Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 12 of 45
Found at i:2311829 original size:18 final size:17
Alignment explanation
Indices: 2311795--2311849 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
2311785 TATTTAAAAT
2311795 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
2311812 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
2311829 A-TTTCTA-TTATATAA
1 ATTTTATATTTATATAA
2311844 ATTTTA
1 ATTTTA
2311850 AAAATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.10
14 2 0.06
15 4 0.13
16 6 0.19
17 7 0.23
18 6 0.19
19 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:2312270 original size:24 final size:24
Alignment explanation
Indices: 2312206--2312268 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
2312196 TCAATAAATT
* **
2312206 TATTTTATTATTAAAAATAAAAAA
1 TATTTTATAATTAAATTTAAAAAA
*
2312230 TATTTTATAATTAAATTTAAATAA
1 TATTTTATAATTAAATTTAAAAAA
*
2312254 TTTTTTATTAATTAA
1 TATTTTA-TAATTAA
2312269 TTACACTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 26 0.79
25 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTTTATAATTAAATTTAAAAAA
Found at i:2312288 original size:16 final size:15
Alignment explanation
Indices: 2312267--2312318 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
2312257 TTTATTAATT
2312267 AATTACACTAAATTTA
1 AATTACA-TAAATTTA
*
2312283 AATTACA-AAATTTT
1 AATTACATAAATTTA
*
2312297 AATTAAATTAATATTTA
1 AATTACA-TAA-ATTTA
2312314 AATTA
1 AATTA
2312319 TTCAAACACA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 12 0.40
16 9 0.30
17 9 0.30
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTACATAAATTTA
Found at i:2321548 original size:27 final size:27
Alignment explanation
Indices: 2321499--2321551 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2321489 AATTCCCCTG
2321499 AAACCCTCAGTTTTCCATATGTATTTC
1 AAACCCTCAGTTTTCCATATGTATTTC
2321526 AAACCCTGCA-TTGTTCCAT-TGTATTT
1 AAACCCT-CAGTT-TTCCATATGTATTT
2321552 TATACTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.42
Consensus pattern (27 bp):
AAACCCTCAGTTTTCCATATGTATTTC
Found at i:2324208 original size:22 final size:21
Alignment explanation
Indices: 2324143--2324213 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 21
2324133 ATATATAAAA
*
2324143 TATAAAATATATAA-TATAATA
1 TATAAAATATA-AATTATAATT
* *
2324164 TA-AAAATAT-ATTTAAAATAT
1 TATAAAATATAAATTATAAT-T
2324184 TATAAAATATAAATTATTAATT
1 TATAAAATATAAATTA-TAATT
*
2324206 TATTAAAT
1 TATAAAAT
2324214 TTATATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.03
19 5 0.13
20 9 0.23
21 9 0.23
22 12 0.31
23 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TATAAAATATAAATTATAATT
Found at i:2324211 original size:82 final size:83
Alignment explanation
Indices: 2324125--2324293 Score: 188
Period size: 82 Copynumber: 2.1 Consensus size: 83
2324115 TTATTATACG
* * *
2324125 ATTAAAAAATATATAAAATATAAAATA-TAT-AATATAATATAAAAATATATTTAAA-ATATT-A
1 ATTAAAAAATATAT-AAATATAAAATATTATAAATATAAT-T-AAAATAAAATAAAATATATTAA
*
2324186 TAAAATATAAAT-TATTAATTT
63 TAAAATATAAATATA-TAAATT
** * *
2324207 ATT-AAATTTATATAAATATAAAATATTTTAAATATAATTAAAATAAAATAAAATATATTAATAT
1 ATTAAAAAATATATAAATATAAAATATTATAAATATAATTAAAATAAAATAAAATATATTAATAA
2324271 AATATAAATATATAAATT
66 AATATAAATATATAAATT
2324289 ATTAA
1 ATTAA
2324294 GTTAAAAGCC
Statistics
Matches: 73, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
80 23 0.32
81 16 0.22
82 31 0.42
83 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (83 bp):
ATTAAAAAATATATAAATATAAAATATTATAAATATAATTAAAATAAAATAAAATATATTAATAA
AATATAAATATATAAATT
Found at i:2324232 original size:7 final size:8
Alignment explanation
Indices: 2324131--2324287 Score: 75
Period size: 7 Copynumber: 19.5 Consensus size: 8
2324121 TACGATTAAA
2324131 AAATATAT
1 AAATATAT
2324139 AAA-ATAT
1 AAATATAT
2324146 AAA-ATAT
1 AAATATAT
*
2324153 ATA-ATAT
1 AAATATAT
*
2324160 -AATATAA
1 AAATATAT
2324167 AAATATATTT
1 AAATATA--T
2324177 AAAATATTAT
1 -AAATA-TAT
2324187 AAA-ATAT
1 AAATATAT
2324194 AAAT-TAT
1 AAATATAT
* *
2324201 TAATTTATT
1 AAATATA-T
2324210 AAATTTATAT
1 AAA--TATAT
2324220 AAATATA-
1 AAATATAT
*
2324227 AAATATTTT
1 AAATA-TAT
2324236 AAATATAAT
1 AAATAT-AT
*
2324245 TAA-A-AT
1 AAATATAT
2324251 AAA-ATA-
1 AAATATAT
2324257 AAATATATT
1 AAATATA-T
2324266 AATATAATAT
1 AA-AT-ATAT
2324276 AAATATAT
1 AAATATAT
2324284 AAAT
1 AAAT
2324288 TATTAAGTTA
Statistics
Matches: 118, Mismatches: 11, Indels: 40
0.70 0.07 0.24
Matches are distributed among these distances:
6 9 0.08
7 41 0.35
8 27 0.23
9 18 0.15
10 10 0.08
11 11 0.09
12 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATATAT
Found at i:2324258 original size:20 final size:21
Alignment explanation
Indices: 2324235--2324284 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
2324225 TAAAATATTT
2324235 TAAATATA-ATTAAAATAAAA
1 TAAATATATATTAAAATAAAA
* *
2324255 TAAA-ATATATTAATATAATA
1 TAAATATATATTAAAATAAAA
2324275 TAAATATATA
1 TAAATATATA
2324285 AATTATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 3 0.12
20 18 0.69
21 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATATATTAAAATAAAA
Found at i:2324280 original size:11 final size:11
Alignment explanation
Indices: 2324216--2324282 Score: 54
Period size: 10 Copynumber: 6.5 Consensus size: 11
2324206 TATTAAATTT
2324216 ATATAAATATAA
1 ATAT-AATATAA
* *
2324228 A-ATATTTTAA
1 ATATAATATAA
2324238 ATATAAT-TAA
1 ATATAATATAA
*
2324248 A-ATAAAATAA
1 ATATAATATAA
*
2324258 A-AT-ATATTA
1 ATATAATATAA
2324267 ATATAATATAA
1 ATATAATATAA
2324278 ATATA
1 ATATA
2324283 TAAATTATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
9 9 0.20
10 18 0.41
11 16 0.36
12 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAATATAA
Found at i:2324418 original size:40 final size:37
Alignment explanation
Indices: 2324374--2324484 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 37
2324364 ACAACCTTAA
2324374 AAATTTTAAAAATTTTATTTAAAATATTTTATATTTATAT
1 AAATTTTAAAAA-TTTATTT-AAATATTTTATA-TTATAT
* * *
2324414 AAATTTT---AATATA-TT-AATAATTTCTATTATAT
1 AAATTTTAAAAATTTATTTAAATATTTTATATTATAT
*
2324446 AAATTTTAAAAATTTATTTATAATATTTTTTAATTATAT
1 AAATTTTAAAAATTTATTTA-AATATTTTAT-ATTATAT
2324485 TATATATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
32 13 0.22
33 9 0.16
35 7 0.12
36 5 0.09
37 2 0.03
38 8 0.14
39 7 0.12
40 7 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (37 bp):
AAATTTTAAAAATTTATTTAAATATTTTATATTATAT
Found at i:2324433 original size:18 final size:17
Alignment explanation
Indices: 2324399--2324453 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
2324389 TATTTAAAAT
2324399 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
2324416 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
2324433 A-TTTCTA-TTATATAA
1 ATTTTATATTTATATAA
2324448 ATTTTA
1 ATTTTA
2324454 AAAATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.10
14 2 0.06
15 4 0.13
16 6 0.19
17 7 0.23
18 6 0.19
19 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:2324473 original size:22 final size:24
Alignment explanation
Indices: 2324376--2324474 Score: 64
Period size: 23 Copynumber: 4.2 Consensus size: 24
2324366 AACCTTAAAA
* *
2324376 ATTTTAA-AAATTTTATTTAAAAT
1 ATTTTAATAAATTCTATTTATAAT
** **
2324399 ATTTTATATTTATATAAATTT-TAAT
1 ATTTTA-ATAAAT-TCTATTTATAAT
* *
2324424 ATATTAATAATTTCTATTATATAA-
1 ATTTTAATAAATTCTATT-TATAAT
2324448 ATTTTAA-AAATT-TATTTATAAT
1 ATTTTAATAAATTCTATTTATAAT
2324470 ATTTT
1 ATTTT
2324475 TTAATTATAT
Statistics
Matches: 57, Mismatches: 13, Indels: 13
0.69 0.16 0.16
Matches are distributed among these distances:
21 5 0.09
22 9 0.16
23 14 0.25
24 11 0.19
25 13 0.23
26 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTAATAAATTCTATTTATAAT
Found at i:2324505 original size:71 final size:69
Alignment explanation
Indices: 2324373--2324518 Score: 165
Period size: 71 Copynumber: 2.1 Consensus size: 69
2324363 CACAACCTTA
* *
2324373 AAAATTTTAAAAATTTTATTTAAAATATTTTATATTTATATAAATTTTAATATATTAATAATTTC
1 AAAATTTTAAAAATTTTATTTAAAATATTTTATAATTATATAAATATTAATATATTAATAATTT-
2324438 TATTAT
65 TATT-T
* * *
2324444 ATAAATTTTAAAAA-TTTATTTATAATATTTTTTAATTATATTATATATTAA-AT-TCGT-ATAA
1 A-AAATTTTAAAAATTTTATTTAAAATATTTTATAATTATA-TAAATATTAATATAT--TAATAA
2324505 TTTTATTT
62 TTTTATTT
2324513 AAAATT
