Multiple sequence alignment - TraesCS2D01G593800

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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 TraesCS2D01G593800 chr2D 100.000 3399 0 0 1 3399 648119928 648123326 0.000000e+00 6277.0
1 TraesCS2D01G593800 chr2D 87.572 1038 116 6 818 1853 648102456 648103482 0.000000e+00 1190.0
2 TraesCS2D01G593800 chr2D 89.613 491 46 5 1890 2377 648103775 648104263 1.340000e-173 619.0
3 TraesCS2D01G593800 chrUn 94.741 2434 97 11 448 2856 31313391 31310964 0.000000e+00 3757.0
4 TraesCS2D01G593800 chrUn 88.383 1033 111 3 826 1856 31327136 31326111 0.000000e+00 1234.0
5 TraesCS2D01G593800 chrUn 88.503 1009 101 9 893 1892 31371334 31370332 0.000000e+00 1206.0
6 TraesCS2D01G593800 chrUn 86.789 598 63 5 1890 2485 31370288 31369705 0.000000e+00 652.0
7 TraesCS2D01G593800 chrUn 90.224 491 43 5 1890 2377 31325877 31325389 1.330000e-178 636.0
8 TraesCS2D01G593800 chrUn 89.776 313 23 5 3093 3399 31310064 31309755 3.180000e-105 392.0
9 TraesCS2D01G593800 chrUn 94.093 237 6 2 3 231 114923986 114923750 1.500000e-93 353.0
10 TraesCS2D01G593800 chrUn 97.183 71 2 0 381 451 114923685 114923615 1.660000e-23 121.0
11 TraesCS2D01G593800 chrUn 97.727 44 1 0 274 317 114923751 114923708 3.640000e-10 76.8
12 TraesCS2D01G593800 chr2B 90.798 2369 144 41 23 2349 781796990 781794654 0.000000e+00 3099.0
13 TraesCS2D01G593800 chr2B 88.333 1080 104 12 818 1892 781828619 781827557 0.000000e+00 1277.0
14 TraesCS2D01G593800 chr2B 86.673 1043 126 6 818 1856 781807211 781806178 0.000000e+00 1144.0
15 TraesCS2D01G593800 chr2B 86.834 676 71 8 1890 2555 781827513 781826846 0.000000e+00 739.0
16 TraesCS2D01G593800 chr2B 88.800 500 44 8 1890 2383 781805973 781805480 1.350000e-168 603.0
17 TraesCS2D01G593800 chr2B 85.496 524 33 10 2377 2859 781794657 781794136 1.090000e-139 507.0
18 TraesCS2D01G593800 chr2B 89.412 85 9 0 2994 3078 781824652 781824568 1.290000e-19 108.0
19 TraesCS2D01G593800 chr5D 79.275 883 151 20 961 1825 5793491 5794359 3.780000e-164 588.0
20 TraesCS2D01G593800 chr5D 77.740 876 165 22 965 1823 5567690 5568552 8.410000e-141 510.0
21 TraesCS2D01G593800 chr5D 93.600 250 12 2 448 694 8377061 8376813 1.490000e-98 370.0
22 TraesCS2D01G593800 chr5D 95.259 232 11 0 448 679 78435980 78435749 5.360000e-98 368.0
23 TraesCS2D01G593800 chr5D 93.249 237 8 2 3 231 8377471 8377235 3.250000e-90 342.0
24 TraesCS2D01G593800 chr5D 92.405 237 10 2 3 231 78436390 78436154 7.030000e-87 331.0
25 TraesCS2D01G593800 chr5D 90.717 237 14 2 3 231 403753337 403753101 3.290000e-80 309.0
26 TraesCS2D01G593800 chr5D 89.091 110 8 2 588 694 403752962 403752854 2.130000e-27 134.0
27 TraesCS2D01G593800 chr5D 79.330 179 35 2 2200 2377 6712219 6712042 1.280000e-24 124.0
28 TraesCS2D01G593800 chr5D 97.183 71 2 0 381 451 8377170 8377100 1.660000e-23 121.0
29 TraesCS2D01G593800 chr5D 97.183 71 2 0 381 451 78436089 78436019 1.660000e-23 121.0
