Multiple sequence alignment - TraesCS2A01G416300

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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 TraesCS2A01G416300 chr2A 100.000 2545 0 0 1 2545 672747301 672744757 0.000000e+00 4700
1 TraesCS2A01G416300 chr2A 95.655 1657 42 17 1 1655 673418935 673420563 0.000000e+00 2634
2 TraesCS2A01G416300 chr2A 96.866 989 15 11 711 1698 673417479 673418452 0.000000e+00 1640
3 TraesCS2A01G416300 chr2A 82.602 684 74 33 807 1468 673451878 673452538 1.710000e-156 562
4 TraesCS2A01G416300 chr2B 87.996 1033 82 26 711 1737 627317418 627318414 0.000000e+00 1182
5 TraesCS2A01G416300 chr2B 86.053 1097 96 33 794 1857 625239186 625238114 0.000000e+00 1125
6 TraesCS2A01G416300 chr2B 90.885 746 50 11 765 1506 627322844 627323575 0.000000e+00 985
7 TraesCS2A01G416300 chr2B 83.490 533 44 19 1882 2378 625238117 625237593 8.300000e-125 457
8 TraesCS2A01G416300 chr2B 90.426 94 7 2 1376 1469 627324438 627324529 3.440000e-24 122
9 TraesCS2A01G416300 chr5A 97.956 685 4 3 1 677 32697963 32698645 0.000000e+00 1179
10 TraesCS2A01G416300 chr2D 87.282 1030 82 16 720 1737 527804870 527803878 0.000000e+00 1131
11 TraesCS2A01G416300 chr2D 87.895 950 59 17 710 1655 528994405 528995302 0.000000e+00 1066
12 TraesCS2A01G416300 chr2D 84.385 602 45 22 1882 2442 527683179 527682586 1.720000e-151 545
13 TraesCS2A01G416300 chr2D 81.671 431 53 18 272 677 365377713 365377284 4.060000e-88 335
14 TraesCS2A01G416300 chr2D 88.115 244 26 2 1617 1857 527803929 527803686 1.150000e-73 287
15 TraesCS2A01G416300 chr2D 86.713 143 10 4 1882 2018 527803689 527803550 1.580000e-32 150
16 TraesCS2A01G416300 chr7D 90.964 664 30 10 721 1375 134467370 134466728 0.000000e+00 867
17 TraesCS2A01G416300 chr7A 88.119 707 57 13 781 1478 133627713 133627025 0.000000e+00 815
18 TraesCS2A01G416300 chr6D 94.430 395 15 3 1 389 37438563 37438170 3.620000e-168 601
19 TraesCS2A01G416300 chr6D 94.898 294 12 3 396 689 37437746 37437456 8.300000e-125 457


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 TraesCS2A01G416300 chr2A 672744757 672747301 2544 True 4700.000000 4700 100.0000 1 2545 1 chr2A.!!$R1 2544
1 TraesCS2A01G416300 chr2A 673417479 673420563 3084 False 2137.000000 2634 96.2605 1 1698 2 chr2A.!!$F2 1697
2 TraesCS2A01G416300 chr2A 673451878 673452538 660 False 562.000000 562 82.6020 807 1468 1 chr2A.!!$F1 661
3 TraesCS2A01G416300 chr2B 627317418 627318414 996 False 1182.000000 1182 87.9960 711 1737 1 chr2B.!!$F1 1026
4 TraesCS2A01G416300 chr2B 625237593 625239186 1593 True 791.000000 1125 84.7715 794 2378 2 chr2B.!!$R1 1584
5 TraesCS2A01G416300 chr2B 627322844 627324529 1685 False 553.500000 985 90.6555 765 1506 2 chr2B.!!$F2 741
6 TraesCS2A01G416300 chr5A 32697963 32698645 682 False 1179.000000 1179 97.9560 1 677 1 chr5A.!!$F1 676
7 TraesCS2A01G416300 chr2D 528994405 528995302 897 False 1066.000000 1066 87.8950 710 1655 1 chr2D.!!$F1 945
8 TraesCS2A01G416300 chr2D 527682586 527683179 593 True 545.000000 545 84.3850 1882 2442 1 chr2D.!!$R2 560
