Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001680.1 Hibiscus syriacus cultivar Beakdansim tig00003358_pilon, whole genome shotgun sequence
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: 103449
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6057 original size:31 final size:31
Alignment explanation
Indices: 5978--6067 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
5968 GGTTCATTTC
* * *
5978 ATCTTTTTGTTCGATTTTTTTTTAATTCCATA
1 ATCTTTTTATTCGA-ATTTTTTTAATTCCTTA
*
6010 A-C--CTTATTCGAA-TTTTTTAATTCCTTA
1 ATCTTTTTATTCGAATTTTTTTAATTCCTTA
*
6037 ATCTTTTTCTTCGAATTTTTTTAATTCCTTA
1 ATCTTTTTATTCGAATTTTTTTAATTCCTTA
6068 TTCCTATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
27 15 0.31
28 1 0.02
29 7 0.15
30 8 0.17
31 16 0.33
32 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.04, T:0.59
Consensus pattern (31 bp):
ATCTTTTTATTCGAATTTTTTTAATTCCTTA
Found at i:8153 original size:26 final size:26
Alignment explanation
Indices: 8117--8169 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
8107 CGCTAGACAC
*
8117 TAGACCTGAATCCAGGAGATCACATG
1 TAGACCCGAATCCAGGAGATCACATG
*
8143 TAGACCCGAATCCAGGAGGTCACATG
1 TAGACCCGAATCCAGGAGATCACATG
8169 T
1 T
8170 CGTATACAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (26 bp):
TAGACCCGAATCCAGGAGATCACATG
Found at i:11096 original size:47 final size:47
Alignment explanation
Indices: 11037--11177 Score: 246
Period size: 47 Copynumber: 3.0 Consensus size: 47
11027 GATTCTCTTA
* * * *
11037 TCATTTCCTCTTTTGACAAACGTAAGAAATTATTTAGGTTAGACCAT
1 TCATGTCCTCTTTTAACAAATGTAAGAAATTATTAAGGTTAGACCAT
11084 TCATGTCCTCTTTTAACAAATGTAAGAAATTATTAAGGTTAGACCAT
1 TCATGTCCTCTTTTAACAAATGTAAGAAATTATTAAGGTTAGACCAT
11131 TCATGTCCTCTTTTAACAAATGTAAGAAATTATTAAGGTTAGACCAT
1 TCATGTCCTCTTTTAACAAATGTAAGAAATTATTAAGGTTAGACCAT
11178 ATAAAATTAT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 90 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (47 bp):
TCATGTCCTCTTTTAACAAATGTAAGAAATTATTAAGGTTAGACCAT
Found at i:11212 original size:19 final size:19
Alignment explanation
Indices: 11176--11214 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11166 AGGTTAGACC
*
11176 ATATAAAATTATAAGTTTA
1 ATATAAAAATATAAGTTTA
11195 ATATAAAAATA-AATGTTTA
1 ATATAAAAATATAA-GTTTA
11214 A
1 A
11215 ATTATACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
ATATAAAAATATAAGTTTA
Found at i:19229 original size:21 final size:23
Alignment explanation
Indices: 19203--19245 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
19193 GTCTCGTGTC
19203 TCATTTT-TTTTT-TATAAATTA
1 TCATTTTATTTTTATATAAATTA
19224 TCATTTTATTTTTATATAAATT
1 TCATTTTATTTTTATATAAATT
19246 TAGTTAACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (23 bp):
TCATTTTATTTTTATATAAATTA
Found at i:21631 original size:20 final size:21
Alignment explanation
Indices: 21606--21646 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
21596 TGAGAGATAA
*
21606 ATTTATTATTATGATT-TTTT
1 ATTTATTATTAAGATTATTTT
*
21626 ATTTATTTTTAAGATTATTTT
1 ATTTATTATTAAGATTATTTT
21647 GTAAACGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
ATTTATTATTAAGATTATTTT
Found at i:27299 original size:28 final size:28
Alignment explanation
Indices: 27264--27323 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
27254 CAGAATATAC
*
27264 TCAACATCCTCCCTGATGCTTCAACTCT
1 TCAACATCCTCCCTGATGCTCCAACTCT
* *
27292 TCAACATCCTTCCTGCTGCTCCAACTCT
1 TCAACATCCTCCCTGATGCTCCAACTCT
27320 TCAA
1 TCAA
27324 AGCAAGAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.40, G:0.07, T:0.32
Consensus pattern (28 bp):
TCAACATCCTCCCTGATGCTCCAACTCT
Found at i:33355 original size:23 final size:24
Alignment explanation
Indices: 33318--33362 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
33308 ATTAAGATTA
33318 ATTATTAAAAATAAAACTATTAAG
1 ATTATTAAAAATAAAACTATTAAG
*
33342 ATTATT-AAAATAAAATTATTA
1 ATTATTAAAAATAAAACTATTA
33363 TAAATTACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTATTAAAAATAAAACTATTAAG
Found at i:33356 original size:28 final size:27
Alignment explanation
Indices: 33302--33357 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
33292 ACTGGCATTT
**
33302 TAAAATATTAAGATTAATTATTAAAAA
1 TAAAATATTAAGATTAATTAAAAAAAA
33329 TAAAACTATTAAGATT-ATTAAAATAAAA
1 TAAAA-TATTAAGATTAATTAAAA-AAAA
33357 T
1 T
33358 TATTATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (27 bp):
TAAAATATTAAGATTAATTAAAAAAAA
Found at i:33369 original size:24 final size:24
Alignment explanation
Indices: 33317--33369 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
33307 TATTAAGATT
33317 AATTATTAAAAATAAAACTATTAA
1 AATTATTAAAAATAAAACTATTAA
* *
33341 GATTATT-AAAATAAAATTATTATA
1 AATTATTAAAAATAAAACTATTA-A
33365 AATTA
1 AATTA
33370 CATTAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AATTATTAAAAATAAAACTATTAA
Found at i:33395 original size:19 final size:18
Alignment explanation
Indices: 33347--33398 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
33337 TTAAGATTAT
33347 TAAAATAA-AATTA-TTA
1 TAAAATAATAATTATTTA
*
33363 TAAATTACATTAATTATTTA
1 TAAAATA-A-TAATTATTTA
33383 CTAAAATAATAATTAT
1 -TAAAATAATAATTAT
33399 ATATTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 6 0.21
17 1 0.03
19 12 0.41
20 4 0.14
21 6 0.21
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATAATAATTATTTA
Found at i:33411 original size:42 final size:40
Alignment explanation
Indices: 33350--33448 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 40
33340 AGATTATTAA
* *
33350 AATAAAATTATTATAAATTACATTAATTATTTACTAAAAT
1 AATAATATTATTATAAATTACATTAATTAATTACTAAAAT
* * * *
33390 AATAATTATATATTATTAATTATATTAATTAATTATTCAAAT
1 AATAA-TAT-TATTATAAATTACATTAATTAATTACTAAAAT
33432 AATAATATTATTA-AAAT
1 AATAATATTATTATAAAT
33449 ATTAAAAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
39 3 0.06
40 10 0.20
41 5 0.10
42 32 0.64
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (40 bp):
AATAATATTATTATAAATTACATTAATTAATTACTAAAAT
Found at i:33426 original size:23 final size:22
Alignment explanation
Indices: 33356--33426 Score: 58
Period size: 23 Copynumber: 3.3 Consensus size: 22
33346 TTAAAATAAA
* *
33356 ATTATTATAAATTACATTAATT
1 ATTATTATTAATTATATTAATT
* * *
33378 A-T-TTACTAA-AATAATAATT
1 ATTATTATTAATTATATTAATT
33397 ATATATTATTAATTATATTAATT
1 AT-TATTATTAATTATATTAATT
33420 AATTATT
1 -ATTATT
33427 CAAATAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
19 8 0.22
20 5 0.14
21 2 0.06
22 7 0.19
23 12 0.33
