Multiple sequence alignment - TraesCS3B01G399300

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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 TraesCS3B01G399300 chr3B 100.000 3378 0 0 1 3378 630403095 630399718 0.000000e+00 6239.0
1 TraesCS3B01G399300 chr3B 97.222 36 1 0 1743 1778 766031802 766031767 1.010000e-05 62.1
2 TraesCS3B01G399300 chr3D 92.561 2124 122 23 299 2399 474217530 474215420 0.000000e+00 3014.0
3 TraesCS3B01G399300 chr3D 90.110 728 36 17 2518 3218 474215338 474214620 0.000000e+00 913.0
4 TraesCS3B01G399300 chr3D 89.216 306 21 6 3 298 474218068 474217765 4.120000e-99 372.0
5 TraesCS3B01G399300 chr3D 80.874 183 20 8 1611 1790 23173709 23173539 2.740000e-26 130.0
6 TraesCS3B01G399300 chr3D 83.486 109 18 0 1608 1716 62329662 62329770 5.960000e-18 102.0
7 TraesCS3B01G399300 chr3A 93.016 1804 105 12 321 2115 616493915 616492124 0.000000e+00 2614.0
8 TraesCS3B01G399300 chr3A 88.380 611 36 20 2515 3106 616491779 616491185 0.000000e+00 702.0
9 TraesCS3B01G399300 chr3A 86.054 294 39 2 5 298 616494487 616494196 7.040000e-82 315.0
10 TraesCS3B01G399300 chr3A 87.645 259 20 8 2151 2399 616492123 616491867 1.190000e-74 291.0
11 TraesCS3B01G399300 chr3A 83.858 254 17 17 3131 3377 616491187 616490951 1.580000e-53 220.0
12 TraesCS3B01G399300 chr3A 100.000 28 0 0 3206 3233 637118005 637117978 6.000000e-03 52.8
13 TraesCS3B01G399300 chr1B 76.568 845 106 58 1062 1835 499895916 499896739 2.460000e-101 379.0
14 TraesCS3B01G399300 chr1D 88.189 254 21 4 1591 1838 375646699 375646449 9.170000e-76 294.0
15 TraesCS3B01G399300 chr1D 75.610 164 35 5 1592 1754 308262107 308262266 3.610000e-10 76.8
16 TraesCS3B01G399300 chr1A 87.402 254 23 4 1591 1838 474450729 474450479 1.980000e-72 283.0
17 TraesCS3B01G399300 chr4A 81.771 192 32 2 1587 1778 717724320 717724132 1.250000e-34 158.0
18 TraesCS3B01G399300 chr7D 80.189 212 37 4 1569 1778 16912137 16911929 1.620000e-33 154.0
19 TraesCS3B01G399300 chr5B 83.784 74 12 0 1643 1716 443698247 443698320 1.680000e-08 71.3


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 TraesCS3B01G399300 chr3B 630399718 630403095 3377 True 6239.0 6239 100.0000 1 3378 1 chr3B.!!$R1 3377
1 TraesCS3B01G399300 chr3D 474214620 474218068 3448 True 1433.0 3014 90.6290 3 3218 3 chr3D.!!$R2 3215
2 TraesCS3B01G399300 chr3A 616490951 616494487 3536 True 828.4 2614 87.7906 5 3377 5 chr3A.!!$R2 3372
3 TraesCS3B01G399300 chr1B 499895916 499896739 823 False 379.0 379 76.5680 1062 1835 1 chr1B.!!$F1 773

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
