Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006985.1 Hibiscus syriacus cultivar Beakdansim tig00017996_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: 663392
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 4 of 5
Found at i:433138 original size:13 final size:13
Alignment explanation
Indices: 433114--433418 Score: 62
Period size: 13 Copynumber: 22.9 Consensus size: 13
433104 AATTGAAAAA
433114 ATATA-ATA-TAT
1 ATATATATATTAT
433125 ATATATATATTAT
1 ATATATATATTAT
433138 AT-T-TATATTAT
1 ATATATATATTAT
*
433149 AAACTATATAATTAT
1 ATA-TATAT-ATTAT
*
433164 -TATA-A-ACTAT
1 ATATATATATTAT
*
433174 ATATATAAATTAT
1 ATATATATATTAT
* *
433187 ATTTATGTGAACTATAT
1 ATATATAT--A-T-TAT
* *
433204 ATATATAAACTAT
1 ATATATATATTAT
* *
433217 GTATATAAACTATAT
1 ATATATATA-T-TAT
* * *
433232 ATGTATAAACTAT
1 ATATATATATTAT
* * *
433245 AAAAAGTATATAAACT
1 ATATA-TATAT-TA-T
433261 ATATATATAGTT-T
1 ATATATATA-TTAT
* * *
433274 ATATTTATATAAC
1 ATATATATATTAT
*
433287 ATATATATA-TAA
1 ATATATATATTAT
*
433299 ACTATATATA-TAA
1 A-TATATATATTAT
*
433312 ACTATATA-AATAT
1 A-TATATATATTAT
* *
433325 AGTTTATATGTTAT
1 A-TATATATATTAT
*
433339 A-ATTTATATTAAT
1 ATATATATATT-AT
433352 ATAGTATATATGTAT
1 ATA-TATATAT-TAT
* * *
433367 GTAAACTAATATAAGT
1 ATATA-T-ATATTA-T
**
433383 A-ATATATAGAAT
1 ATATATATATTAT
433395 ATATATATA-TAT
1 ATATATATATTAT
433407 ATATATATATTA
1 ATATATATATTA
433419 AAGAAACACT
Statistics
Matches: 215, Mismatches: 47, Indels: 62
0.66 0.15 0.19
Matches are distributed among these distances:
10 4 0.02
11 18 0.08
12 29 0.13
13 94 0.44
14 14 0.07
15 36 0.17
16 12 0.06
17 8 0.04
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:433138 original size:15 final size:15
Alignment explanation
Indices: 433114--433416 Score: 62
Period size: 15 Copynumber: 20.0 Consensus size: 15
433104 AATTGAAAAA
*
433114 ATATAATATATATAT
1 ATATATTATATATAT
*
433129 ATATATTATATTTAT
1 ATATATTATATATAT
*
433144 AT-TA-TAAACTATAT
1 ATATATTATA-TATAT
*
433158 A-ATTATTATAAACTAT
1 ATA-TATTATATA-TAT
*
433174 ATATA-TAAAT-TAT
1 ATATATTATATATAT
*
433187 ATTTATGTGA-ACTATAT
1 ATATAT-T-ATA-TATAT
* *
433204 ATATATAAACTATGTAT
1 ATATAT-TA-TATATAT
* * *
433221 ATAAACTATATATGT
1 ATATATTATATATAT
* * *
433236 ATAAACTATA-A-AA
1 ATATATTATATATAT
*
433249 AGTATA-TAAACTATAT
1 A-TATATTATA-TATAT
*
433265 ATATAGTT-TATATTT
1 ATATA-TTATATATAT
**
433280 ATATAACATATATAT
1 ATATATTATATATAT
* *
433295 ATAAACTATATATAT
1 ATATATTATATATAT
* *
433310 AAACTATATAAATATAGT
1 ATA-TAT-TATATATA-T
*
433328 TTATATGT-TATA-AT
1 ATATAT-TATATATAT
*
433342 TTATATTA-ATATAGT
1 ATATATTATATATA-T
* *
433357 ATATATGTATGTAAACT
1 ATATAT-TATATATA-T
*
433374 A-ATATAAGTA-ATAT
1 ATATATTA-TATATAT
* *
433388 ATAGAATATATATAT
1 ATATATTATATATAT
433403 ATATA-TATATATAT
1 ATATATTATATATAT
433417 TAAAGAAACA
Statistics
Matches: 207, Mismatches: 50, Indels: 63
0.65 0.16 0.20
Matches are distributed among these distances:
13 18 0.09
14 32 0.15
15 93 0.45
16 27 0.13
17 34 0.16
18 3 0.01
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (15 bp):
ATATATTATATATAT
Found at i:433227 original size:28 final size:28
Alignment explanation
Indices: 433164--433325 Score: 136
Period size: 28 Copynumber: 5.7 Consensus size: 28
433154 ATATAATTAT
*
433164 TATAAACTATATATATA-AATTA-TATTTA
1 TATAAACTATATATATATAA--ACTATGTA
* *
433192 TGTGAACTATATATATATAAACTATGTA
1 TATAAACTATATATATATAAACTATGTA
*
433220 TATAAACTATATATGTATAAACTATAAAAAGTA
1 TATAAACTATATATATATAAACTAT-----GTA
** *
433253 TATAAACTATATATATAGTTTA-TATTTA
1 TATAAACTATATATATA-TAAACTATGTA
*
433281 TAT-AAC-ATATATATATAAACTATATA
1 TATAAACTATATATATATAAACTATGTA
*
433307 TATAAACTATATAAATATA
1 TATAAACTATATATATATA
433326 GTTTATATGT
Statistics
Matches: 109, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
25 2 0.02
26 17 0.16
27 7 0.06
28 57 0.52
29 2 0.02
33 22 0.20
34 2 0.02
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (28 bp):
TATAAACTATATATATATAAACTATGTA
Found at i:433258 original size:89 final size:86
Alignment explanation
Indices: 433141--433319 Score: 261
Period size: 89 Copynumber: 2.0 Consensus size: 86
433131 ATATTATATT
* * *
433141 TATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTATGTGAACTATATAT
1 TATATTATAAACTATAAAAGTATTATAAACTATATATATAAATTATATTTATAT-AAC-ATATAT
*
433206 ATATAAACTATGTATATAAACTA
64 ATATAAACTATATATATAAACTA
**
433229 TATATGTATAAACTATAAAAAGTA-TATAAACTATATATATAGTTTATATTTATATAACATATAT
1 TATAT-TATAAACTAT-AAAAGTATTATAAACTATATATATAAATTATATTTATATAACATATAT
433293 ATATAAACTATATATATAAACTA
64 ATATAAACTATATATATAAACTA
433316 TATA
1 TATA
433320 AATATAGTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
87 32 0.39
88 8 0.10
89 38 0.46
90 5 0.06
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (86 bp):
TATATTATAAACTATAAAAGTATTATAAACTATATATATAAATTATATTTATATAACATATATAT
ATAAACTATATATATAAACTA
Found at i:433493 original size:14 final size:14
Alignment explanation
Indices: 433474--433515 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
433464 TTATAAAAAT
*
433474 CCTAAATCCTATAC
1 CCTAAATCCTAAAC
* *
433488 CCTAAAACATAAAC
1 CCTAAATCCTAAAC
433502 CCTAAATCCTAAAC
1 CCTAAATCCTAAAC
433516 TTTATAAACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (14 bp):
CCTAAATCCTAAAC
Found at i:433653 original size:20 final size:20
Alignment explanation
Indices: 433630--433699 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
433620 ACAATAGTTA
433630 ATATATGTAACTTATAGTAT
1 ATATATGTAACTTATAGTAT
* * *
433650 ATATATGTATACATGTA-AACT
1 ATATATGTA-ACTTATAGTA-T
*
433671 ATATATGTAACTTATAGTAC
1 ATATATGTAACTTATAGTAT
*
433691 ATGTATGTA
1 ATATATGTA
433700 TAAACTATGT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
20 23 0.59
21 16 0.41
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.41
Consensus pattern (20 bp):
ATATATGTAACTTATAGTAT
Found at i:433835 original size:21 final size:20
Alignment explanation
Indices: 433810--433851 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
433800 TAGTTTATAA
*
433810 AAACCCTAAACTTTAAACCAT
1 AAACCCTAAAC-ATAAACCAT
433831 AAACCCTAAACATAAACCAT
1 AAACCCTAAACATAAACCAT
433851 A
1 A
433852 GTTAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (20 bp):
AAACCCTAAACATAAACCAT
Found at i:433970 original size:15 final size:18
Alignment explanation
Indices: 433950--433990 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
433940 ATGTATAGTG
*
433950 TATATAAACTATA-TATA
1 TATATAACCTATAGTATA
433967 TATATAACCTATAGTATA
1 TATATAACCTATAGTATA
*
433985 TGTATA
1 TATATA
433991 TATACAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (18 bp):
TATATAACCTATAGTATA
Found at i:433990 original size:24 final size:22
Alignment explanation
Indices: 433932--434023 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 22
433922 ATCATGTACG
*
433932 TATAAACTAT-GTATA-GTGTA
1 TATAAACTATAGTATATGTATA
433952 TATAAAC--TA-TATA--TATA
1 TATAAACTATAGTATATGTATA
*
433969 TATAACCTATAGTATATGTATA
1 TATAAACTATAGTATATGTATA
*
433991 TATACAATCTAT-TTATATGT-TA
1 TATA-AA-CTATAGTATATGTATA
434013 TATAAACTATA
1 TATAAACTATA
434024 TATGTAACCT
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
17 9 0.15
18 5 0.08
19 2 0.03
20 15 0.25
21 2 0.03
22 14 0.24
23 8 0.14
24 4 0.07
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (22 bp):
TATAAACTATAGTATATGTATA
Found at i:434008 original size:37 final size:37
Alignment explanation
Indices: 433932--434008 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
433922 ATCATGTACG
*
433932 TATAAACTATGTATAGTGTATATAAACTATATATATA
1 TATAAACTATGTATAGTGTATATAAACAATATATATA
* * * *
433969 TATAACCTATAGTATA-TGTATATATACAATCTATTTA
1 TATAAACTAT-GTATAGTGTATATAAACAATATATATA
434006 TAT
1 TAT
434009 GTTATATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 29 0.85
38 5 0.15
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (37 bp):
TATAAACTATGTATAGTGTATATAAACAATATATATA
Found at i:434121 original size:21 final size:21
Alignment explanation
Indices: 434069--434121 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
434059 TAGTGTACTA
* *
434069 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
* *
434090 TATGGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
434111 TATAGTTTATA
1 TATAGTTTATA
434122 TTAATGTACT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:434201 original size:36 final size:35
Alignment explanation
Indices: 434161--434395 Score: 135
Period size: 34 Copynumber: 6.9 Consensus size: 35
434151 TAATTATCTT
*
434161 AACTATAATTTATATTAATATAGTATATAGTTTATA
1 AACTATAATTTATATTAATATA-TATATAATTTATA
* * *
434197 AACTAT-A-TTATACTAATAT-TAT-T--TATATT
1 AACTATAATTTATATTAATATATATATAATTTATA
* *
434226 AACTATAGTTTATA-AAATATACTATATAATTTAT-
1 AACTATAATTTATATTAATATA-TATATAATTTATA
*
434260 AACATATAATTTATATTAATAT-TA-AT--GTTATA
1 AAC-TATAATTTATATTAATATATATATAATTTATA
* * *
434292 TACTATATTTTATATTAATAT-TAATTATAAATTATA
1 AACTATAATTTATATTAATATAT-A-TATAATTTATA
*
434328 AACTAT-A-TTATATTAATATA-ATTTAATATTAATA
1 AACTATAATTTATATTAATATATATATAAT-TT-ATA
* *
434362 TTAATTAT-ATTAATATTAATTATAATATATAATT
1 --AACTATAATTTATATTAA-TAT-ATATATAATT
434396 ATTATAATAT
Statistics
Matches: 156, Mismatches: 19, Indels: 45
0.71 0.09 0.20
Matches are distributed among these distances:
29 10 0.06
30 5 0.03
31 28 0.18
32 13 0.08
33 6 0.04
34 33 0.21
35 15 0.10
36 27 0.17
37 8 0.05
38 3 0.02
39 2 0.01
40 6 0.04
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (35 bp):
AACTATAATTTATATTAATATATATATAATTTATA
Found at i:434229 original size:65 final size:65
Alignment explanation
Indices: 434139--434393 Score: 256
Period size: 65 Copynumber: 3.9 Consensus size: 65
434129 ACTATATAGT
* * * * *
434139 TTATATTAATGTTAATTATCTTAACTATAATTTATATTAATATAGTATATAGTTTATAAACTATA
1 TTATATTAATATTATTTATATTAACTATAATTTATATTAATATAATATATAATTTATAAACTATA
* * * *
434204 TTATACTAATATTATTTATATTAACTATAGTTTATA-AAATATACTATATAATTTAT-AACATAT
1 TTATATTAATATTATTTATATTAACTATAATTTATATTAATATAATATATAATTTATAAAC-TAT
434267 AA
65 -A
* *
434269 TTTATATTAATATTAATGTTATA-T-ACTATATTTTATATTAATATTAAT-TATAAATTATAAAC
1 -TTATATTAATATT-AT-TTATATTAACTATAATTTATATTAATA-TAATATATAATTTATAAAC
434331 TATA
62 TATA
* *
434335 TTATATTAATATAATTTAATATTAA-TATTAA-TTATATTAATATTAAT-TATAATATATAA
1 TTATATTAATATTATTT-ATATTAACTA-TAATTTATATTAATA-TAATATATAATTTATAA
434394 TTATTATAAT
Statistics
Matches: 161, Mismatches: 17, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
63 5 0.03
64 25 0.16
65 73 0.45
66 28 0.17
67 19 0.12
68 11 0.07
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (65 bp):
TTATATTAATATTATTTATATTAACTATAATTTATATTAATATAATATATAATTTATAAACTATA
Found at i:434274 original size:21 final size:21
Alignment explanation
Indices: 434164--434274 Score: 64
Period size: 21 Copynumber: 5.2 Consensus size: 21
434154 TTATCTTAAC
* *
434164 TATAATTTATATTAATATAGTA
1 TATAATTTATA-AAATATAATA
* * *
434186 TATAGTTTATAAACTATATTA
1 TATAATTTATAAAATATAATA
** *
434207 TACTAATATTAT-TTATATTAA-C
1 TA-TAAT-TTATAAAATA-TAATA
* *
434229 TATAGTTTATAAAATATACTA
1 TATAATTTATAAAATATAATA
* *
434250 TATAATTTATAACATATAATT
1 TATAATTTATAAAATATAATA
434271 TATA
1 TATA
434275 TTAATATTAA
Statistics
Matches: 65, Mismatches: 19, Indels: 11
0.68 0.20 0.12
Matches are distributed among these distances:
20 6 0.09
21 36 0.55
22 17 0.26
23 6 0.09
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (21 bp):
TATAATTTATAAAATATAATA
Found at i:434283 original size:6 final size:6
Alignment explanation
Indices: 434272--434423 Score: 75
Period size: 6 Copynumber: 24.3 Consensus size: 6
434262 CATATAATTT
* * * *
434272 ATATTA ATATTA ATGTTA TATACT- ATATTTT ATATTA ATATTA ATTATAA
1 ATATTA ATATTA ATATTA -ATATTA ATA-TTA ATATTA ATATTA A-TATTA
* *
434322 ATTATAA ACTATATT ATATTA ATA-TA AT-TTA ATATTA ATATT- A-ATT-
1 A-TATTA A-TAT-TA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
*
434368 ATATTA ATATTA AT-TATA ATATATA ATTATTATA ATATTA ATTATAA
1 ATATTA ATATTA ATAT-TA ATAT-TA A-TA-T-TA ATATTA A-TATTA
434415 ATAGTTA AT
1 ATA-TTA AT
434424 TAATAAAAAT
Statistics
Matches: 119, Mismatches: 12, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.03
5 16 0.13
6 50 0.42
7 39 0.33
8 5 0.04
9 5 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:434304 original size:31 final size:30
Alignment explanation
Indices: 434252--434414 Score: 121
Period size: 31 Copynumber: 5.3 Consensus size: 30
434242 ATATACTATA
434252 TAATTTATAACATATAATTTATATTAATAT
1 TAATTTATAACATATAATTTATATTAATAT
*
434282 TAATGTTATATAC-TATATTTTATATTAATAT
1 TAAT-TTATA-ACATATAATTTATATTAATAT
434313 TAA-TTATAA-ATTATAAACTATATTATATTAATA-
1 TAATTTATAACA-TAT--A--AT-TTATATTAATAT
434346 TAATTTAATATTA-ATATTAA-TTATATTAATAT
1 TAATTT-ATA--ACATA-TAATTTATATTAATAT
*
434378 TAA-TTATAATATATAA-TTAT-TATAATAT
1 TAATTTATAACATATAATTTATAT-TAATAT
434406 TAA-TTATAA
1 TAATTTATAA
434415 ATAGTTAATT
Statistics
Matches: 114, Mismatches: 2, Indels: 36
0.75 0.01 0.24
Matches are distributed among these distances:
27 1 0.01
28 24 0.21
29 11 0.10
30 7 0.06
31 39 0.34
32 5 0.04
33 5 0.04
34 13 0.11
