Multiple sequence alignment - TraesCS4B01G366500

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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 TraesCS4B01G366500 chr4B 100.000 3571 0 0 1 3571 654038732 654035162 0.000000e+00 6595.0
1 TraesCS4B01G366500 chr4B 86.332 1017 124 10 1524 2539 12230096 12231098 0.000000e+00 1094.0
2 TraesCS4B01G366500 chrUn 89.614 2773 122 77 673 3381 126673653 126676323 0.000000e+00 3373.0
3 TraesCS4B01G366500 chrUn 88.410 371 31 6 1 365 126670571 126670935 1.520000e-118 436.0
4 TraesCS4B01G366500 chrUn 91.566 83 5 2 363 444 126670889 126670970 2.910000e-21 113.0
5 TraesCS4B01G366500 chrUn 81.148 122 8 7 3432 3551 126676485 126676593 2.280000e-12 84.2
6 TraesCS4B01G366500 chrUn 96.970 33 0 1 3392 3423 9171430 9171398 2.000000e-03 54.7
7 TraesCS4B01G366500 chrUn 96.970 33 0 1 3392 3423 205601066 205601034 2.000000e-03 54.7
8 TraesCS4B01G366500 chr5A 90.311 2312 112 58 651 2901 691671426 691669166 0.000000e+00 2926.0
9 TraesCS4B01G366500 chr5A 80.182 550 47 19 2899 3423 691669249 691668737 4.380000e-94 355.0
10 TraesCS4B01G366500 chr5A 89.720 107 10 1 196 301 338250444 338250338 6.220000e-28 135.0
11 TraesCS4B01G366500 chr5A 89.623 106 10 1 197 301 7183676 7183781 2.240000e-27 134.0
12 TraesCS4B01G366500 chr5A 89.623 106 10 1 197 301 402547779 402547884 2.240000e-27 134.0
13 TraesCS4B01G366500 chr5A 88.679 106 11 1 197 301 709762485 709762380 1.040000e-25 128.0
14 TraesCS4B01G366500 chr5A 87.037 108 10 1 27 130 691673954 691673847 6.260000e-23 119.0
15 TraesCS4B01G366500 chr5A 85.106 94 10 3 386 475 691672712 691672619 3.800000e-15 93.5
16 TraesCS4B01G366500 chr4D 86.444 1018 119 13 1524 2539 6898535 6899535 0.000000e+00 1098.0
17 TraesCS4B01G366500 chr4D 80.000 95 13 4 3034 3127 143277518 143277607 8.280000e-07 65.8
18 TraesCS4B01G366500 chr4A 86.230 1024 127 10 1524 2542 596625635 596624621 0.000000e+00 1098.0
19 TraesCS4B01G366500 chr4A 79.688 128 18 8 15 138 43347057 43347180 6.350000e-13 86.1
20 TraesCS4B01G366500 chr1A 90.476 672 58 5 1895 2566 500563579 500562914 0.000000e+00 881.0
21 TraesCS4B01G366500 chr1A 93.216 398 27 0 999 1396 452018575 452018972 1.430000e-163 586.0
22 TraesCS4B01G366500 chr1A 91.727 278 23 0 1526 1803 452019061 452019338 1.550000e-103 387.0
23 TraesCS4B01G366500 chr1D 90.327 672 59 5 1895 2566 405111093 405110428 0.000000e+00 876.0
24 TraesCS4B01G366500 chr1D 93.467 398 26 0 999 1396 351245580 351245977 3.070000e-165 592.0
25 TraesCS4B01G366500 chr1D 91.727 278 23 0 1526 1803 351246066 351246343 1.550000e-103 387.0
26 TraesCS4B01G366500 chr1D 88.182 110 12 1 197 305 392140978 392141087 2.890000e-26 130.0
27 TraesCS4B01G366500 chr1D 78.571 112 14 6 3034 3144 26248279 26248177 8.280000e-07 65.8
28 TraesCS4B01G366500 chr1B 88.988 672 68 5 1895 2566 544997379 544996714 0.000000e+00 826.0
29 TraesCS4B01G366500 chr1B 87.727 660 75 4 1882 2538 473824101 473824757 0.000000e+00 765.0
30 TraesCS4B01G366500 chr1B 93.719 398 25 0 999 1396 473822306 473822703 6.600000e-167 597.0
31 TraesCS4B01G366500 chr1B 91.727 278 23 0 1526 1803 473822792 473823069 1.550000e-103 387.0
32 TraesCS4B01G366500 chr1B 77.119 118 16 7 3034 3149 107877211 107877319 1.380000e-04 58.4
33 TraesCS4B01G366500 chr1B 77.119 118 16 7 3034 3149 159086820 159086712 1.380000e-04 58.4
34 TraesCS4B01G366500 chr1B 96.970 33 0 1 3392 3423 680742936 680742904 2.000000e-03 54.7
35 TraesCS4B01G366500 chr1B 96.970 33 0 1 3392 3423 682486288 682486256 2.000000e-03 54.7
36 TraesCS4B01G366500 chr6A 92.640 394 29 0 1003 1396 115944849 115945242 5.170000e-158 568.0
37 TraesCS4B01G366500 chr6A 88.679 106 11 1 197 301 53076410 53076305 1.040000e-25 128.0
38 TraesCS4B01G366500 chr6D 92.424 396 30 0 1001 1396 97012775 97013170 1.860000e-157 566.0
39 TraesCS4B01G366500 chr6B 92.172 396 31 0 1001 1396 180922095 180922490 8.660000e-156 560.0
40 TraesCS4B01G366500 chr5B 91.940 397 32 0 1000 1396 594873415 594873811 1.120000e-154 556.0
41 TraesCS4B01G366500 chr2A 88.991 109 11 1 197 304 24058852 24058744 2.240000e-27 134.0
42 TraesCS4B01G366500 chr5D 88.785 107 11 1 196 301 254848671 254848565 2.890000e-26 130.0
43 TraesCS4B01G366500 chr3B 78.814 118 14 7 3034 3149 403426176 403426068 6.400000e-08 69.4
44 TraesCS4B01G366500 chr3B 78.814 118 14 7 3034 3149 776779562 776779670 6.400000e-08 69.4
45 TraesCS4B01G366500 chr2B 78.814 118 14 7 3034 3149 57613720 57613612 6.400000e-08 69.4
46 TraesCS4B01G366500 chr7B 77.966 118 15 7 3034 3149 680513976 680514084 2.980000e-06 63.9


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 TraesCS4B01G366500 chr4B 654035162 654038732 3570 True 6595.000 6595 100.000000 1 3571 1 chr4B.!!$R1 3570
