Multiple sequence alignment - TraesCS2B01G306200

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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 TraesCS2B01G306200 chr2B 100.000 5027 0 0 1 5027 437000098 436995072 0.000000e+00 9284
1 TraesCS2B01G306200 chr2B 96.947 131 4 0 2473 2603 545760388 545760518 2.360000e-53 220
2 TraesCS2B01G306200 chr2D 96.222 2435 58 9 2596 5025 367996031 367993626 0.000000e+00 3956
3 TraesCS2B01G306200 chr2D 97.365 1670 37 2 811 2474 367997696 367996028 0.000000e+00 2833
4 TraesCS2B01G306200 chr2D 91.007 834 48 13 1 811 368001632 368000803 0.000000e+00 1099
5 TraesCS2B01G306200 chr2D 87.234 329 36 5 2644 2971 410406807 410407130 2.210000e-98 370
6 TraesCS2B01G306200 chr2D 96.992 133 4 0 2467 2599 622315790 622315658 1.820000e-54 224
7 TraesCS2B01G306200 chr2D 94.928 138 7 0 2472 2609 619720673 619720536 3.050000e-52 217
8 TraesCS2B01G306200 chr2A 97.042 1555 31 5 2822 4373 498091657 498090115 0.000000e+00 2603
9 TraesCS2B01G306200 chr2A 97.460 866 22 0 1609 2474 498093022 498092157 0.000000e+00 1478
10 TraesCS2B01G306200 chr2A 91.410 908 63 7 703 1603 498093969 498093070 0.000000e+00 1230
11 TraesCS2B01G306200 chr2A 95.575 678 21 5 4350 5025 498089939 498089269 0.000000e+00 1077
12 TraesCS2B01G306200 chr2A 88.710 310 29 4 2653 2961 478504212 478503908 1.710000e-99 374
13 TraesCS2B01G306200 chr2A 90.196 102 7 2 4166 4264 762011811 762011912 4.080000e-26 130
14 TraesCS2B01G306200 chr2A 85.294 102 12 3 1256 1354 498093502 498093401 8.900000e-18 102
15 TraesCS2B01G306200 chr7B 89.103 312 29 3 2652 2962 313152759 313152452 2.840000e-102 383
16 TraesCS2B01G306200 chr7B 94.928 138 6 1 2469 2606 94758960 94759096 1.100000e-51 215
17 TraesCS2B01G306200 chr6D 88.818 313 29 3 2651 2961 445740073 445740381 3.670000e-101 379
18 TraesCS2B01G306200 chr7A 88.103 311 34 3 2653 2961 219650153 219649844 2.860000e-97 366
19 TraesCS2B01G306200 chr7A 88.103 311 31 4 2653 2962 503787766 503787461 1.030000e-96 364
20 TraesCS2B01G306200 chr4B 88.179 313 29 6 2652 2961 484781736 484782043 2.860000e-97 366
21 TraesCS2B01G306200 chr4A 87.697 317 32 5 2646 2961 238410370 238410060 3.700000e-96 363
22 TraesCS2B01G306200 chr5B 96.324 136 5 0 2473 2608 493512568 493512433 1.820000e-54 224
23 TraesCS2B01G306200 chr5B 87.500 120 9 5 4162 4277 698467181 698467298 3.160000e-27 134
24 TraesCS2B01G306200 chr7D 96.296 135 4 1 2466 2599 150359435 150359301 2.360000e-53 220
25 TraesCS2B01G306200 chr6B 96.923 130 4 0 2470 2599 207511030 207510901 8.470000e-53 219
26 TraesCS2B01G306200 chr6B 91.837 98 5 2 4168 4262 684940301 684940398 3.160000e-27 134
27 TraesCS2B01G306200 chr3A 94.928 138 7 0 2470 2607 736073302 736073165 3.050000e-52 217
28 TraesCS2B01G306200 chr3A 92.708 96 5 2 4169 4262 167879795 167879890 2.440000e-28 137
29 TraesCS2B01G306200 chr1B 94.286 140 8 0 2469 2608 409879939 409879800 1.100000e-51 215
30 TraesCS2B01G306200 chr4D 93.137 102 4 2 4165 4263 289339911 289339810 4.060000e-31 147
31 TraesCS2B01G306200 chr5A 91.346 104 6 2 4162 4262 110664983 110665086 6.790000e-29 139
32 TraesCS2B01G306200 chr5D 91.089 101 6 2 4169 4266 134782110 134782210 3.160000e-27 134


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 TraesCS2B01G306200 chr2B 436995072 437000098 5026 True 9284.000000 9284 100.000000 1 5027 1 chr2B.!!$R1 5026
