Multiple sequence alignment - TraesCS2A01G479700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G479700 chr2A 100.000 2609 0 0 1 2609 717879543 717876935 0.000000e+00 4819.0
1 TraesCS2A01G479700 chr2A 76.829 246 53 4 1105 1348 702194070 702193827 4.530000e-28 135.0
2 TraesCS2A01G479700 chr2A 92.473 93 7 0 1636 1728 123533358 123533266 1.630000e-27 134.0
3 TraesCS2A01G479700 chr2A 87.755 98 12 0 1631 1728 320199194 320199291 5.900000e-22 115.0
4 TraesCS2A01G479700 chr2A 92.982 57 4 0 1204 1260 702246232 702246176 1.660000e-12 84.2
5 TraesCS2A01G479700 chr2D 90.934 1103 76 15 537 1631 580004423 580003337 0.000000e+00 1461.0
6 TraesCS2A01G479700 chr2D 92.292 480 26 3 2140 2609 580001347 580000869 0.000000e+00 671.0
7 TraesCS2A01G479700 chr2D 87.269 487 38 11 2129 2597 559294809 559294329 3.820000e-148 534.0
8 TraesCS2A01G479700 chr2D 95.294 170 7 1 203 372 580004595 580004427 4.280000e-68 268.0
9 TraesCS2A01G479700 chr2D 86.818 220 11 10 1943 2148 580003169 580002954 2.020000e-56 230.0
10 TraesCS2A01G479700 chr2D 91.566 166 11 2 1736 1898 580003327 580003162 2.610000e-55 226.0
11 TraesCS2A01G479700 chr2D 77.733 247 49 6 1105 1348 561935308 561935065 2.090000e-31 147.0
12 TraesCS2A01G479700 chr2B 92.626 895 54 4 746 1632 698303320 698302430 0.000000e+00 1277.0
13 TraesCS2A01G479700 chr2B 90.925 562 33 7 2065 2609 698301706 698301146 0.000000e+00 739.0
14 TraesCS2A01G479700 chr2B 82.202 663 99 15 974 1632 671354748 671354101 1.060000e-153 553.0
15 TraesCS2A01G479700 chr2B 95.833 192 8 0 538 729 698951453 698951262 7.010000e-81 311.0
16 TraesCS2A01G479700 chr2B 88.571 175 18 1 1726 1898 698302431 698302257 7.320000e-51 211.0
17 TraesCS2A01G479700 chr2B 94.382 89 4 1 182 270 698951994 698951907 4.530000e-28 135.0
18 TraesCS2A01G479700 chr2B 83.673 147 10 8 1743 1882 671390712 671390573 2.730000e-25 126.0
19 TraesCS2A01G479700 chr2B 75.304 247 55 6 1105 1348 671213657 671213414 2.120000e-21 113.0
20 TraesCS2A01G479700 chr2B 94.118 51 2 1 612 661 698303479 698303429 2.780000e-10 76.8
21 TraesCS2A01G479700 chr2B 95.349 43 1 1 659 701 698303362 698303321 1.680000e-07 67.6
22 TraesCS2A01G479700 chr4A 89.278 485 29 7 2129 2598 667030365 667029889 1.040000e-163 586.0
23 TraesCS2A01G479700 chr4A 92.655 177 12 1 362 537 742467450 742467274 1.200000e-63 254.0
24 TraesCS2A01G479700 chr6B 88.124 421 39 6 2185 2598 27980195 27980611 8.390000e-135 490.0
25 TraesCS2A01G479700 chr6B 89.691 97 10 0 1631 1727 716290394 716290490 9.800000e-25 124.0
26 TraesCS2A01G479700 chr6B 91.549 71 2 1 2129 2199 27980116 27980182 7.690000e-16 95.3
27 TraesCS2A01G479700 chr3D 85.938 320 24 10 2294 2598 94806452 94806139 3.240000e-84 322.0
28 TraesCS2A01G479700 chr3D 94.512 164 9 0 373 536 426479957 426479794 1.200000e-63 254.0
29 TraesCS2A01G479700 chr4B 94.286 175 10 0 360 534 483266366 483266540 4.280000e-68 268.0
30 TraesCS2A01G479700 chr4B 89.474 190 14 5 1 184 438146260 438146071 4.340000e-58 235.0
31 TraesCS2A01G479700 chr4B 88.000 100 12 0 1628 1727 132335766 132335865 4.560000e-23 119.0
32 TraesCS2A01G479700 chr3A 93.678 174 11 0 373 546 659527230 659527403 7.160000e-66 261.0
33 TraesCS2A01G479700 chr3A 91.573 178 15 0 365 542 523738466 523738643 2.010000e-61 246.0
34 TraesCS2A01G479700 chr3A 95.349 86 4 0 1642 1727 649028468 649028553 1.260000e-28 137.0
35 TraesCS2A01G479700 chr7D 94.048 168 9 1 368 535 414094937 414094771 1.200000e-63 254.0
36 TraesCS2A01G479700 chr3B 94.012 167 10 0 372 538 183601248 183601082 1.200000e-63 254.0
37 TraesCS2A01G479700 chr3B 90.722 97 9 0 1631 1727 819036509 819036605 2.110000e-26 130.0
38 TraesCS2A01G479700 chr4D 93.023 172 12 0 364 535 44169149 44169320 4.310000e-63 252.0
39 TraesCS2A01G479700 chr4D 92.982 171 12 0 364 534 484111755 484111925 1.550000e-62 250.0
40 TraesCS2A01G479700 chr4D 89.418 189 14 6 1 183 346140789 346140601 1.560000e-57 233.0
41 TraesCS2A01G479700 chr4D 91.509 106 9 0 1630 1735 59066464 59066359 2.090000e-31 147.0
42 TraesCS2A01G479700 chr4D 88.660 97 11 0 1631 1727 78845853 78845949 4.560000e-23 119.0
43 TraesCS2A01G479700 chr6D 91.304 184 10 5 1 179 151944679 151944861 2.010000e-61 246.0
44 TraesCS2A01G479700 chr6D 90.608 181 15 2 2129 2308 47382190 47382011 3.360000e-59 239.0
45 TraesCS2A01G479700 chr6D 88.776 196 16 6 1 190 455395243 455395048 4.340000e-58 235.0
46 TraesCS2A01G479700 chr1A 90.000 190 13 5 1 184 536806176 536806365 9.330000e-60 241.0
47 TraesCS2A01G479700 chr5D 89.231 195 12 8 1 186 538708377 538708183 4.340000e-58 235.0
48 TraesCS2A01G479700 chr5D 89.062 192 15 5 1 186 500160043 500160234 1.560000e-57 233.0
49 TraesCS2A01G479700 chr5D 89.062 192 14 6 1 186 337722896 337723086 5.620000e-57 231.0
50 TraesCS2A01G479700 chr1D 88.718 195 14 7 1 187 376244675 376244869 5.620000e-57 231.0
51 TraesCS2A01G479700 chr7B 90.722 97 9 0 1631 1727 402800005 402800101 2.110000e-26 130.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G479700 chr2A 717876935 717879543 2608 True 4819.00 4819 100.0000 1 2609 1 chr2A.!!$R4 2608
1 TraesCS2A01G479700 chr2D 580000869 580004595 3726 True 571.20 1461 91.3808 203 2609 5 chr2D.!!$R3 2406
2 TraesCS2A01G479700 chr2B 671354101 671354748 647 True 553.00 553 82.2020 974 1632 1 chr2B.!!$R2 658
3 TraesCS2A01G479700 chr2B 698301146 698303479 2333 True 474.28 1277 92.3178 612 2609 5 chr2B.!!$R4 1997