1 TraesCS4B01G366500 chr4B 12230096 12231098 1002 False 1094.000 1094 86.332000 1524 2539 1 chr4B.!!$F1 1015
2 TraesCS4B01G366500 chrUn 126670571 126676593 6022 False 1001.550 3373 87.684500 1 3551 4 chrUn.!!$F1 3550
3 TraesCS4B01G366500 chr5A 691668737 691673954 5217 True 873.375 2926 85.659000 27 3423 4 chr5A.!!$R3 3396
4 TraesCS4B01G366500 chr4D 6898535 6899535 1000 False 1098.000 1098 86.444000 1524 2539 1 chr4D.!!$F1 1015
5 TraesCS4B01G366500 chr4A 596624621 596625635 1014 True 1098.000 1098 86.230000 1524 2542 1 chr4A.!!$R1 1018
6 TraesCS4B01G366500 chr1A 500562914 500563579 665 True 881.000 881 90.476000 1895 2566 1 chr1A.!!$R1 671
7 TraesCS4B01G366500 chr1A 452018575 452019338 763 False 486.500 586 92.471500 999 1803 2 chr1A.!!$F1 804
8 TraesCS4B01G366500 chr1D 405110428 405111093 665 True 876.000 876 90.327000 1895 2566 1 chr1D.!!$R2 671
9 TraesCS4B01G366500 chr1D 351245580 351246343 763 False 489.500 592 92.597000 999 1803 2 chr1D.!!$F2 804
10 TraesCS4B01G366500 chr1B 544996714 544997379 665 True 826.000 826 88.988000 1895 2566 1 chr1B.!!$R2 671
11 TraesCS4B01G366500 chr1B 473822306 473824757 2451 False 583.000 765 91.057667 999 2538 3 chr1B.!!$F2 1539

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
605 2205 0.162933 GCTTCGTGCAAAATCGACGA 59.837 50.0 0.0 0.0 42.31 4.20 F
897 5480 0.179045 CTAACGCCATCCCCCTCTTG 60.179 60.0 0.0 0.0 0.00 3.02 F
1808 6424 0.179000 CCCCGAGCTGTAAGAAGCAT 59.821 55.0 0.0 0.0 46.08 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 6110 0.107508 CAGATCCGTCAGCCACCATT 60.108 55.0 0.00 0.0 0.00 3.16 R
1878 7048 0.675083 TTCAGGTCGCCGACTGTTTA 59.325 50.0 17.76 0.0 32.47 2.01 R
2931 8520 0.171455 AATCAGACACGAGCGACTCC 59.829 55.0 0.00 0.0 0.00 3.85 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
193 202 7.044181 TCTATGGCTAGCAGATAACAATATGC 58.956 38.462 18.24 0.00 38.91 3.14
202 211 8.159344 AGCAGATAACAATATGCTTTACTTCC 57.841 34.615 1.83 0.00 45.66 3.46
211 220 7.119846 ACAATATGCTTTACTTCCTCTGTTCAC 59.880 37.037 0.00 0.00 0.00 3.18
223 232 7.599245 ACTTCCTCTGTTCACTTTTATAAGACG 59.401 37.037 0.00 0.00 35.30 4.18
243 252 5.043189 ACGTTTTAGACAATTTAGGCAGC 57.957 39.130 0.00 0.00 0.00 5.25
244 253 4.088648 CGTTTTAGACAATTTAGGCAGCG 58.911 43.478 0.00 0.00 0.00 5.18
265 275 3.424962 CGCCAAAGTAGTTCAAAGCTAGC 60.425 47.826 6.62 6.62 0.00 3.42
269 279 5.239525 CCAAAGTAGTTCAAAGCTAGCTGTT 59.760 40.000 20.16 11.83 0.00 3.16
285 295 7.386848 AGCTAGCTGTTCAAAACGTCTTATAAA 59.613 33.333 18.57 0.00 0.00 1.40
289 299 8.185505 AGCTGTTCAAAACGTCTTATAAAAACA 58.814 29.630 0.00 0.00 0.00 2.83
290 300 8.800031 GCTGTTCAAAACGTCTTATAAAAACAA 58.200 29.630 0.00 0.00 0.00 2.83
294 304 8.325367 TCAAAACGTCTTATAAAAACAAACGG 57.675 30.769 0.00 0.00 33.26 4.44
295 305 8.180267 TCAAAACGTCTTATAAAAACAAACGGA 58.820 29.630 0.00 0.00 33.26 4.69
296 306 8.466026 CAAAACGTCTTATAAAAACAAACGGAG 58.534 33.333 0.00 0.00 33.26 4.63
297 307 7.481275 AACGTCTTATAAAAACAAACGGAGA 57.519 32.000 0.00 0.00 33.26 3.71
301 311 7.235080 GTCTTATAAAAACAAACGGAGAGAGC 58.765 38.462 0.00 0.00 0.00 4.09
339 1393 0.527565 CCCAAATGCTTTCTGGACGG 59.472 55.000 12.20 0.00 31.38 4.79
340 1394 1.533625 CCAAATGCTTTCTGGACGGA 58.466 50.000 7.38 0.00 31.38 4.69
341 1395 1.470098 CCAAATGCTTTCTGGACGGAG 59.530 52.381 7.38 0.00 31.38 4.63
342 1396 2.426522 CAAATGCTTTCTGGACGGAGA 58.573 47.619 0.00 0.00 0.00 3.71
343 1397 2.813754 CAAATGCTTTCTGGACGGAGAA 59.186 45.455 0.00 0.00 0.00 2.87
344 1398 3.356529 AATGCTTTCTGGACGGAGAAT 57.643 42.857 0.00 0.00 31.98 2.40
345 1399 2.859165 TGCTTTCTGGACGGAGAATT 57.141 45.000 0.00 0.00 31.98 2.17
346 1400 3.140325 TGCTTTCTGGACGGAGAATTT 57.860 42.857 0.00 0.00 31.98 1.82
347 1401 3.486383 TGCTTTCTGGACGGAGAATTTT 58.514 40.909 0.00 0.00 31.98 1.82
348 1402 3.888930 TGCTTTCTGGACGGAGAATTTTT 59.111 39.130 0.00 0.00 31.98 1.94
371 1425 8.443953 TTTTTGGGTTTGTAGAATTCCAAATG 57.556 30.769 15.61 0.00 41.82 2.32
372 1426 5.146010 TGGGTTTGTAGAATTCCAAATGC 57.854 39.130 11.47 2.73 33.53 3.56
373 1427 4.837860 TGGGTTTGTAGAATTCCAAATGCT 59.162 37.500 11.47 0.00 33.53 3.79
374 1428 5.306678 TGGGTTTGTAGAATTCCAAATGCTT 59.693 36.000 11.47 0.00 33.53 3.91
375 1429 6.183361 TGGGTTTGTAGAATTCCAAATGCTTT 60.183 34.615 11.47 0.00 33.53 3.51
376 1430 6.368791 GGGTTTGTAGAATTCCAAATGCTTTC 59.631 38.462 11.47 1.12 33.53 2.62
377 1431 7.154656 GGTTTGTAGAATTCCAAATGCTTTCT 58.845 34.615 11.47 0.00 33.53 2.52
378 1432 7.116805 GGTTTGTAGAATTCCAAATGCTTTCTG 59.883 37.037 11.47 0.00 33.53 3.02
379 1433 6.271488 TGTAGAATTCCAAATGCTTTCTGG 57.729 37.500 0.65 7.02 0.00 3.86
380 1434 6.009589 TGTAGAATTCCAAATGCTTTCTGGA 58.990 36.000 0.65 10.26 37.47 3.86
381 1435 6.664816 TGTAGAATTCCAAATGCTTTCTGGAT 59.335 34.615 0.65 4.40 38.99 3.41