9 TraesCS2A01G416300 chr2D 527803550 527804870 1320 True 522.666667 1131 87.3700 720 2018 3 chr2D.!!$R3 1298
10 TraesCS2A01G416300 chr7D 134466728 134467370 642 True 867.000000 867 90.9640 721 1375 1 chr7D.!!$R1 654
11 TraesCS2A01G416300 chr7A 133627025 133627713 688 True 815.000000 815 88.1190 781 1478 1 chr7A.!!$R1 697
12 TraesCS2A01G416300 chr6D 37437456 37438563 1107 True 529.000000 601 94.6640 1 689 2 chr6D.!!$R1 688

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
107 1567 1.16527 GAGGCACGCACACCTATTTT 58.835 50.0 0.0 0.0 36.05 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 4394 1.266718 GCGTTCAGAAACAGAATGCCA 59.733 47.619 8.51 0.0 46.91 4.92 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
107 1567 1.165270 GAGGCACGCACACCTATTTT 58.835 50.000 0.00 0.00 36.05 1.82
1284 3213 2.503375 GACGCCGTCACCTACACG 60.503 66.667 13.23 0.00 36.99 4.49
1329 3258 1.359117 CGCCATGGACGTCGTCTAT 59.641 57.895 23.69 20.61 34.14 1.98
1332 3261 0.597637 CCATGGACGTCGTCTATGCC 60.598 60.000 33.94 17.21 45.75 4.40
1425 3375 1.795286 CTTCCTCGTTTGCTCTGTGTC 59.205 52.381 0.00 0.00 0.00 3.67
1432 3382 2.032054 CGTTTGCTCTGTGTCATGTGTT 59.968 45.455 0.00 0.00 0.00 3.32
1433 3383 3.365832 GTTTGCTCTGTGTCATGTGTTG 58.634 45.455 0.00 0.00 0.00 3.33
1508 3467 4.439968 GTTCAGTAGGCTGTGTAATACCC 58.560 47.826 0.00 0.00 43.05 3.69
1509 3468 3.715287 TCAGTAGGCTGTGTAATACCCA 58.285 45.455 0.00 0.00 43.05 4.51
1510 3469 4.098155 TCAGTAGGCTGTGTAATACCCAA 58.902 43.478 0.00 0.00 43.05 4.12
1511 3470 4.532916 TCAGTAGGCTGTGTAATACCCAAA 59.467 41.667 0.00 0.00 43.05 3.28
1512 3471 4.876107 CAGTAGGCTGTGTAATACCCAAAG 59.124 45.833 0.00 0.00 37.92 2.77
1513 3472 4.534897 AGTAGGCTGTGTAATACCCAAAGT 59.465 41.667 0.00 0.00 0.00 2.66
1514 3473 5.722923 AGTAGGCTGTGTAATACCCAAAGTA 59.277 40.000 0.00 0.00 34.76 2.24
1515 3474 5.710409 AGGCTGTGTAATACCCAAAGTAT 57.290 39.130 0.00 0.00 43.85 2.12
1516 3475 5.437060 AGGCTGTGTAATACCCAAAGTATG 58.563 41.667 0.00 0.00 40.98 2.39
1517 3476 5.045140 AGGCTGTGTAATACCCAAAGTATGT 60.045 40.000 0.00 0.00 40.98 2.29
1518 3477 5.650703 GGCTGTGTAATACCCAAAGTATGTT 59.349 40.000 0.00 0.00 40.98 2.71
1519 3478 6.404293 GGCTGTGTAATACCCAAAGTATGTTG 60.404 42.308 0.00 0.00 40.98 3.33
1529 3498 5.596361 ACCCAAAGTATGTTGTGTTCAATGA 59.404 36.000 0.00 0.00 35.92 2.57
1599 3717 5.890334 TGTGTTTTGCTTTTCTAAGACTGG 58.110 37.500 0.00 0.00 32.92 4.00
1611 3729 7.765695 TTTCTAAGACTGGCTGATTTGATTT 57.234 32.000 0.00 0.00 0.00 2.17
1612 3730 6.992063 TCTAAGACTGGCTGATTTGATTTC 57.008 37.500 0.00 0.00 0.00 2.17
1613 3731 6.715280 TCTAAGACTGGCTGATTTGATTTCT 58.285 36.000 0.00 0.00 0.00 2.52
1624 3755 8.465201 GGCTGATTTGATTTCTCTGTTTAGATT 58.535 33.333 0.00 0.00 31.21 2.40
1685 3869 3.510388 TTGAATCTCGTCGCTTCTCAT 57.490 42.857 0.00 0.00 0.00 2.90
1706 3890 8.228464 TCTCATTTTAGATCGTATAGCTGTACG 58.772 37.037 30.34 30.34 46.52 3.67
1708 3892 5.618056 TTTAGATCGTATAGCTGTACGGG 57.382 43.478 33.46 14.34 45.52 5.28
1766 4283 4.212143 TGCAATCTGTACAAGAGATGCT 57.788 40.909 21.85 2.00 45.39 3.79