4 TraesCS2A01G479700 chr2B 698951262 698951994 732 True 223.00 311 95.1075 182 729 2 chr2B.!!$R5 547

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
387 734 0.032017 ATGCTACTCCCTCCGTTCCT 60.032 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 2325 0.179045 GCCACTACGCCCTCATGAAT 60.179 55.0 0.0 0.0 0.0 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 9.649167 GAAACTTCTTTTCATGATGGATCAAAT 57.351 29.630 0.00 0.00 42.95 2.32
74 75 8.997621 AACTTCTTTTCATGATGGATCAAATG 57.002 30.769 0.00 0.00 40.69 2.32
75 76 8.357290 ACTTCTTTTCATGATGGATCAAATGA 57.643 30.769 0.00 0.00 40.69 2.57
76 77 8.978472 ACTTCTTTTCATGATGGATCAAATGAT 58.022 29.630 0.00 0.00 40.69 2.45
77 78 9.817809 CTTCTTTTCATGATGGATCAAATGATT 57.182 29.630 0.00 0.00 40.69 2.57
130 131 8.779354 TTTTTAAACTTGGTTAAACATGCACT 57.221 26.923 6.32 0.00 33.71 4.40
131 132 9.871238 TTTTTAAACTTGGTTAAACATGCACTA 57.129 25.926 6.32 0.00 33.71 2.74
132 133 9.522804 TTTTAAACTTGGTTAAACATGCACTAG 57.477 29.630 6.32 0.00 33.71 2.57
133 134 6.709018 AAACTTGGTTAAACATGCACTAGT 57.291 33.333 6.32 0.00 0.00 2.57
134 135 6.709018 AACTTGGTTAAACATGCACTAGTT 57.291 33.333 6.32 3.55 0.00 2.24
135 136 6.709018 ACTTGGTTAAACATGCACTAGTTT 57.291 33.333 15.33 15.33 40.68 2.66
136 137 6.503524 ACTTGGTTAAACATGCACTAGTTTG 58.496 36.000 18.62 3.06 38.33 2.93
137 138 6.320164 ACTTGGTTAAACATGCACTAGTTTGA 59.680 34.615 18.62 11.10 38.33 2.69
138 139 6.067263 TGGTTAAACATGCACTAGTTTGAC 57.933 37.500 19.26 19.26 41.02 3.18
139 140 5.825679 TGGTTAAACATGCACTAGTTTGACT 59.174 36.000 23.12 6.13 41.30 3.41
140 141 6.320164 TGGTTAAACATGCACTAGTTTGACTT 59.680 34.615 23.12 7.57 41.30 3.01
141 142 7.147983 TGGTTAAACATGCACTAGTTTGACTTT 60.148 33.333 23.12 6.43 41.30 2.66
142 143 7.704899 GGTTAAACATGCACTAGTTTGACTTTT 59.295 33.333 23.12 5.92 41.30 2.27
143 144 8.531530 GTTAAACATGCACTAGTTTGACTTTTG 58.468 33.333 19.76 2.00 39.60 2.44
144 145 6.449635 AACATGCACTAGTTTGACTTTTGA 57.550 33.333 0.00 0.00 0.00 2.69
145 146 6.449635 ACATGCACTAGTTTGACTTTTGAA 57.550 33.333 0.00 0.00 0.00 2.69
146 147 6.862209 ACATGCACTAGTTTGACTTTTGAAA 58.138 32.000 0.00 0.00 0.00 2.69
147 148 7.319646 ACATGCACTAGTTTGACTTTTGAAAA 58.680 30.769 0.00 0.00 0.00 2.29
148 149 7.816995 ACATGCACTAGTTTGACTTTTGAAAAA 59.183 29.630 0.00 0.00 0.00 1.94
178 179 9.774413 AATACAACTTATATAAAGGAACGGAGG 57.226 33.333 0.00 0.00 0.00 4.30
179 180 7.427989 ACAACTTATATAAAGGAACGGAGGA 57.572 36.000 0.00 0.00 0.00 3.71
180 181 7.498443 ACAACTTATATAAAGGAACGGAGGAG 58.502 38.462 0.00 0.00 0.00 3.69
181 182 7.125356 ACAACTTATATAAAGGAACGGAGGAGT 59.875 37.037 0.00 0.00 0.00 3.85
182 183 8.636213 CAACTTATATAAAGGAACGGAGGAGTA 58.364 37.037 0.00 0.00 0.00 2.59
183 184 8.953223 ACTTATATAAAGGAACGGAGGAGTAT 57.047 34.615 0.00 0.00 0.00 2.12
184 185 9.377238 ACTTATATAAAGGAACGGAGGAGTATT 57.623 33.333 0.00 0.00 0.00 1.89
197 198 7.442656 ACGGAGGAGTATTATCTAATTTGTGG 58.557 38.462 0.00 0.00 0.00 4.17
227 228 4.033587 ACGTGTACTGTTGTTACTTTGCTG 59.966 41.667 0.00 0.00 0.00 4.41
266 267 7.787424 AGAATACCTCTCTGGAAACTAGCTAAT 59.213 37.037 0.00 0.00 39.71 1.73
287 634 3.430453 TGGGTCTATTTGAAAAGCAGGG 58.570 45.455 0.00 0.00 0.00 4.45
311 658 0.948678 TTGGAGCAAACGGTAAGTGC 59.051 50.000 3.85 3.85 38.59 4.40
355 702 0.924090 CGACGAGTTTGAGCTATGCC 59.076 55.000 0.00 0.00 0.00 4.40
372 719 0.744874 GCCACATTCTCATGCATGCT 59.255 50.000 22.25 1.07 33.05 3.79
376 723 3.250280 CCACATTCTCATGCATGCTACTC 59.750 47.826 22.25 0.00 33.05 2.59
377 724 3.250280 CACATTCTCATGCATGCTACTCC 59.750 47.826 22.25 0.00 33.05 3.85
378 725 2.627515 TTCTCATGCATGCTACTCCC 57.372 50.000 22.25 0.00 0.00 4.30
379 726 1.798626 TCTCATGCATGCTACTCCCT 58.201 50.000 22.25 0.00 0.00 4.20
380 727 1.690893 TCTCATGCATGCTACTCCCTC 59.309 52.381 22.25 0.00 0.00 4.30
381 728 0.761187 TCATGCATGCTACTCCCTCC 59.239 55.000 22.25 0.00 0.00 4.30
382 729 0.602106 CATGCATGCTACTCCCTCCG 60.602 60.000 20.33 0.00 0.00 4.63
383 730 1.050988 ATGCATGCTACTCCCTCCGT 61.051 55.000 20.33 0.00 0.00 4.69
384 731 1.264749 TGCATGCTACTCCCTCCGTT 61.265 55.000 20.33 0.00 0.00 4.44
385 732 0.530870 GCATGCTACTCCCTCCGTTC 60.531 60.000 11.37 0.00 0.00 3.95
386 733 0.105039 CATGCTACTCCCTCCGTTCC 59.895 60.000 0.00 0.00 0.00 3.62
387 734 0.032017 ATGCTACTCCCTCCGTTCCT 60.032 55.000 0.00 0.00 0.00 3.36
388 735 0.627451 TGCTACTCCCTCCGTTCCTA 59.373 55.000 0.00 0.00 0.00 2.94
389 736 1.006281 TGCTACTCCCTCCGTTCCTAA 59.994 52.381 0.00 0.00 0.00 2.69
390 737 2.105766 GCTACTCCCTCCGTTCCTAAA 58.894 52.381 0.00 0.00 0.00 1.85
391 738 2.699321 GCTACTCCCTCCGTTCCTAAAT 59.301 50.000 0.00 0.00 0.00 1.40
392 739 3.893813 GCTACTCCCTCCGTTCCTAAATA 59.106 47.826 0.00 0.00 0.00 1.40
393 740 4.527427 GCTACTCCCTCCGTTCCTAAATAT 59.473 45.833 0.00 0.00 0.00 1.28
394 741 5.713861 GCTACTCCCTCCGTTCCTAAATATA 59.286 44.000 0.00 0.00 0.00 0.86
395 742 6.210185 GCTACTCCCTCCGTTCCTAAATATAA 59.790 42.308 0.00 0.00 0.00 0.98
396 743 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
397 744 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
398 745 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
399 746 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
400 747 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
401 748 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
402 749 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
