Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold222
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: 358842
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
File 2 of 3
Found at i:170817 original size:44 final size:44
Alignment explanation
Indices: 170753--170841 Score: 128
Period size: 43 Copynumber: 2.0 Consensus size: 44
170743 CGTTCAAATT
* *
170753 ATTTTATATTTAAATTAATTAATTTTAATTTTTTA-ATTAAATTAA
1 ATTTTATATTTAAATGAATTAA-TTAAATTTTTTATATT-AATTAA
170798 ATTTTA-ATTTAAATGAATTAATTAAATTTTTTATATTAATTAA
1 ATTTTATATTTAAATGAATTAATTAAATTTTTTATATTAATTAA
170841 A
1 A
170842 AAATAACCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 18 0.44
44 17 0.41
45 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (44 bp):
ATTTTATATTTAAATGAATTAATTAAATTTTTTATATTAATTAA
Found at i:170853 original size:242 final size:242
Alignment explanation
Indices: 170591--171087 Score: 589
Period size: 242 Copynumber: 2.0 Consensus size: 242
170581 TAAAATATTT
**
170591 TTAACTAAAAAATAACCTAAAAACTTAAAACCCAAATTAACTAAATTTGTTAATTTAATAGATCA
1 TTAACTAAAAAATAACCTAAAAACTTAAAACCCAAATTAACTAAATTCATTAATTTAATAGATCA
* ** * *
170656 TGTTAATTT-TGGATTAATTAATTTAGGTTAAGTCATTTCAAATTTTTAAAATTTTAAGTTATTT
66 GGTTAATTTCAAG-TTAATTAA--T---TTAAGT--TTTCAAATTTTTAAAATTTTAAATCATTT
* * *
170720 TTAGATTTGA-AT-CTTTTTTA-TTT-C-GTTCAAATTATTTTATATTTAAATTAATTAATTTTA
123 TTAAATTT-ACATACTTTTTTATTTTACTATTCAAATTATTTCATATTTAAATTAATTAATTTTA
* *
170780 A-TTTTTTAATT-A-AATTAAATTTTAATTTAAATGAATTAATTAAATTTTTTATA
187 ATTTTTTTAATTAATAATTAAATTTAAATTTAAATGAATTAATTAAACTTTTTATA
* * *
170833 TTAATTAAAAAATAACCTAAAAACTTAAAACCTAAATTAACTAAATTCATTAATTTAATAGATCG
1 TTAACTAAAAAATAACCTAAAAACTTAAAACCCAAATTAACTAAATTCATTAATTTAATAGATCA
*
170898 GGTTAATTTCAAGTTAATTAATTTAAGTTTTTAAATTTTTAAAATTTTAAATCATTTTTAAATTT
66 GGTTAATTTCAAGTTAATTAATTTAAGTTTTCAAATTTTTAAAATTTTAAATCATTTTTAAATTT
*
170963 ACATATTTTTTTATTTTCAAACATTTTAAATTCAAATTATTTCATATTTAAATTAATTAATTTTA
131 ACATACTTTTTTATTTT---AC----T--ATTCAAATTATTTCATATTTAAATTAATTAATTTTA
*
171028 ATTTTTTTAATTAAATTAATTAAATTTAAATTTAAATTAATTAATTAAACTTTTTATA
187 ATTTTTTTAATT-AA-TAATTAAATTTAAATTTAAATGAATTAATTAAACTTTTTATA
171086 TT
1 TT
171088 CAAATTTAAA
Statistics
Matches: 217, Mismatches: 18, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
234 1 0.00
235 35 0.16
236 7 0.03
237 9 0.04
240 1 0.00
241 1 0.00
242 76 0.35
243 1 0.00
248 35 0.16
249 10 0.05
251 1 0.00
253 40 0.18
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (242 bp):
TTAACTAAAAAATAACCTAAAAACTTAAAACCCAAATTAACTAAATTCATTAATTTAATAGATCA
GGTTAATTTCAAGTTAATTAATTTAAGTTTTCAAATTTTTAAAATTTTAAATCATTTTTAAATTT
ACATACTTTTTTATTTTACTATTCAAATTATTTCATATTTAAATTAATTAATTTTAATTTTTTTA
ATTAATAATTAAATTTAAATTTAAATGAATTAATTAAACTTTTTATA
Found at i:171046 original size:9 final size:9
Alignment explanation
Indices: 171010--171075 Score: 53
Period size: 9 Copynumber: 7.0 Consensus size: 9
171000 TATTTCATAT
171010 TTAAATTAA
1 TTAAATTAA
*
171019 TTAATTTTAA
1 TTAA-ATTAA
***
171029 TTTTTTTAA
1 TTAAATTAA
171038 TTAAATTAA
1 TTAAATTAA
171047 TTAAATTTAAA
1 TTAAA-TT-AA
171058 TTTAAATTAA
1 -TTAAATTAA
171068 TT-AATTAA
1 TTAAATTAA
171076 ACTTTTTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
8 6 0.13
9 22 0.47
10 10 0.21
11 4 0.09
12 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTAAATTAA
Found at i:171072 original size:34 final size:34
Alignment explanation
Indices: 171034--171101 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
171024 TTTAATTTTT
*
171034 TTAATTAAA-TTAATTAAATTTAAATTTAAATTAA
1 TTAATTAAACTT-ATTAAATTCAAATTTAAATTAA
* *
171068 TTAATTAAACTTTTTATATTCAAATTTAAATTAA
1 TTAATTAAACTTATTAAATTCAAATTTAAATTAA
171102 CAAATCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (34 bp):
TTAATTAAACTTATTAAATTCAAATTTAAATTAA
Found at i:172004 original size:21 final size:22
Alignment explanation
Indices: 171967--172015 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
171957 CTGCAGCGAG
*
171967 GGAGGTGTTGTTTGAGGA-AGA
1 GGAGGTGTTGTTGGAGGAGAGA
171988 GGAGGATGTTG-TGGAGGAGGAGA
1 GGAGG-TGTTGTTGGAGGA-GAGA
172011 GGAGG
1 GGAGG
172016 GAGAGGGAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.46
22 5 0.21
23 8 0.33
ACGTcount: A:0.24, C:0.00, G:0.55, T:0.20
Consensus pattern (22 bp):
GGAGGTGTTGTTGGAGGAGAGA
Found at i:172033 original size:15 final size:15
Alignment explanation
Indices: 172015--172054 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
172005 AGGAGAGGAG
172015 GGAGAGGGAGGAGAA
1 GGAGAGGGAGGAGAA
* * *
172030 GGAGAGGAAAGATAA
1 GGAGAGGGAGGAGAA
172045 GGAGAGGGAG
1 GGAGAGGGAG
172055 TTTGTCGTGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.55, T:0.03
Consensus pattern (15 bp):
GGAGAGGGAGGAGAA
Found at i:182718 original size:32 final size:32
Alignment explanation
Indices: 182682--182759 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
182672 TTTTATAAAT
182682 TTAAATAAAATTACTCATAAATTTAATAGA-TA
1 TTAAATAAAATTACTCATAAATTTAATA-ATTA
* * * *
182714 TTAAATATAATAACTTATAGATTTAATAATTA
1 TTAAATAAAATTACTCATAAATTTAATAATTA
*
182746 TTAAAAAAAATTAC
1 TTAAATAAAATTAC
182760 CTTATTACTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 1 0.03
32 37 0.97
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (32 bp):
TTAAATAAAATTACTCATAAATTTAATAATTA
Found at i:187724 original size:8 final size:8
Alignment explanation
Indices: 187676--187734 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
187666 AAATATTGAA
187676 AAATATATT
1 AAAT-TATT
187685 AAATTATT
1 AAATTATT
*
187693 ATATT-TT
1 AAATTATT
187700 AAA--ATT
1 AAATTATT
*
187706 TAATTAAATT
1 AAATT--ATT
187716 AAATTATT
1 AAATTATT
187724 AAATTATT
1 AAATTATT
187732 AAA
1 AAA
187735 AATGAACGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
6 4 0.10
7 4 0.10
8 22 0.54
9 4 0.10
10 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AAATTATT
Found at i:188347 original size:17 final size:18
Alignment explanation
Indices: 188317--188360 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
188307 TATATAAATA
188317 TAAATATAGTTTAA-ATTAT
1 TAAATATAG-TTAAGATT-T
188336 TAAATATA-TTAAGATTT
1 TAAATATAGTTAAGATTT
188353 TAAATATA
1 TAAATATA
188361 AATAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 13 0.54
18 3 0.12
19 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
TAAATATAGTTAAGATTT
Found at i:188413 original size:24 final size:24
Alignment explanation
Indices: 188308--188413 Score: 64
Period size: 24 Copynumber: 4.5 Consensus size: 24
188298 CGTATCAGTT
*
188308 ATATAA-ATA-TAAATATAGTTTAA
1 ATATAATATATTAATTATA-TTTAA
*
188331 ATTATTAAATATATTAA-GAT-TTTAA
1 A-TA-T-AATATATTAATTATATTTAA
* * *
188356 ATATAA-ATA-AAATAAATAATTAA
1 ATATAATATATTAAT-TATATTTAA
188379 ATAT-ATCATATTAATTATATTTAA
1 ATATAAT-ATATTAATTATATTTAA
188403 ATATAATATAT
1 ATATAATATAT
188414 CATGTTTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 23
0.68 0.07 0.24
Matches are distributed among these distances:
20 2 0.03
21 3 0.05
22 5 0.08
23 10 0.16
24 22 0.34
25 12 0.19
26 2 0.03
27 5 0.08
28 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (24 bp):
ATATAATATATTAATTATATTTAA
Found at i:190102 original size:20 final size:20
Alignment explanation
Indices: 190064--190102 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
190054 TTATTTTTTA
*
190064 TATTATAATTATATTTAAAG
1 TATTATAATTATATATAAAG
190084 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
190103 TTTTGATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAG
Found at i:190314 original size:19 final size:19
Alignment explanation
Indices: 190292--190342 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
190282 TTTCACTCTT
190292 TTAAAATATAACTATTTTC
1 TTAAAATATAACTATTTTC
*
190311 TTAACCAT-TAAC-ATTTTC
1 TTAA-AATATAACTATTTTC
190329 TTAAAA-A-AACTATT
1 TTAAAATATAACTATT
190343 AACTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
16 3 0.11
17 4 0.15
18 10 0.37
19 8 0.30
20 2 0.07
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAAATATAACTATTTTC
Found at i:190417 original size:2 final size:2
Alignment explanation
Indices: 190410--190434 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
190400 TTATAATGAT
190410 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 T
190435 TCTTTCACGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:190755 original size:11 final size:11
Alignment explanation
Indices: 190724--190758 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
190714 TTTATATCAT
190724 TTATATTTTATA
1 TTATATTTTA-A
190736 TTATATTTTAA
1 TTATATTTTAA
*
190747 TTATTTTTTAA
1 TTATATTTTAA
190758 T
1 T
190759 GACTTCGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:192014 original size:2 final size:2
Alignment explanation
Indices: 192007--192032 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
191997 AGAAAAGAAA
192007 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
192033 GTAGCAGCTC
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):
AT
Found at i:192501 original size:3 final size:3
Alignment explanation
Indices: 192493--192556 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
192483 AAACGATATT
192493 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
192541 GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA G
192557 CTCTCTGGTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:195143 original size:24 final size:24
Alignment explanation
Indices: 195110--195173 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
195100 CAAGAACCAC
* * * * *
195110 TGGAGACAGTTAAACAAGATTCAT
1 TGGAGCCAGTGAAACAACAATCAA
*
195134 TGGTGCCAGTGAAACAACAATCAA
1 TGGAGCCAGTGAAACAACAATCAA
195158 TGGAGCCAGTGAAACA
1 TGGAGCCAGTGAAACA
195174 GGAGCTATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (24 bp):
TGGAGCCAGTGAAACAACAATCAA
Found at i:196993 original size:3 final size:3
Alignment explanation
Indices: 196985--197032 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
196975 GCGAAGAACG
*
196985 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
197033 TATTTCGAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:197477 original size:42 final size:42
Alignment explanation
Indices: 197396--197495 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 42
197386 GTTTATTTTT
* *
197396 TATTAAATTTAATTACTTTTTATTTAAATAGTAAGTAAA-TA
1 TATTTAATTTAATTAATTTTTATTTAAATAGTAAGTAAATTA
*
197437 TATTTAATTTAATTTAATTTTTAATTTATAA-ATTAA-TAAATTA
1 TATTTAATTTAA-TTAATTTTT-ATTTA-AATAGTAAGTAAATTA
*
197480 TAATT-ATTTAAATTAA
1 TATTTAATTT-AATTAA
197496 ATTAAAATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
41 11 0.22
42 20 0.40
43 17 0.34
44 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (42 bp):
TATTTAATTTAATTAATTTTTATTTAAATAGTAAGTAAATTA
Found at i:197491 original size:15 final size:15
Alignment explanation
Indices: 197443--197499 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
197433 AATATATTTA
197443 ATTT-AATT-TAATT