35 4 0.04
36 2 0.02
37 3 0.03
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (30 bp):
TAATTTATAACATATAATTTATATTAATAT
Found at i:434344 original size:34 final size:33
Alignment explanation
Indices: 434287--434416 Score: 125
Period size: 28 Copynumber: 4.0 Consensus size: 33
434277 AATATTAATG
434287 TTATATACTATATTTTATATTAATATTAATTATAAA
1 TTATATACTA-A--TTATATTAATATTAATTATAAA
*
434323 TTATAAACTATATTATATTAATA-TAATT-TAATA
1 TTATATACTA-ATTATATTAATATTAATTATAA-A
*
434356 TTA-ATATTAATTATATTAATATTAATTAT--A
1 TTATATACTAATTATATTAATATTAATTATAAA
434386 --ATATA-TAATTAT-TATAATATTAATTATAAA
1 TTATATACTAATTATAT-TAATATTAATTATAAA
434416 T
1 T
434417 AGTTAATTAA
Statistics
Matches: 83, Mismatches: 3, Indels: 21
0.78 0.03 0.20
Matches are distributed among these distances:
27 1 0.01
28 21 0.25
29 3 0.04
30 2 0.02
31 12 0.14
32 12 0.14
33 10 0.12
34 11 0.13
36 11 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (33 bp):
TTATATACTAATTATATTAATATTAATTATAAA
Found at i:434358 original size:21 final size:20
Alignment explanation
Indices: 434301--434413 Score: 70
Period size: 21 Copynumber: 5.2 Consensus size: 20
434291 ATACTATATT
*
434301 TTATATTAATATTAATTATAAA
1 TTATATTAATATT-A-TATTAA
*
434323 TTATA-AACTATATTATATTAA
1 TTATATTA--ATATTATATTAA
434344 -TATAATTTAATATTAATATTAA
1 TTAT-A-TTAATATT-ATATTAA
434366 TTATATTAATATTA-ATTATAA
1 TTATATTAATATTATA-T-TAA
* *
434387 TATATAATTATTATAATATTAA
1 T-TAT-ATTAATATTATATTAA
434409 TTATA
1 TTATA
434414 AATAGTTAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 26
0.70 0.05 0.25
Matches are distributed among these distances:
19 1 0.01
20 6 0.08
21 27 0.36
22 21 0.28
23 18 0.24
24 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATTAATATTATATTAA
Found at i:434370 original size:131 final size:131
Alignment explanation
Indices: 434132--434412 Score: 309
Period size: 131 Copynumber: 2.2 Consensus size: 131
434122 TTAATGTACT
* * * * **
434132 ATATAGTTTATATTAATGTTAATTATCTTAACTATAATTTATATTAATATAGTATATAGTTTATA
1 ATATAATTTATATTAATATTAATTATCATAACTATAATTTATATTAATATAATATATAAATTATA
* *
434197 AACTATATTATACTAATATTATTTATATTAACTATAGTTTATAAAATATACTATATAATTTATAA
66 AACTATATTATACTAATATAATTTATATTAACTATAGATTATAAAATATACTATATAATTTATAA
434262 C
131 C
*
434263 ATATAATTTATATTAATATTAATGT-T-ATATACTATATTTTATATTAATATTAAT-TATAAATT
1 ATATAATTTATATTAATATTAAT-TATCATA-ACTATAATTTATATTAATA-TAATATATAAATT
* *
434325 ATAAACTATATTATATTAATATAATTTAATATTAA-TATTA-ATTAT---AT-TAATAT-TAA-T
63 ATAAACTATATTATACTAATATAATTT-ATATTAACTA-TAGATTATAAAATATACTATATAATT
*
434382 TATAAT
126 TATAAC
434388 ATATAA-TTAT-TATAATATTAATTAT
1 ATATAATTTATAT-TAATATTAATTAT
434413 AAATAGTTAA
Statistics
Matches: 131, Mismatches: 12, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
123 2 0.02
124 15 0.11
125 12 0.09
126 3 0.02
127 5 0.04
128 2 0.02
130 2 0.02
131 77 0.59
132 13 0.10
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (131 bp):
ATATAATTTATATTAATATTAATTATCATAACTATAATTTATATTAATATAATATATAAATTATA
AACTATATTATACTAATATAATTTATATTAACTATAGATTATAAAATATACTATATAATTTATAA
C
Found at i:434401 original size:16 final size:15
Alignment explanation
Indices: 434332--434425 Score: 80
Period size: 15 Copynumber: 6.7 Consensus size: 15
434322 ATTATAAACT
*
434332 ATATTATATTAATATA
1 ATATTA-ATTATTATA
434348 AT-TTAA-TA-T-TA
1 ATATTAATTATTATA
434359 ATATTAATTA-TATTA
1 ATATTAATTATTA-TA
*
434374 ATATTAATTATAAT-
1 ATATTAATTATTATA
434388 ATA-TAATTATTATA
1 ATATTAATTATTATA
434402 ATATTAATTA-TA-A
1 ATATTAATTATTATA
434415 ATAGTTAATTA
1 ATA-TTAATTA
434426 ATAAAAATTA
Statistics
Matches: 68, Mismatches: 2, Indels: 18
0.77 0.02 0.20
Matches are distributed among these distances:
11 4 0.06
12 5 0.07
13 18 0.26
14 16 0.24
15 22 0.32
16 3 0.04
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
ATATTAATTATTATA
Found at i:434435 original size:28 final size:27
Alignment explanation
Indices: 434332--434435 Score: 86
Period size: 28 Copynumber: 3.7 Consensus size: 27
434322 ATTATAAACT
* * *
434332 ATATTATATTAATATAATTTAA-TATTA
1 ATATTA-ATTAATAAAAATTAATTATAA
* *
434359 ATATTAATTATATTAATATTAATTAT-A
1 ATATTAATTA-ATAAAAATTAATTATAA
* *
434386 ATATATAATTATTATAATATTAATTATAA
1 ATAT-TAATTAATA-AAAATTAATTATAA
434415 ATAGTTAATTAATAAAAATTA
1 ATA-TTAATTAATAAAAATTA
434436 TATAGGGATG
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
26 4 0.06
27 19 0.30
28 27 0.43
29 12 0.19
30 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (27 bp):
ATATTAATTAATAAAAATTAATTATAA
Found at i:435232 original size:6 final size:6
Alignment explanation
Indices: 435223--435480 Score: 114
Period size: 6 Copynumber: 43.8 Consensus size: 6
435213 TTGAACCTTA
* * ** * * *
435223 AACCAG AACCCG AACCCG AACCCA AACTTG AACCCG ACCCCT AA-CCA
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
* ** * * * * *
435270 AACCCG AACCCA AACTTG AACCCG ATCCCT AA-CCA AACCCT AACCCA
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
** * * * * * * *
435317 AACCTA AACCCA AACCC- AACCCCT AA-CCA AACCCA AACCCA AAACCA
1 AACCCG AACCCG AACCCG AA-CCCG AACCCG AACCCG AACCCG AACCCG
* * * ** * * *
435364 AACCCT AACTCA AACCAA AACCCA AACCCG AACCCA AACCCG AA-CCT
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
* * ** *
435411 AACCCA AACCCG AACCTG AACCCG AA-CCG AACCCG AATTCG AACCCA
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
* *
435458 AACCCG AACCCA AATCCG AACCC
1 AACCCG AACCCG AACCCG AACCC
435481 AAATCCTAAC
Statistics
Matches: 192, Mismatches: 53, Indels: 14
0.74 0.20 0.05
Matches are distributed among these distances:
5 23 0.12
6 167 0.87
7 2 0.01
ACGTcount: A:0.41, C:0.45, G:0.07, T:0.07
Consensus pattern (6 bp):
AACCCG
Found at i:435320 original size:29 final size:29
Alignment explanation
Indices: 435300--435420 Score: 129
Period size: 30 Copynumber: 4.1 Consensus size: 29
435290 CCCGATCCCT
*
435300 AACCAAACCCTAACCCAAACCTAAACCCA
1 AACCAAACCCTAACCCAAACCCAAACCCA
*
435329 AACCCAACCCCTAA-CCAAACCCAAACCCAA
1 AA-CCAAACCCTAACCCAAACCCAAACCC-A
* *
435359 AACCAAACCCTAACTCAAACCAAAACCCA
1 AACCAAACCCTAACCCAAACCCAAACCCA
* * * *
435388 AACCCGAACCCAAACCCGAA-CCTAACCCA
1 AA-CCAAACCCTAACCCAAACCCAAACCCA
435417 AACC
1 AACC
435421 CGAACCTGAA
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
28 2 0.03
29 37 0.48
30 38 0.49
ACGTcount: A:0.47, C:0.46, G:0.02, T:0.05
Consensus pattern (29 bp):
AACCAAACCCTAACCCAAACCCAAACCCA
Found at i:435327 original size:35 final size:35
Alignment explanation
Indices: 435235--435438 Score: 187
Period size: 35 Copynumber: 5.8 Consensus size: 35
435225 CCAGAACCCG
* * * *
435235 AACCCGAACCCAAACTTGAACCCGACCCCTAACCA
1 AACCCAAACCCAAACCTGAACCCAAACCCTAACCA
* * * *
435270 AACCCGAACCCAAACTTGAACCCGATCCCTAACCA
1 AACCCAAACCCAAACCTGAACCCAAACCCTAACCA
* * *
435305 AACCCTAACCCAAACCTAAACCCAAACCC-AACCCCT
1 AACCCAAACCCAAACCTGAACCCAAACCCTAA--CCA
** *
435341 AA-CCAAACCCAAACCCAAAACCAAACCCTAACTCA
1 AACCCAAACCCAAACCTGAACCCAAACCCTAAC-CA
* * * *
435376 AACCAAAACCCAAACCCGAACCCAAACCCGAACCT
1 AACCCAAACCCAAACCTGAACCCAAACCCTAACCA
* *
435411 AACCCAAACCCGAACCTGAACCCGAACC
1 AACCCAAACCCAAACCTGAACCCAAACC
435439 GAACCCGAAT
Statistics
Matches: 144, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
34 3 0.02
35 109 0.76
36 32 0.22
ACGTcount: A:0.42, C:0.46, G:0.05, T:0.07
Consensus pattern (35 bp):
AACCCAAACCCAAACCTGAACCCAAACCCTAACCA
Found at i:435403 original size:41 final size:40
Alignment explanation
Indices: 435302--435483 Score: 132
Period size: 41 Copynumber: 4.4 Consensus size: 40
435292 CGATCCCTAA
* * * * *
435302 CCAAACCCTAACCCAAACCTAAACCCAAACCCAACCCCTAAC
1 CCAAACCCGAACCCAAACC-GAA-CCTAACCCAAACCCGAAC
* * * * * **
435344 CAAACC-CAAACCCAAAACCAAACCCTAACTCAAACCAAAAC
1 CCAAACCCGAACCC-AAACCGAA-CCTAACCCAAACCCGAAC
435385 CCAAACCCGAACCCAAACCCGAACCTAACCCAAACCCGAAC
1 CCAAACCCGAACCCAAA-CCGAACCTAACCCAAACCCGAAC
** * * * *
435426 CTGAACCCGAACCGAACCCGAATTCGAACCCAAACCCGAAC
1 CCAAACCCGAACCCAAACCGAA-CCTAACCCAAACCCGAAC
*
435467 CCAAATCCGAACCCAAA
1 CCAAACCCGAACCCAAA
435484 TCCTAACTTG
Statistics
Matches: 110, Mismatches: 26, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
40 5 0.05
41 86 0.78
42 19 0.17
ACGTcount: A:0.44, C:0.45, G:0.05, T:0.05
Consensus pattern (40 bp):
CCAAACCCGAACCCAAACCGAACCTAACCCAAACCCGAAC
Found at i:435421 original size:29 final size:29
Alignment explanation
Indices: 435253--435467 Score: 132
Period size: 29 Copynumber: 7.3 Consensus size: 29
435243 CCCAAACTTG
*
435253 AACCCGACCCCTAA-CCAAACCCGAACCCA
1 AACCCGA-ACCTAACCCAAACCCGAACCCA
** * * * * *
435282 AACTTGAACCCGATCCCTAA-CCAAACCCT
1 AACCCGAA-CCTAACCCAAACCCGAACCCA
* *
435311 AACCCAAACCTAAACCCAAACCC-AACCCCT
1 AACCCGAACCT-AACCCAAACCCGAA-CCCA
* * * * *
435341 AA-CCAAACCCAAACCCAAAACCAAACCCT
1 AACCCGAA-CCTAACCCAAACCCGAACCCA
* * *
435370 AACTCAAACCAAAACCCAAACCCGAACCCA
1 AACCCGAACC-TAACCCAAACCCGAACCCA
**
435400 AACCCGAACCTAACCCAAACCCGAACCTG
1 AACCCGAACCTAACCCAAACCCGAACCCA
* * **
435429 AACCCGAACCGAACCCGAATTCGAACCCA
1 AACCCGAACCTAACCCAAACCCGAACCCA
435458 AACCCGAACC
1 AACCCGAACC
435468 CAAATCCGAA
Statistics
Matches: 146, Mismatches: 31, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
28 2 0.01
29 100 0.68
30 44 0.30
ACGTcount: A:0.42, C:0.46, G:0.06, T:0.07
Consensus pattern (29 bp):
AACCCGAACCTAACCCAAACCCGAACCCA
Found at i:435486 original size:12 final size:12
Alignment explanation
Indices: 435222--435483 Score: 185
Period size: 12 Copynumber: 22.2 Consensus size: 12
435212 CTTGAACCTT
*
435222 AAACCAGAACCC
1 AAACCCGAACCC
*
435234 GAACCCGAACCC
1 AAACCCGAACCC
**
435246 AAACTTGAACCC
1 AAACCCGAACCC
* * *
435258 GACCCCTAA-CC
1 AAACCCGAACCC
435269 AAACCCGAACCC
1 AAACCCGAACCC
**
435281 AAACTTGAACCC
1 AAACCCGAACCC
* * *
435293 GATCCCTAA-CC
1 AAACCCGAACCC
*
435304 AAACCCTAACCC
1 AAACCCGAACCC
**
435316 AAACCTAAACCC
1 AAACCCGAACCC
435328 AAACCC-AACCCC
1 AAACCCGAA-CCC
* *
435340 TAA-CCAAACCC
1 AAACCCGAACCC
* *
435351 AAACCCAAAACC
1 AAACCCGAACCC
* *
435363 AAACCCTAACTC
1 AAACCCGAACCC
**
435375 AAACCAAAACCC
1 AAACCCGAACCC
435387 AAACCCGAACCC
1 AAACCCGAACCC
435399 AAACCCGAA-CC
1 AAACCCGAACCC
* *
435410 TAACCCAAACCC
1 AAACCCGAACCC
* *
435422 GAACCTGAACCC
1 AAACCCGAACCC
*
435434 GAA-CCGAACCC
1 AAACCCGAACCC
* **
435445 GAATTCGAACCC
1 AAACCCGAACCC
435457 AAACCCGAACCC
1 AAACCCGAACCC
*
435469 AAATCCGAACCC
1 AAACCCGAACCC
435481 AAA
1 AAA
435484 TCCTAACTTG
Statistics
Matches: 196, Mismatches: 47, Indels: 14
0.76 0.18 0.05
Matches are distributed among these distances:
11 45 0.23
12 151 0.77
ACGTcount: A:0.42, C:0.44, G:0.07, T:0.06
Consensus pattern (12 bp):
AAACCCGAACCC
Found at i:436020 original size:14 final size:14
Alignment explanation
Indices: 435982--436022 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
435972 TATTTAATTA
435982 TTTATTTTAT-TAT
1 TTTATTTTATCTAT
435995 TTTATTCTTATCT-T
1 TTTATT-TTATCTAT
436009 TTTATCTTTATCTA
1 TTTAT-TTTATCTA
436023 AAATTCTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.25
14 16 0.67
15 2 0.08
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTTATCTAT
Found at i:436154 original size:15 final size:15
Alignment explanation
Indices: 436134--436163 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
436124 GATTGCTATG
436134 AGAACTACCTTGAAT
1 AGAACTACCTTGAAT
436149 AGAACTACCTTGAAT
1 AGAACTACCTTGAAT
436164 TGTTTATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
AGAACTACCTTGAAT
Found at i:437680 original size:63 final size:63
Alignment explanation
Indices: 437602--437730 Score: 258
Period size: 63 Copynumber: 2.0 Consensus size: 63
437592 AACAACTTGA
437602 TTTCCAAGGTTTCCTCCTTTTGCCTTCGTTCTTTAACTCTAGCTTTGATGATGTTTATGCTGG
1 TTTCCAAGGTTTCCTCCTTTTGCCTTCGTTCTTTAACTCTAGCTTTGATGATGTTTATGCTGG
437665 TTTCCAAGGTTTCCTCCTTTTGCCTTCGTTCTTTAACTCTAGCTTTGATGATGTTTATGCTGG
1 TTTCCAAGGTTTCCTCCTTTTGCCTTCGTTCTTTAACTCTAGCTTTGATGATGTTTATGCTGG
437728 TTT
1 TTT
437731 TGATGCATGC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.12, C:0.22, G:0.17, T:0.49
Consensus pattern (63 bp):
TTTCCAAGGTTTCCTCCTTTTGCCTTCGTTCTTTAACTCTAGCTTTGATGATGTTTATGCTGG
Found at i:454684 original size:36 final size:37
Alignment explanation
Indices: 454607--454700 Score: 120
Period size: 36 Copynumber: 2.6 Consensus size: 37
454597 AAAATGAATT
* * * *
454607 GTCTCGTTTGAGACAGTTTTCTCTAAAAGGAAATTTT
1 GTCTCGCTTGAGACATTTTTCTCTAAAAGCAAATTTC
454644 GTCTCGCTTGAGACAATTTTTCTC-AAAA-CAAATTTC
1 GTCTCGCTTGAGAC-ATTTTTCTCTAAAAGCAAATTTC
*
454680 GTCTCGCTTGAGGCATTTTTC
1 GTCTCGCTTGAGACATTTTTC
454701 CTTTGAGATG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
35 7 0.14
36 19 0.37
37 17 0.33
38 8 0.16
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.39
Consensus pattern (37 bp):
GTCTCGCTTGAGACATTTTTCTCTAAAAGCAAATTTC
Found at i:455033 original size:37 final size:36
Alignment explanation
Indices: 454992--455082 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 36
454982 AAATTTGGAA
* *
454992 ATTGTTTCACTTGAAACAAA-ATTGATAAACCTTTGAG
1 ATTGTTTCTCTTGAAACAAATATTG-T-AACCCTTGAG
* **
455029 ATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAG
1 ATTGTTTCTCTTGAAACAAATATTGTAACCCTTGAG
455065 ATTGTTTCTCTTGAAACA
1 ATTGTTTCTCTTGAAACA
455083 CAAAATCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 25 0.52
37 20 0.42
38 3 0.06
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (36 bp):
ATTGTTTCTCTTGAAACAAATATTGTAACCCTTGAG
Found at i:455128 original size:65 final size:66
Alignment explanation
Indices: 455022--455409 Score: 480
Period size: 66 Copynumber: 5.9 Consensus size: 66
455012 ATTGATAAAC
* **
455022 CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGATTGTTTCTCTTGAAACACAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAC-AA
455087 AT
65 AT
* * *
455089 CTTTGA-ATATG-TTCCCTTGAAACAAA-TTTGTCTCCCTTGAGACATTTTCTTTTGAAACATAA
1 CTTTGAGAT-TGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
455151 AT
65 AT
* * * * * * *
455153 CTTTGAGATCGTTTCCCTTGAAACGAATTTTGCCTCTCATGAGACAGTTTCCCTTGAAACACCAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA
455218 T
66 T
* *
455219 CTTTGA-ACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA
455283 T
66 T
* * * * *
455284 CTTTGAGATCGTTTCCCTTGAAA-AGAATTTTGTCTCTCTTGAGACAGTGTCCCTTGAAACACCA
1 CTTTGAGATTGTTTCCCTTGAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
*
455348 AC
65 AT
** ** *
455350 CTTTGAGATTGTTTCCCTTGAAACATGTTTTGTCTCTTTTGAGACGGTTTCTCTTGAAAC
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
455410 CATCATATCC
Statistics
Matches: 274, Mismatches: 40, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
64 11 0.04
65 102 0.37
66 152 0.55
67 9 0.03
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (66 bp):
CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA
T
Found at i:455174 original size:131 final size:131
Alignment explanation
Indices: 455016--455409 Score: 524
Period size: 131 Copynumber: 3.0 Consensus size: 131
455006 AACAAAATTG
* * * * ** *
455016 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGATTGTTTCTCTTGAAA
1 ATAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
* * *
455081 CACAAAATCTTTGAATATG-TTCCCTTGAAACAAA-TTTGTCTCCCTTGAGACATTTTCTTTTGA
66 CAC-CAATCTTTGAAT-TGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGA
455144 AAC
129 AAC
* * *
455147 ATAAATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGCCTCTCATGAGACAGTTTCCCTTGAAA
1 ATAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
*
455212 CACCAATCTTTGAACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAA
66 CACCAATCTTTGAATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAA
455277 C
131 C
* *
455278 ACAAATCTTTGAGATCGTTTCCCTTGAAA-AGAATTTTGTCTCTCTTGAGACAGTGTCCCTTGAA
1 ATAAATCTTTGAGATCGTTTCCCTTGAAACA-AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAA
* ** ** **
455342 ACACCAACCTTTGAGATTGTTTCCCTTGAAACATGTTTTGTCTCTTTTGAGACGGTTTCTCTTGA
65 ACACCAATCTTTGA-ATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGA
455407 AAC
129 AAC
455410 CATCATATCC
Statistics
Matches: 232, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
129 2 0.01
130 25 0.11
131 159 0.69
132 46 0.20
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (131 bp):
ATAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
CACCAATCTTTGAATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAA
C
Found at i:457128 original size:4 final size:4
Alignment explanation
Indices: 457119--457144 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
457109 CTAACCATTG
457119 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
457145 GTTTCTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:457192 original size:139 final size:134
Alignment explanation
Indices: 456947--457223 Score: 412
Period size: 139 Copynumber: 2.0 Consensus size: 134
456937 TATTTCAAGT
* *
456947 TAACTACTGACTTTTATTTTATTGCACTTTAATCATTGCTATTTATTTATTTATTTATTGTTTCT
1 TAACTACTGACTTTTATTTTATTGCACTCTAACCATTGCTATTTATTTATTTATTTATTGTTTCT
* *
457012 AATATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCTACATTATTATGGTTCGAACT
66 AATATTCGAATCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGAACT
457077 CTGC
131 CTGC
*
457081 TAACTACTGACTTTTATTTTATTGCACTCTAACCATTGTTTATTTATTTATTTATTTATTTATTG
1 TAACTACTGACTTTTATTTTATTGCACTCTAACCATTG-----CTATTTATTTATTTATTTATTG
* * *
457146 TTTCTAATATTTGAATCGACCTTGTGGTGATCC-GATCTGGGGTATGATCCGCATTATTATGGTT
61 TTTCTAATATTCGAATCGACCTTGTGGTGA-CCAGATCCGGGGTATGATCCACATTATTATGGTT
*
457210 CGGACTCTGC
125 CGAACTCTGC
457220 TAAC
1 TAAC
457224 CATTAACGTT
Statistics
Matches: 128, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
134 36 0.28
139 90 0.70
140 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (134 bp):
TAACTACTGACTTTTATTTTATTGCACTCTAACCATTGCTATTTATTTATTTATTTATTGTTTCT
AATATTCGAATCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGAACT
CTGC
Found at i:457391 original size:16 final size:17
Alignment explanation
Indices: 457355--457391 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
457345 TCTGCTAATC
*
457355 GCTAACTTTTCTAACAT
1 GCTAACCTTTCTAACAT
457372 -CTAACCTTTCTAAC-T
1 GCTAACCTTTCTAACAT
457387 GCTAA
1 GCTAA
457392 TTACTAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (17 bp):
GCTAACCTTTCTAACAT
Found at i:463210 original size:28 final size:28
Alignment explanation
Indices: 463170--463232 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
463160 AGTTTACAAA
*
463170 ATTTGAAGTTTATGATATAATTCATAGG
1 ATTTGGAGTTTATGATATAATTCATAGG
* *
463198 ATTTGGAGTTTATGATGTAATTTATAGG
1 ATTTGGAGTTTATGATATAATTCATAGG
*
463226 GTTTGGA
1 ATTTGGA
463233 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.44
Consensus pattern (28 bp):
ATTTGGAGTTTATGATATAATTCATAGG
Found at i:465182 original size:68 final size:68
Alignment explanation
Indices: 465002--465249 Score: 259
Period size: 68 Copynumber: 3.6 Consensus size: 68
464992 CCCTTGTGAT
* * * * *
465002 TCACTCTAATCCTT-TGGAGCTCCCGTGCGAGTCAACCAAAATAATTACGATTAGGTGCTCTCGT
1 TCACTCTAATCATTCAGG-GCTCCTGTGCGAGTCACCCAGAATAATTACGATTAGGTGCTC-CGT
*
465066 GCAAG
64 GCGAG
* * * *
465071 TCACTCTAATCATTCGGGGCTCCCGTGCAAGTCATCC-GAAATAATTACGATTAGGTGCTCCGTG
1 TCACTCTAATCATTCAGGGCTCCTGTGCGAGTCACCCAG-AATAATTACGATTAGGTGCTCCGTG
*
465135 TGAG
65 CGAG
* * ** * *
465139 TCACTCTATTCATTCTGGGCTTTTGTGCGAGTCACCCAGAATAATCACGATT-GGTGCTCCCTTG
1 TCACTCTAATCATTCAGGGCTCCTGTGCGAGTCACCCAGAATAATTACGATTAGGTGCT-CCGTG
465203 CGAG
65 CGAG
* * *
465207 TCACTCTAATCCTTCAAGGCTCCTGTGCGAGTCACTCAGAATA
1 TCACTCTAATCATTCAGGGCTCCTGTGCGAGTCACCCAGAATA
465250 CACATTATTA
Statistics
Matches: 151, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
67 6 0.04
68 91 0.60
69 52 0.34
70 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (68 bp):
TCACTCTAATCATTCAGGGCTCCTGTGCGAGTCACCCAGAATAATTACGATTAGGTGCTCCGTGC
GAG
Found at i:465489 original size:25 final size:26
Alignment explanation
Indices: 465456--465504 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
465446 TGAAATGAAT
*
465456 ACATAATTTTAGCACT-AAACTTATG
1 ACATAATTTCAGCACTGAAACTTATG
* *
465481 ACATGATTTCAGCAGTGAAACTTA
1 ACATAATTTCAGCACTGAAACTTA
465505 ACATTGACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (26 bp):
ACATAATTTCAGCACTGAAACTTATG
Found at i:465504 original size:76 final size:76
Alignment explanation
Indices: 465380--466234 Score: 1071
Period size: 76 Copynumber: 11.3 Consensus size: 76
465370 ACATTAACAT
* * * *
465380 GTAATTCCAGCACTAAA-TTAAACACATACAATTCTAGCAGTGAAACTTAACAATGACTTGCACC
1 GTAATTCCAGCACTAAACTT-ATCACAT--AATTCCAGCAGTGAAACTTAACATTGACTTACACC
465444 AGTGAAATGAATAC
63 AGTGAAATGAATAC
* ** * * *
465458 ATAATTTTAGCACTAAACTTATGACATGATTTCAGCAGTGAAACTTAACATTGACTTACACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
465523 GAAATGAATAC
66 GAAATGAATAC
* * * * * * *
465534 GTAATTCAAGCACCAAACTTATCACATCATTTCAGTAGTGAAATTTAACATTGACCTACA-CAG-
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
*
465597 AAAATGAATAC
66 GAAATGAATAC
* * * **
465608 GTAATTCCAGAACTAAACTTATCACATAATTCCAGTAGTGAAACTTAACATTAACTTACACCAAC
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
*
465673 GAAATGAATAT
66 GAAATGAATAC
* * *
465684 GCAATTCCAACACTAAACTTATCACATAATTCCAACAGTGAAACTTAACATTGACTTACACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
*
465749 GAAATGAATAT
66 GAAATGAATAC
* * *
465760 GTAATTTCAGCACTAAACTTATCACCTAATTCCAGCAATGAAA-TTAACATTGACTTACACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
* * *
465824 AAAATAAATAT
66 GAAATGAATAC
* * * *
465835 GTAATTCCAACACTAAACTTATCACATAATTCCAGTAGCGAAACTTAACATTGACTTACATCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
465900 GAAATGAATAC
66 GAAATGAATAC
* * *
465911 GTAATTCTAGCACTAAACTTATCACATAATTCCCA-CAGTGAAATTTAACATTGACTTACACCAA
1 GTAATTCCAGCACTAAACTTATCACATAATT-CCAGCAGTGAAACTTAACATTGACTTACACCAG
*
465975 TGAAACGAATAC
65 TGAAATGAATAC
* * * *
465987 GTAATTCCAGCACTAAACTTATCACATAATTTCTGCAGTGAAACTTGACATTGACTTACACCAGC
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
466052 GAAATGAATAC
66 GAAATGAATAC
* * * * * * *
466063 ATGATTCCAACATTAAA-TTATCACCTAATTCCAGTAGTGAAACTTAACATTGACTTAAACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
*
466127 GAAATGAATAT
66 GAAATGAATAC
* * * *
466138 GTAATTCCAGCACTAAACGTT-TCACATAAGTCAAGGAGTG-AA-TTGAACATTGACTTACACTA
1 GTAATTCCAGCACTAAAC-TTATCACATAATTCCAGCAGTGAAACTT-AACATTGACTTACACCA
466200 GTGAAATGAATAC
64 GTGAAATGAATAC
466213 GTAATTCCAGCACTAAACTTAT
1 GTAATTCCAGCACTAAACTTAT
466235 GATTTCACAT
Statistics
Matches: 671, Mismatches: 96, Indels: 23
0.85 0.12 0.03
Matches are distributed among these distances:
74 66 0.10
75 184 0.27
76 395 0.59
77 5 0.01
78 19 0.03
79 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (76 bp):
GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
GAAATGAATAC
Found at i:465855 original size:151 final size:152
Alignment explanation
Indices: 465378--466234 Score: 1068
Period size: 151 Copynumber: 5.7 Consensus size: 152
465368 GAACATTAAC
* * * * *
465378 ATGTAATTCCAGCACTAAA-TTAAACACATACAATTCTAGCAGTGAAACTTAACAATGACTTGCA
1 ATGTAATTCCAACACTAAACTT-ATCACAT--AATTCCAGCAGTGAAACTTAACATTGACTTACA
* ** * * *
465442 CCAGTGAAATGAATACATAATTTTAGCACTAAACTTATGACATGATTTCAGCAGTGAAACTTAAC
63 CCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAAC
465507 ATTGACTTACACCAGTGAAATGAAT
128 ATTGACTTACACCAGTGAAATGAAT
* * * * * * *
465532 ACGTAATT-CAAGCACCAAACTTATCACATCATTTCAGTAGTGAAATTTAACATTGACCTACA-C
1 ATGTAATTCCAA-CACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACC
* * *
465595 AG-AAAATGAATACGTAATTCCAGAACTAAACTTATCACATAATTCCAGTAGTGAAACTTAACAT
65 AGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACAT
* **
465659 TAACTTACACCAACGAAATGAAT
130 TGACTTACACCAGTGAAATGAAT
* *
465682 ATGCAATTCCAACACTAAACTTATCACATAATTCCAACAGTGAAACTTAACATTGACTTACACCA
1 ATGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
* * * *
465747 GTGAAATGAATATGTAATTTCAGCACTAAACTTATCACCTAATTCCAGCAATGAAA-TTAACATT
66 GTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATT
* *
465811 GACTTACACCAGTAAAATAAAT
131 GACTTACACCAGTGAAATGAAT
* * *
465833 ATGTAATTCCAACACTAAACTTATCACATAATTCCAGTAGCGAAACTTAACATTGACTTACATCA
1 ATGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
* *
465898 GTGAAATGAATACGTAATTCTAGCACTAAACTTATCACATAATTCCCA-CAGTGAAATTTAACAT
66 GTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATT-CCAGCAGTGAAACTTAACAT
* *
465962 TGACTTACACCAATGAAACGAAT
130 TGACTTACACCAGTGAAATGAAT
* * * * *
465985 ACGTAATTCCAGCACTAAACTTATCACATAATTTCTGCAGTGAAACTTGACATTGACTTACACCA
1 ATGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
* * * * * * *
466050 GCGAAATGAATACATGATTCCAACATTAAA-TTATCACCTAATTCCAGTAGTGAAACTTAACATT
66 GTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATT
*
466114 GACTTAAACCAGTGAAATGAAT
131 GACTTACACCAGTGAAATGAAT
* * * *
466136 ATGTAATTCCAGCACTAAACGTT-TCACATAAGTCAAGGAGTG-AA-TTGAACATTGACTTACAC
1 ATGTAATTCCAACACTAAAC-TTATCACATAATTCCAGCAGTGAAACTT-AACATTGACTTACAC
*
466198 TAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
64 CAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
466235 GATTTCACAT
Statistics
Matches: 600, Mismatches: 92, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
149 2 0.00
150 167 0.28
151 224 0.37
152 184 0.31
153 2 0.00
154 19 0.03
155 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (152 bp):
ATGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
GTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATT
GACTTACACCAGTGAAATGAAT
Found at i:465927 original size:227 final size:226
Alignment explanation
Indices: 465380--466234 Score: 1103
Period size: 227 Copynumber: 3.8 Consensus size: 226
465370 ACATTAACAT
* * * * * *
465380 GTAATTCCAGCACTAAATTAAACACATACAATTCTAGCAGTGAAACTTAACAATGACTTGCACCA
1 GTAATTCCAACACTAAATT-ATCACAT--AATTCCAGTAGTGAAACTTAACATTGACTTACACCA
* ** * * * *
465445 GTGAAATGAATACATAATTTTAGCACTAAACTTATGACATGATTTCAGCAGTGAAACTTAACATT
63 GTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAACAGTGAAACTTAACATT
* * * *
465510 GACTTACACCAGTGAAATGAATACGTAATTCAAGCACCAAACTTATCACATCATTTCAGTAGTGA
128 GACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTTCAGCAGTGA
* *
465575 AATTTAACATTGACCTACA-CAGAAAATGAATAC
193 AACTTAACATTGACTTACACCAGAAAATGAATAC
* *
465608 GTAATTCCAGA-ACTAAACTTATCACATAATTCCAGTAGTGAAACTTAACATTAACTTACACCAA
1 GTAATTCCA-ACACTAAA-TTATCACATAATTCCAGTAGTGAAACTTAACATTGACTTACACCAG
* * * *
465672 CGAAATGAATATGCAATTCCAACACTAAACTTATCACATAATTCCAACAGTGAAACTTAACATTG
64 TGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAACAGTGAAACTTAACATTG
* * * * *
465737 ACTTACACCAGTGAAATGAATATGTAATTTCAGCACTAAACTTATCACCTAATTCCAGCAATGAA
129 ACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTTCAGCAGTGAA
* *
465802 A-TTAACATTGACTTACACCAGTAAAATAAATAT
194 ACTTAACATTGACTTACACCAG-AAAATGAATAC
* *
465835 GTAATTCCAACACTAAACTTATCACATAATTCCAGTAGCGAAACTTAACATTGACTTACATCAGT
1 GTAATTCCAACACTAAA-TTATCACATAATTCCAGTAGTGAAACTTAACATTGACTTACACCAGT
* * *
465900 GAAATGAATACGTAATTCTAGCACTAAACTTATCACATAATTCCCACAGTGAAATTTAACATTGA
65 GAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAACAGTGAAACTTAACATTGA
* * *
465965 CTTACACCAATGAAACGAATACGTAATTCCAGCACTAAACTTATCACATAATTTCTGCAGTGAAA
130 CTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTTCAGCAGTGAAA
* *
466030 CTTGACATTGACTTACACCAGCGAAATGAATAC
195 CTTAACATTGACTTACACCAG-AAAATGAATAC
* * * * *
466063 ATGATTCCAACATTAAATTATCACCTAATTCCAGTAGTGAAACTTAACATTGACTTAAACCAGTG
1 GTAATTCCAACACTAAATTATCACATAATTCCAGTAGTGAAACTTAACATTGACTTACACCAGTG
* * *
466128 AAATGAATATGTAATTCCAGCACTAAACGTT-TCACATAAGT-CAAGGAGTG-AA-TTGAACATT
66 AAATGAATACGTAATTCCAGCACTAAAC-TTATCACATAATTCCAA-CAGTGAAACTT-AACATT
*
466189 GACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
128 GACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
466235 GATTTCACAT
Statistics
Matches: 548, Mismatches: 70, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
225 17 0.03
226 199 0.36
227 266 0.49
228 64 0.12
229 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (226 bp):
GTAATTCCAACACTAAATTATCACATAATTCCAGTAGTGAAACTTAACATTGACTTACACCAGTG
AAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAACAGTGAAACTTAACATTGAC
TTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTTCAGCAGTGAAAC
TTAACATTGACTTACACCAGAAAATGAATAC
Found at i:471854 original size:164 final size:160
Alignment explanation
Indices: 471551--471874 Score: 596
Period size: 164 Copynumber: 2.0 Consensus size: 160
471541 CCACAACAAT
471551 AATTTTTTTGTCTTTTTGGTCCTTCCAATTGCTTTTATCAGTGAATGATCTGCTTGCAAATGATA
1 AATTTTTTTGTCTTTTTGGTCCTTCCAATTGCTTTTATCAGTGAATGATCTGCTTGCAAATGATA
471616 AATAAAATTATTTCATTCATATTATAGATAATTCCAATTAAAATTTTCCAATTTAGCTCTTATTT
66 AATAAAATTATTTCATTCATATTATAGATAATTCCAATTAAAATTTTCCAATTTAGCTCTTATTT
471681 GAGGTAAAGCATCATCAATATTCTCCATAA
131 GAGGTAAAGCATCATCAATATTCTCCATAA
471711 AATTTTTCCTTGTCTTTTTTGGTCCTTCCAATTGCTTTTTATCAGTGAATGATCTGCTTGCAAAT
1 AATTTTT--TTGTC-TTTTTGGTCCTTCCAATTGC-TTTTATCAGTGAATGATCTGCTTGCAAAT
471776 GATAAAATAAAATTATTTCATTCATATTATAGATAATTCCAATTAAAATTTTCCAATTTAGCTC-
62 GAT-AAATAAAATTATTTCATTCATATTATAGATAATTCCAATTAAAATTTTCCAATTTAGCTCT
471840 TATTTGAGGTAAAGCATCATCAATATTCTCCATAA
126 TATTTGAGGTAAAGCATCATCAATATTCTCCATAA
471875 CAACTGAACC
Statistics
Matches: 159, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
160 7 0.04
162 5 0.03
163 20 0.13
164 67 0.42
165 60 0.38
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (160 bp):
AATTTTTTTGTCTTTTTGGTCCTTCCAATTGCTTTTATCAGTGAATGATCTGCTTGCAAATGATA
AATAAAATTATTTCATTCATATTATAGATAATTCCAATTAAAATTTTCCAATTTAGCTCTTATTT
GAGGTAAAGCATCATCAATATTCTCCATAA
Found at i:474849 original size:18 final size:18
Alignment explanation
Indices: 474826--474892 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
474816 CAGTCCGATC
474826 GTTGACCATTGATCGACT
1 GTTGACCATTGATCGACT
474844 GTTGACCATTGATCGACT
1 GTTGACCATTGATCGACT
*
474862 GTTGACCGTTGA-C--C-
1 GTTGACCATTGATCGACT
*
474876 GTTGACCGTTGATCGAC
1 GTTGACCATTGATCGAC
474893 CGTTAACTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 12 0.27
15 2 0.04
17 2 0.04
18 29 0.64
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.31
Consensus pattern (18 bp):
GTTGACCATTGATCGACT
Found at i:474872 original size:7 final size:7
Alignment explanation
Indices: 474862--474887 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
474852 TTGATCGACT
474862 GTTGACC
1 GTTGACC
474869 GTTGACC
1 GTTGACC
474876 GTTGACC
1 GTTGACC
474883 GTTGA
1 GTTGA
474888 TCGACCGTTA
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:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (7 bp):
GTTGACC
Found at i:474893 original size:25 final size:25
Alignment explanation
Indices: 474825--474896 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
474815 CCAGTCCGAT
* *
474825 CGTTGACCATTGATCGACTGTTGAC
1 CGTTGACCGTTGATCGACCGTTGAC
* * * *
474850 CATTGATCGACTG-TTGACCGTTGAC
1 CGTTGACCG-TTGATCGACCGTTGAC
474875 CGTTGACCGTTGATCGACCGTT
1 CGTTGACCGTTGATCGACCGTT
474897 AACTTGACTT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
24 2 0.06
25 31 0.89
26 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (25 bp):
CGTTGACCGTTGATCGACCGTTGAC
Found at i:475780 original size:39 final size:39
Alignment explanation
Indices: 475732--475821 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
475722 TTGTTTAGGG
* *
475732 TAAGTCCTTACTACA-GACTCATCTGCTTTGTGCACAGGA
1 TAAGACCTTACTACATG-CTCATATGCTTTGTGCACAGGA
* *
475771 TAAGACCTTACTGCATGCTCCTATGCTTTGTGCACAGGA
1 TAAGACCTTACTACATGCTCATATGCTTTGTGCACAGGA
475810 TAAGACCTTACT
1 TAAGACCTTACT
475822 GCAGGTCTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 45 0.98
40 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (39 bp):
TAAGACCTTACTACATGCTCATATGCTTTGTGCACAGGA
Found at i:476018 original size:169 final size:168
Alignment explanation
Indices: 475739--476077 Score: 644
Period size: 169 Copynumber: 2.0 Consensus size: 168
475729 GGGTAAGTCC
475739 TTACTACAGACTCATCTGCTTTGTGCACAGGATAAGACCTTACTGCATGCTCCTATGCTTTGTGC
1 TTACTACAGACTCATCTGCTTTGTGCACAGGATAAGACCTTACTGCATGCTCCTATGCTTTGTG-
475804 ACAGGATAAGACCTTACTGCAGGTCTCTACCTTATGCACAGGGTAAGCCCTTACTGGGTGTACAG
65 ACAGGATAAGACCTTACTGCAGGTCTCTACCTTATGCACAGGGTAAGCCCTTACTGGGTGTACAG
475869 GTAGGTGTATGGTTCTGGGAAACCTACACATTCTGGTGA
130 GTAGGTGTATGGTTCTGGGAAACCTACACATTCTGGTGA
475908 TTACTACAGACTCATCTGCTTTGTGCACAGGATAAGACCTTACTGCATGCTCCTATGCTTTGTG-
1 TTACTACAGACTCATCTGCTTTGTGCACAGGATAAGACCTTACTGCATGCTCCTATGCTTTGTGA
475972 CAGGATAAGACCTTACTGCAGGCGTCTCTACCTTATGCACAGGGTAAGCCCTTACTGGGTGTACA
66 CAGGATAAGACCTTACTGCA-G-GTCTCTACCTTATGCACAGGGTAAGCCCTTACTGGGTGTACA
476037 GGTAGGTGTATGGTTCTGGGAAACCTACACATTCTGGTGA
129 GGTAGGTGTATGGTTCTGGGAAACCTACACATTCTGGTGA
476077 T
1 T
476078 CAGACGGGGG
Statistics
Matches: 168, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
167 20 0.12
168 1 0.01
169 147 0.88
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (168 bp):
TTACTACAGACTCATCTGCTTTGTGCACAGGATAAGACCTTACTGCATGCTCCTATGCTTTGTGA
CAGGATAAGACCTTACTGCAGGTCTCTACCTTATGCACAGGGTAAGCCCTTACTGGGTGTACAGG
TAGGTGTATGGTTCTGGGAAACCTACACATTCTGGTGA
Found at i:480792 original size:2 final size:2
Alignment explanation
Indices: 480785--480815 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
480775 AAAAATCCAT
480785 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
480816 AACTAACCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:480803 original size:17 final size:17
Alignment explanation
Indices: 480783--480815 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
480773 ATAAAAATCC
480783 ATTATATATATATATAT
1 ATTATATATATATATAT
480800 ATTATATATATATATA
1 ATTATATATATATATA
480816 AACTAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTATATATATATATAT
Found at i:480805 original size:15 final size:15
Alignment explanation
Indices: 480787--480815 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
480777 AAATCCATTA
480787 TATATATATATATAT
1 TATATATATATATAT
480802 TATATATATATATA
1 TATATATATATATA
480816 AACTAACCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:482001 original size:39 final size:39
Alignment explanation
Indices: 481933--482163 Score: 239
Period size: 39 Copynumber: 5.9 Consensus size: 39
481923 CTTTCCGCAT
* * * * *
481933 GCTCATCGGTTTTATGCTCAGGGTAAGTCCTTACAGCAG
1 GCTCCTCGGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
* *
481972 GCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGTAG
1 GCTCCTCGGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
* ** * *
482011 GCTCATCGGCTTTGTGCTTAGGGTAAGTCTTTACTACAG
1 GCTCCTCGGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
* * * * *
482050 ACTTCTCTGCTTTGTGCACAGGATAAGACCTTACTGCAG
1 GCTCCTCGGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
* ** *
482089 GCTCCTCTGCTTTGTGCACAGTATAAGACCTTACTGCAG
1 GCTCCTCGGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
* *
482128 GCGCCTCTGCTTTGTGCACAGGGTAAG-CTCTTACTG
1 GCTCCTCGGCTTTGTGCACAGGGTAAGTC-CTTACTG
482164 GGTGTACAGG
Statistics
Matches: 165, Mismatches: 26, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
38 1 0.01
39 164 0.99
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (39 bp):
GCTCCTCGGCTTTGTGCACAGGGTAAGTCCTTACTGCAG
Found at i:484074 original size:2 final size:2
Alignment explanation
Indices: 484067--484115 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
484057 CAAATTGTAT
484067 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
484107 TA TA -A TA TA
1 TA TA TA TA TA
484116 GCCTTATATG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:484093 original size:15 final size:14
Alignment explanation
Indices: 484067--484115 Score: 77
Period size: 13 Copynumber: 3.7 Consensus size: 14
484057 CAAATTGTAT
484067 TATATATATATATA
1 TATATATATATATA
484081 TATATAT-TATATA
1 TATATATATATATA
484094 TATATATA-ATATA
1 TATATATATATATA
484107 TATA-ATATA
1 TATATATATA
484116 GCCTTATATG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.09
13 23 0.70
14 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATATATATATA
Found at i:486142 original size:69 final size:68
Alignment explanation
Indices: 485964--486142 Score: 216
Period size: 69 Copynumber: 2.6 Consensus size: 68
485954 AAATACCCCT
* * **
485964 TGTGAGTCACTCTAATCATTCGGAGCTCCCGTGCGAGCCAATCGAAATAATTACGATTAGGTGCT
1 TGTGAGTCACTCTAATCCTTCGG-GCTCCCGTGCGAGTCACCCGAAATAATTACGATTAGGTGCT
486029 CCCG
65 CCCG
** *
486033 TGCAAGTCACTCTAATCCTTCGGGGCTCCCGTGC-ATGTCACCCGAGATAATTACGATTAGGTGC
1 TGTGAGTCACTCTAATCCTTC-GGGCTCCCGTGCGA-GTCACCCGAAATAATTACGATTAGGTGC
*
486097 TCCTG
64 TCCCG
* **
486102 TGTGAGTCACTCTATTCCTTCAGGGCTTTCGTGCGAGTCAC
1 TGTGAGTCACTCTAATCCTTC-GGGCTCCCGTGCGAGTCAC
486143 TCTATTCCTT
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
68 1 0.01
69 89 0.96
70 3 0.03
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.28
Consensus pattern (68 bp):
TGTGAGTCACTCTAATCCTTCGGGCTCCCGTGCGAGTCACCCGAAATAATTACGATTAGGTGCTC
CCG
Found at i:486143 original size:31 final size:31
Alignment explanation
Indices: 486105--486173 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
486095 GCTCCTGTGT
486105 GAGTCACTCTATTCCTTCAGGGCTTTCGTGC
1 GAGTCACTCTATTCCTTCAGGGCTTTCGTGC
**
486136 GAGTCACTCTATTCCTTTGGGGCTTTCGTGC
1 GAGTCACTCTATTCCTTCAGGGCTTTCGTGC
486167 GAGTCAC
1 GAGTCAC
486174 CCAGAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.13, C:0.28, G:0.25, T:0.35
Consensus pattern (31 bp):
GAGTCACTCTATTCCTTCAGGGCTTTCGTGC
Found at i:486166 original size:100 final size:100
Alignment explanation
Indices: 486031--486228 Score: 256
Period size: 100 Copynumber: 2.0 Consensus size: 100
486021 TAGGTGCTCC
*
486031 CGTGCAAGTCACTCTAATCCTTCGGGGCTCCCGTGC-ATGTCACCC-GAGATAATTACGATTAGG
1 CGTGCAAGTCACTCTAATCCTTCGGGGCTCCCGTGCGA-GTCACCCAGA-ATAATCACGATTAGG
* * *
486094 TGCTCCTGTGTGAGTCACTCTATTCCTTCAGGGCTTT
64 TGCTCCTGTGCGAATCACTCTAATCCTTCAGGGCTTT
* * * ** *
486131 CGTGCGAGTCACTCTATTCCTTTGGGGCTTTCGTGCGAGTCACCCAGAATAATCATGATTAGGTG
1 CGTGCAAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCACCCAGAATAATCACGATTAGGTG
* *
486196 CTCCTTTGCGAATCACTCTAATCCTTCATGGCT
66 CTCCTGTGCGAATCACTCTAATCCTTCAGGGCT
486229 CCTGTGCCAG
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
100 81 0.96
101 3 0.04
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (100 bp):
CGTGCAAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCACCCAGAATAATCACGATTAGGTG
CTCCTGTGCGAATCACTCTAATCCTTCAGGGCTTT
Found at i:486508 original size:76 final size:76
Alignment explanation
Indices: 486411--486935 Score: 638
Period size: 76 Copynumber: 6.9 Consensus size: 76
486401 AACACATTAC
* * * *
486411 AATTCTAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
* * *
486476 ATTTATGACGT
66 ACTTATCACAT
** * * * *
486487 GCTTTCAGCAGTGAAACTTAACATTAATTTACACCAGTGAAATGAATACGTAATT-CAAGCACCA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAA-CACTA
*
486551 AATTTATCACAT
65 AACTTATCACAT
* * ** * ** * * *
486563 CATTTCAATAGTGAAATTTAACATTGACTTACACCAGCAAAATGAATATGTAATTTCAACGCTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
486628 ACTTATCACAT
66 ACTTATCACAT
* * * ** *