1768 4285 5.922053 TGCAATCTGTACAAGAGATGCTAT 58.078 37.500 21.85 1.26 45.39 2.97
1785 4304 2.969262 GCTATCCTTCCTCAGGTAAGCT 59.031 50.000 0.00 0.00 44.37 3.74
1796 4315 2.362397 TCAGGTAAGCTCATCGTCCATC 59.638 50.000 0.00 0.00 0.00 3.51
1811 4330 3.653344 GTCCATCTTTTGGTTTGGCTTC 58.347 45.455 0.00 0.00 46.52 3.86
1822 4341 0.881118 TTTGGCTTCACTGCGGAATC 59.119 50.000 0.00 0.00 0.00 2.52
1829 4348 1.795768 TCACTGCGGAATCAACTGTC 58.204 50.000 0.00 0.00 0.00 3.51
1831 4350 1.872952 CACTGCGGAATCAACTGTCAA 59.127 47.619 0.00 0.00 0.00 3.18
1853 4372 5.722021 ACTTTTCTGTTGTTTTCAGTGGT 57.278 34.783 0.00 0.00 34.86 4.16
1854 4373 6.827586 ACTTTTCTGTTGTTTTCAGTGGTA 57.172 33.333 0.00 0.00 34.86 3.25
1855 4374 7.404671 ACTTTTCTGTTGTTTTCAGTGGTAT 57.595 32.000 0.00 0.00 34.86 2.73
1856 4375 7.257722 ACTTTTCTGTTGTTTTCAGTGGTATG 58.742 34.615 0.00 0.00 34.86 2.39
1857 4376 5.766150 TTCTGTTGTTTTCAGTGGTATGG 57.234 39.130 0.00 0.00 34.86 2.74
1858 4377 5.042463 TCTGTTGTTTTCAGTGGTATGGA 57.958 39.130 0.00 0.00 34.86 3.41
1859 4378 5.630121 TCTGTTGTTTTCAGTGGTATGGAT 58.370 37.500 0.00 0.00 34.86 3.41
1860 4379 6.774673 TCTGTTGTTTTCAGTGGTATGGATA 58.225 36.000 0.00 0.00 34.86 2.59
1861 4380 6.653320 TCTGTTGTTTTCAGTGGTATGGATAC 59.347 38.462 0.00 0.00 34.86 2.24
1862 4381 6.539173 TGTTGTTTTCAGTGGTATGGATACT 58.461 36.000 0.00 0.00 33.81 2.12
1863 4382 7.681679 TGTTGTTTTCAGTGGTATGGATACTA 58.318 34.615 0.00 0.00 33.81 1.82
1864 4383 8.158132 TGTTGTTTTCAGTGGTATGGATACTAA 58.842 33.333 0.00 0.00 33.81 2.24
1865 4384 9.005777 GTTGTTTTCAGTGGTATGGATACTAAA 57.994 33.333 0.00 0.00 33.81 1.85
1866 4385 9.575868 TTGTTTTCAGTGGTATGGATACTAAAA 57.424 29.630 0.00 0.00 33.81 1.52
1867 4386 9.226606 TGTTTTCAGTGGTATGGATACTAAAAG 57.773 33.333 0.00 0.00 33.81 2.27
1868 4387 8.674607 GTTTTCAGTGGTATGGATACTAAAAGG 58.325 37.037 0.00 0.00 33.81 3.11
1869 4388 7.504926 TTCAGTGGTATGGATACTAAAAGGT 57.495 36.000 0.00 0.00 33.81 3.50
1870 4389 8.612486 TTCAGTGGTATGGATACTAAAAGGTA 57.388 34.615 0.00 0.00 33.81 3.08
1871 4390 8.246430 TCAGTGGTATGGATACTAAAAGGTAG 57.754 38.462 0.00 0.00 33.81 3.18
1872 4391 8.063153 TCAGTGGTATGGATACTAAAAGGTAGA 58.937 37.037 0.00 0.00 33.81 2.59
1873 4392 8.361139 CAGTGGTATGGATACTAAAAGGTAGAG 58.639 40.741 0.00 0.00 33.81 2.43
1874 4393 8.066247 AGTGGTATGGATACTAAAAGGTAGAGT 58.934 37.037 0.00 0.00 33.81 3.24
1875 4394 8.702819 GTGGTATGGATACTAAAAGGTAGAGTT 58.297 37.037 0.00 0.00 33.81 3.01
1876 4395 8.701895 TGGTATGGATACTAAAAGGTAGAGTTG 58.298 37.037 0.00 0.00 33.81 3.16
1877 4396 8.148999 GGTATGGATACTAAAAGGTAGAGTTGG 58.851 40.741 0.00 0.00 33.81 3.77
1878 4397 5.985911 TGGATACTAAAAGGTAGAGTTGGC 58.014 41.667 0.00 0.00 37.61 4.52
1879 4398 5.486063 TGGATACTAAAAGGTAGAGTTGGCA 59.514 40.000 0.00 0.00 37.61 4.92
1880 4399 6.157994 TGGATACTAAAAGGTAGAGTTGGCAT 59.842 38.462 0.00 0.00 37.61 4.40
1993 4518 2.143122 CTGAGGCTCTGCGTTAAACAA 58.857 47.619 16.72 0.00 0.00 2.83
1997 4523 3.900941 AGGCTCTGCGTTAAACAATTTG 58.099 40.909 0.00 0.00 0.00 2.32
1998 4524 3.317993 AGGCTCTGCGTTAAACAATTTGT 59.682 39.130 0.00 0.00 0.00 2.83