436 1490 4.518211 GCACTTGCTAGCATATTCCAATCT 59.482 41.667 20.13 0.00 38.21 2.40
437 1491 5.562307 GCACTTGCTAGCATATTCCAATCTG 60.562 44.000 20.13 1.49 38.21 2.90
475 1640 5.107824 GTCGAATTAGTAACCACCTCCTTC 58.892 45.833 0.00 0.00 0.00 3.46
568 1901 2.154462 CTCTTGATTTGCGTTGTCCCT 58.846 47.619 0.00 0.00 0.00 4.20
574 1907 1.155424 TTTGCGTTGTCCCTGTCGAC 61.155 55.000 9.11 9.11 0.00 4.20
605 2205 0.162933 GCTTCGTGCAAAATCGACGA 59.837 50.000 0.00 0.00 42.31 4.20
609 2209 1.193650 TCGTGCAAAATCGACGAAAGG 59.806 47.619 0.00 0.00 39.07 3.11
619 2219 2.963432 TCGACGAAAGGGATTTGGTAC 58.037 47.619 0.00 0.00 0.00 3.34
640 2240 4.394729 ACGTACCACAGGTTCAAATGATT 58.605 39.130 0.00 0.00 37.09 2.57
649 2249 4.687483 CAGGTTCAAATGATTTCAAGTGCC 59.313 41.667 0.00 0.00 0.00 5.01
692 5239 4.525487 ACCATGATGAAGCAGTCAACAAAT 59.475 37.500 0.00 0.00 41.79 2.32
704 5251 2.962421 GTCAACAAATTTCACCTCCCCA 59.038 45.455 0.00 0.00 0.00 4.96
705 5252 3.578282 GTCAACAAATTTCACCTCCCCAT 59.422 43.478 0.00 0.00 0.00 4.00
708 5255 1.832998 CAAATTTCACCTCCCCATGGG 59.167 52.381 25.30 25.30 46.11 4.00
713 5269 4.348495 ACCTCCCCATGGGACCGT 62.348 66.667 33.62 20.27 46.17 4.83
778 5334 4.794439 GCCGCCCCACGCAAAATC 62.794 66.667 0.00 0.00 41.76 2.17
779 5335 4.474846 CCGCCCCACGCAAAATCG 62.475 66.667 0.00 0.00 41.76 3.34
788 5346 1.978782 CACGCAAAATCGCCTCTTTTC 59.021 47.619 0.00 0.00 0.00 2.29
789 5347 1.880027 ACGCAAAATCGCCTCTTTTCT 59.120 42.857 0.00 0.00 0.00 2.52
897 5480 0.179045 CTAACGCCATCCCCCTCTTG 60.179 60.000 0.00 0.00 0.00 3.02
899 5482 3.801997 CGCCATCCCCCTCTTGCT 61.802 66.667 0.00 0.00 0.00 3.91
902 5485 2.002977 CCATCCCCCTCTTGCTCCA 61.003 63.158 0.00 0.00 0.00 3.86
904 5487 0.554792 CATCCCCCTCTTGCTCCAAT 59.445 55.000 0.00 0.00 0.00 3.16
906 5489 0.625849 TCCCCCTCTTGCTCCAATTC 59.374 55.000 0.00 0.00 0.00 2.17
910 5493 0.332632 CCTCTTGCTCCAATTCCCCA 59.667 55.000 0.00 0.00 0.00 4.96
912 5495 1.821136 CTCTTGCTCCAATTCCCCAAC 59.179 52.381 0.00 0.00 0.00 3.77
913 5496 0.897621 CTTGCTCCAATTCCCCAACC 59.102 55.000 0.00 0.00 0.00 3.77
914 5497 0.544120 TTGCTCCAATTCCCCAACCC 60.544 55.000 0.00 0.00 0.00 4.11
915 5498 1.685765 GCTCCAATTCCCCAACCCC 60.686 63.158 0.00 0.00 0.00 4.95
916 5499 1.001631 CTCCAATTCCCCAACCCCC 59.998 63.158 0.00 0.00 0.00 5.40
982 5569 4.147135 CGAAGGGAAGGGAAGGGA 57.853 61.111 0.00 0.00 0.00 4.20
983 5570 2.383608 CGAAGGGAAGGGAAGGGAA 58.616 57.895 0.00 0.00 0.00 3.97
984 5571 0.253327 CGAAGGGAAGGGAAGGGAAG 59.747 60.000 0.00 0.00 0.00 3.46
985 5572 0.626382 GAAGGGAAGGGAAGGGAAGG 59.374 60.000 0.00 0.00 0.00 3.46
986 5573 0.851332 AAGGGAAGGGAAGGGAAGGG 60.851 60.000 0.00 0.00 0.00 3.95
987 5574 1.230182 GGGAAGGGAAGGGAAGGGA 60.230 63.158 0.00 0.00 0.00 4.20
988 5575 0.849540 GGGAAGGGAAGGGAAGGGAA 60.850 60.000 0.00 0.00 0.00 3.97
989 5576 0.626382 GGAAGGGAAGGGAAGGGAAG 59.374 60.000 0.00 0.00 0.00 3.46
990 5577 0.626382 GAAGGGAAGGGAAGGGAAGG 59.374 60.000 0.00 0.00 0.00 3.46
991 5578 0.198696 AAGGGAAGGGAAGGGAAGGA 59.801 55.000 0.00 0.00 0.00 3.36
992 5579 0.198696 AGGGAAGGGAAGGGAAGGAA 59.801 55.000 0.00 0.00 0.00 3.36
993 5580 1.081481 GGGAAGGGAAGGGAAGGAAA 58.919 55.000 0.00 0.00 0.00 3.13
994 5581 1.006043 GGGAAGGGAAGGGAAGGAAAG 59.994 57.143 0.00 0.00 0.00 2.62
995 5582 1.006043 GGAAGGGAAGGGAAGGAAAGG 59.994 57.143 0.00 0.00 0.00 3.11
996 5583 1.006043 GAAGGGAAGGGAAGGAAAGGG 59.994 57.143 0.00 0.00 0.00 3.95
997 5584 0.851332 AGGGAAGGGAAGGAAAGGGG 60.851 60.000 0.00 0.00 0.00 4.79
1405 5992 1.948144 GCCTCCAAGGTCTCTGCTTTC 60.948 57.143 0.00 0.00 37.80 2.62
1406 5993 1.627834 CCTCCAAGGTCTCTGCTTTCT 59.372 52.381 0.00 0.00 0.00 2.52
1476 6092 4.647615 CGGCGGCGTAGATCTGGG 62.648 72.222 24.74 0.00 0.00 4.45
1481 6097 3.537874 GCGTAGATCTGGGGCGGT 61.538 66.667 5.18 0.00 0.00 5.68
1484 6100 0.536687 CGTAGATCTGGGGCGGTAGA 60.537 60.000 5.18 0.00 0.00 2.59
1488 6104 1.120530 GATCTGGGGCGGTAGAGAAA 58.879 55.000 0.00 0.00 0.00 2.52
1489 6105 1.694696 GATCTGGGGCGGTAGAGAAAT 59.305 52.381 0.00 0.00 0.00 2.17
1491 6107 0.830648 CTGGGGCGGTAGAGAAATGA 59.169 55.000 0.00 0.00 0.00 2.57
1492 6108 0.830648 TGGGGCGGTAGAGAAATGAG 59.169 55.000 0.00 0.00 0.00 2.90
1493 6109 1.120530 GGGGCGGTAGAGAAATGAGA 58.879 55.000 0.00 0.00 0.00 3.27
1494 6110 1.485066 GGGGCGGTAGAGAAATGAGAA 59.515 52.381 0.00 0.00 0.00 2.87
1495 6111 2.093128 GGGGCGGTAGAGAAATGAGAAA 60.093 50.000 0.00 0.00 0.00 2.52
1496 6112 3.433740 GGGGCGGTAGAGAAATGAGAAAT 60.434 47.826 0.00 0.00 0.00 2.17
1497 6113 3.561725 GGGCGGTAGAGAAATGAGAAATG 59.438 47.826 0.00 0.00 0.00 2.32
1498 6114 3.561725 GGCGGTAGAGAAATGAGAAATGG 59.438 47.826 0.00 0.00 0.00 3.16
1803 6419 1.229082 ACCACCCCGAGCTGTAAGA 60.229 57.895 0.00 0.00 34.07 2.10
1807 6423 1.192146 ACCCCGAGCTGTAAGAAGCA 61.192 55.000 0.00 0.00 46.08 3.91