403 750 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
419 766 7.033530 AGTCTTTGTAGAGATTCGACTATGG 57.966 40.000 0.00 0.00 0.00 2.74
420 767 6.829298 AGTCTTTGTAGAGATTCGACTATGGA 59.171 38.462 0.00 0.00 0.00 3.41
421 768 6.913673 GTCTTTGTAGAGATTCGACTATGGAC 59.086 42.308 0.00 0.00 0.00 4.02
422 769 6.829298 TCTTTGTAGAGATTCGACTATGGACT 59.171 38.462 0.00 0.00 0.00 3.85
423 770 7.991460 TCTTTGTAGAGATTCGACTATGGACTA 59.009 37.037 0.00 0.00 0.00 2.59
424 771 7.493743 TTGTAGAGATTCGACTATGGACTAC 57.506 40.000 0.00 0.00 0.00 2.73
425 772 6.589135 TGTAGAGATTCGACTATGGACTACA 58.411 40.000 0.00 0.00 36.46 2.74
426 773 7.225011 TGTAGAGATTCGACTATGGACTACAT 58.775 38.462 0.00 0.00 43.68 2.29
427 774 8.373220 TGTAGAGATTCGACTATGGACTACATA 58.627 37.037 0.00 0.00 41.03 2.29
428 775 7.675962 AGAGATTCGACTATGGACTACATAC 57.324 40.000 0.00 0.00 41.03 2.39
429 776 6.369340 AGAGATTCGACTATGGACTACATACG 59.631 42.308 0.00 0.00 41.03 3.06
430 777 6.228995 AGATTCGACTATGGACTACATACGA 58.771 40.000 0.00 0.00 41.03 3.43
431 778 6.709397 AGATTCGACTATGGACTACATACGAA 59.291 38.462 8.43 8.43 45.89 3.85
432 779 5.919272 TCGACTATGGACTACATACGAAG 57.081 43.478 0.00 0.00 37.51 3.79
433 780 4.212847 TCGACTATGGACTACATACGAAGC 59.787 45.833 0.00 0.00 37.51 3.86
434 781 4.024302 CGACTATGGACTACATACGAAGCA 60.024 45.833 0.00 0.00 41.03 3.91
435 782 5.505159 CGACTATGGACTACATACGAAGCAA 60.505 44.000 0.00 0.00 41.03 3.91
436 783 6.216801 ACTATGGACTACATACGAAGCAAA 57.783 37.500 0.00 0.00 41.03 3.68
437 784 6.636705 ACTATGGACTACATACGAAGCAAAA 58.363 36.000 0.00 0.00 41.03 2.44
438 785 7.272978 ACTATGGACTACATACGAAGCAAAAT 58.727 34.615 0.00 0.00 41.03 1.82
439 786 5.794687 TGGACTACATACGAAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
440 787 5.483811 TGGACTACATACGAAGCAAAATGA 58.516 37.500 0.00 0.00 0.00 2.57
441 788 5.580691 TGGACTACATACGAAGCAAAATGAG 59.419 40.000 0.00 0.00 0.00 2.90
442 789 5.581085 GGACTACATACGAAGCAAAATGAGT 59.419 40.000 0.00 0.00 0.00 3.41
443 790 6.408858 ACTACATACGAAGCAAAATGAGTG 57.591 37.500 0.00 0.00 0.00 3.51
444 791 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
445 792 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
446 793 5.689819 ACATACGAAGCAAAATGAGTGAAC 58.310 37.500 0.00 0.00 0.00 3.18
447 794 3.626028 ACGAAGCAAAATGAGTGAACC 57.374 42.857 0.00 0.00 0.00 3.62
448 795 3.214328 ACGAAGCAAAATGAGTGAACCT 58.786 40.909 0.00 0.00 0.00 3.50
449 796 4.385825 ACGAAGCAAAATGAGTGAACCTA 58.614 39.130 0.00 0.00 0.00 3.08
450 797 4.213482 ACGAAGCAAAATGAGTGAACCTAC 59.787 41.667 0.00 0.00 0.00 3.18
451 798 4.213270 CGAAGCAAAATGAGTGAACCTACA 59.787 41.667 0.00 0.00 0.00 2.74
452 799 5.438761 AAGCAAAATGAGTGAACCTACAC 57.561 39.130 0.00 0.00 40.60 2.90
465 812 7.796958 GTGAACCTACACTTTAAAATGCATC 57.203 36.000 0.00 0.00 37.73 3.91
466 813 7.593825 GTGAACCTACACTTTAAAATGCATCT 58.406 34.615 0.00 0.00 37.73 2.90
467 814 8.726988 GTGAACCTACACTTTAAAATGCATCTA 58.273 33.333 0.00 0.00 37.73 1.98
468 815 9.461312 TGAACCTACACTTTAAAATGCATCTAT 57.539 29.630 0.00 0.00 0.00 1.98
484 831 9.788889 AATGCATCTATATACATCCATATGTGG 57.211 33.333 0.00 1.19 45.99 4.17
485 832 8.322905 TGCATCTATATACATCCATATGTGGT 57.677 34.615 8.51 0.00 45.99 4.16
486 833 8.424133 TGCATCTATATACATCCATATGTGGTC 58.576 37.037 8.51 0.00 45.99 4.02
487 834 8.646004 GCATCTATATACATCCATATGTGGTCT 58.354 37.037 8.51 0.00 45.99 3.85
495 842 7.855784 ACATCCATATGTGGTCTATAGTGAA 57.144 36.000 8.51 0.00 44.79 3.18
496 843 8.262601 ACATCCATATGTGGTCTATAGTGAAA 57.737 34.615 8.51 0.00 44.79 2.69
497 844 8.884323 ACATCCATATGTGGTCTATAGTGAAAT 58.116 33.333 8.51 0.00 44.79 2.17
529 876 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
530 877 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
531 878 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
532 879 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
533 880 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
534 881 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
535 882 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
552 899 5.346181 AGTACAAGGCAGGTCTAAATCTC 57.654 43.478 0.00 0.00 0.00 2.75
554 901 4.851639 ACAAGGCAGGTCTAAATCTCAT 57.148 40.909 0.00 0.00 0.00 2.90
600 947 5.743872 CAGAAGAAAAGGTTGTACAAAGCAC 59.256 40.000 10.51 0.00 0.00 4.40
610 957 4.811555 TGTACAAAGCACTGATGTTGAC 57.188 40.909 0.00 0.00 0.00 3.18
663 1080 8.647796 TCCCCATTTGTACTGTTATATGTAGAG 58.352 37.037 0.00 0.00 0.00 2.43
705 1122 6.542005 TCAAGTTGCTCAAAGAATGTGTTCTA 59.458 34.615 0.00 0.00 43.80 2.10
767 1184 1.282817 GCCATGCACGTACACGAATA 58.717 50.000 9.04 0.00 43.02 1.75
881 1303 5.307196 GTGGACTAATAGGAAGGGAAGCATA 59.693 44.000 0.00 0.00 0.00 3.14
947 1370 2.892852 TGCAAGAAATCAAACCCTCCAG 59.107 45.455 0.00 0.00 0.00 3.86
957 1380 4.403734 TCAAACCCTCCAGAAACCATTAC 58.596 43.478 0.00 0.00 0.00 1.89
983 1406 4.133013 AGAAATCAATGCCTGCCATTTC 57.867 40.909 0.00 0.00 42.15 2.17
1012 1435 2.776312 TATCTCGATGACGGTCTTGC 57.224 50.000 9.88 0.00 40.21 4.01
1050 1473 3.961838 TACACACAATCCCGGCCGC 62.962 63.158 22.85 0.00 0.00 6.53
1068 1493 1.753956 GCTTGCTACCAACACAAACG 58.246 50.000 0.00 0.00 0.00 3.60
1095 1520 1.526917 CATGGGGCCTTCACGATCC 60.527 63.158 0.84 0.00 0.00 3.36
1096 1521 2.000701 ATGGGGCCTTCACGATCCA 61.001 57.895 0.84 0.00 0.00 3.41