30 TraesCS2D01G593800 chr5D 97.183 71 2 0 381 451 403753036 403752966 1.660000e-23 121.0
31 TraesCS2D01G593800 chr5D 97.727 44 1 0 274 317 8377236 8377193 3.640000e-10 76.8
32 TraesCS2D01G593800 chr5D 97.727 44 1 0 274 317 78436155 78436112 3.640000e-10 76.8
33 TraesCS2D01G593800 chr7D 92.188 256 16 2 442 694 567809495 567809749 3.220000e-95 359.0
34 TraesCS2D01G593800 chr7D 93.191 235 10 3 3 231 567809093 567809327 1.170000e-89 340.0
35 TraesCS2D01G593800 chr7D 76.780 646 114 24 1226 1850 489903278 489902648 2.530000e-86 329.0
36 TraesCS2D01G593800 chr7D 95.775 71 3 0 381 451 567809392 567809462 7.710000e-22 115.0
37 TraesCS2D01G593800 chr7D 75.000 196 34 10 370 563 489904275 489904093 3.640000e-10 76.8
38 TraesCS2D01G593800 chr7D 97.727 44 1 0 274 317 567809326 567809369 3.640000e-10 76.8
39 TraesCS2D01G593800 chr7A 92.400 250 14 3 448 694 186108012 186107765 5.400000e-93 351.0
40 TraesCS2D01G593800 chr7A 97.183 71 2 0 381 451 186108121 186108051 1.660000e-23 121.0
41 TraesCS2D01G593800 chr3A 91.016 256 19 2 442 694 731602475 731602729 3.250000e-90 342.0
42 TraesCS2D01G593800 chr3A 89.035 228 17 2 12 231 731602080 731602307 3.340000e-70 276.0
43 TraesCS2D01G593800 chr3A 94.366 71 4 0 381 451 731602372 731602442 3.590000e-20 110.0
44 TraesCS2D01G593800 chr4A 90.234 256 21 2 442 694 53815243 53815497 7.030000e-87 331.0
45 TraesCS2D01G593800 chr4A 91.630 227 11 2 13 231 53814850 53815076 1.180000e-79 307.0
46 TraesCS2D01G593800 chr4A 82.650 317 23 12 28 316 59281556 59281868 5.630000e-63 252.0
47 TraesCS2D01G593800 chr4A 83.333 144 23 1 1950 2093 614982831 614982973 7.650000e-27 132.0
48 TraesCS2D01G593800 chr4A 80.000 180 32 4 1950 2129 614908012 614908187 2.750000e-26 130.0
49 TraesCS2D01G593800 chr4A 95.775 71 3 0 381 451 53815141 53815211 7.710000e-22 115.0
50 TraesCS2D01G593800 chr4A 100.000 44 0 0 274 317 53815075 53815118 7.820000e-12 82.4
51 TraesCS2D01G593800 chr7B 76.780 646 114 25 1226 1850 518395096 518394466 2.530000e-86 329.0
52 TraesCS2D01G593800 chr2A 90.598 234 14 2 6 231 477282057 477281824 1.530000e-78 303.0
53 TraesCS2D01G593800 chr4B 80.923 325 20 17 28 316 496546579 496546897 5.710000e-53 219.0
54 TraesCS2D01G593800 chr4D 94.444 126 7 0 3 128 119793720 119793595 9.620000e-46 195.0


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 TraesCS2D01G593800 chr2D 648119928 648123326 3398 False 6277.000000 6277 100.000000 1 3399 1 chr2D.!!$F1 3398
1 TraesCS2D01G593800 chr2D 648102456 648104263 1807 False 904.500000 1190 88.592500 818 2377 2 chr2D.!!$F2 1559
2 TraesCS2D01G593800 chrUn 31309755 31313391 3636 True 2074.500000 3757 92.258500 448 3399 2 chrUn.!!$R1 2951
3 TraesCS2D01G593800 chrUn 31325389 31327136 1747 True 935.000000 1234 89.303500 826 2377 2 chrUn.!!$R2 1551
4 TraesCS2D01G593800 chrUn 31369705 31371334 1629 True 929.000000 1206 87.646000 893 2485 2 chrUn.!!$R3 1592