1999 4525 3.668656 GGCTCTGCGTTAAACAATTTGTC 59.331 43.478 1.83 0.00 0.00 3.18
2003 4529 6.125327 TCTGCGTTAAACAATTTGTCTTCA 57.875 33.333 1.83 0.00 0.00 3.02
2069 4617 6.983906 AAAATCTTGTTTCTCACTGGGATT 57.016 33.333 0.00 0.00 0.00 3.01
2072 4620 8.655935 AAATCTTGTTTCTCACTGGGATTTAT 57.344 30.769 0.00 0.00 32.32 1.40
2128 4676 6.512297 TCTTTTTGAGAAATTGTAAGGTGCC 58.488 36.000 0.00 0.00 0.00 5.01
2146 4705 0.549950 CCATCTGGAGCAGGGATTGT 59.450 55.000 0.00 0.00 37.39 2.71
2164 4751 6.328714 GGATTGTTTGTGTTTTGCCAAATTT 58.671 32.000 0.00 0.00 33.53 1.82
2214 4801 2.778299 GACATGGTCAAGGCAAGTGTA 58.222 47.619 0.00 0.00 32.09 2.90
2226 4813 0.673644 CAAGTGTAGGGTCTTGCGGG 60.674 60.000 0.00 0.00 35.42 6.13
2258 4848 1.896465 AGCTGGTAGGAGTGTTGAGTC 59.104 52.381 0.00 0.00 0.00 3.36
2259 4849 1.066787 GCTGGTAGGAGTGTTGAGTCC 60.067 57.143 0.00 0.00 41.62 3.85
2267 4860 2.613223 GGAGTGTTGAGTCCTAACTGCC 60.613 54.545 0.00 0.00 38.55 4.85
2297 4890 7.224557 ACCAAACTTTGTTTCTATCAAATGCAC 59.775 33.333 0.00 0.00 34.88 4.57
2298 4891 7.224362 CCAAACTTTGTTTCTATCAAATGCACA 59.776 33.333 0.00 0.00 34.88 4.57
2308 4901 9.624697 TTTCTATCAAATGCACAAAGATACAAC 57.375 29.630 0.00 0.00 0.00 3.32
2316 4909 4.201960 TGCACAAAGATACAACGCTTTTGA 60.202 37.500 2.19 0.00 32.36 2.69
2354 4950 3.343617 TCCTTTTACTGCCAAATCTCCG 58.656 45.455 0.00 0.00 0.00 4.63
2368 4964 5.590259 CCAAATCTCCGATCTTTTGGTACAT 59.410 40.000 5.35 0.00 41.94 2.29
2393 4989 2.550606 TGAAATTGGTCGTTGTAGTGCC 59.449 45.455 0.00 0.00 0.00 5.01
2410 5006 0.249911 GCCGTCACTTTGAGGTGAGT 60.250 55.000 0.00 0.00 45.31 3.41
2421 5017 5.585047 ACTTTGAGGTGAGTTTAGACAACAC 59.415 40.000 0.00 0.00 35.85 3.32
2427 5023 2.158871 TGAGTTTAGACAACACCGGCTT 60.159 45.455 0.00 0.00 0.00 4.35
2429 5025 0.948678 TTTAGACAACACCGGCTTGC 59.051 50.000 0.00 0.23 0.00 4.01
2442 5038 1.723870 GCTTGCGCCATCTAAGGTG 59.276 57.895 4.18 0.00 42.11 4.00
2444 5040 0.729116 CTTGCGCCATCTAAGGTGTG 59.271 55.000 4.18 0.00 41.26 3.82
2446 5042 2.472909 GCGCCATCTAAGGTGTGCC 61.473 63.158 0.00 0.00 41.26 5.01
2447 5043 1.078497 CGCCATCTAAGGTGTGCCA 60.078 57.895 0.00 0.00 37.19 4.92
2448 5044 0.464373 CGCCATCTAAGGTGTGCCAT 60.464 55.000 0.00 0.00 37.19 4.40
2449 5045 1.202639 CGCCATCTAAGGTGTGCCATA 60.203 52.381 0.00 0.00 37.19 2.74
2451 5047 3.306710 CGCCATCTAAGGTGTGCCATATA 60.307 47.826 0.00 0.00 37.19 0.86
2452 5048 4.623886 CGCCATCTAAGGTGTGCCATATAT 60.624 45.833 0.00 0.00 37.19 0.86
2463 5059 3.465990 CCATATATGGCCCGAGCTG 57.534 57.895 18.77 0.00 41.75 4.24
2464 5060 0.745845 CCATATATGGCCCGAGCTGC 60.746 60.000 18.77 0.00 41.75 5.25
2465 5061 1.086067 CATATATGGCCCGAGCTGCG 61.086 60.000 0.00 0.00 39.73 5.18
2481 5077 4.514577 CGGCCCATCGAGAGCGTT 62.515 66.667 0.00 0.00 38.98 4.84
2482 5078 2.586357 GGCCCATCGAGAGCGTTC 60.586 66.667 0.00 0.00 38.98 3.95
2483 5079 2.496817 GCCCATCGAGAGCGTTCT 59.503 61.111 0.00 0.00 38.98 3.01
2484 5080 1.734137 GCCCATCGAGAGCGTTCTA 59.266 57.895 0.21 0.00 38.98 2.10
2485 5081 0.318275 GCCCATCGAGAGCGTTCTAG 60.318 60.000 0.21 1.77 38.98 2.43