1117 1542 3.151022 CCTGCCTCGTCCTCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
1120 1545 3.213402 GCCTCGTCCTCCTCCTCG 61.213 72.222 0.00 0.00 0.00 4.63
1311 1736 3.558411 GCCAGCAGCATCGTCGAC 61.558 66.667 5.18 5.18 42.97 4.20
1366 1791 2.281345 GCATCCAGATGGGCCTCG 60.281 66.667 4.53 0.00 39.16 4.63
1374 1799 2.680352 ATGGGCCTCGACGACTGT 60.680 61.111 4.53 0.00 0.00 3.55
1377 1802 2.179517 GGCCTCGACGACTGTGAG 59.820 66.667 0.00 0.00 0.00 3.51
1411 1836 2.024871 CCGTGGACGAGCTCGATC 59.975 66.667 40.58 30.05 43.02 3.69
1517 1942 3.744719 CTGCGAGACCGGGTTCGA 61.745 66.667 27.31 14.55 39.06 3.71
1523 1948 1.655885 GAGACCGGGTTCGAGGAGAC 61.656 65.000 6.32 0.00 39.00 3.36
1578 2003 4.079901 TCCGAGTTCACTAAGGAGGTCTAT 60.080 45.833 0.73 0.00 31.85 1.98
1635 2060 5.980025 GCTTGATTAGAAGCGAATTAGTCC 58.020 41.667 0.00 0.00 39.10 3.85
1636 2061 5.050023 GCTTGATTAGAAGCGAATTAGTCCC 60.050 44.000 0.00 0.00 39.10 4.46
1637 2062 5.871396 TGATTAGAAGCGAATTAGTCCCT 57.129 39.130 0.00 0.00 0.00 4.20
1638 2063 6.235231 TGATTAGAAGCGAATTAGTCCCTT 57.765 37.500 0.00 0.00 0.00 3.95
1639 2064 6.281405 TGATTAGAAGCGAATTAGTCCCTTC 58.719 40.000 0.00 0.00 40.22 3.46
1640 2065 3.166489 AGAAGCGAATTAGTCCCTTCG 57.834 47.619 2.17 0.63 43.29 3.79
1641 2066 2.496470 AGAAGCGAATTAGTCCCTTCGT 59.504 45.455 2.17 0.00 43.29 3.85
1642 2067 3.056035 AGAAGCGAATTAGTCCCTTCGTT 60.056 43.478 2.17 0.00 43.29 3.85
1643 2068 3.329929 AGCGAATTAGTCCCTTCGTTT 57.670 42.857 6.56 0.00 44.54 3.60
1644 2069 3.259902 AGCGAATTAGTCCCTTCGTTTC 58.740 45.455 6.56 0.00 44.54 2.78
1645 2070 2.997986 GCGAATTAGTCCCTTCGTTTCA 59.002 45.455 6.56 0.00 44.54 2.69
1646 2071 3.434299 GCGAATTAGTCCCTTCGTTTCAA 59.566 43.478 6.56 0.00 44.54 2.69
1647 2072 4.083696 GCGAATTAGTCCCTTCGTTTCAAA 60.084 41.667 6.56 0.00 44.54 2.69
1648 2073 5.561339 GCGAATTAGTCCCTTCGTTTCAAAA 60.561 40.000 6.56 0.00 44.54 2.44
1649 2074 6.608610 CGAATTAGTCCCTTCGTTTCAAAAT 58.391 36.000 0.00 0.00 39.42 1.82
1650 2075 7.624764 GCGAATTAGTCCCTTCGTTTCAAAATA 60.625 37.037 6.56 0.00 44.54 1.40
1651 2076 7.903431 CGAATTAGTCCCTTCGTTTCAAAATAG 59.097 37.037 0.00 0.00 39.42 1.73
1652 2077 8.857694 AATTAGTCCCTTCGTTTCAAAATAGA 57.142 30.769 0.00 0.00 0.00 1.98
1653 2078 9.462606 AATTAGTCCCTTCGTTTCAAAATAGAT 57.537 29.630 0.00 0.00 0.00 1.98
1654 2079 6.743575 AGTCCCTTCGTTTCAAAATAGATG 57.256 37.500 0.00 0.00 0.00 2.90
1655 2080 6.472887 AGTCCCTTCGTTTCAAAATAGATGA 58.527 36.000 0.00 0.00 0.00 2.92
1656 2081 7.112779 AGTCCCTTCGTTTCAAAATAGATGAT 58.887 34.615 0.00 0.00 0.00 2.45
1657 2082 7.281100 AGTCCCTTCGTTTCAAAATAGATGATC 59.719 37.037 0.00 0.00 0.00 2.92
1658 2083 6.542370 TCCCTTCGTTTCAAAATAGATGATCC 59.458 38.462 0.00 0.00 0.00 3.36
1659 2084 6.318648 CCCTTCGTTTCAAAATAGATGATCCA 59.681 38.462 0.00 0.00 0.00 3.41
1660 2085 7.148086 CCCTTCGTTTCAAAATAGATGATCCAA 60.148 37.037 0.00 0.00 0.00 3.53
1661 2086 8.408601 CCTTCGTTTCAAAATAGATGATCCAAT 58.591 33.333 0.00 0.00 0.00 3.16
1662 2087 9.793252 CTTCGTTTCAAAATAGATGATCCAATT 57.207 29.630 0.00 0.00 0.00 2.32
1722 2147 8.726870 TGAGTTATCTATTTTAAAACGGAGGG 57.273 34.615 1.97 0.00 0.00 4.30
1723 2148 8.542080 TGAGTTATCTATTTTAAAACGGAGGGA 58.458 33.333 1.97 0.00 0.00 4.20
1724 2149 8.959705 AGTTATCTATTTTAAAACGGAGGGAG 57.040 34.615 1.97 0.00 0.00 4.30
1725 2150 8.546322 AGTTATCTATTTTAAAACGGAGGGAGT 58.454 33.333 1.97 0.00 0.00 3.85
1726 2151 9.822185 GTTATCTATTTTAAAACGGAGGGAGTA 57.178 33.333 1.97 0.00 0.00 2.59
1756 2181 1.212688 TCATCCGTTCATCTGGCCATT 59.787 47.619 5.51 0.00 0.00 3.16
1762 2187 1.901833 GTTCATCTGGCCATTTGGGTT 59.098 47.619 5.51 0.00 39.65 4.11
1777 2202 8.925159 GCCATTTGGGTTAGAGTTTTCTCATGA 61.925 40.741 0.00 0.00 43.47 3.07
1835 2263 0.319900 ACTGAACGTCGCAATCTGCT 60.320 50.000 0.00 0.00 42.25 4.24
1863 2291 0.107268 CGGTGATCATGGCCTCATCA 59.893 55.000 3.32 6.01 0.00 3.07
1892 2320 6.753107 TTCACACATCAGTCTAGACGATAA 57.247 37.500 21.61 13.56 36.20 1.75
1893 2321 6.944234 TCACACATCAGTCTAGACGATAAT 57.056 37.500 21.61 14.18 36.20 1.28
1894 2322 8.446599 TTCACACATCAGTCTAGACGATAATA 57.553 34.615 21.61 6.97 36.20 0.98
1895 2323 7.862648 TCACACATCAGTCTAGACGATAATAC 58.137 38.462 21.61 0.00 36.20 1.89
1896 2324 7.715686 TCACACATCAGTCTAGACGATAATACT 59.284 37.037 21.61 1.53 36.20 2.12
1897 2325 8.989980 CACACATCAGTCTAGACGATAATACTA 58.010 37.037 21.61 3.83 36.20 1.82
1898 2326 9.727859 ACACATCAGTCTAGACGATAATACTAT 57.272 33.333 21.61 0.28 36.20 2.12
1907 2335 9.397280 TCTAGACGATAATACTATTCATGAGGG 57.603 37.037 0.00 0.00 0.00 4.30
1908 2336 6.868622 AGACGATAATACTATTCATGAGGGC 58.131 40.000 0.00 0.00 0.00 5.19
1909 2337 5.651530 ACGATAATACTATTCATGAGGGCG 58.348 41.667 0.00 0.00 0.00 6.13
1910 2338 5.185249 ACGATAATACTATTCATGAGGGCGT 59.815 40.000 0.00 0.00 0.00 5.68
1911 2339 6.376299 ACGATAATACTATTCATGAGGGCGTA 59.624 38.462 0.00 0.00 0.00 4.42
1912 2340 6.913132 CGATAATACTATTCATGAGGGCGTAG 59.087 42.308 0.00 0.00 0.00 3.51
1913 2341 7.415318 CGATAATACTATTCATGAGGGCGTAGT 60.415 40.741 0.00 4.21 0.00 2.73
1914 2342 3.735237 ACTATTCATGAGGGCGTAGTG 57.265 47.619 0.00 0.00 0.00 2.74
1915 2343 2.365617 ACTATTCATGAGGGCGTAGTGG 59.634 50.000 0.00 0.00 0.00 4.00
1916 2344 0.179045 ATTCATGAGGGCGTAGTGGC 60.179 55.000 0.00 0.00 43.88 5.01
1930 2358 4.835456 TGGCCCCCGGGAGCTATT 62.835 66.667 27.66 0.00 37.50 1.73
1931 2359 2.528378 GGCCCCCGGGAGCTATTA 60.528 66.667 27.66 0.00 37.50 0.98