855 1135 0.037975 CAAGGCCCAATCACAAGCAC 60.038 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 2795 0.66297 CCAAATTTCACACCGGTGCG 60.663 55.0 34.26 25.66 44.87 5.34 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
24 25 2.035961 GACAGAATATCCACCGCTGCTA 59.964 50.000 0.00 0.00 0.00 3.49
27 28 3.255888 CAGAATATCCACCGCTGCTACTA 59.744 47.826 0.00 0.00 0.00 1.82
46 47 1.064003 ACACAACCATGCCCTCTACA 58.936 50.000 0.00 0.00 0.00 2.74
48 49 2.041620 ACACAACCATGCCCTCTACATT 59.958 45.455 0.00 0.00 0.00 2.71
100 101 0.460459 GAGGGCTACCAGACGAAAGC 60.460 60.000 0.00 0.00 40.13 3.51
114 115 4.733725 AAGCCCTCCCTACCGCCA 62.734 66.667 0.00 0.00 0.00 5.69
143 144 1.003233 GACCAGTGTCAGGGTTTAGGG 59.997 57.143 0.00 0.00 41.37 3.53
191 192 3.468326 GAAGCGGGGATGGAGAGGC 62.468 68.421 0.00 0.00 0.00 4.70
217 218 3.199071 AGATGGTGGCTTATGTTTCGGTA 59.801 43.478 0.00 0.00 0.00 4.02
224 225 3.181487 GGCTTATGTTTCGGTACCTACGA 60.181 47.826 10.90 0.00 38.78 3.43
247 258 6.018433 ACTATCAAAAGGGAGGCACATATT 57.982 37.500 0.00 0.00 0.00 1.28
262 273 4.576053 GCACATATTCTATGTGGTGCAAGA 59.424 41.667 22.19 0.00 46.85 3.02
263 274 5.240183 GCACATATTCTATGTGGTGCAAGAT 59.760 40.000 22.19 0.00 46.85 2.40
267 278 8.408601 ACATATTCTATGTGGTGCAAGATTTTC 58.591 33.333 0.00 0.00 0.00 2.29
309 582 6.646240 GTCTGCCACAATAAACATGTTCATTT 59.354 34.615 12.39 3.30 0.00 2.32
311 584 8.363390 TCTGCCACAATAAACATGTTCATTTAA 58.637 29.630 12.39 0.00 0.00 1.52
313 586 8.933807 TGCCACAATAAACATGTTCATTTAATG 58.066 29.630 12.39 6.55 30.72 1.90
319 592 2.159114 ACATGTTCATTTAATGCCCCGC 60.159 45.455 0.00 0.00 0.00 6.13
331 604 4.864334 CCCCGCAGCCATCCAGAC 62.864 72.222 0.00 0.00 0.00 3.51
332 605 4.864334 CCCGCAGCCATCCAGACC 62.864 72.222 0.00 0.00 0.00 3.85
334 607 2.434843 CCGCAGCCATCCAGACCTA 61.435 63.158 0.00 0.00 0.00 3.08
356 629 1.661990 ATGCCCTACTCCTCCCGGTA 61.662 60.000 0.00 0.00 0.00 4.02
357 630 1.155624 GCCCTACTCCTCCCGGTAT 59.844 63.158 0.00 0.00 0.00 2.73
397 670 4.101448 GGATGTCCCCACGCTGCT 62.101 66.667 0.00 0.00 0.00 4.24
426 699 2.303163 TGGTGATATTTGGTCGTCGG 57.697 50.000 0.00 0.00 0.00 4.79
430 703 2.997986 GTGATATTTGGTCGTCGGTTGT 59.002 45.455 0.00 0.00 0.00 3.32
449 722 5.189180 GTTGTTCTCTCCTTGCTATGGAAT 58.811 41.667 0.00 0.00 32.61 3.01
479 753 6.646653 GGGATTCCAGAAACAATTTGTCTTTC 59.353 38.462 4.80 4.36 0.00 2.62
498 772 1.300697 GCAACGAACTCCACTCCGT 60.301 57.895 0.00 0.00 36.77 4.69
559 833 8.336080 ACTCTTTGAACTTTCAGATACGAAAAC 58.664 33.333 0.00 0.00 38.61 2.43
579 853 2.691011 ACGTCTCTAAGAAGGATGCCTC 59.309 50.000 0.00 0.00 30.89 4.70
583 857 4.835615 GTCTCTAAGAAGGATGCCTCCATA 59.164 45.833 10.92 0.00 44.79 2.74
588 862 7.191918 TCTAAGAAGGATGCCTCCATATCATA 58.808 38.462 10.92 2.88 44.79 2.15
609 883 1.476891 GCGTCAATACCTCTCCTCACA 59.523 52.381 0.00 0.00 0.00 3.58