24 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTATTATTAATTATATTAATT
Found at i:33464 original size:15 final size:15
Alignment explanation
Indices: 33441--33470 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33431 TAATAATATT
33441 ATTAAAATATTAAAA
1 ATTAAAATATTAAAA
*
33456 ATTATAATATTAAAA
1 ATTAAAATATTAAAA
33471 CAAAAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAAAATATTAAAA
Found at i:33972 original size:31 final size:31
Alignment explanation
Indices: 33937--34021 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 31
33927 TATTTCGTCG
* *
33937 TTAGTACATAAACTATCAATTTTGGTTTGTT
1 TTAGTACATAAACTATCAATTTTGGTCTATT
33968 TTAGTATC-TAAACTAT-AATTTTTGGTCTATT
1 TTAGTA-CATAAACTATCAA-TTTTGGTCTATT
* *
33999 TTAGTACATAAACTTTCATTTTT
1 TTAGTACATAAACTATCAATTTT
34022 TTTTCAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 3 0.07
31 41 0.89
32 2 0.04
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (31 bp):
TTAGTACATAAACTATCAATTTTGGTCTATT
Found at i:37783 original size:22 final size:23
Alignment explanation
Indices: 37753--37796 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
37743 TTTATTTATT
37753 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
37776 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
37797 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:37790 original size:31 final size:30
Alignment explanation
Indices: 37745--37914 Score: 104
Period size: 31 Copynumber: 5.7 Consensus size: 30
37735 AAATATTATT
*
37745 TATT-TATTTATTAATATTTATAATAATATAA
1 TATTATATTT-TTAATA-ATATAATAATATAA
* *
37776 TATTATATTTTTAATATTAT-ATAAAATAA
1 TATTATATTTTTAATAATATAATAATATAA
* * *
37805 TCAATTATA-TTATAATAATATAA-GATATTA
1 T--ATTATATTTTTAATAATATAATAATATAA
* *
37835 TATT-TTTATTTTAATAATAT-ATAATAAAAA
1 TATTATAT-TTTTAATAATATAATAAT-ATAA
* * * *
37865 AATTTATATATTTAATAAT-GAATAATATTA
1 TA-TTATATTTTTAATAATATAATAATATAA
37895 T-TTATATATTTTAATAATAT
1 TATTATAT-TTTTAATAATAT
37915 TTTAATAAAG
Statistics
Matches: 106, Mismatches: 20, Indels: 27
0.69 0.13 0.18
Matches are distributed among these distances:
27 1 0.01
28 10 0.09
29 31 0.29
30 24 0.23
31 33 0.31
32 7 0.07
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
TATTATATTTTTAATAATATAATAATATAA
Found at i:37872 original size:54 final size:51
Alignment explanation
Indices: 37760--37872 Score: 122
Period size: 54 Copynumber: 2.1 Consensus size: 51
37750 ATTTATTAAT
* **
37760 ATTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATT
1 ATTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAAAA
*
37811 ATATTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAAAAA
1 AT-TTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAAT-AAAAA
37866 ATTTATA
1 ATTTATA
37873 TATTTAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
51 2 0.04
52 16 0.31
53 7 0.13
54 23 0.44
55 4 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAAAA
Found at i:37880 original size:28 final size:29
Alignment explanation
Indices: 37849--37912 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
37839 TTTATTTTAA
37849 TAATATAT-AATAAAAAAATTTATATA-TT
1 TAATA-ATGAATAAAAAAATTTATATATTT
* **
37877 TAATAATGAATAATATTATTTATATATTT
1 TAATAATGAATAAAAAAATTTATATATTT
37906 TAATAAT
1 TAATAAT
37913 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 20 0.65
29 9 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TAATAATGAATAAAAAAATTTATATATTT
Found at i:37882 original size:24 final size:28
Alignment explanation
Indices: 37764--37913 Score: 94
Period size: 29 Copynumber: 5.1 Consensus size: 28
37754 ATTAATATTT
37764 ATAATAATATAATATTATAT-TTTTAATA
1 ATAATAATATAAT-TTATATATTTTAATA
* * ** *
37792 TTATATAAAATAATCAATTATATTATAATA
1 ATA-ATAATATAATTTA-TATATTTTAATA
37822 AT-ATAAGATATTATATTT-T-TATTTTAATA
1 ATAAT-A-ATA-TA-ATTTATATATTTTAATA
*
37851 ATATATAATAAAAAAATTTATATA-TTTAATA
1 ATA-ATAAT---ATAATTTATATATTTTAATA
*
37882 ATGAATAATATTATTTATATATTTTAATA
1 AT-AATAATATAATTTATATATTTTAATA
37911 ATA
1 ATA
37914 TTTTAATAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 32
0.67 0.09 0.23
Matches are distributed among these distances:
28 16 0.17
29 35 0.38
30 16 0.17
31 20 0.22
32 6 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
ATAATAATATAATTTATATATTTTAATA
Found at i:37892 original size:19 final size:19
Alignment explanation
Indices: 37870--37922 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
37860 AAAAAAATTT
37870 ATATATTTAATAATGAATA
1 ATATATTTAATAATGAATA
* *
37889 ATATTATTTATATATTTTAATA
1 ATA-TATTTA-ATA-ATGAATA
37911 ATAT-TTTAATAA
1 ATATATTTAATAA
37923 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATATTTAATAATGAATA
Found at i:37930 original size:14 final size:11
Alignment explanation
Indices: 37885--37922 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
37875 TTTAATAATG
37885 AATAATATTATT
1 AATAATATT-TT
*
37897 TAT-ATATTTT
1 AATAATATTTT
37907 AATAATATTTT
1 AATAATATTTT
37918 AATAA
1 AATAA
37923 AGATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.74
12 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATAATATTTT
Found at i:37943 original size:23 final size:23
Alignment explanation
Indices: 37917--37961 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
37907 AATAATATTT
37917 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
37940 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
37962 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:38039 original size:29 final size:29
Alignment explanation
Indices: 38005--38062 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
37995 TAATTTATAA
*
38005 TATTTTATT-TTACTAAAATATATAAAAAT
1 TATTTTATTATTAATAAAAT-TATAAAAAT
*
38034 TATTTTTTTATTAATAAAATTATAAAAAT
1 TATTTTATTATTAATAAAATTATAAAAAT
38063 AATATTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
TATTTTATTATTAATAAAATTATAAAAAT
Found at i:38341 original size:21 final size:21
Alignment explanation
Indices: 38315--38384 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
38305 AGAATTCAAA
38315 TTCCAGTAATTCATTTTCCAG
1 TTCCAGTAATTCATTTTCCAG
*
38336 TTCCAGTAATTCA------AA
1 TTCCAGTAATTCATTTTCCAG
38351 TTCCAGTAATTCATTTTCCAG
1 TTCCAGTAATTCATTTTCCAG
*
38372 TTCCAATAATTCA
1 TTCCAGTAATTCA
38385 AATTCCAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
15 14 0.35
21 26 0.65
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (21 bp):
TTCCAGTAATTCATTTTCCAG
Found at i:38348 original size:36 final size:36
Alignment explanation
Indices: 38307--38403 Score: 167