1808 6424 0.179000 CCCCGAGCTGTAAGAAGCAT 59.821 55.000 0.00 0.00 46.08 3.79
1857 7019 3.811722 TGTCGTTTGATGATTGCTGAC 57.188 42.857 0.00 0.00 0.00 3.51
1858 7020 2.483877 TGTCGTTTGATGATTGCTGACC 59.516 45.455 0.00 0.00 0.00 4.02
1859 7021 2.744202 GTCGTTTGATGATTGCTGACCT 59.256 45.455 0.00 0.00 0.00 3.85
1861 7023 2.743664 CGTTTGATGATTGCTGACCTCA 59.256 45.455 0.00 0.00 0.00 3.86
1862 7024 3.189080 CGTTTGATGATTGCTGACCTCAA 59.811 43.478 0.00 0.00 0.00 3.02
1863 7025 4.670992 CGTTTGATGATTGCTGACCTCAAG 60.671 45.833 0.00 0.00 0.00 3.02
1875 7045 5.159209 GCTGACCTCAAGAATCAAACAATG 58.841 41.667 0.00 0.00 0.00 2.82
1876 7046 5.048504 GCTGACCTCAAGAATCAAACAATGA 60.049 40.000 0.00 0.00 43.67 2.57
1877 7047 6.515531 GCTGACCTCAAGAATCAAACAATGAA 60.516 38.462 0.00 0.00 42.54 2.57
1878 7048 7.528996 TGACCTCAAGAATCAAACAATGAAT 57.471 32.000 0.00 0.00 42.54 2.57
1879 7049 8.634335 TGACCTCAAGAATCAAACAATGAATA 57.366 30.769 0.00 0.00 42.54 1.75
2267 7839 1.276989 GAGTGGATCCCCAACAACGTA 59.723 52.381 9.90 0.00 45.59 3.57
2551 8123 3.186730 CGAGCTCGAGGACGACGA 61.187 66.667 32.06 0.00 43.81 4.20
2580 8152 1.008327 TCCAGGGCTAGAGATCAACCA 59.992 52.381 0.00 0.00 0.00 3.67
2586 8158 3.707102 GGGCTAGAGATCAACCAAGTACT 59.293 47.826 0.00 0.00 0.00 2.73
2587 8159 4.894114 GGGCTAGAGATCAACCAAGTACTA 59.106 45.833 0.00 0.00 0.00 1.82
2588 8160 5.221283 GGGCTAGAGATCAACCAAGTACTAC 60.221 48.000 0.00 0.00 0.00 2.73
2589 8161 5.595133 GGCTAGAGATCAACCAAGTACTACT 59.405 44.000 0.00 0.00 0.00 2.57
2595 8167 4.164822 TCAACCAAGTACTACTGCGTAC 57.835 45.455 0.00 0.00 39.97 3.67
2602 8174 5.850128 CCAAGTACTACTGCGTACGATTATC 59.150 44.000 21.65 0.45 43.42 1.75
2614 8186 5.331383 GCGTACGATTATCGGTTCTTTTCTC 60.331 44.000 21.65 0.00 45.59 2.87
2720 8292 0.251297 CATGGAAGGGTGGTTGCTGA 60.251 55.000 0.00 0.00 0.00 4.26
2735 8307 3.920231 TGCTGATGAGATAGCTTGGTT 57.080 42.857 0.00 0.00 40.52 3.67
2736 8308 3.538591 TGCTGATGAGATAGCTTGGTTG 58.461 45.455 0.00 0.00 40.52 3.77
2737 8309 2.877168 GCTGATGAGATAGCTTGGTTGG 59.123 50.000 0.00 0.00 36.99 3.77
2738 8310 3.683847 GCTGATGAGATAGCTTGGTTGGT 60.684 47.826 0.00 0.00 36.99 3.67
2739 8311 4.443457 GCTGATGAGATAGCTTGGTTGGTA 60.443 45.833 0.00 0.00 36.99 3.25
2740 8312 5.023533 TGATGAGATAGCTTGGTTGGTAC 57.976 43.478 0.00 0.00 0.00 3.34
2741 8313 4.716784 TGATGAGATAGCTTGGTTGGTACT 59.283 41.667 0.00 0.00 0.00 2.73
2749 8321 8.008922 AGATAGCTTGGTTGGTACTATAACCTA 58.991 37.037 20.12 14.86 45.16 3.08
2773 8345 2.443887 ACAATTGCTGTGGAATGTGC 57.556 45.000 5.05 0.00 36.69 4.57
2774 8346 1.687660 ACAATTGCTGTGGAATGTGCA 59.312 42.857 5.05 0.00 36.69 4.57
2776 8348 2.734606 CAATTGCTGTGGAATGTGCAAG 59.265 45.455 0.00 0.00 46.37 4.01
2777 8349 0.032403 TTGCTGTGGAATGTGCAAGC 59.968 50.000 0.00 0.00 39.98 4.01
2802 8374 3.826637 GCCCTGTTGCGTTCTACTA 57.173 52.632 0.00 0.00 0.00 1.82
2805 8377 2.607187 CCCTGTTGCGTTCTACTAGTG 58.393 52.381 5.39 0.00 0.00 2.74
2819 8408 2.679082 ACTAGTGGTGTCCAGTGTCTT 58.321 47.619 0.00 0.00 37.77 3.01
2820 8409 2.628657 ACTAGTGGTGTCCAGTGTCTTC 59.371 50.000 0.00 0.00 37.77 2.87
2858 8447 9.713740 CAAATCTAATGTAATCTGAAGTTGCTC 57.286 33.333 0.00 0.00 0.00 4.26
2930 8519 7.946918 TCGTGTTAAATCTTAATGCAATTCG 57.053 32.000 0.00 0.00 37.87 3.34
2931 8520 6.964370 TCGTGTTAAATCTTAATGCAATTCGG 59.036 34.615 0.00 0.00 37.87 4.30
2936 8525 5.757850 AATCTTAATGCAATTCGGGAGTC 57.242 39.130 0.00 0.00 37.87 3.36
2968 8557 5.416639 TCTGATTTCAGTCCATGATTTGTGG 59.583 40.000 7.42 0.00 44.12 4.17
2969 8558 5.078949 TGATTTCAGTCCATGATTTGTGGT 58.921 37.500 0.00 0.00 37.89 4.16
2970 8559 6.244654 TGATTTCAGTCCATGATTTGTGGTA 58.755 36.000 0.00 0.00 37.89 3.25
2971 8560 6.375174 TGATTTCAGTCCATGATTTGTGGTAG 59.625 38.462 0.00 0.00 37.89 3.18
2977 8566 5.104360 AGTCCATGATTTGTGGTAGTATGCT 60.104 40.000 0.00 0.00 37.96 3.79
2980 8569 6.326323 TCCATGATTTGTGGTAGTATGCTCTA 59.674 38.462 0.00 0.00 37.96 2.43
2989 8578 6.263392 TGTGGTAGTATGCTCTAGATCTTGTC 59.737 42.308 0.00 0.00 0.00 3.18
2994 8583 4.935352 ATGCTCTAGATCTTGTCCTGTC 57.065 45.455 0.00 0.00 0.00 3.51
3000 8589 5.760131 TCTAGATCTTGTCCTGTCTCATGA 58.240 41.667 0.00 0.00 0.00 3.07
3015 8604 6.327154 TGTCTCATGATGTGAAATGAAATGC 58.673 36.000 0.00 0.00 36.14 3.56
3042 8631 5.760743 GCACCACTAGTTTCTTTCTTCTTCT 59.239 40.000 0.00 0.00 0.00 2.85
3044 8633 7.201741 GCACCACTAGTTTCTTTCTTCTTCTTT 60.202 37.037 0.00 0.00 0.00 2.52
3046 8635 8.047310 ACCACTAGTTTCTTTCTTCTTCTTTCA 58.953 33.333 0.00 0.00 0.00 2.69
3082 8674 5.469760 TGTCGATCTGCAAATGGTATTATGG 59.530 40.000 0.00 0.00 0.00 2.74
3087 8679 5.765510 TCTGCAAATGGTATTATGGTTCCT 58.234 37.500 0.00 0.00 0.00 3.36
3088 8680 6.194235 TCTGCAAATGGTATTATGGTTCCTT 58.806 36.000 0.00 0.00 0.00 3.36
3089 8681 6.096705 TCTGCAAATGGTATTATGGTTCCTTG 59.903 38.462 0.00 0.00 0.00 3.61