1 TraesCS2B01G306200 chr2D 367993626 368001632 8006 True 2629.333333 3956 94.864667 1 5025 3 chr2D.!!$R3 5024
2 TraesCS2B01G306200 chr2A 498089269 498093969 4700 True 1298.000000 2603 93.356200 703 5025 5 chr2A.!!$R2 4322

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
950 4082 0.116541 TCCCCGTTCCTCTTCTTCCT 59.883 55.000 0.0 0.0 0.00 3.36 F
2488 5675 0.911769 TAGTACTCCTTCCGTCCGGA 59.088 55.000 0.0 0.0 43.52 5.14 F
3027 6499 1.207089 TCACGAAGGCGGATTCTTCAT 59.793 47.619 0.0 0.0 43.17 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2584 5771 0.388294 GGAAATACTCCCTCCGTCCG 59.612 60.0 0.0 0.0 38.44 4.79 R
3702 7175 0.713883 GAACATGTACGCCTGACACG 59.286 55.0 0.0 0.0 0.00 4.49 R
4584 8262 0.179001 ACAGTTTGTGGGCCAGTACC 60.179 55.0 6.4 0.0 0.00 3.34 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
95 99 2.202756 GGCGCGGTCTGGAGTAAG 60.203 66.667 8.83 0.00 0.00 2.34
129 133 2.357517 CTCTTCCTTGGCACGCGT 60.358 61.111 5.58 5.58 0.00 6.01
132 136 4.555709 TTCCTTGGCACGCGTGGT 62.556 61.111 37.47 0.46 0.00 4.16
156 160 1.450025 GAAGGGTTGATTCCGGTGAC 58.550 55.000 0.00 0.00 0.00 3.67
220 224 1.097547 CCTGGCATAGAAGGCAACGG 61.098 60.000 0.00 0.00 43.93 4.44
232 236 4.953868 CAACGGCGGTGGTGACGA 62.954 66.667 19.01 0.00 0.00 4.20
235 239 4.735132 CGGCGGTGGTGACGACAT 62.735 66.667 0.00 0.00 39.94 3.06
243 247 1.169661 TGGTGACGACATGGTTTGGC 61.170 55.000 0.00 0.00 0.00 4.52
248 252 2.961768 GACATGGTTTGGCGGTGG 59.038 61.111 0.00 0.00 0.00 4.61
264 268 0.460987 GTGGTGGCGAGAAGAGATGG 60.461 60.000 0.00 0.00 0.00 3.51
305 309 5.128663 GGGAGCAGCCAAAAATTATCCTAAA 59.871 40.000 0.00 0.00 38.95 1.85
315 319 9.203421 CCAAAAATTATCCTAAAAAGTGGTGTC 57.797 33.333 0.00 0.00 0.00 3.67
334 338 6.103997 GGTGTCGGTCAAGTATATTTGAGAA 58.896 40.000 10.65 0.00 37.72 2.87
351 355 4.398319 TGAGAAAGTTAGGCTCCCTTTTG 58.602 43.478 11.29 0.00 34.61 2.44
379 383 8.814038 ATAACTCATTAACATTTTGCTCCTCT 57.186 30.769 0.00 0.00 0.00 3.69
382 386 8.635765 ACTCATTAACATTTTGCTCCTCTAAA 57.364 30.769 0.00 0.00 0.00 1.85
398 402 4.715297 CCTCTAAACCTCCTAAACCTAGCA 59.285 45.833 0.00 0.00 0.00 3.49
402 406 5.369409 AAACCTCCTAAACCTAGCATACC 57.631 43.478 0.00 0.00 0.00 2.73
406 410 2.101917 TCCTAAACCTAGCATACCACGC 59.898 50.000 0.00 0.00 0.00 5.34
443 447 9.559958 CTTTATTAACTTTCTGATGCGTTTCAT 57.440 29.630 0.00 0.00 38.32 2.57
469 473 6.091986 ACAAAACACCAACTTGCTTGTAATTG 59.908 34.615 12.74 12.74 28.79 2.32
497 501 2.618053 CCACACGGATTCAAGTCCTAC 58.382 52.381 0.00 0.00 36.07 3.18
507 511 3.217242 AAGTCCTACACTTGCGCAG 57.783 52.632 11.31 7.81 44.28 5.18
508 512 0.679505 AAGTCCTACACTTGCGCAGA 59.320 50.000 11.31 0.00 44.28 4.26
551 556 2.401583 TGCACGCTTTCCATCACTAT 57.598 45.000 0.00 0.00 0.00 2.12
560 565 6.024049 CGCTTTCCATCACTATTCTTTCAAC 58.976 40.000 0.00 0.00 0.00 3.18
566 571 8.722480 TCCATCACTATTCTTTCAACAGTATG 57.278 34.615 0.00 0.00 46.00 2.39
580 585 1.072266 AGTATGGTGTGCCCCTCAAA 58.928 50.000 0.00 0.00 0.00 2.69
581 586 1.640670 AGTATGGTGTGCCCCTCAAAT 59.359 47.619 0.00 0.00 0.00 2.32
593 598 3.680475 GCCCCTCAAATATGACGTGTACA 60.680 47.826 0.00 0.00 0.00 2.90
620 625 6.238484 GGCGACTTTGCAATATAAAGATCTGT 60.238 38.462 0.00 0.00 38.26 3.41
636 641 5.303971 AGATCTGTGTCAGTTTCTTGAAGG 58.696 41.667 0.00 0.00 32.61 3.46
720 740 7.087007 TGACATAAGCACGCAAAATAAAATGA 58.913 30.769 0.00 0.00 0.00 2.57
726 746 5.630680 AGCACGCAAAATAAAATGAGAACAG 59.369 36.000 0.00 0.00 0.00 3.16
