Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold263
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: 1338270
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 10
Found at i:173862 original size:22 final size:22
Alignment explanation
Indices: 173825--173915 Score: 59
Period size: 23 Copynumber: 4.2 Consensus size: 22
173815 TTTAAAATTT
*
173825 ATATTATATTTATATTATTTTAA
1 ATATAATA-TTATATTATTTTAA
173848 ATATAATA-T-TA-TATTTT-A
1 ATATAATATTATATTATTTTAA
* *
173866 ATA-ATTTTTATATTATATTTAA
1 ATATAATATTATATTAT-TTTAA
* *
173888 ATA-ATATAATTATATTATATTCA
1 ATATA-AT-ATTATATTATTTTAA
173911 ATATA
1 ATATA
173916 CCTGAAGACA
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
17 2 0.04
18 5 0.09
19 8 0.15
20 5 0.09
21 4 0.08
22 5 0.09
23 14 0.26
24 10 0.19
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATAATATTATATTATTTTAA
Found at i:173865 original size:29 final size:29
Alignment explanation
Indices: 173803--173873 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
173793 TTAATTATCT
* *
173803 TTTTATTTTATTTTTAAAATTTATATTATA
1 TTTTATATTA-TTTTAAAATTAATATTATA
173833 -TTTATATTATTTT-AAATATAATATTATA
1 TTTTATATTATTTTAAAAT-TAATATTATA
*
173861 TTTTA-ATAATTTT
1 TTTTATATTATTTT
173874 TATATTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 4 0.11
28 20 0.56
29 12 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTATATTATTTTAAAATTAATATTATA
Found at i:173905 original size:24 final size:22
Alignment explanation
Indices: 173834--173908 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
173824 TATATTATAT
173834 TTATATTAT-TTTAAAT-A-TA
1 TTATATTATATTTAAATAATTA
* *
173853 --ATATTATATTTTAATAATTT
1 TTATATTATATTTAAATAATTA
173873 TTATATTATATTTAAATAATATAA
1 TTATATTATATTTAAATAAT-T-A
173897 TTATATTATATT
1 TTATATTATATT
173909 CAATATACCT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
17 7 0.16
18 6 0.13
19 1 0.02
20 1 0.02
22 17 0.38
23 1 0.02
24 12 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATATTATATTTAAATAATTA
Found at i:173907 original size:13 final size:11
Alignment explanation
Indices: 173821--173908 Score: 62
Period size: 11 Copynumber: 8.3 Consensus size: 11
173811 TATTTTTAAA
173821 ATTTATATTAT
1 ATTTATATTAT
173832 ATTTATATTAT
1 ATTTATATTAT
173843 -TTTA-A--AT
1 ATTTATATTAT
*
173850 A-TAATATTAT
1 ATTTATATTAT
*
173860 ATTT-TAATAAT
1 ATTTAT-ATTAT
*
173871 TTTTATATTAT
1 ATTTATATTAT
*
173882 ATTTAAATAATAT
1 ATTT--ATATTAT
*
173895 AATTATATTAT
1 ATTTATATTAT
173906 ATT
1 ATT
173909 CAATATACCT
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
7 4 0.07
8 1 0.02
9 1 0.02
10 8 0.14
11 34 0.59
12 1 0.02
13 9 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:176876 original size:2 final size:2
Alignment explanation
Indices: 176871--176900 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
176861 ATAAATAAGA
176871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176901 TCTGCCGGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:179410 original size:30 final size:30
Alignment explanation
Indices: 179376--179440 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
179366 CTTATTTTAT
179376 TTTGAATGAAATATTAGACATAAATATATA
1 TTTGAATGAAATATTAGACATAAATATATA
*
179406 TTTGAATGAAATATTAGATATAAATATATA
1 TTTGAATGAAATATTAGACATAAATATATA
179436 TTTGA
1 TTTGA
179441 TACGTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.40
Consensus pattern (30 bp):
TTTGAATGAAATATTAGACATAAATATATA
Found at i:179436 original size:17 final size:17
Alignment explanation
Indices: 179386--179442 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
179376 TTTGAATGAA
*
179386 ATATTAGACATAAATAT
1 ATATTAGATATAAATAT
* *
179403 ATATTTGA-AT-GA-A-
1 ATATTAGATATAAATAT
179416 ATATTAGATATAAATAT
1 ATATTAGATATAAATAT
*
179433 ATATTTGATA
1 ATATTAGATA
179443 CGTTAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
13 7 0.23
14 3 0.10
15 2 0.06
16 3 0.10
17 16 0.52
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (17 bp):
ATATTAGATATAAATAT
Found at i:185333 original size:2 final size:2
Alignment explanation
Indices: 185326--185375 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
185316 TACAACCTCT
* * *
185326 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA AA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
185368 TA TA TA TA
1 TA TA TA TA
185376 AAATAAAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:188475 original size:3 final size:3
Alignment explanation
Indices: 188467--188495 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
188457 CTTTGAACCA
188467 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
188496 CAAAATCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:194608 original size:14 final size:15
Alignment explanation
Indices: 194589--194625 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
194579 TGTGTTATCT
194589 TTTTTTTCTTTTT-C
1 TTTTTTTCTTTTTGC
194603 TTTTTTT-TTTTTGC
1 TTTTTTTCTTTTTGC
*
194617 ATTTTTTCT
1 TTTTTTTCT
194626 CAATATGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 14 0.70
15 1 0.05
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTTTGC
Found at i:200070 original size:3 final size:3
Alignment explanation
Indices: 200062--200108 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
200052 ATGACGACAG
200062 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
200109 CAGGAAATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:203282 original size:2 final size:2
Alignment explanation
Indices: 203275--203313 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
203265 TGAATTCAAC
203275 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
203314 TTCATTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:205735 original size:14 final size:15
Alignment explanation
Indices: 205711--205748 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
205701 CATAAGATCC
*
205711 TTTTTTATTTTTTAA
1 TTTTTTATTTTTCAA
205726 TTTTTT-TTTTTCAA
1 TTTTTTATTTTTCAA
205740 TTTTATTAT
1 TTTT-TTAT
205749 GTTTGTAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.55
15 8 0.40
16 1 0.05
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTATTTTTCAA
Found at i:209383 original size:2 final size:2
Alignment explanation
Indices: 209341--209365 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
209331 TTCTACAATA
209341 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
209366 AGGCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:224095 original size:24 final size:24
Alignment explanation
Indices: 224067--224118 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
224057 TTTCACCTTT
224067 TTGTCAGATTACGCTTTT-CAGTTG
1 TTGTCAGATTACGCTTTTCCA-TTG
* **
224091 TTGTCTGATTTTGCTTTTCCATTG
1 TTGTCAGATTACGCTTTTCCATTG
224115 TTGT
1 TTGT
224119 GAAACTGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.12, C:0.15, G:0.19, T:0.54
Consensus pattern (24 bp):
TTGTCAGATTACGCTTTTCCATTG
Found at i:227230 original size:23 final size:24
Alignment explanation
Indices: 227193--227240 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
227183 TAAAACTTAA
227193 ATAAATAAAATAAATTTGATATTG
1 ATAAATAAAATAAATTTGATATTG
*
227217 ATAAAT-AAATAAATTTGTTATTG
1 ATAAATAAAATAAATTTGATATTG
227240 A
1 A
227241 CAAGTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (24 bp):
ATAAATAAAATAAATTTGATATTG
Found at i:230027 original size:3 final size:3
Alignment explanation
Indices: 230019--230074 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