1 AAAATT
2324519 AAGAAGACTA
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
68 5 0.08
69 2 0.03
70 5 0.08
71 33 0.50
72 21 0.32
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (69 bp):
AAAATTTTAAAAATTTTATTTAAAATATTTTATAATTATATAAATATTAATATATTAATAATTTT
ATTT
Found at i:2324870 original size:25 final size:24
Alignment explanation
Indices: 2324811--2324873 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
2324801 CAATAAATTT
2324811 ATTTTATTATTAA--AAATATAAAA
1 ATTTT-TTATTAATTAAATATAAAA
* *
2324834 ATATTTTA-TAATTAAATTTAAATA
1 ATTTTTTATTAATTAAATATAAA-A
2324858 ATTTTTTATTAATTAA
1 ATTTTTTATTAATTAA
2324874 TTACACTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.09
22 3 0.09
23 12 0.36
24 8 0.24
25 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTTTTATTAATTAAATATAAAA
Found at i:2324875 original size:24 final size:23
Alignment explanation
Indices: 2324811--2324875 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
2324801 CAATAAATTT
* *
2324811 ATTTTATTATTAA-AAATATAAAA
1 ATTTT-TTATTAATTAATTTAAAA
*
2324834 ATATTTTA-TAATTAAATTTAAATA
1 ATTTTTTATTAATT-AATTTAAA-A
2324858 ATTTTTTATTAATTAATT
1 ATTTTTTATTAATTAATT
2324876 ACACTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 3 0.09
22 3 0.09
23 11 0.32
24 12 0.35
25 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTTTTATTAATTAATTTAAAA
Found at i:2324893 original size:16 final size:15
Alignment explanation
Indices: 2324872--2324923 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
2324862 TTTATTAATT
2324872 AATTACACTAAATTTA
1 AATTACA-TAAATTTA
*
2324888 AATTACA-AAATTTT
1 AATTACATAAATTTA
*
2324902 AATTAAATTAATATTTA
1 AATTACA-TAA-ATTTA
2324919 AATTA
1 AATTA
2324924 ATTCAAACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 12 0.40
16 9 0.30
17 9 0.30
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTACATAAATTTA
Found at i:2325315 original size:16 final size:17
Alignment explanation
Indices: 2325296--2325334 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2325286 ATTTATACTT
2325296 AAATAA-TTTTAATATA
1 AAATAACTTTTAATATA
* *
2325312 AAATAACTTTTTATTTA
1 AAATAACTTTTAATATA
2325329 AAATAA
1 AAATAA
2325335 AGATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAACTTTTAATATA
Found at i:2325396 original size:28 final size:27
Alignment explanation
Indices: 2325365--2325429 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
2325355 TGGGACAAGG
2325365 ATTTTTTTAAATATAATAAA-AAATAAAA
1 ATTTTTTTAAA-A-AATAAATAAATAAAA
*
2325393 ATTTATTTTAAAAAATAAATTCAATAAAA
1 ATTT-TTTTAAAAAATAAA-TAAATAAAA
*
2325422 TTTTTTTT
1 ATTTTTTT
2325430 TTATTTTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 6 0.19
28 9 0.28
29 17 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTTTTTTAAAAAATAAATAAATAAAA
Found at i:2336229 original size:23 final size:22
Alignment explanation
Indices: 2336159--2336233 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 22
2336149 AATTACATAT
*
2336159 AAAAATTTAATTATAATATTAGTA
1 AAAAATTTAATTA-AA-ATAAGTA
* *
2336183 ATAAATTTTA-TATAAATATA-TA
1 AAAAATTTAATTA-AAATA-AGTA
2336205 AAAAATTTAATGTAAAATAAGTA
1 AAAAATTTAAT-TAAAATAAGTA
2336228 AAAAAT
1 AAAAAT
2336234 AAAAAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 13 0.31
23 19 0.45
24 10 0.24
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
AAAAATTTAATTAAAATAAGTA
Found at i:2347013 original size:3 final size:3
Alignment explanation
Indices: 2347005--2347040 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2346995 AGCAGAACGT
2347005 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2347041 CACTAATGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2347137 original size:9 final size:9
Alignment explanation
Indices: 2347123--2347231 Score: 92
Period size: 9 Copynumber: 10.7 Consensus size: 9
2347113 TAAATTTTTT
2347123 TTAAAATTA
1 TTAAAATTA
2347132 TTAAAATTATA
1 TTAAAA-T-TA
2347143 TCTAAAATTA
1 T-TAAAATTA
2347153 TTAAAATTA
1 TTAAAATTA
2347162 TATAAAAAATTA
1 T-T--AAAATTA
2347174 TTAAAATTA
1 TTAAAATTA
*
2347183 TTACAGTAATCA
1 TTA-A--AATTA
2347195 TTAAAATTA
1 TTAAAATTA
2347204 TATAAAAATTA
1 T-T-AAAATTA
2347215 TTAAAAATATA
1 TT-AAAAT-TA
2347226 TTAAAA
1 TTAAAA
2347232 GGGATCAAAA
Statistics
Matches: 86, Mismatches: 2, Indels: 23
0.77 0.02 0.21
Matches are distributed among these distances:
9 30 0.35
10 18 0.21
11 18 0.21
12 20 0.23
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (9 bp):
TTAAAATTA
Found at i:2347148 original size:12 final size:11
Alignment explanation
Indices: 2347130--2347334 Score: 80
Period size: 11 Copynumber: 19.7 Consensus size: 11
2347120 TTTTTAAAAT
2347130 TATTAAAATTA
1 TATTAAAATTA
2347141 TATCTAAAA-T-
1 TAT-TAAAATTA
2347151 TATTAAAATTA
1 TATTAAAATTA
* *
2347162 TATAAAAAAT-
1 TATTAAAATTA
2347172 TATTAAAA-T-
1 TATTAAAATTA
* * *
2347181 TATTACAGTAA
1 TATTAAAATTA
2347192 TCATTAAAATTA
1 T-ATTAAAATTA
*
2347204 TA-TAAAAAT-
1 TATTAAAATTA
*
2347213 TATTAAAAATA
1 TATTAAAATTA
**
2347224 TATTAAAA-GG
1 TATTAAAATTA
* *
2347234 GATCAAAATTA
1 TATTAAAATTA
*
2347245 TATCAAAATTA
1 TATTAAAATTA
*
2347256 T-TT-AAACTA
1 TATTAAAATTA
* *
2347265 TATCAAATGTTA
1 TATTAAA-ATTA
** *
2347277 -ACCAAAACTA
1 TATTAAAATTA
*
2347287 TA--AAAAAT-
1 TATTAAAATTA
2347295 TATTAAAATTA
1 TATTAAAATTA
* *
2347306 TA-TCAAATTT
1 TATTAAAATTA
*
2347316 TATCAAAATTA
1 TATTAAAATTA
2347327 TATTAAAA
1 TATTAAAA
2347335 ATCATCAAAT
Statistics
Matches: 144, Mismatches: 33, Indels: 34
0.68 0.16 0.16
Matches are distributed among these distances:
8 2 0.01
9 25 0.17
10 47 0.33
11 55 0.38
12 15 0.10
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:2347148 original size:21 final size:19
Alignment explanation
Indices: 2347124--2347362 Score: 147
Period size: 21 Copynumber: 11.6 Consensus size: 19
2347114 AAATTTTTTT
2347124 TAAAATTATTAAAATTATA
1 TAAAATTATTAAAATTATA
2347143 TCTAAAATTATTAAAATTATA
1 --TAAAATTATTAAAATTATA
2347164 TAAAAAATTATTAAAATTAT-
1 T--AAAATTATTAAAATTATA
*
2347184 TACAGTAATCATTAAAATTATA
1 TA-A--AATTATTAAAATTATA
*
2347206 TAAAAATTATTAAAAATATA
1 T-AAAATTATTAAAATTATA
** *
2347226 TTAAAAGGGATCAAAATTATA
1 -TAAAA-TTATTAAAATTATA
* *
2347247 TCAAAATTATTTAAACTATA
1 T-AAAATTATTAAAATTATA
* ** *
2347267 TCAAATGTTAACCAAAACTATA
1 T-AAA-ATT-ATTAAAATTATA
*
2347289 AAAAATTATTAAAATTATA
1 TAAAATTATTAAAATTATA
* *
2347308 TCAAATTTTATCAAAATTATA
1 T-AAA-ATTATTAAAATTATA
* * *
2347329 TTAAAAATCATCAAATTTATA
1 -T-AAAATTATTAAAATTATA
2347350 TAAAAATTATTAA
1 T-AAAATTATTAA
2347363 TAGTATATTA
Statistics
Matches: 173, Mismatches: 30, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.01
19 11 0.06
20 50 0.29
21 95 0.55
22 15 0.09
23 1 0.01
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAAATTATTAAAATTATA
Found at i:2347242 original size:41 final size:40
Alignment explanation
Indices: 2347125--2347359 Score: 170
Period size: 41 Copynumber: 5.7 Consensus size: 40
2347115 AATTTTTTTT
* *
2347125 AAAATTATTAAAATTATATCTAAAATTATTAAAATTATATAA
1 AAAATTATTAAAAATATAT-TAAAATTATCAAAATTATAT-A
* *
2347167 AAAATTATT-AAAAT-TATTACAGTAATCATTAAAATTATATA
1 AAAATTATTAAAAATATATTA-A--AATTATCAAAATTATATA
** *
2347208 AAAATTATTAAAAATATATTAAAAGGGATCAAAATTATATC
1 AAAATTATTAAAAATATATTAAAA-TTATCAAAATTATATA
* * * * * *
2347249 AAAATTATTTAAACTATATCAAATGTTAACCAAAACTATA-A
1 AAAATTATTAAAAATATATTAAA-ATT-ATCAAAATTATATA
* * *
2347290 AAAATTATTAAAATTATATCAAATTTTATCAAAATTATATTA
1 AAAATTATTAAAAATATATTAAA-ATTATCAAAATTATA-TA
* * ** *
2347332 AAAATCATCAAATTTATATAAAAATTAT
1 AAAATTATTAAAAATATATTAAAATTAT
2347360 TAATAGTATA
Statistics
Matches: 158, Mismatches: 25, Indels: 21
0.77 0.12 0.10
Matches are distributed among these distances:
39 2 0.01
40 16 0.10
41 74 0.47
42 61 0.39
43 5 0.03
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (40 bp):
AAAATTATTAAAAATATATTAAAATTATCAAAATTATATA
Found at i:2347326 original size:30 final size:30
Alignment explanation
Indices: 2347285--2347362 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
2347275 TAACCAAAAC
2347285 TATA-AAAAATTATTAAAATTAT-ATCAAATT
1 TATATAAAAATTATTAAAA--ATCATCAAATT
*
2347315 T-TATCAAAATTATATTAAAAATCATCAAATT
1 TATAT-AAAAAT-TATTAAAAATCATCAAATT
2347346 TATATAAAAATTATTAA
1 TATATAAAAATTATTAA
2347363 TAGTATATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
29 2 0.05