615 891 3.671740 ATACCTCTCCTCACACTAGCA 57.328 47.619 0.00 0.00 0.00 3.49
631 907 2.607631 AGCACACAATTGCAAAGCTT 57.392 40.000 1.71 0.00 45.62 3.74
644 920 0.319813 AAAGCTTGCCATTTGGTCGC 60.320 50.000 0.00 0.00 37.57 5.19
651 927 0.316841 GCCATTTGGTCGCCTTTGAA 59.683 50.000 0.00 0.00 37.57 2.69
663 939 3.625313 TCGCCTTTGAATAATGCATTCGA 59.375 39.130 16.86 12.25 45.25 3.71
672 949 6.710278 TGAATAATGCATTCGATAGGGATCA 58.290 36.000 16.86 2.61 45.25 2.92
726 1003 9.849166 TCAATTCCTTCGGTTAAAATAATTCAC 57.151 29.630 0.00 0.00 0.00 3.18
855 1135 0.037975 CAAGGCCCAATCACAAGCAC 60.038 55.000 0.00 0.00 0.00 4.40
973 1253 2.359355 CGGTCCTCCCCTATATAGGCAT 60.359 54.545 21.75 0.00 42.26 4.40
989 1269 1.919600 GCATGCCTCCTTCCACCTCT 61.920 60.000 6.36 0.00 0.00 3.69
1029 1314 4.838152 TCCTCCATTGCTCGCCGC 62.838 66.667 0.00 0.00 39.77 6.53
1520 1853 4.954933 GGTAAGCCGCCATCTTCA 57.045 55.556 0.00 0.00 0.00 3.02
1549 1882 2.798976 TCTTGTGCTTGGATTGTTGC 57.201 45.000 0.00 0.00 0.00 4.17
1553 1886 1.755959 TGTGCTTGGATTGTTGCTTGT 59.244 42.857 0.00 0.00 0.00 3.16
1555 1888 2.540931 GTGCTTGGATTGTTGCTTGTTG 59.459 45.455 0.00 0.00 0.00 3.33
1556 1889 2.168106 TGCTTGGATTGTTGCTTGTTGT 59.832 40.909 0.00 0.00 0.00 3.32
1557 1890 3.197265 GCTTGGATTGTTGCTTGTTGTT 58.803 40.909 0.00 0.00 0.00 2.83
1559 1892 3.176552 TGGATTGTTGCTTGTTGTTGG 57.823 42.857 0.00 0.00 0.00 3.77
1560 1893 2.499289 TGGATTGTTGCTTGTTGTTGGT 59.501 40.909 0.00 0.00 0.00 3.67
1625 1963 1.262640 GGGGCTGAAGAAGTACGGGA 61.263 60.000 0.00 0.00 0.00 5.14
1630 1968 1.135333 CTGAAGAAGTACGGGAGAGGC 59.865 57.143 0.00 0.00 0.00 4.70
1651 1989 1.227089 CTGGAGGAACATCTCGCGG 60.227 63.158 6.13 0.00 34.74 6.46
2014 2361 0.975040 ACTCGCTCCTCCTGCAGATT 60.975 55.000 17.39 0.00 0.00 2.40
2104 2451 1.422388 CACCTATCACCATCATCGCG 58.578 55.000 0.00 0.00 0.00 5.87
2214 2561 0.736672 TCTCTCTCGACCGACACTCG 60.737 60.000 0.00 0.00 40.07 4.18
2294 2641 0.460987 GGTCTGCGTCCATGGAGAAG 60.461 60.000 16.81 13.29 38.10 2.85
2311 2659 2.503356 AGAAGCTCAAGAACCCATCGAT 59.497 45.455 0.00 0.00 0.00 3.59
2333 2681 1.997606 GTGCCGTCCAGTGTACATAAC 59.002 52.381 0.00 0.00 0.00 1.89
2334 2682 1.066716 TGCCGTCCAGTGTACATAACC 60.067 52.381 0.00 0.00 0.00 2.85
2343 2691 0.691332 TGTACATAACCCCGCCACAA 59.309 50.000 0.00 0.00 0.00 3.33
2344 2692 1.339247 TGTACATAACCCCGCCACAAG 60.339 52.381 0.00 0.00 0.00 3.16
2345 2693 0.985760 TACATAACCCCGCCACAAGT 59.014 50.000 0.00 0.00 0.00 3.16
2347 2695 1.562475 ACATAACCCCGCCACAAGTAT 59.438 47.619 0.00 0.00 0.00 2.12
2348 2696 2.773087 ACATAACCCCGCCACAAGTATA 59.227 45.455 0.00 0.00 0.00 1.47
2349 2697 2.985957 TAACCCCGCCACAAGTATAC 57.014 50.000 0.00 0.00 0.00 1.47