230009 TATAGCAATG
230019 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
230067 ATT ATT AT
1 ATT ATT AT
230075 CAGAATTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:232939 original size:36 final size:35
Alignment explanation
Indices: 232898--232973 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
232888 GGATTCGCTT
232898 GGATTGGTGAAACCATTGACGGAGGAAATGAAGCAG
1 GGATTGGTGAAACCATTGACGGAGGAAATG-AGCAG
** * * *
232934 GGATTGGTGAAGGCGTTGACGGAGGGAATGAGCAT
1 GGATTGGTGAAACCATTGACGGAGGAAATGAGCAG
232969 GGATT
1 GGATT
232974 TCACAGAGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 9 0.26
36 26 0.74
ACGTcount: A:0.30, C:0.09, G:0.41, T:0.20
Consensus pattern (35 bp):
GGATTGGTGAAACCATTGACGGAGGAAATGAGCAG
Found at i:238819 original size:3 final size:3
Alignment explanation
Indices: 238811--238842 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
238801 CCAATGTGCA
238811 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
238843 AAGTAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:239505 original size:23 final size:24
Alignment explanation
Indices: 239454--239506 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
239444 AATTAATTTA
* *
239454 TATAATAATATTAAATAATAATAT
1 TATAATAAAATTAAATAATAAAAT
*
239478 T-TAATAAAATTAAA-ATTAAAAT
1 TATAATAAAATTAAATAATAAAAT
239500 TATAATA
1 TATAATA
239507 TTTATAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 7 0.28
23 17 0.68
24 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TATAATAAAATTAAATAATAAAAT
Found at i:242372 original size:23 final size:23
Alignment explanation
Indices: 242328--242378 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
242318 AAAATTCATC
242328 ATTTTATTTAAATAAATATTTTA
1 ATTTTATTTAAATAAATATTTTA
242351 ATTTATATTTAAATAAAT-TTTTA
1 ATTT-TATTTAAATAAATATTTTA
242374 ATTTT
1 ATTTT
242379 TAATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 1 0.04
23 13 0.48
24 13 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTTTATTTAAATAAATATTTTA
Found at i:242384 original size:24 final size:24
Alignment explanation
Indices: 242329--242385 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
242319 AAATTCATCA
242329 TTTTATTTAAATAAATATTTTAAT
1 TTTTATTTAAATAAATATTTTAAT
*
242353 TTATATTTAAATAAAT-TTTTAAT
1 TTTTATTTAAATAAATATTTTAAT
242376 TTTTAATTTA
1 TTTT-ATTTA
242386 TATTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATTTAAATAAATATTTTAAT
Found at i:243632 original size:23 final size:24
Alignment explanation
Indices: 243603--243650 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
243593 TATAGGCATG
243603 TATAAGCTAAATATAA-ATATAAA
1 TATAAGCTAAATATAACATATAAA
*
243626 TATAAGCTAAATATAACTTATAAA
1 TATAAGCTAAATATAACATATAAA
243650 T
1 T
243651 GAAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.33
Consensus pattern (24 bp):
TATAAGCTAAATATAACATATAAA
Found at i:244495 original size:2 final size:2
Alignment explanation
Indices: 244488--244512 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
244478 CTTTTATTCT
244488 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
244513 TAGAGTTTGT
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:244727 original size:3 final size:3
Alignment explanation
Indices: 244719--244743 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
244709 AATTTAAAAT
244719 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
244744 AGTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:245255 original size:16 final size:16
Alignment explanation
Indices: 245234--245267 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
245224 CTTTTAATTC
*
245234 ATTGAAATGAAATAGA
1 ATTGAAATAAAATAGA
245250 ATTGAAATAAAATAGA
1 ATTGAAATAAAATAGA
245266 AT
1 AT
245268 AATTATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (16 bp):
ATTGAAATAAAATAGA
Found at i:245665 original size:2 final size:2
Alignment explanation
Indices: 245658--245694 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
245648 AGTGGTAACT
245658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
245695 GATGAAATTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:246011 original size:79 final size:79
Alignment explanation
Indices: 245911--246066 Score: 278
Period size: 79 Copynumber: 2.0 Consensus size: 79
245901 TACGTATATG
*
245911 AAGCTTGAGTTGCCTGCATAGACTCTATTTTTATAAAATAAAGAATTATTAAACCTGTAAAGTTG
1 AAGCTTGAGTTGCCTGCATAGACTCTATTTTTATAAAATAAAGAATTATTAAACCGGTAAAGTTG
245976 GTATATAATATACC
66 GTATATAATATACC
*
245990 AAGCTTGAGTTG-TTAGCATAGACTCTATTTTTATAAAATAAAGAATTATTAAACCGGTAAAGTT
1 AAGCTTGAGTTGCCT-GCATAGACTCTATTTTTATAAAATAAAGAATTATTAAACCGGTAAAGTT
246054 GGTATATAATATA
65 GGTATATAATATA
246067 ATATAATATA
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
78 1 0.01
79 73 0.99
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (79 bp):
AAGCTTGAGTTGCCTGCATAGACTCTATTTTTATAAAATAAAGAATTATTAAACCGGTAAAGTTG
GTATATAATATACC
Found at i:246067 original size:5 final size:5
Alignment explanation
Indices: 246057--246096 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
246047 TAAAGTTGGT
246057 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
246097 TCTGTTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:246619 original size:5 final size:5
Alignment explanation
Indices: 246609--246663 Score: 110
Period size: 5 Copynumber: 11.0 Consensus size: 5
246599 AGAAGCATAT
246609 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
246659 TTATA
1 TTATA
246664 GAGAGAGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:246891 original size:32 final size:29
Alignment explanation
Indices: 246854--246930 Score: 111
Period size: 32 Copynumber: 2.6 Consensus size: 29
246844 ATATATAATT
246854 ATATAAATATTTTAAAATTTATATTATACGAA
1 ATATAAATATTTTAAAATTTATATTA-A--AA
*
246886 TTATAAATATTTTAAAATTTATATTAAAA
1 ATATAAATATTTTAAAATTTATATTAAAA
246915 ATA-AAATATTTTAAAA
1 ATATAAATATTTTAAAA
246931 ATAGTTATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 13 0.30
29 4 0.09
31 1 0.02
32 25 0.58
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATAAATATTTTAAAATTTATATTAAAA
Found at i:246907 original size:18 final size:17
Alignment explanation
Indices: 246855--246930 Score: 53
Period size: 14 Copynumber: 4.9 Consensus size: 17
246845 TATATAATTA
246855 TATAAATATTTTAAAAT
1 TATAAATATTTTAAAAT
* *
246872 T-T--ATATTATACGAAT
1 TATAAATATTTTA-AAAT
246887 TATAAATATTTTAAAAT
1 TATAAATATTTTAAAAT
*
246904 T-T--ATA--TTAAAAA
1 TATAAATATTTTAAAAT
246916 TA-AAATATTTTAAAA
1 TATAAATATTTTAAAA
246931 ATAGTTATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 19
0.65 0.07 0.28
Matches are distributed among these distances:
12 7 0.16
14 13 0.29
15 4 0.09
16 9 0.20
17 5 0.11
18 7 0.16
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TATAAATATTTTAAAAT
Found at i:253431 original size:2 final size:2
Alignment explanation
Indices: 253426--253451 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
253416 TTAAAGAGCT
253426 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
253452 GATATTGGAC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:259738 original size:8 final size:8
Alignment explanation
Indices: 259725--260047 Score: 391
Period size: 8 Copynumber: 40.9 Consensus size: 8
259715 GACTTATAAT
259725 ATATATAC
1 ATATATAC
259733 ATATATAC
1 ATATATAC
259741 ATATATATAC
1 --ATATATAC
259751 ATATATAC
1 ATATATAC
259759 ATATATAC
1 ATATATAC
259767 ATATATAC
1 ATATATAC
*
259775 ATATATATAT
1 --ATATATAC