5 TraesCS2D01G593800 chr2B 781794136 781796990 2854 True 1803.000000 3099 88.147000 23 2859 2 chr2B.!!$R1 2836
6 TraesCS2D01G593800 chr2B 781805480 781807211 1731 True 873.500000 1144 87.736500 818 2383 2 chr2B.!!$R2 1565
7 TraesCS2D01G593800 chr2B 781824568 781828619 4051 True 708.000000 1277 88.193000 818 3078 3 chr2B.!!$R3 2260
8 TraesCS2D01G593800 chr5D 5793491 5794359 868 False 588.000000 588 79.275000 961 1825 1 chr5D.!!$F2 864
9 TraesCS2D01G593800 chr5D 5567690 5568552 862 False 510.000000 510 77.740000 965 1823 1 chr5D.!!$F1 858
10 TraesCS2D01G593800 chr5D 8376813 8377471 658 True 227.450000 370 95.439750 3 694 4 chr5D.!!$R2 691
11 TraesCS2D01G593800 chr5D 78435749 78436390 641 True 224.200000 368 95.643500 3 679 4 chr5D.!!$R3 676
12 TraesCS2D01G593800 chr7D 567809093 567809749 656 False 222.700000 359 94.720250 3 694 4 chr7D.!!$F1 691
13 TraesCS2D01G593800 chr7D 489902648 489904275 1627 True 202.900000 329 75.890000 370 1850 2 chr7D.!!$R1 1480
14 TraesCS2D01G593800 chr3A 731602080 731602729 649 False 242.666667 342 91.472333 12 694 3 chr3A.!!$F1 682
15 TraesCS2D01G593800 chr4A 53814850 53815497 647 False 208.850000 331 94.409750 13 694 4 chr4A.!!$F4 681
16 TraesCS2D01G593800 chr7B 518394466 518395096 630 True 329.000000 329 76.780000 1226 1850 1 chr7B.!!$R1 624

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
706 880 0.109723 TGCTACCCGGTTCAGCTTTT 59.89 50.0 17.08 0.0 36.26 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 3098 1.344114 GCACATGAAAGCTGGGGAAAA 59.656 47.619 0.0 0.0 0.0 2.29 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
231 243 6.956202 AGCAAATCTGGGAAGATAAAGATG 57.044 37.500 0.00 0.00 29.93 2.90
232 244 6.430007 AGCAAATCTGGGAAGATAAAGATGT 58.570 36.000 0.00 0.00 29.93 3.06
233 245 7.577303 AGCAAATCTGGGAAGATAAAGATGTA 58.423 34.615 0.00 0.00 29.93 2.29
234 246 7.500559 AGCAAATCTGGGAAGATAAAGATGTAC 59.499 37.037 0.00 0.00 29.93 2.90
235 247 7.283127 GCAAATCTGGGAAGATAAAGATGTACA 59.717 37.037 0.00 0.00 29.93 2.90
236 248 9.177608 CAAATCTGGGAAGATAAAGATGTACAA 57.822 33.333 0.00 0.00 29.93 2.41
237 249 9.927081 AAATCTGGGAAGATAAAGATGTACAAT 57.073 29.630 0.00 0.00 29.93 2.71
238 250 9.927081 AATCTGGGAAGATAAAGATGTACAATT 57.073 29.630 0.00 0.00 29.93 2.32
239 251 8.737168 TCTGGGAAGATAAAGATGTACAATTG 57.263 34.615 3.24 3.24 0.00 2.32
240 252 8.548025 TCTGGGAAGATAAAGATGTACAATTGA 58.452 33.333 13.59 0.00 0.00 2.57
241 253 9.347240 CTGGGAAGATAAAGATGTACAATTGAT 57.653 33.333 13.59 0.00 0.00 2.57
268 280 4.508662 ACAGTGCTCCTGCTTTCTTATAC 58.491 43.478 4.17 0.00 45.68 1.47
353 386 6.121590 TGATGCTTCCTGCTTGTATGAATTA 58.878 36.000 0.00 0.00 43.37 1.40
354 387 6.261603 TGATGCTTCCTGCTTGTATGAATTAG 59.738 38.462 0.00 0.00 43.37 1.73
355 388 5.500234 TGCTTCCTGCTTGTATGAATTAGT 58.500 37.500 0.00 0.00 43.37 2.24
356 389 6.649155 TGCTTCCTGCTTGTATGAATTAGTA 58.351 36.000 0.00 0.00 43.37 1.82
357 390 7.109501 TGCTTCCTGCTTGTATGAATTAGTAA 58.890 34.615 0.00 0.00 43.37 2.24