Period size: 36 Copynumber: 2.7 Consensus size: 36
38297 CATTTTCTAG
*
38307 AATTCAAATTCCAGTAATTCATTTTCCAGTTCCAGT
1 AATTCAAATTCCAGTAATTCATTTTCCAGTTCCAAT
38343 AATTCAAATTCCAGTAATTCATTTTCCAGTTCCAAT
1 AATTCAAATTCCAGTAATTCATTTTCCAGTTCCAAT
* *
38379 AATTCAAATTCCAATAATTTATTTT
1 AATTCAAATTCCAGTAATTCATTTT
38404 TCGAAAAACC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (36 bp):
AATTCAAATTCCAGTAATTCATTTTCCAGTTCCAAT
Found at i:38372 original size:15 final size:15
Alignment explanation
Indices: 38291--38336 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
38281 TTCCAGAAAT
*
38291 GTAATTCATTTTCTA
1 GTAATTCATTTTCCA
**
38306 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
38320 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
38335 GT
1 GT
38337 TCCAGTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:39687 original size:18 final size:19
Alignment explanation
Indices: 39652--39691 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
39642 ATTTAAAAAT
*
39652 TAAATTAATATGAATGAAA
1 TAAAATAATATGAATGAAA
39671 TAAAATAATAT-AATGAAA
1 TAAAATAATATGAATGAAA
39689 TAA
1 TAA
39692 GCAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:39747 original size:2 final size:2
Alignment explanation
Indices: 39742--39786 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
39732 ACACACATAA
* * *
39742 AT AT AT AT AT AC AT AA AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39784 AT A
1 AT A
39787 ATAAAACATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:39757 original size:16 final size:16
Alignment explanation
Indices: 39736--39784 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
39726 AATTAAACAC
39736 ACATAAATATATATAT
1 ACATAAATATATATAT
39752 ACATAAATATATATAT
1 ACATAAATATATATAT
*
39768 ACATATATATATATAT
1 ACATAAATATATATAT
39784 A
1 A
39785 TAATAAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
ACATAAATATATATAT
Found at i:39884 original size:16 final size:16
Alignment explanation
Indices: 39865--39899 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39855 TTTAAAAAAC
* *
39865 AAAAGGACTAAATTAT
1 AAAAGGACAAAATAAT
39881 AAAAGGACAAAATAAT
1 AAAAGGACAAAATAAT
39897 AAA
1 AAA
39900 GCATAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (16 bp):
AAAAGGACAAAATAAT
Found at i:41239 original size:12 final size:12
Alignment explanation
Indices: 41214--41275 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
41204 CCTACGAAAA
41214 AAAATGTAAT-AT
1 AAAAT-TAATAAT
41226 AAAATTAATAAT
1 AAAATTAATAAT
* *
41238 AATATT-A-AAC
1 AAAATTAATAAT
41248 AAAA-TAATAAT
1 AAAATTAATAAT
*
41259 AATAATAAATAAT
1 AA-AATTAATAAT
41272 AAAA
1 AAAA
41276 AAAAAAGACC
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
9 1 0.03
10 6 0.15
11 9 0.22
12 16 0.40
13 8 0.20
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (12 bp):
AAAATTAATAAT
Found at i:41257 original size:21 final size:22
Alignment explanation
Indices: 41226--41267 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
41216 AATGTAATAT
*
41226 AAAATTAATAATAATATTAAAC
1 AAAATTAATAATAATAATAAAC
41248 AAAA-TAATAATAATAATAAA
1 AAAATTAATAATAATAATAAA
41268 TAATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATTAATAATAATAATAAAC
Found at i:41503 original size:43 final size:43
Alignment explanation
Indices: 41441--41588 Score: 142
Period size: 43 Copynumber: 3.5 Consensus size: 43
41431 ACACTGCTCA
**
41441 TACATGATGAAGAGTTCTGGTCGTCTAAAGGTGACAAGGTTCC
1 TACATGATGAAGAAATCTGGTCGTCTAAAGGTGACAAGGTTCC
* * * ** * *
41484 TACATGATGAGGAAATCT-G--GTC-AAGGGATGATATTGCTCA
1 TACATGATGAAGAAATCTGGTCGTCTAAAGG-TGACAAGGTTCC
** *
41524 TACATGATGAAGAGTTTTGGTCGTCTAAAGGTGACAAGGTTCC
1 TACATGATGAAGAAATCTGGTCGTCTAAAGGTGACAAGGTTCC
*
41567 TACATGATGAGGAAATCTGGTC
1 TACATGATGAAGAAATCTGGTC
41589 AAGGGATGAC
Statistics
Matches: 77, Mismatches: 23, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
39 4 0.05
40 24 0.31
41 1 0.01
42 1 0.01
43 43 0.56
44 4 0.05
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (43 bp):
TACATGATGAAGAAATCTGGTCGTCTAAAGGTGACAAGGTTCC
Found at i:41545 original size:40 final size:40
Alignment explanation
Indices: 41425--41629 Score: 144
Period size: 40 Copynumber: 5.0 Consensus size: 40
41415 TTGGTTGTTG
* *
41425 GGGACGACACTGCTCATACATGATGAAGAGTTCTGGTCGTCTAA
1 GGGATGACATTGCTCATACATGATGAAGAGTTCT-G--GTC-AA
* ** * * * **
41469 AGG-TGACAAGGTTCCTACATGATGAGGAAATCTGGTCAA
1 GGGATGACATTGCTCATACATGATGAAGAGTTCTGGTCAA
* *
41508 GGGATGATATTGCTCATACATGATGAAGAGTTTTGGTCGTCTAA
1 GGGATGACATTGCTCATACATGATGAAGAGTTCT-G--GTC-AA
* ** * * * **
41552 AGG-TGACAAGGTTCCTACATGATGAGGAAATCTGGTCAA
1 GGGATGACATTGCTCATACATGATGAAGAGTTCTGGTCAA
41591 GGGATGACATTGCTCATACATGATGAAGAGTTCTGGTCA
1 GGGATGACATTGCTCATACATGATGAAGAGTTCTGGTCA
41630 TCTTTAGGAG
Statistics
Matches: 118, Mismatches: 37, Indels: 16
0.69 0.22 0.09
Matches are distributed among these distances:
39 8 0.07
40 55 0.47
41 1 0.01
42 2 0.02
43 46 0.39
44 6 0.05
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGATGACATTGCTCATACATGATGAAGAGTTCTGGTCAA
Found at i:41574 original size:83 final size:83
Alignment explanation
Indices: 41425--41628 Score: 372
Period size: 83 Copynumber: 2.5 Consensus size: 83
41415 TTGGTTGTTG
* *
41425 GGGACGACACTGCTCATACATGATGAAGAGTTCTGGTCGTCTAAAGGTGACAAGGTTCCTACATG
1 GGGATGACATTGCTCATACATGATGAAGAGTTCTGGTCGTCTAAAGGTGACAAGGTTCCTACATG
41490 ATGAGGAAATCTGGTCAA
66 ATGAGGAAATCTGGTCAA
* *
41508 GGGATGATATTGCTCATACATGATGAAGAGTTTTGGTCGTCTAAAGGTGACAAGGTTCCTACATG
1 GGGATGACATTGCTCATACATGATGAAGAGTTCTGGTCGTCTAAAGGTGACAAGGTTCCTACATG
41573 ATGAGGAAATCTGGTCAA
66 ATGAGGAAATCTGGTCAA
41591 GGGATGACATTGCTCATACATGATGAAGAGTTCTGGTC
1 GGGATGACATTGCTCATACATGATGAAGAGTTCTGGTC
41629 ATCTTTAGGA
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 115 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (83 bp):
GGGATGACATTGCTCATACATGATGAAGAGTTCTGGTCGTCTAAAGGTGACAAGGTTCCTACATG
ATGAGGAAATCTGGTCAA
Found at i:41793 original size:133 final size:134
Alignment explanation
Indices: 41555--41904 Score: 479
Period size: 133 Copynumber: 2.6 Consensus size: 134
41545 CGTCTAAAGG
* * ** * * *
41555 TGACAAGGTTCCTACATGATGAGGAAATCTGGTCAAGGGATGACATTGCTCATACATGATGAAGA
1 TGACAAGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
* *
41620 GTTCTGGTCATCTTTAGGAGGAGTGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTA
66 GTTCTGGCCATCTTTAGGAGGAGCGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTA
41685 -GGA
131 TGGA
* *
41688 TGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGGCACTGCTCATACGTGATGAAGA
1 TGACAAGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
*
41753 GTTCTGGCCATCTTTAGGTAGG-GCGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
66 GTTCTGGCCATCTTTAGG-AGGAGCGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCT
*
41817 ATGGT
130 ATGGA
* * * * * *
41822 TGACATGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGGTTCCTATGTGATGAGGA
1 TGACAAGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
* * *
41887 CTACTGGCCATCTCTAGG
66 GTTCTGGCCATCTTTAGG
41905 GATAATGGTT
Statistics
Matches: 192, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
133 114 0.59
134 78 0.41
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (134 bp):
TGACAAGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
GTTCTGGCCATCTTTAGGAGGAGCGATAACACGATTCCTACGTGATGAGGACGGCTGGTTATCTA
TGGA
Found at i:42410 original size:12 final size:12
Alignment explanation
Indices: 42393--42417 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42383 AGAGATTCAA
42393 TGATTTTTTTTT
1 TGATTTTTTTTT
42405 TGATTTTTTTTT
1 TGATTTTTTTTT
42417 T
1 T
42418 AAAACATTGT
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (12 bp):
TGATTTTTTTTT
Found at i:43125 original size:37 final size:36
Alignment explanation
Indices: 43074--43194 Score: 114
Period size: 37 Copynumber: 3.5 Consensus size: 36
43064 ATTCAAAGAT
43074 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAATTATCTTAA-AGAGACAAAA
* **
43111 TTTTGTTTCCAAAG-AA--A-C----AGACTCAAAGA
1 TTTTGTTTCAAAAGAAATTATCTTAAAGAGACAAA-A
43140 TTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAA
1 -TTTTGTTTCAAAAGAAATTATCTT-AAAGAGACAAAA
*
43178 TTTTGTTTCCAAAGAAA
1 TTTTGTTTCAAAAGAAA
43195 CAAACTCAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
28 7 0.11
29 1 0.02
30 13 0.20
31 2 0.03
33 2 0.03
34 2 0.03
36 2 0.03
37 29 0.44
38 1 0.02
39 7 0.11
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAATTATCTTAAAGAGACAAAA
Found at i:43145 original size:30 final size:30
Alignment explanation
Indices: 43111--43241 Score: 106
Period size: 30 Copynumber: 4.1 Consensus size: 30
43101 AGAGACAAAA
*
43111 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
**
43141 TTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAA-A-
1 TTTTGTTTCAAAAG-AA--A-C-----AGACTCAAAGAT
* *
43178 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
43208 TTTTGTTTCAAAAGAAACA-ATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGA-CTCAAAGAT
43238 TTTT
1 TTTT
43242 TCGCAAAATT
Statistics
Matches: 81, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
28 6 0.07
29 2 0.02
30 44 0.54
31 2 0.02
33 2 0.02
34 2 0.02
36 2 0.02
37 13 0.16
38 1 0.01
39 7 0.09
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:43147 original size:67 final size:67
Alignment explanation
Indices: 43056--43224 Score: 311
Period size: 67 Copynumber: 2.5 Consensus size: 67
43046 TCATTTTAAG
* *
43056 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
43121 AA
66 AA
43123 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
43188 AA
66 AA
*
43190 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAA
43225 CAATCTCAAA
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 99 1.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
AA
Found at i:43248 original size:29 final size:30
Alignment explanation
Indices: 43188--43249 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
43178 TTTTGTTTCC
**
43188 AAAGAAACAAACTCAAAGATTTTTGTTTCA
1 AAAGAAACAAACTCAAAGATTTTTGTCGCA
*
43218 AAAGAAACAATCTCAAAGATTTTT-TCGCA
1 AAAGAAACAAACTCAAAGATTTTTGTCGCA
43247 AAA
1 AAA
43250 TTATCTCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (30 bp):
AAAGAAACAAACTCAAAGATTTTTGTCGCA
Found at i:43308 original size:51 final size:52
Alignment explanation
Indices: 43229--43327 Score: 164
Period size: 51 Copynumber: 1.9 Consensus size: 52
43219 AAGAAACAAT
*
43229 CTCAAAGATTTTTTCGCAAAATTATCTCAAGAGAGACAAAACTTTGTTCAGA
1 CTCAAAGATTTTTTCACAAAATTATCTCAAGAGAGACAAAACTTTGTTCAGA
* *
43281 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTT
1 CTCAAAGATTTTTTCACAAAATTATCTCAAGAGAGACAAAACTTTGTT
43328 TCAAAATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 36 0.82
52 8 0.18
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (52 bp):
CTCAAAGATTTTTTCACAAAATTATCTCAAGAGAGACAAAACTTTGTTCAGA
Found at i:43357 original size:28 final size:28
Alignment explanation
Indices: 43326--43450 Score: 155
Period size: 29 Copynumber: 4.5 Consensus size: 28
43316 CAAAACTTTG
* * *
43326 TTTCAAAATAAATAGACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
43354 TTTCAAAAGAAAC-AACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
* *
43381 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
*
43410 TGTTCAAAAGGAACAAACTCAAAGA-TTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
*
43438 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
43451 TGTCTTTAAG
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
27 24 0.28
28 26 0.30
29 36 0.42
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.29
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:43409 original size:29 final size:28
Alignment explanation
Indices: 43341--43440 Score: 157
Period size: 29 Copynumber: 3.5 Consensus size: 28
43331 AAATAAATAG
*
43341 ACTCAAAGATTTTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
43368 ACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
*
43397 ACTCCAAGATTTTTGTTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
43426 ACTCAAAGATTTTTT
1 ACTCAAAGATTTTTT
43441 CAAGAGAAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
27 14 0.21
28 12 0.18
29 41 0.61
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (28 bp):
ACTCAAAGATTTTTTTCAAAAGGAACAA
Found at i:43773 original size:36 final size:35
Alignment explanation
Indices: 43689--43786 Score: 110
Period size: 36 Copynumber: 2.8 Consensus size: 35
43679 GAGAAAATGA
* *
43689 TGTCTCAAGCGAGACGAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGATAT
* **
43723 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGCA-AT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AG-ATAT
*
43759 TGTCTCAAGCGAGACAAAGTTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
43787 GAGAAAACGA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
34 19 0.37
35 4 0.08
36 28 0.54
37 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGATAT
Found at i:43801 original size:36 final size:36
Alignment explanation