1 ATTTAAATTATAATT
*
197456 -TTTAATTTATAAATT
1 ATTTAAATTAT-AATT
*
197471 A-ATAAATTATAATT
1 ATTTAAATTATAATT
197485 ATTTAAATTA-AATT
1 ATTTAAATTATAATT
197499 A
1 A
197500 AAATTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
12 3 0.09
13 3 0.09
14 11 0.31
15 18 0.51
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAAATTATAATT
Found at i:199973 original size:15 final size:16
Alignment explanation
Indices: 199940--199970 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
199930 GCATGGCAGG
*
199940 TTTTTTTTTTTTCAAA
1 TTTTTTGTTTTTCAAA
199956 TTTTTTGTTTTTCAA
1 TTTTTTGTTTTTCAA
199971 TTTATAATCT
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:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTTGTTTTTCAAA
Found at i:202432 original size:23 final size:24
Alignment explanation
Indices: 202405--202452 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
202395 TTTATAGTTA
202405 TGTATCTTGA-AATT-AATAGCAAT
1 TGTATCTT-ATAATTAAATAGCAAT
*
202428 TGTATCTTATAATTAAATATCAAT
1 TGTATCTTATAATTAAATAGCAAT
202452 T
1 T
202453 ACCTTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 12 0.55
24 9 0.41
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (24 bp):
TGTATCTTATAATTAAATAGCAAT
Found at i:202853 original size:21 final size:20
Alignment explanation
Indices: 202828--202885 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
202818 TTCTTTTACC
202828 ATATTTAAACATATTAAATT
1 ATATTTAAACATATTAAATT
* *
202848 AATATTTAAATATTTTAAATT
1 -ATATTTAAACATATTAAATT
**
202869 ATATTTTTACATATTAA
1 ATATTTAAACATATTAA
202886 TATATGTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTTAAACATATTAAATT
Found at i:206204 original size:22 final size:23
Alignment explanation
Indices: 206179--206228 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
206169 ATAAACTAAA
206179 ATATTTAAAAATAT-ATAAAAAT
1 ATATTTAAAAATATCATAAAAAT
** *
206201 ATATTTTCAAATATCATTAAAAT
1 ATATTTAAAAATATCATAAAAAT
206224 A-ATTT
1 ATATTT
206229 TATCAATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATTTAAAAATATCATAAAAAT
Found at i:206234 original size:24 final size:22
Alignment explanation
Indices: 206187--206229 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
206177 AAATATTTAA
206187 AAATATATAAAAATATATTTTC
1 AAATATATAAAAATATATTTTC
*
206209 AAATATCATTAAAATA-ATTTT
1 AAATAT-ATAAAAATATATTTT
206230 ATCAATACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATATATAAAAATATATTTTC
Found at i:206415 original size:19 final size:19
Alignment explanation
Indices: 206391--206429 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
206381 ATAGAGCCTC
206391 TGGCAGAGGTTTAGAATGT
1 TGGCAGAGGTTTAGAATGT
*
206410 TGGCAGATGTTTAGAATGT
1 TGGCAGAGGTTTAGAATGT
206429 T
1 T
206430 TGAAAGTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.36
Consensus pattern (19 bp):
TGGCAGAGGTTTAGAATGT
Found at i:206746 original size:17 final size:20
Alignment explanation
Indices: 206707--206743 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
206697 TATTTTAGAG
*
206707 TATTATTTTAAATTTATTAT
1 TATTATTTTAAATATATTAT
206727 TATT-TTTTAAATATATT
1 TATTATTTTAAATATATT
206744 TATAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTATTTTAAATATATTAT
Found at i:206784 original size:2 final size:2
Alignment explanation
Indices: 206773--206841 Score: 56
Period size: 2 Copynumber: 35.5 Consensus size: 2
206763 TTTTAATAAA
* *
206773 AT AT AT -T AT AT AT AT AT AT AT GT AA AT AT ACT -T CA- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT
* *
206813 AT AT AT AT AT AT AT TT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
206842 AATTTAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
1 4 0.08
2 48 0.91
3 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:206914 original size:30 final size:29
Alignment explanation
Indices: 206833--206923 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 29
206823 ATATTTATAT
*
206833 ATAA-ATAT-AAATTTAAAAATTATAAATAA
1 ATAATATATAAAATTTTAAAA--ATAAATAA
* * *
206862 TTAATATCTAAAATTTTTAAAATCAAATAA
1 ATAATATATAAAATTTTAAAAAT-AAATAA
206892 ATAA-ATATAAAATATTTAAAAATATAATAA
1 ATAATATATAAAAT-TTTAAAAATA-AATAA
206922 AT
1 AT
206924 TATTATTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
29 14 0.28
30 27 0.54
31 9 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (29 bp):
ATAATATATAAAATTTTAAAAATAAATAA
Found at i:207013 original size:27 final size:29
Alignment explanation
Indices: 206976--207032 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
206966 TTTTTGTGTG
*
206976 TAATTATAAAAAATAAAAT-ATTAAAAAT
1 TAATTATAAAAAATAAAATAAATAAAAAT
* *
207004 TAATT-TAAAAAGTTAAATAAATAAAAAT
1 TAATTATAAAAAATAAAATAAATAAAAAT
207032 T
1 T
207033 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
TAATTATAAAAAATAAAATAAATAAAAAT
Found at i:208912 original size:53 final size:53
Alignment explanation
Indices: 208816--208916 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
208806 TGATCGAAAT
* *
208816 CTAATTAATTTGAGTATTAAACTTAATTGATCTGAACTTAAAATGACTCTGAC
1 CTAATTAATTTGAATATTAAACTTAATTGATCTGAACTAAAAATGACTCTGAC
* * *
208869 CTAATTAATTTGAATATTAAACTTGATTGCTTTGAAAC-AAAAATGACT
1 CTAATTAATTTGAATATTAAACTTAATTGATCTG-AACTAAAAATGACT
208917 AAAACCTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 39 0.93
54 3 0.07
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.38
Consensus pattern (53 bp):
CTAATTAATTTGAATATTAAACTTAATTGATCTGAACTAAAAATGACTCTGAC
Found at i:216395 original size:26 final size:26
Alignment explanation
Indices: 216366--216422 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
216356 AAAACAATAG
*
216366 AGAAG-TTCTCAATAAAGGGAGAGCAA
1 AGAAGATTCCCAA-AAAGGGAGAGCAA
* *
216392 AGAAGATTTCCCAACAAGGGGGAGCAA
1 AGAAGA-TTCCCAAAAAGGGAGAGCAA
216419 AGAA
1 AGAA
216423 ATATCAAGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 5 0.19
27 15 0.58
28 6 0.23
ACGTcount: A:0.46, C:0.14, G:0.28, T:0.12
Consensus pattern (26 bp):
AGAAGATTCCCAAAAAGGGAGAGCAA
Found at i:226110 original size:15 final size:14
Alignment explanation
Indices: 226086--226176 Score: 57
Period size: 14 Copynumber: 6.6 Consensus size: 14
226076 CATTGACACA
226086 AATA-TTAAATTATT
1 AATATTTAAA-TATT
226100 AATATTTAAATATT
1 AATATTTAAATATT
* **
226114 AAGAACT--AT-TT
1 AATATTTAAATATT
* *
226125 ATTTTTTAAATATT
1 AATATTTAAATATT
*
226139 AATATTTCAAATAAT
1 AATATTT-AAATATT
*
226154 AATATTTTAATCA-T
1 AATATTTAAAT-ATT
226168 AATATTTAA
1 AATATTTAA
226177 TACTAAAATA
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
11 4 0.07
12 2 0.03
13 2 0.03
14 31 0.53
15 19 0.33
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.48
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:226291 original size:15 final size:17
Alignment explanation
Indices: 226255--226291 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
226245 AATATTTTAA
226255 AATATTATCTTATTATT
1 AATATTATCTTATTATT
*
226272 TATATTAT-TTA-TATT
1 AATATTATCTTATTATT
226287 AATAT
1 AATAT
226292 AATAATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 8 0.44
16 3 0.17
17 7 0.39
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
AATATTATCTTATTATT
Found at i:226595 original size:21 final size:22
Alignment explanation
Indices: 226553--226600 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
226543 ATGCTATTTC
226553 TATTAATTTTTTATACTATTAAAA
1 TATTAATTTTTTATA-TATT-AAA
226577 TATTAA-TTTTTAT-TATTAAA
1 TATTAATTTTTTATATATTAAA
226597 TATT
1 TATT
226601 TATAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.29
21 4 0.17
23 7 0.29
24 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTAATTTTTTATATATTAAA
Found at i:226674 original size:16 final size:15
Alignment explanation
Indices: 226639--226707 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 15
226629 CAGATAAAAT
*
226639 AATAATATTTTCATTG
1 AATAATATTTT-ATTA
226655 AATAATATTTTATTAA
1 AATAATATTTTATT-A
*
226671 AATAATAAATTATATT-
1 AATAAT--ATTTTATTA
226687 AATAA-ATTATTATTA
1 AATAATATT-TTATTA
226702 AA-AATA
1 AATAATA
226708 ATATTATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
13 3 0.07
14 6 0.14
15 6 0.14
16 22 0.50
18 7 0.16
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (15 bp):
AATAATATTTTATTA
Found at i:226691 original size:32 final size:35
Alignment explanation
Indices: 226633--226714 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 35
226623 TATAGTCAGA
*
226633 TAAAATAATAATATTTTCATTGAATAATATT-TTAT
1 TAAAATAATAATATTATCATTGAATAA-ATTATTAT
226668 TAAAATAATAA-ATTAT-ATT-AATAAATTATTAT
1 TAAAATAATAATATTATCATTGAATAAATTATTAT
226700 T-AAA-AATAATATTAT
1 TAAAATAATAATATTAT
226715 ATAATATGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
30 5 0.11
31 11 0.25
32 10 0.23
33 3 0.07
34 4 0.09
35 11 0.25
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (35 bp):
TAAAATAATAATATTATCATTGAATAAATTATTAT
Found at i:226696 original size:13 final size:13
Alignment explanation
Indices: 226673--226718 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
226663 TTTATTAAAA
226673 TAATAAATTATAT
1 TAATAAATTATAT
226686 TAATAAATTATTAT
1 TAATAAATTA-TAT
*
226700 TAA-AAATAATAT
1 TAATAAATTATAT
226712 TATATAA
1 TA-ATAA
226719 TATGTATGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.17
13 16 0.55
14 8 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATAAATTATAT
Found at i:227570 original size:14 final size:13
Alignment explanation
Indices: 227546--227580 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
227536 AAATATTCTC
*
227546 TTCTCTTTCCTTT
1 TTCTTTTTCCTTT
227559 TTCCTTTTTCCTTT
1 TT-CTTTTTCCTTT
227573 TTCTTTTT
1 TTCTTTTT
227581 TTTTCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTCTTTTTCCTTT
Found at i:227581 original size:7 final size:7
Alignment explanation
Indices: 227551--227580 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
227541 TTCTCTTCTC
227551 TTTCCTT
1 TTTCCTT
227558 TTTCCTT
1 TTTCCTT
227565 TTTCCTT
1 TTTCCTT
227572 TTT-CTT
1 TTTCCTT
227578 TTT
1 TTT
227581 TTTTCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTCCTT
Found at i:230087 original size:34 final size:34
Alignment explanation
Indices: 230030--230214 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
230020 GCATGTAATA
*
230030 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
230063 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
230097 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
230131 ATTATTGATTAAATGGGTGATTTGATGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
230165 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTACC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
230199 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
230215 TGGTTTTTAC
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
33 17 0.13
34 113 0.86
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:230130 original size:68 final size:68
Alignment explanation
Indices: 230030--230214 Score: 282