2486 5082 1.309950 CCCATCGAGAGCGTTCTAGA 58.690 55.000 13.92 13.92 39.05 2.43
2487 5083 1.002251 CCCATCGAGAGCGTTCTAGAC 60.002 57.143 13.85 0.00 37.80 2.59
2488 5084 1.671328 CCATCGAGAGCGTTCTAGACA 59.329 52.381 13.85 0.00 37.80 3.41
2489 5085 2.292016 CCATCGAGAGCGTTCTAGACAT 59.708 50.000 13.85 0.00 37.80 3.06
2490 5086 3.295785 CATCGAGAGCGTTCTAGACATG 58.704 50.000 13.85 6.44 37.80 3.21
2491 5087 1.671328 TCGAGAGCGTTCTAGACATGG 59.329 52.381 7.96 0.00 38.98 3.66
2492 5088 1.402259 CGAGAGCGTTCTAGACATGGT 59.598 52.381 0.21 0.00 32.53 3.55
2493 5089 2.159366 CGAGAGCGTTCTAGACATGGTT 60.159 50.000 0.21 0.00 32.53 3.67
2494 5090 3.440228 GAGAGCGTTCTAGACATGGTTC 58.560 50.000 0.21 0.00 32.53 3.62
2495 5091 3.093057 AGAGCGTTCTAGACATGGTTCT 58.907 45.455 0.00 0.00 0.00 3.01
2496 5092 3.511934 AGAGCGTTCTAGACATGGTTCTT 59.488 43.478 0.00 0.00 0.00 2.52
2497 5093 4.021016 AGAGCGTTCTAGACATGGTTCTTT 60.021 41.667 0.00 0.00 0.00 2.52
2498 5094 5.185249 AGAGCGTTCTAGACATGGTTCTTTA 59.815 40.000 0.00 0.00 0.00 1.85
2499 5095 5.790593 AGCGTTCTAGACATGGTTCTTTAA 58.209 37.500 0.00 0.00 0.00 1.52
2500 5096 6.228258 AGCGTTCTAGACATGGTTCTTTAAA 58.772 36.000 0.00 0.00 0.00 1.52
2501 5097 6.879458 AGCGTTCTAGACATGGTTCTTTAAAT 59.121 34.615 0.00 0.00 0.00 1.40
2502 5098 7.064728 AGCGTTCTAGACATGGTTCTTTAAATC 59.935 37.037 0.00 0.00 0.00 2.17
2503 5099 7.064728 GCGTTCTAGACATGGTTCTTTAAATCT 59.935 37.037 0.00 0.00 0.00 2.40
2504 5100 8.936864 CGTTCTAGACATGGTTCTTTAAATCTT 58.063 33.333 0.00 0.00 0.00 2.40
2510 5106 9.300681 AGACATGGTTCTTTAAATCTTCATTGA 57.699 29.630 0.00 0.00 0.00 2.57
2527 5123 9.013229 TCTTCATTGATTAAGCTAAAAAGCTCA 57.987 29.630 0.00 0.00 45.54 4.26
2528 5124 9.798994 CTTCATTGATTAAGCTAAAAAGCTCAT 57.201 29.630 0.00 0.00 45.54 2.90
2529 5125 9.793252 TTCATTGATTAAGCTAAAAAGCTCATC 57.207 29.630 0.00 6.49 45.54 2.92
2530 5126 8.959548 TCATTGATTAAGCTAAAAAGCTCATCA 58.040 29.630 13.98 13.98 45.54 3.07
2531 5127 9.017669 CATTGATTAAGCTAAAAAGCTCATCAC 57.982 33.333 16.20 4.28 45.54 3.06
2532 5128 7.928307 TGATTAAGCTAAAAAGCTCATCACT 57.072 32.000 13.98 0.00 45.54 3.41
2533 5129 9.448438 TTGATTAAGCTAAAAAGCTCATCACTA 57.552 29.630 16.20 6.06 45.54 2.74
2534 5130 9.448438 TGATTAAGCTAAAAAGCTCATCACTAA 57.552 29.630 13.98 4.59 45.54 2.24
2537 5133 7.693969 AAGCTAAAAAGCTCATCACTAATGT 57.306 32.000 0.00 0.00 45.54 2.71
2538 5134 7.081526 AGCTAAAAAGCTCATCACTAATGTG 57.918 36.000 0.00 0.00 42.12 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 1567 9.629878 TTAAACTAAACTTGAACCAGAACCATA 57.370 29.630 0.00 0.00 0.00 2.74
351 1814 0.828762 TGGCCATCCATGCATTAGCC 60.829 55.000 0.00 12.87 37.43 3.93
394 2274 8.637986 AGTTGTGCCTTGACATCTTTATTTTTA 58.362 29.630 0.00 0.00 0.00 1.52
506 2386 4.454728 ACATCCAAAAGCGCATTTGTAT 57.545 36.364 29.59 20.61 38.37 2.29
1425 3375 2.749076 CCCATCTACCACACAACACATG 59.251 50.000 0.00 0.00 0.00 3.21
1432 3382 4.625324 GCAGTAAATCCCATCTACCACACA 60.625 45.833 0.00 0.00 0.00 3.72
1433 3383 3.877508 GCAGTAAATCCCATCTACCACAC 59.122 47.826 0.00 0.00 0.00 3.82