2350 2698 0.108041 AACCCCGCCACAAGTATACG 60.108 55.000 0.00 0.00 0.00 3.06
2351 2699 1.227438 CCCCGCCACAAGTATACGG 60.227 63.158 0.00 0.00 43.44 4.02
2379 2735 6.653320 ACTGTACCGAAAATCTGAAATAAGCA 59.347 34.615 0.00 0.00 0.00 3.91
2380 2736 7.072177 TGTACCGAAAATCTGAAATAAGCAG 57.928 36.000 0.00 0.00 34.71 4.24
2382 2738 6.575162 ACCGAAAATCTGAAATAAGCAGTT 57.425 33.333 0.00 0.00 34.98 3.16
2383 2739 6.612306 ACCGAAAATCTGAAATAAGCAGTTC 58.388 36.000 0.00 0.00 34.98 3.01
2395 2751 7.174772 TGAAATAAGCAGTTCATGAAGCTTGTA 59.825 33.333 30.58 19.50 45.91 2.41
2399 2755 3.181526 GCAGTTCATGAAGCTTGTACTCG 60.182 47.826 8.80 0.00 0.00 4.18
2400 2756 3.990469 CAGTTCATGAAGCTTGTACTCGT 59.010 43.478 8.80 0.00 0.00 4.18
2401 2757 4.449068 CAGTTCATGAAGCTTGTACTCGTT 59.551 41.667 8.80 0.00 0.00 3.85
2402 2758 4.686554 AGTTCATGAAGCTTGTACTCGTTC 59.313 41.667 8.80 0.00 0.00 3.95
2404 2760 1.415374 TGAAGCTTGTACTCGTTCGC 58.585 50.000 2.10 0.00 0.00 4.70
2405 2761 0.714439 GAAGCTTGTACTCGTTCGCC 59.286 55.000 2.10 0.00 0.00 5.54
2406 2762 1.007336 AAGCTTGTACTCGTTCGCCG 61.007 55.000 0.00 0.00 38.13 6.46
2408 2764 1.280206 GCTTGTACTCGTTCGCCGTT 61.280 55.000 0.00 0.00 37.94 4.44
2409 2765 0.433492 CTTGTACTCGTTCGCCGTTG 59.567 55.000 0.00 0.00 37.94 4.10
2410 2766 0.248990 TTGTACTCGTTCGCCGTTGT 60.249 50.000 0.00 0.00 37.94 3.32
2411 2767 0.661187 TGTACTCGTTCGCCGTTGTC 60.661 55.000 0.00 0.00 37.94 3.18
2412 2768 1.440850 TACTCGTTCGCCGTTGTCG 60.441 57.895 0.00 0.00 37.94 4.35
2442 2798 2.440247 TCCGATCAGGAGCTCGCA 60.440 61.111 7.83 0.00 45.98 5.10
2461 2817 2.034812 GCACCGGTGTGAAATTTGGTTA 59.965 45.455 33.92 0.00 45.76 2.85
2464 2820 3.818773 ACCGGTGTGAAATTTGGTTAGAG 59.181 43.478 6.12 0.00 0.00 2.43
2467 2838 3.234386 GTGTGAAATTTGGTTAGAGCGC 58.766 45.455 0.00 0.00 0.00 5.92
2472 2843 4.518970 TGAAATTTGGTTAGAGCGCTTCTT 59.481 37.500 13.26 2.94 37.36 2.52
2474 2845 4.686839 ATTTGGTTAGAGCGCTTCTTTC 57.313 40.909 13.26 0.00 37.36 2.62
2475 2846 2.831685 TGGTTAGAGCGCTTCTTTCA 57.168 45.000 13.26 5.43 37.36 2.69
2476 2847 2.688507 TGGTTAGAGCGCTTCTTTCAG 58.311 47.619 13.26 0.00 37.36 3.02
2478 2849 3.067833 GGTTAGAGCGCTTCTTTCAGTT 58.932 45.455 13.26 0.00 37.36 3.16
2480 2851 4.689345 GGTTAGAGCGCTTCTTTCAGTTTA 59.311 41.667 13.26 0.00 37.36 2.01
2481 2852 5.351740 GGTTAGAGCGCTTCTTTCAGTTTAT 59.648 40.000 13.26 0.00 37.36 1.40
2482 2853 6.455780 GGTTAGAGCGCTTCTTTCAGTTTATC 60.456 42.308 13.26 0.00 37.36 1.75
2483 2854 3.614616 AGAGCGCTTCTTTCAGTTTATCG 59.385 43.478 13.26 0.00 29.61 2.92
2484 2855 3.326747 AGCGCTTCTTTCAGTTTATCGT 58.673 40.909 2.64 0.00 0.00 3.73
2486 2857 3.840763 GCGCTTCTTTCAGTTTATCGTTG 59.159 43.478 0.00 0.00 0.00 4.10