3090 8682 5.954752 TGCAAATGGTATTATGGTTCCTTGA 59.045 36.000 0.00 0.00 0.00 3.02
3091 8683 6.096705 TGCAAATGGTATTATGGTTCCTTGAG 59.903 38.462 0.00 0.00 0.00 3.02
3092 8684 6.507023 CAAATGGTATTATGGTTCCTTGAGC 58.493 40.000 0.00 0.00 0.00 4.26
3093 8685 5.653255 ATGGTATTATGGTTCCTTGAGCT 57.347 39.130 0.00 0.00 0.00 4.09
3094 8686 5.450818 TGGTATTATGGTTCCTTGAGCTT 57.549 39.130 0.00 0.00 0.00 3.74
3095 8687 5.192927 TGGTATTATGGTTCCTTGAGCTTG 58.807 41.667 0.00 0.00 0.00 4.01
3096 8688 5.045213 TGGTATTATGGTTCCTTGAGCTTGA 60.045 40.000 0.00 0.00 0.00 3.02
3120 8713 4.452114 TGATGACAGATTGTTGCACACTAC 59.548 41.667 0.00 0.00 0.00 2.73
3150 8743 7.432252 GCTGTTCCAGTGTTTACATATTATTGC 59.568 37.037 0.00 0.00 33.43 3.56
3151 8744 8.574251 TGTTCCAGTGTTTACATATTATTGCT 57.426 30.769 0.00 0.00 0.00 3.91
3152 8745 9.019656 TGTTCCAGTGTTTACATATTATTGCTT 57.980 29.630 0.00 0.00 0.00 3.91
3153 8746 9.289303 GTTCCAGTGTTTACATATTATTGCTTG 57.711 33.333 0.00 0.00 0.00 4.01
3154 8747 7.479980 TCCAGTGTTTACATATTATTGCTTGC 58.520 34.615 0.00 0.00 0.00 4.01
3155 8748 7.121907 TCCAGTGTTTACATATTATTGCTTGCA 59.878 33.333 0.00 0.00 0.00 4.08
3179 8772 1.600957 GCAGTACACATATGCCAGCAG 59.399 52.381 1.58 0.00 33.81 4.24
3190 8783 4.069869 CCAGCAGTGTCTGGTTGG 57.930 61.111 19.62 4.26 46.59 3.77
3222 8815 2.681848 CCATGGATCTTGTTCTCTGCAC 59.318 50.000 5.56 0.00 0.00 4.57
3245 8838 1.065053 TGCACCACAGTAACAGTTGGT 60.065 47.619 0.00 0.00 0.00 3.67
3246 8839 1.333619 GCACCACAGTAACAGTTGGTG 59.666 52.381 14.75 14.75 46.70 4.17
3254 8866 3.253188 CAGTAACAGTTGGTGATGGTTGG 59.747 47.826 0.00 0.00 0.00 3.77
3265 8877 0.819582 GATGGTTGGTTGGGCAGATG 59.180 55.000 0.00 0.00 0.00 2.90
3300 8912 4.360027 GTGTCGCAGCACAGCACG 62.360 66.667 0.00 0.00 39.07 5.34
3334 8946 1.000274 CAAAGTTGCTCCTTTTCCCCG 60.000 52.381 0.00 0.00 32.42 5.73
3338 8950 0.538746 TTGCTCCTTTTCCCCGTTCC 60.539 55.000 0.00 0.00 0.00 3.62
3366 8978 1.975660 TTACAAACTCCCCTGTGCAC 58.024 50.000 10.75 10.75 0.00 4.57
3381 8993 2.029020 TGTGCACGGGATAGATCTATGC 60.029 50.000 22.38 22.38 33.76 3.14
3419 9031 4.081309 CCTCCGTCCCAAATTACTTGTCTA 60.081 45.833 0.00 0.00 32.65 2.59
3420 9032 5.080969 TCCGTCCCAAATTACTTGTCTAG 57.919 43.478 0.00 0.00 32.65 2.43
3422 9034 5.424252 TCCGTCCCAAATTACTTGTCTAGAT 59.576 40.000 0.00 0.00 32.65 1.98
3423 9035 5.753921 CCGTCCCAAATTACTTGTCTAGATC 59.246 44.000 0.00 0.00 32.65 2.75
3425 9037 6.477033 CGTCCCAAATTACTTGTCTAGATCAG 59.523 42.308 0.00 0.00 32.65 2.90
3426 9038 7.556844 GTCCCAAATTACTTGTCTAGATCAGA 58.443 38.462 0.00 0.00 32.65 3.27
3448 9178 9.175312 TCAGACTTGTATACTAAGTTGTCCTAG 57.825 37.037 16.62 0.00 38.42 3.02
3480 9210 4.629200 GGTCTTATCTCAAGTTGCTGTGAG 59.371 45.833 0.00 0.00 42.23 3.51
3485 9215 4.613925 TCTCAAGTTGCTGTGAGATTCT 57.386 40.909 0.00 0.00 44.12 2.40
3486 9216 4.313282 TCTCAAGTTGCTGTGAGATTCTG 58.687 43.478 0.00 0.00 44.12 3.02
3487 9217 4.063689 CTCAAGTTGCTGTGAGATTCTGT 58.936 43.478 0.00 0.00 43.32 3.41
3488 9218 4.060900 TCAAGTTGCTGTGAGATTCTGTC 58.939 43.478 0.00 0.00 0.00 3.51
3489 9219 3.051081 AGTTGCTGTGAGATTCTGTCC 57.949 47.619 0.00 0.00 0.00 4.02
3506 9236 2.159181 CCGTTTGACCGGTCATCAC 58.841 57.895 36.52 30.81 43.07 3.06
3514 9244 0.762418 ACCGGTCATCACCTTGTTCA 59.238 50.000 0.00 0.00 41.17 3.18
3517 9247 2.009774 CGGTCATCACCTTGTTCATCC 58.990 52.381 0.00 0.00 41.17 3.51
3520 9250 0.734889 CATCACCTTGTTCATCCCGC 59.265 55.000 0.00 0.00 0.00 6.13
3521 9251 0.620556 ATCACCTTGTTCATCCCGCT 59.379 50.000 0.00 0.00 0.00 5.52
3522 9252 0.321564 TCACCTTGTTCATCCCGCTG 60.322 55.000 0.00 0.00 0.00 5.18
3523 9253 1.675641 ACCTTGTTCATCCCGCTGC 60.676 57.895 0.00 0.00 0.00 5.25
3551 9281 9.103861 GCTCTGTTTCTGAGCTAATTTTATACT 57.896 33.333 17.09 0.00 46.81 2.12
3553 9283 9.601217 TCTGTTTCTGAGCTAATTTTATACTCC 57.399 33.333 0.00 0.00 0.00 3.85
3554 9284 8.732746 TGTTTCTGAGCTAATTTTATACTCCC 57.267 34.615 0.00 0.00 0.00 4.30
3555 9285 8.548877 TGTTTCTGAGCTAATTTTATACTCCCT 58.451 33.333 0.00 0.00 0.00 4.20
3556 9286 9.047371 GTTTCTGAGCTAATTTTATACTCCCTC 57.953 37.037 0.00 0.00 0.00 4.30
3557 9287 7.304497 TCTGAGCTAATTTTATACTCCCTCC 57.696 40.000 0.00 0.00 0.00 4.30
3558 9288 6.015350 TCTGAGCTAATTTTATACTCCCTCCG 60.015 42.308 0.00 0.00 0.00 4.63
3559 9289 5.601313 TGAGCTAATTTTATACTCCCTCCGT 59.399 40.000 0.00 0.00 0.00 4.69
3560 9290 6.099269 TGAGCTAATTTTATACTCCCTCCGTT 59.901 38.462 0.00 0.00 0.00 4.44
3561 9291 6.896883 AGCTAATTTTATACTCCCTCCGTTT 58.103 36.000 0.00 0.00 0.00 3.60
3562 9292 6.990939 AGCTAATTTTATACTCCCTCCGTTTC 59.009 38.462 0.00 0.00 0.00 2.78
3563 9293 6.990939 GCTAATTTTATACTCCCTCCGTTTCT 59.009 38.462 0.00 0.00 0.00 2.52
3564 9294 7.498239 GCTAATTTTATACTCCCTCCGTTTCTT 59.502 37.037 0.00 0.00 0.00 2.52