Indices: 43690--43808 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 36
43680 AGAAAATGAT
* * *
43690 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGA-AAAC
** * **
43724 GTCTCAAATGAGACAAAATTTGTTTTTAGAGCAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
43760 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
43795 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
43809 TCAACTTTGT
Statistics
Matches: 67, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
34 19 0.28
35 11 0.16
36 37 0.55
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:43939 original size:105 final size:101
Alignment explanation
Indices: 43760--43992 Score: 276
Period size: 105 Copynumber: 2.3 Consensus size: 101
43750 TAGAGCAATT
*
43760 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
*
43824 GTGAAACAAATTCGAAATTTGGATCTCAAAGTG-AAAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAAG-GAAAAAG
* *
43862 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTGTTT
* * * *
43926 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AAT-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
43967 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
43993 AAAATTTTCA
Statistics
Matches: 114, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 6 0.05
105 80 0.70
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:44560 original size:4 final size:4
Alignment explanation
Indices: 44469--44547 Score: 75
Period size: 4 Copynumber: 21.8 Consensus size: 4
44459 GTATGTGTTG
* *
44469 ATGT ATGT ATAT ATGT ATGT ATG- A-GT -TG- ATGT ATGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
44513 ATGT ATG- A-GT -TG- ATGT ATGT ATAT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
44548 AGTTGATGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
2 2 0.03
3 8 0.13
4 51 0.84
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:44573 original size:28 final size:28
Alignment explanation
Indices: 44457--44560 Score: 199
Period size: 28 Copynumber: 3.7 Consensus size: 28
44447 TGTAACATGC
*
44457 ATGTATGTGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
44485 ATGTATGAGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
44513 ATGTATGAGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
44541 ATGTATGAGTTGATGTATGT
1 ATGTATGAGTTGATGTATGT
44561 TTCTCAATCT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (28 bp):
ATGTATGAGTTGATGTATGTATATATGT
Found at i:48426 original size:29 final size:32
Alignment explanation
Indices: 48368--48427 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
48358 TGACAAAATG
48368 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
48400 ACACAAACAAAAGAG-A-AAA-AAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
48428 CATGTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 9 0.32
30 3 0.11
31 1 0.04
32 15 0.54
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:50138 original size:18 final size:19
Alignment explanation
Indices: 50103--50142 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
50093 ATTTAAAAAT
*
50103 TAAATTAATATGAATGAAA
1 TAAAATAATATGAATGAAA
50122 TAAAATAATAT-AATGAAA
1 TAAAATAATATGAATGAAA
50140 TAA
1 TAA
50143 GCAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:50204 original size:14 final size:14
Alignment explanation
Indices: 50187--50234 Score: 80
Period size: 14 Copynumber: 3.5 Consensus size: 14
50177 AATTAAACAC
50187 ACATAAATATATAT
1 ACATAAATATATAT
50201 ACATAAATATATAT
1 ACATAAATATATAT
*
50215 ACATATATATATAT
1 ACATAAATATATAT
50229 A-ATAAA
1 ACATAAA
50235 ACATCTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 4 0.12
14 28 0.88
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (14 bp):
ACATAAATATATAT
Found at i:50327 original size:16 final size:16
Alignment explanation
Indices: 50308--50342 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
50298 TTTAAAAAAC
* *
50308 AAAAGGACTAAATTAT
1 AAAAGGACAAAATAAT
50324 AAAAGGACAAAATAAT
1 AAAAGGACAAAATAAT
50340 AAA
1 AAA
50343 GCATAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (16 bp):
AAAAGGACAAAATAAT
Found at i:51697 original size:21 final size:22
Alignment explanation
Indices: 51666--51712 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
51656 AATGTAATAT
*
51666 AAAATTAATAATAATATTAAAC
1 AAAATTAATAATAATAATAAAC
*
51688 AAAA-TAATAATAATAATAAAT
1 AAAATTAATAATAATAATAAAC
51709 AAAA
1 AAAA
51713 AAAAAAAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATTAATAATAATAATAAAC
Found at i:52883 original size:3 final size:3
Alignment explanation
Indices: 52875--52913 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
52865 TTGTCCGGGA
52875 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
52914 ATAATAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:63001 original size:51 final size:51
Alignment explanation
Indices: 62945--64185 Score: 936
Period size: 54 Copynumber: 23.3 Consensus size: 51
62935 TGAAGCGGAA
* *
62945 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCGTTT
1 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
* * *
62996 GAAGATG-TCTGAGTTCCATACTCCCTAAAGAAAGAGGGAGTGATCCCGTGT
1 GAAGATGTTC-GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
* * *
63047 GAAGTTATTGGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
1 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
* * * * * *
63098 GAAGTTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGT
* *
63149 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGA
1 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
* * * * * *
63200 GAAGTTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGT
* * * *
63251 GAAGAATATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAG---ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGT
63305 GAAGAAAATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
1 GAAG---ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
* * * * * *
63359 GAAGTTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGT
* * * * *
63410 GAAGAAGATGTCTGAGTTCTATACTTCCT-GAAGAAAGAGGGAGAGAACCCGTTT
1 GAAGATG-T-TC-GAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGT
*
63464 AAAGAAGATGTTCGTGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
1 ---GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
* * * * * * * *
63518 GAAGTTATTGGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAACCCGAAAGGA
1 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG---TGT
* * *