486639 AATTCCAGTAGTGAAACTTAACATTAACTTACACTAACGAAATGAATACGTGATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
486704 ACTTATCACAT
66 ACTTATCACAT
* **
486715 AATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGGACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
*
486780 ACTTATCACCT
66 ACTTATCACAT
* * *
486791 AATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
*
486856 ACTTATCACGT
66 ACTTATCACAT
* * * * * *
486867 AATTCCAGCAGCGAAACTTAACATTGATTTACATCAGCGAAATGAATACATAACTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
486932 ACTT
66 ACTT
486936 TGAAGCTTAA
Statistics
Matches: 384, Mismatches: 63, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
75 1 0.00
76 380 0.99
77 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (76 bp):
AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
ACTTATCACAT
Found at i:486817 original size:228 final size:227
Alignment explanation
Indices: 486411--487299 Score: 1002
Period size: 228 Copynumber: 4.0 Consensus size: 227
486401 AACACATTAC
* * * * *
486411 AATTCTAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCAACACTAA
* ** * * *
486476 ATTTATGACGTGCTTTCAGCAGTGAAACTTAACATTAATTTACACCAGTGAAATGAATACGTAAT
66 ATTTATCAC-TAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
* * * * * * *
486541 TCAAGCACCAAATTTATCACATCATTTCAATAGTGAAATTTAACATTGACTTACACCAGCAAAAT
130 TCCAGCACTAAACTTATCACATAATTCCAGTAGTGAAATTTAACATTGACTTACACCAGTAAAAT
* * *
486606 GAATATGTAATTTCAACGCTAAACTTATCACAT
195 GAATACGTAATTCCAACACTAAACTTATCACAT
* * * * *
486639 AATTCCAGTAGTGAAACTTAACATTAACTTACACTAACGAAATGAATACGTGATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCAACACTAA
* *
486704 ACTTATCACATAATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
66 ATTTATCAC-TAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
* * * *
486769 TCCAGGACTAAACTTATCACCTAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAAT
130 TCCAGCACTAAACTTATCACATAATTCCAGTAGTGAAATTTAACATTGACTTACACCAGTAAAAT
*
486834 GAATACGTAATTCCAACACTAAACTTATCACGT
195 GAATACGTAATTCCAACACTAAACTTATCACAT
* * * * *
486867 AATTCCAGCAGCGAAACTTAACATTGATTTACATCAGCGAAATGAATACATAACTCCAACACT--
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCAACACTAA
* * * * *
486930 A---A--AC---TT-------TGAAGCTTAACATTGACTTACATCATTGAAATGAAAATGTAATT
66 ATTTATCACTAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATT
* * * * * *
486980 CTACCACTAAACTTGTCACATAATTCCCGTAGTGAAATTTAACATTGACTTACAACAGTGAAATG
131 CCAGCACTAAACTTATCACATAATTCCAGTAGTGAAATTTAACATTGACTTACACCAGTAAAATG
* * *
487045 AATACGTAATTCTAGCACTAAACTTTTCACAT
196 AATACGTAATTCCAACACTAAACTTATCACAT
* * *
487077 AATTCCTGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCAGCATTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCAACACTAA
* * * *
487142 ATTTATCACCTAATTCCAGTAGTGAAACTTAACATTGACTTAAACCAGTGAAGTGAATACGTCAT
66 ATTTATCA-CTAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
* * * * ** * * * *
487207 TCCATCACTAAACTTTTCACATAAGTCAAGGGGTGAAATTGAACATTAACTTACACTAGTGAAAT
130 TCCAGCACTAAACTTATCACATAATTCCAGTAGTGAAATTTAACATTGACTTACACCAGTAAAAT
*
487272 CAATACGTAATTCCAACACTAAACTTAT
195 GAATACGTAATTCCAACACTAAACTTAT
487300 GATTTCACAT
Statistics
Matches: 548, Mismatches: 95, Indels: 36
0.81 0.14 0.05
Matches are distributed among these distances:
210 177 0.32
212 1 0.00
215 1 0.00
217 3 0.01
218 1 0.00
221 4 0.01
223 1 0.00
226 1 0.00
228 359 0.66
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (227 bp):
AATTCCAGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCAACACTAA
ATTTATCACTAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATT
CCAGCACTAAACTTATCACATAATTCCAGTAGTGAAATTTAACATTGACTTACACCAGTAAAATG
AATACGTAATTCCAACACTAAACTTATCACAT
Found at i:486993 original size:210 final size:210
Alignment explanation
Indices: 486726--487134 Score: 593
Period size: 210 Copynumber: 1.9 Consensus size: 210
486716 ATTCCAACAG
* ** *
486726 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGGACTAAACTTATCACCT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAAAACGTAATTCCACCACTAAACTTATCACAT
*
486791 AATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAACACTAA
66 AATTCCAGCAATGAAATTTAACATTGACTTACAACAGTAAAATGAATACGTAATTCCAACACTAA
* * * *
486856 ACTTATCACGTAATTCCAGCAGCGAAACTTAACATTGATTTACATCAGCGAAATGAATACATAAC
131 ACTTATCACATAATTCCAGCAGCGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAAC
486921 TCCAACACTAAACTT
196 TCCAACACTAAACTT
* * * * * *
486936 TGAAGCTTAACATTGACTTACATCATTGAAATGAAAATGTAATTCTACCACTAAACTTGTCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAAAACGTAATTCCACCACTAAACTTATCACAT
* * * * * *
487001 AATTCCCGTAGTGAAATTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCTAGCACTAA
66 AATTCCAGCAATGAAATTTAACATTGACTTACAACAGTAAAATGAATACGTAATTCCAACACTAA
* * * *
487066 ACTTTTCACATAATTCCTGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAAT
131 ACTTATCACATAATTCCAGCAGCGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAAC
487131 TCCA
196 TCCA
487135 GCATTAAATT
Statistics
Matches: 174, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
210 174 1.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (210 bp):
TGAAACTTAACATTGACTTACACCAGTGAAATGAAAACGTAATTCCACCACTAAACTTATCACAT
AATTCCAGCAATGAAATTTAACATTGACTTACAACAGTAAAATGAATACGTAATTCCAACACTAA
ACTTATCACATAATTCCAGCAGCGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAAC
TCCAACACTAAACTT
Found at i:487048 original size:134 final size:134
Alignment explanation
Indices: 486808--487070 Score: 346
Period size: 134 Copynumber: 2.0 Consensus size: 134
486798 GCAATGAAAT
* *
486808 TTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACGTAATTCC
1 TTAACATTGACTTACACCAGTAAAATGAAAACGTAATTCCAACACTAAACTTATCACATAATTCC
* *
486873 AGCAGCGAAACTTAACATTGATTTACATCAGCGAAATGAATACATAACTCCAACACTAAACTTTG
66 AGCAGCGAAACTTAACATTGACTTACAACAGCGAAATGAATACATAACTCCAACACTAAACTTTG
486938 AAGC
131 AAGC
* * * * * * *
486942 TTAACATTGACTTACATCATTGAAATGAAAATGTAATTCTACCACTAAACTTGTCACATAATTCC
1 TTAACATTGACTTACACCAGTAAAATGAAAACGTAATTCCAACACTAAACTTATCACATAATTCC
* * * * * * * * *
487007 CGTAGTGAAATTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCTAGCACTAAACTTT
66 AGCAGCGAAACTTAACATTGACTTACAACAGCGAAATGAATACATAACTCCAACACTAAACTTT
487071 TCACATAATT
Statistics
Matches: 109, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
134 109 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (134 bp):
TTAACATTGACTTACACCAGTAAAATGAAAACGTAATTCCAACACTAAACTTATCACATAATTCC
AGCAGCGAAACTTAACATTGACTTACAACAGCGAAATGAATACATAACTCCAACACTAAACTTTG
AAGC
Found at i:487068 original size:76 final size:76
Alignment explanation
Indices: 486936--487297 Score: 399
Period size: 76 Copynumber: 4.8 Consensus size: 76
486926 CACTAAACTT
* * * * * * * *
486936 TGAAGCTTAACATTGACTTACATCATTGAAATGAAAATGTAATTCTACCACTAAACTTGTCACAT
1 TGAAACTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCCAGCACTAAACTTTTCACAT
*
487001 AATTCCCGTAG
66 AATTCCAGTAG
* *
487012 TGAAATTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCTAGCACTAAACTTTTCACAT
1 TGAAACTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCCAGCACTAAACTTTTCACAT
* *
487077 AATTCCTGCAG
66 AATTCCAGTAG
* * * * * *
487088 TGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCAGCATTAAA-TTTATCACC
1 TGAAACTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCCAGCACTAAACTTT-TCACA
487152 TAATTCCAGTAG
65 TAATTCCAGTAG
* * *
487164 TGAAACTTAACATTGACTTA-AACCAGTGAAGTGAATACGTCATTCCATCACTAAACTTTTCACA
1 TGAAACTTAACATTGACTTACAA-CAGTGAAATGAATACGTAATTCCAGCACTAAACTTTTCACA
* * **
487228 TAAGTCAAGGGG
65 TAATTCCAGTAG
* * *
487240 TGAAA-TTGAACATTAACTTAC-ACTAGTGAAATCAATACGTAATTCCAACACTAAACTT
1 TGAAACTT-AACATTGACTTACAAC-AGTGAAATGAATACGTAATTCCAGCACTAAACTT
487298 ATGATTTCAC
Statistics
Matches: 242, Mismatches: 38, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
75 7 0.03
76 232 0.96
77 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.30
Consensus pattern (76 bp):
TGAAACTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCCAGCACTAAACTTTTCACAT
AATTCCAGTAG
Found at i:487217 original size:152 final size:152
Alignment explanation
Indices: 486936--487299 Score: 444
Period size: 152 Copynumber: 2.4 Consensus size: 152
486926 CACTAAACTT
* * * * * * * *
486936 TGAAGCTTAACATTGACTTACATCATTGAAATGAAAATGTAATTCTACCACTAAACTTGTCACAT
1 TGAAACTTAACATTAACTTACACCAGTGAAATGAATACGTAATTCCACCACTAAACTTATCACAT
* * *
487001 AATTCCCGTAGTGAAATTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCTAGCACTAA
66 AATTCCAGTAGTGAAACTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCCAGCACTAA
* **
487066 ACTTTTCACATAATTCCTGCAG
131 ACTTTTCACATAAGTCAAGCAG
* * * * * *
487088 TGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCAGCATTAAATTTATCACCT
1 TGAAACTTAACATTAACTTACACCAGTGAAATGAATACGTAATTCCACCACTAAACTTATCACAT
* * *
487153 AATTCCAGTAGTGAAACTTAACATTGACTTA-AACCAGTGAAGTGAATACGTCATTCCATCACTA
66 AATTCCAGTAGTGAAACTTAACATTGACTTACAA-CAGTGAAATGAATACGTAATTCCAGCACTA
**
487217 AACTTTTCACATAAGTCAAGGGG
130 AACTTTTCACATAAGTCAAGCAG
* * *
487240 TGAAA-TTGAACATTAACTTACACTAGTGAAATCAATACGTAATTCCAACACTAAACTTAT
1 TGAAACTT-AACATTAACTTACACCAGTGAAATGAATACGTAATTCCACCACTAAACTTAT
487300 GATTTCACAT
Statistics
Matches: 178, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
151 4 0.02
152 174 0.98
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.30
Consensus pattern (152 bp):
TGAAACTTAACATTAACTTACACCAGTGAAATGAATACGTAATTCCACCACTAAACTTATCACAT
AATTCCAGTAGTGAAACTTAACATTGACTTACAACAGTGAAATGAATACGTAATTCCAGCACTAA
ACTTTTCACATAAGTCAAGCAG
Found at i:487289 original size:362 final size:362
Alignment explanation
Indices: 486580--487297 Score: 958
Period size: 362 Copynumber: 2.0 Consensus size: 362
486570 ATAGTGAAAT
* *
486580 TTAACATTGACTTACACCAGCAAAATGAATATGTAATTTCAACGCTAAACTTATCACATAATTCC
1 TTAACATTGACTTACACCAGCAAAATGAAAATGTAATTTCAACACTAAACTTATCACATAATTCC
*
486645 AGTAGTGAAACTTAACATTAACTTACACTAACGAAATGAATACGTGATTCCAACACTAAACTTAT
66 AGTAGTGAAACTTAACATTAACTTACACTAACGAAATGAATACGTAATTCCAACACTAAACTTAT
* * * *
486710 CACATAATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGG
131 CACATAATTCCAACAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCAGC
* *
486775 ACTAAACTTATCACCTAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATAC
196 ACTAAACTTATCACCTAATTCCAGCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAATAC
* * * * *
486840 GTAATTCCAACACTAAACTTATCACGTAATTCCAGCAGCGAAACTTAACATTGATTTACATCAGC
261 GTAATTCCAACACTAAACTTATCACATAAGTCAAGCAGCGAAACTTAACATTAACTTACATCAGC
*
486905 GAAATGAATACATAACTCCAACACTAAACTTTGAAGC
326 GAAATCAATACATAACTCCAACACTAAACTTTGAAGC
* *** * *
486942 TTAACATTGACTTACATCATTGAAATGAAAATGTAA-TTCTACCACTAAACTTGTCACATAATTC
1 TTAACATTGACTTACACCAGCAAAATGAAAATGTAATTTC-AACACTAAACTTATCACATAATTC
* * * ** * *
487006 CCGTAGTGAAATTTAACATTGACTTACAAC-AGTGAAATGAATACGTAATTCTAGCACTAAACTT
65 CAGTAGTGAAACTTAACATTAACTTAC-ACTAACGAAATGAATACGTAATTCCAACACTAAACTT
* **
487070 TTCACATAATTCCTGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCA
129 ATCACATAATTCCAACAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCA
* * * * * *
487135 GCATTAAATTTATCACCTAATTCCAGTAGTGAAACTTAACATTGACTTAAACCAGTGAAGTGAAT
194 GCACTAAACTTATCACCTAATTCCAGCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAAT
* * * ** *
487200 ACGTCATTCCATCACTAAACTTTTCACATAAGTCAAGGGGTGAAA-TTGAACATTAACTTACA-C
259 ACGTAATTCCAACACTAAACTTATCACATAAGTCAAGCAGCGAAACTT-AACATTAACTTACATC
* * *
487263 TAGTGAAATCAATACGTAATTCCAACACTAAACTT
323 -AGCGAAATCAATACATAACTCCAACACTAAACTT
487298 ATGATTTCAC
Statistics
Matches: 306, Mismatches: 46, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
361 6 0.02
362 298 0.97
363 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.29
Consensus pattern (362 bp):
TTAACATTGACTTACACCAGCAAAATGAAAATGTAATTTCAACACTAAACTTATCACATAATTCC
AGTAGTGAAACTTAACATTAACTTACACTAACGAAATGAATACGTAATTCCAACACTAAACTTAT
CACATAATTCCAACAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTCCAGC
ACTAAACTTATCACCTAATTCCAGCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAATAC
GTAATTCCAACACTAAACTTATCACATAAGTCAAGCAGCGAAACTTAACATTAACTTACATCAGC
GAAATCAATACATAACTCCAACACTAAACTTTGAAGC
Found at i:488012 original size:21 final size:21
Alignment explanation
Indices: 487986--488047 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
487976 TTGTTTAAAG
*
487986 AAATAAAATGAGATAAAGATT
1 AAATAAAATGAGATAAAGAAT
*
488007 AAATAAAAT-A-ATAAAAAAAT
1 AAATAAAATGAGAT-AAAGAAT
488027 AAATAAAATTGAGATAAAGAA
1 AAATAAAA-TGAGATAAAGAA
488048 AACTTATGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 2 0.06
20 14 0.41
21 10 0.29
22 6 0.18
23 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (21 bp):
AAATAAAATGAGATAAAGAAT
Found at i:489431 original size:12 final size:12
Alignment explanation
Indices: 489408--489451 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
489398 GCCCCGATTA
*
489408 CCCGATTACCCGC
1 CCCGA-TACCCGG
489421 CCCGATACCCGG
1 CCCGATACCCGG
489433 CCCGATACCCGG
1 CCCGATACCCGG
489445 CCCGATA
1 CCCGATA