30 9 0.22
31 19 0.46
32 11 0.27
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (30 bp):
TATATAAAAATTATTAAAAATCATCAAATT
Found at i:2347334 original size:32 final size:32
Alignment explanation
Indices: 2347285--2347359 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
2347275 TAACCAAAAC
*
2347285 TATAAAAAAT-TATTAAAATTAT-ATCAAATTT-
1 TATAAAAATTATATTAAAA--ATCATCAAATTTA
*
2347316 TATCAAAATTATATTAAAAATCATCAAATTTA
1 TATAAAAATTATATTAAAAATCATCAAATTTA
2347348 TATAAAAATTAT
1 TATAAAAATTAT
2347360 TAATAGTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 2 0.05
31 17 0.45
32 19 0.50
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (32 bp):
TATAAAAATTATATTAAAAATCATCAAATTTA
Found at i:2347764 original size:2 final size:2
Alignment explanation
Indices: 2347757--2347781 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2347747 ATCCCTTGAA
2347757 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2347782 ACTTGCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2349494 original size:6 final size:7
Alignment explanation
Indices: 2349459--2349493 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2349449 TGAAATATAT
*
2349459 ATTAACA
1 ATTAAAA
*
2349466 ATAAAAA
1 ATTAAAA
2349473 ATTAAAA
1 ATTAAAA
2349480 ATTAAAA
1 ATTAAAA
2349487 ATTAAAA
1 ATTAAAA
2349494 TCATAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (7 bp):
ATTAAAA
Found at i:2356992 original size:2 final size:2
Alignment explanation
Indices: 2356985--2357041 Score: 62
Period size: 2 Copynumber: 28.5 Consensus size: 2
2356975 TAGTAGGTAA
* * *
2356985 AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AG GT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
*
2357028 AA AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT A
2357042 CACATATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2357014 original size:35 final size:34
Alignment explanation
Indices: 2356972--2357041 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 34
2356962 CCGACCATAA
*
2356972 ATATAGTAGGTAAATATATATATATATATATATAT
1 ATATAGTAGGTAAATATATATAAATATATA-ATAT
2357007 ATATAGTAGGTAAATATATATAAATATATAATAT
1 ATATAGTAGGTAAATATATATAAATATATAATAT
2357041 A
1 A
2357042 CACATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 5 0.15
35 29 0.85
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (34 bp):
ATATAGTAGGTAAATATATATAAATATATAATAT
Found at i:2357142 original size:35 final size:35
Alignment explanation
Indices: 2357101--2357171 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
2357091 TATCATTTAC
2357101 TTCGATATACATAATTCACTGTTAAATATATCTTT
1 TTCGATATACATAATTCACTGTTAAATATATCTTT
*
2357136 TTCGATATACATAATTCACTGTTAGATATATCTTT
1 TTCGATATACATAATTCACTGTTAAATATATCTTT
2357171 T
1 T
2357172 GTTGATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (35 bp):
TTCGATATACATAATTCACTGTTAAATATATCTTT
Found at i:2361350 original size:15 final size:14
Alignment explanation
Indices: 2361309--2361350 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2361299 TTTTATATTA
*
2361309 TAAAAATTAAAATT
1 TAAAAATTATAATT
2361323 TAAAAAATT-TAATT
1 T-AAAAATTATAATT
2361337 TAAATAATTATAAT
1 TAAA-AATTATAAT
2361351 ATTTTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.12
14 10 0.42
15 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAAATTATAATT
Found at i:2364189 original size:69 final size:69
Alignment explanation
Indices: 2364091--2364247 Score: 199
Period size: 69 Copynumber: 2.3 Consensus size: 69
2364081 TGAAAGTCGT
* * *
2364091 GGTGATAATGAGAACAAGGGCAAGGAAGAATCTCATTCTGAAGCCTTG-GGAAAGACGAATGGTG
1 GGTGATAATGAGCACAAGGGCAAGGAAGAATCACATTCTGAAGCC-GGAGGAAAGACGAATGGTG
*
2364155 TAAAA
65 AAAAA
* * * * *
2364160 GGTGATAATGAGCACAGGGGTAAGGAAGAATCACATTTTGAAGCCGGAGGAAAGGCGGATGGTGA
1 GGTGATAATGAGCACAAGGGCAAGGAAGAATCACATTCTGAAGCCGGAGGAAAGACGAATGGTGA
2364225 AAAA
66 AAAA
* *
2364229 GGTGACAATAAGCACAAGG
1 GGTGATAATGAGCACAAGG
2364248 TTCAGGAATC
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
68 1 0.01
69 74 0.99
ACGTcount: A:0.39, C:0.11, G:0.33, T:0.17
Consensus pattern (69 bp):
GGTGATAATGAGCACAAGGGCAAGGAAGAATCACATTCTGAAGCCGGAGGAAAGACGAATGGTGA
AAAA
Found at i:2364458 original size:141 final size:142
Alignment explanation
Indices: 2364227--2364566 Score: 341
Period size: 141 Copynumber: 2.4 Consensus size: 142
2364217 GATGGTGAAA
* * * * * * *
2364227 AAGGTGACAATAAGCACAAGGTTCA-G--GAATCGAATGTTGAATCTAAAGGAATGACGGATAGT
1 AAGGTGACAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGACGGATAGC
* * * * *
2364289 ATGAAGGAAGGCAATAATGAGCACAAGGGTGAGGAAG-ATCCAAATGTTGAATCCAACGGAACGA
66 ATGAAAGAAGGCAATAATGAGCACAAGGGTCAGGAAGAATCCAAAT-TCGAAGCCAACGGAAAGA
2364353 CT-A-ATGATAAAG
130 -TGAGATGATAAAG
* *
2364365 AAGGTGACAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGATGGATGGC
1 AAGGTGACAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGACGGATAGC
** * ** *
2364430 ATGAAAGAAGGTGATAATGTGCTTAAGGGTCAGGAAGAATCCAAATTCGAAGCCAATGGAAAGAT
66 ATGAAAGAAGGCAATAATGAGCACAAGGGTCAGGAAGAATCCAAATTCGAAGCCAACGGAAAGAT
*
2364495 GGATGGTGATAAAG
131 -GA-GATGATAAAG
* * * * ** **
2364509 AAGGTAATAATGTGCAAAAGGGTCAGGAAGAGGCAAATAATGAAGCCAAAGGAAAGAC
1 AAGGTGACAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGAC
2364567 ATATGGTGGG
Statistics
Matches: 164, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
138 23 0.14
139 1 0.01
140 1 0.01
141 73 0.45
142 9 0.05
144 57 0.35
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (142 bp):
AAGGTGACAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGACGGATAGC
ATGAAAGAAGGCAATAATGAGCACAAGGGTCAGGAAGAATCCAAATTCGAAGCCAACGGAAAGAT
GAGATGATAAAG
Found at i:2364460 original size:72 final size:70
Alignment explanation
Indices: 2364158--2364565 Score: 303
Period size: 72 Copynumber: 5.8 Consensus size: 70
2364148 AATGGTGTAA
* * * * * ** **
2364158 AAGGTGATAATGAGCACAGGGGTAAGGAAGAATCACATTTTGAAGCCGGAGGAAAGGCGGATGG-
1 AAGGTAATAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGATGGATGGA
2364222 TGAAA-
66 T-AAAG
* * * * * * * * * *
2364227 AAGGTGACAATAAGCACAAGGTTCA-G--GAATCGAATGTTGAATCTAAAGGAATGACGGATAGT
1 AAGGTAATAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGATGGAT-GG
*
2364289 ATGAAGG
65 AT-AAAG
* * * * * *
2364296 AAGGCAATAATGAGCACAAGGGTGAGGAAG-ATCCAAATGTTGAATCCAACGGAACGACT-AAT-
1 AAGGTAATAATGAGCACAAGGGTCAGGAAGAAT-CAAATGTTGAAGCCAAAGGAAAGA-TGGATG
2364358 GATAAAG
64 GATAAAG
* *
2364365 AAGGTGACAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGATGGATGGC
1 AAGGTAATAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGATGGATGG-
2364430 ATGAAAG
65 AT-AAAG
* * ** * *
2364437 AAGGTGATAATGTGCTTAAGGGTCAGGAAGAATCCAAAT-TCGAAGCCAATGGAAAGATGGATGG
1 AAGGTAATAATGAGCACAAGGGTCAGGAAGAAT-CAAATGTTGAAGCCAAAGGAAAGATGGAT-G
2364501 TGATAAAG
64 -GATAAAG
* * ** **
2364509 AAGGTAATAATGTGCAAAAGGGTCAGGAAGAGGCAAATAATGAAGCCAAAGGAAAGA
1 AAGGTAATAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGA
2364566 CATATGGTGG
Statistics
Matches: 270, Mismatches: 52, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
66 24 0.09
67 1 0.00
68 6 0.02
69 91 0.34
70 6 0.02
71 9 0.03
72 124 0.46
73 8 0.03
74 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (70 bp):
AAGGTAATAATGAGCACAAGGGTCAGGAAGAATCAAATGTTGAAGCCAAAGGAAAGATGGATGGA
TAAAG
Found at i:2367423 original size:31 final size:33
Alignment explanation
Indices: 2367372--2367436 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 33
2367362 ACATCAATTT
2367372 TTAAACATTTATATATTATAAA-ATATTAAAATA
1 TTAAACATTTATATATTATAAATAT-TTAAAATA
2367405 TTAAA-ATTTATATA-TATAAATATTTAAAATA
1 TTAAACATTTATATATTATAAATATTTAAAATA
2367436 T
1 T
2367437 AATTATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 15 0.48
32 11 0.35
33 5 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (33 bp):
TTAAACATTTATATATTATAAATATTTAAAATA
Found at i:2367436 original size:15 final size:15
Alignment explanation
Indices: 2367392--2367438 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
2367382 ATATATTATA
2367392 AAATA-TTAAAATATT
1 AAATATTTAAAATA-T
*
2367407 AAA-ATTTATATATAT
1 AAATATTTA-AAATAT
2367422 AAATATTTAAAATAT
1 AAATATTTAAAATAT
2367437 AA
1 AA
2367439 TTATAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 1 0.04
15 17 0.63
16 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATATTTAAAATAT
Found at i:2367443 original size:23 final size:22
Alignment explanation
Indices: 2367393--2367443 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
2367383 TATATTATAA
2367393 AATAT-TA-AAATATTAAAATT
1 AATATATATAAATATTAAAATT
*
2367413 TATATATATAAATATTTAAAATAT
1 AATATATATAAATA-TTAAAAT-T
2367437 AAT-TATA
1 AATATATA
2367444 ATTTTACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 4 0.16
21 2 0.08
22 5 0.20
23 11 0.44
24 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATATATAAATATTAAAATT
Found at i:2369804 original size:32 final size:33
Alignment explanation
Indices: 2369750--2369837 Score: 101
Period size: 32 Copynumber: 2.7 Consensus size: 33
2369740 TTTTATAATT
* * *
2369750 ATATTTAAAATAATATAT-TTATATAAATTTTA
1 ATATTTATAATAATTTATATTATATAAATTTAA
*
2369782 TTATTT-TAATAATTTATATTATATAAATTTAA
1 ATATTTATAATAATTTATATTATATAAATTTAA
2369814 ATATTTATATTATAATTTA-ATTAT
1 ATATTTATA--ATAATTTATATTAT
2369838 TTTACAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
31 9 0.19
32 23 0.49
33 2 0.04
34 5 0.11
35 8 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
ATATTTATAATAATTTATATTATATAAATTTAA
Found at i:2369832 original size:20 final size:21
Alignment explanation
Indices: 2369778--2369839 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
2369768 TTATATAAAT
* *
2369778 TTTATTATTTTAATAATTTATA
1 TTTATAATTTAAAT-ATTTATA
2369800 TTATATAAATTTAAATATTTATA
1 TT-TAT-AATTTAAATATTTATA
*
2369823 -TTATAATTTAATTATTT
1 TTTATAATTTAAATATTT
2369840 TACAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 12 0.34
21 3 0.09
22 3 0.09
23 10 0.29
24 7 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATAATTTAAATATTTATA
Found at i:2374033 original size:21 final size:21
Alignment explanation
Indices: 2373983--2374033 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
2373973 TAATATTTAA
2373983 AATTAAA-TTTAAATAAAAAT
1 AATTAAATTTTAAATAAAAAT
* **
2374003 ATTTTTATTTTAAA-AATAAAT
1 AATTAAATTTTAAATAA-AAAT
2374024 AATTAAATTT
1 AATTAAATTT
2374034 ATTCAATTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTAAATTTTAAATAAAAAT
Found at i:2376142 original size:22 final size:21
Alignment explanation
Indices: 2376109--2376152 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
2376099 TTAAATTTAA
2376109 TTATAAATATA-TAAATATTT
1 TTATAAATATATTAAATATTT
2376129 TTATAAAATAATATTAAATATTT
1 TTAT-AAAT-ATATTAAATATTT
2376152 T
1 T
2376153 AAATTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 4 0.19
22 3 0.14
23 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATAAATATATTAAATATTT
Found at i:2376161 original size:22 final size:25
Alignment explanation
Indices: 2376106--2376161 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 25
2376096 TATTTAAATT
2376106 TAATTATAAATATATAAATATTTTTA
1 TAATTAT-AATATATAAATATTTTTA
*
2376132 TAA-AATAATAT-TAAATA-TTTTA
1 TAATTATAATATATAAATATTTTTA
2376154 -AATTATAA
1 TAATTATAA
2376162 AATAAGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 2 0.07
22 9 0.33
23 6 0.22
24 5 0.19
25 2 0.07
26 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATTATAATATATAAATATTTTTA
Found at i:2377617 original size:23 final size:21
Alignment explanation
Indices: 2377571--2377617 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
2377561 AATGTGTATA
* *
2377571 TTTAAAATAAAAAATTAATTT
1 TTTAAAATAAAAAATAAATAT
2377592 TTTAAATATATAAAAATAAATAT
1 TTTAAA-ATA-AAAAATAAATAT
2377615 TTT
1 TTT
2377618 CACCTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 3 0.14
23 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAAAATAAAAAATAAATAT
Found at i:2382900 original size:25 final size:25
Alignment explanation
Indices: 2382866--2382915 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2382856 ACTTAAACAA
* *
2382866 CTCAAGTATGAGTGTTAAATATAAG
1 CTCAACTATGAGTGTCAAATATAAG
*
2382891 CTCAACTATGTGTGTCAAATATAAG
1 CTCAACTATGAGTGTCAAATATAAG
2382916 TATGTCTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (25 bp):
CTCAACTATGAGTGTCAAATATAAG
Found at i:2385563 original size:18 final size:18
Alignment explanation
Indices: 2385540--2385576 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2385530 CCAGACACTC
2385540 TCTCCCTTATTCTCTTCT
1 TCTCCCTTATTCTCTTCT
* *
2385558 TCTCCCTTCTTCTGTTCT
1 TCTCCCTTATTCTCTTCT
2385576 T
1 T
2385577 TCTCAGGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.38, G:0.03, T:0.57
Consensus pattern (18 bp):
TCTCCCTTATTCTCTTCT
Found at i:2386544 original size:11 final size:11
Alignment explanation
Indices: 2386524--2386669 Score: 55
Period size: 11 Copynumber: 14.0 Consensus size: 11
2386514 AAATACGAAA
2386524 AATA-AAATAT
1 AATATAAATAT
2386534 AATATAAATAT
1 AATATAAATAT
* *
2386545 AACATTAATAT
1 AATATAAATAT
* * * *
2386556 ATTATTTATTTT
1 AATA-TAAATAT
*
2386568 AA-ATTATATAT
1 AATA-TAAATAT
2386579 AATATAAAT-T
1 AATATAAATAT
*
2386589 -AT-TAATTAT
1 AATATAAATAT
***
2386598 CAATATTTGTAT
1 -AATATAAATAT
2386610 AATATAAATAT
1 AATATAAATAT
*
2386621 -TTA-AAATAT
1 AATATAAATAT
2386630 AATTATAAA-AT
1 AA-TATAAATAT
2386641 -A-ATAAA-AT
1 AATATAAATAT
*
2386649 -ATATAAATAA
1 AATATAAATAT
2386659 AATATAAATAT
1 AATATAAATAT
2386670 TAAAATATAC
Statistics
Matches: 100, Mismatches: 23, Indels: 25
0.68 0.16 0.17
Matches are distributed among these distances:
8 12 0.12
9 14 0.14
10 9 0.09
11 51 0.51
12 14 0.14
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
AATATAAATAT
Found at i:2386638 original size:21 final size:20
Alignment explanation
Indices: 2386607--2386666 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
2386597 TCAATATTTG
*
2386607 TATAATAT-AAATATTTAAAA
1 TATAATATAAAATA-ATAAAA
2386627 TATAATTATAAAATAATAAAA
1 TATAA-TATAAAATAATAAAA
*
2386648 TATATAAATAAAAT-ATAAA
1 TATA-ATATAAAATAATAAA
2386667 TATTAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 10 0.29
21 19 0.54
22 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TATAATATAAAATAATAAAA
Found at i:2386640 original size:13 final size:12
Alignment explanation
Indices: 2386607--2386678 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 12
2386597 TCAATATTTG
2386607 TATAATAT-AAA
1 TATAATATAAAA
2386618 TAT--T-TAAAA
1 TATAATATAAAA
2386627 TATAAT-TATAAA
1 TATAATATA-AAA
2386639 -ATAATA-AAATA
1 TATAATATAAA-A
2386650 TATAA-ATAAAA
1 TATAATATAAAA
2386661 TATAAATATTAAAA
1 TAT-AATA-TAAAA
2386675 TATA
1 TATA
2386679 CAAATTACCG
Statistics
Matches: 50, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
8 1 0.02
9 7 0.14
10 2 0.04
11 18 0.36
12 12 0.24
13 2 0.04
14 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TATAATATAAAA
Found at i:2386677 original size:8 final size:7
Alignment explanation
Indices: 2386610--2386683 Score: 64
Period size: 8 Copynumber: 10.4 Consensus size: 7
2386600 ATATTTGTAT
2386610 AATATAA
1 AATATAA
*
2386617 ATATTTAA
1 A-ATATAA
2386625 AATAT-A
1 AATATAA
*
2386631 ATTATAA
1 AATATAA
2386638 AATAATAA
1 AAT-ATAA
*
2386646 AATATAT
1 AATATAA
2386653 AA-ATAA
1 AATATAA
2386659 AATAT-A
1 AATATAA
2386665 AATATTAA
1 AATA-TAA
2386673 AATATACA
1 AATATA-A
2386681 AAT
1 AAT
2386684 TACCGAATCT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
6 15 0.28
7 17 0.31
8 22 0.41
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (7 bp):
AATATAA
Found at i:2386685 original size:14 final size:13
Alignment explanation
Indices: 2386633--2386685 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
2386623 AAAATATAAT
2386633 TATAAAATAATAAAA
1 TATAAAAT--TAAAA
2386648 TATATAAA-TAAAA
1 TATA-AAATTAAAA
2386661 TATAAATATTAAAA
1 TATAAA-ATTAAAA
2386675 TATACAAATTA
1 TATA-AAATTA
2386686 CCGAATCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.06
13 10 0.29
14 13 0.38
15 6 0.18
16 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAAAATTAAAA
Found at i:2388922 original size:2 final size:2
Alignment explanation
Indices: 2388915--2388941 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2388905 TGTCAATTAG
2388915 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 T
2388942 TTTAGTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2391006 original size:20 final size:22
Alignment explanation
Indices: 2390981--2391030 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2390971 TAAAATATTT
*
2390981 TATATTTAT-ATTTATTTTA-A