259785 ATATATAC
1 ATATATAC
*
259793 ATACATAC
1 ATATATAC
259801 ATATATAC
1 ATATATAC
*
259809 ATACATAC
1 ATATATAC
*
259817 ATACATAC
1 ATATATAC
*
259825 ATACAT--
1 ATATATAC
*
259831 ATACATAC
1 ATATATAC
*
259839 ATACATAC
1 ATATATAC
259847 ATATATAC
1 ATATATAC
259855 ATATATAC
1 ATATATAC
259863 ATATATAC
1 ATATATAC
259871 ATATAT--
1 ATATATAC
259877 ATATATAC
1 ATATATAC
259885 ATATATAC
1 ATATATAC
259893 --ATATAC
1 ATATATAC
259899 ATATATAC
1 ATATATAC
259907 ATATATAC
1 ATATATAC
259915 ATATATAC
1 ATATATAC
259923 ATATATAC
1 ATATATAC
259931 ATATATAC
1 ATATATAC
*
259939 ATATATAT
1 ATATATAC
259947 ATATACATAC
1 ATAT--ATAC
259957 ATATATAC
1 ATATATAC
259965 ATATATAC
1 ATATATAC
259973 ----ATAC
1 ATATATAC
259977 ATATATAC
1 ATATATAC
259985 ATATAT--
1 ATATATAC
259991 ATATATAC
1 ATATATAC
259999 ATATATAC
1 ATATATAC
260007 ATATATATAC
1 --ATATATAC
*
260017 ATACATAC
1 ATATATAC
*
260025 ATATATAT
1 ATATATAC
*
260033 ATATATAT
1 ATATATAC
260041 ATATATA
1 ATATATA
260048 TGATTTTGTT
Statistics
Matches: 284, Mismatches: 11, Indels: 40
0.85 0.03 0.12
Matches are distributed among these distances:
4 4 0.01
6 24 0.08
8 226 0.80
10 30 0.11
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATATAC
Found at i:259778 original size:42 final size:42
Alignment explanation
Indices: 259725--260048 Score: 412
Period size: 42 Copynumber: 7.8 Consensus size: 42
259715 GACTTATAAT
259725 ATATATACATATATACATATATATACATATATACATATATAC
1 ATATATACATATATACATATATATACATATATACATATATAC
* *
259767 ATATATACATATATATATATATATACATACATACATATATAC
1 ATATATACATATATACATATATATACATATATACATATATAC
* * *
259809 ATACATACATACATACATACATATACATACATACATACATATATAC
1 AT--AT--ATACATATATACATATATATACATATATACATATATAC
259855 ATATATACATATATAC--ATATAT--ATATATACATATATAC
1 ATATATACATATATACATATATATACATATATACATATATAC
259893 --ATATACATATATAC--ATATATACATATATACATATATAC
1 ATATATACATATATACATATATATACATATATACATATATAC
* *
259931 ATATATACATATATATATATACATACATATATACATATATAC
1 ATATATACATATATACATATATATACATATATACATATATAC
* * * *
259973 ATACATATATACATATATATATATACATATATACATATATATAC
1 ATATATACATATATACATATATATACATATATAC--ATATATAC
* * *
260017 ATACATACATATATATATATATATATATATAT
1 ATATATACATATATACATATATATACATATAT
260049 GATTTTGTTC
Statistics
Matches: 253, Mismatches: 17, Indels: 22
0.87 0.06 0.08
Matches are distributed among these distances:
36 20 0.08
38 31 0.12
40 18 0.07
42 106 0.42
44 41 0.16
46 37 0.15
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (42 bp):
ATATATACATATATACATATATATACATATATACATATATAC
Found at i:259791 original size:46 final size:46
Alignment explanation
Indices: 259723--260048 Score: 366
Period size: 46 Copynumber: 7.2 Consensus size: 46
259713 CAGACTTATA
* * *
259723 ATATATATACATATATACATATATATACATATATACATATATACAT
1 ATATACATATATATATATATATATATACATATATACATATATACAT
*
259769 ATATAC----ATATATATATATATATACATACATACATATATACAT
1 ATATACATATATATATATATATATATACATATATACATATATACAT
* * * * * *
259811 ACATACATACATACATACATATACATACATACATACATATATACAT
1 ATATACATATATATATATATATATATACATATATACATATATACAT
*
259857 ATATACATATATACATATATATATATACATATATAC--ATATACAT
1 ATATACATATATATATATATATATATACATATATACATATATACAT
*
259901 ATATACATATATACATATATACATATATACATATATACATATAT--AT
1 ATATACATATAT--ATATATATATATATACATATATACATATATACAT
* *
259947 ATATACATACATATATACATATATACATACATATATACATATAT--AT
1 ATATACAT--ATATATATATATATATATACATATATACATATATACAT
* * * * *
259993 ATATACATATATACATATATATACATACATACATATATATATATAT
1 ATATACATATATATATATATATATATACATATATACATATATACAT
*
260039 ATATATATAT
1 ATATACATAT
260049 GATTTTGTTC
Statistics
Matches: 246, Mismatches: 22, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
42 39 0.16
44 50 0.20
46 149 0.61
48 8 0.03
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (46 bp):
ATATACATATATATATATATATATATACATATATACATATATACAT
Found at i:269065 original size:3 final size:3
Alignment explanation
Indices: 269057--269166 Score: 87
Period size: 3 Copynumber: 36.7 Consensus size: 3
269047 TGGAGTGAAT
* * * * *
269057 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCA TCA TCA TCA TCA
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
* * * * * * * *
269105 TCA TCA TCC TCT TCT TCT TCC TCT TCC TCC TCC T-C TTC TTC TCCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC T-CC
269150 TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TC
269167 ATAATCCTCG
Statistics
Matches: 98, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
2 2 0.02
3 94 0.96
4 2 0.02
ACGTcount: A:0.06, C:0.55, G:0.00, T:0.39
Consensus pattern (3 bp):
TCC
Found at i:269306 original size:12 final size:12
Alignment explanation
Indices: 269289--269322 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
269279 ATCTTGCTCA
*
269289 CCTCTTCCTCTT
1 CCTCTTCATCTT
269301 CCTCTTCATCTT
1 CCTCTTCATCTT
*
269313 CCTCCTCATC
1 CCTCTTCATC
269323 GACAAAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.50, G:0.00, T:0.44
Consensus pattern (12 bp):
CCTCTTCATCTT
Found at i:270701 original size:18 final size:19
Alignment explanation
Indices: 270678--270728 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
270668 GATAAAAAAA
270678 ATATAAATATAAAT-AATT
1 ATATAAATATAAATAAATT
*
270696 ATATAAATAT-ATTAAATT
1 ATATAAATATAAATAAATT
*
270714 TTATATAATATAAAT
1 ATATA-AATATAAAT
270729 TTATTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 2 0.07
18 18 0.67
19 5 0.19
20 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAAATATAAATAAATT
Found at i:271222 original size:16 final size:17
Alignment explanation
Indices: 271192--271236 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
271182 ATAAATTAAT
271192 TATTAATATTATATAAA
1 TATTAATATTATATAAA
271209 TATTAATA-TATATAAA
1 TATTAATATTATATAAA
271225 T-TT-ATATTATAT
1 TATTAATATTATAT
271237 TATCGTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.11
15 7 0.26
16 9 0.33
17 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTAATATTATATAAA
Found at i:273104 original size:2 final size:2
Alignment explanation
Indices: 273097--273121 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
273087 TCCATAATTT
273097 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
273122 GTTTAGTTCT
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:274042 original size:16 final size:16
Alignment explanation
Indices: 274021--274052 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
274011 TCAAATTCGT
274021 TTTGGGTTTTTCAAGA
1 TTTGGGTTTTTCAAGA
*
274037 TTTGGGTTTTTGAAGA
1 TTTGGGTTTTTCAAGA
274053 CAAGTGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (16 bp):
TTTGGGTTTTTCAAGA
Found at i:275154 original size:28 final size:28
Alignment explanation
Indices: 275122--275180 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
275112 GTTAGTGTTC
275122 CAAAAATTTATCTTCTTCATAACACCTA
1 CAAAAATTTATCTTCTTCATAACACCTA
*
275150 CAAAAATTTATCTTCTTCATAACATCTA
1 CAAAAATTTATCTTCTTCATAACACCTA
275178 CAA
1 CAA
275181 CAACAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.36
Consensus pattern (28 bp):
CAAAAATTTATCTTCTTCATAACACCTA
Found at i:281314 original size:17 final size:17
Alignment explanation
Indices: 281294--281335 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
281284 AATTAAATTT
281294 TTATAAATAAAAAATAA
1 TTATAAATAAAAAATAA
281311 TTATAACAT-AAAAATAA
1 TTATAA-ATAAAAAATAA
281328 -TATAAATA
1 TTATAAATA
281336 TAATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.09
16 5 0.22
17 14 0.61
18 2 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TTATAAATAAAAAATAA