731 751 7.805071 ACGCAAAATAAAATGAGAACAGAGAAG 59.195 33.333 0.00 0.00 0.00 2.85
950 4082 0.116541 TCCCCGTTCCTCTTCTTCCT 59.883 55.000 0.00 0.00 0.00 3.36
984 4116 1.157585 GCTCGTTTCAAACCCTCCTC 58.842 55.000 0.00 0.00 0.00 3.71
1045 4177 1.003718 GAAACCGACCTGACCCTGG 60.004 63.158 0.00 0.00 0.00 4.45
1218 4351 1.134521 ACAACAGAGACAGTTTGCGGA 60.135 47.619 0.00 0.00 0.00 5.54
1518 4663 3.780850 ACAAGGAGATTCCCGGTAATTCT 59.219 43.478 0.00 0.00 37.19 2.40
1519 4664 4.130118 CAAGGAGATTCCCGGTAATTCTG 58.870 47.826 0.00 0.00 37.19 3.02
1843 5030 2.002586 CGCCTGGTGAAGATGTTACTG 58.997 52.381 0.00 0.00 0.00 2.74
1896 5083 3.274288 GGAGTGTTTGATGATGACCTCC 58.726 50.000 0.00 0.00 0.00 4.30
1917 5104 3.521937 CCCCTATTCTCTACCACCAACAA 59.478 47.826 0.00 0.00 0.00 2.83
2004 5191 6.239148 GGAGCTTGATACTGAGTATGTCATCA 60.239 42.308 10.29 0.03 33.51 3.07
2010 5197 4.801330 ACTGAGTATGTCATCAACGGAA 57.199 40.909 0.00 0.00 33.51 4.30
2067 5254 2.562738 GGTGCAGCCCTAATTCACTTTT 59.437 45.455 4.03 0.00 0.00 2.27
2154 5341 1.763770 CCACTCCTCCAAACTGGCT 59.236 57.895 0.00 0.00 37.47 4.75
2474 5661 4.152580 GCTGTCTTTCTTGCCAAGTAGTAC 59.847 45.833 4.04 0.00 0.00 2.73
2475 5662 5.542779 CTGTCTTTCTTGCCAAGTAGTACT 58.457 41.667 4.04 0.00 0.00 2.73
2476 5663 5.539048 TGTCTTTCTTGCCAAGTAGTACTC 58.461 41.667 2.58 0.00 0.00 2.59
2477 5664 4.930405 GTCTTTCTTGCCAAGTAGTACTCC 59.070 45.833 2.58 0.00 0.00 3.85
2478 5665 4.838986 TCTTTCTTGCCAAGTAGTACTCCT 59.161 41.667 2.58 0.00 0.00 3.69
2479 5666 5.307196 TCTTTCTTGCCAAGTAGTACTCCTT 59.693 40.000 2.58 0.00 0.00 3.36
2480 5667 4.803098 TCTTGCCAAGTAGTACTCCTTC 57.197 45.455 2.58 0.00 0.00 3.46
2481 5668 3.514309 TCTTGCCAAGTAGTACTCCTTCC 59.486 47.826 2.58 0.00 0.00 3.46
2482 5669 1.822990 TGCCAAGTAGTACTCCTTCCG 59.177 52.381 2.58 0.00 0.00 4.30
2483 5670 1.823610 GCCAAGTAGTACTCCTTCCGT 59.176 52.381 2.58 0.00 0.00 4.69
2484 5671 2.159268 GCCAAGTAGTACTCCTTCCGTC 60.159 54.545 2.58 0.00 0.00 4.79
2485 5672 2.426381 CCAAGTAGTACTCCTTCCGTCC 59.574 54.545 2.58 0.00 0.00 4.79
2486 5673 2.035530 AGTAGTACTCCTTCCGTCCG 57.964 55.000 0.00 0.00 0.00 4.79
2487 5674 1.020437 GTAGTACTCCTTCCGTCCGG 58.980 60.000 0.00 0.00 0.00 5.14
2488 5675 0.911769 TAGTACTCCTTCCGTCCGGA 59.088 55.000 0.00 0.00 43.52 5.14
2498 5685 2.660189 TCCGTCCGGAAATACTTGTC 57.340 50.000 5.23 0.00 42.05 3.18
2499 5686 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2500 5687 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2501 5688 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2502 5689 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2503 5690 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2504 5691 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2505 5692 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2506 5693 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2507 5694 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2508 5695 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
2509 5696 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
2510 5697 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
2511 5698 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
2517 5704 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
2518 5705 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
2519 5706 6.259893 TGTCATCAAAATGGATAAAAGGGGA 58.740 36.000 0.00 0.00 33.42 4.81
2520 5707 6.902416 TGTCATCAAAATGGATAAAAGGGGAT 59.098 34.615 0.00 0.00 33.42 3.85