63572 GAATATTGTTCGAGTTCC-TACTCCCTAAAGAAAGAGGGAGCGAACCCGAAATGA
1 GAAGA-TGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG---TGT
* *
63626 GAAGATTGTTCGAGTTCC-TACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGCAT
1 GAAGA-TGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TG--T
* * * * *
63681 -AAGATCGTTCGAGTTCC-TACTCCCTAAAGAAAGATGGAGCAAACCCATAAGCA
1 GAAGAT-GTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT--G-T
* * *
63734 GAAGATCGTTCGAGTTCC-TACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGGA
1 GAAGAT-GTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG---TGT
* * * *
63788 GAAGATTGTTCGAGTTCC-TACTCCCTAAAGAAAGAGGGAGCGAACCTGAAAGCA
1 GAAGA-TGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TG-T
* * *
63842 GAAGATTGTTCGAGTTCC-TACACCCTAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCGTA
1 GAAGA-TGTTCGAGTTCCATACTCCCTAG-----A------GAA---AGAGGGAGCGAACCCGT-
*
63906 AACAT
50 ---GT
*
63911 -AAGATCGTTCGAGTTCC-TACTCCCTAAAGAAAGAGGGAGCGAACCCGTAG-
1 GAAGAT-GTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT-GT
*
63961 GCAAAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
1 G---AAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
* * * * *
64015 GAAGTTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTGT
1 GAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGT
* * * * * *
64066 GAAGTTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGT
* * * *
64117 AAAGAAGATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 ---GAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGT
64171 GAAGATTGTTCGAGT
1 GAAGA-TGTTCGAGT
64186 CCTTTACTCT
Statistics
Matches: 1014, Mismatches: 114, Indels: 123
0.81 0.09 0.10
Matches are distributed among these distances:
50 6 0.01
51 400 0.39
52 11 0.01
53 19 0.02
54 512 0.50
55 15 0.01
56 1 0.00
57 8 0.01
59 1 0.00
63 1 0.00
65 2 0.00
67 1 0.00
68 37 0.04
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (51 bp):
GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
Found at i:63364 original size:159 final size:159
Alignment explanation
Indices: 62942--64174 Score: 1231
Period size: 159 Copynumber: 7.7 Consensus size: 159
62932 TAGTGAAGCG
* *
62942 GAAGAAGATGTTCGAGTTCCATACTCCCT-AGAGAAAGAGAGAGCGAACCCGTTTGAAG---ATG
1 GAAGAAGATGTTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAAATG
* * * *
63003 -TCTGAGTTCCATACTCCCTAAAGAAAGAGGGAGTGATCCCGTGTGAAGTTATTGGAGTTCCATA
65 TTC-GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATA
* *
63067 CTCCCTAGAGAAAGAGGGAGCGAACCCG--T
129 CTTCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * * *
63096 G-TGAAGTTATTGGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAG---ATGT
1 GAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAAATGT
* *
63157 CCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAGAAGTTATTGGAGTTCTATACT
66 TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATACT
*
63222 TCCTGAAGAAAGAGGGAGCGAACCCGTTT
131 TCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * *
63251 GAAGAATATGTCCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAAATGT
1 GAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAAATGT
63316 TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATACT
66 TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATACT
*
63381 TCCTGAAGAAAGAGGGAGCGAACCCGTTT
131 TCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
63410 GAAGAAGATG-TCTGAGTTCTATACTTCCTGAAGAAAGAGGGAGAGAACCCGTTTAAAGAAGATG
1 GAAGAAGATGTTC-GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAAATG
*
63474 TTCGTGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATAC
65 TTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATAC
***
63539 TTCCTAAAGAAAGAGGGAGCGAACCCGAAA
130 TTCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * * ** *
63569 GGAGAATATTGTTCGAGTTC-CTACTCCCTAAAGAAAGAGGGAGCGAACCCGAAATG-AGAAGAT
1 GAAGAAGA-TGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TTTGAAGAA-AA
* * ** *
63632 TGTTCGAGTTCC-TACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGCAT-AAGATCGTTCGAGT
63 TGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TG--TGAAG-TTATTGGAGT
* * * * * **
63695 TC-CTACTCCCTAAAGAAAGATGGAGCAAACCCATAA
123 TCTATACTTCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *** * *
63731 GCAGAAGATCGTTCGAGTTC-CTACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGGAGAAGATT
1 GAAGAAGAT-GTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAA-AAT
* * * * * *
63795 GTTCGAGTTCC-TACTCCCTAAAGAAAGAGGGAGCGAACCTGAAAGCAGAAGATTGTTCGAGTTC
64 GTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TG-TGAAG-TTATTGGAGTT-
* *
63859 CTACACCCTAGTTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCG-TA
124 CT--A---TA----CT--T-CCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * * ** *
63906 AACATAAGATCGTTCGAGTTC-CTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAA-AAGA
1 GA-AGAAGAT-GTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTG-AAGAAAA
*
63969 TTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTAT
63 TGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTAT
*
64034 ACTTCCTGAAGAAAGAGGGAGCGAACCCG--T
128 ACTTCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * * * * *
64064 G-TGAAGTTATTGGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTAAAGAAGATGT
1 GAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAAATGT
* * * *
64128 CCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAG
66 TCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGTGAAG
64175 ATTGTTCGAG
Statistics
Matches: 932, Mismatches: 106, Indels: 80
0.83 0.09 0.07
Matches are distributed among these distances:
153 131 0.14
154 3 0.00
155 13 0.01
156 130 0.14
158 1 0.00
159 332 0.36
160 21 0.02
161 7 0.01
162 146 0.16
163 11 0.01
166 2 0.00
169 3 0.00
171 2 0.00
172 9 0.01
173 6 0.01
174 1 0.00
175 12 0.01
176 101 0.11
177 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (159 bp):
GAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAAATGT
TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATACT
TCCTAAAGAAAGAGGGAGCGAACCCGTTT
Found at i:63891 original size:68 final size:68
Alignment explanation
Indices: 63800--63936 Score: 213
Period size: 68 Copynumber: 2.0 Consensus size: 68
63790 AGATTGTTCG
* *
63800 AGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCTG-AAAGCAGAAGATTGTTCGAGTTCCTACA
1 AGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAA-CAGAAGATCGTTCGAGTTCCTACA
63864 CCCT
65 CCCT