358 391 7.280876 TGCTTCCTGCTTGTATGAATTAGTAAG 59.719 37.037 0.00 0.00 43.37 2.34
359 392 7.281100 GCTTCCTGCTTGTATGAATTAGTAAGT 59.719 37.037 0.00 0.00 38.95 2.24
360 393 9.817809 CTTCCTGCTTGTATGAATTAGTAAGTA 57.182 33.333 0.00 0.00 0.00 2.24
361 394 9.595823 TTCCTGCTTGTATGAATTAGTAAGTAC 57.404 33.333 0.00 0.00 0.00 2.73
362 395 8.978472 TCCTGCTTGTATGAATTAGTAAGTACT 58.022 33.333 0.00 0.00 40.24 2.73
363 396 9.250624 CCTGCTTGTATGAATTAGTAAGTACTC 57.749 37.037 0.00 0.00 37.73 2.59
364 397 9.803315 CTGCTTGTATGAATTAGTAAGTACTCA 57.197 33.333 0.00 0.00 37.73 3.41
508 584 5.808366 TTTCTGTCTGTGACTGATTACCT 57.192 39.130 7.83 0.00 39.51 3.08
555 631 3.120060 CCATCTTTGCTGCTACTGTTGAC 60.120 47.826 0.00 0.00 0.00 3.18
631 727 7.232118 ACTTTTGGAAGAAGTGATTATTGGG 57.768 36.000 0.00 0.00 36.08 4.12
702 876 2.436115 GGTGCTACCCGGTTCAGC 60.436 66.667 11.21 11.21 35.82 4.26
706 880 0.109723 TGCTACCCGGTTCAGCTTTT 59.890 50.000 17.08 0.00 36.26 2.27
840 1049 7.001922 CGCTGAACTATATGCGTTTACATAAC 58.998 38.462 0.00 0.00 42.93 1.89
1018 1256 0.038166 AATGTCGGCACCAACATCCT 59.962 50.000 0.00 0.00 35.10 3.24
1167 1405 0.955428 TCTCACCAAGATGGCGCAAC 60.955 55.000 10.83 0.00 42.67 4.17
1175 1413 0.037590 AGATGGCGCAACCTTTGGTA 59.962 50.000 10.83 0.00 40.22 3.25
1479 1759 4.941713 TGAAACATGGGTTATTTAGGCCT 58.058 39.130 11.78 11.78 35.82 5.19
1549 1829 2.616510 GGTTTCTGTGACCATGAGGAGG 60.617 54.545 0.00 0.00 38.69 4.30
1805 2107 1.893808 CCACAACGTTGGAGCTGCT 60.894 57.895 30.34 0.00 39.24 4.24
1853 2156 4.280174 GGGTTCTTTTCTGTTTCTTACCCC 59.720 45.833 0.00 0.00 37.34 4.95
1910 2475 2.832563 TGTTGCTTTCGTGTCTGATGA 58.167 42.857 0.00 0.00 0.00 2.92
2145 2712 6.087522 GCTACAACTCTTACTGACACTACTG 58.912 44.000 0.00 0.00 0.00 2.74
2154 2724 2.005451 CTGACACTACTGCCTTGATGC 58.995 52.381 0.00 0.00 0.00 3.91
2360 2938 2.769621 AGCGGCCCAGATCCATGA 60.770 61.111 0.00 0.00 0.00 3.07
2370 2949 4.689705 GCCCAGATCCATGATAACCAAGAA 60.690 45.833 0.00 0.00 0.00 2.52
2377 2956 4.935205 TCCATGATAACCAAGAACTCGTTG 59.065 41.667 0.00 0.00 0.00 4.10
2470 3052 2.084610 TGGATCTGAACTGCTTCGTG 57.915 50.000 0.00 0.00 0.00 4.35
2485 3067 2.380084 TCGTGAATGTAGGCTGGTTC 57.620 50.000 0.00 0.00 0.00 3.62
2512 3098 5.308237 GGATTCTGGTGGGTATTCAGTCTAT 59.692 44.000 0.00 0.00 0.00 1.98
2527 3113 4.042809 TCAGTCTATTTTCCCCAGCTTTCA 59.957 41.667 0.00 0.00 0.00 2.69
2595 3210 2.632377 TCGAATGGAATGTGAGCTTCC 58.368 47.619 0.00 0.00 42.15 3.46
2641 3257 6.938698 TCCCCGGTTATATTAGCTATCAAA 57.061 37.500 0.00 0.00 0.00 2.69
2714 3330 4.326504 ACTTTCATGTGCTGGGAAAAAG 57.673 40.909 0.00 0.00 30.87 2.27
2715 3331 3.960102 ACTTTCATGTGCTGGGAAAAAGA 59.040 39.130 5.14 0.00 30.87 2.52
2776 3570 7.882271 ACAGTAAAGAATTCTCTCATGCTTTCT 59.118 33.333 8.78 0.00 0.00 2.52
2790 3584 5.125257 TCATGCTTTCTGAAAATGGCGATTA 59.875 36.000 12.47 0.00 0.00 1.75
2898 5249 9.769093 GTACAAAACCAATATCTTATGTGTCAC 57.231 33.333 0.00 0.00 0.00 3.67