Found at i:281345 original size:11 final size:11
Alignment explanation
Indices: 281295--281348 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
281285 ATTAAATTTT
*
281295 TATAAATAAAA
1 TATAAATATAA
* *
281306 AATAATTATAA
1 TATAAATATAA
* *
281317 CATAAAAATAA
1 TATAAATATAA
281328 TATAAATATAA
1 TATAAATATAA
281339 TATAAATATA
1 TATAAATATA
281349 TAAAATTTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
TATAAATATAA
Found at i:281346 original size:17 final size:16
Alignment explanation
Indices: 281295--281348 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
281285 ATTAAATTTT
*
281295 TATAAATAAAAAATAAT
1 TATAAAT-AAAAATAAA
281312 TATAACATAAAAAT-AA
1 TATAA-ATAAAAATAAA
*
281328 TATAAATATAATATAAA
1 TATAAATA-AAAATAAA
281345 TATA
1 TATA
281349 TAAAATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 3 0.09
16 10 0.31
17 17 0.53
18 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
TATAAATAAAAATAAA
Found at i:283164 original size:6 final size:6
Alignment explanation
Indices: 283153--283178 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
283143 AGCAAACGGT
283153 TGAAAA TGAAAA TGAAAA TGAAAA TG
1 TGAAAA TGAAAA TGAAAA TGAAAA TG
283179 GGTTGGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAAAA
Found at i:289488 original size:2 final size:2
Alignment explanation
Indices: 289481--289515 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
289471 TCATAACAAA
289481 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
289516 CCTAGAGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:290714 original size:12 final size:12
Alignment explanation
Indices: 290697--290730 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
290687 AGGAGATGGA
290697 GCAGCGGCAGAG
1 GCAGCGGCAGAG
*
290709 GCAGCGGCAGGG
1 GCAGCGGCAGAG
*
290721 GCAGCAGCAG
1 GCAGCGGCAG
290731 CAGGGGCAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.50, T:0.00
Consensus pattern (12 bp):
GCAGCGGCAGAG
Found at i:290733 original size:15 final size:15
Alignment explanation
Indices: 290709--290744 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
290699 AGCGGCAGAG
*
290709 GCAGCGGCAGGGGCA
1 GCAGCAGCAGGGGCA
290724 GCAGCAGCAGGGGCA
1 GCAGCAGCAGGGGCA
290739 GCAGCA
1 GCAGCA
290745 ACTCCAGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.28, G:0.47, T:0.00
Consensus pattern (15 bp):
GCAGCAGCAGGGGCA
Found at i:293192 original size:20 final size:19
Alignment explanation
Indices: 293167--293215 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
293157 AATCAAACAT
*
293167 AAATAAACAAAGGATAAAGC
1 AAATAAACAAAGGA-AAAGA
* *
293187 AAATAAAAAAAATGAAAAGA
1 AAAT-AAACAAAGGAAAAGA
293207 AAATAAACA
1 AAATAAACA
293216 CAAGAACACA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.17
20 12 0.50
21 8 0.33
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.10
Consensus pattern (19 bp):
AAATAAACAAAGGAAAAGA
Found at i:296999 original size:61 final size:61
Alignment explanation
Indices: 296904--297026 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
296894 TTTTGGGTTT
*
296904 TGAATCCTAAGCCCAATCTGAACCCAATCTCCCAAATCAATTCGGCCCTATTGTTTCCTCC
1 TGAATCATAAGCCCAATCTGAACCCAATCTCCCAAATCAATTCGGCCCTATTGTTTCCTCC
296965 TGAATCATAAGCCCAATCTGAACCCAATCTCCCAAATCAATTCGGCCCTATTGTTTCCTCC
1 TGAATCATAAGCCCAATCTGAACCCAATCTCCCAAATCAATTCGGCCCTATTGTTTCCTCC
297026 T
1 T
297027 AAATGCCCTA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.27, C:0.35, G:0.10, T:0.28
Consensus pattern (61 bp):
TGAATCATAAGCCCAATCTGAACCCAATCTCCCAAATCAATTCGGCCCTATTGTTTCCTCC
Found at i:297458 original size:17 final size:17
Alignment explanation
Indices: 297436--297470 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
297426 TTAACATTTA
297436 TAATATTATTTTATTAT
1 TAATATTATTTTATTAT
*
297453 TAATATTTTTTTATTAT
1 TAATATTATTTTATTAT
297470 T
1 T
297471 GGGTTGCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TAATATTATTTTATTAT
Found at i:297674 original size:24 final size:23
Alignment explanation
Indices: 297639--297686 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
297629 TTGAATTATT
*
297639 ATTTATTAATAAAAAATTATTTAA
1 ATTTATTAAT-AAAAATTAATTAA
297663 ATTTAATT-ATAAAAATTAATTAA
1 ATTT-ATTAATAAAAATTAATTAA
297686 A
1 A
297687 ATAGTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 13 0.59
24 6 0.27
25 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTATTAATAAAAATTAATTAA
Found at i:307874 original size:6 final size:6
Alignment explanation
Indices: 307865--307890 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
307855 CCACATAAGC
307865 GCTAAT GCTAAT GCTAAT GCTAAT GC
1 GCTAAT GCTAAT GCTAAT GCTAAT GC
307891 CGATGCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (6 bp):
GCTAAT
Found at i:309294 original size:32 final size:32
Alignment explanation
Indices: 309258--309343 Score: 113
Period size: 31 Copynumber: 2.7 Consensus size: 32
309248 TAATAAAAAT
*
309258 TAATATAAATATTTTAAATTTTAAATTTTATA
1 TAATATAAATATTTTAAATTTTAAAATTTATA
*
309290 TAATA-AAA-ATTATTAAATATTAAAATTTATA
1 TAATATAAATATT-TTAAATTTTAAAATTTATA
309321 TAAATATAAAATATTTTAAATTT
1 T-AATAT-AAATATTTTAAATTT
309344 AATTATATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
30 3 0.07
31 21 0.46
32 9 0.20
34 10 0.22
35 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TAATATAAATATTTTAAATTTTAAAATTTATA
Found at i:309378 original size:64 final size:61
Alignment explanation
Indices: 309259--309387 Score: 140
Period size: 64 Copynumber: 2.0 Consensus size: 61
309249 AATAAAAATT
* *
309259 AATATAAATATTTTAAATTTTAAATTTTATATAATAAAAATTATTAAATATTAAAATTTATATA
1 AATATAAATATTTTAAATTTTAAATTATATATAATAAAAATAATT-AATATTAAAA--TATATA
309323 AATATAAAATATTTTAAA-TTT-AATTATATTATAATAAATACATAATT-ATGA-TAAAATATAT
1 AATAT-AAATATTTTAAATTTTAAATTATA-TATAATAAA-A-ATAATTAAT-ATTAAAATATAT
309384 A
61 A
309385 AAT
1 AAT
309388 TATTAGGTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
62 9 0.16
63 6 0.10
64 24 0.41
65 14 0.24
66 5 0.09
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (61 bp):
AATATAAATATTTTAAATTTTAAATTATATATAATAAAAATAATTAATATTAAAATATATA
Found at i:311108 original size:9 final size:10
Alignment explanation
Indices: 311079--311140 Score: 63
Period size: 11 Copynumber: 6.0 Consensus size: 10
311069 TTTTAATTAT
311079 ATAATATATAA
1 ATAATATA-AA
*
311090 TTAATATAAA
1 ATAATATAAA
311100 ATAAT-TAAA
1 ATAATATAAA
311109 ATAATATAAAA
1 ATAATAT-AAA
*
311120 ATTATATAAAA
1 ATAATAT-AAA
*
311131 ATTATATAAA
1 ATAATATAAA
311141 CATTTAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
9 9 0.20
10 10 0.22
11 27 0.59
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATAATATAAA
Found at i:311173 original size:13 final size:14
Alignment explanation
Indices: 311073--311174 Score: 61
Period size: 14 Copynumber: 7.0 Consensus size: 14
311063 GGTTTTTTTT
311073 AATTATATAATATA
1 AATTATATAATATA
*
311087 TAATTAATATAAAAT-
1 -AATT-ATATAATATA
*
311102 AATTAAAATAATATAAA
1 AATT-ATATAATAT--A
311119 AATTATAT-A-A-A
1 AATTATATAATATA
*
311130 AATTATATAAACATTTAA
1 AATTATAT--A-ATAT-A
311148 AATTATATAATATA
1 AATTATATAATATA
311162 AATTAT-TAATATA
1 AATTATATAATATA
311175 TTAAAATATA
Statistics
Matches: 70, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
11 9 0.13
13 7 0.10
14 20 0.29
15 9 0.13
16 12 0.17
17 4 0.06
18 9 0.13
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTATATAATATA
Found at i:314066 original size:18 final size:18
Alignment explanation
Indices: 314040--314075 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