2490 2861 6.244275 GCTTCTTTCAGTTTATCGTTGCTAG 58.756 40.000 0.00 0.00 0.00 3.42
2492 2863 7.571428 GCTTCTTTCAGTTTATCGTTGCTAGTT 60.571 37.037 0.00 0.00 0.00 2.24
2495 2866 8.869897 TCTTTCAGTTTATCGTTGCTAGTTATG 58.130 33.333 0.00 0.00 0.00 1.90
2496 2867 6.583912 TCAGTTTATCGTTGCTAGTTATGC 57.416 37.500 0.00 0.00 0.00 3.14
2497 2868 5.231357 TCAGTTTATCGTTGCTAGTTATGCG 59.769 40.000 0.00 0.00 0.00 4.73
2498 2869 5.005394 CAGTTTATCGTTGCTAGTTATGCGT 59.995 40.000 0.00 0.00 0.00 5.24
2499 2870 5.005394 AGTTTATCGTTGCTAGTTATGCGTG 59.995 40.000 0.00 0.00 0.00 5.34
2500 2871 2.357327 TCGTTGCTAGTTATGCGTGT 57.643 45.000 0.00 0.00 0.00 4.49
2501 2872 1.989864 TCGTTGCTAGTTATGCGTGTG 59.010 47.619 0.00 0.00 0.00 3.82
2502 2873 1.989864 CGTTGCTAGTTATGCGTGTGA 59.010 47.619 0.00 0.00 0.00 3.58
2503 2874 2.028045 CGTTGCTAGTTATGCGTGTGAG 59.972 50.000 0.00 0.00 0.00 3.51
2504 2875 3.250744 GTTGCTAGTTATGCGTGTGAGA 58.749 45.455 0.00 0.00 0.00 3.27
2505 2876 3.586100 TGCTAGTTATGCGTGTGAGAA 57.414 42.857 0.00 0.00 0.00 2.87
2506 2877 3.511699 TGCTAGTTATGCGTGTGAGAAG 58.488 45.455 0.00 0.00 0.00 2.85
2507 2878 2.282820 GCTAGTTATGCGTGTGAGAAGC 59.717 50.000 0.00 0.00 0.00 3.86
2508 2879 2.751166 AGTTATGCGTGTGAGAAGCT 57.249 45.000 0.00 0.00 0.00 3.74
2509 2880 3.045601 AGTTATGCGTGTGAGAAGCTT 57.954 42.857 0.00 0.00 0.00 3.74
2510 2881 3.403038 AGTTATGCGTGTGAGAAGCTTT 58.597 40.909 0.00 0.00 0.00 3.51
2511 2882 3.433615 AGTTATGCGTGTGAGAAGCTTTC 59.566 43.478 0.00 0.94 0.00 2.62
2512 2883 0.792640 ATGCGTGTGAGAAGCTTTCG 59.207 50.000 0.00 0.96 34.02 3.46
2513 2884 1.154580 GCGTGTGAGAAGCTTTCGC 60.155 57.895 0.00 7.73 35.86 4.70
2531 2902 2.589492 CGAGATCCGTCGCCATTGC 61.589 63.158 0.00 0.00 32.22 3.56
2538 2909 4.465512 GTCGCCATTGCTGCACCG 62.466 66.667 0.00 3.30 34.43 4.94
2608 2990 2.679349 GCTCACCTCACCTGAAATCCTC 60.679 54.545 0.00 0.00 0.00 3.71
2609 2991 1.909302 TCACCTCACCTGAAATCCTCC 59.091 52.381 0.00 0.00 0.00 4.30
2610 2992 1.630369 CACCTCACCTGAAATCCTCCA 59.370 52.381 0.00 0.00 0.00 3.86
2611 2993 2.240667 CACCTCACCTGAAATCCTCCAT 59.759 50.000 0.00 0.00 0.00 3.41
2612 2994 2.240667 ACCTCACCTGAAATCCTCCATG 59.759 50.000 0.00 0.00 0.00 3.66
2669 3055 2.158449 GGCTTCTCATTAATGCCGATCG 59.842 50.000 8.51 8.51 33.96 3.69
2670 3056 3.059884 GCTTCTCATTAATGCCGATCGA 58.940 45.455 18.66 0.00 0.00 3.59
2671 3057 3.681897 GCTTCTCATTAATGCCGATCGAT 59.318 43.478 18.66 0.00 0.00 3.59
2672 3058 4.201666 GCTTCTCATTAATGCCGATCGATC 60.202 45.833 18.66 15.68 0.00 3.69
2686 3072 0.460109 TCGATCTCGTTCCGTCCGTA 60.460 55.000 0.00 0.00 40.80 4.02
2713 3099 4.946772 TCCGCCACAAATATTGAATTCTCA 59.053 37.500 7.05 0.00 0.00 3.27