2521 5708 7.147689 TGTCATCAAAATGGATAAAAGGGGATG 60.148 37.037 0.00 0.00 33.42 3.51
2522 5709 6.902416 TCATCAAAATGGATAAAAGGGGATGT 59.098 34.615 0.00 0.00 33.42 3.06
2523 5710 8.064389 TCATCAAAATGGATAAAAGGGGATGTA 58.936 33.333 0.00 0.00 33.42 2.29
2524 5711 8.873144 CATCAAAATGGATAAAAGGGGATGTAT 58.127 33.333 0.00 0.00 0.00 2.29
2525 5712 8.477419 TCAAAATGGATAAAAGGGGATGTATC 57.523 34.615 0.00 0.00 0.00 2.24
2526 5713 8.288812 TCAAAATGGATAAAAGGGGATGTATCT 58.711 33.333 0.00 0.00 0.00 1.98
2527 5714 9.586732 CAAAATGGATAAAAGGGGATGTATCTA 57.413 33.333 0.00 0.00 0.00 1.98
2528 5715 9.813826 AAAATGGATAAAAGGGGATGTATCTAG 57.186 33.333 0.00 0.00 0.00 2.43
2529 5716 8.757307 AATGGATAAAAGGGGATGTATCTAGA 57.243 34.615 0.00 0.00 0.00 2.43
2530 5717 8.940012 ATGGATAAAAGGGGATGTATCTAGAT 57.060 34.615 10.73 10.73 0.00 1.98
2531 5718 8.150827 TGGATAAAAGGGGATGTATCTAGATG 57.849 38.462 15.79 0.00 0.00 2.90
2532 5719 7.739444 TGGATAAAAGGGGATGTATCTAGATGT 59.261 37.037 15.79 1.25 0.00 3.06
2533 5720 9.268282 GGATAAAAGGGGATGTATCTAGATGTA 57.732 37.037 15.79 4.44 0.00 2.29
2540 5727 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
2564 5751 9.607333 AGTTCTAGATACATCTCCATTTATCCA 57.393 33.333 0.00 0.00 38.32 3.41
2573 5760 8.771521 ACATCTCCATTTATCCATTTTGATGA 57.228 30.769 0.00 0.00 33.85 2.92
2574 5761 8.636213 ACATCTCCATTTATCCATTTTGATGAC 58.364 33.333 0.00 0.00 33.85 3.06
2575 5762 8.635328 CATCTCCATTTATCCATTTTGATGACA 58.365 33.333 0.00 0.00 32.05 3.58
2576 5763 8.592529 TCTCCATTTATCCATTTTGATGACAA 57.407 30.769 0.00 0.00 0.00 3.18
2577 5764 8.689061 TCTCCATTTATCCATTTTGATGACAAG 58.311 33.333 0.00 0.00 37.32 3.16
2578 5765 8.365060 TCCATTTATCCATTTTGATGACAAGT 57.635 30.769 0.00 0.00 37.32 3.16
2579 5766 9.473007 TCCATTTATCCATTTTGATGACAAGTA 57.527 29.630 0.00 0.00 37.32 2.24
2585 5772 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
2586 5773 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
2587 5774 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2588 5775 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2589 5776 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2590 5777 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2591 5778 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2592 5779 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2593 5780 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2594 5781 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2595 5782 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2596 5783 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2597 5784 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
2598 5785 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2770 5957 3.350833 TCCTCGGACTAGTAACCTGTTC 58.649 50.000 0.00 0.00 0.00 3.18
2845 6317 2.366266 AGTTTTCTTGCATGCATGTGGT 59.634 40.909 26.79 10.71 0.00 4.16
2881 6353 8.891671 TCCTAGTAAACGAAAAGAAAAGCTAA 57.108 30.769 0.00 0.00 0.00 3.09
3027 6499 1.207089 TCACGAAGGCGGATTCTTCAT 59.793 47.619 0.00 0.00 43.17 2.57
3552 7025 6.469782 AAACCAAATCTTATGCACCCTATG 57.530 37.500 0.00 0.00 0.00 2.23
3554 7027 5.133221 ACCAAATCTTATGCACCCTATGTC 58.867 41.667 0.00 0.00 0.00 3.06
3602 7075 9.536558 GTGTTTTGTTGAACTTTAAAATGAACC 57.463 29.630 0.00 0.00 0.00 3.62
3702 7175 8.924511 TGATTAACCTCATTCTTATCCAATCC 57.075 34.615 0.00 0.00 0.00 3.01