1932 2360 2.593956 GGCCCCCGGGAGCTATTAG 61.594 68.421 27.66 4.35 37.50 1.73
1933 2361 1.535687 GCCCCCGGGAGCTATTAGA 60.536 63.158 26.32 0.00 37.50 2.10
1934 2362 1.828461 GCCCCCGGGAGCTATTAGAC 61.828 65.000 26.32 0.00 37.50 2.59
1935 2363 0.471211 CCCCCGGGAGCTATTAGACA 60.471 60.000 26.32 0.00 37.50 3.41
1936 2364 1.645710 CCCCGGGAGCTATTAGACAT 58.354 55.000 26.32 0.00 0.00 3.06
1937 2365 1.978580 CCCCGGGAGCTATTAGACATT 59.021 52.381 26.32 0.00 0.00 2.71
1938 2366 2.372172 CCCCGGGAGCTATTAGACATTT 59.628 50.000 26.32 0.00 0.00 2.32
1939 2367 3.557264 CCCCGGGAGCTATTAGACATTTC 60.557 52.174 26.32 0.00 0.00 2.17
1940 2368 3.325135 CCCGGGAGCTATTAGACATTTCT 59.675 47.826 18.48 0.00 35.66 2.52
1941 2369 4.561105 CCGGGAGCTATTAGACATTTCTC 58.439 47.826 0.00 0.00 32.75 2.87
1942 2370 4.282195 CCGGGAGCTATTAGACATTTCTCT 59.718 45.833 0.00 0.00 32.75 3.10
1943 2371 5.477291 CCGGGAGCTATTAGACATTTCTCTA 59.523 44.000 0.00 0.00 32.75 2.43
1955 2383 9.908747 TTAGACATTTCTCTAGTACTAAGCTCT 57.091 33.333 3.76 0.00 32.75 4.09
1972 2405 2.354203 GCTCTCAGGGATTGAAACGTCT 60.354 50.000 0.00 0.00 34.81 4.18
2016 2450 2.734606 CGCTCAATTGGTCAGTTCGTTA 59.265 45.455 5.42 0.00 0.00 3.18
2040 2477 4.513406 AGGTTTTTGGGAGAAGTGTACA 57.487 40.909 0.00 0.00 0.00 2.90
2050 2511 6.774673 TGGGAGAAGTGTACAAACATATTCA 58.225 36.000 0.00 0.00 38.08 2.57
2079 2943 5.278758 GGAGAATGGTTTCGGAATTTGTCAA 60.279 40.000 0.00 0.00 36.93 3.18
2145 4622 4.213270 CACGAAATGCTTGAAGGTTCAGTA 59.787 41.667 0.00 0.00 38.61 2.74
2195 4672 9.720667 CATTTCGTGATGAGCAAATTTAAGATA 57.279 29.630 0.00 0.00 0.00 1.98
2245 4723 1.067516 CCAATCCAATGGGTCGAATGC 59.932 52.381 0.00 0.00 36.79 3.56
2275 4753 5.071115 ACCTCTTGGCAGGTAAGAATCTATC 59.929 44.000 0.00 0.00 45.71 2.08
2425 4910 5.289675 CACTTTTAGCTCTGTTACATCCTCG 59.710 44.000 0.00 0.00 0.00 4.63
2444 4929 5.065218 TCCTCGCAGATTGAGCTTTATTTTC 59.935 40.000 0.00 0.00 33.89 2.29
2446 4931 4.699735 TCGCAGATTGAGCTTTATTTTCCA 59.300 37.500 0.00 0.00 0.00 3.53
2500 4985 7.611387 TCGTAAAATACATACGCACATGTAAC 58.389 34.615 10.47 0.00 42.92 2.50
2511 4996 2.210116 CACATGTAACCCGGATAGCAC 58.790 52.381 0.73 0.00 0.00 4.40
2559 5053 7.343316 TGTTTAATCTTCTCCCAACCTTTTTCA 59.657 33.333 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.846248 GTCTTGCAGATGTTGTTATTTTATTCT 57.154 29.630 0.00 0.00 0.00 2.40
5 6 9.076596 GGTCTTGCAGATGTTGTTATTTTATTC 57.923 33.333 0.00 0.00 0.00 1.75
6 7 8.806146 AGGTCTTGCAGATGTTGTTATTTTATT 58.194 29.630 0.00 0.00 0.00 1.40
7 8 8.353423 AGGTCTTGCAGATGTTGTTATTTTAT 57.647 30.769 0.00 0.00 0.00 1.40
8 9 7.759489 AGGTCTTGCAGATGTTGTTATTTTA 57.241 32.000 0.00 0.00 0.00 1.52
9 10 6.655078 AGGTCTTGCAGATGTTGTTATTTT 57.345 33.333 0.00 0.00 0.00 1.82
10 11 7.759489 TTAGGTCTTGCAGATGTTGTTATTT 57.241 32.000 0.00 0.00 0.00 1.40
11 12 7.944729 ATTAGGTCTTGCAGATGTTGTTATT 57.055 32.000 0.00 0.00 0.00 1.40
12 13 8.486210 TCTATTAGGTCTTGCAGATGTTGTTAT 58.514 33.333 0.00 0.00 0.00 1.89
13 14 7.847096 TCTATTAGGTCTTGCAGATGTTGTTA 58.153 34.615 0.00 0.00 0.00 2.41
14 15 6.711277 TCTATTAGGTCTTGCAGATGTTGTT 58.289 36.000 0.00 0.00 0.00 2.83
15 16 6.299805 TCTATTAGGTCTTGCAGATGTTGT 57.700 37.500 0.00 0.00 0.00 3.32
16 17 8.893219 TTATCTATTAGGTCTTGCAGATGTTG 57.107 34.615 0.00 0.00 0.00 3.33
17 18 9.905713 TTTTATCTATTAGGTCTTGCAGATGTT 57.094 29.630 0.00 0.00 0.00 2.71
47 48 9.649167 ATTTGATCCATCATGAAAAGAAGTTTC 57.351 29.630 0.00 0.00 38.29 2.78
48 49 9.431887 CATTTGATCCATCATGAAAAGAAGTTT 57.568 29.630 0.00 0.00 36.56 2.66
49 50 8.809066 TCATTTGATCCATCATGAAAAGAAGTT 58.191 29.630 0.00 0.00 36.56 2.66
50 51 8.357290 TCATTTGATCCATCATGAAAAGAAGT 57.643 30.769 0.00 0.00 36.56 3.01
51 52 9.817809 AATCATTTGATCCATCATGAAAAGAAG 57.182 29.630 0.00 0.00 36.56 2.85
105 106 8.779354 AGTGCATGTTTAACCAAGTTTAAAAA 57.221 26.923 0.00 0.00 33.71 1.94
106 107 9.522804 CTAGTGCATGTTTAACCAAGTTTAAAA 57.477 29.630 0.00 0.00 33.71 1.52
107 108 8.688151 ACTAGTGCATGTTTAACCAAGTTTAAA 58.312 29.630 0.00 0.00 0.00 1.52
108 109 8.228035 ACTAGTGCATGTTTAACCAAGTTTAA 57.772 30.769 0.00 0.00 0.00 1.52
109 110 7.811117 ACTAGTGCATGTTTAACCAAGTTTA 57.189 32.000 0.00 0.00 0.00 2.01
110 111 6.709018 ACTAGTGCATGTTTAACCAAGTTT 57.291 33.333 0.00 0.00 0.00 2.66
111 112 6.709018 AACTAGTGCATGTTTAACCAAGTT 57.291 33.333 0.00 0.00 0.00 2.66
112 113 6.320164 TCAAACTAGTGCATGTTTAACCAAGT 59.680 34.615 12.69 0.00 35.01 3.16
113 114 6.636850 GTCAAACTAGTGCATGTTTAACCAAG 59.363 38.462 12.69 3.64 35.01 3.61
114 115 6.320164 AGTCAAACTAGTGCATGTTTAACCAA 59.680 34.615 12.69 0.00 35.01 3.67
115 116 5.825679 AGTCAAACTAGTGCATGTTTAACCA 59.174 36.000 12.69 0.00 35.01 3.67
116 117 6.313744 AGTCAAACTAGTGCATGTTTAACC 57.686 37.500 12.69 6.43 35.01 2.85
117 118 8.531530 CAAAAGTCAAACTAGTGCATGTTTAAC 58.468 33.333 12.69 10.12 35.01 2.01
118 119 8.462811 TCAAAAGTCAAACTAGTGCATGTTTAA 58.537 29.630 12.69 0.08 35.01 1.52
119 120 7.990917 TCAAAAGTCAAACTAGTGCATGTTTA 58.009 30.769 12.69 3.29 35.01 2.01
120 121 6.862209 TCAAAAGTCAAACTAGTGCATGTTT 58.138 32.000 0.00 8.84 36.91 2.83
121 122 6.449635 TCAAAAGTCAAACTAGTGCATGTT 57.550 33.333 0.00 0.00 0.00 2.71
122 123 6.449635 TTCAAAAGTCAAACTAGTGCATGT 57.550 33.333 0.00 0.00 0.00 3.21
123 124 7.754069 TTTTCAAAAGTCAAACTAGTGCATG 57.246 32.000 0.00 0.00 0.00 4.06
152 153 9.774413 CCTCCGTTCCTTTATATAAGTTGTATT 57.226 33.333 0.00 0.00 0.00 1.89
