1 TGGCTCGAGCTCTGGCTC
20024126 TGGCTCTG-GCTCTGGCTC
1 TGGCTC-GAGCTCTGGCTC
20024144 GGCCTCTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.02, C:0.28, G:0.35, T:0.35
Consensus pattern (18 bp):
TGGCTCGAGCTCTGGCTC
Found at i:20024127 original size:6 final size:6
Alignment explanation
Indices: 20024102--20024143 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
20024092 GCTCGAGCTT
*
20024102 TGGCTC TGGCT- TGGGCTC TGGTTC TGGCTC TGGCTC TGGCTC
1 TGGCTC TGGCTC T-GGCTC TGGCTC TGGCTC TGGCTC TGGCTC
20024144 GGCCTCTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 30 0.94
7 1 0.03
ACGTcount: A:0.00, C:0.29, G:0.36, T:0.36
Consensus pattern (6 bp):
TGGCTC
Found at i:20024803 original size:14 final size:14
Alignment explanation
Indices: 20024784--20024818 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
20024774 CAAATTACAT
20024784 GTTAGAATAGTATC
1 GTTAGAATAGTATC
20024798 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
20024812 ATTAGAA
1 GTTAGAA
20024819 AAAAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:20027282 original size:52 final size:50
Alignment explanation
Indices: 20027220--20027316 Score: 167
Period size: 50 Copynumber: 1.9 Consensus size: 50
20027210 ATAATTCTTG
*
20027220 CAACATGCCATTTAGGTTTTTTTAAAAAAAATATTATTTGGGTAAAAAAACC
1 CAACATGCCATTTAGG-GTTTTT-AAAAAAATATTATTTGGGTAAAAAAACC
20027272 CAACATGCCATTTAGGGTTTTTAAAAAAATATTATTTGGGTAAAA
1 CAACATGCCATTTAGGGTTTTTAAAAAAATATTATTTGGGTAAAA
20027317 CACCCCGTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 23 0.52
51 5 0.11
52 16 0.36
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (50 bp):
CAACATGCCATTTAGGGTTTTTAAAAAAATATTATTTGGGTAAAAAAACC
Found at i:20028873 original size:25 final size:24
Alignment explanation
Indices: 20028839--20028891 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
20028829 ATATGGAAAG
*
20028839 AAATAACAAAGATTTTTATACTAAT
1 AAATAACAAAGA-TATTATACTAAT
* * *
20028864 AAATATCAAATATATTATGCTAAT
1 AAATAACAAAGATATTATACTAAT
20028888 AAAT
1 AAAT
20028892 GCTAAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.36
Consensus pattern (24 bp):
AAATAACAAAGATATTATACTAAT
Found at i:20028886 original size:24 final size:24
Alignment explanation
Indices: 20028854--20028906 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
20028844 ACAAAGATTT
* *
20028854 TTATACTAATAAAT-ATCAAATATA
1 TTATGCTAATAAATGCT-AAATATA
20028878 TTATGCTAATAAATGCTAAATATA
1 TTATGCTAATAAATGCTAAATATA
20028902 TTATG
1 TTATG
20028907 TTAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (24 bp):
TTATGCTAATAAATGCTAAATATA
Found at i:20029573 original size:12 final size:12
Alignment explanation
Indices: 20029551--20029587 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
20029541 AGATCATCAA
20029551 AACTTTCATCTTC
1 AACTTT-ATCTTC
*
20029564 ATCTTTATCTTC
1 AACTTTATCTTC
20029576 AACTTTATCTTC
1 AACTTTATCTTC
20029588 TCAATCGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (12 bp):
AACTTTATCTTC
Found at i:20039589 original size:28 final size:29
Alignment explanation
Indices: 20039558--20039617 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
20039548 CCTAAACCTT
20039558 AAAATCCTAAACCCAAATTTA-ATTTTCA
1 AAAATCCTAAACCCAAATTTATATTTTCA
* *
20039586 AAAATCCTAAACCCTAATTTATTTTTTCA