314030 GCTGGTTGAA
314040 AAAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAAGAAAAG
* *
314058 AAAAGAAAAAAAGGAAAG
1 AAAAAAAAAAAAGAAAAG
314076 CAATAAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAGAAAAG
Found at i:317366 original size:16 final size:15
Alignment explanation
Indices: 317347--317379 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
317337 TTTATCATTT
317347 AATTAATTAATTTATA
1 AATTAATTAATTT-TA
317363 AATTAATTAATTTTA
1 AATTAATTAATTTTA
317378 AA
1 AA
317380 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAATTAATTTTA
Found at i:317486 original size:17 final size:17
Alignment explanation
Indices: 317465--317512 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
317455 AATATATTTA
317465 TTTATATATTTTT-ATG
1 TTTATATATTTTTAATG
317481 TATTATAATTATTTTTAATG
1 T-TTAT-A-TATTTTTAATG
317501 TTTAATATATTT
1 TTT-ATATATTT
317513 AATATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.04
17 4 0.15
18 6 0.22
19 10 0.37
20 6 0.22
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTATATATTTTTAATG
Found at i:317572 original size:24 final size:23
Alignment explanation
Indices: 317519--317575 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
317509 ATTTAATATA
* *
317519 TTAATAATATATATTATATAATT
1 TTAATATTACATATTATATAATT
*
317542 TTAAATATTACATATGTATATTATT
1 TT-AATATTACATAT-TATATAATT
317567 TTAATATTA
1 TTAATATTA
317576 TCTAAATCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 17 0.59
25 10 0.34
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAATATTACATATTATATAATT
Found at i:318027 original size:22 final size:21
Alignment explanation
Indices: 318005--318061 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
317995 TTATATCTTA
318005 AATATATATTAAAATAATATT
1 AATATATATTAAAATAATATT
*
318026 AATATTATATTAAAAAAATA-T
1 AATA-TATATTAAAATAATATT
*
318047 AATAAATATTAAAAT
1 AATATATATTAAAAT
318062 TATGTTCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.28
21 9 0.28
22 14 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATATATTAAAATAATATT
Found at i:318922 original size:14 final size:16
Alignment explanation
Indices: 318905--318941 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
318895 ACATATTCGG
318905 ATATAAATA-TTAAA-
1 ATATAAATAGTTAAAT
*
318919 ATATAATTAGTTAAAT
1 ATATAAATAGTTAAAT
318935 ATATAAA
1 ATATAAA
318942 AATTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 8 0.42
15 5 0.26
16 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATAAATAGTTAAAT
Found at i:319521 original size:20 final size:21
Alignment explanation
Indices: 319496--319541 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
319486 TATTTTTATT
319496 TATTATA-A-TTATATTTAAAA
1 TATTATATATTTAT-TTTAAAA
*
319516 TATTATATATTTATTTTAATA
1 TATTATATATTTATTTTAAAA
319537 TATTA
1 TATTA
319542 ATAAAACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 12 0.52
22 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTATATATTTATTTTAAAA
Found at i:319538 original size:16 final size:16
Alignment explanation
Indices: 319492--319539 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
319482 TATATATTTT
319492 TATTTATTATAAT-TA
1 TATTTATTATAATATA
** *
319507 TATTTAAAATATTATA
1 TATTTATTATAATATA
*
319523 TATTTATTTTAATATA
1 TATTTATTATAATATA
319539 T
1 T
319540 TAATAAAACT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTATTATAATATA
Found at i:319539 original size:21 final size:19
Alignment explanation
Indices: 319486--319541 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
319476 TTTAATTATA
* *
319486 TATTTTTATTTATTATAAT
1 TATTTTAATATATTATAAT
*
319505 TATATTTAAAATATTATATATT
1 TAT-TTTAATATATTATA-A-T
319527 TATTTTAATATATTA
1 TATTTTAATATATTA
319542 ATAAAACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.10
20 11 0.37
21 12 0.40
22 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTAATATATTATAAT
Found at i:319596 original size:14 final size:16
Alignment explanation
Indices: 319565--319597 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
319555 TATTTAAATA
319565 ATTTTGTTATATTTAT
1 ATTTTGTTATATTTAT
319581 ATTTT-TTATA-TTAT
1 ATTTTGTTATATTTAT
319595 ATT
1 ATT
319598 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 5 0.29
16 5 0.29
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
ATTTTGTTATATTTAT
Found at i:319601 original size:19 final size:20
Alignment explanation
Indices: 319571--319637 Score: 90
Period size: 18 Copynumber: 3.6 Consensus size: 20
319561 AATAATTTTG
319571 TTATATTTATATTTTTTATA
1 TTATATTTATATTTTTTATA
319591 TTATA-TTATA-TTTTTA-A
1 TTATATTTATATTTTTTATA
*
319608 TTAAATTT-TATTTTTT-TA
1 TTATATTTATATTTTTTATA
319626 TTATATTTATAT
1 TTATATTTATAT
319638 CAAATAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 7 0.17
18 21 0.51
19 8 0.20
20 5 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATATTTATATTTTTTATA
Found at i:319646 original size:37 final size:36
Alignment explanation
Indices: 319575--319657 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 36
319565 ATTTTGTTAT
***
319575 ATTTATATTTTTTATATTATATTATATTTTTAATTAA
1 ATTT-TATTTTTTATATTATATTATATAAATAATTAA
*
319612 ATTTTATTTTTT-TATTATATTTATATCAAATAATTAT
1 ATTTTATTTTTTATATTATA-TTATAT-AAATAATTAA
*
319649 ATTATATTT
1 ATTTTATTT
319658 AAAATTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
35 7 0.18
36 14 0.36
37 18 0.46
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (36 bp):
ATTTTATTTTTTATATTATATTATATAAATAATTAA
Found at i:319885 original size:20 final size:20
Alignment explanation
Indices: 319846--319885 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
319836 ATAATATATT
*
319846 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
319866 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
319886 TTTAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:319912 original size:31 final size:33
Alignment explanation
Indices: 319876--319937 Score: 110
Period size: 32 Copynumber: 1.9 Consensus size: 33
319866 ATATTATATA
319876 TTTATATAAA-TTTAATATATTAATA-ATTTCT
1 TTTATATAAATTTTAATATATTAATATATTTCT
319907 TTTATATAAATTTTAATATATTAATATATTT
1 TTTATATAAATTTTAATATATTAATATATTT
319938 AATTCTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 10 0.34
32 15 0.52
33 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (33 bp):
TTTATATAAATTTTAATATATTAATATATTTCT
Found at i:320135 original size:3 final size:3
Alignment explanation
Indices: 320122--320157 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
320112 CAAGATTTAG
*
320122 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
320158 ATTCTTGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:321129 original size:30 final size:31
Alignment explanation
Indices: 321085--321145 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
321075 ATTTAATTAA
* *
321085 AAATATTAATATTAAT-ATAAAATAA-TATTT
1 AAATAATAAAATTAATAAT-AAATAACTATTT
321115 AAATAATAAAATTAATAATAAATAACTATTT
1 AAATAATAAAATTAATAATAAATAACTATTT
321146 TAGGTCGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
AAATAATAAAATTAATAATAAATAACTATTT
Found at i:321136 original size:19 final size:19
Alignment explanation
Indices: 321089--321139 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
321079 AATTAAAAAT
*
321089 ATTAAT-ATTAAT-ATAAA
1 ATTAATAATAAATAATAAA
*
321106 A-TAATATTTAAATAATAAA
1 ATTAATA-ATAAATAATAAA
321125 ATTAATAATAAATAA
1 ATTAATAATAAATAA
321140 CTATTTTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 4 0.15