2762 3148 2.654079 CCTCGTGCTCCTTGCTCCT 61.654 63.158 0.00 0.00 43.37 3.69
2868 3267 4.339247 CAGTTGCTGGGAGAAAGAAAGAAA 59.661 41.667 0.00 0.00 0.00 2.52
2972 3375 7.378966 GCAGCATCAATATACTGTAGGAGTAA 58.621 38.462 0.00 0.00 40.67 2.24
2983 3386 2.453601 TGTAGGAGTAATAGGGAGGGGG 59.546 54.545 0.00 0.00 0.00 5.40
3066 3473 1.675310 CCAACAGCAGCGAATCCCA 60.675 57.895 0.00 0.00 0.00 4.37
3111 3522 0.768997 TTCGTCCCCTTCCTTCCCAA 60.769 55.000 0.00 0.00 0.00 4.12
3114 3525 0.612174 GTCCCCTTCCTTCCCAAAGC 60.612 60.000 0.00 0.00 0.00 3.51
3120 3531 2.037641 CCTTCCTTCCCAAAGCAAAAGG 59.962 50.000 0.00 0.00 39.73 3.11
3129 3540 3.313249 CCCAAAGCAAAAGGAAAGCAAAG 59.687 43.478 0.00 0.00 0.00 2.77
3130 3541 3.242837 CCAAAGCAAAAGGAAAGCAAAGC 60.243 43.478 0.00 0.00 0.00 3.51
3131 3542 2.245159 AGCAAAAGGAAAGCAAAGCC 57.755 45.000 0.00 0.00 0.00 4.35
3132 3543 1.764723 AGCAAAAGGAAAGCAAAGCCT 59.235 42.857 0.00 0.00 0.00 4.58
3134 3545 2.397549 CAAAAGGAAAGCAAAGCCTCG 58.602 47.619 0.00 0.00 0.00 4.63
3135 3546 0.961753 AAAGGAAAGCAAAGCCTCGG 59.038 50.000 0.00 0.00 0.00 4.63
3136 3547 1.527433 AAGGAAAGCAAAGCCTCGGC 61.527 55.000 0.00 0.00 42.33 5.54
3174 3587 0.037697 TGTACGCTCGCACCATTCTT 60.038 50.000 0.00 0.00 0.00 2.52
3277 3695 1.376424 ACTCATCACCCAGCTTGCG 60.376 57.895 0.00 0.00 0.00 4.85
3318 3742 2.202401 GTCTCCGGACGTACGTGC 60.202 66.667 28.16 27.85 32.47 5.34
3319 3743 2.669229 TCTCCGGACGTACGTGCA 60.669 61.111 33.96 18.31 36.19 4.57
3320 3744 2.202440 CTCCGGACGTACGTGCAG 60.202 66.667 33.96 25.66 36.19 4.41
3321 3745 4.409218 TCCGGACGTACGTGCAGC 62.409 66.667 33.96 17.08 36.19 5.25
3322 3746 4.710695 CCGGACGTACGTGCAGCA 62.711 66.667 33.96 0.00 36.19 4.41
3323 3747 2.506217 CGGACGTACGTGCAGCAT 60.506 61.111 33.96 6.35 36.19 3.79
3324 3748 2.788176 CGGACGTACGTGCAGCATG 61.788 63.158 33.96 17.19 36.19 4.06
3374 3803 0.164647 GCGCACAGTGATTGTCTGTC 59.835 55.000 4.15 0.00 43.14 3.51
3377 3806 2.212652 GCACAGTGATTGTCTGTCACA 58.787 47.619 4.15 0.00 46.46 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.414181 AGCGGTGGATATTCTGTCCAG 59.586 52.381 0.00 0.00 45.91 3.86
1 2 1.138859 CAGCGGTGGATATTCTGTCCA 59.861 52.381 6.74 0.00 43.26 4.02
3 4 1.202580 AGCAGCGGTGGATATTCTGTC 60.203 52.381 17.54 0.00 0.00 3.51
7 8 2.821991 AGTAGCAGCGGTGGATATTC 57.178 50.000 17.54 0.00 0.00 1.75
24 25 1.362224 AGAGGGCATGGTTGTGTAGT 58.638 50.000 0.00 0.00 0.00 2.73
27 28 1.064003 TGTAGAGGGCATGGTTGTGT 58.936 50.000 0.00 0.00 0.00 3.72
46 47 7.658525 TGCAATCTATGAATGGTGGTTTAAT 57.341 32.000 0.00 0.00 0.00 1.40
48 49 7.275888 GATGCAATCTATGAATGGTGGTTTA 57.724 36.000 0.00 0.00 41.17 2.01
100 101 4.798682 AGGTGGCGGTAGGGAGGG 62.799 72.222 0.00 0.00 0.00 4.30