1 AAAATCCTAAACCCAAATTTATATTTTCA
20039615 AAA
1 AAA
20039618 GCCTTACCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATCCTAAACCCAAATTTATATTTTCA
Found at i:20039604 original size:79 final size:78
Alignment explanation
Indices: 20039472--20039617 Score: 220
Period size: 79 Copynumber: 1.9 Consensus size: 78
20039462 ACCTATTAAA
* * * *
20039472 AAACCCTAAAATCCTAAACCCATATTTATTTTTTAAAAAACATAAACCTTAATTTATTTTTTTCA
1 AAACCCTAAAATCCTAAACCCAAATTTAATTTTCAAAAAACATAAACCCTAATTTA-TTTTTTCA
20039537 AAAACCCTAACCCT
65 AAAACCCTAACCCT
* * *
20039551 AAACCTTAAAATCCTAAACCCAAATTTAATTTTCAAAAATCCTAAACCCTAATTTATTTTTTCAA
1 AAACCCTAAAATCCTAAACCCAAATTTAATTTTCAAAAAACATAAACCCTAATTTATTTTTTCAA
20039616 AA
66 AA
20039618 GCCTTACCCA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
78 11 0.18
79 49 0.82
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (78 bp):
AAACCCTAAAATCCTAAACCCAAATTTAATTTTCAAAAAACATAAACCCTAATTTATTTTTTCAA
AAACCCTAACCCT
Found at i:20039822 original size:26 final size:27
Alignment explanation
Indices: 20039793--20039849 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 27
20039783 CGTTTTGAGT
*
20039793 TTTTTAGT-CCATTT-CAGTAAATAATA
1 TTTTAAGTGCCATTTCCA-TAAATAATA
20039819 TTTTAAGTGGCCCATTTCCATAAATAATA
1 TTTTAAGT-G-CCATTTCCATAAATAATA
20039848 TT
1 TT
20039850 AGAAATCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 7 0.27
29 17 0.65
30 2 0.08
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (27 bp):
TTTTAAGTGCCATTTCCATAAATAATA
Found at i:20040002 original size:14 final size:14
Alignment explanation
Indices: 20039983--20040012 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20039973 GTTTGACCAA
20039983 AAGAATTCATTTTC
1 AAGAATTCATTTTC
20039997 AAGAATTCATTTTC
1 AAGAATTCATTTTC
20040011 AA
1 AA
20040013 AAACACGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (14 bp):
AAGAATTCATTTTC
Found at i:20040126 original size:16 final size:16
Alignment explanation
Indices: 20040105--20040137 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20040095 GGTCAGCCTC
*
20040105 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
20040121 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
20040137 T
1 T
20040138 TCTCTTCGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:20045294 original size:20 final size:19
Alignment explanation
Indices: 20045239--20045308 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 19
20045229 GAATAATTAG
* *
20045239 ATACCAAAATTTCTAATCA
1 ATACCAAAATTTTTAATGA
* ** * *
20045258 TTATTAAAACTTGTAATGAA
1 ATACCAAAATTTTTAATG-A
* *
20045278 ATATCAAAATTTTTAATGG
1 ATACCAAAATTTTTAATGA
20045297 ATACCAAAATTT
1 ATACCAAAATTT
20045309 CAAACTAAAT
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
19 23 0.61
20 15 0.39
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (19 bp):
ATACCAAAATTTTTAATGA
Found at i:20054364 original size:16 final size:17
Alignment explanation
Indices: 20054334--20054373 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
20054324 TTGGATCCAG
20054334 AAAGCAAAAATGAAAAAA
1 AAAG-AAAAATGAAAAAA
*
20054352 AAAGAAAAA-GAAAAAG
1 AAAGAAAAATGAAAAAA
20054368 AAAGAA
1 AAAGAA
20054374 CAGAGAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
17 5 0.24
18 4 0.19
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAGAAAAATGAAAAAA
Found at i:20055788 original size:17 final size:16
Alignment explanation
Indices: 20055766--20055829 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 16
20055756 TTAAGGAGAT
20055766 AAAAATAAATAAATAAC
1 AAAAATAAATAAAT-AC
20055783 AAAAATAAATAAATAC
1 AAAAATAAATAAATAC
*
20055799 GAAAAATAAACAAATGAC
1 -AAAAATAAATAAAT-AC
* *
20055817 TAAAATCAATAAA
1 AAAAATAAATAAA
20055830 CCAATCAGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
16 2 0.05
17 37 0.90
18 2 0.05
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAATAAATAAATAC
Found at i:20059964 original size:35 final size:35
Alignment explanation
Indices: 20059924--20059997 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
20059914 CCATAAAACA
*
20059924 CCAATGCTTATAAGAGCTAATCTAACCGAAACACG
1 CCAATGCTCATAAGAGCTAATCTAACCGAAACACG
*
20059959 CCAATGCTCATAAGAGCTAATCTAACCGAAATACG
1 CCAATGCTCATAAGAGCTAATCTAACCGAAACACG
20059994 CCAA
1 CCAA
20059998 ATAGAGAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.19
Consensus pattern (35 bp):
CCAATGCTCATAAGAGCTAATCTAACCGAAACACG
Found at i:20068353 original size:20 final size:20
Alignment explanation
Indices: 20068315--20068354 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20068305 AATATTTTTC
* *
20068315 AGTAAATCATTTTATAGAAA
1 AGTAAAACATTTTACAGAAA
*
20068335 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
20068355 TCATTTTACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:20068356 original size:34 final size:35
Alignment explanation
Indices: 20068303--20068369 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
20068293 CAAACACCAG
* * *
20068303 AAAATATTTTTCAGTAAATCATTTTATAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
20068338 AAAACATTTTCCAG-AAATCATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
20068370 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:20068361 original size:14 final size:14
Alignment explanation
Indices: 20068338--20068377 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
20068328 ATAGAAAAGT
*
20068338 AAAACATTTTCCAG
1 AAAACATTTTACAG
*
20068352 AAATCATTTTACAG
1 AAAACATTTTACAG
20068366 AAAACATTTTAC
1 AAAACATTTTAC
20068378 TGGCAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:20075924 original size:43 final size:41
Alignment explanation
Indices: 20075843--20075968 Score: 130
Period size: 43 Copynumber: 2.9 Consensus size: 41
20075833 AGGATTCCGT
20075843 TATGTGTTATCGTGTAAGACCACGTCTAGGACGTTGGCATCGAC
1 TATGTGTTA-CGTGTAAGA-CACGTCTAGGACGTTGGCATCG-C
* *
20075887 T-TGTGTTTACGTGTAAGACACTGTCTGGGACAG-TGGCATCGT
1 TATGTG-TTACGTGTAAGACAC-GTCTAGGAC-GTTGGCATCGC
* *
20075929 TATGTGATTACGTGTAAGACAACATCTGGGACGTTGGCAT
1 TATGTG-TTACGTGTAAGAC-ACGTCTAGGACGTTGGCAT
20075969 TGTACGATAT
Statistics
Matches: 72, Mismatches: 4, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
42 5 0.07
43 60 0.83
44 7 0.10
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (41 bp):
TATGTGTTACGTGTAAGACACGTCTAGGACGTTGGCATCGC
Found at i:20085363 original size:13 final size:13
Alignment explanation
Indices: 20085345--20085369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20085335 AATATATAAA
20085345 AAAACAAAAAAAC
1 AAAACAAAAAAAC
20085358 AAAACAAAAAAA
1 AAAACAAAAAAA
20085370 TTTGCAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAC
Found at i:20085450 original size:27 final size:27
Alignment explanation
Indices: 20085420--20085486 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
20085410 CGCCAATGGT
20085420 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* *
20085447 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
20085474 ATTGGCGGCACCA
1 ATTGGCGGCACCA
20085487 GTTAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:20085537 original size:4 final size:4
Alignment explanation
Indices: 20085528--20085657 Score: 85
Period size: 4 Copynumber: 32.0 Consensus size: 4
20085518 GAAGGAGAGG
* *
20085528 GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
* *
20085576 GAAAA GGAAA G-GA GAAGA GAAA AAAA GAAA G-AA G-AA G-AA GAAAA
1 G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
*
20085620 GGAAAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 -G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
20085658 AGGAAAGGAG
Statistics
Matches: 103, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
3 18 0.17
4 57 0.55
5 21 0.20
6 7 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:20085557 original size:18 final size:19
Alignment explanation
Indices: 20085530--20085687 Score: 116
Period size: 18 Copynumber: 8.2 Consensus size: 19
20085520 AGGAGAGGGA
*
20085530 AAGAAAGAAAGAAAGAAAG
1 AAGAAGGAAAGAAAGAAAG
*
20085549 GAG-AGGAAAGAAAGAAA-
1 AAGAAGGAAAGAAAGAAAG
20085566 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAG-AAA-GAAAG
* *
20085587 GAGAAGAGAAAAAAAGAAAG
1 AAGAAG-GAAAGAAAGAAAG
20085607 AAGAA-G-AAGAAAAGGAAA-
1 AAGAAGGAAAG-AAA-GAAAG
20085625 AGAGAA-GAAA-AAAGAAAG
1 A-AGAAGGAAAGAAAGAAAG
20085643 AAAGAAGGAAAGAAAAGGAAAG
1 -AAGAAGGAAAG-AAA-GAAAG
* *
20085665 GAGAAGAGAAA-AAAAAAAG
1 AAGAAG-GAAAGAAAGAAAG
20085684 AAGA
1 AAGA
20085688 GGAGGGAAGG
Statistics
Matches: 113, Mismatches: 10, Indels: 32
0.73 0.06 0.21
Matches are distributed among these distances:
17 8 0.07
18 32 0.28
19 26 0.23
20 18 0.16
21 16 0.14
22 13 0.12
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAGAAGGAAAGAAAGAAAG
Found at i:20085630 original size:39 final size:39
Alignment explanation
Indices: 20085544--20085687 Score: 190
Period size: 39 Copynumber: 3.7 Consensus size: 39
20085534 AAGAAAGAAA
*
20085544 GAAAGGAG-AG-GAAAGAAAGAAA-AAGAAGGAAAGAAAAG
1 GAAAGGAGAAGAGAAAAAAAGAAAGAAGAA-G-AAGAAAAG
20085582 GAAAGGAGAAGAGAAAAAAAGAAAGAAGAAGAAGAAAAG
1 GAAAGGAGAAGAGAAAAAAAGAAAGAAGAAGAAGAAAAG
* * *
20085621 GAAAAGAGAAGAAAAAAGAAAGAAAGAAGGA-AAGAAAAG
1 GAAAGGAGAAGAGAAAA-AAAGAAAGAAGAAGAAGAAAAG
20085660 GAAAGGAGAAGAGAAAAAAA-AAAGAAGA
1 GAAAGGAGAAGAGAAAAAAAGAAAGAAGA
20085688 GGAGGGAAGG
Statistics
Matches: 95, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
37 7 0.07
38 11 0.12
39 48 0.51
40 24 0.25
41 5 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (39 bp):
GAAAGGAGAAGAGAAAAAAAGAAAGAAGAAGAAGAAAAG
Found at i:20086880 original size:162 final size:162
Alignment explanation
Indices: 20086711--20087218 Score: 537
Period size: 162 Copynumber: 3.2 Consensus size: 162
20086701 AAGAAAATGT
20086711 ACTGAAATAATATAAAACAATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCG
1 ACTGAAATAATATAAAACAATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCG
20086776 AGAAAATAATACGAGCAAAGGGCAGGGGTAAGGGTTATTTTTTTACACCAAATTAATTTAAATAA
66 AGAAAATAATACGAGCAAAGGGCAGGGGTAAGGGTTATTTTTTTACACCAAATTAATTTAAATAA
20086841 CACACTAGAGTAATAAATTTCAAACATTATGC
131 CACACTAGAGTAATAAATTTCAAACATTATGC
* ** *
20086873 ACTGAAATAATGTAAAATTATAAAATTA-GA-AAT--TATGATATTT-TTTAAAGTAAT-AAAAT
1 ACTGAAATAATATAAAACAATAAAA-TACGAGAATAATAT-ATTTTTATTTAAAGTAATAAAAAT
* * ** * *
20086932 GCGGAGAGAAA-AATACGAACAAATGGCAGAAGTAAGAGTGTATTACTAACTTTTATA--AAATT
64 -C-GAGA-AAATAATACGAGCAAAGGGCAGGGGTAAGGGT-TATT--T---TTTTACACCAAATT
* * * * * * ** *
20086994 CA--GAAATAATTA-A-TACA--AA-ATATTTCAAAGAAAATGT
120 AATTTAAATAA-CACACTAGAGTAATAAATTTCAAACATTATGC
20087031 ACTGAAATAATATAAAACAATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCG
1 ACTGAAATAATATAAAACAATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCG
* * * * *
20087096 AGAAAATAATACGAG-TAAGAGACAGGGTTAAGGGTTATTTTTTGACACCAAAATAATTTAAATA
66 AGAAAATAATACGAGCAAAG-GGCAGGGGTAAGGGTTATTTTTTTACACCAAATTAATTTAAATA
20087160 ACACACTAGAGTAATAAATTTCAAACATTATGC
130 ACACACTAGAGTAATAAATTTCAAACATTATGC
* **
20087193 ACTGAAATAATGTAAAATTATAAAAT
1 ACTGAAATAATATAAAACAATAAAAT
20087219 TAGAAATTTT
Statistics
Matches: 271, Mismatches: 46, Indels: 58
0.72 0.12 0.15
Matches are distributed among these distances:
154 5 0.02
156 5 0.02
157 4 0.01
158 49 0.18
159 32 0.12
160 58 0.21
161 30 0.11
162 72 0.27
163 4 0.01
164 6 0.02
166 6 0.02
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (162 bp):
ACTGAAATAATATAAAACAATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCG
AGAAAATAATACGAGCAAAGGGCAGGGGTAAGGGTTATTTTTTTACACCAAATTAATTTAAATAA
CACACTAGAGTAATAAATTTCAAACATTATGC
Found at i:20087100 original size:320 final size:320
Alignment explanation
Indices: 20086530--20087305 Score: 1331
Period size: 320 Copynumber: 2.4 Consensus size: 320
20086520 CACAGTAAAT
* * **
20086530 TAATAAATTTCAAACATGATGCACTGAAATAATGTAAAATTATAAAAGACTA-AGTTTATGATAT
1 TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTAT-AAA-ATTAGAAATTATGATAT
** *
20086594 TTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGAAAAAAGTAAGAGTGTATTACT
64 TTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCAGAAGTAAGAGTGTATTACT
20086659 AACTTTTATAAAATTCAAAAATAATTAATACAAAATATTTCAAAGAAAATGTACTGAAATAATAT
129 AACTTTTATAAAATTCAAAAATAATTAATACAAAATATTTCAAAGAAAATGTACTGAAATAATAT
20086724 AAAACAATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCGAGAAAATAATACG
194 AAAACAATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCGAGAAAATAATACG
* * *
20086789 AGCAAAG-GGCAGGGGTAAGGGTTATTTTTTTACACCAAATTAATTTAAATAACACACTAGAG
259 AG-AAAGAGACAGGGGTAAGGGTTATTTTTTGACACCAAAATAATTTAAATAACACACTAGAG
20086851 TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATTT
1 TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATTT
*
20086916 TTTAAAGTAATAAAATGCGGAGAGAAAAATACGAACAAATGGCAGAAGTAAGAGTGTATTACTAA
66 TTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCAGAAGTAAGAGTGTATTACTAA
*
20086981 CTTTTATAAAATTCAGAAATAATTAATACAAAATATTTCAAAGAAAATGTACTGAAATAATATAA
131 CTTTTATAAAATTCAAAAATAATTAATACAAAATATTTCAAAGAAAATGTACTGAAATAATATAA
20087046 AACAATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCGAGAAAATAATACGAG
196 AACAATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCGAGAAAATAATACGAG
* *