1508 3467 9.247126 TGATTTCATTGAACACAACATACTTTG 57.753 29.630 0.00 0.00 0.00 2.77
1509 3468 9.467258 CTGATTTCATTGAACACAACATACTTT 57.533 29.630 0.00 0.00 0.00 2.66
1510 3469 8.632679 ACTGATTTCATTGAACACAACATACTT 58.367 29.630 0.00 0.00 0.00 2.24
1511 3470 8.169977 ACTGATTTCATTGAACACAACATACT 57.830 30.769 0.00 0.00 0.00 2.12
1512 3471 8.801715 AACTGATTTCATTGAACACAACATAC 57.198 30.769 0.00 0.00 0.00 2.39
1513 3472 8.628280 TGAACTGATTTCATTGAACACAACATA 58.372 29.630 0.00 0.00 39.45 2.29
1514 3473 7.490840 TGAACTGATTTCATTGAACACAACAT 58.509 30.769 0.00 0.00 39.45 2.71
1515 3474 6.861144 TGAACTGATTTCATTGAACACAACA 58.139 32.000 0.00 1.91 39.45 3.33
1516 3475 7.754069 TTGAACTGATTTCATTGAACACAAC 57.246 32.000 0.00 0.00 43.99 3.32
1517 3476 8.945481 AATTGAACTGATTTCATTGAACACAA 57.055 26.923 0.00 0.00 43.99 3.33
1518 3477 8.415553 AGAATTGAACTGATTTCATTGAACACA 58.584 29.630 0.00 2.08 43.99 3.72
1519 3478 8.807667 AGAATTGAACTGATTTCATTGAACAC 57.192 30.769 0.00 0.00 43.99 3.32
1529 3498 9.778993 CGTCATGATTTAGAATTGAACTGATTT 57.221 29.630 0.00 0.00 0.00 2.17
1539 3508 8.461222 TGAAGCATTTCGTCATGATTTAGAATT 58.539 29.630 0.00 0.00 32.90 2.17
1545 3514 5.048504 ACAGTGAAGCATTTCGTCATGATTT 60.049 36.000 0.00 0.00 32.90 2.17
1550 3519 3.814842 TCAACAGTGAAGCATTTCGTCAT 59.185 39.130 0.00 0.00 35.71 3.06
1599 3717 9.286946 CAATCTAAACAGAGAAATCAAATCAGC 57.713 33.333 0.00 0.00 0.00 4.26
1611 3729 5.118990 GCAGCCATACAATCTAAACAGAGA 58.881 41.667 0.00 0.00 0.00 3.10
1612 3730 4.877823 TGCAGCCATACAATCTAAACAGAG 59.122 41.667 0.00 0.00 0.00 3.35
1613 3731 4.635765 GTGCAGCCATACAATCTAAACAGA 59.364 41.667 0.00 0.00 0.00 3.41
1624 3755 4.129380 GACATATTCAGTGCAGCCATACA 58.871 43.478 0.00 0.00 0.00 2.29
1627 3758 3.572632 AGACATATTCAGTGCAGCCAT 57.427 42.857 0.00 0.00 0.00 4.40
1662 3846 4.993905 TGAGAAGCGACGAGATTCAAATA 58.006 39.130 13.80 0.00 46.94 1.40
1669 3853 5.250235 TCTAAAATGAGAAGCGACGAGAT 57.750 39.130 0.00 0.00 0.00 2.75
1670 3854 4.696899 TCTAAAATGAGAAGCGACGAGA 57.303 40.909 0.00 0.00 0.00 4.04
1676 3860 6.804295 AGCTATACGATCTAAAATGAGAAGCG 59.196 38.462 0.00 0.00 35.01 4.68
1708 3892 2.652941 TTGCAAATGAAAGGGCGATC 57.347 45.000 0.00 0.00 0.00 3.69
1750 4267 5.303078 GGAAGGATAGCATCTCTTGTACAGA 59.697 44.000 0.00 0.00 0.00 3.41
1756 4273 4.885413 CTGAGGAAGGATAGCATCTCTTG 58.115 47.826 0.00 0.00 0.00 3.02
1796 4315 2.204237 GCAGTGAAGCCAAACCAAAAG 58.796 47.619 0.00 0.00 0.00 2.27
1811 4330 1.511850 TGACAGTTGATTCCGCAGTG 58.488 50.000 0.00 0.00 0.00 3.66
1831 4350 5.722021 ACCACTGAAAACAACAGAAAAGT 57.278 34.783 0.00 0.00 38.55 2.66
1853 4372 7.346175 TGCCAACTCTACCTTTTAGTATCCATA 59.654 37.037 0.00 0.00 0.00 2.74
1854 4373 6.157994 TGCCAACTCTACCTTTTAGTATCCAT 59.842 38.462 0.00 0.00 0.00 3.41
1855 4374 5.486063 TGCCAACTCTACCTTTTAGTATCCA 59.514 40.000 0.00 0.00 0.00 3.41
1856 4375 5.985911 TGCCAACTCTACCTTTTAGTATCC 58.014 41.667 0.00 0.00 0.00 2.59
1857 4376 7.988028 AGAATGCCAACTCTACCTTTTAGTATC 59.012 37.037 0.00 0.00 0.00 2.24
1858 4377 7.770897 CAGAATGCCAACTCTACCTTTTAGTAT 59.229 37.037 0.00 0.00 0.00 2.12