3711 7184 2.158957 TCTTATCCAATCCGTGTCAGGC 60.159 50.000 0.00 0.00 0.00 4.85
3736 7209 4.624015 ACATGTTCAGCATTTCCAAACTG 58.376 39.130 0.00 0.00 35.19 3.16
3752 7225 2.128771 ACTGGCATACATTTTCCGCT 57.871 45.000 0.00 0.00 0.00 5.52
4089 7562 4.589216 ATGTGGAATTTTCAGTGTGGTG 57.411 40.909 0.00 0.00 0.00 4.17
4107 7580 0.753867 TGTCTGTTGTACGCCTTCCA 59.246 50.000 0.00 0.00 0.00 3.53
4300 7775 1.961793 TATTTATGTCCCAGCGGCAC 58.038 50.000 1.45 0.00 0.00 5.01
4399 8073 3.795688 TTGAAGAGGTGCCATTTCTCT 57.204 42.857 0.00 0.00 39.31 3.10
4414 8088 6.366061 GCCATTTCTCTCCACATTTTGTAAAC 59.634 38.462 0.00 0.00 0.00 2.01
4422 8096 3.679025 CCACATTTTGTAAACGCATGCAT 59.321 39.130 19.57 0.00 0.00 3.96
4423 8097 4.152045 CCACATTTTGTAAACGCATGCATT 59.848 37.500 19.57 14.28 0.00 3.56
4424 8098 5.333952 CCACATTTTGTAAACGCATGCATTT 60.334 36.000 16.71 16.71 0.00 2.32
4572 8250 1.342074 AAGCTCTGCCAGTAGTGACA 58.658 50.000 0.00 0.00 0.00 3.58
4584 8262 0.976641 TAGTGACACCTGAAGCCCTG 59.023 55.000 0.84 0.00 0.00 4.45
4633 8311 2.616376 TGTATTGTGTCGCAACAGCTTT 59.384 40.909 0.00 0.00 40.28 3.51
4754 8432 8.492673 ACTGAAGCAGATAAAAATGTATTCGA 57.507 30.769 0.82 0.00 35.18 3.71
4755 8433 8.391106 ACTGAAGCAGATAAAAATGTATTCGAC 58.609 33.333 0.82 0.00 35.18 4.20
4758 8436 8.492673 AAGCAGATAAAAATGTATTCGACTGA 57.507 30.769 0.00 0.00 0.00 3.41
4759 8437 8.492673 AGCAGATAAAAATGTATTCGACTGAA 57.507 30.769 0.00 0.00 38.76 3.02
4760 8438 8.607459 AGCAGATAAAAATGTATTCGACTGAAG 58.393 33.333 0.00 0.00 37.57 3.02
4761 8439 7.852945 GCAGATAAAAATGTATTCGACTGAAGG 59.147 37.037 0.00 0.00 37.57 3.46
4762 8440 9.098355 CAGATAAAAATGTATTCGACTGAAGGA 57.902 33.333 0.00 0.00 37.57 3.36
5025 8703 9.631257 TTTCATGAAATCATCTTCTAGCCATAA 57.369 29.630 16.91 0.00 33.61 1.90
5026 8704 9.803507 TTCATGAAATCATCTTCTAGCCATAAT 57.196 29.630 5.45 0.00 33.61 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.637489 CTCCCGCTGCTCCGATCG 62.637 72.222 8.51 8.51 0.00 3.69
15 16 4.537433 CTAGCACCCTCCCGCTGC 62.537 72.222 0.00 0.00 39.30 5.25
129 133 0.856982 AATCAACCCTTCCACCACCA 59.143 50.000 0.00 0.00 0.00 4.17
132 136 0.037590 CGGAATCAACCCTTCCACCA 59.962 55.000 3.26 0.00 41.94 4.17
220 224 3.118454 CCATGTCGTCACCACCGC 61.118 66.667 0.00 0.00 0.00 5.68
232 236 2.197324 ACCACCGCCAAACCATGT 59.803 55.556 0.00 0.00 0.00 3.21
243 247 1.949847 ATCTCTTCTCGCCACCACCG 61.950 60.000 0.00 0.00 0.00 4.94
248 252 1.880340 CGCCATCTCTTCTCGCCAC 60.880 63.158 0.00 0.00 0.00 5.01
305 309 3.764237 ATACTTGACCGACACCACTTT 57.236 42.857 0.00 0.00 0.00 2.66
315 319 8.818057 CCTAACTTTCTCAAATATACTTGACCG 58.182 37.037 0.00 0.00 32.00 4.79
334 338 2.070573 TCCCAAAAGGGAGCCTAACTT 58.929 47.619 0.00 0.00 40.01 2.66
351 355 7.068716 AGGAGCAAAATGTTAATGAGTTATCCC 59.931 37.037 0.00 0.00 0.00 3.85
361 365 7.122799 GGAGGTTTAGAGGAGCAAAATGTTAAT 59.877 37.037 0.00 0.00 0.00 1.40
366 370 4.593956 AGGAGGTTTAGAGGAGCAAAATG 58.406 43.478 0.00 0.00 0.00 2.32
379 383 5.965705 TGGTATGCTAGGTTTAGGAGGTTTA 59.034 40.000 0.00 0.00 30.25 2.01
382 386 3.710165 GTGGTATGCTAGGTTTAGGAGGT 59.290 47.826 0.00 0.00 30.25 3.85
398 402 3.334583 AGTTTGTCATCTGCGTGGTAT 57.665 42.857 0.00 0.00 0.00 2.73
402 406 7.298122 AGTTAATAAAGTTTGTCATCTGCGTG 58.702 34.615 0.00 0.00 0.00 5.34
443 447 4.792521 ACAAGCAAGTTGGTGTTTTGTA 57.207 36.364 8.61 0.00 40.90 2.41
469 473 1.017387 GAATCCGTGTGGGCAGATTC 58.983 55.000 0.00 0.00 38.25 2.52
497 501 4.744136 AATATGATCATCTGCGCAAGTG 57.256 40.909 12.53 13.52 41.68 3.16