3565 9295 9.392259 CTAATTTTATACTCCCTCCGTTTCTTT 57.608 33.333 0.00 0.00 0.00 2.52
3566 9296 8.645814 AATTTTATACTCCCTCCGTTTCTTTT 57.354 30.769 0.00 0.00 0.00 2.27
3567 9297 8.645814 ATTTTATACTCCCTCCGTTTCTTTTT 57.354 30.769 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 232 3.851969 GCGCTGCCTAAATTGTCTAAAAC 59.148 43.478 0.00 0.00 0.00 2.43
239 248 0.591170 TTGAACTACTTTGGCGCTGC 59.409 50.000 7.64 0.00 0.00 5.25
243 252 3.424962 GCTAGCTTTGAACTACTTTGGCG 60.425 47.826 7.70 0.00 0.00 5.69
244 253 3.753797 AGCTAGCTTTGAACTACTTTGGC 59.246 43.478 12.68 0.00 0.00 4.52
250 260 5.924475 TTGAACAGCTAGCTTTGAACTAC 57.076 39.130 16.46 1.85 0.00 2.73
251 261 6.511121 CGTTTTGAACAGCTAGCTTTGAACTA 60.511 38.462 16.46 0.00 0.00 2.24
256 266 3.952535 ACGTTTTGAACAGCTAGCTTTG 58.047 40.909 16.46 8.63 0.00 2.77
269 279 8.180267 TCCGTTTGTTTTTATAAGACGTTTTGA 58.820 29.630 0.83 0.00 0.00 2.69
285 295 2.614057 CAAGTGCTCTCTCCGTTTGTTT 59.386 45.455 0.00 0.00 0.00 2.83
289 299 0.759346 ACCAAGTGCTCTCTCCGTTT 59.241 50.000 0.00 0.00 0.00 3.60
290 300 0.759346 AACCAAGTGCTCTCTCCGTT 59.241 50.000 0.00 0.00 0.00 4.44
292 302 1.294659 GCAACCAAGTGCTCTCTCCG 61.295 60.000 0.00 0.00 41.51 4.63
301 311 2.012673 GGATCTGCTAGCAACCAAGTG 58.987 52.381 19.86 5.16 0.00 3.16
346 1400 7.012799 GCATTTGGAATTCTACAAACCCAAAAA 59.987 33.333 10.78 0.00 43.91 1.94
347 1401 6.484977 GCATTTGGAATTCTACAAACCCAAAA 59.515 34.615 10.78 0.00 43.91 2.44
348 1402 5.994668 GCATTTGGAATTCTACAAACCCAAA 59.005 36.000 10.78 8.54 44.53 3.28
349 1403 5.306678 AGCATTTGGAATTCTACAAACCCAA 59.693 36.000 10.78 0.44 39.15 4.12
350 1404 4.837860 AGCATTTGGAATTCTACAAACCCA 59.162 37.500 10.78 0.00 39.15 4.51
351 1405 5.405935 AGCATTTGGAATTCTACAAACCC 57.594 39.130 10.78 6.47 39.15 4.11
352 1406 7.116805 CAGAAAGCATTTGGAATTCTACAAACC 59.883 37.037 10.78 6.73 39.27 3.27
353 1407 7.116805 CCAGAAAGCATTTGGAATTCTACAAAC 59.883 37.037 10.78 2.40 39.27 2.93
354 1408 7.015098 TCCAGAAAGCATTTGGAATTCTACAAA 59.985 33.333 10.91 10.91 39.27 2.83
355 1409 6.493115 TCCAGAAAGCATTTGGAATTCTACAA 59.507 34.615 5.23 0.00 39.27 2.41
356 1410 6.009589 TCCAGAAAGCATTTGGAATTCTACA 58.990 36.000 5.23 0.00 39.27 2.74
357 1411 6.515272 TCCAGAAAGCATTTGGAATTCTAC 57.485 37.500 5.23 0.00 39.27 2.59
358 1412 6.097270 CCATCCAGAAAGCATTTGGAATTCTA 59.903 38.462 5.23 0.00 43.69 2.10
359 1413 5.105064 CCATCCAGAAAGCATTTGGAATTCT 60.105 40.000 5.23 0.00 43.69 2.40
360 1414 5.105228 TCCATCCAGAAAGCATTTGGAATTC 60.105 40.000 5.98 0.00 43.69 2.17
361 1415 4.778958 TCCATCCAGAAAGCATTTGGAATT 59.221 37.500 5.98 0.00 43.69 2.17
362 1416 4.355549 TCCATCCAGAAAGCATTTGGAAT 58.644 39.130 5.98 0.00 43.69 3.01
363 1417 3.765511 CTCCATCCAGAAAGCATTTGGAA 59.234 43.478 5.98 0.00 43.69 3.53
364 1418 3.010472 TCTCCATCCAGAAAGCATTTGGA 59.990 43.478 4.57 4.57 44.52 3.53
365 1419 3.359033 TCTCCATCCAGAAAGCATTTGG 58.641 45.455 0.00 0.00 39.27 3.28
366 1420 5.593679 ATTCTCCATCCAGAAAGCATTTG 57.406 39.130 0.00 0.00 39.27 2.32
367 1421 6.616237 AAATTCTCCATCCAGAAAGCATTT 57.384 33.333 0.00 0.00 43.98 2.32
368 1422 6.616237 AAAATTCTCCATCCAGAAAGCATT 57.384 33.333 0.00 0.00 35.99 3.56
369 1423 6.616237 AAAAATTCTCCATCCAGAAAGCAT 57.384 33.333 0.00 0.00 35.99 3.79
454 1619 4.081309 TGGAAGGAGGTGGTTACTAATTCG 60.081 45.833 0.00 0.00 0.00 3.34
520 1853 1.286305 TTTAGGGGGATGGCTGGGTC 61.286 60.000 0.00 0.00 0.00 4.46
524 1857 0.113190 GGGATTTAGGGGGATGGCTG 59.887 60.000 0.00 0.00 0.00 4.85
534 1867 5.379706 AATCAAGAGGTGAGGGATTTAGG 57.620 43.478 0.00 0.00 40.43 2.69
568 1901 1.285950 CAGCGAGGTGAAGTCGACA 59.714 57.895 19.50 0.00 39.92 4.35
574 1907 1.373497 ACGAAGCAGCGAGGTGAAG 60.373 57.895 6.46 0.00 34.83 3.02
619 2219 5.049060 TGAAATCATTTGAACCTGTGGTACG 60.049 40.000 0.00 0.00 33.12 3.67
649 2249 4.157656 TGGTGAAACTCAACAAAGTCAAGG 59.842 41.667 0.00 0.00 41.82 3.61
708 5255 1.152922 TTGGTTTGGGTGGACGGTC 60.153 57.895 0.00 0.00 0.00 4.79
709 5256 1.152839 CTTGGTTTGGGTGGACGGT 60.153 57.895 0.00 0.00 0.00 4.83
713 5269 3.558033 GTTACTTCTTGGTTTGGGTGGA 58.442 45.455 0.00 0.00 0.00 4.02
722 5278 3.732212 GTGGTAACGGTTACTTCTTGGT 58.268 45.455 25.36 0.00 42.51 3.67
777 5333 3.400188 GGGGGAGAAAAGAGGCGA 58.600 61.111 0.00 0.00 0.00 5.54
799 5357 4.219919 AGGGGGAGTTCGAATTTTGAAAA 58.780 39.130 0.00 0.00 0.00 2.29
897 5480 1.685765 GGGGTTGGGGAATTGGAGC 60.686 63.158 0.00 0.00 0.00 4.70
899 5482 3.196461 GGGGGTTGGGGAATTGGA 58.804 61.111 0.00 0.00 0.00 3.53
957 5540 2.722201 CCTTCCCTTCGGAGGACGG 61.722 68.421 12.85 4.29 46.74 4.79
978 5565 0.851332 CCCCTTTCCTTCCCTTCCCT 60.851 60.000 0.00 0.00 0.00 4.20
981 5568 1.670059 TCTCCCCTTTCCTTCCCTTC 58.330 55.000 0.00 0.00 0.00 3.46
982 5569 1.925959 CATCTCCCCTTTCCTTCCCTT 59.074 52.381 0.00 0.00 0.00 3.95
983 5570 1.082879 TCATCTCCCCTTTCCTTCCCT 59.917 52.381 0.00 0.00 0.00 4.20