1859 4378 7.103641 CAGAATGCCAACTCTACCTTTTAGTA 58.896 38.462 0.00 0.00 0.00 1.82
1860 4379 5.940470 CAGAATGCCAACTCTACCTTTTAGT 59.060 40.000 0.00 0.00 0.00 2.24
1861 4380 5.940470 ACAGAATGCCAACTCTACCTTTTAG 59.060 40.000 0.00 0.00 42.53 1.85
1862 4381 5.876357 ACAGAATGCCAACTCTACCTTTTA 58.124 37.500 0.00 0.00 42.53 1.52
1863 4382 4.729868 ACAGAATGCCAACTCTACCTTTT 58.270 39.130 0.00 0.00 42.53 2.27
1864 4383 4.373156 ACAGAATGCCAACTCTACCTTT 57.627 40.909 0.00 0.00 42.53 3.11
1865 4384 4.373156 AACAGAATGCCAACTCTACCTT 57.627 40.909 0.00 0.00 42.53 3.50
1866 4385 4.042187 AGAAACAGAATGCCAACTCTACCT 59.958 41.667 0.00 0.00 42.53 3.08
1867 4386 4.154918 CAGAAACAGAATGCCAACTCTACC 59.845 45.833 0.00 0.00 42.53 3.18
1868 4387 4.997395 TCAGAAACAGAATGCCAACTCTAC 59.003 41.667 0.00 0.00 42.53 2.59
1869 4388 5.227569 TCAGAAACAGAATGCCAACTCTA 57.772 39.130 0.00 0.00 42.53 2.43
1870 4389 4.090761 TCAGAAACAGAATGCCAACTCT 57.909 40.909 0.00 0.00 42.53 3.24
1871 4390 4.540824 GTTCAGAAACAGAATGCCAACTC 58.459 43.478 0.00 0.00 42.53 3.01
1872 4391 3.003689 CGTTCAGAAACAGAATGCCAACT 59.996 43.478 0.00 0.00 42.53 3.16
1873 4392 3.300009 CGTTCAGAAACAGAATGCCAAC 58.700 45.455 0.00 0.00 42.53 3.77
1874 4393 2.287547 GCGTTCAGAAACAGAATGCCAA 60.288 45.455 8.51 0.00 46.91 4.52
1875 4394 1.266718 GCGTTCAGAAACAGAATGCCA 59.733 47.619 8.51 0.00 46.91 4.92
1876 4395 1.969103 GCGTTCAGAAACAGAATGCC 58.031 50.000 8.51 0.00 46.91 4.40
1878 4397 4.990543 TGTAGCGTTCAGAAACAGAATG 57.009 40.909 0.00 0.00 46.00 2.67
1879 4398 5.237815 TGATGTAGCGTTCAGAAACAGAAT 58.762 37.500 0.00 0.00 34.93 2.40
1880 4399 4.627058 TGATGTAGCGTTCAGAAACAGAA 58.373 39.130 0.00 0.00 34.93 3.02
1953 4472 6.150976 CCTCAGATAGTCAGTATTAGAGGCAG 59.849 46.154 7.78 0.00 36.48 4.85
2045 4591 6.983906 ATCCCAGTGAGAAACAAGATTTTT 57.016 33.333 0.00 0.00 0.00 1.94
2046 4592 6.983906 AATCCCAGTGAGAAACAAGATTTT 57.016 33.333 0.00 0.00 0.00 1.82
2047 4593 6.983906 AAATCCCAGTGAGAAACAAGATTT 57.016 33.333 0.00 0.00 0.00 2.17
2069 4617 4.408921 ACCTATGAGCTGGTTGCACTATAA 59.591 41.667 0.00 0.00 45.94 0.98
2072 4620 2.187958 ACCTATGAGCTGGTTGCACTA 58.812 47.619 0.00 0.00 45.94 2.74
2083 4631 4.940654 AGAAAAGAGAAGCAACCTATGAGC 59.059 41.667 0.00 0.00 0.00 4.26
2128 4676 2.426024 CAAACAATCCCTGCTCCAGATG 59.574 50.000 0.00 0.00 32.44 2.90
2146 4705 5.159209 CAAGCAAATTTGGCAAAACACAAA 58.841 33.333 17.70 0.00 40.44 2.83
2226 4813 2.202623 CCAGCTAGGTGTCGCGAC 60.203 66.667 31.66 31.66 0.00 5.19
2258 4848 0.598065 GTTTGGTGCTGGCAGTTAGG 59.402 55.000 17.16 0.00 0.00 2.69
2259 4849 1.609208 AGTTTGGTGCTGGCAGTTAG 58.391 50.000 17.16 0.00 0.00 2.34
2267 4860 5.830912 TGATAGAAACAAAGTTTGGTGCTG 58.169 37.500 22.48 0.00 36.72 4.41
2297 4890 5.108385 ACCTCAAAAGCGTTGTATCTTTG 57.892 39.130 3.52 0.00 33.29 2.77
2298 4891 5.767816 AACCTCAAAAGCGTTGTATCTTT 57.232 34.783 3.52 0.00 34.30 2.52
2342 4938 2.754552 CCAAAAGATCGGAGATTTGGCA 59.245 45.455 14.88 0.00 44.00 4.92
2343 4939 3.427161 CCAAAAGATCGGAGATTTGGC 57.573 47.619 14.88 0.00 44.00 4.52