Period size: 68 Copynumber: 2.7 Consensus size: 68
230020 GCATGTAATA
* * * * *
230030 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGATGGCTT
*
230094 GCC
66 ACC
*
230097 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTT
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGATGGCTT
230162 ACC
66 ACC
* *
230165 ATTGTTGACTAAATGGTAGATTTGGTAGGTTACCATTGTTGATTAAATGG
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGG
230215 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 13 0.12
68 94 0.88
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (68 bp):
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGATGGCTT
ACC
Found at i:234682 original size:34 final size:34
Alignment explanation
Indices: 234625--234809 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
234615 AAGTGGGAGA
*
234625 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
234658 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
234692 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
234726 ATTATTGATTAAATGGGTGATTTGATGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
234760 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTACC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
234794 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
234810 TAGTTTTTAC
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
33 17 0.13
34 113 0.86
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:234725 original size:68 final size:68
Alignment explanation
Indices: 234625--234809 Score: 282
Period size: 68 Copynumber: 2.7 Consensus size: 68
234615 AAGTGGGAGA
* * * * *
234625 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGATGGCTT
*
234689 GCC
66 ACC
*
234692 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTT
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGATGGCTT
234757 ACC
66 ACC
* *
234760 ATTGTTGACTAAATGGTAGATTTGGTAGGTTACCATTGTTGATTAAATGG
1 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGG
234810 TAGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 13 0.12
68 94 0.88
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (68 bp):
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGATGGCTT
ACC
Found at i:240539 original size:24 final size:21
Alignment explanation
Indices: 240491--240539 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
240481 ATCCTGATTC
*
240491 ATTTTTATTGTATAATATATT
1 ATTTTTATTGTATAATATATA
*
240512 ATTTTTATATTTATAAATTATATA
1 ATTTTTAT-TGTAT-AA-TATATA
240536 ATTT
1 ATTT
240540 AAATAATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
23 2 0.09
24 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTATTGTATAATATATA
Found at i:241654 original size:2 final size:2
Alignment explanation
Indices: 241647--241683 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
241637 CCATCAATGC
241647 AT AT 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 AT AT A
241684 AATCCATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:244165 original size:32 final size:32
Alignment explanation
Indices: 244126--244219 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 32
244116 AATTTTTATC
244126 TTTTAAAAATAATTATTAATTATTTTTAATTT
1 TTTTAAAAATAATTATTAATTATTTTTAATTT
* * * *
244158 TTTTAAAACT-TTTA-AAATTAATTTTATATTT
1 TTTTAAAAATAATTATTAATTATTTTTA-ATTT
* * *
244189 TTTTTAAAATAACTATTAATTATCTTTAATT
1 TTTTAAAAATAATTATTAATTATTTTTAATT
244220 CTTTCAAATT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
30 10 0.21
31 15 0.31
32 14 0.29
33 9 0.19
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (32 bp):
TTTTAAAAATAATTATTAATTATTTTTAATTT
Found at i:244217 original size:63 final size:61
Alignment explanation
Indices: 244096--244219 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 61
244086 TAATTTCTCA
* * *
244096 TTTTTAAACTTTTTAAAGTCAATTTTTATCTTTTAAAAATAATTATTAATTATTTTTAATT
1 TTTTTAAACTTTTTAAAATCAATTTTTATCTTTTAAAAATAACTATTAATTATCTTTAATT
* * *
244157 TTTTTAAAAC-TTTTAAAATTAATTTTATATTTTTTTTAAAATAACTATTAATTATCTTTAATT
1 TTTTT-AAACTTTTTAAAATCAATTTT-TA-TCTTTTAAAAATAACTATTAATTATCTTTAATT
244220 CTTTCAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
61 19 0.35
62 6 0.11
63 29 0.54
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (61 bp):
TTTTTAAACTTTTTAAAATCAATTTTTATCTTTTAAAAATAACTATTAATTATCTTTAATT
Found at i:245636 original size:20 final size:20
Alignment explanation
Indices: 245585--245637 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 20
245575 ATATAATTAT
*
245585 TATTT-TTTTATAGAAAGATA
1 TATTTATTTGATA-AAAGATA
245605 TATTTA---GATAAAAGATA
1 TATTTATTTGATAAAAGATA
245622 TATTTATTTGATAAAA
1 TATTTATTTGATAAAA
245638 TAATATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
17 13 0.46
18 3 0.11
20 12 0.43
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (20 bp):
TATTTATTTGATAAAAGATA
Found at i:245643 original size:21 final size:21
Alignment explanation
Indices: 245605--245644 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
245595 TAGAAAGATA
*
245605 TATTTAGATAAAAGATATATT
1 TATTTAGATAAAAAATATATT
245626 TATTT-GATAAAATAATATA
1 TATTTAGATAAAA-AATATA
245645 ATTGTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (21 bp):
TATTTAGATAAAAAATATATT
Found at i:249678 original size:97 final size:97
Alignment explanation
Indices: 249511--249727 Score: 316
Period size: 97 Copynumber: 2.2 Consensus size: 97
249501 ATACTTCAAC
*
249511 CCCATT-CTTCTGA-GAGGATACT-TCAACCCGGTTTTTAAACTTATCAAGATTTAAATCTTATT
1 CCCATTCCTTC-GAGGA-GATACTCTCAACCCCGTTTTTAAACTTATCAAGATTTAAATCTTATT
* **
249573 TTTACCTAAATTATCATTGTCGGGGACACTCCAA
64 TTGACCTAAATTATCATTGTCGAAGACACTCCAA
249607 TCCCATTCCTTCGAGGAGATACTCT-AACCCCGTTTTTAAACTTATCAAGATTTAAATCTTATTT
1 -CCCATTCCTTCGAGGAGATACTCTCAACCCCGTTTTTAAACTTATCAAGATTTAAATCTTATTT
*
249671 TGGCCTAAATTATCATTGTCGAAGACACTCCAA
65 TGACCTAAATTATCATTGTCGAAGACACTCCAA
*
249704 CCCTATTCCTCCGAGGAGATACTC
1 CCC-ATTCCTTCGAGGAGATACTC
249728 AAGGCTCGTA
Statistics
Matches: 110, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
96 3 0.03
97 100 0.91
98 7 0.06
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (97 bp):
CCCATTCCTTCGAGGAGATACTCTCAACCCCGTTTTTAAACTTATCAAGATTTAAATCTTATTTT
GACCTAAATTATCATTGTCGAAGACACTCCAA
Found at i:252970 original size:70 final size:70
Alignment explanation
Indices: 252849--253058 Score: 262
Period size: 70 Copynumber: 3.0 Consensus size: 70
252839 ATGGGCTAAC
*
252849 GATTGCGAGGGTACTTGTAGG-ACAAGCCACACGGCCCAAGAGGGAAA-ATCCAAGTATGGTGAT
1 GATTGTGAGGGTACTTG-AGGTACAAGCCACACGGCCCAAGA-GGAAACATCCAAGTATGGTGAT
252912 CATCAAT
64 CATCAAT
* * * *
252919 GATTGTGAGGGTTCTTGAGGTACGAGCCGCACGGCCCAAGAGGAAACATCCAAGTATGTTGATCA
1 GATTGTGAGGGTACTTGAGGTACAAGCCACACGGCCCAAGAGGAAACATCCAAGTATGGTGATCA
*
252984 TCGAT
66 TCAAT
** * * * *
252989 GATTGTGACTGTACTTGAAGTACACAAGCCACACGACCCAAGAGGAAACAACCAAGTGTGGTGAT
1 GATTGTGAGGGTACTTGAGGT--ACAAGCCACACGGCCCAAGAGGAAACATCCAAGTATGGTGAT
253054 CATCA
64 CATCA
253059 TTCAAGCATG
Statistics
Matches: 119, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
69 8 0.07
70 71 0.60
72 40 0.34
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (70 bp):
GATTGTGAGGGTACTTGAGGTACAAGCCACACGGCCCAAGAGGAAACATCCAAGTATGGTGATCA
TCAAT
Found at i:254114 original size:8 final size:8
Alignment explanation
Indices: 254101--254203 Score: 52
Period size: 8 Copynumber: 12.0 Consensus size: 8
254091 CATAATACAT
254101 ATATATAA
1 ATATATAA
254109 ATATATAA
1 ATATATAA
254117 ATATATCAA
1 ATATAT-AA
* *
254126 A-ATTTAT
1 ATATATAA
254133 ATAATATAA
1 AT-ATATAA
254142 AT-TATTAA
1 ATATA-TAA
254150 CATAT-TAAA
1 -ATATAT-AA
254159 ATAAATATAA
1 AT--ATATAA
254169 ATATAT-A
1 ATATATAA
*
254176 ATACTTTAA
1 ATA-TATAA
254185 ATATAATTAAA
1 ATAT-A-T-AA
254196 ATATATAA
1 ATATATAA
254204 CAATTTATAA
Statistics
Matches: 74, Mismatches: 6, Indels: 30
0.67 0.05 0.27
Matches are distributed among these distances:
7 8 0.11
8 32 0.43
9 18 0.24
10 9 0.12
11 7 0.09
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAA
Found at i:254160 original size:32 final size:32
Alignment explanation
Indices: 254099--254176 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 32
254089 AACATAATAC
*
254099 ATATATATAAATATATAAATATATCAAAATTT
1 ATATATATAAATATATAAACATATCAAAATTT
* *
254131 ATATAATATAAAT-TATTAACATATTAAAA--T
1 ATAT-ATATAAATATATAAACATATCAAAATTT
254161 A-A-ATATAAATATATAA
1 ATATATATAAATATATAA
254177 TACTTTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 8 0.20
28 4 0.10
29 1 0.03
30 2 0.05
32 17 0.43
33 8 0.20
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (32 bp):
ATATATATAAATATATAAACATATCAAAATTT
Found at i:254184 original size:27 final size:27
Alignment explanation
Indices: 254111--254232 Score: 94
Period size: 27 Copynumber: 4.5 Consensus size: 27
254101 ATATATAAAT
*
254111 ATATAAATATATCAA-AATTT-ATAT-A
1 ATATAAATATAT-AACAATTTAAAATAA
254136 ATATAAAT-TATTAAC-ATATTAAAATAA
1 ATATAAATATA-TAACAAT-TTAAAATAA
* *
254163 ATATAAATATATAATACTTTAAATATAA
1 ATATAAATATATAACAATTTAAA-ATAA
* *
254191 TTA-AAATATATAACAATTTATAAAAATA
1 ATATAAATATATAACAATTTA-AAATA-A
*
254219 ATATAAATGTATAA
1 ATATAAATATATAA
254233 ACTATTATAC
Statistics
Matches: 77, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
24 6 0.08
25 11 0.14
26 3 0.04
27 34 0.44
28 14 0.18
29 9 0.12
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (27 bp):
ATATAAATATATAACAATTTAAAATAA
Found at i:254189 original size:54 final size:53
Alignment explanation
Indices: 254102--254233 Score: 130
Period size: 52 Copynumber: 2.5 Consensus size: 53
254092 ATAATACATA
* *
254102 TATATAAAT-ATATAAATATATCAAAATTTATATAATATAAATTAT-TAAC-A--
1 TATAAAAATAATATAAATATAT-AAAATTTATATAAT-TAAAATATATAACAATT
* *
254152 TATTAAAATAAATATAAATATATAATACTTTAAATATAATTAAAATATATAACAATT
1 TATAAAAAT-AATATAAATATATAA-AATTT--ATATAATTAAAATATATAACAATT
*
254209 TATAAAAATAATATAAATGTATAAA
1 TATAAAAATAATATAAATATATAAA
254234 CTATTATACA
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
50 7 0.10
51 2 0.03
52 16 0.24
53 7 0.10
54 11 0.16
55 2 0.03
56 14 0.21
57 8 0.12
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (53 bp):
TATAAAAATAATATAAATATATAAAATTTATATAATTAAAATATATAACAATT
Found at i:255532 original size:6 final size:6
Alignment explanation
Indices: 255523--255578 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
255513 TAATTTATGC
* * * *
255523 TTATAT TTATAT TTACAT TTATAT TT-TA- ATATAA ATATAAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTAT-AT TTATAT
255570 TTATAT TTA
1 TTATAT TTA
255579 CATATATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
4 1 0.02
5 4 0.10
6 33 0.79
7 4 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (6 bp):
TTATAT
Found at i:255589 original size:29 final size:28
Alignment explanation
Indices: 255524--255594 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
255514 AATTTATGCT
*
255524 TATATTTATATTTACATTTATATTTTAA
1 TATATATATATTTACATTTATATTTTAA