153 154 9.151177 TCCTCCGTTCCTTTATATAAGTTGTAT 57.849 33.333 0.00 0.00 0.00 2.29
154 155 8.537728 TCCTCCGTTCCTTTATATAAGTTGTA 57.462 34.615 0.00 0.00 0.00 2.41
155 156 7.125356 ACTCCTCCGTTCCTTTATATAAGTTGT 59.875 37.037 0.00 0.00 0.00 3.32
156 157 7.498443 ACTCCTCCGTTCCTTTATATAAGTTG 58.502 38.462 0.00 0.00 0.00 3.16
157 158 7.672122 ACTCCTCCGTTCCTTTATATAAGTT 57.328 36.000 0.00 0.00 0.00 2.66
158 159 8.953223 ATACTCCTCCGTTCCTTTATATAAGT 57.047 34.615 0.00 0.00 0.00 2.24
162 163 9.771140 AGATAATACTCCTCCGTTCCTTTATAT 57.229 33.333 0.00 0.00 0.00 0.86
164 165 9.597681 TTAGATAATACTCCTCCGTTCCTTTAT 57.402 33.333 0.00 0.00 0.00 1.40
165 166 9.597681 ATTAGATAATACTCCTCCGTTCCTTTA 57.402 33.333 0.00 0.00 0.00 1.85
166 167 7.909485 TTAGATAATACTCCTCCGTTCCTTT 57.091 36.000 0.00 0.00 0.00 3.11
167 168 8.493787 AATTAGATAATACTCCTCCGTTCCTT 57.506 34.615 0.00 0.00 0.00 3.36
168 169 8.368668 CAAATTAGATAATACTCCTCCGTTCCT 58.631 37.037 0.00 0.00 0.00 3.36
169 170 8.148999 ACAAATTAGATAATACTCCTCCGTTCC 58.851 37.037 0.00 0.00 0.00 3.62
170 171 8.979574 CACAAATTAGATAATACTCCTCCGTTC 58.020 37.037 0.00 0.00 0.00 3.95
171 172 7.931948 CCACAAATTAGATAATACTCCTCCGTT 59.068 37.037 0.00 0.00 0.00 4.44
172 173 7.442656 CCACAAATTAGATAATACTCCTCCGT 58.557 38.462 0.00 0.00 0.00 4.69
173 174 6.369065 GCCACAAATTAGATAATACTCCTCCG 59.631 42.308 0.00 0.00 0.00 4.63
174 175 6.655425 GGCCACAAATTAGATAATACTCCTCC 59.345 42.308 0.00 0.00 0.00 4.30
175 176 7.454225 AGGCCACAAATTAGATAATACTCCTC 58.546 38.462 5.01 0.00 0.00 3.71
176 177 7.394144 AGGCCACAAATTAGATAATACTCCT 57.606 36.000 5.01 0.00 0.00 3.69
177 178 9.569122 TTAAGGCCACAAATTAGATAATACTCC 57.431 33.333 5.01 0.00 0.00 3.85
180 181 9.659830 CGTTTAAGGCCACAAATTAGATAATAC 57.340 33.333 5.01 0.00 0.00 1.89
181 182 9.398538 ACGTTTAAGGCCACAAATTAGATAATA 57.601 29.630 5.01 0.00 0.00 0.98
182 183 8.188139 CACGTTTAAGGCCACAAATTAGATAAT 58.812 33.333 5.01 0.00 0.00 1.28
183 184 7.175293 ACACGTTTAAGGCCACAAATTAGATAA 59.825 33.333 5.01 0.00 0.00 1.75
184 185 6.655848 ACACGTTTAAGGCCACAAATTAGATA 59.344 34.615 5.01 0.00 0.00 1.98
197 198 4.541085 AACAACAGTACACGTTTAAGGC 57.459 40.909 0.00 0.00 0.00 4.35
266 267 3.075283 TCCCTGCTTTTCAAATAGACCCA 59.925 43.478 0.00 0.00 0.00 4.51
287 634 4.679654 CACTTACCGTTTGCTCCAAAATTC 59.320 41.667 0.00 0.00 35.03 2.17
311 658 3.114065 GGTATCCTAGCTCGACAAAACG 58.886 50.000 0.00 0.00 0.00 3.60
355 702 3.250280 GGAGTAGCATGCATGAGAATGTG 59.750 47.826 30.64 2.71 32.93 3.21
372 719 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
376 723 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
377 724 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
378 725 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
393 740 8.622157 CCATAGTCGAATCTCTACAAAGACTTA 58.378 37.037 0.00 0.00 38.30 2.24
394 741 7.339721 TCCATAGTCGAATCTCTACAAAGACTT 59.660 37.037 0.00 0.00 38.30 3.01
395 742 6.829298 TCCATAGTCGAATCTCTACAAAGACT 59.171 38.462 0.00 0.91 40.16 3.24
396 743 6.913673 GTCCATAGTCGAATCTCTACAAAGAC 59.086 42.308 0.00 0.00 0.00 3.01
397 744 6.829298 AGTCCATAGTCGAATCTCTACAAAGA 59.171 38.462 0.00 0.00 0.00 2.52
398 745 7.033530 AGTCCATAGTCGAATCTCTACAAAG 57.966 40.000 0.00 0.00 0.00 2.77
399 746 7.555195 TGTAGTCCATAGTCGAATCTCTACAAA 59.445 37.037 0.00 0.00 34.46 2.83
400 747 7.052248 TGTAGTCCATAGTCGAATCTCTACAA 58.948 38.462 0.00 0.00 34.46 2.41
401 748 6.589135 TGTAGTCCATAGTCGAATCTCTACA 58.411 40.000 0.00 0.49 34.82 2.74
402 749 7.675962 ATGTAGTCCATAGTCGAATCTCTAC 57.324 40.000 0.00 0.00 29.82 2.59
403 750 7.544915 CGTATGTAGTCCATAGTCGAATCTCTA 59.455 40.741 0.00 0.00 36.71 2.43
404 751 6.369340 CGTATGTAGTCCATAGTCGAATCTCT 59.631 42.308 0.00 0.00 36.71 3.10
405 752 6.368243 TCGTATGTAGTCCATAGTCGAATCTC 59.632 42.308 0.00 0.00 36.71 2.75
406 753 6.228995 TCGTATGTAGTCCATAGTCGAATCT 58.771 40.000 0.00 0.00 36.71 2.40
407 754 6.477669 TCGTATGTAGTCCATAGTCGAATC 57.522 41.667 0.00 0.00 36.71 2.52
408 755 6.568081 GCTTCGTATGTAGTCCATAGTCGAAT 60.568 42.308 0.00 0.00 40.61 3.34
409 756 5.277683 GCTTCGTATGTAGTCCATAGTCGAA 60.278 44.000 0.00 0.00 39.87 3.71
410 757 4.212847 GCTTCGTATGTAGTCCATAGTCGA 59.787 45.833 0.00 0.00 36.71 4.20
411 758 4.024302 TGCTTCGTATGTAGTCCATAGTCG 60.024 45.833 0.00 0.00 36.71 4.18
412 759 5.434352 TGCTTCGTATGTAGTCCATAGTC 57.566 43.478 0.00 0.00 36.71 2.59
413 760 5.847111 TTGCTTCGTATGTAGTCCATAGT 57.153 39.130 0.00 0.00 36.71 2.12
414 761 7.438160 TCATTTTGCTTCGTATGTAGTCCATAG 59.562 37.037 0.00 0.00 36.71 2.23
415 762 7.269316 TCATTTTGCTTCGTATGTAGTCCATA 58.731 34.615 0.00 0.00 34.86 2.74
416 763 6.112734 TCATTTTGCTTCGTATGTAGTCCAT 58.887 36.000 0.00 0.00 37.58 3.41
417 764 5.483811 TCATTTTGCTTCGTATGTAGTCCA 58.516 37.500 0.00 0.00 0.00 4.02
418 765 5.581085 ACTCATTTTGCTTCGTATGTAGTCC 59.419 40.000 0.00 0.00 0.00 3.85
419 766 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
420 767 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
421 768 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
422 769 6.128391 GGTTCACTCATTTTGCTTCGTATGTA 60.128 38.462 0.00 0.00 0.00 2.29
423 770 5.334879 GGTTCACTCATTTTGCTTCGTATGT 60.335 40.000 0.00 0.00 0.00 2.29
424 771 5.088739 GGTTCACTCATTTTGCTTCGTATG 58.911 41.667 0.00 0.00 0.00 2.39
425 772 5.003804 AGGTTCACTCATTTTGCTTCGTAT 58.996 37.500 0.00 0.00 0.00 3.06
426 773 4.385825 AGGTTCACTCATTTTGCTTCGTA 58.614 39.130 0.00 0.00 0.00 3.43