1 TATATTTATAATTTATCTTATA
*
2391001 TATATTAATAATTTATCTTATA
1 TATATTTATAATTTATCTTATA
*
2391023 TAAATTTA
1 TATATTTA
2391031 AAAAATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 8 0.33
21 9 0.38
22 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATTTATAATTTATCTTATA
Found at i:2391055 original size:25 final size:25
Alignment explanation
Indices: 2391027--2391074 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2391017 CTTATATAAA
*
2391027 TTTAAAAAATATATTCATATTATTT
1 TTTAAAAAATATATACATATTATTT
* *
2391052 TTTAAAAATTTTATACATATTAT
1 TTTAAAAAATATATACATATTAT
2391075 ATTTATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTAAAAAATATATACATATTATTT
Found at i:2391106 original size:20 final size:21
Alignment explanation
Indices: 2391077--2391115 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2391067 CATATTATAT
*
2391077 TTATATAA-TTATATTCAAAA
1 TTATAAAATTTATATTCAAAA
2391097 TTATAAAATTTATATTCAA
1 TTATAAAATTTATATTCAA
2391116 TCCTAACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATAAAATTTATATTCAAAA
Found at i:2391160 original size:31 final size:31
Alignment explanation
Indices: 2391125--2391189 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
2391115 ATCCTAACAA
2391125 TTTATTTATACATCTTGTGTTTTATATTTGG
1 TTTATTTATACATCTTGTGTTTTATATTTGG
* *
2391156 TTTATTTATACATCTTTTGTTTTATCTTTGG
1 TTTATTTATACATCTTGTGTTTTATATTTGG
2391187 TTT
1 TTT
2391190 TTGTGTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.65
Consensus pattern (31 bp):
TTTATTTATACATCTTGTGTTTTATATTTGG
Found at i:2398208 original size:2 final size:2
Alignment explanation
Indices: 2398196--2398240 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2398186 CCTGTTTATT
*
2398196 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2398238 TA T
1 TA T
2398241 GTGAAGGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2399106 original size:29 final size:28
Alignment explanation
Indices: 2399041--2399106 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 28
2399031 AATATATCAC
2399041 CTTTATATAAAAATATAAATTTATAAATT
1 CTTTAT-TAAAAATATAAATTTATAAATT
*
2399070 CATT-TTAAAAATAATTAAATTTA-AATATT
1 CTTTATTAAAAAT-A-TAAATTTATAA-ATT
2399099 -TTTATTAA
1 CTTTATTAA
2399107 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
27 7 0.23
28 6 0.19
29 18 0.58
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
CTTTATTAAAAATATAAATTTATAAATT
Found at i:2399676 original size:16 final size:16
Alignment explanation
Indices: 2399655--2399707 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
2399645 AATTGAATTG
2399655 ATTAATTAAATTAAAA
1 ATTAATTAAATTAAAA
* *
2399671 ATTAATTAATTTAATA
1 ATTAATTAAATTAAAA
* *
2399687 ATTTATTATA-TATAAA
1 ATTAATTAAATTA-AAA
2399703 ATTAA
1 ATTAA
2399708 ATTTTTATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 2 0.07
16 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAATTAAATTAAAA
Found at i:2400259 original size:46 final size:46
Alignment explanation
Indices: 2400186--2400277 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
2400176 CAATTGTATA
* *
2400186 AATATAAAATTACAATAGAGGAATGATTTTTTAGCGACAGAAATGT
1 AATATAAAATTACAATAAAGGAATGATTTTTTAGCAACAGAAATGT
*
2400232 AATATAAAATTACAATAAAGGAGTGATTTTTTAGCAACAGAAATGT
1 AATATAAAATTACAATAAAGGAATGATTTTTTAGCAACAGAAATGT
2400278 TTCGATGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (46 bp):
AATATAAAATTACAATAAAGGAATGATTTTTTAGCAACAGAAATGT
Found at i:2400601 original size:22 final size:20
Alignment explanation
Indices: 2400562--2400601 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2400552 TTAAAGATAC
*
2400562 CATATTTATCTTATTTTAAA
1 CATATTTATATTATTTTAAA
2400582 CATATATTATATTATATTTA
1 CATAT-TTATATTAT-TTTA
2400602 TTATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
CATATTTATATTATTTTAAA
Found at i:2400886 original size:12 final size:12
Alignment explanation
Indices: 2400867--2400896 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2400857 TGTATAATTA
2400867 AAAATTTTTTAT
1 AAAATTTTTTAT
*
2400879 ATAATTTTTTAT
1 AAAATTTTTTAT
2400891 AAAATT
1 AAAATT
2400897 AAAATTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
AAAATTTTTTAT
Found at i:2402152 original size:21 final size:21
Alignment explanation
Indices: 2402137--2402194 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
2402127 ATTTTATCAA
2402137 ATTATA-ATAATATTTTAAAT
1 ATTATATATAATATTTTAAAT
2402157 ATTATATATAATA-TTTAATAT
1 ATTATATATAATATTTTAA-AT
* *
2402178 ATT-TTTATTATATTTTA
1 ATTATATATAATATTTTA
2402195 TTAATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATATATAATATTTTAAAT
Found at i:2408450 original size:9 final size:9
Alignment explanation
Indices: 2408433--2408467 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2408423 AAAATCTATT
2408433 ATGATGAAG
1 ATGATGAAG
*
2408442 ATCATGAAG
1 ATGATGAAG
*
2408451 ATGATGATG
1 ATGATGAAG
2408460 ATGATGAA
1 ATGATGAA
2408468 ACAGTGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.43, C:0.03, G:0.29, T:0.26
Consensus pattern (9 bp):
ATGATGAAG
Found at i:2415484 original size:37 final size:34
Alignment explanation
Indices: 2415441--2415527 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 34
2415431 AATATCTTTG
* * *
2415441 TTAAGTGTGTTAGGTGGTATGTTAAGTAAGTAATATA
1 TTAAGTGTATTAGGTAGTATGTTAAGT-A--AACATA
* *
2415478 TTAAGTGTATTAGGTAGTGTGTTAGGTAAACATA
1 TTAAGTGTATTAGGTAGTATGTTAAGTAAACATA
2415512 TTAAGTGTATTAGGTA
1 TTAAGTGTATTAGGTA
2415528 AATATATTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 21 0.47
36 1 0.02
37 23 0.51
ACGTcount: A:0.32, C:0.01, G:0.26, T:0.40
Consensus pattern (34 bp):
TTAAGTGTATTAGGTAGTATGTTAAGTAAACATA
Found at i:2415519 original size:22 final size:22
Alignment explanation
Indices: 2415493--2415548 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
2415483 TGTATTAGGT
2415493 AGTGTGTTAGGTAAACATATTA
1 AGTGTGTTAGGTAAACATATTA
* *
2415515 AGTGTATTAGGTAAATATATTA
1 AGTGTGTTAGGTAAACATATTA
*
2415537 GGTGTGTTAGGT
1 AGTGTGTTAGGT
2415549 GAACTTATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.39
Consensus pattern (22 bp):
AGTGTGTTAGGTAAACATATTA
Found at i:2417805 original size:14 final size:14
Alignment explanation
Indices: 2417786--2417834 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
2417776 TATTCAAATT
2417786 ATATATAAATTTTA
1 ATATATAAATTTTA
2417800 ATATATTAATAATTTATA
1 ATATA-T-A-AATTT-TA
*
2417818 TTATATAAATTTTA
1 ATATATAAATTTTA
2417832 ATA
1 ATA
2417835 CATTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.31
15 6 0.21
16 2 0.07
17 6 0.21
18 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATAAATTTTA
Found at i:2417828 original size:32 final size:31
Alignment explanation
Indices: 2417787--2417852 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 31
2417777 ATTCAAATTA
*
2417787 TATATAAATTTTAATATATTAATAATTTATAT
1 TATATAAATTTTAATACATTAAT-ATTTATAT
* *
2417819 TATATAAATTTTAATACATTTATTTTTATAT
1 TATATAAATTTTAATACATTAATATTTATAT
2417850 TAT
1 TAT
2417853 TTTTTTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (31 bp):
TATATAAATTTTAATACATTAATATTTATAT
Found at i:2420317 original size:27 final size:30
Alignment explanation
Indices: 2420252--2420327 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
2420242 TCCATGTCAT
2420252 TTTTAATCAAAAATAAAAATTAAGTGAAAAA
1 TTTTAATCAAAAATAAAAA-TAAGTGAAAAA
*
2420283 TTCT-ATCAAAAATAAAAA-AA-TG-AAAA
1 TTTTAATCAAAAATAAAAATAAGTGAAAAA
2420309 TTTTAATC--AAATAAAAATA
1 TTTTAATCAAAAATAAAAATA
2420328 GGATAACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
25 9 0.22
26 8 0.20
27 5 0.12
28 2 0.05
30 14 0.34
31 3 0.07
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (30 bp):
TTTTAATCAAAAATAAAAATAAGTGAAAAA
Found at i:2421579 original size:268 final size:264
Alignment explanation
Indices: 2421100--2421636 Score: 788
Period size: 268 Copynumber: 2.0 Consensus size: 264
2421090 ATCTATGAAC
**
2421100 ATAATGTTGTACCATGCTTGGGATGCATATTAAAAGCACGAGCATGTGTCGCAGGTCACACAAAT
1 ATAATGTTGTACCATGCTTGGGATGCATATTAAAAGCACGAGCATGTGTCGCAGACCACACAAAT
* * * *
2421165 TCAGATTTAATAATTTGAAATATATAAAATATTTTGATTCATTAAAATAAATTTAATATTCGAAA
66 TCAGATTCAATAATTTGAAATATATAAAATAATTTAATTCATTAAAATAAATTCAATATTCGAAA
*
2421230 AGATTTAAAAAATTCAGTTTATTTAAAAACGTAAAAAGTTAGATAACTATAACTACTTCAATTTA