984 5571 1.492599 CTCATCTCCCCTTTCCTTCCC 59.507 57.143 0.00 0.00 0.00 3.97
985 5572 1.492599 CCTCATCTCCCCTTTCCTTCC 59.507 57.143 0.00 0.00 0.00 3.46
986 5573 1.492599 CCCTCATCTCCCCTTTCCTTC 59.507 57.143 0.00 0.00 0.00 3.46
987 5574 1.082879 TCCCTCATCTCCCCTTTCCTT 59.917 52.381 0.00 0.00 0.00 3.36
988 5575 0.725133 TCCCTCATCTCCCCTTTCCT 59.275 55.000 0.00 0.00 0.00 3.36
989 5576 1.135960 CTCCCTCATCTCCCCTTTCC 58.864 60.000 0.00 0.00 0.00 3.13
990 5577 2.182516 TCTCCCTCATCTCCCCTTTC 57.817 55.000 0.00 0.00 0.00 2.62
991 5578 2.698653 GGATCTCCCTCATCTCCCCTTT 60.699 54.545 0.00 0.00 0.00 3.11
992 5579 1.132560 GGATCTCCCTCATCTCCCCTT 60.133 57.143 0.00 0.00 0.00 3.95
993 5580 0.491371 GGATCTCCCTCATCTCCCCT 59.509 60.000 0.00 0.00 0.00 4.79
994 5581 0.491371 AGGATCTCCCTCATCTCCCC 59.509 60.000 0.00 0.00 43.31 4.81
995 5582 1.643310 CAGGATCTCCCTCATCTCCC 58.357 60.000 0.00 0.00 45.60 4.30
996 5583 0.975887 GCAGGATCTCCCTCATCTCC 59.024 60.000 0.00 0.00 45.60 3.71
997 5584 1.344114 GTGCAGGATCTCCCTCATCTC 59.656 57.143 0.00 0.00 45.60 2.75
1405 5992 3.753797 CGGAGAAAGGGGAAGAAGAAAAG 59.246 47.826 0.00 0.00 0.00 2.27
1406 5993 3.137728 ACGGAGAAAGGGGAAGAAGAAAA 59.862 43.478 0.00 0.00 0.00 2.29
1476 6092 3.561725 CCATTTCTCATTTCTCTACCGCC 59.438 47.826 0.00 0.00 0.00 6.13
1481 6097 5.045651 TCAGCCACCATTTCTCATTTCTCTA 60.046 40.000 0.00 0.00 0.00 2.43
1484 6100 3.760684 GTCAGCCACCATTTCTCATTTCT 59.239 43.478 0.00 0.00 0.00 2.52
1488 6104 1.679944 CCGTCAGCCACCATTTCTCAT 60.680 52.381 0.00 0.00 0.00 2.90
1489 6105 0.321564 CCGTCAGCCACCATTTCTCA 60.322 55.000 0.00 0.00 0.00 3.27
1491 6107 0.620556 ATCCGTCAGCCACCATTTCT 59.379 50.000 0.00 0.00 0.00 2.52
1492 6108 1.017387 GATCCGTCAGCCACCATTTC 58.983 55.000 0.00 0.00 0.00 2.17
1493 6109 0.620556 AGATCCGTCAGCCACCATTT 59.379 50.000 0.00 0.00 0.00 2.32
1494 6110 0.107508 CAGATCCGTCAGCCACCATT 60.108 55.000 0.00 0.00 0.00 3.16
1495 6111 1.267574 ACAGATCCGTCAGCCACCAT 61.268 55.000 0.00 0.00 0.00 3.55
1496 6112 1.913262 ACAGATCCGTCAGCCACCA 60.913 57.895 0.00 0.00 0.00 4.17
1497 6113 1.448540 CACAGATCCGTCAGCCACC 60.449 63.158 0.00 0.00 0.00 4.61
1498 6114 2.103042 GCACAGATCCGTCAGCCAC 61.103 63.158 0.00 0.00 0.00 5.01
1803 6419 3.950395 GCTACAGAAATGGAGGAATGCTT 59.050 43.478 0.00 0.00 0.00 3.91
1807 6423 5.163478 GCAAATGCTACAGAAATGGAGGAAT 60.163 40.000 0.00 0.00 38.21 3.01
1808 6424 4.158394 GCAAATGCTACAGAAATGGAGGAA 59.842 41.667 0.00 0.00 38.21 3.36
1838 6696 2.744202 AGGTCAGCAATCATCAAACGAC 59.256 45.455 0.00 0.00 0.00 4.34
1857 7019 9.695526 TGTTTATTCATTGTTTGATTCTTGAGG 57.304 29.630 0.00 0.00 33.34 3.86
1861 7023 9.398170 CGACTGTTTATTCATTGTTTGATTCTT 57.602 29.630 0.00 0.00 33.34 2.52
1862 7024 8.023128 CCGACTGTTTATTCATTGTTTGATTCT 58.977 33.333 0.00 0.00 33.34 2.40
1863 7025 7.201350 GCCGACTGTTTATTCATTGTTTGATTC 60.201 37.037 0.00 0.00 33.34 2.52
1875 7045 1.659098 CAGGTCGCCGACTGTTTATTC 59.341 52.381 17.76 0.00 32.47 1.75
1876 7046 1.274167 TCAGGTCGCCGACTGTTTATT 59.726 47.619 17.76 0.00 32.47 1.40
1877 7047 0.892755 TCAGGTCGCCGACTGTTTAT 59.107 50.000 17.76 0.00 32.47 1.40
1878 7048 0.675083 TTCAGGTCGCCGACTGTTTA 59.325 50.000 17.76 0.00 32.47 2.01
1879 7049 0.878961 GTTCAGGTCGCCGACTGTTT 60.879 55.000 17.76 0.00 32.47 2.83
2267 7839 2.414179 TCGCACACCGTCGACTTT 59.586 55.556 14.70 0.00 38.35 2.66
2399 7971 0.949105 CCGTGTACCAGTGCAGGAAC 60.949 60.000 9.68 0.00 33.89 3.62
2566 8138 6.500041 CAGTAGTACTTGGTTGATCTCTAGC 58.500 44.000 0.00 0.00 0.00 3.42
2586 8158 3.561310 AGAACCGATAATCGTACGCAGTA 59.439 43.478 11.24 3.94 37.23 2.74
2587 8159 2.357009 AGAACCGATAATCGTACGCAGT 59.643 45.455 11.24 1.59 40.34 4.40
2588 8160 2.996155 AGAACCGATAATCGTACGCAG 58.004 47.619 11.24 0.00 38.40 5.18
2589 8161 3.425577 AAGAACCGATAATCGTACGCA 57.574 42.857 11.24 0.00 38.40 5.24
2595 8167 6.589830 ACATGAGAAAAGAACCGATAATCG 57.410 37.500 0.00 0.00 40.07 3.34
2602 8174 8.853345 CATCAAATTAACATGAGAAAAGAACCG 58.147 33.333 0.00 0.00 0.00 4.44
2614 8186 8.545420 GCCTAAAGCAATCATCAAATTAACATG 58.455 33.333 0.00 0.00 42.97 3.21
2720 8292 8.368668 GTTATAGTACCAACCAAGCTATCTCAT 58.631 37.037 0.00 0.00 0.00 2.90
2735 8307 6.757173 ATTGTGCCATAGGTTATAGTACCA 57.243 37.500 0.00 0.00 40.82 3.25
2736 8308 6.072673 GCAATTGTGCCATAGGTTATAGTACC 60.073 42.308 7.40 0.00 45.68 3.34
2737 8309 6.899114 GCAATTGTGCCATAGGTTATAGTAC 58.101 40.000 7.40 0.00 45.68 2.73
2772 8344 4.712425 CAGGGCGTTGCTGCTTGC 62.712 66.667 0.00 1.86 43.25 4.01
2773 8345 2.848858 AACAGGGCGTTGCTGCTTG 61.849 57.895 0.00 0.00 36.12 4.01
2774 8346 2.519302 AACAGGGCGTTGCTGCTT 60.519 55.556 0.00 0.00 36.12 3.91
2802 8374 1.139058 GTGAAGACACTGGACACCACT 59.861 52.381 0.00 0.00 42.99 4.00
2847 8436 2.140065 TCAGACACGAGCAACTTCAG 57.860 50.000 0.00 0.00 0.00 3.02