* *
255552 TATAAATATAATTTATATTTATA-TTTACA
1 TATATATAT-ATTTACATTTATATTTTA-A
*
255581 TATATATATTTTTA
1 TATATATATATTTA
255595 ATCTAGTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATATATATTTACATTTATATTTTAA
Found at i:259284 original size:79 final size:79
Alignment explanation
Indices: 259179--259350 Score: 231
Period size: 79 Copynumber: 2.2 Consensus size: 79
259169 ACCATCAGGG
* *
259179 ATACTCCAATCCCGTTATTTCCGAGGGAATACTCCAACC-CTGATTTTATTTTTAAAATA-TCGA
1 ATACTCCAACCCCGTTATTTCCGAGGGAATACTCCAACCTC-GATTTTATTTTTAAAACACT-GA
259242 TTTTTCACCATCGAAA
64 TTTTTCACCATCGAAA
* * *
259258 ATACTCCAACCCCGTTATTTCTGAGGGGATACTCTAACCTCGATTTTATTTTTAAAACACTGATT
1 ATACTCCAACCCCGTTATTTCCGAGGGAATACTCCAACCTCGATTTTATTTTTAAAACACTGATT
* **
259323 TTTCACTATCGAGG
66 TTTCACCATCGAAA
*
259337 ATACTTCAACCCCG
1 ATACTCCAACCCCG
259351 GTTTTATTTC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
79 80 0.98
80 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (79 bp):
ATACTCCAACCCCGTTATTTCCGAGGGAATACTCCAACCTCGATTTTATTTTTAAAACACTGATT
TTTCACCATCGAAA
Found at i:259390 original size:51 final size:52
Alignment explanation
Indices: 259282--259403 Score: 128
Period size: 51 Copynumber: 2.4 Consensus size: 52
259272 TTATTTCTGA
* * * * *
259282 GGGGATAC-TCTAACCTCGATTTTATTTTTAAAACACTGATTTTTCACTATC
1 GGGGATACTTCTAACCCCGATTTTATTTCTAAAACACTAATTTTCCACCATC
* * *
259333 GAGGATACTTC-AACCCCGGTTTTATTTCTAAAACA-TCAATTTTCCACCATT
1 GGGGATACTTCTAACCCCGATTTTATTTCTAAAACACT-AATTTTCCACCATC
259384 GGGGATAC-TCTAA-CCCGATT
1 GGGGATACTTCTAACCCCGATT
259404 ATTTCTGAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
50 9 0.16
51 47 0.81
52 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (52 bp):
GGGGATACTTCTAACCCCGATTTTATTTCTAAAACACTAATTTTCCACCATC
Found at i:259425 original size:78 final size:78
Alignment explanation
Indices: 259335--259555 Score: 279
Period size: 78 Copynumber: 2.8 Consensus size: 78
259325 TCACTATCGA
* * *
259335 GGATACTTCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACCATTGGGGATACTCTAACCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTT-CACTATCGGGGATACTCTAACCC
**
259400 -GATTATTTCTGA-G
65 TG-TTATTTCCAAGG
* *
259413 GGATACTCCAACCTCGGTTCTATTTCTAAAACA-CTAATTGTTCACTATCGGGGATACTAC-AAC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATC-AATT-TTCACTATCGGGGATACT-CTAAC
259476 CCTGTTATTTCCAAGG
63 CCTGTTATTTCCAAGG
* *
259492 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCGATTTTTCACTATCGAGGATACTCTAACC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATC-AATTTTCACTATCGGGGATACTCTAACC
259556 TAGGTTTTAT
Statistics
Matches: 124, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
77 1 0.01
78 62 0.50
79 57 0.46
80 4 0.03
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (78 bp):
GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTCACTATCGGGGATACTCTAACCCT
GTTATTTCCAAGG
Found at i:259476 original size:129 final size:130
Alignment explanation
Indices: 259207--259477 Score: 339
Period size: 129 Copynumber: 2.1 Consensus size: 130
259197 TTCCGAGGGA
* * * * * *
259207 ATACTCCAACCCTGATTTTATTTTTAAAATATCGATTTTTCACCATCGAAAATACTCCAACCCCG
1 ATACTACAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATCGAAAATACTCCAACCCCG
* * * * *
259272 TTATTTCTGAGGGGATACTCTAACCTCGATTTTATTTTTAAAACACTGATTTTTCACTATCGAGG
66 TTATTTCTGAGGGGATACTCCAACCTCGATTCTATTTCTAAAACACTAATTGTTCACTATCGAGG
* * * *** *
259337 ATACTTCAACCCCGGTTTTATTTCTAAAACATCAATTTTCCACCATTGGGGATACTCTAA-CCCG
1 ATACTACAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATCGAAAATACTCCAACCCCG
* *
259401 ATTATTTCTGA-GGGATACTCCAACCTCGGTTCTATTTCTAAAACACTAATTGTTCACTATCGGG
66 -TTATTTCTGAGGGGATACTCCAACCTCGATTCTATTTCTAAAACACTAATTGTTCACTATCGAG
259465 G
130 G
259466 ATACTACAACCC
1 ATACTACAACCC
259478 TGTTATTTCC
Statistics
Matches: 120, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
129 62 0.52
130 58 0.48
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (130 bp):
ATACTACAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATCGAAAATACTCCAACCCCG
TTATTTCTGAGGGGATACTCCAACCTCGATTCTATTTCTAAAACACTAATTGTTCACTATCGAGG
Found at i:259515 original size:208 final size:206
Alignment explanation
Indices: 259143--259708 Score: 674
Period size: 208 Copynumber: 2.7 Consensus size: 206
259133 CATTTATGTT
* * * * * * *
259143 TTTTCTTTCTAAAATACCGATTTTCTACCATCAGGGATACTCCAATCCCG-TTATTTCCGAGGGA
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCTAA-CCCGATTATTTCTGAGGG-
* * * * **
259207 ATACTCCAACCCTGATTTTATTTTTAAAATATCGATTTTTCACCATCGAAAATACTCCAACCCCG
64 ATACTCCAACCCTGGTTTTATTTCTAAAATA-CTAATTTTCACCATCGAGGATACT-CAACCCCG
* * * *
259272 TTATTTCTGAGGGGATACTCTAACCTCGATTTTATTTTTAAAACA-CTGATTTTTCACTATCGAG
127 TTATTTCTAAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATC-GATTTTTCACTATCGAG
*
259336 GATACT-TCAACCCCGG
191 GATACTCT-AACCCAGG
* *
259352 TTTTATTTCTAAAACATCAATTTTCCACCATTGGGGATACTCTAACCCGATTATTTCTGAGGGAT
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCTAACCCGATTATTTCTGAGGGAT
* * * * *
259417 ACTCCAA-CCTCGGTTCTATTTCTAAAACACTAATTGTTCACTATCGGGGATACTACAACCCTGT
66 ACTCCAACCCT-GGTTTTATTTCTAAAATACTAATT-TTCACCATCGAGGATACT-CAACCCCGT
* *
259481 TATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCGATTTTTCACTATCGAGGA
128 TATTTCTAAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACTATCGAGGA
*
259546 TACTCTAACCTAGG
193 TACTCTAACCCAGG
* * *
259560 TTTTATTTCTAAAACATCGATTTTTCACCATCGGGGATACT-TCAACCCCATTATTTTTGAGGGG
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCT-AACCCGATTATTTCTGA-GGG
* *
259624 ATACTCCAACCCTGGTTTTATTTCTAAAATACTAATTTTCCACCATCGTGGATACTCTAACCCCA
64 ATACTCCAACCCTGGTTTTATTTCTAAAATACTAATTTT-CACCATCGAGGATACTC-AACCCCG
*
259689 TTATTTCTAAGGAGATACTC
127 TTATTTCTAAGGGGATACTC
259709 TAACACTGAT
Statistics
Matches: 305, Mismatches: 42, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
207 8 0.03
208 172 0.56
209 122 0.40
210 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (206 bp):
TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCTAACCCGATTATTTCTGAGGGAT
ACTCCAACCCTGGTTTTATTTCTAAAATACTAATTTTCACCATCGAGGATACTCAACCCCGTTAT
TTCTAAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCACTATCGAGGATAC
TCTAACCCAGG
Found at i:259568 original size:51 final size:51
Alignment explanation
Indices: 259492--259607 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
259482 ATTTCCAAGG
* *
259492 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCGATTTTTCACTATCGA
1 GGATACTCCAACCCAGGTTTTATTTCTAAAACATCGATTTTTCACCATCGA
* * *
259543 GGATACTCTAACCTAGGTTTTATTTCTAAAACATCGATTTTTCACCATCGG
1 GGATACTCCAACCCAGGTTTTATTTCTAAAACATCGATTTTTCACCATCGA
*
259594 GGATACTTCAACCC
1 GGATACTCCAACCC
259608 CATTATTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (51 bp):
GGATACTCCAACCCAGGTTTTATTTCTAAAACATCGATTTTTCACCATCGA
Found at i:259587 original size:130 final size:130
Alignment explanation
Indices: 259413--259685 Score: 352
Period size: 130 Copynumber: 2.1 Consensus size: 130
259403 TATTTCTGAG
* * *
259413 GGATACTCCAACCTCGGTTCTATTTCTAAAACACTAATTGTTCACTATCGGGGATACTACAACCC
1 GGATACTCTAACCTAGGTTCTATTTCTAAAACACTAATTGTTCACCATCGGGGATACTACAACCC
** * * *
259478 TGTTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA-TCGATTTTTCACTATCG
66 CATTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACT-AATTTTCCACCATCG
259542 A
130 A
* * * *
259543 GGATACTCTAACCTAGGTTTTATTTCTAAAACA-TCGATTTTTCACCATCGGGGATACTTCAACC
1 GGATACTCTAACCTAGGTTCTATTTCTAAAACACT-AATTGTTCACCATCGGGGATACTACAACC
*** * *
259607 CCATTATTTTTGAGGGGATACTCCAACCCTGGTTTTATTTCTAAAATACTAATTTTCCACCATCG
65 CCATTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCACCATCG
*
259672 T
130 A
259673 GGATACTCTAACC
1 GGATACTCTAACC
259686 CCATTATTTC
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
129 1 0.01
130 121 0.98
131 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (130 bp):
GGATACTCTAACCTAGGTTCTATTTCTAAAACACTAATTGTTCACCATCGGGGATACTACAACCC
CATTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCACCATCGA
Found at i:259643 original size:79 final size:79
Alignment explanation
Indices: 259543--259708 Score: 212
Period size: 79 Copynumber: 2.1 Consensus size: 79
259533 TCACTATCGA
* * *
259543 GGATACTCTAACCTAGGTTTTATTTCTAAAACA-TCGATTTTTCACCATCGGGGATACT-TCAAC
1 GGATACTCCAACCTAGGTTTTATTTCTAAAACACT-AATTTTCCACCATCGGGGATACTCT-AAC
* *
259606 CCCATTATTTTTGAGG
64 CCCATTATTTCTAAGG
* *
259622 GGATACTCCAACCCT-GGTTTTATTTCTAAAATACTAATTTTCCACCATCGTGGATACTCTAACC
1 GGATACTCCAA-CCTAGGTTTTATTTCTAAAACACTAATTTTCCACCATCGGGGATACTCTAACC
259686 CCATTATTTCTAAGG
65 CCATTATTTCTAAGG
*
259701 AGATACTC
1 GGATACTC
259709 TAACACTGAT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
79 71 0.93
80 5 0.07
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (79 bp):
GGATACTCCAACCTAGGTTTTATTTCTAAAACACTAATTTTCCACCATCGGGGATACTCTAACCC
CATTATTTCTAAGG
Found at i:261842 original size:4 final size:4
Alignment explanation
Indices: 261833--261870 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
261823 ATTGAGGTGC
*
261833 TTAT TTAT TTAT TTAT TCAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
261871 TGTTTTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:272149 original size:11 final size:11
Alignment explanation
Indices: 272118--272157 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
272108 CTTTCTTTTC
**
272118 AAAAAAAAATC
1 AAAAAAAAAAG
*
272129 AACAAAAAAAG
1 AAAAAAAAAAG
272140 AAAAAAAAAAG
1 AAAAAAAAAAG
272151 AAAAAAA
1 AAAAAAA
272158 TGGAAAGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.88, C:0.05, G:0.05, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:272156 original size:21 final size:21
Alignment explanation
Indices: 272118--272177 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
272108 CTTTCTTTTC
**
272118 AAAAAAAAATCAACAAAAAAAG
1 AAAAAAAAAAGAA-AAAAAAAG
**
272140 AAAAAAAAAAGAAAAAAATGG
1 AAAAAAAAAAGAAAAAAAAAG
* *
272161 AAAGAGAAAAGAAAAAA
1 AAAAAAAAAAGAAAAAA
272178 GAACTTGCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAGAAAAAAAAAG
Found at i:273235 original size:61 final size:61
Alignment explanation
Indices: 273152--273798 Score: 543
Period size: 61 Copynumber: 10.4 Consensus size: 61
273142 AACCTTTTAT
* * **
273152 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGATA
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
273213 CCTTCCAGTCCTCAAAGAGCAGGA--CATTTTCCTTTCAAAGCCCACATAAGTTGGTGGTA
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * ** *
273272 CTTTCCAGTCCTCAAAAAGCAAGATGCCTTCTCCTTGCAAAGCCCACGCAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * ** *
273333 CCTTCCAATCCTCAAAGAGCAGGACACCTTTTCC-TATAGAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTA-AAGCCCACACAAGTTGGTGGCA
* * * ** * *
273394 CCTTTTAGT-CTCGAAGAGCAAGA--CACTTCTTTTTTTTTAAGCCCACACAAGTTGGTGGCT
1 CCTTCTAGTCCTCAAAGAGCAGGATGC-CTT-TTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