131 AGATTTAAAAAATTCAGTTTATTTAAAAACGTAAAAAGTCAGATAACTATAACTACTTCAATTTA
* * * *
2421295 TTTAAAATTTTATAAAATTATAGTAATAGAGTTTAAACTTATATGAAATTTTAGATTTTATAAAT
196 CTTAAAATTTTATAAAAGTACAGTAATAGAATTTAAACTTATATGAAATTTTAGATTTTATAAAT
2421360 AAAT
261 AAAT
* *
2421364 ATAATTTTGTACCATGCTTGGGATGCATATTACAAGCACGAGCATGTGTCGCAGACCACACAAAT
1 ATAATGTTGTACCATGCTTGGGATGCATATTAAAAGCACGAGCATGTGTCGCAGACCACAC--A-
* * * * *
2421429 TAATTCAGATTCAATGATTTGAAATATATAAAGTAATTTAATTTATTAAAATAAGTTCGATA-TC
63 -AATTCAGATTCAATAATTTGAAATATATAAAATAATTTAATTCATTAAAATAAATTCAATATTC
* * * * * *
2421493 TGAAGAGTTTTAAAAAATTTAGTTTATTTAAAAGCTTAAAAAGTCAGATAACTATAACTATTTCA
127 -GAAAAGATTTAAAAAATTCAGTTTATTTAAAAACGTAAAAAGTCAGATAACTATAACTACTTCA
* *
2421558 ATTTACTTAAAATTTTATAAAAGTACAGTGATAGAATTTAAATTTATATGAAATTTTAGATTTTA
191 ATTTACTTAAAATTTTATAAAAGTACAGTAATAGAATTTAAACTTATATGAAATTTTAGATTTTA
2421623 TAAATAAAT
256 TAAATAAAT
2421632 ATAAT
1 ATAAT
2421637 CATAATCATT
Statistics
Matches: 242, Mismatches: 26, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
264 57 0.24
266 1 0.00
267 2 0.01
268 182 0.75
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (264 bp):
ATAATGTTGTACCATGCTTGGGATGCATATTAAAAGCACGAGCATGTGTCGCAGACCACACAAAT
TCAGATTCAATAATTTGAAATATATAAAATAATTTAATTCATTAAAATAAATTCAATATTCGAAA
AGATTTAAAAAATTCAGTTTATTTAAAAACGTAAAAAGTCAGATAACTATAACTACTTCAATTTA
CTTAAAATTTTATAAAAGTACAGTAATAGAATTTAAACTTATATGAAATTTTAGATTTTATAAAT
AAAT
Found at i:2422454 original size:27 final size:28
Alignment explanation
Indices: 2422383--2422461 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 28
2422373 AAATAACAAG
*
2422383 CCACCATTTTTTACAAA-AAAAAAGTAA
1 CCACCATTTTTTACAAACAAAAATGTAA
*
2422410 CCACCATTTTTTACAAACACAAATG-AA
1 CCACCATTTTTTACAAACAAAAATGTAA
* * *
2422437 CTACCATTTTTGACAAACAGAAATG
1 CCACCATTTTTTACAAACAAAAATG
2422462 GTGACTTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 41 0.89
28 5 0.11
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.27
Consensus pattern (28 bp):
CCACCATTTTTTACAAACAAAAATGTAA
Found at i:2426931 original size:24 final size:24
Alignment explanation
Indices: 2426902--2426947 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2426892 AATAAAAATT
*
2426902 AGCTACTAATTTTGACAAATAACA
1 AGCTACCAATTTTGACAAATAACA
* *
2426926 AGCTACCATTTTTTACAAATAA
1 AGCTACCAATTTTGACAAATAA
2426948 AAAGGAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (24 bp):
AGCTACCAATTTTGACAAATAACA
Found at i:2426971 original size:27 final size:28
Alignment explanation
Indices: 2426933--2427009 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
2426923 ACAAGCTACC
*
2426933 ATTTTTTACAAATA-AAAAGGAATCATT
1 ATTTTTTACAAATACAAAAGGAACCATT
* **
2426960 ATTTTTGACAAATATTAAA-GAACCATT
1 ATTTTTTACAAATACAAAAGGAACCATT
*
2426987 ATTTTTTACAAACACAAAAGGAA
1 ATTTTTTACAAATACAAAAGGAA
2427010 ACTTTTGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 35 0.85
28 6 0.15
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (28 bp):
ATTTTTTACAAATACAAAAGGAACCATT
Found at i:2427608 original size:2 final size:2
Alignment explanation
Indices: 2427601--2427629 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2427591 AGCATTAATT
2427601 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2427630 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2427634 original size:2 final size:2
Alignment explanation
Indices: 2427629--2427654 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2427619 TCTCTCTCTC
2427629 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2427655 AGAGTAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2428287 original size:19 final size:18
Alignment explanation
Indices: 2428255--2428311 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
2428245 AATTAAATTG
*
2428255 ATATCAAAAATTAATTAA
1 ATATTAAAAATTAATTAA
* *
2428273 ATATTAATTAATTAATAAA
1 ATATTAA-AAATTAATTAA
*
2428292 ATTTTAAAAACTTAATTAA
1 ATATTAAAAA-TTAATTAA
2428311 A
1 A
2428312 CTAACAGTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 8 0.26
19 23 0.74
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTAAAAATTAATTAA
Found at i:2428620 original size:23 final size:22
Alignment explanation
Indices: 2428572--2428625 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
2428562 TTATAGATTT
2428572 TATTAA-AATTTATATTTGATA
1 TATTAATAATTTATATTTGATA
2428593 TATTAATAATTTATAAATTT-ATA
1 TATTAATAATTTAT--ATTTGATA
*
2428616 TATTATTAAT
1 TATTAATAAT
2428626 AAATCAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 6 0.21
22 7 0.24
23 12 0.41
24 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TATTAATAATTTATATTTGATA
Found at i:2428637 original size:26 final size:26
Alignment explanation
Indices: 2428608--2428657 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2428598 ATAATTTATA
* *
2428608 AATTTATATATTATTAATAAATCAAT
1 AATTTATACACTATTAATAAATCAAT
*
2428634 AATTTATACACTGTTAATAAATCA
1 AATTTATACACTATTAATAAATCA
2428658 GTTAATTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (26 bp):
AATTTATACACTATTAATAAATCAAT
Found at i:2433253 original size:17 final size:15
Alignment explanation
Indices: 2433230--2433272 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 15
2433220 GAATAATATT
2433230 AATAAAAAATATTAA
1 AATAAAAAATATTAA
2433245 ATTATAAAAAAT-TTAA
1 A--ATAAAAAATATTAA
2433261 AATAAAAAATAT
1 AATAAAAAATAT
2433273 ATTATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 9 0.36
15 2 0.08
16 5 0.20
17 9 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAAAAATATTAA
Found at i:2433559 original size:25 final size:26
Alignment explanation
Indices: 2433526--2433580 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
2433516 TTTCTTTTTA
*
2433526 AAAATAAAAAA-TATAGTAAACCAGT
1 AAAATAAAAAATTATAGTAAACCAAT
*
2433551 AAAATAAAAAATTATAGTGAACCAAT
1 AAAATAAAAAATTATAGTAAACCAAT
2433577 AAAA
1 AAAA
2433581 AATTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.20
Consensus pattern (26 bp):
AAAATAAAAAATTATAGTAAACCAAT
Found at i:2433715 original size:11 final size:12
Alignment explanation
Indices: 2433691--2433723 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2433681 ATTTTATTAA
2433691 TTAATTATTATAT
1 TTAA-TATTATAT
2433704 TTAATATT-TAT
1 TTAATATTATAT
2433715 TTAATATTA
1 TTAATATTA
2433724 AAACTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 4 0.21
13 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTAATATTATAT
Found at i:2434031 original size:20 final size:19
Alignment explanation
Indices: 2434012--2434059 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
2434002 TATTTAATTA
2434012 ATAAAATATAAATTTTATT
1 ATAAAATATAAATTTTATT
* *
2434031 ATAAATATATAAATATTAAT
1 ATAAA-ATATAAATTTTATT
2434051 ATAAAATAT
1 ATAAAATAT
2434060 TTTTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAAATATAAATTTTATT
Found at i:2434087 original size:32 final size:32
Alignment explanation
Indices: 2433991--2434092 Score: 84
Period size: 34 Copynumber: 3.1 Consensus size: 32
2433981 AGAAAAGATT
*
2433991 TTTTTAATTATTATTTAATTAATAAAATATAAAT-
1 TTTTTAATAATT-TTTAA-TAATAAAATA-AAATA
* * * *
2434025 TTTATT-ATAAATATATAAATATTAATATAAAATA
1 TTT-TTAAT-AAT-TTTTAATAATAAAATAAAATA
2434059 TTTTTAATAATTTTTAATAATAAAAT-AAATA
1 TTTTTAATAATTTTTAATAATAAAATAAAATA
2434090 TTT
1 TTT
2434093 AAATTTTATA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
31 8 0.15
32 11 0.20
33 9 0.17
34 18 0.33
35 7 0.13
36 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
TTTTTAATAATTTTTAATAATAAAATAAAATA
Found at i:2434099 original size:26 final size:26
Alignment explanation
Indices: 2434031--2434121 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 26
2434021 AAATTTTATT
* *
2434031 ATAAATATATAAATATTAAT-ATAAA
1 ATAAATATTTAAATTTTAATAATAAA
*
2434056 AT--ATTTTTAATAATTTTTAATAATAAA
1 ATAAATATTT-A-AA-TTTTAATAATAAA
**
2434083 ATAAATATTTAAATTTT-ATAAATTTA
1 ATAAATATTTAAATTTTAAT-AATAAA
2434109 ATAAAT-TTTAAAT
1 ATAAATATTTAAAT
2434122 AAATAAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
23 4 0.08
24 1 0.02
25 13 0.25
26 20 0.38
27 9 0.17
28 1 0.02
29 5 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAAATATTTAAATTTTAATAATAAA
Found at i:2436044 original size:3 final size:3
Alignment explanation
Indices: 2436036--2436092 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
2436026 TTATCACGTT