177 178 3.554342 CCTGCCTCTCCATCCCCG 61.554 72.222 0.00 0.00 0.00 5.73
179 180 0.473501 ATCTCCTGCCTCTCCATCCC 60.474 60.000 0.00 0.00 0.00 3.85
191 192 3.287867 AACATAAGCCACCATCTCCTG 57.712 47.619 0.00 0.00 0.00 3.86
217 218 3.705072 CCTCCCTTTTGATAGTCGTAGGT 59.295 47.826 0.00 0.00 0.00 3.08
224 225 5.653255 ATATGTGCCTCCCTTTTGATAGT 57.347 39.130 0.00 0.00 0.00 2.12
247 258 6.258230 CAAGAAAATCTTGCACCACATAGA 57.742 37.500 7.13 0.00 46.03 1.98
262 273 9.630098 CAGACATAATGCAAAGTACAAGAAAAT 57.370 29.630 0.00 0.00 0.00 1.82
263 274 7.594758 GCAGACATAATGCAAAGTACAAGAAAA 59.405 33.333 0.00 0.00 43.31 2.29
267 278 5.106197 TGGCAGACATAATGCAAAGTACAAG 60.106 40.000 0.00 0.00 45.68 3.16
270 281 4.155826 TGTGGCAGACATAATGCAAAGTAC 59.844 41.667 0.00 0.00 45.68 2.73
319 592 1.727062 ATCCTAGGTCTGGATGGCTG 58.273 55.000 9.08 0.00 42.22 4.85
331 604 1.551329 GGAGGAGTAGGGCATCCTAGG 60.551 61.905 0.82 0.82 46.12 3.02
332 605 1.551329 GGGAGGAGTAGGGCATCCTAG 60.551 61.905 0.00 0.00 46.12 3.02
356 629 2.522923 AGCTCGATGGAGGGCGAT 60.523 61.111 6.88 0.00 40.80 4.58
357 630 3.219928 GAGCTCGATGGAGGGCGA 61.220 66.667 6.88 0.00 40.80 5.54
426 699 4.207891 TCCATAGCAAGGAGAGAACAAC 57.792 45.455 0.00 0.00 0.00 3.32
430 703 7.000472 CCAAATATTCCATAGCAAGGAGAGAA 59.000 38.462 0.00 0.00 36.33 2.87
449 722 7.972301 ACAAATTGTTTCTGGAATCCCAAATA 58.028 30.769 0.00 0.00 42.98 1.40
479 753 2.372690 CGGAGTGGAGTTCGTTGCG 61.373 63.158 0.00 0.00 0.00 4.85
498 772 6.214399 GCTAAATTTCTAGCGCTAGTCCTTA 58.786 40.000 36.45 26.54 35.31 2.69
508 782 7.253817 GTGAAGTCACTAGCTAAATTTCTAGCG 60.254 40.741 11.85 5.22 44.33 4.26
559 833 2.035321 GGAGGCATCCTTCTTAGAGACG 59.965 54.545 10.91 0.00 42.94 4.18
579 853 6.214191 AGAGGTATTGACGCTATGATATGG 57.786 41.667 0.00 0.00 0.00 2.74
583 857 4.411927 AGGAGAGGTATTGACGCTATGAT 58.588 43.478 0.00 0.00 0.00 2.45
588 862 1.751924 GTGAGGAGAGGTATTGACGCT 59.248 52.381 0.00 0.00 0.00 5.07
609 883 2.624838 AGCTTTGCAATTGTGTGCTAGT 59.375 40.909 7.40 0.00 45.17 2.57
631 907 0.825425 TCAAAGGCGACCAAATGGCA 60.825 50.000 0.00 0.00 39.32 4.92
635 911 4.081752 TGCATTATTCAAAGGCGACCAAAT 60.082 37.500 0.00 0.00 0.00 2.32
639 915 3.715628 ATGCATTATTCAAAGGCGACC 57.284 42.857 0.00 0.00 0.00 4.79
644 920 6.430925 TCCCTATCGAATGCATTATTCAAAGG 59.569 38.462 12.97 13.58 44.42 3.11
651 927 7.134362 AGATGATCCCTATCGAATGCATTAT 57.866 36.000 12.97 5.91 34.60 1.28
672 949 2.022035 TGACCAATCACTAGGGGGAGAT 60.022 50.000 0.00 0.00 0.00 2.75
726 1003 4.923893 TGTCTTGCTTTTTCAGACATGTG 58.076 39.130 1.15 0.00 35.00 3.21
855 1135 4.861102 AGATGAGCAAAAAGAAAGTGGG 57.139 40.909 0.00 0.00 0.00 4.61