427 774 3.214328 AGGTTCACTCATTTTGCTTCGT 58.786 40.909 0.00 0.00 0.00 3.85
428 775 3.904136 AGGTTCACTCATTTTGCTTCG 57.096 42.857 0.00 0.00 0.00 3.79
429 776 5.239525 AGTGTAGGTTCACTCATTTTGCTTC 59.760 40.000 0.00 0.00 44.07 3.86
430 777 5.133221 AGTGTAGGTTCACTCATTTTGCTT 58.867 37.500 0.00 0.00 44.07 3.91
431 778 4.718961 AGTGTAGGTTCACTCATTTTGCT 58.281 39.130 0.00 0.00 44.07 3.91
432 779 5.438761 AAGTGTAGGTTCACTCATTTTGC 57.561 39.130 0.00 0.00 46.25 3.68
433 780 9.796120 TTTTAAAGTGTAGGTTCACTCATTTTG 57.204 29.630 0.00 0.00 46.25 2.44
435 782 9.965824 CATTTTAAAGTGTAGGTTCACTCATTT 57.034 29.630 2.68 0.00 46.25 2.32
436 783 8.082242 GCATTTTAAAGTGTAGGTTCACTCATT 58.918 33.333 11.77 0.00 46.25 2.57
437 784 7.230510 TGCATTTTAAAGTGTAGGTTCACTCAT 59.769 33.333 11.77 0.00 46.25 2.90
438 785 6.544197 TGCATTTTAAAGTGTAGGTTCACTCA 59.456 34.615 11.77 0.00 46.25 3.41
439 786 6.966021 TGCATTTTAAAGTGTAGGTTCACTC 58.034 36.000 11.77 0.00 46.25 3.51
441 788 7.593825 AGATGCATTTTAAAGTGTAGGTTCAC 58.406 34.615 11.77 0.00 38.46 3.18
442 789 7.759489 AGATGCATTTTAAAGTGTAGGTTCA 57.241 32.000 11.77 1.68 0.00 3.18
503 850 8.645110 CCCTCCGTTCCTAAATATAAGTCTTTA 58.355 37.037 0.00 0.00 0.00 1.85
504 851 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
505 852 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
506 853 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
507 854 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
508 855 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
509 856 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
510 857 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
511 858 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
512 859 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
513 860 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
514 861 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
515 862 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
516 863 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
517 864 2.622452 CCTTGTACTCCCTCCGTTCCTA 60.622 54.545 0.00 0.00 0.00 2.94
518 865 1.558233 CTTGTACTCCCTCCGTTCCT 58.442 55.000 0.00 0.00 0.00 3.36
519 866 0.535797 CCTTGTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
520 867 0.108281 GCCTTGTACTCCCTCCGTTC 60.108 60.000 0.00 0.00 0.00 3.95
521 868 0.834687 TGCCTTGTACTCCCTCCGTT 60.835 55.000 0.00 0.00 0.00 4.44
522 869 1.229082 TGCCTTGTACTCCCTCCGT 60.229 57.895 0.00 0.00 0.00 4.69
523 870 1.517832 CTGCCTTGTACTCCCTCCG 59.482 63.158 0.00 0.00 0.00 4.63
524 871 0.910088 ACCTGCCTTGTACTCCCTCC 60.910 60.000 0.00 0.00 0.00 4.30
525 872 0.537653 GACCTGCCTTGTACTCCCTC 59.462 60.000 0.00 0.00 0.00 4.30
526 873 0.117340 AGACCTGCCTTGTACTCCCT 59.883 55.000 0.00 0.00 0.00 4.20
527 874 1.861982 TAGACCTGCCTTGTACTCCC 58.138 55.000 0.00 0.00 0.00 4.30
528 875 3.975168 TTTAGACCTGCCTTGTACTCC 57.025 47.619 0.00 0.00 0.00 3.85
529 876 5.105310 TGAGATTTAGACCTGCCTTGTACTC 60.105 44.000 0.00 0.00 0.00 2.59
530 877 4.777896 TGAGATTTAGACCTGCCTTGTACT 59.222 41.667 0.00 0.00 0.00 2.73
531 878 5.086104 TGAGATTTAGACCTGCCTTGTAC 57.914 43.478 0.00 0.00 0.00 2.90
532 879 5.425217 TGATGAGATTTAGACCTGCCTTGTA 59.575 40.000 0.00 0.00 0.00 2.41
533 880 4.225942 TGATGAGATTTAGACCTGCCTTGT 59.774 41.667 0.00 0.00 0.00 3.16
534 881 4.774124 TGATGAGATTTAGACCTGCCTTG 58.226 43.478 0.00 0.00 0.00 3.61
535 882 5.441718 TTGATGAGATTTAGACCTGCCTT 57.558 39.130 0.00 0.00 0.00 4.35
552 899 7.977904 TGTATAAAGTGCATCTCAGTTTGATG 58.022 34.615 7.70 0.00 45.30 3.07
554 901 7.386059 TCTGTATAAAGTGCATCTCAGTTTGA 58.614 34.615 7.70 0.00 45.30 2.69
600 947 3.877559 TGCCTATTCCAGTCAACATCAG 58.122 45.455 0.00 0.00 0.00 2.90
663 1080 3.823304 ACTTGAGAGGATTTGGCTTTGAC 59.177 43.478 0.00 0.00 0.00 3.18
705 1122 2.915657 AGGAGGGAGTAAACCGTAGT 57.084 50.000 0.00 0.00 0.00 2.73
767 1184 8.748412 TGATTTCTGGATTCAAATCGGTAATTT 58.252 29.630 0.00 0.00 40.50 1.82
810 1227 1.027357 GGTCGTCCGATTGGCTAGTA 58.973 55.000 0.00 0.00 34.14 1.82
881 1303 7.510675 TTTACTTCCAGAGATACAGGGAATT 57.489 36.000 0.00 0.00 38.63 2.17
947 1370 7.412237 GCATTGATTTCTTGCTGTAATGGTTTC 60.412 37.037 0.00 0.00 33.61 2.78
957 1380 2.268298 GCAGGCATTGATTTCTTGCTG 58.732 47.619 0.00 0.00 36.62 4.41
983 1406 3.615110 CGTCATCGAGATAAATGGGAGGG 60.615 52.174 0.00 0.00 39.71 4.30
1012 1435 9.841880 GTGTGTACTGTAGATGGTATATATGTG 57.158 37.037 0.00 0.00 0.00 3.21
1050 1473 2.598907 CGACGTTTGTGTTGGTAGCAAG 60.599 50.000 7.79 0.00 0.00 4.01
1068 1493 0.898326 AAGGCCCCATGGTTTTCGAC 60.898 55.000 11.73 0.00 0.00 4.20
1095 1520 2.765807 AGGACGAGGCAGGGGATG 60.766 66.667 0.00 0.00 0.00 3.51
1096 1521 2.444895 GAGGACGAGGCAGGGGAT 60.445 66.667 0.00 0.00 0.00 3.85
1117 1542 2.024871 GGACGAGGCGATGACGAG 59.975 66.667 0.00 0.00 42.66 4.18
1120 1545 1.064946 CTCTGGACGAGGCGATGAC 59.935 63.158 0.00 0.00 36.06 3.06
1366 1791 3.318017 AGTACAATTGCTCACAGTCGTC 58.682 45.455 5.05 0.00 0.00 4.20
1374 1799 1.725641 CCTGCGAGTACAATTGCTCA 58.274 50.000 5.05 0.00 34.24 4.26
1377 1802 1.429423 GGCCTGCGAGTACAATTGC 59.571 57.895 5.05 0.00 0.00 3.56
1411 1836 3.849953 GACGCCTTTAGCCGCACG 61.850 66.667 0.00 0.00 38.78 5.34
1517 1942 4.680537 ACTCCACGCCCGTCTCCT 62.681 66.667 0.00 0.00 0.00 3.69
1578 2003 3.751698 AGTGCACTATATCGAGCGTGATA 59.248 43.478 20.16 3.84 35.43 2.15
1632 2057 6.737254 TCATCTATTTTGAAACGAAGGGAC 57.263 37.500 0.00 0.00 0.00 4.46