2899 5250 7.826690 ACAAAACCAATATCTTATGTGTCACC 58.173 34.615 0.00 0.00 0.00 4.02
2900 5251 6.677781 AAACCAATATCTTATGTGTCACCG 57.322 37.500 0.00 0.00 0.00 4.94
2901 5252 5.353394 ACCAATATCTTATGTGTCACCGT 57.647 39.130 0.00 0.00 0.00 4.83
2903 5254 6.880484 ACCAATATCTTATGTGTCACCGTTA 58.120 36.000 0.00 0.00 0.00 3.18
2904 5255 6.984474 ACCAATATCTTATGTGTCACCGTTAG 59.016 38.462 0.00 0.00 0.00 2.34
2906 5257 4.737855 ATCTTATGTGTCACCGTTAGCT 57.262 40.909 0.00 0.00 0.00 3.32
2907 5258 5.847111 ATCTTATGTGTCACCGTTAGCTA 57.153 39.130 0.00 0.00 0.00 3.32
2908 5259 4.990257 TCTTATGTGTCACCGTTAGCTAC 58.010 43.478 0.00 0.00 0.00 3.58
2910 5261 2.717580 TGTGTCACCGTTAGCTACAG 57.282 50.000 0.00 0.00 0.00 2.74
2911 5262 1.271379 TGTGTCACCGTTAGCTACAGG 59.729 52.381 11.13 11.13 0.00 4.00
2912 5263 1.271656 GTGTCACCGTTAGCTACAGGT 59.728 52.381 12.28 12.28 35.13 4.00
2913 5264 1.965643 TGTCACCGTTAGCTACAGGTT 59.034 47.619 14.75 1.23 33.38 3.50
2914 5265 2.366266 TGTCACCGTTAGCTACAGGTTT 59.634 45.455 14.75 0.00 33.38 3.27
2915 5266 2.735134 GTCACCGTTAGCTACAGGTTTG 59.265 50.000 14.75 7.11 33.38 2.93
2916 5267 1.463444 CACCGTTAGCTACAGGTTTGC 59.537 52.381 14.75 0.00 33.38 3.68
2917 5268 1.346722 ACCGTTAGCTACAGGTTTGCT 59.653 47.619 12.28 0.00 40.43 3.91
2965 5317 8.778358 CCTTATTTGAATCTAACTATCCAGTGC 58.222 37.037 0.00 0.00 34.36 4.40
2974 5326 6.366340 TCTAACTATCCAGTGCTAGCTAAGT 58.634 40.000 17.23 5.90 34.36 2.24
3005 5360 0.037139 TGCCAATGCATGCCAACTTC 60.037 50.000 16.68 0.57 44.23 3.01
3013 5368 2.694628 TGCATGCCAACTTCTTGAAAGT 59.305 40.909 16.68 0.00 0.00 2.66
3017 5372 5.565439 GCATGCCAACTTCTTGAAAGTGTAT 60.565 40.000 6.36 0.00 0.00 2.29
3065 5420 4.637483 ATTCATGGCCACAAATTACTCG 57.363 40.909 8.16 0.00 0.00 4.18
3087 5442 4.565166 CGTAAGAAATACTCGCCAACATGA 59.435 41.667 0.00 0.00 43.02 3.07
3088 5443 5.234329 CGTAAGAAATACTCGCCAACATGAT 59.766 40.000 0.00 0.00 43.02 2.45
3089 5444 6.238103 CGTAAGAAATACTCGCCAACATGATT 60.238 38.462 0.00 0.00 43.02 2.57
3099 5869 6.767902 ACTCGCCAACATGATTATAAAGACAT 59.232 34.615 0.00 0.00 0.00 3.06
3101 5871 6.017192 TCGCCAACATGATTATAAAGACATGG 60.017 38.462 22.39 14.15 42.66 3.66
3119 5889 6.429385 AGACATGGTTTCTGTTCAAAGATCTC 59.571 38.462 0.00 0.00 0.00 2.75
3124 5894 1.623311 TCTGTTCAAAGATCTCCGGCA 59.377 47.619 0.00 0.00 0.00 5.69
3145 5915 0.107945 GAGAGCACACAGATCCCCAC 60.108 60.000 0.00 0.00 31.44 4.61
3157 5927 1.343142 GATCCCCACCACAAAACCAAC 59.657 52.381 0.00 0.00 0.00 3.77
3167 5937 5.691305 CACCACAAAACCAACATCTTATGTG 59.309 40.000 0.00 0.00 44.07 3.21
3168 5938 5.362430 ACCACAAAACCAACATCTTATGTGT 59.638 36.000 0.00 0.00 44.07 3.72
3170 5940 7.083858 CCACAAAACCAACATCTTATGTGTAG 58.916 38.462 0.00 0.00 44.07 2.74
3171 5941 7.040755 CCACAAAACCAACATCTTATGTGTAGA 60.041 37.037 0.00 0.00 44.07 2.59
3172 5942 8.514594 CACAAAACCAACATCTTATGTGTAGAT 58.485 33.333 0.00 0.00 44.07 1.98
3202 5972 4.018597 ACTGGAATCTGATGCTCTCCTTTT 60.019 41.667 7.43 0.00 0.00 2.27