* * *
63868 AGTTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCGTAAACATAAGATCGTTCGAGTTCCTACTC
1 AGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAACAGAAGATCGTTCGAGTTCCTACAC
63933 CCT
66 CCT
63936 A
1 A
63937 AAGAAAGAGG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 60 0.95
69 3 0.05
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (68 bp):
AGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAACAGAAGATCGTTCGAGTTCCTACAC
CCT
Found at i:63901 original size:122 final size:122
Alignment explanation
Indices: 63746--63991 Score: 379
Period size: 122 Copynumber: 2.0 Consensus size: 122
63736 AGATCGTTCG
* *
63746 AGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCG-AAAGGAGAAGATTGTTCGAGTTCCTACT
1 AGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAA-CAGAAGATCGTTCGAGTTCCTACT
* *
63810 CCCTAAAGAAAGAGGGAGCGAACCTGAAAGCAGAAGATTGTTCGAGTTCC-TACACCCT
65 CCCTAAAGAAAGAGGGAGCGAACCCGAAAGCAAAAGATT-TTCGAGTTCCATACACCCT
* *
63868 AGTTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCGTAAACATAAGATCGTTCGAGTTCCTACTC
1 AGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAACAGAAGATCGTTCGAGTTCCTACTC
* * *
63933 CCTAAAGAAAGAGGGAGCGAACCCGTAGGCAAAAGATTTTCGAGTTCCATACTCCCT
66 CCTAAAGAAAGAGGGAGCGAACCCGAAAGCAAAAGATTTTCGAGTTCCATACACCCT
63990 AG
1 AG
63992 AGAAAGAGGG
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
121 10 0.09
122 100 0.88
123 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (122 bp):
AGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAACAGAAGATCGTTCGAGTTCCTACTC
CCTAAAGAAAGAGGGAGCGAACCCGAAAGCAAAAGATTTTCGAGTTCCATACACCCT
Found at i:63988 original size:176 final size:176
Alignment explanation
Indices: 63692--64009 Score: 523
Period size: 176 Copynumber: 1.8 Consensus size: 176
63682 AGATCGTTCG
* *
63692 AGTTCCTACTCCCTAAAGAAAGATGGAGCAAACCCATAAGCAGAAGATCGTTCGAGTTCCTACTC
1 AGTTCCTACTCCCTAAAGAAAGAGGGAGCAAACCCATAAACAGAAGATCGTTCGAGTTCCTACTC
*
63757 CCTAAAGAAAGAGGGAGCGAACCCGAAAGGAGAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAG
66 CCTAAAGAAAGAGGGAGCGAACCCGAAAGGAAAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAG
63822 AGGGAGCGAACCTGAAAGCAGAAGATTGTTCGAGTTCCTACACCCT
131 AGGGAGCGAACCTGAAAGCAGAAGATTGTTCGAGTTCCTACACCCT
** * *
63868 AGTTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCGTAAACATAAGATCGTTCGAGTTCCTACTC
1 AGTTCCTACTCCCTAAAGAAAGAGGGAGCAAACCCATAAACAGAAGATCGTTCGAGTTCCTACTC
* *
63933 CCTAAAGAAAGAGGGAGCGAACCCG-TAGGCAAAAGATT-TTCGAGTTCCATACTCCCTAGAGAA
66 CCTAAAGAAAGAGGGAGCGAACCCGAAAGG-AAAAGATTGTTCGAGTTCC-TACTCCCTAAAGAA
63996 AGAGGGAGCGAACC
129 AGAGGGAGCGAACC
64010 CGTGTGAAGT
Statistics
Matches: 131, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
175 13 0.10
176 118 0.90
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (176 bp):
AGTTCCTACTCCCTAAAGAAAGAGGGAGCAAACCCATAAACAGAAGATCGTTCGAGTTCCTACTC
CCTAAAGAAAGAGGGAGCGAACCCGAAAGGAAAAGATTGTTCGAGTTCCTACTCCCTAAAGAAAG
AGGGAGCGAACCTGAAAGCAGAAGATTGTTCGAGTTCCTACACCCT
Found at i:64247 original size:55 final size:55
Alignment explanation
Indices: 64169--64622 Score: 558
Period size: 55 Copynumber: 8.3 Consensus size: 55
64159 GCGAACCCGT
* * *
64169 TTGAAGATTGTTCGAGTCCTT-TACTCTCTGAAGATATAGGGAGCAGGCGCGATTG
1 TTGAAGATTGTTCGAGT-CTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * * *
64224 TTGAAGATTGTTCTAGTCTTTTACTCTCTGAAGATATAGGGAGCAGGCGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * * *
64279 TTGAAAATTGTTCGAGTCTTTTACTCTCTGAAGATATAGGGAGCAGGCGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * *
64334 TTGAAAATTGTTCGAGTCTTATACACTCTGAAGAAATAGGGGGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * *
64389 ATGAAGATTG-TAG-GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * * *
64442 TTGAAGATGGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGTTTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * *
64497 TTGAAGATGGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACAAGTTTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * *
64552 TTGAAGA-TGATTCGAGTCTTATACTCTCTGAAGAAATAGAGAACAGATACGATTG
1 TTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
64607 TTGAAGA-TGTTCGAGT
1 TTGAAGATTGTTCGAGT
64623 TCCATTTTTC
Statistics
Matches: 368, Mismatches: 27, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
53 45 0.12
54 15 0.04
55 308 0.84
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
Found at i:64448 original size:218 final size:218
Alignment explanation
Indices: 64190--64590 Score: 552
Period size: 218 Copynumber: 1.8 Consensus size: 218
64180 TCGAGTCCTT
* * * * * * *
64190 TACTCTCTGAAGATATAGGGAGCAGGCGCGATTGTTGAAGATTGTTCTAGTCTTTTACTCTCTGA
1 TACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATGGTTCGAGTCTTATACTCTCTGA
* * ** * * * *
64255 AGATATAGGGAGCAGGCGCGATTGTTGAAAATTGTTCGAGTCTTTTACTCTCTGAAGATATAGGG
66 AGAAATAGGGAGCAGACAAGATTATTGAAAATGGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
* **
64320 AGCAGGCGCGATTGTTGAAAATTG-TTCGAGTCTTATACACTCTGAAGAAATAGGGGGCAGACGC
131 AGCAGACAAGATTGTTGAAAA-TGATTCGAGTCTTATACACTCTGAAGAAATAGGGGGCAGACGC
64384 GATTGATGAAGATTGTAGGTCTTA
195 GATTGATGAAGATTGTAGGTCTTA
*
64408 TACTCTCTGAAGAAATAGGGGGCAGACACGATTATTGAAGATGGTTCGAGTCTTATACTCTCTGA
1 TACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATGGTTCGAGTCTTATACTCTCTGA
* * *
64473 AGAAATAGGGGGCAGACAAGTTTATTGAAGATGGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
66 AGAAATAGGGAGCAGACAAGATTATTGAAAATGGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
* * * *
64538 GGCAGACAAGTTTGTTGAAGATGATTCGAGTCTTATACTCTCTGAAGAAATAG
131 AGCAGACAAGATTGTTGAAAATGATTCGAGTCTTATACACTCTGAAGAAATAG
64591 AGAACAGATA
Statistics
Matches: 156, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
217 2 0.01
218 154 0.99
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (218 bp):
TACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATGGTTCGAGTCTTATACTCTCTGA
AGAAATAGGGAGCAGACAAGATTATTGAAAATGGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
AGCAGACAAGATTGTTGAAAATGATTCGAGTCTTATACACTCTGAAGAAATAGGGGGCAGACGCG
ATTGATGAAGATTGTAGGTCTTA
Found at i:67278 original size:12 final size:12
Alignment explanation
Indices: 67261--67285 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
67251 TATACACTTA
67261 TAAAAATATATT
1 TAAAAATATATT
67273 TAAAAATATATT
1 TAAAAATATATT
67285 T
1 T
67286 TGATGACGTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATATATT
Found at i:68524 original size:20 final size:21
Alignment explanation