20087111 TAAGAGACAGGGTTAAGGGTTATTTTTTGACACCAAAATAATTTAAATAACACACTAGAG
261 AAAGAGACAGGGGTAAGGGTTATTTTTTGACACCAAAATAATTTAAATAACACACTAGAG
*
20087171 TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTTTGATATTT
1 TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATTT
* * * * *
20087236 TTTAAAGTAATAAAATGCGGAGAAAAAAATACGAATAAATGGCTGAAGTAAGATTTTTTTACTAA
66 TTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCAGAAGTAAGAGTGTATTACTAA
20087301 CTTTT
131 CTTTT
20087306 TTTTCAACTT
Statistics
Matches: 432, Mismatches: 21, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
319 6 0.01
320 384 0.89
321 42 0.10
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.30
Consensus pattern (320 bp):
TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATTT
TTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCAGAAGTAAGAGTGTATTACTAA
CTTTTATAAAATTCAAAAATAATTAATACAAAATATTTCAAAGAAAATGTACTGAAATAATATAA
AACAATAAAATACGAGAATAATATATTTTTATTTAAAGTAATAAAAATCGAGAAAATAATACGAG
AAAGAGACAGGGGTAAGGGTTATTTTTTGACACCAAAATAATTTAAATAACACACTAGAG
Found at i:20087236 original size:162 final size:159
Alignment explanation
Indices: 20086530--20087269 Score: 527
Period size: 160 Copynumber: 4.6 Consensus size: 159
20086520 CACAGTAAAT
* * **
20086530 TAATAAATTTCAAACATGATGCACTGAAATAATGTAAAATTATAAAAGACTA-AGTTTATGATAT
1 TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTAT-AAA-ATTAGAAATTATGATAT
* * *** ** * **
20086594 TTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGAAAAAAGTAAGAGTGTA-TTAC
64 TTTTTAAAGTAATAAAATGCGGAGAAAATAATACGAGCAAA-GGGCAGGGTAAGGGT-TATTTTT
*** * * * *
20086658 TAACTTTTATAA-AATTCAAA-AATA-ATTA-A-
127 TAAC-ACCAAAATAATTTAAATAACACACTAGAG
* * ** * * **
20086687 TACAAAATATTTCAAAGAAAATGTACTGAAATAATATAAAACAATAAAA-TACGAGAATAATAT-
1 TA-ATAA-ATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTA-GA-AAT--TATG
*
20086750 ATTTTTATTTAAAGTAATAAAAAT-C-GAGAAAATAATACGAGCAAAGGGCAGGGGTAAGGGTTA
60 ATATTT-TTTAAAGTAAT-AAAATGCGGAGAAAATAATACGAGCAAAGGGCA-GGGTAAGGGTTA
* *
20086813 TTTTTTTACACCAAATTAATTTAAATAACACACTAGAG
122 TTTTTTAACACCAAAATAATTTAAATAACACACTAGAG
20086851 TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATTT
1 TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATTT
* * * * **
20086916 TTTAAAGTAATAAAATGCGGAGAGAAA-AATACGAACAAATGGCAGAAGTAAGAGTGTA-TTACT
66 TTTAAAGTAATAAAATGCGGAGA-AAATAATACGAGCAAAGGGCAG-GGTAAGGGT-TATTTTTT
*** * * * * *
20086979 AACTTTTATAA-AATTCAGA-AATA-ATTA-A-
128 AAC-ACCAAAATAATTTAAATAACACACTAGAG
* * ** * * **
20087007 TACAAAATATTTCAAAGAAAATGTACTGAAATAATATAAAACAATAAAA-TACGAGAATAATAT-
1 TA-ATAA-ATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTA-GA-AAT--TATG
* * *
20087070 ATTTTTATTTAAAGTAATAAAAAT-C-GAGAAAATAATACGAG-TAAGAGACAGGGTTAAGGGTT
60 ATATTT-TTTAAAGTAAT-AAAATGCGGAGAAAATAATACGAGCAAAG-GGCAGGG-TAAGGGTT
*
20087132 ATTTTTTGACACCAAAATAATTTAAATAACACACTAGAG
121 ATTTTTTAACACCAAAATAATTTAAATAACACACTAGAG
*
20087171 TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTTTGATATTT
1 TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATTT
*
20087236 TTTAAAGTAATAAAATGCGGAGAAAAAAATACGA
66 TTTAAAGTAATAAAATGCGGAGAAAATAATACGA
20087270 ATAAATGGCT
Statistics
Matches: 446, Mismatches: 92, Indels: 87
0.71 0.15 0.14
Matches are distributed among these distances:
156 4 0.01
157 9 0.02
158 56 0.13
159 84 0.19
160 140 0.31
161 49 0.11
162 88 0.20
163 12 0.03
164 4 0.01
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (159 bp):
TAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATGATATTT
TTTAAAGTAATAAAATGCGGAGAAAATAATACGAGCAAAGGGCAGGGTAAGGGTTATTTTTTAAC
ACCAAAATAATTTAAATAACACACTAGAG
Found at i:20092571 original size:3 final size:3
Alignment explanation
Indices: 20092563--20092600 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
20092553 TCTTAATACT
20092563 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
20092601 TAATAATACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:20092868 original size:27 final size:27
Alignment explanation
Indices: 20092822--20092922 Score: 116
Period size: 27 Copynumber: 3.7 Consensus size: 27
20092812 AATACGAATA
*
20092822 GTGCCGCCAAT--CAATATGGCATCATTG
1 GTGCCGCCAATGGC-AT-TGGCACCATTG
20092849 GTGCCGCCAATGGCATTGGCACCATTG
1 GTGCCGCCAATGGCATTGGCACCATTG
* ** *
20092876 GTGCCGCTAATGGTTTTGGCACCTTTG
1 GTGCCGCCAATGGCATTGGCACCATTG
*
20092903 GTGCCGCCAATGCCATTGGC
1 GTGCCGCCAATGGCATTGGC
20092923 GTGACCAAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
27 60 0.95
28 2 0.03
29 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.27
Consensus pattern (27 bp):
GTGCCGCCAATGGCATTGGCACCATTG
Found at i:20093000 original size:26 final size:28
Alignment explanation
Indices: 20092971--20093042 Score: 96
Period size: 26 Copynumber: 2.6 Consensus size: 28
20092961 CAGGTTTTTT
20092971 TTATATATATTTTGGTAAAT-AAAAAA-
1 TTATATATATTTTGGTAAATAAAAAAAG
* *
20092997 TTATATATTTTTTGGAAAATAAAAAAAAG
1 TTATATATATTTTGGTAAAT-AAAAAAAG
20093026 TTATA-ATATTTTGGTAA
1 TTATATATATTTTGGTAA
20093043 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 18 0.46
28 16 0.41
29 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (28 bp):
TTATATATATTTTGGTAAATAAAAAAAG
Found at i:20093537 original size:3 final size:3
Alignment explanation
Indices: 20093529--20093563 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20093519 TCGCAAAAAG
20093529 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20093564 GTAGAAGAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20093765 original size:3 final size:3
Alignment explanation
Indices: 20093759--20093811 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
20093749 CTCCTCCTCC
* * *
20093759 TCT TCT T-T TTT TCT TCT TCT TTT TCT TCT TCT TCT TCT T-T GCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
20093805 TTT TCT T
1 TCT TCT T
20093812 TTGCTGCCGA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
2 3 0.07
3 38 0.93
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.74
Consensus pattern (3 bp):
TCT
Found at i:20093791 original size:26 final size:26
Alignment explanation
Indices: 20093759--20093811 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
20093749 CTCCTCCTCC
*
20093759 TCTTCTT-TTTTTC-TT-CTTCTTTT
1 TCTTCTTCTTCTTCTTTGCTTCTTTT
20093782 TCTTCTTCTTCTTCTTTGCTTCTTTT
1 TCTTCTTCTTCTTCTTTGCTTCTTTT
20093808 TCTT
1 TCTT
20093812 TTGCTGCCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 7 0.27
24 5 0.19
25 2 0.08
26 12 0.46
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.74
Consensus pattern (26 bp):
TCTTCTTCTTCTTCTTTGCTTCTTTT
Done.