3227 6002 7.429636 TTCTGAAAACGGAACTTATACTTGG 57.570 36.000 0.00 0.00 0.00 3.61
3228 6003 5.935789 TCTGAAAACGGAACTTATACTTGGG 59.064 40.000 0.00 0.00 0.00 4.12
3231 6006 3.622166 ACGGAACTTATACTTGGGTGG 57.378 47.619 0.00 0.00 0.00 4.61
3247 6022 5.290493 TGGGTGGACAAATACTAGCATAG 57.710 43.478 0.00 0.00 46.50 2.23
3279 6055 0.038599 ATGGATCACACCAGCAAGCA 59.961 50.000 0.00 0.00 43.49 3.91
3308 6084 5.588648 TGGAAATGGAACCATTAATCGTCTC 59.411 40.000 17.73 10.42 44.86 3.36
3310 6086 6.238484 GGAAATGGAACCATTAATCGTCTCAG 60.238 42.308 17.73 0.00 44.86 3.35
3313 6089 3.557595 GGAACCATTAATCGTCTCAGCTG 59.442 47.826 7.63 7.63 0.00 4.24
3316 6092 4.832248 ACCATTAATCGTCTCAGCTGAAA 58.168 39.130 18.85 0.21 0.00 2.69
3355 6131 2.731968 CGTCACAAATAACCATGCAGGC 60.732 50.000 0.00 0.00 43.14 4.85
3374 6150 7.857569 TGCAGGCTAATTAACAATACGATTAC 58.142 34.615 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 261 3.311048 GCAGTATAAGAAAGCAGGAGCAC 59.689 47.826 0.00 0.00 45.49 4.40
258 270 5.647658 TGACACCAATGGCAGTATAAGAAAG 59.352 40.000 0.00 0.00 39.72 2.62
259 271 5.565509 TGACACCAATGGCAGTATAAGAAA 58.434 37.500 0.00 0.00 39.72 2.52
260 272 5.172687 TGACACCAATGGCAGTATAAGAA 57.827 39.130 0.00 0.00 39.72 2.52
261 273 4.835284 TGACACCAATGGCAGTATAAGA 57.165 40.909 0.00 0.00 39.72 2.10
613 709 9.586435 CAAAATAACCCAATAATCACTTCTTCC 57.414 33.333 0.00 0.00 0.00 3.46
840 1049 1.725625 GCGGTCACACAATGCAACG 60.726 57.895 0.00 0.00 0.00 4.10
1018 1256 1.478654 GCTCTTGGAACCACAGGGAAA 60.479 52.381 0.00 0.00 38.05 3.13
1052 1290 0.037326 GAGCCTGTCGACACCATTCA 60.037 55.000 15.76 0.00 0.00 2.57
1175 1413 1.831106 TGCGGATGAATGGTGTAGAGT 59.169 47.619 0.00 0.00 0.00 3.24
1267 1535 3.262420 CTTCATCCAAGGAAGTGGTACG 58.738 50.000 0.00 0.00 39.88 3.67
1479 1759 0.888619 CAGGGCAGTCGTAGTTCAGA 59.111 55.000 0.00 0.00 0.00 3.27
1549 1829 3.007398 ACCTTGAGTGACCTTGATGAGAC 59.993 47.826 0.00 0.00 0.00 3.36
1677 1969 4.561530 GCTGTTACCAGACAAGACAGATCA 60.562 45.833 6.03 0.00 41.50 2.92
1805 2107 2.700722 TACCTCATGTAATGGCGCAA 57.299 45.000 10.83 0.00 46.73 4.85
1853 2156 5.524971 ACATTGGGCATGTTTCATCATAG 57.475 39.130 0.00 0.00 44.40 2.23
1910 2475 2.282701 ATGCGCGCTTCAAATTCATT 57.717 40.000 33.29 0.00 0.00 2.57
2145 2712 2.882761 TGCAGAATATCAGCATCAAGGC 59.117 45.455 0.00 0.00 33.88 4.35
2154 2724 4.760204 TGCATTCATCCTGCAGAATATCAG 59.240 41.667 17.39 1.12 44.30 2.90
2360 2938 3.134574 TGCCAACGAGTTCTTGGTTAT 57.865 42.857 3.95 0.00 40.46 1.89
2370 2949 3.130340 ACAAATCAACTTTGCCAACGAGT 59.870 39.130 0.00 0.00 46.81 4.18
2377 2956 5.005682 GTCTCAACAACAAATCAACTTTGCC 59.994 40.000 0.00 0.00 46.81 4.52
2470 3052 3.281727 TCCATGAACCAGCCTACATTC 57.718 47.619 0.00 0.00 0.00 2.67
2485 3067 4.139786 CTGAATACCCACCAGAATCCATG 58.860 47.826 0.00 0.00 0.00 3.66
2512 3098 1.344114 GCACATGAAAGCTGGGGAAAA 59.656 47.619 0.00 0.00 0.00 2.29
2527 3113 6.186957 TCCAGGTATAATTGTTCAAGCACAT 58.813 36.000 0.00 0.00 0.00 3.21