*
2436036 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2436084 TTA TTA TTA
1 TTA TTA TTA
2436093 ATTTTTAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2436353 original size:127 final size:127
Alignment explanation
Indices: 2436127--2436380 Score: 472
Period size: 127 Copynumber: 2.0 Consensus size: 127
2436117 AGGGCCAAGG
*
2436127 TTTCAATAAAGGCTTCCTCAAATGAATGTAGTTTGACCTCGAGCGTGGGCTAGCTTCATCAGCTT
1 TTTCAATAAAGGCCTCCTCAAATGAATGTAGTTTGACCTCGAGCGTGGGCTAGCTTCATCAGCTT
*
2436192 AATGCGATAGGCTTATTCATTCGAGTTCTCTTTGAAATTAAATTTAAATATATATTATAATT
66 AATGCGATAGGCCTATTCATTCGAGTTCTCTTTGAAATTAAATTTAAATATATATTATAATT
* *
2436254 TTTCAATAAAGGCCTCCTCAAGTGGATGTAGTTTGACCTCGAGCGTGGGCTAGCTTCATCAGCTT
1 TTTCAATAAAGGCCTCCTCAAATGAATGTAGTTTGACCTCGAGCGTGGGCTAGCTTCATCAGCTT
2436319 AATGCGATAGGCCTATTCATTCGAGTTCTCTTTGAAATTAAATTTAAATATATATTATAATT
66 AATGCGATAGGCCTATTCATTCGAGTTCTCTTTGAAATTAAATTTAAATATATATTATAATT
2436381 AAAATTTTAA
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 123 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (127 bp):
TTTCAATAAAGGCCTCCTCAAATGAATGTAGTTTGACCTCGAGCGTGGGCTAGCTTCATCAGCTT
AATGCGATAGGCCTATTCATTCGAGTTCTCTTTGAAATTAAATTTAAATATATATTATAATT
Found at i:2436878 original size:17 final size:17
Alignment explanation
Indices: 2436835--2436889 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
2436825 TATTTTAATT
*
2436835 ATTTATTA-CTTTTTAA
1 ATTTATTATATTTTTAA
*
2436851 ATATTA-AATATTTTTAA
1 AT-TTATTATATTTTTAA
* *
2436868 ATTTATTATATATATAA
1 ATTTATTATATTTTTAA
2436885 ATTTA
1 ATTTA
2436890 AATTTTACAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.19
17 25 0.81
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATTATATTTTTAA
Found at i:2436880 original size:19 final size:17
Alignment explanation
Indices: 2436821--2436869 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
2436811 ATCATCACAT
* *
2436821 AATATATTTTAATTATTT
1 AATAT-TTTTAAATATTA
*
2436839 ATTACTTTTTAAATATTA
1 AATA-TTTTTAAATATTA
2436857 AATATTTTTAAAT
1 AATATTTTTAAAT
2436870 TTATTATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.35
18 16 0.62
19 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTTTTAAATATTA
Found at i:2445326 original size:2 final size:2
Alignment explanation
Indices: 2445319--2445351 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2445309 TGGCCCATTC
2445319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2445352 CATTTACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2451643 original size:18 final size:18
Alignment explanation
Indices: 2451580--2451643 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
2451570 TTTAGATATT
* *
2451580 ATTAAATATTAAATAATTTA
1 ATTAAATATT-ATTAA-TAA
*
2451600 ATTTAAT-TTATTAATAA
1 ATTAAATATTATTAATAA
* *
2451617 TTTATATATTATTAATAA
1 ATTAAATATTATTAATAA
2451635 ATTAAATAT
1 ATTAAATAT
2451644 AAATCTGTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
17 6 0.17
18 21 0.60
19 2 0.06
20 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAAATATTATTAATAA
Found at i:2452186 original size:16 final size:14
Alignment explanation
Indices: 2452155--2452196 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2452145 AATATTTAAT
2452155 TTTTATTTTAATTA
1 TTTTATTTTAATTA
2452169 TTTTATATTTAA-TA
1 TTTTAT-TTTAATTA
* *
2452183 TATTATTTTTATTA
1 TTTTATTTTAATTA
2452197 AATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 4 0.17
14 15 0.62
15 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTTAATTA
Found at i:2454862 original size:33 final size:33
Alignment explanation
Indices: 2454825--2454888 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
2454815 AGTCATTGGA
*
2454825 AGGTTGCATATCCATCGACTTACACTGCTAGGG
1 AGGTTGCATATCCATCAACTTACACTGCTAGGG
*
2454858 AGGTTGCATATCCTTCAACTTACACTGCTAG
1 AGGTTGCATATCCATCAACTTACACTGCTAG
2454889 TTTTAACTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (33 bp):
AGGTTGCATATCCATCAACTTACACTGCTAGGG
Found at i:2456465 original size:144 final size:144
Alignment explanation
Indices: 2456205--2456478 Score: 539
Period size: 144 Copynumber: 1.9 Consensus size: 144
2456195 CACGGTGCTG
2456205 GCATCTTGGCTTTTCACCTTTTTTCACATCCTTTTAAAGTGAGAATGTGACAATTCAGCTGTATT
1 GCATCTTGGCTTTTCACCTTTTTTCACATCCTTTTAAAGTGAGAATGTGACAATTCAGCTGTATT
*
2456270 TCTAGGTTCCATCTGAATCAGGGATATGTATAGTGGTTTCCTTTCACTTTCTAGGTTCTAGGTTC
66 TCTAGGTTCCATATGAATCAGGGATATGTATAGTGGTTTCCTTTCACTTTCTAGGTTCTAGGTTC
2456335 ACTTTCTAGGTTCA
131 ACTTTCTAGGTTCA
2456349 GCATCTTGGCTTTTCACCTTTTTTCACATCCTTTTAAAGTGAGAATGTGACAATTCAGCTGTATT
1 GCATCTTGGCTTTTCACCTTTTTTCACATCCTTTTAAAGTGAGAATGTGACAATTCAGCTGTATT
2456414 TCTAGGTTCCATATGAATCAGGGATATGTATAGTGGTTTCCTTTCACTTTCTAGGTTCTAGGTTC
66 TCTAGGTTCCATATGAATCAGGGATATGTATAGTGGTTTCCTTTCACTTTCTAGGTTCTAGGTTC
2456479 CCTTGAGCAC
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 129 1.00
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (144 bp):
GCATCTTGGCTTTTCACCTTTTTTCACATCCTTTTAAAGTGAGAATGTGACAATTCAGCTGTATT
TCTAGGTTCCATATGAATCAGGGATATGTATAGTGGTTTCCTTTCACTTTCTAGGTTCTAGGTTC
ACTTTCTAGGTTCA
Found at i:2456556 original size:4 final size:4
Alignment explanation
Indices: 2456547--2456573 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2456537 CGTTCGAGAA
2456547 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
2456574 TCCATATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2457858 original size:2 final size:2
Alignment explanation
Indices: 2457851--2457890 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2457841 CAAATGTTGA
2457851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2457891 TGTATTTCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2462865 original size:13 final size:13
Alignment explanation
Indices: 2462844--2462899 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
2462834 TACCTTTTTT
2462844 TAATATATAATTA
1 TAATATATAATTA
* *
2462857 TATTATATAAATA
1 TAATATATAATTA
*
2462870 TAATAAATAATTA
1 TAATATATAATTA
*
2462883 -AA-ATA-AAATA
1 TAATATATAATTA
2462893 TAATATA
1 TAATATA
2462900 AATAAATAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
10 4 0.12
11 4 0.12
12 5 0.15
13 21 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATATATAATTA
Found at i:2462903 original size:29 final size:29
Alignment explanation
Indices: 2462861--2462925 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
2462851 TAATTATATT
*
2462861 ATATAAATATAATAAATAATTAAAATAAA
1 ATATAAATATAATAAATAAGTAAAATAAA
**
2462890 ATAT-AATATAAATAAATAAGTAAAATGTA
1 ATATAAATAT-AATAAATAAGTAAAATAAA
2462919 ATATAAA
1 ATATAAA
2462926 CTATGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 5 0.16
29 24 0.77
30 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (29 bp):
ATATAAATATAATAAATAAGTAAAATAAA
Found at i:2462920 original size:24 final size:25
Alignment explanation
Indices: 2462865--2462925 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
2462855 TATATTATAT
*
2462865 AAATAT-A-ATAAATAATTAAAATA
1 AAATATAATATAAATAAATAAAATA
*
2462888 AAATATAATATAAATAAAT-AAGTA
1 AAATATAATATAAATAAATAAAATA
*
2462912 AAATGTAATATAAA
1 AAATATAATATAAA
2462926 CTATGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.18
24 18 0.55
25 9 0.27
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (25 bp):
AAATATAATATAAATAAATAAAATA
Found at i:2462975 original size:19 final size:18
Alignment explanation
Indices: 2462947--2462982 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2462937 TATGATCATA
2462947 AAAATATATAAATATATC
1 AAAATATATAAATATATC
*
2462965 AAAATATTATATATATAT
1 AAAATA-TATAAATATAT
2462983 ATATATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATATATAAATATATC
Found at i:2462975 original size:21 final size:21
Alignment explanation
Indices: 2462934--2462984 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2462924 AACTATGAAA
2462934 AAATATGATCATAAAAATATAT
1 AAATAT-ATCATAAAAATATAT
*
2462956 AAATATATCA-AAATATTATAT
1 AAATATATCATAAA-AATATAT
*
2462977 ATATATAT
1 AAATATAT
2462985 ATATATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 17 0.65
22 6 0.23
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATATATCATAAAAATATAT
Found at i:2463049 original size:24 final size:24
Alignment explanation
Indices: 2463020--2463069 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2463010 TAATGTTTTG