2858 8447 5.791367 ATCATGAACTGAAATCAGACACG 57.209 39.130 16.93 9.09 46.59 4.49
2919 8508 1.134521 AGCGACTCCCGAATTGCATTA 60.135 47.619 0.00 0.00 41.76 1.90
2924 8513 1.153823 ACGAGCGACTCCCGAATTG 60.154 57.895 0.00 0.00 41.76 2.32
2930 8519 1.658686 ATCAGACACGAGCGACTCCC 61.659 60.000 0.00 0.00 0.00 4.30
2931 8520 0.171455 AATCAGACACGAGCGACTCC 59.829 55.000 0.00 0.00 0.00 3.85
2936 8525 1.651138 GACTGAAATCAGACACGAGCG 59.349 52.381 16.93 0.00 46.59 5.03
2968 8557 6.488683 ACAGGACAAGATCTAGAGCATACTAC 59.511 42.308 11.20 0.00 0.00 2.73
2969 8558 6.606069 ACAGGACAAGATCTAGAGCATACTA 58.394 40.000 11.20 0.00 0.00 1.82
2970 8559 5.454062 ACAGGACAAGATCTAGAGCATACT 58.546 41.667 11.20 0.00 0.00 2.12
2971 8560 5.534654 AGACAGGACAAGATCTAGAGCATAC 59.465 44.000 11.20 0.00 0.00 2.39
2977 8566 5.760131 TCATGAGACAGGACAAGATCTAGA 58.240 41.667 0.00 0.00 0.00 2.43
2980 8569 4.715792 ACATCATGAGACAGGACAAGATCT 59.284 41.667 0.09 0.00 0.00 2.75
2989 8578 6.505044 TTTCATTTCACATCATGAGACAGG 57.495 37.500 0.09 0.00 38.99 4.00
2994 8583 5.575019 TCGCATTTCATTTCACATCATGAG 58.425 37.500 0.09 0.00 38.99 2.90
3000 8589 3.504863 GTGCTCGCATTTCATTTCACAT 58.495 40.909 0.00 0.00 0.00 3.21
3015 8604 3.654414 AGAAAGAAACTAGTGGTGCTCG 58.346 45.455 0.00 0.00 0.00 5.03
3082 8674 4.005650 TGTCATCATCAAGCTCAAGGAAC 58.994 43.478 0.00 0.00 0.00 3.62
3087 8679 5.250982 ACAATCTGTCATCATCAAGCTCAA 58.749 37.500 0.00 0.00 0.00 3.02
3088 8680 4.840271 ACAATCTGTCATCATCAAGCTCA 58.160 39.130 0.00 0.00 0.00 4.26
3089 8681 5.570344 CAACAATCTGTCATCATCAAGCTC 58.430 41.667 0.00 0.00 0.00 4.09
3090 8682 4.142447 GCAACAATCTGTCATCATCAAGCT 60.142 41.667 0.00 0.00 0.00 3.74
3091 8683 4.103357 GCAACAATCTGTCATCATCAAGC 58.897 43.478 0.00 0.00 0.00 4.01
3092 8684 5.093457 GTGCAACAATCTGTCATCATCAAG 58.907 41.667 0.00 0.00 36.32 3.02
3093 8685 5.050644 GTGCAACAATCTGTCATCATCAA 57.949 39.130 0.00 0.00 36.32 2.57
3094 8686 4.690184 GTGCAACAATCTGTCATCATCA 57.310 40.909 0.00 0.00 36.32 3.07
3153 8746 2.223340 GGCATATGTGTACTGCAACTGC 60.223 50.000 4.29 10.99 37.64 4.40
3154 8747 3.009026 TGGCATATGTGTACTGCAACTG 58.991 45.455 4.29 3.67 37.64 3.16
3155 8748 3.273434 CTGGCATATGTGTACTGCAACT 58.727 45.455 4.29 0.00 37.64 3.16
3179 8772 1.134220 TGGACAACTCCAACCAGACAC 60.134 52.381 0.00 0.00 44.26 3.67
3236 8829 2.430332 CAACCAACCATCACCAACTGTT 59.570 45.455 0.00 0.00 0.00 3.16
3237 8830 2.031120 CAACCAACCATCACCAACTGT 58.969 47.619 0.00 0.00 0.00 3.55
3238 8831 1.340889 CCAACCAACCATCACCAACTG 59.659 52.381 0.00 0.00 0.00 3.16
3239 8832 1.703411 CCAACCAACCATCACCAACT 58.297 50.000 0.00 0.00 0.00 3.16
3241 8834 1.118356 GCCCAACCAACCATCACCAA 61.118 55.000 0.00 0.00 0.00 3.67
3245 8838 0.409092 ATCTGCCCAACCAACCATCA 59.591 50.000 0.00 0.00 0.00 3.07
3246 8839 0.819582 CATCTGCCCAACCAACCATC 59.180 55.000 0.00 0.00 0.00 3.51
3254 8866 0.966875 TGTGATGCCATCTGCCCAAC 60.967 55.000 6.21 0.00 40.16 3.77
3287 8899 4.318021 AAAGCGTGCTGTGCTGCG 62.318 61.111 0.00 0.00 43.14 5.18
3334 8946 3.972403 AGTTTGTAAACCAATGCGGAAC 58.028 40.909 4.00 0.00 39.71 3.62
3338 8950 2.352323 GGGGAGTTTGTAAACCAATGCG 60.352 50.000 4.00 0.00 39.71 4.73
3366 8978 7.495901 AGTAAATGATGCATAGATCTATCCCG 58.504 38.462 12.50 3.42 0.00 5.14
3381 8993 5.701290 GGGACGGAGGAAATAGTAAATGATG 59.299 44.000 0.00 0.00 0.00 3.07
3395 9007 2.640826 ACAAGTAATTTGGGACGGAGGA 59.359 45.455 0.00 0.00 41.25 3.71
3419 9031 8.688151 GGACAACTTAGTATACAAGTCTGATCT 58.312 37.037 16.13 3.24 35.19 2.75
3420 9032 8.688151 AGGACAACTTAGTATACAAGTCTGATC 58.312 37.037 16.13 12.30 35.19 2.92
3422 9034 9.175312 CTAGGACAACTTAGTATACAAGTCTGA 57.825 37.037 16.13 4.52 35.19 3.27
3423 9035 8.407064 CCTAGGACAACTTAGTATACAAGTCTG 58.593 40.741 1.05 16.54 35.19 3.51
3425 9037 8.291191 ACCTAGGACAACTTAGTATACAAGTC 57.709 38.462 17.98 9.52 35.19 3.01
3426 9038 8.661752 AACCTAGGACAACTTAGTATACAAGT 57.338 34.615 17.98 9.73 37.85 3.16
3427 9039 9.367444 CAAACCTAGGACAACTTAGTATACAAG 57.633 37.037 17.98 9.14 0.00 3.16
3428 9040 9.092338 TCAAACCTAGGACAACTTAGTATACAA 57.908 33.333 17.98 0.00 0.00 2.41
3430 9042 8.747471 AGTCAAACCTAGGACAACTTAGTATAC 58.253 37.037 17.98 0.00 36.50 1.47
3431 9043 8.746530 CAGTCAAACCTAGGACAACTTAGTATA 58.253 37.037 17.98 0.00 36.50 1.47
3435 9047 5.221661 ACCAGTCAAACCTAGGACAACTTAG 60.222 44.000 17.98 9.07 36.50 2.18
3448 9178 5.552178 ACTTGAGATAAGACCAGTCAAACC 58.448 41.667 0.00 0.00 0.00 3.27
3489 9219 2.159181 GGTGATGACCGGTCAAACG 58.841 57.895 39.04 0.00 43.58 3.60
3501 9231 0.734889 GCGGGATGAACAAGGTGATG 59.265 55.000 0.00 0.00 0.00 3.07
3506 9236 1.377725 AGCAGCGGGATGAACAAGG 60.378 57.895 0.00 0.00 0.00 3.61
3542 9272 8.645814 AAAAAGAAACGGAGGGAGTATAAAAT 57.354 30.769 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.