17 1 0.04
18 4 0.15
19 13 0.48
20 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTAATAATAAATAATAAA
Found at i:321249 original size:15 final size:17
Alignment explanation
Indices: 321231--321270 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
321221 GATATATAAA
321231 AAAATTAT-AAAT-ATT
1 AAAATTATAAAATAATT
321246 AAAATT-TAAAATAATT
1 AAAATTATAAAATAATT
321262 AAATATTAT
1 AAA-ATTAT
321271 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 10 0.48
16 6 0.29
17 3 0.14
18 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTATAAAATAATT
Found at i:331361 original size:12 final size:10
Alignment explanation
Indices: 331333--331357 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
331323 CATCCTAAAA
331333 TTTTTAATAT
1 TTTTTAATAT
331343 TTTTTAATAT
1 TTTTTAATAT
331353 TTTTT
1 TTTTT
331358 TTAAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:332517 original size:21 final size:21
Alignment explanation
Indices: 332476--332518 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
332466 ATGGTGAAAG
* *
332476 TGATGAGATTAATTATTATAA
1 TGATAAGATTAATAATTATAA
332497 TGATAAGATTAA-AATTAATAA
1 TGATAAGATTAATAATT-ATAA
332518 T
1 T
332519 AAATTATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (21 bp):
TGATAAGATTAATAATTATAA
Found at i:332614 original size:27 final size:28
Alignment explanation
Indices: 332576--332628 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
332566 ATTTTGAGAA
332576 AAAAATAAATATTAA-AAAT-ATTAAATT
1 AAAAATAAATA-TAATAAATAATTAAATT
*
332603 AAAAATATATATAATAAATAATTAAA
1 AAAAATAAATATAATAAATAATTAAA
332629 ATTATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 14 0.61
28 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAAATAAATATAATAAATAATTAAATT
Found at i:332648 original size:23 final size:23
Alignment explanation
Indices: 332593--332649 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
332583 AATATTAAAA
332593 ATATT-AAATTAAAAATATATAT
1 ATATTAAAATTAAAAATATATAT
* * *
332615 A-ATAAATAATTAAAATTATATTT
1 ATATTAA-AATTAAAAATATATAT
332638 ATATTAAAATTA
1 ATATTAAAATTA
332650 GATTAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 2 0.07
22 2 0.07
23 20 0.71
24 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATTAAAATTAAAAATATATAT
Found at i:332658 original size:17 final size:17
Alignment explanation
Indices: 332623--332658 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
332613 ATAATAAATA
* *
332623 ATTAAAATTATATTTAT
1 ATTAAAATTAGATTAAT
332640 ATTAAAATTAGATTAAT
1 ATTAAAATTAGATTAAT
332657 AT
1 AT
332659 AAATAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTAAAATTAGATTAAT
Found at i:333071 original size:23 final size:21
Alignment explanation
Indices: 333044--333100 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 21
333034 TTAATATATT
333044 TTATATTTATATAAATTTTAAA
1 TTATATTTATATAAATTTT-AA
*
333066 TATATATTTATATTATATTTTAA
1 T-TATATTTATA-TAAATTTTAA
333089 TTAT-TTTATATA
1 TTATATTTATATA
333101 TATATATCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.06
21 6 0.19
22 4 0.12
23 13 0.41
24 7 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATTTATATAAATTTTAA
Found at i:333082 original size:11 final size:11
Alignment explanation
Indices: 333002--333105 Score: 50
Period size: 11 Copynumber: 9.8 Consensus size: 11
332992 AAGTTTAATA
333002 ATATGTATATTT
1 ATAT-TATATTT
333014 -TATTATATTT
1 ATATTATATTT
333024 -TAATTATGATTT
1 AT-ATTAT-ATTT
333036 A-A-TATA--T
1 ATATTATATTT
333043 -T-TTATATTT
1 ATATTATATTT
*
333052 ATA-TAAATTTT
1 ATATTATA-TTT
*
333063 AAATATATATTT
1 ATAT-TATATTT
333075 ATATTATATTT
1 ATATTATATTT
333086 -TAATTAT-TTT
1 AT-ATTATATTT
333096 ATATATATAT
1 ATAT-TATAT
333106 ATCATAATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 32
0.67 0.04 0.30
Matches are distributed among these distances:
7 5 0.07
9 2 0.03
10 21 0.29
11 30 0.42
12 11 0.15
13 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
ATATTATATTT
Found at i:333115 original size:21 final size:18
Alignment explanation
Indices: 333037--333136 Score: 59
Period size: 17 Copynumber: 5.7 Consensus size: 18
333027 TTATGATTTA
*
333037 ATAT-ATTTTATATTTAT
1 ATATAATTTTATAATTAT
333054 ATA-AATTTTA-AA-TAT
1 ATATAATTTTATAATTAT
* * *
333069 ATATTTATATTAT-ATTTT
1 ATA-TAATTTTATAATTAT
*
333087 A-ATTATTTTATATATATAT
1 ATATAATTTTATA-AT-TAT
*
333106 ATCATAATTTTGTAATTAT
1 AT-ATAATTTTATAATTAT
*
333125 ATATAATATTAT
1 ATATAATTTTAT
333137 TTCATTTTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
15 6 0.10
16 9 0.14
17 16 0.25
18 13 0.21
19 8 0.13
20 2 0.03
21 9 0.14
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (18 bp):
ATATAATTTTATAATTAT
Found at i:338927 original size:30 final size:30
Alignment explanation
Indices: 338875--338932 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
338865 AAACTAAAAT
* * *
338875 TTCAAACGATATTTTTTTACATATTTAAGA
1 TTCAAACGAAATTCTTTCACATATTTAAGA
*
338905 TTCAAATGAAATTCTTTCACATATTTAA
1 TTCAAACGAAATTCTTTCACATATTTAA
338933 ATATTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (30 bp):
TTCAAACGAAATTCTTTCACATATTTAAGA
Found at i:345521 original size:2 final size:2
Alignment explanation
Indices: 345516--345558 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
345506 TTTATGCGTT
345516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
345558 T
1 T
345559 TCTAGGGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:354796 original size:17 final size:17
Alignment explanation
Indices: 354774--354806 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
354764 AAAAAACCAG
*
354774 AAATATGAATAAAATAT
1 AAATATAAATAAAATAT
354791 AAATATAAATAAAATA
1 AAATATAAATAAAATA
354807 CCTTTCCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
AAATATAAATAAAATAT
Found at i:355411 original size:2 final size:2
Alignment explanation
Indices: 355399--355430 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
355389 GGACCATGTT
*
355399 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
355431 CTTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:356294 original size:11 final size:11
Alignment explanation
Indices: 356261--356301 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
356251 TTGGTTTGTA
356261 ATTTAAATTTT
1 ATTTAAATTTT
*
356272 -TTTAATTTTT
1 ATTTAAATTTT
*
356282 ATTCAAATTTT
1 ATTTAAATTTT
356293 ATTTAAATT
1 ATTTAAATT
356302 AACTCATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTTAAATTTT
Found at i:358861 original size:2 final size:2
Alignment explanation
Indices: 358856--358882 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
358846 TATATATATA
358856 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
358883 ACATATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:359593 original size:20 final size:21
Alignment explanation
Indices: 359568--359615 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
359558 GTTTATAATT
*
359568 TTTTTACATTAAA-AAAATAA
1 TTTTTAAATTAAATAAAATAA
*
359588 TTTTTAAATTAAATAAAATTA
1 TTTTTAAATTAAATAAAATAA
*
359609 TATTTAA
1 TTTTTAA
359616 TAATTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTTAAATTAAATAAAATAA
Found at i:359614 original size:21 final size:20
Alignment explanation
Indices: 359570--359615 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
359560 TTATAATTTT
* *
359570 TTTACATTAAAAAAATAATT
1 TTTAAATTAAAAAAATAATA
*
359590 TTTAAATTAAATAAAATTATA
1 TTTAAATTAAA-AAAATAATA
359611 TTTAA
1 TTTAA