Indices: 68478--68525 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
68468 GTGTTATATT
**
68478 ATATTTTAAAAATATTAATTAGT
1 ATATTTT--AAATATTAATTAAA
68501 ATATTTTAAATATT-ATTAAA
1 ATATTTTAAATATTAATTAAA
68521 ATATT
1 ATATT
68526 ATTAGATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 7 0.30
23 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATTTTAAATATTAATTAAA
Found at i:68612 original size:27 final size:27
Alignment explanation
Indices: 68551--68633 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 27
68541 TAATATTAAA
*
68551 TATAAATAATATTATTCATTATTAATAAT
1 TATAAATAATATTATT-TTTA-TAATAAT
68580 T-T-AATAATATTATTTTTATAA-AAT
1 TATAAATAATATTATTTTTATAATAAT
* *
68604 TAATAAATAATATAAATTTTATTAATAAT
1 T-ATAAATAATATTATTTTTA-TAATAAT
68633 T
1 T
68634 TATTATATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 4 0.09
25 3 0.07
26 4 0.09
27 26 0.57
28 4 0.09
29 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (27 bp):
TATAAATAATATTATTTTTATAATAAT
Found at i:68643 original size:27 final size:27
Alignment explanation
Indices: 68569--68643 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 27
68559 ATATTATTCA
* * *
68569 TTATTAATAATTTAATA-ATATTATTT
1 TTATTAATAATTTATTATATATAAATT
* *
68595 TTA-TAA-AATTAATAAATAATATAAATT
1 TTATTAATAATTTAT-TAT-ATATAAATT
68622 TTATTAATAATTTATTATATAT
1 TTATTAATAATTTATTATATAT
68644 TATCAAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
24 5 0.14
25 4 0.11
26 3 0.08
27 14 0.38
28 5 0.14
29 6 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTATTAATAATTTATTATATATAAATT
Found at i:68655 original size:54 final size:53
Alignment explanation
Indices: 68552--68656 Score: 122
Period size: 54 Copynumber: 1.9 Consensus size: 53
68542 AATATTAAAT
* ****
68552 ATAAATAATATTATTCATTATTAATAATTTAATAATATTATTTTTATAAAATTA
1 ATAAATAATATAATT-ATTATTAATAATTTAATAATATTATCAAAATAAAATTA
*
68606 ATAAATAATATAAATT-TTATTAATAATTTATTATATATTATCAAAATAAAA
1 ATAAATAATAT-AATTATTATTAATAATTTAATA-ATATTATCAAAATAAAA
68657 ATATATTATC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
53 16 0.37
54 24 0.56
55 3 0.07
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (53 bp):
ATAAATAATATAATTATTATTAATAATTTAATAATATTATCAAAATAAAATTA
Found at i:68728 original size:21 final size:21
Alignment explanation
Indices: 68699--68746 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
68689 ACTATTTTTT
68699 TATAATATTAAAAATATTATA
1 TATAATATTAAAAATATTATA
* *
68720 TATATTATTAGAAATATTA-A
1 TATAATATTAAAAATATTATA
68740 TA-AATAT
1 TATAATAT
68747 AGTTGAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.17
20 3 0.12
21 17 0.71
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TATAATATTAAAAATATTATA
Found at i:71018 original size:21 final size:21
Alignment explanation
Indices: 70992--71033 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
70982 AAGCATATAT
70992 AAATATACCATAAAGACATAA
1 AAATATACCATAAAGACATAA
*
71013 AAATATATCATAAAGACATAA
1 AAATATACCATAAAGACATAA
71034 TTATTCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.21
Consensus pattern (21 bp):
AAATATACCATAAAGACATAA
Found at i:76136 original size:29 final size:29
Alignment explanation
Indices: 76102--76160 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
76092 CCTAAATTAA
*
76102 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
76131 TTTGATGTAATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
76160 T
1 T
76161 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTAATTGCTTACATCAATTTAGT
Found at i:76171 original size:29 final size:29
Alignment explanation
Indices: 76111--76168 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
76101 ATTTGATGTC
* *
76111 ATTGCTTACATCAATTTAGTTTTGATGTA
1 ATTGCTTACATCAATTTAGTTTAGATGAA
*
76140 ATTGCTTACATCAATTTAG-TTAGGTGAA
1 ATTGCTTACATCAATTTAGTTTAGATGAA
76168 A
1 A
76169 ATTAAGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (29 bp):
ATTGCTTACATCAATTTAGTTTAGATGAA
Found at i:80801 original size:29 final size:29
Alignment explanation
Indices: 80767--80825 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
80757 CCTAAATTAA
80767 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
80796 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
80825 T
1 T
80826 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:89331 original size:21 final size:21
Alignment explanation
Indices: 89282--89336 Score: 92
Period size: 22 Copynumber: 2.6 Consensus size: 21
89272 AGATGTCTGG
89282 GCCTGAGAAGCAGTTGTTACT
1 GCCTGAGAAGCAGTTGTTACT
*
89303 GCCCTGAGAAGCAGTTGTTCCT
1 G-CCTGAGAAGCAGTTGTTACT
89325 GCCTGAGAAGCA
1 GCCTGAGAAGCA
89337 ACCTGAGTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (21 bp):
GCCTGAGAAGCAGTTGTTACT
Found at i:92935 original size:12 final size:12
Alignment explanation
Indices: 92918--92942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
92908 CCAGGATAGA
92918 ATTGTATATATT
1 ATTGTATATATT
92930 ATTGTATATATT
1 ATTGTATATATT
92942 A
1 A
92943 ACTTTAGATA
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
ATTGTATATATT
Found at i:93120 original size:2 final size:2
Alignment explanation
Indices: 93113--93138 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
93103 AGTAATGAAG
93113 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
93139 AACAAGTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:98553 original size:30 final size:31
Alignment explanation
Indices: 98489--98591 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 31
98479 GAAAGCAAAC
* *
98489 CAAAGAAAGA-AAAAACCCACCACAAC-AAAC
1 CAAAGAAA-ACAAAAACCCATCACAACAAAAA
* *
98519 CAAAGAAAACAAAAACCC-TCACAGCAAAAG
1 CAAAGAAAACAAAAACCCATCACAACAAAAA
* *
98549 CAAAGGAAACAAAAGCCCATCACAACAAAAA
1 CAAAGAAAACAAAAACCCATCACAACAAAAA
98580 CAAAG-AAACAAA
1 CAAAGAAAACAAA
98592 TATAGGGGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
29 6 0.10
30 42 0.67
31 15 0.24
ACGTcount: A:0.63, C:0.26, G:0.09, T:0.02
Consensus pattern (31 bp):
CAAAGAAAACAAAAACCCATCACAACAAAAA
Found at i:100368 original size:34 final size:34
Alignment explanation
Indices: 100330--100399 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
100320 GTCATGCATA
100330 CTGCATGTTATAGAAAATAATCCAAAAAATTAAG
1 CTGCATGTTATAGAAAATAATCCAAAAAATTAAG
*
100364 CTGCATGTTATAGAAAATAATCCAAACAATTAAG
1 CTGCATGTTATAGAAAATAATCCAAAAAATTAAG
100398 CT
1 CT
100400 TCAAGTAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.27
Consensus pattern (34 bp):
CTGCATGTTATAGAAAATAATCCAAAAAATTAAG
Done.