551 556 3.568007 GGCACACCATACTGTTGAAAGAA 59.432 43.478 0.00 0.00 35.26 2.52
560 565 0.327924 TTGAGGGGCACACCATACTG 59.672 55.000 0.00 0.00 42.91 2.74
566 571 2.024414 GTCATATTTGAGGGGCACACC 58.976 52.381 0.00 0.00 39.11 4.16
580 585 2.426024 AGTCGCCTTGTACACGTCATAT 59.574 45.455 0.00 0.00 0.00 1.78
581 586 1.814394 AGTCGCCTTGTACACGTCATA 59.186 47.619 0.00 0.00 0.00 2.15
593 598 6.543831 AGATCTTTATATTGCAAAGTCGCCTT 59.456 34.615 1.71 0.00 35.08 4.35
620 625 4.584874 TGAACACCTTCAAGAAACTGACA 58.415 39.130 0.00 0.00 33.20 3.58
631 636 6.126507 ACACCATATCCATATGAACACCTTCA 60.127 38.462 3.65 0.00 42.05 3.02
632 637 6.205464 CACACCATATCCATATGAACACCTTC 59.795 42.308 3.65 0.00 42.05 3.46
636 641 4.083855 CGCACACCATATCCATATGAACAC 60.084 45.833 3.65 0.00 42.05 3.32
720 740 2.262915 CGGCGCCTTCTCTGTTCT 59.737 61.111 26.68 0.00 0.00 3.01
748 768 1.332028 CGGATGCGAGCATTAAACGTC 60.332 52.381 12.16 0.00 36.70 4.34
751 771 3.148823 GCGGATGCGAGCATTAAAC 57.851 52.632 12.10 0.00 36.70 2.01
806 827 0.994263 GTTCGGTCCGTGGTATTTCG 59.006 55.000 11.88 0.00 0.00 3.46
809 3941 0.686224 TTGGTTCGGTCCGTGGTATT 59.314 50.000 11.88 0.00 0.00 1.89
817 3949 2.741211 GCGTCCTTGGTTCGGTCC 60.741 66.667 8.35 0.00 0.00 4.46
923 4055 2.606826 GGAACGGGGAGGAGTGGT 60.607 66.667 0.00 0.00 0.00 4.16
1045 4177 4.131088 GAGGTCACCCGAGACGGC 62.131 72.222 4.57 0.00 46.86 5.68
1055 4187 0.038526 ACCGTTGTCATCGAGGTCAC 60.039 55.000 4.86 0.00 0.00 3.67
1218 4351 3.325135 AGAGATTCTTCTGAACCAACGGT 59.675 43.478 0.00 0.00 34.71 4.83
1501 4640 2.158813 TGCCAGAATTACCGGGAATCTC 60.159 50.000 13.67 12.32 0.00 2.75
1518 4663 2.063015 AATCCCAACCGTGAGTGCCA 62.063 55.000 0.00 0.00 0.00 4.92
1519 4664 0.035820 TAATCCCAACCGTGAGTGCC 60.036 55.000 0.00 0.00 0.00 5.01
1603 4748 6.918022 GCATGGTTAGTTTTCAATATGGTAGC 59.082 38.462 0.00 0.00 0.00 3.58
1617 4804 4.456911 CAGTGACATCAAGCATGGTTAGTT 59.543 41.667 10.31 0.00 36.72 2.24
1618 4805 4.005650 CAGTGACATCAAGCATGGTTAGT 58.994 43.478 10.31 9.33 36.72 2.24
1697 4884 3.009723 CAACTGCTCCATACCGAAATGT 58.990 45.455 0.00 0.00 0.00 2.71
1783 4970 5.070981 ACAATAGATAGGACCATGACACCAG 59.929 44.000 0.00 0.00 0.00 4.00
1843 5030 2.094417 GCCTTACGCAGAGTCAATTGAC 59.906 50.000 27.69 27.69 40.47 3.18
1896 5083 4.019681 TGTTGTTGGTGGTAGAGAATAGGG 60.020 45.833 0.00 0.00 0.00 3.53
1917 5104 1.971357 AGTTGGTACTACTGCTGCTGT 59.029 47.619 16.37 16.37 31.21 4.40
2479 5666 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2480 5667 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2481 5668 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2482 5669 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2483 5670 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
2484 5671 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
2485 5672 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
2491 5678 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
2492 5679 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
2493 5680 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
2494 5681 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
2495 5682 6.259893 TCCCCTTTTATCCATTTTGATGACA 58.740 36.000 0.00 0.00 0.00 3.58
2496 5683 6.790232 TCCCCTTTTATCCATTTTGATGAC 57.210 37.500 0.00 0.00 0.00 3.06
2497 5684 6.902416 ACATCCCCTTTTATCCATTTTGATGA 59.098 34.615 0.00 0.00 32.39 2.92