*
2463020 AATACAATTAT-GATATAAAAATAT
1 AATACAAATATAG-TATAAAAATAT
*
2463044 AATACAAATATAGTATAAATATAT
1 AATACAAATATAGTATAAAAATAT
2463068 AA
1 AA
2463070 ATTATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (24 bp):
AATACAAATATAGTATAAAAATAT
Found at i:2463223 original size:20 final size:21
Alignment explanation
Indices: 2463186--2463224 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2463176 ATTTATCTAA
2463186 AATTTAAATTTATTTATTACC
1 AATTTAAATTTATTTATTACC
*
2463207 AATTTATATTT-TTTATTA
1 AATTTAAATTTATTTATTA
2463225 TAATCCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTTAAATTTATTTATTACC
Found at i:2463820 original size:2 final size:2
Alignment explanation
Indices: 2463815--2463848 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2463805 ACACACACAC
2463815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2463849 TACGTCGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2464552 original size:13 final size:13
Alignment explanation
Indices: 2464515--2464552 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2464505 AAACCATATC
*
2464515 TTTTTCCTTTTCT
1 TTTTTCCTTTTTT
*
2464528 TTTTTCTTTTTTT
1 TTTTTCCTTTTTT
2464541 TTTTTCCTTTTT
1 TTTTTCCTTTTT
2464553 GTTTCTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCCTTTTTT
Found at i:2467881 original size:2 final size:2
Alignment explanation
Indices: 2467833--2467864 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2467823 AACTATTTAT
*
2467833 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2467865 CACAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2469110 original size:7 final size:7
Alignment explanation
Indices: 2469100--2469136 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
2469090 ATAAAAATAT
2469100 AACCCTA
1 AACCCTA
2469107 AACCCTA
1 AACCCTA
2469114 AACCCTA
1 AACCCTA
2469121 AACCCTA
1 AACCCTA
2469128 AACCCTA
1 AACCCTA
2469135 AA
1 AA
2469137 TTTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.46, C:0.41, G:0.00, T:0.14
Consensus pattern (7 bp):
AACCCTA
Found at i:2469115 original size:21 final size:21
Alignment explanation
Indices: 2469091--2469136 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2469081 AGTTAAAAAA
2469091 TAAA-AATATAACCCTAAACCC
1 TAAACAATA-AACCCTAAACCC
**
2469112 TAAACCCTAAACCCTAAACCC
1 TAAACAATAAACCCTAAACCC
2469133 TAAA
1 TAAA
2469137 TTTAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACAATAAACCCTAAACCC
Found at i:2469151 original size:13 final size:13
Alignment explanation
Indices: 2469133--2469157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2469123 CCCTAAACCC
2469133 TAAATTTAATTAT
1 TAAATTTAATTAT
2469146 TAAATTTAATTA
1 TAAATTTAATTA
2469158 ATAATTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAATTTAATTAT
Found at i:2469224 original size:17 final size:19
Alignment explanation
Indices: 2469185--2469225 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
2469175 TTAAAAATAT
*
2469185 TATTTATTTGATATTTAAA
1 TATTTATTTAATATTTAAA
2469204 -ATTT-TTTAATA-TTAAA
1 TATTTATTTAATATTTAAA
2469220 TATTTA
1 TATTTA
2469226 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTTATTTAATATTTAAA
Found at i:2472785 original size:2 final size:2
Alignment explanation
Indices: 2472778--2472827 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
2472768 TATTTGCATC
* * *
2472778 AT AT AT AT AT AT AT AT AT GAT AT AA AT AT AA AA AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
2472819 AT AT AT AT A
1 AT AT AT AT A
2472828 AACTTTGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2476853 original size:16 final size:16
Alignment explanation
Indices: 2476832--2476862 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2476822 TATATTTACA
*
2476832 AATTTTATTTTTTTAT
1 AATTTTATTATTTTAT
2476848 AATTTTATTATTTTA
1 AATTTTATTATTTTA
2476863 AAAAATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
AATTTTATTATTTTAT
Found at i:2477129 original size:7 final size:7
Alignment explanation
Indices: 2477117--2477148 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2477107 TATCTCCTGG
2477117 TTTTTTC
1 TTTTTTC
2477124 TTTTTT-
1 TTTTTTC
2477130 TTTTTTC
1 TTTTTTC
2477137 TTTTTTC
1 TTTTTTC
2477144 TTTTT
1 TTTTT
2477149 ACTGGTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTTC
Found at i:2477135 original size:13 final size:14
Alignment explanation
Indices: 2477117--2477148 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2477107 TATCTCCTGG
2477117 TTTTTTCTTTTTT-
1 TTTTTTCTTTTTTC
2477130 TTTTTTCTTTTTTC
1 TTTTTTCTTTTTTC
2477144 TTTTT
1 TTTTT
2477149 ACTGGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTCTTTTTTC
Found at i:2478788 original size:24 final size:22
Alignment explanation
Indices: 2478757--2478800 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
2478747 TTGTTTGAGT
2478757 ATAAT-AAATGTATAAGAATTTTC
1 ATAATAAAAT-TATAA-AATTTTC
2478780 ATAAGTAAAATTATAAAATTT
1 ATAA-TAAAATTATAAAATTT
2478801 AAGTGCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 9 0.47
24 6 0.32
25 4 0.21
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (22 bp):
ATAATAAAATTATAAAATTTTC
Found at i:2478953 original size:19 final size:20
Alignment explanation
Indices: 2478921--2478964 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
2478911 ATTAACAAGT
2478921 TAAAAAATATATTTAAAAAA
1 TAAAAAATATATTTAAAAAA
*
2478941 TAAAAAATA-ATTTTAAAAA
1 TAAAAAATATATTTAAAAAA
2478960 TAAAA
1 TAAAA
2478965 CGTTTGACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAAATATATTTAAAAAA
Found at i:2481141 original size:27 final size:27
Alignment explanation
Indices: 2481111--2481169 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
2481101 CCATAATTAT
*
2481111 ATTTAAAATATTATATA-TTTATATATA
1 ATTTAAAATACTA-ATACTTTATATATA
* *
2481138 ATTTAATATACTAATACTTTTTATATA
1 ATTTAAAATACTAATACTTTATATATA
2481165 ATTTA
1 ATTTA
2481170 TTTATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTAAAATACTAATACTTTATATATA
Found at i:2485659 original size:17 final size:17
Alignment explanation
Indices: 2485617--2485665 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2485607 AAAAATAATT
*
2485617 AATTTATGACATGATATA
1 AATTTATAACAT-ATATA
* *
2485635 AATGTATAACATATTTA
1 AATTTATAACATATATA
*
2485652 AATTTATATCATAT
1 AATTTATAACATAT
2485666 GAATTATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (17 bp):
AATTTATAACATATATA
Found at i:2485839 original size:17 final size:17
Alignment explanation
Indices: 2485756--2485858 Score: 68
Period size: 18 Copynumber: 5.9 Consensus size: 17
2485746 ATTTTATTTT
*
2485756 ATTATTTAAATTATATAA
1 ATTATTTAAATTAAAT-A
* *
2485774 AATATTTAAAATAAA-A
1 ATTATTTAAATTAAATA
* *
2485790 TATT-TTTATTATTTAATTA
1 -ATTATTTA--AATTAAATA
* *
2485809 ATGATTTAAATTAAATC
1 ATTATTTAAATTAAATA
*
2485826 A-TATTTAAATTTAAAAA
1 ATTATTTAAA-TTAAATA
2485843 ATTATTTAAATTAAAT
1 ATTATTTAAATTAAAT
2485859 TAAATTTATT
Statistics
Matches: 63, Mismatches: 15, Indels: 15
0.68 0.16 0.16
Matches are distributed among these distances:
16 12 0.19
17 20 0.32
18 26 0.41
19 5 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (17 bp):
ATTATTTAAATTAAATA
Found at i:2485850 original size:34 final size:33
Alignment explanation
Indices: 2485758--2485858 Score: 96
Period size: 34 Copynumber: 3.0 Consensus size: 33
2485748 TTTATTTTAT
* *
2485758 TATTTAAATTATATAAAA-TATTTAAAATAAAATA
1 TATTTAAATT-TAAAAAATTATTT-AAATTAAATA
* * ** *
2485792 TTTTTATTATTTAATTAATGATTTAAATTAAATCA
1 TATTTA-AATTTAAAAAATTATTTAAATTAAAT-A
2485827 TATTTAAATTTAAAAAATTATTTAAATTAAAT
1 TATTTAAATTTAAAAAATTATTTAAATTAAAT
2485859 TAAATTTATT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
34 39 0.75
35 13 0.25
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
TATTTAAATTTAAAAAATTATTTAAATTAAATA
Found at i:2486302 original size:16 final size:16
Alignment explanation
Indices: 2486283--2486331 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
2486273 TAATTAATTT
2486283 TATTTTATTTAAATAA
1 TATTTTATTTAAATAA
2486299 TATTTAATAATTTAAA-AA
1 TATTT--T-ATTTAAATAA
2486317 TATTTTTATTTAAAT
1 TA-TTTTATTTAAAT
2486332 TTAATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 12 0.43
17 1 0.04
18 5 0.18
19 10 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTATTTAAATAA
Done.