2354 4950 7.273381 CCAATTTCAACGATGTACCAAAAGATC 59.727 37.037 0.00 0.00 0.00 2.75
2368 4964 4.025563 CACTACAACGACCAATTTCAACGA 60.026 41.667 0.00 0.00 0.00 3.85
2393 4989 4.444720 GTCTAAACTCACCTCAAAGTGACG 59.555 45.833 0.00 0.00 41.78 4.35
2401 4997 3.491964 CGGTGTTGTCTAAACTCACCTCA 60.492 47.826 10.22 0.00 42.85 3.86
2410 5006 0.948678 GCAAGCCGGTGTTGTCTAAA 59.051 50.000 16.96 0.00 0.00 1.85
2427 5023 1.745115 GCACACCTTAGATGGCGCA 60.745 57.895 10.83 0.00 0.00 6.09
2429 5025 1.078497 TGGCACACCTTAGATGGCG 60.078 57.895 0.00 0.00 41.57 5.69
2446 5042 1.086067 CGCAGCTCGGGCCATATATG 61.086 60.000 2.00 5.68 39.73 1.78
2447 5043 1.219124 CGCAGCTCGGGCCATATAT 59.781 57.895 2.00 0.00 39.73 0.86
2448 5044 2.656646 CGCAGCTCGGGCCATATA 59.343 61.111 2.00 0.00 39.73 0.86
2464 5060 4.514577 AACGCTCTCGATGGGCCG 62.515 66.667 0.00 0.00 39.41 6.13
2465 5061 1.735376 TAGAACGCTCTCGATGGGCC 61.735 60.000 0.00 0.00 39.41 5.80
2466 5062 0.318275 CTAGAACGCTCTCGATGGGC 60.318 60.000 0.00 0.00 39.41 5.36
2467 5063 1.002251 GTCTAGAACGCTCTCGATGGG 60.002 57.143 0.00 0.00 39.41 4.00
2468 5064 1.671328 TGTCTAGAACGCTCTCGATGG 59.329 52.381 0.00 0.00 39.41 3.51
2469 5065 3.295785 CATGTCTAGAACGCTCTCGATG 58.704 50.000 0.00 0.00 39.41 3.84
2470 5066 2.292016 CCATGTCTAGAACGCTCTCGAT 59.708 50.000 0.00 0.00 39.41 3.59
2471 5067 1.671328 CCATGTCTAGAACGCTCTCGA 59.329 52.381 0.00 0.00 39.41 4.04
2472 5068 1.402259 ACCATGTCTAGAACGCTCTCG 59.598 52.381 0.00 0.00 42.43 4.04
2473 5069 3.129638 AGAACCATGTCTAGAACGCTCTC 59.870 47.826 0.00 0.00 32.70 3.20
2474 5070 3.093057 AGAACCATGTCTAGAACGCTCT 58.907 45.455 0.00 0.00 35.52 4.09
2475 5071 3.512033 AGAACCATGTCTAGAACGCTC 57.488 47.619 0.00 0.00 0.00 5.03
2476 5072 3.963428 AAGAACCATGTCTAGAACGCT 57.037 42.857 0.00 0.00 0.00 5.07
2477 5073 6.476243 TTTAAAGAACCATGTCTAGAACGC 57.524 37.500 0.00 0.00 0.00 4.84
2478 5074 8.480643 AGATTTAAAGAACCATGTCTAGAACG 57.519 34.615 0.00 0.00 0.00 3.95
2484 5080 9.300681 TCAATGAAGATTTAAAGAACCATGTCT 57.699 29.630 0.00 0.00 0.00 3.41
2501 5097 9.013229 TGAGCTTTTTAGCTTAATCAATGAAGA 57.987 29.630 0.00 0.00 46.36 2.87
2502 5098 9.798994 ATGAGCTTTTTAGCTTAATCAATGAAG 57.201 29.630 0.00 0.00 46.36 3.02
2503 5099 9.793252 GATGAGCTTTTTAGCTTAATCAATGAA 57.207 29.630 14.08 0.00 46.36 2.57
2504 5100 8.959548 TGATGAGCTTTTTAGCTTAATCAATGA 58.040 29.630 17.12 0.00 46.36 2.57
2505 5101 9.017669 GTGATGAGCTTTTTAGCTTAATCAATG 57.982 33.333 19.35 0.00 46.36 2.82
2506 5102 8.964772 AGTGATGAGCTTTTTAGCTTAATCAAT 58.035 29.630 19.35 17.20 46.36 2.57
2507 5103 8.340618 AGTGATGAGCTTTTTAGCTTAATCAA 57.659 30.769 19.35 8.54 46.36 2.57
2508 5104 7.928307 AGTGATGAGCTTTTTAGCTTAATCA 57.072 32.000 16.19 16.19 46.36 2.57
2511 5107 9.231297 ACATTAGTGATGAGCTTTTTAGCTTAA 57.769 29.630 1.26 0.00 46.36 1.85
2512 5108 8.792830 ACATTAGTGATGAGCTTTTTAGCTTA 57.207 30.769 1.26 0.00 46.36 3.09
2513 5109 7.693969 ACATTAGTGATGAGCTTTTTAGCTT 57.306 32.000 1.26 0.00 46.36 3.74


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

AutoCloner maintained by Alex Coulton.