2498 5685 7.128234 ACATCCCCTTTTATCCATTTTGATG 57.872 36.000 0.00 0.00 33.80 3.07
2499 5686 9.093458 GATACATCCCCTTTTATCCATTTTGAT 57.907 33.333 0.00 0.00 0.00 2.57
2500 5687 8.288812 AGATACATCCCCTTTTATCCATTTTGA 58.711 33.333 0.00 0.00 0.00 2.69
2501 5688 8.482852 AGATACATCCCCTTTTATCCATTTTG 57.517 34.615 0.00 0.00 0.00 2.44
2502 5689 9.813826 CTAGATACATCCCCTTTTATCCATTTT 57.186 33.333 0.00 0.00 0.00 1.82
2503 5690 9.182642 TCTAGATACATCCCCTTTTATCCATTT 57.817 33.333 0.00 0.00 0.00 2.32
2504 5691 8.757307 TCTAGATACATCCCCTTTTATCCATT 57.243 34.615 0.00 0.00 0.00 3.16
2505 5692 8.776119 CATCTAGATACATCCCCTTTTATCCAT 58.224 37.037 4.54 0.00 0.00 3.41
2506 5693 7.739444 ACATCTAGATACATCCCCTTTTATCCA 59.261 37.037 4.54 0.00 0.00 3.41
2507 5694 8.152023 ACATCTAGATACATCCCCTTTTATCC 57.848 38.462 4.54 0.00 0.00 2.59
2514 5701 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
2538 5725 9.607333 TGGATAAATGGAGATGTATCTAGAACT 57.393 33.333 0.00 0.00 37.25 3.01
2547 5734 9.865152 TCATCAAAATGGATAAATGGAGATGTA 57.135 29.630 0.00 0.00 33.42 2.29
2548 5735 8.636213 GTCATCAAAATGGATAAATGGAGATGT 58.364 33.333 0.00 0.00 33.42 3.06
2549 5736 8.635328 TGTCATCAAAATGGATAAATGGAGATG 58.365 33.333 0.00 0.00 33.42 2.90
2550 5737 8.771521 TGTCATCAAAATGGATAAATGGAGAT 57.228 30.769 0.00 0.00 33.42 2.75
2551 5738 8.592529 TTGTCATCAAAATGGATAAATGGAGA 57.407 30.769 0.00 0.00 33.42 3.71
2552 5739 8.472413 ACTTGTCATCAAAATGGATAAATGGAG 58.528 33.333 0.00 0.00 33.42 3.86
2553 5740 8.365060 ACTTGTCATCAAAATGGATAAATGGA 57.635 30.769 0.00 0.00 33.42 3.41
2560 5747 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
2561 5748 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2562 5749 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2563 5750 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2564 5751 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2565 5752 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2566 5753 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2567 5754 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2568 5755 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2569 5756 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2570 5757 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2571 5758 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2572 5759 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2573 5760 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2574 5761 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2575 5762 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2576 5763 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2577 5764 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2578 5765 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2579 5766 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2580 5767 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2581 5768 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
2582 5769 1.753073 GAAATACTCCCTCCGTCCGAA 59.247 52.381 0.00 0.00 0.00 4.30
2583 5770 1.396653 GAAATACTCCCTCCGTCCGA 58.603 55.000 0.00 0.00 0.00 4.55
2584 5771 0.388294 GGAAATACTCCCTCCGTCCG 59.612 60.000 0.00 0.00 38.44 4.79
2585 5772 1.790818 AGGAAATACTCCCTCCGTCC 58.209 55.000 0.00 0.00 46.81 4.79
2586 5773 4.799917 GCATTAGGAAATACTCCCTCCGTC 60.800 50.000 0.00 0.00 46.81 4.79
2587 5774 3.071167 GCATTAGGAAATACTCCCTCCGT 59.929 47.826 0.00 0.00 46.81 4.69