2595 3210 7.254084 GGGAAGCGTGAATTTGCTAATAATTTG 60.254 37.037 0.00 0.00 41.46 2.32
2596 3211 6.756542 GGGAAGCGTGAATTTGCTAATAATTT 59.243 34.615 0.00 0.00 41.46 1.82
2641 3257 7.839680 AGTTTATTTTGTGGAAGACTGGAAT 57.160 32.000 0.00 0.00 0.00 3.01
2753 3547 8.261492 TCAGAAAGCATGAGAGAATTCTTTAC 57.739 34.615 9.87 5.13 32.53 2.01
2768 3562 4.460948 AATCGCCATTTTCAGAAAGCAT 57.539 36.364 6.46 0.00 0.00 3.79
2790 3584 7.661968 ACATCTGTCAATTATGTACTAGCGAT 58.338 34.615 0.00 0.00 32.21 4.58
2803 3597 5.441718 ACTGACCCATACATCTGTCAATT 57.558 39.130 0.00 0.00 37.29 2.32
2875 5226 6.966632 CGGTGACACATAAGATATTGGTTTTG 59.033 38.462 8.08 0.00 0.00 2.44
2878 5229 5.741011 ACGGTGACACATAAGATATTGGTT 58.259 37.500 8.08 0.00 0.00 3.67
2879 5230 5.353394 ACGGTGACACATAAGATATTGGT 57.647 39.130 8.08 0.00 0.00 3.67
2880 5231 6.073765 GCTAACGGTGACACATAAGATATTGG 60.074 42.308 8.08 0.00 0.00 3.16
2881 5232 6.701841 AGCTAACGGTGACACATAAGATATTG 59.298 38.462 8.08 0.00 0.00 1.90
2882 5233 6.817184 AGCTAACGGTGACACATAAGATATT 58.183 36.000 8.08 0.00 0.00 1.28
2885 5236 4.737855 AGCTAACGGTGACACATAAGAT 57.262 40.909 8.08 0.00 0.00 2.40
2886 5237 4.460034 TGTAGCTAACGGTGACACATAAGA 59.540 41.667 8.08 0.00 0.00 2.10
2887 5238 4.740268 TGTAGCTAACGGTGACACATAAG 58.260 43.478 8.08 0.39 0.00 1.73
2888 5239 4.381185 CCTGTAGCTAACGGTGACACATAA 60.381 45.833 8.08 0.00 31.96 1.90
2890 5241 2.094182 CCTGTAGCTAACGGTGACACAT 60.094 50.000 8.08 0.00 31.96 3.21
2891 5242 1.271379 CCTGTAGCTAACGGTGACACA 59.729 52.381 8.08 0.00 31.96 3.72
2892 5243 1.271656 ACCTGTAGCTAACGGTGACAC 59.728 52.381 12.97 0.00 34.88 3.67
2893 5244 1.624336 ACCTGTAGCTAACGGTGACA 58.376 50.000 12.97 0.00 34.88 3.58
2894 5245 2.735134 CAAACCTGTAGCTAACGGTGAC 59.265 50.000 14.14 0.00 35.87 3.67
2895 5246 2.868839 GCAAACCTGTAGCTAACGGTGA 60.869 50.000 14.14 0.00 35.87 4.02
2896 5247 1.463444 GCAAACCTGTAGCTAACGGTG 59.537 52.381 14.14 6.07 35.87 4.94
2898 5249 1.732259 CAGCAAACCTGTAGCTAACGG 59.268 52.381 0.00 1.06 36.73 4.44
2899 5250 2.683968 TCAGCAAACCTGTAGCTAACG 58.316 47.619 0.00 0.00 42.38 3.18
2900 5251 5.393962 CAAATCAGCAAACCTGTAGCTAAC 58.606 41.667 0.00 0.00 42.38 2.34
2901 5252 4.082787 GCAAATCAGCAAACCTGTAGCTAA 60.083 41.667 0.00 0.00 42.38 3.09
2903 5254 2.229784 GCAAATCAGCAAACCTGTAGCT 59.770 45.455 0.00 0.00 42.38 3.32
2904 5255 2.229784 AGCAAATCAGCAAACCTGTAGC 59.770 45.455 0.00 0.00 42.38 3.58
2906 5257 3.253188 GTCAGCAAATCAGCAAACCTGTA 59.747 43.478 0.00 0.00 42.38 2.74
2907 5258 2.035066 GTCAGCAAATCAGCAAACCTGT 59.965 45.455 0.00 0.00 42.38 4.00
2908 5259 2.034939 TGTCAGCAAATCAGCAAACCTG 59.965 45.455 0.00 0.00 43.17 4.00
2910 5261 2.223782 TGTGTCAGCAAATCAGCAAACC 60.224 45.455 0.00 0.00 36.85 3.27
2911 5262 3.082698 TGTGTCAGCAAATCAGCAAAC 57.917 42.857 0.00 0.00 36.85 2.93
2912 5263 3.644823 CATGTGTCAGCAAATCAGCAAA 58.355 40.909 0.00 0.00 36.85 3.68
2913 5264 2.608506 GCATGTGTCAGCAAATCAGCAA 60.609 45.455 0.00 0.00 36.85 3.91