1633 2058 6.542370 GGATCATCTATTTTGAAACGAAGGGA 59.458 38.462 0.00 0.00 0.00 4.20
1634 2059 6.318648 TGGATCATCTATTTTGAAACGAAGGG 59.681 38.462 0.00 0.00 0.00 3.95
1635 2060 7.320443 TGGATCATCTATTTTGAAACGAAGG 57.680 36.000 0.00 0.00 0.00 3.46
1636 2061 9.793252 AATTGGATCATCTATTTTGAAACGAAG 57.207 29.630 0.00 0.00 0.00 3.79
1696 2121 9.169592 CCCTCCGTTTTAAAATAGATAACTCAA 57.830 33.333 3.52 0.00 0.00 3.02
1697 2122 8.542080 TCCCTCCGTTTTAAAATAGATAACTCA 58.458 33.333 3.52 0.00 0.00 3.41
1698 2123 8.953368 TCCCTCCGTTTTAAAATAGATAACTC 57.047 34.615 3.52 0.00 0.00 3.01
1699 2124 8.546322 ACTCCCTCCGTTTTAAAATAGATAACT 58.454 33.333 3.52 0.00 0.00 2.24
1700 2125 8.728337 ACTCCCTCCGTTTTAAAATAGATAAC 57.272 34.615 3.52 0.00 0.00 1.89
1703 2128 9.916360 AAATACTCCCTCCGTTTTAAAATAGAT 57.084 29.630 3.52 0.00 0.00 1.98
1704 2129 9.743581 AAAATACTCCCTCCGTTTTAAAATAGA 57.256 29.630 3.52 3.61 0.00 1.98
1732 2157 3.118075 TGGCCAGATGAACGGATGAATTA 60.118 43.478 0.00 0.00 0.00 1.40
1734 2159 1.212688 TGGCCAGATGAACGGATGAAT 59.787 47.619 0.00 0.00 0.00 2.57
1756 2181 8.477419 AATTTCATGAGAAAACTCTAACCCAA 57.523 30.769 0.00 0.00 46.06 4.12
1815 2241 0.512952 GCAGATTGCGACGTTCAGTT 59.487 50.000 0.00 0.00 31.71 3.16
1863 2291 6.016693 CGTCTAGACTGATGTGTGAATATCCT 60.017 42.308 20.34 0.00 0.00 3.24
1892 2320 4.220821 CCACTACGCCCTCATGAATAGTAT 59.779 45.833 0.00 0.00 0.00 2.12
1893 2321 3.572682 CCACTACGCCCTCATGAATAGTA 59.427 47.826 0.00 0.00 0.00 1.82
1894 2322 2.365617 CCACTACGCCCTCATGAATAGT 59.634 50.000 0.00 0.00 0.00 2.12
1895 2323 2.868044 GCCACTACGCCCTCATGAATAG 60.868 54.545 0.00 0.00 0.00 1.73
1896 2324 1.070134 GCCACTACGCCCTCATGAATA 59.930 52.381 0.00 0.00 0.00 1.75
1897 2325 0.179045 GCCACTACGCCCTCATGAAT 60.179 55.000 0.00 0.00 0.00 2.57
1898 2326 1.220749 GCCACTACGCCCTCATGAA 59.779 57.895 0.00 0.00 0.00 2.57
1899 2327 2.731571 GGCCACTACGCCCTCATGA 61.732 63.158 0.00 0.00 43.66 3.07
1900 2328 2.203070 GGCCACTACGCCCTCATG 60.203 66.667 0.00 0.00 43.66 3.07
1913 2341 3.413915 TAATAGCTCCCGGGGGCCA 62.414 63.158 42.12 31.58 34.68 5.36
1914 2342 2.528378 TAATAGCTCCCGGGGGCC 60.528 66.667 42.12 23.99 34.68 5.80
1915 2343 1.535687 TCTAATAGCTCCCGGGGGC 60.536 63.158 39.67 39.67 34.68 5.80
1916 2344 0.471211 TGTCTAATAGCTCCCGGGGG 60.471 60.000 23.50 21.45 0.00 5.40
1917 2345 1.645710 ATGTCTAATAGCTCCCGGGG 58.354 55.000 23.50 13.02 0.00 5.73
1918 2346 3.325135 AGAAATGTCTAATAGCTCCCGGG 59.675 47.826 16.85 16.85 29.93 5.73
1919 2347 4.282195 AGAGAAATGTCTAATAGCTCCCGG 59.718 45.833 0.00 0.00 32.80 5.73
1920 2348 5.461032 AGAGAAATGTCTAATAGCTCCCG 57.539 43.478 0.00 0.00 32.80 5.14
1921 2349 7.533289 ACTAGAGAAATGTCTAATAGCTCCC 57.467 40.000 0.00 0.00 32.80 4.30
1922 2350 9.292195 AGTACTAGAGAAATGTCTAATAGCTCC 57.708 37.037 0.00 0.00 32.80 4.70
1929 2357 9.908747 AGAGCTTAGTACTAGAGAAATGTCTAA 57.091 33.333 2.23 0.00 32.80 2.10
1930 2358 9.550406 GAGAGCTTAGTACTAGAGAAATGTCTA 57.450 37.037 2.23 0.00 32.80 2.59
1931 2359 8.050325 TGAGAGCTTAGTACTAGAGAAATGTCT 58.950 37.037 2.23 0.00 36.55 3.41
1932 2360 8.215926 TGAGAGCTTAGTACTAGAGAAATGTC 57.784 38.462 2.23 3.82 0.00 3.06
1933 2361 7.284489 CCTGAGAGCTTAGTACTAGAGAAATGT 59.716 40.741 2.23 0.00 0.00 2.71
1934 2362 7.255451 CCCTGAGAGCTTAGTACTAGAGAAATG 60.255 44.444 2.23 0.00 0.00 2.32
1935 2363 6.775629 CCCTGAGAGCTTAGTACTAGAGAAAT 59.224 42.308 2.23 0.00 0.00 2.17
1936 2364 6.069556 TCCCTGAGAGCTTAGTACTAGAGAAA 60.070 42.308 2.23 0.00 0.00 2.52
1937 2365 5.429109 TCCCTGAGAGCTTAGTACTAGAGAA 59.571 44.000 2.23 0.00 0.00 2.87
1938 2366 4.969999 TCCCTGAGAGCTTAGTACTAGAGA 59.030 45.833 2.23 0.00 0.00 3.10
1939 2367 5.298989 TCCCTGAGAGCTTAGTACTAGAG 57.701 47.826 2.23 5.41 0.00 2.43
1940 2368 5.915744 ATCCCTGAGAGCTTAGTACTAGA 57.084 43.478 2.23 0.00 0.00 2.43
1941 2369 6.065374 TCAATCCCTGAGAGCTTAGTACTAG 58.935 44.000 2.23 0.00 0.00 2.57
1942 2370 6.014771 TCAATCCCTGAGAGCTTAGTACTA 57.985 41.667 0.00 0.00 0.00 1.82
1943 2371 4.873010 TCAATCCCTGAGAGCTTAGTACT 58.127 43.478 0.00 0.00 0.00 2.73
1955 2383 2.105821 ACCAAGACGTTTCAATCCCTGA 59.894 45.455 0.00 0.00 0.00 3.86
1972 2405 2.591429 CACAGCCTGTCGCACCAA 60.591 61.111 0.00 0.00 41.38 3.67
2016 2450 4.251103 ACACTTCTCCCAAAAACCTTCT 57.749 40.909 0.00 0.00 0.00 2.85
2040 2477 6.256053 ACCATTCTCCCAAGTGAATATGTTT 58.744 36.000 0.00 0.00 35.09 2.83
2050 2511 1.702957 TCCGAAACCATTCTCCCAAGT 59.297 47.619 0.00 0.00 33.17 3.16
2079 2943 2.863884 TCTCCCCATCTGGATTTTCCT 58.136 47.619 0.00 0.00 37.46 3.36
2145 4622 5.246307 GGGCAACAAGAAGTATGTAGTTCT 58.754 41.667 4.64 4.64 45.32 3.01
2212 4690 6.181908 CCATTGGATTGGGAAAAATTGATGT 58.818 36.000 0.00 0.00 32.80 3.06
2245 4723 0.608640 ACCTGCCAAGAGGTAAGACG 59.391 55.000 0.00 0.00 45.09 4.18
2299 4777 8.810652 TCCTTGTTTATGTAAAGTGCAAATTC 57.189 30.769 0.00 0.00 0.00 2.17
2395 4873 6.223852 TGTAACAGAGCTAAAAGTGGAAGAG 58.776 40.000 0.00 0.00 0.00 2.85
2425 4910 5.233689 GCATGGAAAATAAAGCTCAATCTGC 59.766 40.000 0.00 0.00 0.00 4.26
2444 4929 3.125316 CGCTTAATCAAAATGGGCATGG 58.875 45.455 0.00 0.00 0.00 3.66
2446 4931 2.483538 GGCGCTTAATCAAAATGGGCAT 60.484 45.455 7.64 0.00 38.14 4.40
2500 4985 2.036958 TGACAAATGTGCTATCCGGG 57.963 50.000 0.00 0.00 0.00 5.73
2559 5053 8.515695 TTGTATCAGCTCAAGAAATGATCATT 57.484 30.769 15.36 15.36 37.44 2.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.