2588 5775 3.325135 AGCATTAGGAAATACTCCCTCCG 59.675 47.826 0.00 0.00 46.81 4.63
2589 5776 4.103311 ACAGCATTAGGAAATACTCCCTCC 59.897 45.833 0.00 0.00 46.81 4.30
2590 5777 5.059833 CACAGCATTAGGAAATACTCCCTC 58.940 45.833 0.00 0.00 46.81 4.30
2591 5778 4.687219 GCACAGCATTAGGAAATACTCCCT 60.687 45.833 0.00 0.00 46.81 4.20
2592 5779 3.565902 GCACAGCATTAGGAAATACTCCC 59.434 47.826 0.00 0.00 46.81 4.30
2593 5780 4.274459 CAGCACAGCATTAGGAAATACTCC 59.726 45.833 0.00 0.00 45.81 3.85
2594 5781 4.878397 ACAGCACAGCATTAGGAAATACTC 59.122 41.667 0.00 0.00 0.00 2.59
2595 5782 4.848357 ACAGCACAGCATTAGGAAATACT 58.152 39.130 0.00 0.00 0.00 2.12
2596 5783 4.878397 AGACAGCACAGCATTAGGAAATAC 59.122 41.667 0.00 0.00 0.00 1.89
2597 5784 4.877823 CAGACAGCACAGCATTAGGAAATA 59.122 41.667 0.00 0.00 0.00 1.40
2598 5785 3.693085 CAGACAGCACAGCATTAGGAAAT 59.307 43.478 0.00 0.00 0.00 2.17
2708 5895 4.039973 CCTCGATTACTATTGGTGGCCTTA 59.960 45.833 3.32 0.00 0.00 2.69
2810 5997 4.344359 AGAAAACTGAGTGGAGGAAGAC 57.656 45.455 0.00 0.00 0.00 3.01
3027 6499 0.112995 AGTCTGGCCAGCCAAATGAA 59.887 50.000 28.91 4.97 46.63 2.57
3535 7008 4.978099 CCTGACATAGGGTGCATAAGATT 58.022 43.478 0.00 0.00 43.33 2.40
3552 7025 1.144057 CCATGTAGGACGGCCTGAC 59.856 63.158 23.83 14.90 46.45 3.51
3554 7027 3.628989 TCCATGTAGGACGGCCTG 58.371 61.111 23.83 2.90 46.45 4.85
3602 7075 5.964958 TCAGCTTCTGGTTTAAAAGGATG 57.035 39.130 0.00 0.00 31.51 3.51
3702 7175 0.713883 GAACATGTACGCCTGACACG 59.286 55.000 0.00 0.00 0.00 4.49
3711 7184 4.418013 TTGGAAATGCTGAACATGTACG 57.582 40.909 0.00 0.00 39.60 3.67
3736 7209 1.680338 AGGAGCGGAAAATGTATGCC 58.320 50.000 0.00 0.00 0.00 4.40
4089 7562 1.529865 GTTGGAAGGCGTACAACAGAC 59.470 52.381 21.42 0.00 42.88 3.51
4300 7775 4.058721 TGATCTTCATGTACCATCACGG 57.941 45.455 0.00 0.00 42.50 4.94
4399 8073 3.243535 TGCATGCGTTTACAAAATGTGGA 60.244 39.130 14.09 0.00 0.00 4.02
4486 8164 5.903010 TGATCCCTATTCTTAGGCTTGTACA 59.097 40.000 0.00 0.00 43.34 2.90
4487 8165 6.183360 TGTGATCCCTATTCTTAGGCTTGTAC 60.183 42.308 0.00 0.00 43.34 2.90
4488 8166 5.903010 TGTGATCCCTATTCTTAGGCTTGTA 59.097 40.000 0.00 0.00 43.34 2.41
4572 8250 1.201429 CCAGTACCAGGGCTTCAGGT 61.201 60.000 0.00 0.00 39.41 4.00
4584 8262 0.179001 ACAGTTTGTGGGCCAGTACC 60.179 55.000 6.40 0.00 0.00 3.34
4633 8311 1.973515 AGAGGCTCAATGTCACTCACA 59.026 47.619 18.26 0.00 40.18 3.58
4753 8431 5.295540 GCCTCTCAAATGTTATCCTTCAGTC 59.704 44.000 0.00 0.00 0.00 3.51
4754 8432 5.189180 GCCTCTCAAATGTTATCCTTCAGT 58.811 41.667 0.00 0.00 0.00 3.41
4755 8433 5.188434 TGCCTCTCAAATGTTATCCTTCAG 58.812 41.667 0.00 0.00 0.00 3.02
4758 8436 5.574188 AGTTGCCTCTCAAATGTTATCCTT 58.426 37.500 0.00 0.00 36.26 3.36
4759 8437 5.045286 AGAGTTGCCTCTCAAATGTTATCCT 60.045 40.000 7.75 0.00 45.08 3.24
4760 8438 5.065731 CAGAGTTGCCTCTCAAATGTTATCC 59.934 44.000 7.75 0.00 45.08 2.59
4761 8439 5.645497 ACAGAGTTGCCTCTCAAATGTTATC 59.355 40.000 7.75 0.00 45.08 1.75
4762 8440 5.564550 ACAGAGTTGCCTCTCAAATGTTAT 58.435 37.500 7.75 0.00 45.08 1.89
4764 8442 3.825328 ACAGAGTTGCCTCTCAAATGTT 58.175 40.909 7.75 0.00 45.08 2.71
4765 8443 3.498774 ACAGAGTTGCCTCTCAAATGT 57.501 42.857 7.75 1.87 45.08 2.71
4850 8528 7.493645 TGCACAACATGTATTTGATTGAACAAA 59.506 29.630 0.00 0.00 42.58 2.83
4872 8550 2.680312 TGCTGGAATAGAGAGTGCAC 57.320 50.000 9.40 9.40 0.00 4.57


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

AutoCloner maintained by Alex Coulton.