2914 5265 1.068125 GCATGTGTCAGCAAATCAGCA 60.068 47.619 0.00 0.00 36.85 4.41
2915 5266 1.068125 TGCATGTGTCAGCAAATCAGC 60.068 47.619 0.00 0.00 37.90 4.26
2916 5267 3.291809 TTGCATGTGTCAGCAAATCAG 57.708 42.857 0.00 0.00 46.65 2.90
2965 5317 3.380004 CACAGGACAGGAGACTTAGCTAG 59.620 52.174 0.00 0.00 40.21 3.42
2974 5326 0.325933 CATTGGCACAGGACAGGAGA 59.674 55.000 0.00 0.00 42.39 3.71
3005 5360 8.915654 GTGGCAAAATCTTTATACACTTTCAAG 58.084 33.333 0.00 0.00 0.00 3.02
3013 5368 5.954752 TCATGGGTGGCAAAATCTTTATACA 59.045 36.000 0.00 0.00 0.00 2.29
3017 5372 6.438741 TGTAATCATGGGTGGCAAAATCTTTA 59.561 34.615 0.00 0.00 0.00 1.85
3053 5408 7.839837 GCGAGTATTTCTTACGAGTAATTTGTG 59.160 37.037 0.00 0.00 35.84 3.33
3065 5420 6.604735 ATCATGTTGGCGAGTATTTCTTAC 57.395 37.500 0.00 0.00 0.00 2.34
3078 5433 7.042797 ACCATGTCTTTATAATCATGTTGGC 57.957 36.000 16.89 0.00 36.81 4.52
3079 5434 9.520204 GAAACCATGTCTTTATAATCATGTTGG 57.480 33.333 16.89 10.07 36.81 3.77
3082 5437 9.466497 ACAGAAACCATGTCTTTATAATCATGT 57.534 29.630 16.89 8.52 36.81 3.21
3085 5440 9.513906 TGAACAGAAACCATGTCTTTATAATCA 57.486 29.630 0.00 0.00 0.00 2.57
3089 5444 9.567776 TCTTTGAACAGAAACCATGTCTTTATA 57.432 29.630 0.00 0.00 0.00 0.98
3099 5869 4.065088 CGGAGATCTTTGAACAGAAACCA 58.935 43.478 0.00 0.00 0.00 3.67
3101 5871 3.120165 GCCGGAGATCTTTGAACAGAAAC 60.120 47.826 5.05 0.00 0.00 2.78
3119 5889 2.046988 TGTGTGCTCTCATGCCGG 60.047 61.111 0.00 0.00 0.00 6.13
3124 5894 0.835941 GGGGATCTGTGTGCTCTCAT 59.164 55.000 0.00 0.00 0.00 2.90
3145 5915 5.841810 ACACATAAGATGTTGGTTTTGTGG 58.158 37.500 9.44 0.00 42.70 4.17
3202 5972 7.040961 CCCAAGTATAAGTTCCGTTTTCAGAAA 60.041 37.037 0.00 0.00 0.00 2.52
3213 5983 4.563140 TGTCCACCCAAGTATAAGTTCC 57.437 45.455 0.00 0.00 0.00 3.62
3220 5995 5.190925 TGCTAGTATTTGTCCACCCAAGTAT 59.809 40.000 0.00 0.00 0.00 2.12
3225 6000 4.719773 ACTATGCTAGTATTTGTCCACCCA 59.280 41.667 0.00 0.00 37.23 4.51
3227 6002 8.726870 TTTAACTATGCTAGTATTTGTCCACC 57.273 34.615 0.00 0.00 38.26 4.61
3228 6003 9.379791 ACTTTAACTATGCTAGTATTTGTCCAC 57.620 33.333 0.00 0.00 38.26 4.02
3247 6022 6.206634 TGGTGTGATCCATTCTGAACTTTAAC 59.793 38.462 0.00 0.00 31.96 2.01
3263 6039 0.109412 GCTTGCTTGCTGGTGTGATC 60.109 55.000 0.00 0.00 0.00 2.92
3279 6055 6.564557 ATTAATGGTTCCATTTCCATGCTT 57.435 33.333 20.02 0.00 42.73 3.91
3308 6084 1.030457 GATGGCCTCCATTTCAGCTG 58.970 55.000 7.63 7.63 45.26 4.24
3310 6086 1.030457 CTGATGGCCTCCATTTCAGC 58.970 55.000 3.32 0.00 45.26 4.26
3313 6089 1.030457 CAGCTGATGGCCTCCATTTC 58.970 55.000 8.42 0.00 45.26 2.17
3335 6111 2.493278 AGCCTGCATGGTTATTTGTGAC 59.507 45.455 0.00 0.00 38.35 3.67
3355 6131 7.007697 GCCAGCGTAATCGTATTGTTAATTAG 58.992 38.462 0.00 0.00 39.49 1.73
3374 6150 4.095410 TGAAGACAATTAATTGCCAGCG 57.905 40.909 24.82 4.02 41.38 5.18


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

AutoCloner maintained by Alex Coulton.