489452 AATATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 25 0.83
13 5 0.17
ACGTcount: A:0.18, C:0.50, G:0.20, T:0.11
Consensus pattern (12 bp):
CCCGATACCCGG
Found at i:489574 original size:12 final size:12
Alignment explanation
Indices: 489557--489587 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
489547 TTAAATATAT
489557 ATACCCGACCCG
1 ATACCCGACCCG
*
489569 ATACCCGGCCCG
1 ATACCCGACCCG
489581 ATACCCG
1 ATACCCG
489588 TTTAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.48, G:0.19, T:0.10
Consensus pattern (12 bp):
ATACCCGACCCG
Found at i:489711 original size:25 final size:25
Alignment explanation
Indices: 489677--489728 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
489667 AAATCCCCGC
* *
489677 GGTTTTTTAAGCGGGGACGGGTACG
1 GGTTTTTTAAACGGGGACGGGGACG
*
489702 GGTTTTTTAAACGTGGACGGGGACG
1 GGTTTTTTAAACGGGGACGGGGACG
489727 GG
1 GG
489729 GACGGGGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (25 bp):
GGTTTTTTAAACGGGGACGGGGACG
Found at i:493733 original size:23 final size:22
Alignment explanation
Indices: 493696--493738 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
493686 GTTTTTATAA
*
493696 AAGTTTTTTTCTTTTCCTTTTC
1 AAGTTTTTTTATTTTCCTTTTC
*
493718 AAGTTCTTTTTATTTTTCTTT
1 AAGTT-TTTTTATTTTCCTTT
493739 ATTTTCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.70
Consensus pattern (22 bp):
AAGTTTTTTTATTTTCCTTTTC
Found at i:502405 original size:13 final size:13
Alignment explanation
Indices: 502387--502444 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
502377 GTCATAAATC
502387 TATGACGCGCATT
1 TATGACGCGCATT
*
502400 TATGACGCTCATT
1 TATGACGCGCATT
*
502413 TATGACGCGTATT
1 TATGACGCGCATT
* * *
502426 TATGATGCACATG
1 TATGACGCGCATT
502439 TATGAC
1 TATGAC
502445 TTACATTGCG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:502419 original size:26 final size:26
Alignment explanation
Indices: 502387--502444 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
502377 GTCATAAATC
* *
502387 TATGACGCGCATTTATGACGCTCATT
1 TATGACGCGCATTTATGACGCACATG
* *
502413 TATGACGCGTATTTATGATGCACATG
1 TATGACGCGCATTTATGACGCACATG
502439 TATGAC
1 TATGAC
502445 TTACATTGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (26 bp):
TATGACGCGCATTTATGACGCACATG
Found at i:502526 original size:85 final size:85
Alignment explanation
Indices: 502435--502730 Score: 486
Period size: 85 Copynumber: 3.5 Consensus size: 85
502425 TTATGATGCA
502435 CATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAATATGACACACATTTGTG
1 CATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAATATGACACACATTTGTG
502500 CGTCATAAATTTATGACACG
66 CGTCATAAATTTATGACACG
* *
502520 CATGTATGACTTACATTGCGCGTCATTAAAGCCCCCGTCATAAATTAAGATGACACACATTTGTG
1 CATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAATATGACACACATTTGTG
502585 CGTCATAAATTTATGACACG
66 CGTCATAAATTTATGACACG
** *
502605 CATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTTGCT-TGACATACATTTGT
1 CATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAA-TTAATATGACACACATTTGT
*
502669 GTGTCATAAATTTATGACACG
65 GCGTCATAAATTTATGACACG
* * * *
502690 CATATATGACTTACATTGCGTGTCATTGAAGCACACGTCAT
1 CATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCAT
502731 TTAAAAAGAC
Statistics
Matches: 198, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
85 196 0.99
86 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (85 bp):
CATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATTAATATGACACACATTTGTG
CGTCATAAATTTATGACACG
Found at i:502785 original size:2 final size:2
Alignment explanation
Indices: 502778--502818 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
502768 ATTCGGAAAT
502778 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
502819 TGTAGATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:514356 original size:21 final size:20
Alignment explanation
Indices: 514322--514364 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
514312 CAAATAACAC
514322 AAAAAGAAAG-AAAATAAATA
1 AAAAAGAAAGAAAAAT-AATA
*
514342 AAAAAGAAAATAAAAATAATA
1 AAAAAG-AAAGAAAAATAATA
514363 AA
1 AA
514365 CCATAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 9 0.45
22 5 0.25
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (20 bp):
AAAAAGAAAGAAAAATAATA
Found at i:514380 original size:5 final size:5
Alignment explanation
Indices: 514370--514461 Score: 88
Period size: 5 Copynumber: 18.8 Consensus size: 5
514360 ATAAACCATA
*
514370 ATAAT ATAAT A-AAT A-ATAT ATAAT AT-A- ATACT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
514417 ATAAT ATATAT ACAAT ATAAT AT-AT A-ATAT ATAAT ATAAAT ATAA
1 ATAAT ATA-AT ATAAT ATAAT ATAAT ATA-AT ATAAT AT-AAT ATAA
514462 ATATTTTCAA
Statistics
Matches: 74, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
3 2 0.03
4 9 0.12
5 52 0.70
6 11 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:514399 original size:37 final size:40
Alignment explanation
Indices: 514357--514465 Score: 106
Period size: 37 Copynumber: 2.8 Consensus size: 40
514347 GAAAATAAAA
*
514357 ATAATAAACCAT-A-ATAATATAATA-AATA-ATATATAAT
1 ATAAT-AACCATAATATAATATAATATAATATATATACAAT
*
514394 ATAAT-ACTATAATATAATATAATATAATATATATACAAT
1 ATAATAACCATAATATAATATAATATAATATATATACAAT
**
514433 ATAATATATAAT-ATATAATATAAATATAA-ATAT
1 ATAATA-ACCATAATATAATAT-AATATAATATAT
514466 TTTCAAAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
35 4 0.07
36 1 0.02
37 16 0.26
38 4 0.07
39 13 0.21
40 13 0.21
41 10 0.16
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (40 bp):
ATAATAACCATAATATAATATAATATAATATATATACAAT
Found at i:514413 original size:23 final size:22
Alignment explanation
Indices: 514371--514461 Score: 90
Period size: 19 Copynumber: 4.4 Consensus size: 22
514361 TAAACCATAA
514371 TAATATAATA-AATA-AT-ATA
1 TAATATAATATAATATATAATA
514390 TAATATAATACT-ATAATATAATA
1 TAATATAATA-TAAT-ATATAATA
*
514413 TAATATAATAT-ATATACAATA
1 TAATATAATATAATATATAATA
514434 T-A-AT-ATATAATATATAATA
1 TAATATAATATAATATATAATA
514453 TAAATATAA
1 T-AATATAA
514462 ATATTTTCAA
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
18 4 0.07
19 22 0.37
20 3 0.05
21 10 0.17
22 7 0.12
23 14 0.23
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATATAATATAATATATAATA
Found at i:514481 original size:46 final size:46
Alignment explanation
Indices: 514370--514488 Score: 127
Period size: 46 Copynumber: 2.6 Consensus size: 46
514360 ATAAACCATA
*
514370 ATAATATAATAAATAATAT-ATAATATAATACTATAATATAATATAAT
1 ATAATATAA-AAACAATATAAT-ATATAATACTATAATATAATATAAT
* *
514417 ATAATATATATACAATATAATATATAATA-TATAATATAAATATAA-
1 ATAATATAAAAACAATATAATATATAATACTATAATAT-AATATAAT
* * *
514462 ATATTTTCAAAAACTATATAATATATA
1 ATAATAT-AAAAACAATATAATATATA
514489 TATTTTCAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 13 0.21
46 38 0.62
47 10 0.16
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (46 bp):
ATAATATAAAAACAATATAATATATAATACTATAATATAATATAAT
Found at i:514506 original size:37 final size:37
Alignment explanation
Indices: 514460--514944 Score: 399
Period size: 37 Copynumber: 13.9 Consensus size: 37
514450 ATATAAATAT
*
514460 AAATATTTTCAAAAACTATATAATATATATATTTTCA
1 AAATGTTTTCAAAAACTATATAATATATATATTTTCA
* * *
514497 AAATGTTTTCAAAAACTATATATTAAACATATGTTTTCA
1 AAATGTTTTCAAAAACTATATA--ATATATATATTTTCA
514536 AAATGTTTTCAAAAA-T-TAT-ATATAT-T-TTTTC-
1 AAATGTTTTCAAAAACTATATAATATATATATTTTCA
*
514567 AAA----------AACTATATATTATATATATTTTCA
1 AAATGTTTTCAAAAACTATATAATATATATATTTTCA
* *
514594 AAATGTTTTCAAAAACTATATTATATATATATATTCA
1 AAATGTTTTCAAAAACTATATAATATATATATTTTCA
*
514631 AAATGTTTTCAAAAAATATATTATATATATATATATATATTCA
1 AAATGTTTTC-AAAAA-CTA-TATA-ATATATATAT-T-TTCA
514674 AAATGTTTTCAAAAACTATAT-AT-TATATA---T--
1 AAATGTTTTCAAAAACTATATAATATATATATTTTCA
*
514704 --ATGTTTTCAAAAACTATATATTATATA-----T--
1 AAATGTTTTCAAAAACTATATAATATATATATTTTCA
*
514732 --ATGTTTTCAAAAACTATATATTATATAT-------
1 AAATGTTTTCAAAAACTATATAATATATATATTTTCA
* *
514760 --ATGTTTTCAAAAACTATATATTATATATATTCTCA
1 AAATGTTTTCAAAAACTATATAATATATATATTTTCA
* *
514795 AAATGTTTTCAAAGACTATATATTATATATATATTCTCA
1 AAATGTTTTCAAAAACTATATA--ATATATATATTTTCA
*
514834 AAATGTTTTCAAAAACTATATATTATATATATTTTTTCA
1 AAATGTTTTCAAAAACTATATA--ATATATATATTTTCA
* *
514873 AAATGTTTTCAAAAACTATATATTATACATATTTTCA
1 AAATGTTTTCAAAAACTATATAATATATATATTTTCA
*
514910 AAATGTTTTCAAAAACTATATATTATATATATTTT
1 AAATGTTTTCAAAAACTATATAATATATATATTTT
514945 TTCAAAAAAA
Statistics
Matches: 386, Mismatches: 24, Indels: 76
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.01
22 1 0.00
23 3 0.01
24 5 0.01
25 1 0.00
26 5 0.01
27 3 0.01
28 75 0.19
29 1 0.00
30 4 0.01
31 3 0.01
32 6 0.02
33 1 0.00
34 4 0.01
37 126 0.33
38 8 0.02
39 101 0.26
40 6 0.02
41 12 0.03
42 5 0.01
43 14 0.04
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
AAATGTTTTCAAAAACTATATAATATATATATTTTCA
Found at i:514519 original size:39 final size:38
Alignment explanation
Indices: 514460--514951 Score: 219
Period size: 39 Copynumber: 14.1 Consensus size: 38
514450 ATATAAATAT
* * *
514460 AAATATTTTCAAAAACTATATA-ATATATATATTTTCA
1 AAATGTTTTCAAAAACTATATATAAACATATATTTTCA
*
514497 AAATGTTTTCAAAAACTATATATTAAACATATGTTTTCA
1 AAATGTTTTCAAAAACTATATA-TAAACATATATTTTCA
*
514536 AAATGTTTTCAAAAA-T-TATAT----ATATTTTTTC-
1 AAATGTTTTCAAAAACTATATATAAACATATATTTTCA
* *
514567 AAA----------AACTATATAT-TATATATATTTTCA
1 AAATGTTTTCAAAAACTATATATAAACATATATTTTCA
* * *
514594 AAATGTTTTCAAAAACTATAT-TATATATATATATTCA
1 AAATGTTTTCAAAAACTATATATAAACATATATTTTCA
* *
514631 AAATGTTTTCAAAAAATATATTATATATATATATATATATTCA
1 AAATGTTTTCAAAAACTATA-TATA-A-ACATATAT-T-TTCA
514674 AAATGTTTTCAAAAACTATATAT-----TATA---T--
1 AAATGTTTTCAAAAACTATATATAAACATATATTTTCA
* * *
514702 ATATGTTTTCAAAAACTATATAT-TATATATAT-----
1 AAATGTTTTCAAAAACTATATATAAACATATATTTTCA
* * *
514734 ----GTTTTCAAAAACTATATATTATATATATGTTTTC-
1 AAATGTTTTCAAAAACTATATA-TAAACATATATTTTCA
* * *
514768 AAA----------AACTATATAT-TATATATATTCTCA
1 AAATGTTTTCAAAAACTATATATAAACATATATTTTCA
* * * *
514795 AAATGTTTTCAAAGACTATATATTATATATATATTCTCA
1 AAATGTTTTCAAAAACTATATA-TAAACATATATTTTCA
* * *
514834 AAATGTTTTCAAAAACTATATATTATATATATTTTTTCA
1 AAATGTTTTCAAAAACTATATA-TAAACATATATTTTCA
*
514873 AAATGTTTTCAAAAACTATATATTATAC--ATATTTTCA
1 AAATGTTTTCAAAAACTATATA-TAAACATATATTTTCA
* * *
514910 AAATGTTTTCAAAAACTATATATTATATATATTTTTTCA
1 AAATGTTTTCAAAAACTATATA-TAAACATATATTTTCA
514949 AAA
1 AAA
514952 AAATTTATGT
Statistics
Matches: 378, Mismatches: 23, Indels: 106
0.75 0.05 0.21
Matches are distributed among these distances:
21 2 0.01
22 1 0.00
23 5 0.01
26 20 0.05
27 7 0.02
28 49 0.13
29 1 0.00
30 9 0.02
31 3 0.01
32 13 0.03
35 4 0.01
36 2 0.01
37 108 0.29
38 3 0.01
39 117 0.31
41 8 0.02
42 3 0.01
43 23 0.06
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (38 bp):
AAATGTTTTCAAAAACTATATATAAACATATATTTTCA
Found at i:514566 original size:97 final size:95
Alignment explanation
Indices: 514456--514658 Score: 307
Period size: 97 Copynumber: 2.1 Consensus size: 95
514446 TATAATATAA
*
514456 ATATAAATATTTTCAAAAACTATATAATATATATATTTTCAAAATGTTTTCAAAAACTATATATT
1 ATATATATATTTTCAAAAACTATATAATATATATATTTTCAAAATGTTTTCAAAAAC--TATATT
* * *
514521 AAACATATGTTTTCAAAATGTTTTCAAAAATT
64 AAACATATATATTCAAAATGTTTTCAAAAAAT
* * *
514553 ATATATATTTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATTAT
1 ATATATATATTTTCAAAAACTATATAATATATATATTTTCAAAATGTTTTCAAAAACTATATTAA
*
514618 ATATATATATTCAAAATGTTTTCAAAAAAT
66 ACATATATATTCAAAATGTTTTCAAAAAAT
514648 ATATTATATAT
1 ATA-TATATAT
514659 ATATATATAT
Statistics
Matches: 96, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
95 36 0.38
96 6 0.06
97 54 0.56
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (95 bp):
ATATATATATTTTCAAAAACTATATAATATATATATTTTCAAAATGTTTTCAAAAACTATATTAA
ACATATATATTCAAAATGTTTTCAAAAAAT
Found at i:514602 original size:58 final size:60
Alignment explanation
Indices: 514502--514619 Score: 186
Period size: 58 Copynumber: 2.0 Consensus size: 60
514492 TTTCAAAATG
* *
514502 TTTTCAAAAACTATATATTAAACATATGTTTTCAAAATGTTTTCAAAAATTATA-TATATT
1 TTTTCAAAAACTATATATT-AACATATATTTTCAAAATGTTTTCAAAAACTATATTATATT
*
514562 TTTTCAAAAACTATATATT-ATATATATTTTCAAAATGTTTTCAAAAACTATATTATAT
1 TTTTCAAAAACTATATATTAACATATATTTTCAAAATGTTTTCAAAAACTATATTATAT
514620 ATATATATTC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 30 0.56
59 5 0.09
60 19 0.35
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (60 bp):
TTTTCAAAAACTATATATTAACATATATTTTCAAAATGTTTTCAAAAACTATATTATATT
Found at i:514694 original size:28 final size:28
Alignment explanation
Indices: 514676--514789 Score: 228
Period size: 28 Copynumber: 4.1 Consensus size: 28
514666 TATATTCAAA
514676 ATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAT
514704 ATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAT
514732 ATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAT
514760 ATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAT
514788 AT
1 AT
514790 TCTCAAAATG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 86 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (28 bp):