273454 CCTTCTAGTCCTCAAAAAGCAGGATGCCTTTCTCCTTTTCCATCTTATAGCCCACACGAGTTGGT
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTT-TCCTTTT--A----A-AGCCCACACAAGTTGGT
*
273519 GACA
58 GGCA
* * * * * *
273523 CCTTTTAGTCTTCAAAGTGCAGGATACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
* ** * * ** *
273585 CCTTTCTAGTCCACAAAGAATAGGATGCCTTTTTCTTTTCAAAGCCTACATGAGTTGGTAGCA
1 CC-TTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
* * * * * **
273648 CCCTTCTAGTCCTCAAAGAGCAAGACGCATTTT-CTCTTAAAGCCCATAGGAGTTGGTGGCA
1 -CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
273709 CCTTTTAATCCTCAAAGAACAGGATGCTTTCTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
1 CCTTCTAGTCCTCAAAGAGCAGGATGC---C--TTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
273774 A
61 A
* *
273775 CCTTTTAGTCGTCAAAGAGCAGGA
1 CCTTCTAGTCCTCAAAGAGCAGGA
273799 ATCATTTCCT
Statistics
Matches: 475, Mismatches: 86, Indels: 45
0.78 0.14 0.07
Matches are distributed among these distances:
58 1 0.00
59 55 0.12
60 67 0.14
61 138 0.29
62 34 0.07
63 76 0.16
64 2 0.00
65 4 0.01
66 45 0.09
67 2 0.00
68 7 0.01
69 44 0.09
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (61 bp):
CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:273423 original size:120 final size:118
Alignment explanation
Indices: 273152--273795 Score: 432
Period size: 120 Copynumber: 5.2 Consensus size: 118
273142 AACCTTTTAT
* * **
273152 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGATACCTT
1 CCTTTTAGTCCTCAAAGAGCAAGA--CCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * *
273217 CCAGTCCTCAAAGAGCAGGACATTTTCCTTTCAAAGCCCACATAAGTTGGTGGTA
64 CCAGTCCTCAAAGAGCAGGACATTTTCCTATCAAAGCCCACACAAGTTGGTGGCA
* * ** *
273272 -CTTTCCAGTCCTCAAAAAGCAAGATGCCTTCTCCTTGCAAAGCCCACGCAAGTTGGTGGCACCT
1 CCTTT-TAGTCCTCAAAGAGCAAGA--CCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
*
273336 TCCAATCCTCAAAGAGCAGGACACCTTTTCCTAT-AGAAGCCCACACAAGTTGGTGGCA
63 TCCAGTCCTCAAAGAGCAGGACA--TTTTCCTATCA-AAGCCCACACAAGTTGGTGGCA
* ** * *
273394 CCTTTTAGT-CTCGAAGAGCAAGACACTTCTTTTTTTTTAAGCCCACACAAGTTGGTGGCTCCTT
1 CCTTTTAGTCCTCAAAGAGCAAGAC-CTTC-TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * * * * *
273458 CTAGTCCTCAAAAAGCAGGATGCCTTTCTCCTTTTCCATCTTATAGCCCACACGAGTTGGTGACA
64 CCAGTCCTCAAAGAGCAGGA--CATTT-TCC---T--ATC--AAAGCCCACACAAGTTGGTGGCA
* * * * * *
273523 CCTTTTAGTCTTCAAAGTGCAGGATACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
1 CCTTTTAGTCCTCAAAGAGCA--AGACCTTCTCCTTTT-AAAGCCCACACAAGTTGGTGGCACC-
* * ** * * * * ** *
273588 TTCTAGTCCACAAAGAATAGGATGCCTTTTTCTTTTCAAAGCCTACATGAGTTGGTAGCA
62 TTCCAGTCCTCAAAGAGCAGGA---CATTTTCCTATCAAAGCCCACACAAGTTGGTGGCA
* * * * **
273648 CCCTTCTAGTCCTCAAAGAGCAAGACGCATT-TTCTCTTAAAGCCCATAGGAGTTGGTGGCACCT
1 -CCTTTTAGTCCTCAAAGAGCAAGAC-C-TTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
** * * * * *
273712 TTTAATCCTCAAAGAACAGGATGCTTTCTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
63 TCCAGTCCTCAAAGAGCAGGA------C-ATTTTCCTATCAAAGCCCACACAAGTTGGTGGCA
*
273775 CCTTTTAGTCGTCAAAGAGCA
1 CCTTTTAGTCCTCAAAGAGCA
273796 GGAATCATTT
Statistics
Matches: 418, Mismatches: 75, Indels: 56
0.76 0.14 0.10
Matches are distributed among these distances:
119 5 0.01
120 75 0.18
121 60 0.14
122 34 0.08
123 23 0.06
124 26 0.06
125 26 0.06
126 41 0.10
127 32 0.08
129 29 0.07
130 15 0.04
131 25 0.06
132 23 0.06
133 4 0.01
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (118 bp):
CCTTTTAGTCCTCAAAGAGCAAGACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCC
AGTCCTCAAAGAGCAGGACATTTTCCTATCAAAGCCCACACAAGTTGGTGGCA
Found at i:273545 original size:69 final size:62
Alignment explanation
Indices: 273502--273798 Score: 244
Period size: 63 Copynumber: 4.7 Consensus size: 62
273492 TCCATCTTAT
* * ** *
273502 AGCCCACACGAGTTGGTGACACCTTTTAGTCTTCAAAGTGCAGGATACCTTTTTCTTTTCAA
1 AGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCAGGATACCTTTTCCTTTTCAA
* * * *
273564 AGCCCACACGAGTTGGTGGCACCTTTCTAGTCCACAAAGAA-TAGGATGCCTTTTTCTTTTCAA
1 AGCCCACACGAGTTGGTGGCACCTTT-TAGTCCTCAAA-AAGCAGGATACCTTTTCCTTTTCAA
* * * * * * ** * *
273627 AGCCTACATGAGTTGGTAGCACCCTTCTAGTCCTCAAAGAGCAAGACGCATTTT-CTCTT-AA
1 AGCCCACACGAGTTGGTGGCA-CCTTTTAGTCCTCAAAAAGCAGGATACCTTTTCCTTTTCAA
* * * *
273688 AGCCCATAGGAGTTGGTGGCACCTTTTAATCCTCAAAGAA-CAGGATGCTTTCTTTTTTCCTTTT
1 AGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAA-AAGCAGGATAC---C--TTTTCCTTTT
273752 -AA
60 CAA
* * *
273754 AGCCCACACAAGTTGGTGGCACCTTTTAGTCGTCAAAGAGCAGGA
1 AGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCAGGA
273799 ATCATTTCCT
Statistics
Matches: 188, Mismatches: 35, Indels: 20
0.77 0.14 0.08
Matches are distributed among these distances:
60 20 0.11
61 20 0.11
62 30 0.16
63 66 0.35
64 4 0.02
65 5 0.03
66 43 0.23
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (62 bp):
AGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCAGGATACCTTTTCCTTTTCAA
Found at i:273939 original size:75 final size:75
Alignment explanation
Indices: 273811--274062 Score: 278
Period size: 75 Copynumber: 3.4 Consensus size: 75
273801 CATTTCCTTA
* * * * * *
273811 TTTTCCTTTTATCCTCAAAGAGC-AGAACACACTTCATTTCTCTTTTCCTGTGTCCCCAAAGAGC
1 TTTTCC-TTTGTCCTCAAGGAGCAAG-ACCCATTTCA-TTCTCTTTTCCTGTGTCCTCGAAGAGC
*
273875 AAGATGTACTCCT
63 AAGACGTACTCCT
* * *
273888 TTTTCCTTTGCCCTCAAGGAGCAAGACCCATTTCATTCTCTTTTCCTGTGTCTTCGAAGAGCAGG
1 TTTTCCTTTGTCCTCAAGGAGCAAGACCCATTTCATTCTCTTTTCCTGTGTCCTCGAAGAGCAAG
* *
273953 ACATACTCTT
66 ACGTACTCCT
* * * * *
273963 TTTTCCTTTGTTCTCAAGGAGCAAGACCCATTTCGTTCTTTTTTCCTTTGTCCTCGATGAGC-AG
1 TTTTCCTTTGTCCTCAAGGAGCAAGACCCATTTCATTCTCTTTTCCTGTGTCCTCGAAGAGCAAG
274027 AACGTACTCC-
66 -ACGTACTCCT
*
274037 -TTTCCTTTGTCCTCAAAGAGCAAGAC
1 TTTTCCTTTGTCCTCAAGGAGCAAGAC
274063 ATGCCTTCTT
Statistics
Matches: 149, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
73 24 0.16
74 1 0.01
75 95 0.64
76 21 0.14
77 8 0.05
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (75 bp):
TTTTCCTTTGTCCTCAAGGAGCAAGACCCATTTCATTCTCTTTTCCTGTGTCCTCGAAGAGCAAG
ACGTACTCCT
Found at i:273950 original size:40 final size:40
Alignment explanation
Indices: 273887--274025 Score: 114
Period size: 40 Copynumber: 3.6 Consensus size: 40
273877 GATGTACTCC
* *
273887 TTTTTCCTTTGCCCTC-AAGGAGCAAGACCCATTTCATTCT
1 TTTTTCCTTTGTCTTCGAA-GAGCAAGACCCATTTCATTCT
* * * *
273927 CTTTTCCTGTGTCTTCGAAGAGCAGGA--CA--T-ACTCT
1 TTTTTCCTTTGTCTTCGAAGAGCAAGACCCATTTCATTCT
*
273962 TTTTTCCTTTGT-TCTC-AAGGAGCAAGACCCATTTCGTTCT
1 TTTTTCCTTTGTCT-TCGAA-GAGCAAGACCCATTTCATTCT
* *
274002 TTTTTCCTTTGTCCTCGATGAGCA
1 TTTTTCCTTTGTCTTCGAAGAGCA
274026 GAACGTACTC
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
34 3 0.04
35 23 0.30
36 1 0.01
37 2 0.03
38 2 0.03
39 1 0.01
40 41 0.54
41 3 0.04
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.40
Consensus pattern (40 bp):
TTTTTCCTTTGTCTTCGAAGAGCAAGACCCATTTCATTCT
Found at i:274660 original size:21 final size:20
Alignment explanation
Indices: 274634--274688 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
274624 CATAAGTAAA
**
274634 TGTATCGATACATTTACTGTT
1 TGTATCGATACATTT-CTCAT
* *
274655 TGTATCGATATATTTTTCAT
1 TGTATCGATACATTTCTCAT
274675 TGTATCGATACATT
1 TGTATCGATACATT
274689 CTGGGTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (20 bp):
TGTATCGATACATTTCTCAT
Found at i:278759 original size:20 final size:20
Alignment explanation
Indices: 278734--278872 Score: 96
Period size: 20 Copynumber: 6.8 Consensus size: 20
278724 ATTTGCCTGC
278734 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
278754 ATGTATCGATACATCTGGGTAAAATTCCCA
1 ATGTATCGATACAT-T--G---AA-T---A
**
278784 GATGTATCGATACAAAG-ATCA
1 -ATGTATCGATACATTGAAT-A
278805 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
278825 ATGTATCGATAC-------A
1 ATGTATCGATACATTGAATA
278838 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
278858 ATGTATCGATACATT
1 ATGTATCGATACATT
278873 TCCTTGGCAA
Statistics
Matches: 96, Mismatches: 4, Indels: 38
0.70 0.03 0.28
Matches are distributed among these distances:
13 13 0.14
20 57 0.59
21 5 0.05
23 2 0.02
24 1 0.01
26 2 0.02
27 1 0.01
28 1 0.01
30 1 0.01
31 13 0.14
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:278842 original size:13 final size:13
Alignment explanation
Indices: 278824--278850 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
278814 TACATTGAAT
278824 AATGTATCGATAC
1 AATGTATCGATAC
278837 AATGTATCGATAC
1 AATGTATCGATAC
278850 A
1 A
278851 TTGAATAATG
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:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:278845 original size:33 final size:33
Alignment explanation
Indices: 278803--278870 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
278793 ATACAAAGAT
278803 CAATGTATCGATACATTGAATAATGTATCGATA
1 CAATGTATCGATACATTGAATAATGTATCGATA
278836 CAATGTATCGATACATTGAATAATGTATCGATA
1 CAATGTATCGATACATTGAATAATGTATCGATA
278869 CA
1 CA
278871 TTTCCTTGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACATTGAATAATGTATCGATA
Found at i:280805 original size:79 final size:79
Alignment explanation
Indices: 280675--281271 Score: 566
Period size: 79 Copynumber: 7.6 Consensus size: 79
280665 TTATTATTTG
280675 TTATTTCT-AAACACCGATTTTCTACCATCAGGGATACTCCAACCCCGTTATTTTCGAGGGAATA
1 TTATTTCTAAAACACCGATTTTCTACCATCAGGGATACTCCAACCCCGTTATTTTCGAGGGAATA
280739 CTCCAACCCCGATT
66 CTCCAACCCCGATT
* * * * * * *
280753 TTATTTCTAAAATACCAATTTTATACTATCAGAGATACTCCAACCCCGTTATTTTTGAGGGGATA
1 TTATTTCTAAAACACCGATTTTCTACCATCAGGGATACTCCAACCCCGTTATTTTCGAGGGAATA
**
280818 CTCCAACTTCGATT
66 CTCCAACCCCGATT
** * * *
280832 TTATTTCTAAAACACCGATTTTCTACCATTGGGGATACTCCAACCCTGTTATTTCCGA-GAAGAT
1 TTATTTCTAAAACACCGATTTTCTACCATCAGGGATACTCCAACCCCGTTATTTTCGAGGGA-AT
*
280896 ACTCTAACCCCGATT
65 ACTCCAACCCCGATT
* * * ** * *
280911 TTATTTCTAAAACATCAATTTTCCACCATTGGGGATACTCCAACCCTGTTA-TTTCTGAGGGGAT
1 TTATTTCTAAAACACCGATTTTCTACCATCAGGGATACTCCAACCCCGTTATTTTC-GAGGGAAT
*
280975 ACTCCAACCTCGATT
65 ACTCCAACCCCGATT
* * * * * *
280990 TTATTTCTAAAACACTGATTTT-TCACCAT-TGGGAATATTCCAACCCTGTTATTTTTGAAAGG-
1 TTATTTCTAAAACACCGATTTTCT-ACCATCAGGG-ATACTCCAACCCCGTTATTTTCG-AGGGA
* * *
281052 ATACTCCATCTCCGGTT
63 ATACTCCAACCCCGATT
* * * * * * * *
281069 TTATTTCTAAAACATCGATTTTCCACCATTAGGGGTACTCTAACCCCGTTA-TTCCAAAGGGGAT
1 TTATTTCTAAAACACCGATTTTCTACCATCAGGGATACTCCAACCCCGTTATTTTC-GAGGGAAT
*
281133 ACTCCAACCCCCATT
65 ACTCCAACCCCGATT
* * * * * * *
281148 TTATTTCTAAAATATCAGTTTTTC-ACTATC-GGAGATACTTCAACCCCGTTATTTCCAAGGGAA
1 TTATTTCTAAAACA-CCGATTTTCTACCATCAGG-GATACTCCAACCCCGTTATTTTCGAGGGAA
* *
281211 TACTCCAACCTCGGTT
64 TACTCCAACCCCGATT
* * *
281227 TTATTTCTAAAACATCGATTTCCCACCATC-GAGGATACTCCAACC
1 TTATTTCTAAAACACCGATTTTCTACCATCAG-GGATACTCCAACC
281272 TCGATTTTAT
Statistics
Matches: 422, Mismatches: 80, Indels: 33
0.79 0.15 0.06
Matches are distributed among these distances:
78 27 0.06
79 374 0.89
80 21 0.05
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (79 bp):
TTATTTCTAAAACACCGATTTTCTACCATCAGGGATACTCCAACCCCGTTATTTTCGAGGGAATA
CTCCAACCCCGATT
Found at i:280971 original size:158 final size:158
Alignment explanation
Indices: 280675--281271 Score: 673
Period size: 158 Copynumber: 3.8 Consensus size: 158
280665 TTATTATTTG
* * *
280675 TTATTTCT-AAACACCGATTTTCTACCATCAGGGATACTCCAACCCCGTTATTTTCGAGGGAATA
1 TTATTTCTAAAACACCGATTTTCTACCATCGGGGATACTCCAACCCCGTTATTTCCGAGAGAATA
* * ** * * *
280739 CTCCAACCCCGATTTTATTTCTAAAATACCAATTTTATACTATCAGAGATACTCCAACCCCGTTA
66 CTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATCGGGGATACTCCAACCCCGTTA
* *
280804 TTTTTGAGGGGATACTCCAACTTCGATT
131 TTTCTGAGGGGATACTCCAACCTCGATT
* *
280832 TTATTTCTAAAACACCGATTTTCTACCATTGGGGATACTCCAACCCTGTTATTTCCGAGA-AGAT
1 TTATTTCTAAAACACCGATTTTCTACCATCGGGGATACTCCAACCCCGTTATTTCCGAGAGA-AT
* * *
280896 ACTCTAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATTGGGGATACTCCAACCCTGTT
65 ACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATCGGGGATACTCCAACCCCGTT
280961 ATTTCTGAGGGGATACTCCAACCTCGATT
130 ATTTCTGAGGGGATACTCCAACCTCGATT
* * * * * ** * *
280990 TTATTTCTAAAACACTGATTTT-TCACCATTGGGAATATTCCAACCCTGTTATTTTTGAAAGGAT
1 TTATTTCTAAAACACCGATTTTCT-ACCATCGGGGATACTCCAACCCCGTTATTTCCGAGAGAAT
* * * * * *
281054 ACTCCATCTCCGGTTTTATTTCTAAAACATCGATTTTCCACCATTAGGGG-TACTCTAACCCCGT
65 ACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCA-TCGGGGATACTCCAACCCCGT
* ** * *
281118 TATTCCAAAGGGGATACTCCAACCCCCATT
129 TATTTCTGAGGGGATACTCCAACCTCGATT
* * * * * * * *
281148 TTATTTCTAAAATATCAGTTTTTC-ACTATCGGAGATACTTCAACCCCGTTATTTCCAAGGGAAT
1 TTATTTCTAAAACA-CCGATTTTCTACCATCGGGGATACTCCAACCCCGTTATTTCCGAGAGAAT
* * * * *
281212 ACTCCAACCTCGGTTTTATTTCTAAAACATCGATTTCCCACCATCGAGGATACTCCAACC
65 ACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATCGGGGATACTCCAACC
281272 TCGATTTTAT
Statistics
Matches: 372, Mismatches: 60, Indels: 15
0.83 0.13 0.03
Matches are distributed among these distances:
157 14 0.04
158 347 0.93
159 11 0.03
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (158 bp):
TTATTTCTAAAACACCGATTTTCTACCATCGGGGATACTCCAACCCCGTTATTTCCGAGAGAATA
CTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATCGGGGATACTCCAACCCCGTTA
TTTCTGAGGGGATACTCCAACCTCGATT
Found at i:281136 original size:237 final size:237
Alignment explanation
Indices: 280675--281271 Score: 695
Period size: 237 Copynumber: 2.5 Consensus size: 237
280665 TTATTATTTG
* * * *
280675 TTATTTCT-AAACACCGATTTTCTACCATCAGGGATACTCCAACCCCGTTATTT-TCGAGGGAAT
1 TTATTTCTAAAACATCAATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTCT-GAGGGAAT
* * *
280738 ACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTATACTATCAGAGATACTCCAACCCCGTT
65 ACTCCAACCTCGATTTTATTTCTAAAACACCAATTTTATACCATCAGAGATACTCCAACCCCGTT
** * *
280803 ATTTTTGAGGGGATACTCCAACTTCGATTTTATTTCTAAAACACCGATTTTCTACCATTGGGGAT
130 ATTTTTGAAAGGATACTCCAACTCCGATTTTATTTCTAAAACACCGATTTTCCACCATTGGGGAT
* * * *
280868 ACTCCAACCCTGTTATTTCCGAGAAGATACTCTAACCCCGATT
195 ACTCCAACCCCGTTATTTCCAAGAAGATACTCCAACCCCCATT
* * *
280911 TTATTTCTAAAACATCAATTTTCCACCATTGGGGATACTCCAACCCTGTTATTTCTGAGGGGATA
1 TTATTTCTAAAACATCAATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGAATA
** * * * *
280976 CTCCAACCTCGATTTTATTTCTAAAACACTGATTTT-TCACCAT-TGGGAATATTCCAACCCTGT
66 CTCCAACCTCGATTTTATTTCTAAAACACCAATTTTAT-ACCATCAGAG-ATACTCCAACCCCGT
* * *
281039 TATTTTTGAAAGGATACTCCATCTCCGGTTTTATTTCTAAAACATCGATTTTCCACCATTAGGGG
129 TATTTTTGAAAGGATACTCCAACTCCGATTTTATTTCTAAAACACCGATTTTCCACCATT-GGGG
* **
281104 -TACTCTAACCCCGTTA-TTCCAAAGGGGATACTCCAACCCCCATT
193 ATACTCCAACCCCGTTATTTCC-AAGAAGATACTCCAACCCCCATT
* * * * * * **
281148 TTATTTCTAAAATATCAGTTTTTCACTATCGGAGATACTTCAACCCCGTTATTTCCAAGGGAATA
1 TTATTTCTAAAACATCAATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGAATA
* * * ***
281213 CTCCAACCTCGGTTTTATTTCTAAAACATCGATTTCCCACCATC-GAGGATACTCCAACC
66 CTCCAACCTCGATTTTATTTCTAAAACACCAATTTTATACCATCAGA-GATACTCCAACC
281272 TCGATTTTAT
Statistics
Matches: 304, Mismatches: 48, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
236 15 0.05
237 283 0.93
238 6 0.02
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (237 bp):
TTATTTCTAAAACATCAATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGAATA
CTCCAACCTCGATTTTATTTCTAAAACACCAATTTTATACCATCAGAGATACTCCAACCCCGTTA
TTTTTGAAAGGATACTCCAACTCCGATTTTATTTCTAAAACACCGATTTTCCACCATTGGGGATA
CTCCAACCCCGTTATTTCCAAGAAGATACTCCAACCCCCATT
Found at i:281269 original size:51 final size:51
Alignment explanation
Indices: 281210--281325 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
281200 TTCCAAGGGA
*
281210 ATACTCCAACCTCGGTTTTATTTCTAAAACATCGATTTCCCACCATCGAGG
1 ATACTCCAACCTCGATTTTATTTCTAAAACATCGATTTCCCACCATCGAGG
* **
281261 ATACTCCAACCTCGATTTTATTTCTAAAACATTGATTTTTCACCATCGAGG
1 ATACTCCAACCTCGATTTTATTTCTAAAACATCGATTTCCCACCATCGAGG
* *
281312 ATAATCGAACCTCG
1 ATACTCCAACCTCG
281326 TTATTTTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (51 bp):
ATACTCCAACCTCGATTTTATTTCTAAAACATCGATTTCCCACCATCGAGG
Found at i:281303 original size:130 final size:129
Alignment explanation
Indices: 281129--281402 Score: 331
Period size: 130 Copynumber: 2.1 Consensus size: 129
281119 ATTCCAAAGG
* * *
281129 GGATACTCCAACCCCCATTTTATTTCTAAAATATCAGTTTTTCACTATCG-GAGATACTTC-AAC
1 GGATACTCCAACCCCCATTTTATTTCTAAAACATCAGTTTTTCACCATCGAG-GATA-ATCGAAC
*
281192 CCCGTTATTTCCAAGGGAATACTCCAACCT-CGGTTTTATTTCTAAAACATCGATTTCCCACCAT
64 CCCGTTATTTCCAAGGGAATACTCCAA-CTAC-GTTTTATTTCTAAAACATCAATTTCCCACCAT
281256 CGA
127 CGA
* * *
281259 GGATACTCCAACCTCGATTTTATTTCTAAAACAT-TGATTTTTCACCATCGAGGATAATCGAACC
1 GGATACTCCAACCCCCATTTTATTTCTAAAACATCAG-TTTTTCACCATCGAGGATAATCGAACC
* *** * * * * *
281323 TCGTTATTTTTTAGGGGATACTCCAACTACGTTTTATTTCTAAAGCATCAATTTTCCACCATTGG
65 CCGTTATTTCCAAGGGAATACTCCAACTACGTTTTATTTCTAAAACATCAATTTCCCACCATCGA
281388 GGATACTCCAACCCC
1 GGATACTCCAACCCC
281403 GTTTTTCCGA
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
129 49 0.40
130 73 0.59
131 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (129 bp):
GGATACTCCAACCCCCATTTTATTTCTAAAACATCAGTTTTTCACCATCGAGGATAATCGAACCC
CGTTATTTCCAAGGGAATACTCCAACTACGTTTTATTTCTAAAACATCAATTTCCCACCATCGA
Found at i:281437 original size:78 final size:78
Alignment explanation
Indices: 281259--281434 Score: 196
Period size: 78 Copynumber: 2.3 Consensus size: 78
281249 CCACCATCGA
** * * *
281259 GGATACTCCAACCTCGATTTTATTTCTAAAACATTGATTTTTCACCATCGAGGATAATCGAACCT
1 GGATACTCCAACCTCG-TTTTATTTCTAAAACATCAATTTTCCACCATCGAGGATAATCCAACCC
***
281324 CGTTATTTTTTAGG
65 CGTTATTTCCGAGG
* * * *
281338 GGATACTCCAA-CTACGTTTTATTTCTAAAGCATCAATTTTCCACCATTGGGGATACTCCAACCC
1 GGATACTCCAACCT-CGTTTTATTTCTAAAACATCAATTTTCCACCATCGAGGATAATCCAACCC
281402 CGTT-TTTCCGAGG
65 CGTTATTTCCGAGG
281415 GGATACTCCAAACCT-GTTTT
1 GGATACTCC-AACCTCGTTTT
281435 TATCTCCAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
77 20 0.24
78 47 0.57
79 15 0.18
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (78 bp):
GGATACTCCAACCTCGTTTTATTTCTAAAACATCAATTTTCCACCATCGAGGATAATCCAACCCC
GTTATTTCCGAGG
Found at i:282215 original size:20 final size:19
Alignment explanation
Indices: 282190--282261 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
282180 TACCCAGATG
282190 TATCGATACATTTTTCAATA
1 TATCGATACATTTTT-AATA
* * *
282210 TATCGATACATGTATGAATG
1 TATCGATACAT-TTTTAATA
* *
282230 TATCGATATATGCTTTAATA
1 TATCGATACAT-TTTTAATA
282250 TATCGATACATT
1 TATCGATACATT
282262 CTATCTTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (19 bp):
TATCGATACATTTTTAATA
Found at i:287906 original size:17 final size:18
Alignment explanation
Indices: 287865--287922 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
287855 AGGTTTAGGT
287865 AAGAAAGAAAGAAAGAAGA
1 AAGAAAGAAAGAAAGAA-A
287884 TGAAG-AAGAAAGAAAGAAA
1 --AAGAAAGAAAGAAAGAAA
* *
287903 AAGAAAAAAAAAAAGAAA
1 AAGAAAGAAAGAAAGAAA
287921 AA
1 AA
287923 AATATGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 3 0.09
18 14 0.41
19 1 0.03
20 13 0.38
21 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
AAGAAAGAAAGAAAGAAA
Found at i:287917 original size:12 final size:12
Alignment explanation
Indices: 287889--287924 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
287879 GAAGATGAAG
287889 AAGAAAGAAAGAAA
1 AAGAAA-AAA-AAA
287903 AAGAAAAAAAAA
1 AAGAAAAAAAAA
287915 AAGAAAAAAA
1 AAGAAAAAAA
287925 TATGAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.59
13 3 0.14
14 6 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:288300 original size:20 final size:20
Alignment explanation
Indices: 288259--288307 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
288249 TGATGTTTGC
288259 ATTTATTTTTTTATTATCAT
1 ATTTATTTTTTTATTATCAT
288279 ATTT-TTTTTTGTATATAT-AT
1 ATTTATTTTTT-TAT-TATCAT
*
288299 ATATATTTT
1 ATTTATTTT
288308 GAATATCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTTATTTTTTTATTATCAT
Found at i:291795 original size:18 final size:18
Alignment explanation
Indices: 291772--291808 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
291762 GAATTACAGC
291772 GTGAAGAAATCAGAGTTG
1 GTGAAGAAATCAGAGTTG
291790 GTGAAGAAATCAGAGTTG
1 GTGAAGAAATCAGAGTTG
291808 G
1 G
291809 CAAAGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22
Consensus pattern (18 bp):
GTGAAGAAATCAGAGTTG
Found at i:291814 original size:18 final size:18
Alignment explanation
Indices: 291775--291816 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
291765 TTACAGCGTG
**
291775 AAGAAATCAGAGTTGGTG
1 AAGAAATCAGAGTTGGCA
291793 AAGAAATCAGAGTTGGCA
1 AAGAAATCAGAGTTGGCA
291811 AAGAAA
1 AAGAAA
291817 AGCTCGTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.07, G:0.29, T:0.17
Consensus pattern (18 bp):
AAGAAATCAGAGTTGGCA
Found at i:301825 original size:19 final size:19
Alignment explanation
Indices: 301801--301898 Score: 76
Period size: 19 Copynumber: 5.7 Consensus size: 19
301791 TAGCTTACAT
301801 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
301820 TGTATCGAT---ATA--T-
1 TGTATCGATACAAAACTTA
*
301833 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
301852 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
301865 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAAC-TTA
301885 TGTATCGATACAAA
1 TGTATCGATACAAA
301899 TCGTTGAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 25
0.69 0.03 0.27
Matches are distributed among these distances:
13 20 0.32
14 2 0.03
16 6 0.10
18 1 0.02
19 21 0.33
20 13 0.21
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:301840 original size:32 final size:32
Alignment explanation
Indices: 301796--301896 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
301786 GGCAGTAGCT
*
301796 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
301828 TATATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