359616 TAATTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAAATTAAAAAAATAATA
Found at i:359638 original size:13 final size:13
Alignment explanation
Indices: 359605--359688 Score: 64
Period size: 14 Copynumber: 6.1 Consensus size: 13
359595 ATTAAATAAA
359605 ATTATATTTA-AT
1 ATTATATTTATAT
359617 AATTAATATCTT-TAT
1 -ATT-ATAT-TTATAT
359632 ATTATATTTATAT
1 ATTATATTTATAT
*
359645 ATTTTTATTTATTAT
1 A-TTATATTTA-TAT
*
359660 AATTATATTTAAAAT
1 -ATTATATTT-ATAT
*
359675 TTTATATTTATAT
1 ATTATATTTATAT
359688 A
1 A
359689 AATTTTAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
12 2 0.04
13 14 0.25
14 23 0.40
15 16 0.28
16 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTATATTTATAT
Found at i:359651 original size:21 final size:22
Alignment explanation
Indices: 359615--359667 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
359605 ATTATATTTA
359615 ATAATTA-ATATCTTTA-TATT
1 ATAATTATATATCTTTATTATT
* *
359635 ATATTTATATATTTTTATTTATT
1 ATAATTATATATCTTTA-TTATT
359658 ATAATTATAT
1 ATAATTATAT
359668 TTAAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.22
21 8 0.30
23 13 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATAATTATATATCTTTATTATT
Found at i:359665 original size:23 final size:21
Alignment explanation
Indices: 359606--359667 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
359596 TTAAATAAAA
359606 TTATATTTAATAATTA-ATATCT
1 TTATA-TT-ATAATTATATATCT
* *
359628 TTATATTATATTTATATATTT
1 TTATATTATAATTATATATCT
359649 TTATTTATTATAATTATAT
1 TTA--TATTATAATTATAT
359668 TTAAAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 6 0.18
21 10 0.29
22 5 0.15
23 13 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATATTATAATTATATATCT
Found at i:359669 original size:29 final size:29
Alignment explanation
Indices: 359604--359689 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 29
359594 AATTAAATAA
* *
359604 AATTATATTTAATAA-TTAATATCT-TTAT
1 AATTATATTTAA-AATTTTATATTTATTAT
*
359632 -ATTATATTTATATATTTT-TATTTATTAT
1 AATTATATTTA-AAATTTTATATTTATTAT
359660 AATTATATTTAAAATTTTATATTTA-TAT
1 AATTATATTTAAAATTTTATATTTATTAT
359688 AA
1 AA
359690 ATTTTAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
27 15 0.31
28 18 0.37
29 16 0.33
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (29 bp):
AATTATATTTAAAATTTTATATTTATTAT
Found at i:359692 original size:29 final size:29
Alignment explanation
Indices: 359603--359692 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
359593 AAATTAAATA
*
359603 AAATTATATTTAATAA-TTAATATCTT-TAT
1 AAATTATATTTAA-AATTTTATAT-TTATAT
*
359632 --ATTATATTTATATATTTT-TATTTAT-T
1 AAATTATATTTA-AAATTTTATATTTATAT
359658 ATAATTATATTTAAAATTTTATATTTATAT
1 A-AATTATATTTAAAATTTTATATTTATAT
359688 AAATT
1 AAATT
359693 TTAATATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
26 3 0.06
27 15 0.30
28 9 0.18
29 21 0.42
30 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (29 bp):
AAATTATATTTAAAATTTTATATTTATAT
Found at i:359695 original size:25 final size:28
Alignment explanation
Indices: 359607--359703 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 28
359597 TAAATAAAAT
* * *
359607 TATATTTAATAA-TTAATATCT-TTATAT
1 TATATTTAA-AATTTTATATTTATTATAA
*
359634 TATATTTATATATTTT-TATTTATTATAA
1 TATATTTA-AAATTTTATATTTATTATAA
359662 TTATATTTAAAATTTTATATTTA-TATAA
1 -TATATTTAAAATTTTATATTTATTATAA
*
359690 -AT-TTTAATATTTTA
1 TATATTTAAAATTTTA
359704 ACAATTTATA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
25 11 0.19
26 2 0.03
27 13 0.22
28 19 0.32
29 14 0.24
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
TATATTTAAAATTTTATATTTATTATAA
Found at i:359699 original size:18 final size:17
Alignment explanation
Indices: 359633--359727 Score: 63
Period size: 14 Copynumber: 6.2 Consensus size: 17
359623 TATCTTTATA
359633 TTATATTTATAT--ATT
1 TTATATTTATATAAATT
359648 TT-TATTTAT-TATAA--
1 TTATATTTATATA-AATT
359662 TTATA-TT-TA-AAATT
1 TTATATTTATATAAATT
359676 TTATATTTATATAAATT
1 TTATATTTATATAAATT
359693 TTAATATTT-TA-ACAA-T
1 TT-ATATTTATATA-AATT
*
359709 TTATA-TTATATTAATT
1 TTATATTTATATAAATT
359725 TTA
1 TTA
359728 ATAATTTAGA
Statistics
Matches: 64, Mismatches: 1, Indels: 29
0.68 0.01 0.31
Matches are distributed among these distances:
12 2 0.03
13 3 0.05
14 18 0.28
15 13 0.20
16 11 0.17
17 11 0.17
18 6 0.09
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:359718 original size:32 final size:33
Alignment explanation
Indices: 359666--359735 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
359656 TTATAATTAT
359666 ATTTAAAATTTTATATTTATATAAATTTTAATA
1 ATTTAAAATTTTATATTTATATAAATTTTAATA
* *
359699 TTTTAACAA-TTTATA-TTATATTAATTTTAATA
1 ATTTAA-AATTTTATATTTATATAAATTTTAATA
359731 ATTTA
1 ATTTA
359736 GATATATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 20 0.61
33 11 0.33
34 2 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (33 bp):
ATTTAAAATTTTATATTTATATAAATTTTAATA
Found at i:360282 original size:2 final size:2
Alignment explanation
Indices: 360275--360301 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
360265 ACAGTACCCT
360275 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
360302 GAATAGTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:360693 original size:2 final size:2
Alignment explanation
Indices: 360686--360722 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
360676 CTGTGGTCAG
360686 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
360723 ATATGGAACT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:367178 original size:20 final size:20
Alignment explanation
Indices: 367153--367222 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
367143 AATATATATT
367153 TAATAAATATAAAATTAATA
1 TAATAAATATAAAATTAATA
* * * *
367173 TAATAAACATCATA-TATATT
1 TAATAAATATAAAATTA-ATA
367193 TAATAAATATAAAATTAATA
1 TAATAAATATAAAATTAATA
367213 TAATAAATAT
1 TAATAAATAT
367223 CACATAATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.05
20 36 0.90
21 2 0.05
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATAAATATAAAATTAATA
Found at i:367188 original size:40 final size:40
Alignment explanation
Indices: 367144--367232 Score: 153
Period size: 40 Copynumber: 2.2 Consensus size: 40
367134 CGACGTAAAA
367144 ATATATATTTAATAAATATAAAATTAATATAATAAACATC
1 ATATATATTTAATAAATATAAAATTAATATAATAAACATC
*
367184 ATATATATTTAATAAATATAAAATTAATATAATAAATATC
1 ATATATATTTAATAAATATAAAATTAATATAATAAACATC
*
367224 ACATA-ATTT
1 ATATATATTT
367233 TTTGTTAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 4 0.09
40 43 0.91
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.39
Consensus pattern (40 bp):
ATATATATTTAATAAATATAAAATTAATATAATAAACATC
Found at i:368611 original size:180 final size:179
Alignment explanation
Indices: 368224--368662 Score: 535
Period size: 180 Copynumber: 2.4 Consensus size: 179
368214 TTAAAATGTA
* *
368224 AACTGCATTATAGGCTATTTGTTTTGGTGCAAGTAGTGATCTTTGTCAACC-ACCTAAAACAAAA
1 AACTGCATTATAGGCTATTTGTTTTGGTGCAAGTAGTGATCTTTCTCAACCAACC-AAAACAGAA
* * *
368288 TGGCATCCAAAGCACAATCGAAGAATGCATTCATCCATGGATATAGCGCACTTATTATTCAGGAA
65 TGGCATACAAAGCACAATCAAAGAATGCATCCATCCATGGATATAGCGCACTTATTATTCAGGAA
* * *
368353 CAATCATGAATCATTAAGAATCACAGGTTAAGCAAATTATCAGAACAACAT
130 CAATCATGAATCACTAAGAAGCACAGGTTAAGCAAA-TACCAGAACAACAT
* * * *
368404 AACTGCATTATTGGCTATTTGTTTTGGTACAAGTATTAATCTTTCTCAACCAACCAAAACAGAAT
1 AACTGCATTATAGGCTATTTGTTTTGGTGCAAGTAGTGATCTTTCTCAACCAACCAAAACAGAAT
* * * * *
368469 GGCATTCAAAGCACAATCAAAGAATGTATCCTTCCATGGATCTAGCGCAGTTATTATTCAGGAAC