ATGTTTTCAAAAACTATATATTATATAT
Found at i:514854 original size:65 final size:67
Alignment explanation
Indices: 514456--514952 Score: 262
Period size: 65 Copynumber: 7.3 Consensus size: 67
514446 TATAATATAA
* * *
514456 ATATAAATATTTTCAAAAACTATATA--ATATATATATTTTCAAAATGTTTTCAAAAACTATATA
1 ATATATATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACTATATA
514519 TT
66 TT
* * * * * *
514521 AAACATATGTTTTC-AAAA-TGT-T-TTCA-A-A-A-ATTAT-ATATATTTTTTCAAAAACTATA
1 ATATATATGTTTTCAAAAACTATATATT-ATATATATATTCTCA-AAATGTTTTCAAAAACTATA
514577 TATTAT
64 TA-T-T
514583 ATATATTTTCAAAATGTTTTCAAAAAC--TATATTATATATATATAT-TCAAAATGTTTTCAAAA
1 ATATA---T----ATGTTTTCAAAAACTATATATTATATATATAT-TCTCAAAATGTTTTCAAAA
*
514645 AATATATTATAT
58 ACTATA-TAT-T
* ** * * * * *
514657 ATATATATATATATTCAAAATGT-TTTCA-AAAACTATATATTAT-ATATATGTTTTCAAAAACT
1 ATATATATGT-T-TTCAAAAACTATAT-ATTATA-TATATATTCTCA-AAATGTTTTCAAAAACT
514719 ATATATT
61 ATATATT
* * ** * **
514726 ATATATATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAA-ACTAT-ATATTA-TATAT
1 ATATATATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCA-AAAACTATAT
514788 ATT
65 ATT
* * *
514791 CTCA-AAATGTTTTCAAAGACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACTATAT
1 AT-ATATATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACTATAT
514855 ATT
65 ATT
* * * * * *
514858 ATATATATTTTTTCAAAATGTTTTCAAAAACTATATATTATACATATTTTCAAAATGTTTTCAAA
1 ATATATATGTTTTCAAAA-----AC-TATA-TAT-TA-TATATATATTCTCAAAATGTTTTCAAA
514923 AACTATATATT
57 AACTATATATT
*
514934 ATATATATTTTTTCAAAAA
1 ATATATATGTTTTCAAAAA
514953 AATTTATGTA
Statistics
Matches: 328, Mismatches: 55, Indels: 92
0.69 0.12 0.19
Matches are distributed among these distances:
59 1 0.00
60 24 0.07
61 2 0.01
62 6 0.02
63 3 0.01
64 5 0.02
65 59 0.18
66 10 0.03
67 43 0.13
68 7 0.02
69 26 0.08
70 15 0.05
71 31 0.09
72 2 0.01
73 3 0.01
74 31 0.09
75 6 0.02
76 54 0.16
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (67 bp):
ATATATATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACTATATA
TT
Found at i:515686 original size:14 final size:14
Alignment explanation
Indices: 515669--515700 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
515659 AATATGAGAT
515669 ATTTTAAAAATCAA
1 ATTTTAAAAATCAA
*
515683 ATTTTAAAAATTAA
1 ATTTTAAAAATCAA
515697 ATTT
1 ATTT
515701 GTTTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTAAAAATCAA
Found at i:524929 original size:26 final size:26
Alignment explanation
Indices: 524900--524968 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
524890 CGGTTTGGTT
524900 TGGTTCAGTTCGGGTTTACCTTTAAA
1 TGGTTCAGTTCGGGTTTACCTTTAAA
*
524926 TGGTTCGGTTCGGGTTTACCTTTAAA
1 TGGTTCAGTTCGGGTTTACCTTTAAA
* *
524952 CGGTTCGATTTCGGGTT
1 TGGTTC-AGTTCGGGTT
524969 GATTTAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
26 30 0.79
27 8 0.21
ACGTcount: A:0.14, C:0.16, G:0.28, T:0.42
Consensus pattern (26 bp):
TGGTTCAGTTCGGGTTTACCTTTAAA
Found at i:527245 original size:3 final size:3
Alignment explanation
Indices: 527229--527284 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
527219 AAACACATAT
* *
527229 ATA ATA A-A AGTA ATA ATA ATA ATA ATA ATA ATA ATG ATAA ATA ATT
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
527275 ATA ATA ATA A
1 ATA ATA ATA A
527285 CAAATATAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 40 0.87
4 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:527554 original size:20 final size:20
Alignment explanation
Indices: 527531--527595 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
527521 CTCGAAAGGC
527531 TTACAGATGACCCGAAGGAT
1 TTACAGATGACCCGAAGGAT
* * * * *
527551 TTACACATCATGCTCGAAAGAC
1 TTACAGATGA--CCCGAAGGAT
527573 TTACAGATGACCCGAAGGAT
1 TTACAGATGACCCGAAGGAT
527593 TTA
1 TTA
527596 AAAAATCAAG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 18 0.55
22 15 0.45
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (20 bp):
TTACAGATGACCCGAAGGAT
Found at i:527566 original size:42 final size:42
Alignment explanation
Indices: 527514--527595 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
527504 AAGGACTTAT
* *
527514 CATCTTGCTCGAAAGGCTTACAGATGACCCGAAGGATTTACA
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTACA
527556 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
527596 AAAAATCAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTACA
Found at i:527763 original size:39 final size:39
Alignment explanation
Indices: 527717--528079 Score: 546
Period size: 39 Copynumber: 9.3 Consensus size: 39
527707 ATAGTTTCTT
* * *
527717 ATAAAATCTTTTGTTTCAAGAGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* *
527756 ACAAAATCTTCTATTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* *
527795 ACAAAATCTTCTATTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
*
527834 ATAAAATCTTCTGTTTCGAGGTAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
527873 AGAAAATCTTCTGTTTTGAGGGAAATTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
*
527912 ATAAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
527951 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
527990 ATAAAATCTTATATTTCAAGGGAAACTACCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
528029 ATACAATCTTCTGTTTCAAGGGAAACTACCTCAAGCGAG
1 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
*
528068 ATACAATCTTCT
1 ATAAAATCTTCT
528080 TTAAAAACAA
Statistics
Matches: 300, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 300 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (39 bp):
ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
Found at i:528393 original size:75 final size:76
Alignment explanation
Indices: 528082--528395 Score: 408
Period size: 76 Copynumber: 4.1 Consensus size: 76
528072 AATCTTCTTT
*
528082 AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAA-ATCGTCTCAAGCCAGACAAA
1 AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAACAT-GTCTCAAGCGAGACAAA
528146 TCTTGTTTTAAG
65 TCTTGTTTTAAG
* * *
528158 AAAAACAATCTTGAGTGAAAT-AAATCTTCTTATTTCGAGTAAAAAATGTCTCAAGCGAGACAAA
1 AAAAACAATCTTGAGTGAAATGAAAT-GTCTTCTTTCGAGTAAAACATGTCTCAAGCGAGACAAA
528222 TCTTGTTTTAAG
65 TCTTGTTTTAAG
* * * * *
528234 AAAAACAA-CATGTAGTGAAATGAAATGTCTTACTTT-GAATAAAACCTATATCAAGCGAGACAA
1 AAAAACAATCTTG-AGTGAAATGAAATGTCTT-CTTTCGAGTAAAACATGTCTCAAGCGAGACAA
*
528297 ATCTTATTTTAAG
64 ATCTTGTTTTAAG
* * *
528310 AAAAACAATCTTGAGTCAAATAAAATGTCTTCTTTC-AGGTAAAACA-GTCTCAAGTGAGACAAA
1 AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGA-GTAAAACATGTCTCAAGCGAGACAAA
528373 GT-TTGTTTTAAG
65 -TCTTGTTTTAAG
528385 AAAAACAATCT
1 AAAAACAATCT
528396 CCAGTGAGAT
Statistics
Matches: 208, Mismatches: 21, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
75 46 0.22
76 150 0.72
77 12 0.06
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (76 bp):
AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAACATGTCTCAAGCGAGACAAAT
CTTGTTTTAAG
Found at i:529517 original size:13 final size:13
Alignment explanation
Indices: 529499--529525 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
529489 AAGATCTTTG
529499 ACTTGACAATTAC
1 ACTTGACAATTAC
529512 ACTTGACAATTAC
1 ACTTGACAATTAC
529525 A
1 A
529526 GTGGAGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTGACAATTAC
Found at i:532688 original size:42 final size:40
Alignment explanation
Indices: 532622--532699 Score: 102
Period size: 42 Copynumber: 1.9 Consensus size: 40
532612 TTGTTAAAGA
** *
532622 ATCCTACCCTCACATGCTAGCTACCCTCACATGCTTTATCAG
1 ATCCTACCCGAACATGATAGCTACCC-C-CATGCTTTATCAG
*
532664 ATCCTACCCGAACATGATATCTACCCCCATGCTTTA
1 ATCCTACCCGAACATGATAGCTACCCCCATGCTTTA
532700 CTTGAACATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 9 0.28
41 1 0.03
42 22 0.69
ACGTcount: A:0.26, C:0.37, G:0.09, T:0.28
Consensus pattern (40 bp):
ATCCTACCCGAACATGATAGCTACCCCCATGCTTTATCAG
Found at i:534395 original size:19 final size:19
Alignment explanation
Indices: 534373--534410 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
534363 TAAATATATC
534373 AATAAAACATAAAAGGACT
1 AATAAAACATAAAAGGACT
*
534392 AATAAAACATACAAGGACT
1 AATAAAACATAAAAGGACT
534411 GAAATGCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.13, G:0.11, T:0.16
Consensus pattern (19 bp):
AATAAAACATAAAAGGACT
Found at i:535671 original size:3 final size:3
Alignment explanation
Indices: 535655--535719 Score: 87
Period size: 3 Copynumber: 21.3 Consensus size: 3
535645 AAACACATAT
*
535655 ATA ATA A-A ATTA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATAA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
535701 ATA ATT ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
535720 ATATAATATT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 48 0.87
4 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:546911 original size:8 final size:9
Alignment explanation
Indices: 546886--546911 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
546876 AAGATTTCTC
546886 AAAATTTTT
1 AAAATTTTT
546895 AAAATTTTT
1 AAAATTTTT
546904 AAAATTTT
1 AAAATTTT
546912 CGAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AAAATTTTT
Found at i:548452 original size:25 final size:25
Alignment explanation
Indices: 548418--548478 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 25
548408 TGTTAAAACA
*
548418 TTTTGAATGTTTTTGGATTTGTGTG
1 TTTTGGATGTTTTTGGATTTGTGTG
* *
548443 TTTTGGATG--TTTGGATTTTTGTT
1 TTTTGGATGTTTTTGGATTTGTGTG
548466 TGTTTGGATGTTT
1 T-TTTGGATGTTT
548479 AAATTTGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 13 0.43
24 8 0.27
25 8 0.27
26 1 0.03
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (25 bp):
TTTTGGATGTTTTTGGATTTGTGTG
Found at i:548476 original size:24 final size:23
Alignment explanation
Indices: 548429--548478 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
548419 TTTGAATGTT
548429 TTTGGATTTGTGTGTTTTGGATG
1 TTTGGATTTGTGTGTTTTGGATG
* *
548452 TTTGGATTTTTGTTTGTTTGGATG
1 TTTGGATTTGTGTGT-TTTGGATG
548476 TTT
1 TTT
548479 AAATTTGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.08, C:0.00, G:0.30, T:0.62
Consensus pattern (23 bp):
TTTGGATTTGTGTGTTTTGGATG
Found at i:548484 original size:24 final size:25
Alignment explanation
Indices: 548435--548484 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
548425 TGTTTTTGGA
**
548435 TTTGTGTGTTTTGGATGTTTGGATT
1 TTTGTGTGTTTTGGATGTTTAAATT
*
548460 TTTGTTTG-TTTGGATGTTTAAATT
1 TTTGTGTGTTTTGGATGTTTAAATT
548484 T
1 T
548485 GGTTTGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.12, C:0.00, G:0.26, T:0.62
Consensus pattern (25 bp):
TTTGTGTGTTTTGGATGTTTAAATT
Found at i:548776 original size:13 final size:13
Alignment explanation
Indices: 548747--548781 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
548737 GGGGAGTAAT
*
548747 TTTTCAAAATTGA
1 TTTTCAAAAATGA
548760 -TTTCAAAAATGA
1 TTTTCAAAAATGA
548772 TTTTCAAAAA
1 TTTTCAAAAA
548782 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:551041 original size:3 final size:3
Alignment explanation
Indices: 551033--551060 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
551023 ATGAGTAAAT
551033 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
551061 ATAAAGGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:551537 original size:9 final size:9
Alignment explanation
Indices: 551514--551634 Score: 68
Period size: 9 Copynumber: 13.0 Consensus size: 9
551504 AAAAAGGTAG
551514 AAAAG-AAA
1 AAAAGAAAA
*
551522 TAAAGAAAA
1 AAAAGAAAA
*
551531 AATAG-AAA
1 AAAAGAAAA
*
551539 AAGAGAAAA
1 AAAAGAAAA
*
551548 AAATGAAAAA
1 AAAAG-AAAA
551558 GAAGAAGAAAAA
1 -AA-AAG-AAAA
551570 AAAAGAAAA
1 AAAAGAAAA
*
551579 AACAGAAAA
1 AAAAGAAAA
*
551588 AAAGGAAAA
1 AAAAGAAAA
**
551597 GAAAA-AGGA
1 -AAAAGAAAA
*
551606 AAAGGAAAA
1 AAAAGAAAA
*
551615 GAAAGAAAGA
1 AAAAGAAA-A
551625 AGAAAGAAAA
1 A-AAAGAAAA
551635 CTGATCAAAT
Statistics
Matches: 85, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
8 14 0.16
9 41 0.48
10 12 0.14
11 11 0.13
12 7 0.08
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.02
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:551539 original size:8 final size:8
Alignment explanation
Indices: 551514--551602 Score: 55
Period size: 8 Copynumber: 11.4 Consensus size: 8
551504 AAAAAGGTAG
551514 AAAAGA-A
1 AAAAGAGA
551521 ATAAAGA-A
1 A-AAAGAGA
*
551529 AAAATAGA
1 AAAAGAGA
551537 AAAAGAGA
1 AAAAGAGA
*
551545 AAAAAATGA
1 AAAAGA-GA
551554 AAAAGAAGA
1 AAAAG-AGA
551563 AGAAA-A-A
1 A-AAAGAGA
551570 AAAAGA-A
1 AAAAGAGA
*
551577 AAAACAGA
1 AAAAGAGA
* *
551585 AAAAAAGG
1 AAAAGAGA
551593 AAAAGA-A
1 AAAAGAGA
551600 AAA
1 AAA
551603 GGAAAAGGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
6 3 0.05
7 17 0.26
8 33 0.50
9 9 0.14
10 4 0.06
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (8 bp):
AAAAGAGA
Found at i:551559 original size:40 final size:38
Alignment explanation
Indices: 551514--551608 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 38
551504 AAAAAGGTAG
*
551514 AAAAGAAATAAAGAAAAAATAG-AAAAAGAGAAAAAAATGA