301860 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
301893 TACA
1 TACA
301897 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 50 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:301870 original size:13 final size:13
Alignment explanation
Indices: 301820--301876 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
301810 ACAAAACTTA
*
301820 TGTATCGATATAT
1 TGTATCGATACAT
301833 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
301851 ATGTATCGATACAT
1 -TGTATCGATACAT
301865 TGTATCGATACA
1 TGTATCGATACA
301877 ACACTTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 21 0.57
14 1 0.03
16 5 0.14
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:304609 original size:29 final size:30
Alignment explanation
Indices: 304577--304640 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
304567 CCTTTACACC
304577 CAAAAAAAAAACAAAAAATA-AAAAAAAAA
1 CAAAAAAAAAACAAAAAATAGAAAAAAAAA
** * *
304606 CAAAAAACCAAGAAAAAATAGCAAAAAAAA
1 CAAAAAAAAAACAAAAAATAGAAAAAAAAA
*
304636 GAAAA
1 CAAAA
304641 GGGTCTAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.83, C:0.09, G:0.05, T:0.03
Consensus pattern (30 bp):
CAAAAAAAAAACAAAAAATAGAAAAAAAAA
Found at i:304637 original size:19 final size:19
Alignment explanation
Indices: 304580--304640 Score: 72
Period size: 18 Copynumber: 3.2 Consensus size: 19
304570 TTACACCCAA
*
304580 AAAAAAAACAAAAAATAA-
1 AAAAAAAACAAAAAACAAG
304598 AAAAAAAACAAAAAACCAAG
1 AAAAAAAACAAAAAA-CAAG
*
304618 AAAAAATAGCAAAAAA-AAG
1 AAAAAA-AACAAAAAACAAG
304637 AAAA
1 AAAA
304641 GGGTCTAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
18 15 0.39
19 9 0.24
20 6 0.16
21 8 0.21
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.03
Consensus pattern (19 bp):
AAAAAAAACAAAAAACAAG
Found at i:305891 original size:29 final size:29
Alignment explanation
Indices: 305853--306537 Score: 851
Period size: 29 Copynumber: 23.9 Consensus size: 29
305843 TGTTCATCCC
* *
305853 TTTCAAAGCCCACAAGTCAATGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
305882 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
305910 TTTCAAAGCCCACAAGTCATTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
305939 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * * *
305968 TTCCAAAGCTCACAAATTAGTGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
305997 TTTCAAAGCCCACAAGTCAATGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
306025 TTTCAAAGCCGACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
306054 TTTCAAAGCCTACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
306083 TTTCAAAGCCTACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
306112 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
306140 TTTCAAAG-CCACAATTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
306168 TTTCAAAGCCCACAAATTAGTGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
306197 TTTCAAAGCCCACAAGTCAGTAGTGC-C-C-
1 TTTCAAAGCCCACAAGTCAGT-G-GCACTCT
306225 TTTCAAAG-CC-CAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
306252 TTTCAAAGCCCACAAATCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
306281 TTTCAAAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
306309 ---CAAAGCCGACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
306335 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
306364 TTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
306392 GTTCAAAGCCCACGAGTTAGTGGTACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
306421 TTTCAAAGCTCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
306449 TTTCAAAGCCCACAAGTCAGTGGCATTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
**
306478 TTTCAAAGCCCACACGAGTTGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-ACTCT
*
306510 TTTCAAAGCCCACACAAGTTAGTGGCAC
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC
306538 CATTTTTTTT
Statistics
Matches: 573, Mismatches: 61, Indels: 42
0.85 0.09 0.06
Matches are distributed among these distances:
24 2 0.00
25 25 0.04
26 10 0.02
27 26 0.05
28 126 0.22
29 343 0.60
30 2 0.00
31 12 0.02
32 21 0.04
33 2 0.00
34 4 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:305919 original size:57 final size:57
Alignment explanation
Indices: 305850--306538 Score: 806
Period size: 57 Copynumber: 12.0 Consensus size: 57
305840 GAATGTTCAT
* *
305850 CCCTTTCAAAGCCCACAAGTCAATGGCACTTTTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
305907 CCCTTTCAAAGCCCACAAGTCATTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * * * *
305964 CTCTTTCCAAAGCTCACAAATTAGTGGCACTTTTTTCAAAGCCCACAAGTCAATGGCA
1 CCCTTT-CAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
306022 CCCTTTCAAAGCCGACAAGTCAGTGGCACTCCTTTCAAAGCCTACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
*
306079 CTCCTTTCAAAGCCTACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
306137 CCCTTTCAAAG-CCACAATTCAGTGGCACTCTTTTCAAAGCCCACAAATTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
**
306193 CTTTTTTCAAAGCCCACAAGTCAGTAGTGC-C-C-TTTCAAAG-CC-CAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGT-G-GCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
306248 CTCTTTTCAAAGCCCACAAATCAATGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
306306 --C-TCCAAAGCCGACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAATCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * ** * * *
306360 CTCTTTTCAAAGCCCACAAGTTAGTGGCAC-CCGTTCAAAGCCCACGAGTTAGTGGTA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
306417 CTCTTTTCAAAGCTCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
* * ** *
306474 TTCTTTTCAAAGCCCACACGAGTTGGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCA
1 -CCCTTTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTTCAAAG-CC-CACAAGTCAGTGGCA
306537 CC
1 CC
306539 ATTTTTTTTA
Statistics
Matches: 545, Mismatches: 65, Indels: 39
0.84 0.10 0.06
Matches are distributed among these distances:
53 2 0.00
54 49 0.09
55 34 0.06
56 52 0.10
57 218 0.40
58 150 0.28
59 10 0.02
60 4 0.01
61 9 0.02
62 3 0.01
63 14 0.03
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (57 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:306029 original size:86 final size:85
Alignment explanation
Indices: 305853--306537 Score: 848
Period size: 86 Copynumber: 8.0 Consensus size: 85
305843 TGTTCATCCC
* * *
305853 TTTCAAAGCCCACAAGTCAATGGCACTTTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCAC-TCTTTCAAAG-CCACAAGTCAGTGGCACTCTTTTCAAA
*
305917 GCCCACAAGTCATTGGCACTCT
64 GCCCACAAGTCAGTGGCACTCT
* * * *
305939 TTTCAAAGCCCACAAATCAGTGGCACTCTTTCCAAAGCTCACAAATTAGTGGCACTTTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTT-CAAAGC-CACAAGTCAGTGGCACTCTTTTCAAA
* *
306004 GCCCACAAGTCAATGGCAC-CC
64 GCCCACAAGTCAGTGGCACTCT
* *
306025 TTTCAAAGCCGACAAGTCAGTGGCACTCCTTTCAAAGCCTACAAGTCAGTGGCACTCCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCC-ACAAGTCAGTGGCACTCTTTTCAAA
*
306090 GCCTACAAGTCAGTGGCACTCT
64 GCCCACAAGTCAGTGGCACTCT
* *
306112 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCACAATTCAGTGGCACTCTTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
306177 CCACAAATTAGTGGCACTTT
66 CCACAAGTCAGTGGCACTCT
306197 TTTCAAAGCCCACAAGTCAGTAGTGC-C-CTTTCAAAGCC-CAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGT-G-GCACTCTTTCAAAGCCACAAGTCAGTGGCACTCTTTTCAAA
* *
306259 GCCCACAAATCAATGGCACTCT
64 GCCCACAAGTCAGTGGCACTCT
*
306281 TTTCAAAGCCCACAAGTCAGTGGCACTC---CAAAGCCGACAAGTCAGTGGCACCCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCC-ACAAGTCAGTGGCACTCTTTTCAAAG
*
306343 CCCACAAATCAGTGGCACTCT
65 CCCACAAGTCAGTGGCACTCT
* * * * * *
306364 TTTCAAAGCCCACAAGTTAGTGGCACCCGTTCAAAGCCCACGAGTTAGTGGTACTCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAG-CCACAAGTCAGTGGCACTCTTTTCAAAG
* *
306429 CTCACAAGTCAGTGGCAC-CC
65 CCCACAAGTCAGTGGCACTCT
* **
306449 TTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAGCCCACACGAGTTGGTGGCAACTCTTTTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAG-CCACA--AGTCAGTGGC-ACTCTTTTC
*
306514 AAAGCCCACACAAGTTAGTGGCAC
61 AAAG-CC-CACAAGTCAGTGGCAC
306538 CATTTTTTTT
Statistics
Matches: 527, Mismatches: 50, Indels: 39
0.86 0.08 0.06
Matches are distributed among these distances:
81 7 0.01
82 2 0.00
83 72 0.14
84 64 0.12
85 105 0.20
86 181 0.34
87 59 0.11
88 8 0.02
89 13 0.02
90 1 0.00
91 15 0.03
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (85 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCACAAGTCAGTGGCACTCTTTTCAAAGC
CCACAAGTCAGTGGCACTCT
Found at i:306058 original size:115 final size:114
Alignment explanation
Indices: 305852--306537 Score: 797
Period size: 115 Copynumber: 6.0 Consensus size: 114
305842 ATGTTCATCC
* *
305852 CTTT-CAAAGCCCACAAGTCAATGGCACTTTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1 CTTTCCAAAG-CCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
*
305916 AGCCCACAAGTCATTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACT
65 AGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACT
* * * *
305966 CTTTCCAAAGCTCACAAATTAGTGGCACTTTTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAA
1 CTTTCCAAAGC-CACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
* * * *
306031 AGCCGACAAGTCAGTGGCACTCCTTTCAAAGCCTACAAGTCAGTGGCACT
65 AGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACT
306081 CCTTT-CAAAGCCTACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
1 -CTTTCCAAAGCC-ACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
* *
306145 AAG-CCACAATTCAGTGGCACTCTTTTCAAAGCCCACAAATTAGTGGCACT
64 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACT
* * *
306195 TTTTTCAAAGCCCACAAGTCAGTAGTGC-C-C-TTTCAAAG-CC-CAAGTCAGTGGCACTCTTTT
1 CTTTCCAAAG-CCACAAGTCAGT-G-GCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTT
* * *
306255 CAAAGCCCACAAATCAATGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA--
62 CAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACT
* * *
306306 C--TCCAAAGCCGACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCA
1 CTTTCCAAAGCC-ACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
* ** * * * *
306369 AAGCCCACAAGTTAGTGGCAC-CCGTTCAAAGCCCACGAGTTAGTGGTACT
64 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACT
* * * *
306419 CTTTTCAAAGCTCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCA
1 CTTTCCAAAGC-CACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCA
** *
306483 AAGCCCACACGAGTTGGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCAC
64 AAGCCCACA--AGTCAGTGGC-ACTCTTTTCAAAGCCCACA-AA-TCAGTGGCAC
306538 CATTTTTTTT
Statistics
Matches: 498, Mismatches: 46, Indels: 50
0.84 0.08 0.08
Matches are distributed among these distances:
107 2 0.00
108 4 0.01
109 17 0.03
110 8 0.02
111 38 0.08
112 50 0.10
113 53 0.11
114 104 0.21
115 181 0.36
116 16 0.03
117 2 0.00
118 13 0.03
119 1 0.00
120 9 0.02
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (114 bp):
CTTTCCAAAGCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
GCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACT
Found at i:311079 original size:17 final size:17
Alignment explanation
Indices: 311059--311091 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
311049 ATTCAAAACA
311059 TTTGTA-TATTCTATTTG
1 TTTGTATTATT-TATTTG
311076 TTTGTATTATTTATTT
1 TTTGTATTATTTATTT
311092 ATATATGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.70
Consensus pattern (17 bp):
TTTGTATTATTTATTTG
Found at i:312543 original size:18 final size:18
Alignment explanation
Indices: 312520--312554 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
312510 TAAATTTAAC
312520 AAATTAATTTTATATAAT
1 AAATTAATTTTATATAAT
312538 AAATTAATTTTATATAA
1 AAATTAATTTTATATAA
312555 AGCTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTAATTTTATATAAT
Found at i:312816 original size:8 final size:8
Alignment explanation
Indices: 312790--312842 Score: 52
Period size: 9 Copynumber: 6.0 Consensus size: 8
312780 TAGTCTTTAA
312790 TTATATAAT
1 TTATAT-AT
312799 TTATATTAT
1 TTATA-TAT
*
312808 TTTTATAT
1 TTATATAT
312816 TTATATAT
1 TTATATAT
312824 ATTATATAAT
1 -TTATAT-AT
312834 TTATCATAT
1 TTAT-ATAT
312843 AAATATTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 10 0.26
9 23 0.61
10 5 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
TTATATAT
Found at i:312831 original size:17 final size:18
Alignment explanation
Indices: 312789--312843 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
312779 TTAGTCTTTA
312789 ATTATATAATTTATAT-T
1 ATTATATAATTTATATAT
*
312806 ATT-TTTATATTTATATAT
1 ATTATATA-ATTTATATAT
312824 ATTATATAATTTATCATAT
1 ATTATATAATTTAT-ATAT
312843 A
1 A
312844 AATATTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 3 0.09
17 11 0.34
18 10 0.31
19 8 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATATAATTTATATAT
Found at i:312893 original size:28 final size:26
Alignment explanation
Indices: 312842--312919 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 26
312832 ATTTATCATA
* *
312842 TAAATATTAAAAAATATATTAAATTATT
1 TAAATTTTAAAAAATATA-TAAAATA-T
*
312870 TATATTTTAAAAAATA-ATAAAAATAT
1 TAAATTTTAAAAAATATAT-AAAATAT
*
312896 TAAATTATAAAAAAATTATATAAA
1 TAAATT-TTAAAAAA-TATATAAA
312920 TAAATTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 7 0.17
27 13 0.32
28 19 0.46
29 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TAAATTTTAAAAAATATATAAAATAT
Found at i:312905 original size:16 final size:16
Alignment explanation
Indices: 312881--312923 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
312871 ATATTTTAAA
*
312881 AAATAATAAAAATATT
1 AAATAATAAAAAAATT
*
312897 AAATTATAAAAAAATT
1 AAATAATAAAAAAATT
*
312913 ATATAAATAAA
1 AAAT-AATAAA
312924 TTTAAATGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAATAAAAAAATT
Found at i:313256 original size:26 final size:27
Alignment explanation
Indices: 313227--313288 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
313217 TTCAATCATG
313227 ATATTATTATAT-ATTA-TTCATCATTA
1 ATATTATTATATAATTATTTCAT-ATTA
* *
313253 ATA-TGTTATGTAATTATTTCATATTA
1 ATATTATTATATAATTATTTCATATTA
*
313279 AAATTATTAT
1 ATATTATTAT
313289 TTTTATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 6 0.21
26 13 0.45
27 10 0.34
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (27 bp):
ATATTATTATATAATTATTTCATATTA
Found at i:313316 original size:25 final size:24
Alignment explanation
Indices: 313288--313335 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
313278 AAAATTATTA
313288 TTTTTATAAATTATTAATCATTTAC
1 TTTTTATAAATTATT-ATCATTTAC
* *
313313 TTTTTATTAGTTATTATCATTTA
1 TTTTTATAAATTATTATCATTTA
313336 GTATTTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTATAAATTATTATCATTTAC
Found at i:313953 original size:16 final size:16
Alignment explanation
Indices: 313934--314045 Score: 107
Period size: 16 Copynumber: 7.4 Consensus size: 16
313924 AATATATGTA
313934 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
313950 AATTTAAATTTAAAA-
1 AATTTAAATTTAAAAT
*
313965 CA-TTAAA---AATAAT
1 AATTTAAATTTAA-AAT
*
313978 AA-AT-AATTTAAAAT
1 AATTTAAATTTAAAAT
313992 AATTTAAATTTAAAA-
1 AATTTAAATTTAAAAT
* *
314007 AATTTTAATAT-AAAT
1 AATTTAAATTTAAAAT
314022 AATTTTAAATTTAAAAT
1 AA-TTTAAATTTAAAAT
314039 AATTTAA
1 AATTTAA
314046 TACAAATCAA
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
11 2 0.03
12 4 0.05
13 2 0.03
14 13 0.17
15 15 0.19
16 36 0.46
17 6 0.08
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:313972 original size:47 final size:46
Alignment explanation
Indices: 313921--314045 Score: 159
Period size: 42 Copynumber: 2.8 Consensus size: 46
313911 AAAAATATTA
* *
313921 TAAAATATATGTAAATTTAAATTTAAAATAATTTAAATTTAAAACAT
1 TAAAATATA-ATAAATTTAAATTTAAAATAATTTAAATTTAAAAAAT
313968 TAAAA-ATAATAAA--T-AATTTAAAATAATTTAAATTTAAAAAAT
1 TAAAATATAATAAATTTAAATTTAAAATAATTTAAATTTAAAAAAT
** *
314010 TTTAATATAAATAATTTTAAATTTAAAATAATTTAA
1 TAAAATAT-AATAAATTTAAATTTAAAATAATTTAA
314046 TACAAATCAA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
42 30 0.44
43 3 0.04
44 5 0.07
45 4 0.06
46 4 0.06
47 22 0.32
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (46 bp):
TAAAATATAATAAATTTAAATTTAAAATAATTTAAATTTAAAAAAT
Found at i:313990 original size:17 final size:17
Alignment explanation
Indices: 313899--313994 Score: 51
Period size: 17 Copynumber: 5.8 Consensus size: 17
313889 TTATTACATT
* *
313899 TAATATAAAATAAAAAA
1 TAATTTAAAATAATAAA
**
313916 T-ATTATAAAAT-ATATG
1 TAATT-TAAAATAATAAA
* *
313932 TAAATTTAAATTTA-AAA
1 T-AATTTAAAATAATAAA
*
313949 TAATTT-AAAT-TTAAA
1 TAATTTAAAATAATAAA
*
313964 -ACATTAAAAATAATAAA
1 TA-ATTTAAAATAATAAA
313981 TAATTTAAAATAAT
1 TAATTTAAAATAAT
313995 TTAAATTTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
14 1 0.02
15 9 0.16
16 14 0.24
17 29 0.50
18 5 0.09
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (17 bp):
TAATTTAAAATAATAAA
Found at i:314020 original size:15 final size:16
Alignment explanation
Indices: 313981--314043 Score: 85
Period size: 15 Copynumber: 4.0 Consensus size: 16
313971 AAATAATAAA
313981 TAATTTAAAATAATTT
1 TAATTTAAAATAATTT
*
313997 AAATTTAAAA-AATTT
1 TAATTTAAAATAATTT
*
314012 TAATAT-AAATAATTT
1 TAATTTAAAATAATTT
314027 TAAATTTAAAATAATTT
1 T-AATTTAAAATAATTT
314044 AATACAAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
14 3 0.08
15 15 0.38
16 13 0.32
17 9 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATTTAAAATAATTT
Found at i:314060 original size:31 final size:30
Alignment explanation
Indices: 313988--314061 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 30
313978 AAATAATTTA
*
313988 AAATAATTTAAATTTAAAAAATTTTAATAT
1 AAATAATTTAAATTTAAAAAATTTTAATAC
314018 AAATAATTTTAAATTTAAAATAA-TTTAATAC
1 AAATAA-TTTAAATTTAAAA-AATTTTAATAC
314049 AAATCAATTTAAA
1 AAAT-AATTTAAA
314062 CTTCGAATGC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
30 6 0.15
31 30 0.75
32 4 0.10
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATAATTTAAATTTAAAAAATTTTAATAC
Found at i:314262 original size:20 final size:22
Alignment explanation
Indices: 314237--314276 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
314227 TTAAACTTAA
*
314237 TTATA-TAAATAAT-TTTTATC
1 TTATATTAAAAAATATTTTATC
314257 TTATATTAAAAAATATTTTA
1 TTATATTAAAAAATATTTTA
314277 AAAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATATTAAAAAATATTTTATC
Found at i:314279 original size:12 final size:12
Alignment explanation
Indices: 314262--314301 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
314252 TTATCTTATA
314262 TTAAAAAATATT
1 TTAAAAAATATT
*
314274 TTAAAAAATTTAT
1 TTAAAAAATAT-T
314287 TTAAATAAATATT
1 TTAAA-AAATATT
314300 TT
1 TT
314302 TATTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.42
13 9 0.38
14 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:314311 original size:27 final size:27
Alignment explanation
Indices: 314257--314369 Score: 101
Period size: 28 Copynumber: 4.1 Consensus size: 27
314247 AATTTTTATC
**
314257 TTATATTAAA-AAATATTTTA-AAAAAT
1 TTAT-TTAAATAAATATTTTATATTAAT
314283 TTATTTAAATAAATATTTT-TATTATATTT
1 TTATTTAAATAAATATTTTATATTA-A--T
314312 TTATTT-AATAAATATTTTATATTAAT
1 TTATTTAAATAAATATTTTATATTAAT
*
314338 ATTA-TTAAATAAATATTTATATGTTAAAT
1 -TTATTTAAATAAATATTT-TATATT-AAT
314367 TTA
1 TTA
314370 ATTATGACAT
Statistics
Matches: 74, Mismatches: 3, Indels: 18
0.78 0.03 0.19
Matches are distributed among these distances:
25 5 0.07
26 18 0.24
27 15 0.20
28 21 0.28
29 15 0.20
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
TTATTTAAATAAATATTTTATATTAAT
Found at i:314326 original size:17 final size:17
Alignment explanation
Indices: 314290--314338 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 17
314280 AATTTATTTA
314290 AATAAATATTTT-TATT
1 AATAAATATTTTATATT
314306 -AT--AT-TTTTAT-TT
1 AATAAATATTTTATATT
314318 AATAAATATTTTATATT
1 AATAAATATTTTATATT
314335 AATA
1 AATA
314339 TTATTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 11
0.71 0.00 0.29
Matches are distributed among these distances:
12 6 0.22
13 5 0.19
15 4 0.15
16 6 0.22
17 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATAAATATTTTATATT
Found at i:314343 original size:16 final size:16
Alignment explanation
Indices: 314282--314338 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
314272 TTTTAAAAAA
314282 TTTATTTAAATAAATAT
1 TTTATTT-AATAAATAT
314299 TTT-TATT-AT--AT-T
1 TTTAT-TTAATAAATAT
314311 TTTATTTAATAAATAT
1 TTTATTTAATAAATAT
314327 TTTATATTAATA
1 TTTAT-TTAATA
314339 TTATTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
12 6 0.18
13 5 0.15
15 4 0.12
16 7 0.21
17 11 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATTTAATAAATAT
Found at i:314581 original size:3 final size:3
Alignment explanation
Indices: 314573--314602 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
314563 TATTTGTGTA
314573 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
314603 GTCGTAACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:315230 original size:20 final size:21
Alignment explanation
Indices: 315205--315249 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
315195 GTTTGGGATG
315205 ATGAAACAT-GC-TATAAATGC
1 ATGAAACATAGCTTA-AAATGC
315225 ATGAAACATAGCTTAAAATGC
1 ATGAAACATAGCTTAAAATGC
315246 ATGA
1 ATGA
315250 TTCATGGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.39
21 12 0.52
22 2 0.09
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (21 bp):
ATGAAACATAGCTTAAAATGC
Found at i:316250 original size:52 final size:52
Alignment explanation
Indices: 316102--316230 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
316092 CGAAATATGA
316102 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
316154 AAATTTGCATGTATGTATCGATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
316206 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
316231 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Done.