66 GGCATACAAAGCACAATCAAAGAATGCATCCATCCATGGATATAGCGCACTTATTATTCAGGAAC
* ** * ** *
368534 AATGATGAATTGCTAAGAAGCACGGGTTAAGC-AA-ACCATTACAATAT
131 AATCATGAATCACTAAGAAGCACAGGTTAAGCAAATACCAGAACAACAT
* * * *
368581 AACTGCATTATAGGCTATTTGTTTTTTTGGTGCAAGTAGTGGTCTCTCACAACCCAA-CTAAACA
1 AACTGCATTATAGGCTATTTG---TTTTGGTGCAAGTAGTGATCTTTCTCAA-CCAACCAAAACA
*
368645 GAAAGGCATACAAAGCAC
62 GAATGGCATACAAAGCAC
368663 GAACCAACAA
Statistics
Matches: 221, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
177 29 0.13
179 2 0.01
180 183 0.83
181 7 0.03
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (179 bp):
AACTGCATTATAGGCTATTTGTTTTGGTGCAAGTAGTGATCTTTCTCAACCAACCAAAACAGAAT
GGCATACAAAGCACAATCAAAGAATGCATCCATCCATGGATATAGCGCACTTATTATTCAGGAAC
AATCATGAATCACTAAGAAGCACAGGTTAAGCAAATACCAGAACAACAT
Found at i:372400 original size:3 final size:3
Alignment explanation
Indices: 372394--372420 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
372384 GCGATTAAGG
372394 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
372421 CTAATTAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:372598 original size:20 final size:18
Alignment explanation
Indices: 372573--372638 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 18
372563 ATTCATGATA
372573 ATTTATATAATTATATTAAT
1 ATTTAT-TAATTATA-TAAT
*
372593 ATTTATTAAATATATAAT
1 ATTTATTAATTATATAAT
*
372611 -TTTAATTTTAATTTTATAAT
1 ATTT-A--TTAATTATATAAT
372631 ATTTATTA
1 ATTTATTA
372639 TTTTTAAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.08
18 8 0.21
19 7 0.18
20 18 0.46
21 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTATTAATTATATAAT
Found at i:373174 original size:16 final size:16
Alignment explanation
Indices: 373149--373188 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
373139 TAATATAATC
*
373149 ATTTAATTCATTAAAT
1 ATTTAATTCATGAAAT
*
373165 ATTTATTTCATGAAAT
1 ATTTAATTCATGAAAT
*
373181 AATTAATT
1 ATTTAATT
373189 TTAATCTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTAATTCATGAAAT
Found at i:378155 original size:15 final size:16
Alignment explanation
Indices: 378137--378169 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
378127 AAATTAATTT
378137 ATAA-TAATTTAAAAA
1 ATAATTAATTTAAAAA
*
378152 ATAATTAATTTTAAAA
1 ATAATTAATTTAAAAA
378168 AT
1 AT
378170 TTTTATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATTAATTTAAAAA
Found at i:378243 original size:6 final size:6
Alignment explanation
Indices: 378232--378259 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
378222 ATCTTAGATC
378232 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
378260 ATACCAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:379380 original size:14 final size:14
Alignment explanation
Indices: 379363--379389 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
379353 AATTTAATTA
379363 TTTTTTATAATATT
1 TTTTTTATAATATT
379377 TTTTTTATAATAT
1 TTTTTTATAATAT
379390 CATTATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTATAATATT
Found at i:379741 original size:25 final size:25
Alignment explanation
Indices: 379695--379742 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
379685 TTTAATATGA
* *
379695 ATATATTTAAAATTTTTAATTTTTT
1 ATATATTTAAAAATTATAATTTTTT
379720 ATATATTTAAAAAATTAT-ATTTT
1 ATATATTT-AAAAATTATAATTTT
379743 AATATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATATTTAAAAATTATAATTTTTT
Found at i:384157 original size:25 final size:28
Alignment explanation
Indices: 384129--384184 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
384119 TAATTATTAA
384129 TTAAAAAA-T-TATTTAAT-TATAATTT
1 TTAAAAAATTATATTTAATATATAATTT
*
384154 TTAAAAAATTATATTTAATATATTATTT
1 TTAAAAAATTATATTTAATATATAATTT
384182 TTA
1 TTA
384185 TTAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.30
26 1 0.04
27 8 0.30
28 10 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAAAAAATTATATTTAATATATAATTT
Found at i:384181 original size:39 final size:38
Alignment explanation
Indices: 384136--384232 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 38
384126 TAATTAAAAA
*
384136 ATTATTTAATTATAATTTTTAAAAAAT-TATATTTAATAT
1 ATTATTTAATTATAATTTTTAAAAAATATATA-CTAAT-T
*
384175 ATTATTTTTATTA-AATTTTTAAAAAATATATACTAATT
1 ATTA-TTTAATTATAATTTTTAAAAAATATATACTAATT
* *
384213 ATTTTTTAATATATCATTTT
1 ATTATTTAAT-TATAATTTT
384233 AACCAACATC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
37 5 0.10
38 6 0.12
39 27 0.55
40 11 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (38 bp):
ATTATTTAATTATAATTTTTAAAAAATATATACTAATT
Found at i:384779 original size:16 final size:18
Alignment explanation
Indices: 384758--384804 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
384748 TAAATTTTAT
384758 TTAAACAT-ATAATAAC-
1 TTAAACATAATAATAACA
*
384774 TTAAACATAATTATAACA
1 TTAAACATAATAATAACA
384792 TTAAA-A-AATAATA
1 TTAAACATAATAATA
384805 CAATTATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 14 0.52
17 8 0.30
18 5 0.19
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAAACATAATAATAACA
Found at i:386186 original size:15 final size:15
Alignment explanation
Indices: 386104--386176 Score: 62
Period size: 15 Copynumber: 5.0 Consensus size: 15
386094 TTACTCGATT
*
386104 TAAA-AAAATAATTA
1 TAAATAAAATAAATA
* *
386118 AAAATAATATAAATA
1 TAAATAAAATAAATA
* * *
386133 TAATGTTATATAAA-A
1 TAA-ATAAAATAAATA
386148 -AAATAAAATAAATA
1 TAAATAAAATAAATA
386162 TAAATAAAATAAATA
1 TAAATAAAATAAATA
386177 GTATTAAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
13 7 0.15
14 6 0.13
15 25 0.54
16 8 0.17
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (15 bp):
TAAATAAAATAAATA
Found at i:386216 original size:22 final size:22
Alignment explanation
Indices: 386165--386217 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
386155 ATAAATATAA
386165 ATAAAATAAATAGTATTAAAATTT
1 ATAAAATAAATAGTATTAAAA--T
* *
386189 ATAATATAAAT--TATTAATAT
1 ATAAAATAAATAGTATTAAAAT
386209 ATAAAATAA
1 ATAAAATAA
386218 TATAATACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.35
22 7 0.27
24 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAAAATAAATAGTATTAAAAT
Found at i:386217 original size:20 final size:21
Alignment explanation
Indices: 386165--386285 Score: 67
Period size: 22 Copynumber: 5.8 Consensus size: 21
386155 ATAAATATAA
*
386165 ATAAAATA-AATAGTATTAAAAT
1 ATAAAATATAAT--TATTAATAT
* *
386187 TTATAATATAAATTATTAATAT
1 ATAAAATAT-AATTATTAATAT
*
386209 AT-AAA-ATAA-TA-TAATAC
1 ATAAAATATAATTATTAATAT
* *
386226 ATTAAATATAATTA-TAATAC
1 ATAAAATATAATTATTAATAT
**
386246 ATGAAAATATAAAAATATAATAT
1 AT-AAAATATAATTAT-TAATAT
386269 A-AAAATATTAATTATTA
1 ATAAAATA-TAATTATTA
386286 GATTCCAAAC
Statistics
Matches: 78, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
17 7 0.09
18 5 0.06
19 6 0.08
20 12 0.15
21 19 0.24
22 20 0.26
23 6 0.08
24 3 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAAAATATAATTATTAATAT
Found at i:386232 original size:17 final size:20
Alignment explanation
Indices: 386191--386257 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
386181 TAAAATTTAT
*
386191 AATATAAATTATTAATATA-TA
1 AATAT-AATTA-TAATACATTA
386212 AA-ATAA-TATAATACATTA
1 AATATAATTATAATACATTA
*
386230 AATATAATTATAATACATGAA
1 AATATAATTATAATACAT-TA
386251 AATATAA
1 AATATAA
386258 AAATATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 6 0.15
18 6 0.15
19 6 0.15
20 12 0.30
21 10 0.25
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (20 bp):
AATATAATTATAATACATTA
Done.