1 AAAAGAAA-AAAGAAAAAA-AGAAAAAACAGAAAAAAA-GA
*
551554 AAAAGAAGAAGAA-AAAAAAAGAAAAAACAGAAAAAAAGG
1 AAAAGAA-AA-AAGAAAAAAAGAAAAAACAGAAAAAAAGA
*
551593 AAAAGAAAAAGGAAAA
1 AAAAGAAAAAAGAAAA
551609 GGAAAAGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
37 1 0.02
38 6 0.12
39 10 0.21
40 28 0.58
41 3 0.06
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (38 bp):
AAAAGAAAAAAGAAAAAAAGAAAAAACAGAAAAAAAGA
Found at i:551587 original size:17 final size:16
Alignment explanation
Indices: 551514--551596 Score: 73
Period size: 17 Copynumber: 5.1 Consensus size: 16
551504 AAAAAGGTAG
*
551514 AAAAGAAATAAAGAAA
1 AAAAGAAAAAAAGAAA
*
551530 AAATAGAAAAAGAGAAA
1 AAA-AGAAAAAAAGAAA
551547 AAAATG--AAAAAGAAGA
1 AAAA-GAAAAAAAGAA-A
*
551563 AGAA-AAAAAAAGAAA
1 AAAAGAAAAAAAGAAA
*
551578 AAACAGAAAAAAAGGAA
1 AAA-AGAAAAAAAGAAA
551595 AA
1 AA
551597 GAAAAAGGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
15 10 0.19
16 17 0.31
17 27 0.50
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAGAAAAAAAGAAA
Found at i:551618 original size:23 final size:21
Alignment explanation
Indices: 551523--551634 Score: 76
Period size: 23 Copynumber: 5.4 Consensus size: 21
551513 GAAAAGAAAT
*
551523 AAAGAAAA-AATAGAAAAAGA
1 AAAGAAAAGAAAAGAAAAAGA
*
551543 GAAA-AAAATGAAAAAGAAGAAGA
1 -AAAGAAAA-G-AAAAGAAAAAGA
* *
551566 AAAAAAAAG-AAA-AAACAGA
1 AAAGAAAAGAAAAGAAAAAGA
*
551585 AAA-AAAGGAAAAGAAAAAGGA
1 AAAGAAAAGAAAAGAAAAA-GA
551606 AAAGGAAAAG-AAAGAAAGAAG-
1 AAA-GAAAAGAAAAGAAA-AAGA
551627 AAAGAAAA
1 AAAGAAAA
551635 CTGATCAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 21
0.73 0.07 0.21
Matches are distributed among these distances:
18 4 0.05
19 11 0.15
20 16 0.22
21 11 0.15
22 12 0.16
23 20 0.27
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAGAAAAGAAAAGAAAAAGA
Found at i:551629 original size:22 final size:22
Alignment explanation
Indices: 551555--551629 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
551545 AAAAAATGAA
*
551555 AAAG-AAGAAGAAAA-AAAAAG
1 AAAGAAAGAAGAAAAGGAAAAG
* *
551575 AAAAAACAGAAAAAAAGGAAAAG
1 AAAGAA-AGAAGAAAAGGAAAAG
551598 -AA-AAAG--GAAAAGGAAAAG
1 AAAGAAAGAAGAAAAGGAAAAG
551616 AAAGAAAGAAGAAA
1 AAAGAAAGAAGAAA
551630 GAAAACTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 11 0.25
19 2 0.05
20 9 0.20
21 3 0.07
22 14 0.32
23 5 0.11
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAGAAAAGGAAAAG
Found at i:552316 original size:28 final size:28
Alignment explanation
Indices: 552254--552317 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
552244 TGCAATAAGC
*
552254 CAACCTGAAACACATTACCTCCCCAAAT
1 CAACCTAAAACACATTACCTCCCCAAAT
* * *
552282 TAACCTAAAACACATTACCTTCCCAAGT
1 CAACCTAAAACACATTACCTCCCCAAAT
*
552310 CAGCCTAA
1 CAACCTAA
552318 GCCTTTTATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.39, C:0.36, G:0.05, T:0.20
Consensus pattern (28 bp):
CAACCTAAAACACATTACCTCCCCAAAT
Found at i:553812 original size:42 final size:40
Alignment explanation
Indices: 553750--553852 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 40
553740 GACGAGTAAG
*
553750 TCCTTCGGGCCATCAGTAAGTCTTTCGAGC-ATGATGTTTAAA
1 TCCTTCGGGCCATCA-TAAGTCTTTCGAGCTA-GATG-ATAAA
* *
553792 TCCTTCGGGTCATCTATAAGTCTTTCGAGCTAGATGATAAG
1 TCCTTCGGGCCATC-ATAAGTCTTTCGAGCTAGATGATAAA
553833 TCCTTCGGGCCATCCATAAG
1 TCCTTCGGGCCAT-CATAAG
553853 ACCTTCAGGA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
41 20 0.37
42 32 0.59
43 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (40 bp):
TCCTTCGGGCCATCATAAGTCTTTCGAGCTAGATGATAAA
Found at i:554127 original size:41 final size:41
Alignment explanation
Indices: 554066--554143 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
554056 TGATGCTTAA
* * * * *
554066 ATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAC
1 ATCCTTCAGGCCATCCATAAGACCTTCGAGCAAGATGATAC
*
554107 ATCCTTCAGGCCATCCATAAGACCTTCGGGCAAGATG
1 ATCCTTCAGGCCATCCATAAGACCTTCGAGCAAGATG
554144 TTTTCAAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (41 bp):
ATCCTTCAGGCCATCCATAAGACCTTCGAGCAAGATGATAC
Found at i:554243 original size:58 final size:55
Alignment explanation
Indices: 554156--554363 Score: 178
Period size: 58 Copynumber: 3.7 Consensus size: 55
554146 TTCAAATGAG
* * *
554156 TTTTTAGA-AACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCTAAAGAA
1 TTTTTAAAGAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCT-AAAAGAA
* * * * *
554211 TTTTTAAAGGAAGCTAAGCCTAATTTTTAGGGGGTCCTTGATGA-CAACTGAAAATGAAAGA
1 TTTTTAAA-GAA-CTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCT-AAAA-G--A-A
* *
554272 TTCTTAAA-AACTAAGCCTGATTTTCAGGGGTTTCTTGATG-TT-T-TAAAAGAA
1 TTTTTAAAGAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTAAAAGAA
*
554323 TTTTTGAAAGAAACTAAACCTAATTTT-AGGGGTTTCTTGAT
1 TTTTT-AAAG-AACTAAGCCTAATTTTCAGGGGTTTCTTGAT
554364 AACTATAAAT
Statistics
Matches: 123, Mismatches: 19, Indels: 24
0.74 0.11 0.14
Matches are distributed among these distances:
51 5 0.04
52 4 0.03
53 14 0.11
54 15 0.12
55 11 0.09
56 1 0.01
57 8 0.07
58 54 0.44
59 2 0.02
60 1 0.01
61 8 0.07
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (55 bp):
TTTTTAAAGAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTAAAAGAA
Found at i:555306 original size:117 final size:117
Alignment explanation
Indices: 555089--555413 Score: 517
Period size: 117 Copynumber: 2.8 Consensus size: 117
555079 AAGATAAACT
* *
555089 GATCAACATTT-CAAGTGGAGAGTTTATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GATCAATATTTCCAA-TGGAGAGTTCATAATGAGAAGAACTCATCCGA-AGAGGGAGAAGAAGTT
* *
555153 CATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGGTG
64 CATAATGAGAAGAACTTGTTCAACCTCGGTTCGATTCCATCACAGAAGGAGGTG
* * *
555207 GATCAATATTTCCAATGGAGGGTTCATAACGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
1 GATCAATATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGGAGAAGAAGTTCA
*
555272 TAATGAGAAGAACTTGTTCAACCTCGGTTTGATTCCATCACAGAAGGAGGTG
66 TAATGAGAAGAACTTGTTCAACCTCGGTTCGATTCCATCACAGAAGGAGGTG
*
555324 GATCAATATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTC
1 GATCAATATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCG-AAGAGGGAGAAGAAGTTC
* *
555389 ATAATGAGAAGAGCTTGTTCGACCT
65 ATAATGAGAAGAACTTGTTCAACCT
555414 ATCACTTGAT
Statistics
Matches: 191, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
117 109 0.57
118 79 0.41
119 3 0.02
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (117 bp):
GATCAATATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTCGGTTCGATTCCATCACAGAAGGAGGTG
Found at i:555639 original size:139 final size:139
Alignment explanation
Indices: 555323--555965 Score: 805
Period size: 139 Copynumber: 4.6 Consensus size: 139
555313 AGAAGGAGGT
* * * * *
555323 GGATCAATATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTT
1 GGATCAACATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCG-ATGAGGGAGAAGAAGTT
* * * * * * **
555388 CATAATGAGAAGAGCTTGTTCGACCTATCA-CTTGATTCATGACCT-T----TCGAATCAGTGAC
65 CATAATGAGAAGAACTTGTTCAACCT-T-AGCTCGATTCATCACATATGGAGTTGAATCAGCAAC
* * * *
555447 GCCTCGCTTGAT
128 ACCTCACTCGAG
* * * * * * *
555459 GGATTAACATTTCAAATGGAGAGTTCATAATGATAAGAACTCGTCCGATGAGGGAGAATAAGTTC
1 GGATCAACATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
555524 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
66 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
555589 TCACTCGAG
131 TCACTCGAG
* * * *
555598 GGATCAACATTTCCAGCAAAGAGTTCATAATGAGAAAAACTCGTCCGATGAGGGAGAAGAAGTTC
1 GGATCAACATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
* ** *
555663 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTAATTGCATATGGAGTTGAATCAGCAACAAC
66 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
*
555728 TCACT-TATG
131 TCACTCGA-G
* * * *
555737 GGATTAACATTTCTAGTAGAGAGTTCATAATGAGAAGAACTCATTCGATGAGGGAGAAAAAGTTC
1 GGATCAACATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
* * *
555802 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGGATCAGTAACACA
66 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
*
555867 TTACTCGAG
131 TCACTCGAG
* * *
555876 GGATCAATATTTCCAGTGGTGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
1 GGATCAACATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
555941 ATAATGAGAAGAACTTGTTCAACCT
66 ATAATGAGAAGAACTTGTTCAACCT
555966 CAACAGTTGC
Statistics
Matches: 443, Mismatches: 56, Indels: 13
0.87 0.11 0.03
Matches are distributed among these distances:
133 1 0.00
134 13 0.03
135 40 0.09
136 43 0.10
138 1 0.00
139 344 0.78
140 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (139 bp):
GGATCAACATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
TCACTCGAG
Found at i:561443 original size:8 final size:7
Alignment explanation
Indices: 561429--561545 Score: 95
Period size: 7 Copynumber: 16.6 Consensus size: 7
561419 AAAAGGGTAG
561429 AAAAGAA
1 AAAAGAA
561436 ATAAAGAAA
1 A-AAAG-AA
561445 AAAGAGAA
1 AAA-AGAA
561453 AAAAGAA
1 AAAAGAA
561460 AAGAAG-A
1 AA-AAGAA
*
561467 AGAAGAA
1 AAAAGAA
561474 AAAA-ACA
1 AAAAGA-A
561481 GAAAA-AA
1 -AAAAGAA
561488 AAAAG-A
1 AAAAGAA
561494 AAAAGAA
1 AAAAGAA
561501 AAAA-AA
1 AAAAGAA
*
561507 AAGAAAAA
1 AA-AAGAA
561515 AAAAGAA
1 AAAAGAA
561522 AAAA-AA
1 AAAAGAA
561528 AGAAA-AA
1 A-AAAGAA
561535 AAAAGAA
1 AAAAGAA
561542 AAAA
1 AAAA
561546 AAGAGGAAAA
Statistics
Matches: 94, Mismatches: 3, Indels: 26
0.76 0.02 0.21
Matches are distributed among these distances:
6 24 0.26
7 42 0.45
8 23 0.24
9 5 0.05
ACGTcount: A:0.85, C:0.01, G:0.14, T:0.01
Consensus pattern (7 bp):
AAAAGAA
Found at i:561464 original size:21 final size:20
Alignment explanation
Indices: 561442--561561 Score: 108
Period size: 19 Copynumber: 6.0 Consensus size: 20
561432 AGAAATAAAG
561442 AAAAAAGAGAAAAAAGAAAA
1 AAAAAAGAGAAAAAAGAAAA
*
561462 GAAGAAGAAGA-AAAAAACAGAAA
1 -AA-AA-AAGAGAAAAAAGA-AAA
561485 AAAAAA-AG-AAAAAGAAAA
1 AAAAAAGAGAAAAAAGAAAA
561503 AAAAAAGA-AAAAAA-AAGAA
1 AAAAAAGAGAAAAAAGAA-AA
*
561522 AAAAAA-AGAAAAAAAAAGAA
1 AAAAAAGAGAAAAAAGAA-AA
* *
561542 AAAAAAGAGGAAAATGAAAA
1 AAAAAAGAGAAAAAAGAAAA
561562 GAAAGAAAAC
Statistics
Matches: 84, Mismatches: 5, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
18 12 0.14
19 27 0.32
20 15 0.18
21 12 0.14
22 11 0.13
23 7 0.08
ACGTcount: A:0.83, C:0.01, G:0.15, T:0.01
Consensus pattern (20 bp):
AAAAAAGAGAAAAAAGAAAA
Found at i:561469 original size:27 final size:26
Alignment explanation
Indices: 561439--561538 Score: 93
Period size: 23 Copynumber: 3.8 Consensus size: 26
561429 AAAAGAAATA
561439 AAGAAAAAAGAGAAAAAAGAAAAGAAGAAG
1 AAGAAAAAAGAG--AAAA-AAAA-AAGAAG
* *
561469 AAGAAAAAAACAGAAAAAAAAAAGAAA
1 AAG-AAAAAAGAGAAAAAAAAAAGAAG
561496 AAGAAAAAA-A-AAAGAAAAAAA-AAG
1 AAGAAAAAAGAGAAA-AAAAAAAGAAG
561520 AA-AAAAAA-AGAAAAAAAAA
1 AAGAAAAAAGAGAAAAAAAAA
561539 GAAAAAAAAG
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
23 13 0.20
24 10 0.16
25 8 0.12
26 6 0.09
27 8 0.12
28 4 0.06
29 4 0.06
30 3 0.05
31 8 0.12
ACGTcount: A:0.85, C:0.01, G:0.14, T:0.00
Consensus pattern (26 bp):
AAGAAAAAAGAGAAAAAAAAAAGAAG
Found at i:561475 original size:30 final size:30
Alignment explanation
Indices: 561427--561549 Score: 144
Period size: 30 Copynumber: 4.1 Consensus size: 30
561417 AAAAAAGGGT
* * *
561427 AGAAAAGAAATA-AAGAAAAAAGAGAAAAA
1 AGAAAAGAAAAAGAAAAAAAAAGAAAAAAA
* * *
561456 AGAAAAGAAGAAGAAGAAAAAAACAGAAAAA
1 AGAAAAGAAAAAGAA-AAAAAAAGAAAAAAA
561487 A-AAAAGAAAAAGAAAAAAAAAAGAAAAAAAA
1 AGAAAAGAAAAAG-AAAAAAAAAG-AAAAAAA
561518 AGAAAA-AAAAAGAAAAAAAAAGAAAAAAA
1 AGAAAAGAAAAAGAAAAAAAAAGAAAAAAA
561547 AGA
1 AGA
561550 GGAAAATGAA
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
29 20 0.24
30 29 0.35
31 29 0.35
32 4 0.05
ACGTcount: A:0.84, C:0.01, G:0.15, T:0.01
Consensus pattern (30 bp):
AGAAAAGAAAAAGAAAAAAAAAGAAAAAAA
Found at i:561478 original size:1 final size:1
Alignment explanation
Indices: 561472--561547 Score: 80
Period size: 1 Copynumber: 76.0 Consensus size: 1
561462 GAAGAAGAAG
* * * * * * *
561472 AAAAAAACAGAAAAAAAAAAGAAAAAGAAAAAAAAAAGAAAAAAAAAGAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
561537 AAGAAAAAAAA
1 AAAAAAAAAAA
561548 GAGGAAAATG
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.89, C:0.01, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:561484 original size:48 final size:47
Alignment explanation
Indices: 561429--561570 Score: 139
Period size: 48 Copynumber: 3.0 Consensus size: 47
561419 AAAAGGGTAG
* *
561429 AAAAGAAATAAAGAAAAAAGAGAAAAAAGAAAAGAAGAAGAAGAAAAA
1 AAAAGAAA-AAAGAAAAAAGAGAAAAAAGAAAAGAAAAAAAAGAAAAA
* * *
561477 AACAGAAAAAAAAAAGAAAAAGAAAAAA-AAAAGAAAAAAAAAGAAAAA
1 AAAAGAAAAAAGAAA-AAAGAGAAAAAAGAAAAG-AAAAAAAAGAAAAA
* *
561525 AAAAGAAAAAA-AAAGAAA-A-AAAAGAGGAAAATGAAAAGAAAGAAAA
1 AAAAGAAAAAAGAAA-AAAGAGAAAA-AAGAAAA-GAAAAAAAAGAAAA
561571 CTGATCAAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
45 4 0.05
46 2 0.02
47 34 0.42
48 41 0.51
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.01
Consensus pattern (47 bp):
AAAAGAAAAAAGAAAAAAGAGAAAAAAGAAAAGAAAAAAAAGAAAAA
Done.