973 1253 1.613630 GGAGAGGTGGAAGGAGGCA 60.614 63.158 0.00 0.00 0.00 4.75
989 1269 1.846124 AGGAAAGTGGCGAAGGGGA 60.846 57.895 0.00 0.00 0.00 4.81
1029 1314 1.139853 CTACCTGAGCTGGCTTAAGGG 59.860 57.143 21.23 12.91 35.65 3.95
1138 1429 2.356313 CCACGACGCTCTTGCTGT 60.356 61.111 0.00 0.00 36.97 4.40
1171 1471 1.807814 ACACCTTGTTCTCCTCCAGT 58.192 50.000 0.00 0.00 0.00 4.00
1345 1645 2.467962 CGAGCTGTCGTAGTGAGGA 58.532 57.895 0.00 0.00 41.57 3.71
1520 1853 4.914983 TCCAAGCACAAGAAGAAGATCAT 58.085 39.130 0.00 0.00 0.00 2.45
1549 1882 4.916983 TCAGATTTCCACCAACAACAAG 57.083 40.909 0.00 0.00 0.00 3.16
1553 1886 3.501828 CACGATCAGATTTCCACCAACAA 59.498 43.478 0.00 0.00 0.00 2.83
1555 1888 3.074412 ACACGATCAGATTTCCACCAAC 58.926 45.455 0.00 0.00 0.00 3.77
1556 1889 3.417069 ACACGATCAGATTTCCACCAA 57.583 42.857 0.00 0.00 0.00 3.67
1557 1890 3.334691 GAACACGATCAGATTTCCACCA 58.665 45.455 0.00 0.00 0.00 4.17
1559 1892 2.993899 ACGAACACGATCAGATTTCCAC 59.006 45.455 0.00 0.00 0.00 4.02
1560 1893 2.993220 CACGAACACGATCAGATTTCCA 59.007 45.455 0.00 0.00 0.00 3.53
1625 1963 0.616111 ATGTTCCTCCAGTCGCCTCT 60.616 55.000 0.00 0.00 0.00 3.69
1630 1968 0.526524 GCGAGATGTTCCTCCAGTCG 60.527 60.000 0.00 0.00 0.00 4.18
1651 1989 2.150837 GCGGCTCGTCACGTAGTTC 61.151 63.158 0.00 0.00 41.61 3.01
1696 2034 1.482593 AGCCGGATGAAGTACTTCTGG 59.517 52.381 30.47 25.59 46.04 3.86
1933 2280 1.664649 CTCGAGCTTCACGTTGCCA 60.665 57.895 0.00 0.00 0.00 4.92
2014 2361 3.057548 CACAGCTGGCCGCATTGA 61.058 61.111 19.93 0.00 42.61 2.57
2120 2467 4.767255 CTGCCTCGTCCCTGGTGC 62.767 72.222 0.00 0.00 0.00 5.01
2140 2487 3.426568 GGCAAGCAGAGCACGTCC 61.427 66.667 0.00 0.00 0.00 4.79
2142 2489 2.358003 GAGGCAAGCAGAGCACGT 60.358 61.111 0.00 0.00 0.00 4.49
2145 2492 2.223200 CTCTCGAGGCAAGCAGAGCA 62.223 60.000 13.56 0.00 0.00 4.26
2148 2495 2.278330 TGCTCTCGAGGCAAGCAGA 61.278 57.895 19.99 2.50 40.91 4.26
2214 2561 1.089481 TCGCTTGCGTTCCATCATCC 61.089 55.000 14.70 0.00 0.00 3.51
2294 2641 1.212616 CGATCGATGGGTTCTTGAGC 58.787 55.000 10.26 0.00 0.00 4.26
2333 2681 1.227438 CCGTATACTTGTGGCGGGG 60.227 63.158 0.56 0.00 38.86 5.73
2334 2682 1.885850 GCCGTATACTTGTGGCGGG 60.886 63.158 4.08 0.00 42.34 6.13
2343 2691 1.027357 CGGTACAGTGGCCGTATACT 58.973 55.000 16.98 0.00 42.73 2.12
2344 2692 3.557207 CGGTACAGTGGCCGTATAC 57.443 57.895 16.98 0.00 42.73 1.47
2350 2698 1.737793 CAGATTTTCGGTACAGTGGCC 59.262 52.381 0.00 0.00 0.00 5.36
2351 2699 2.695359 TCAGATTTTCGGTACAGTGGC 58.305 47.619 0.00 0.00 0.00 5.01
2379 2735 4.258702 ACGAGTACAAGCTTCATGAACT 57.741 40.909 3.38 4.47 0.00 3.01
2380 2736 4.433022 CGAACGAGTACAAGCTTCATGAAC 60.433 45.833 3.38 2.06 0.00 3.18
2382 2738 3.242518 CGAACGAGTACAAGCTTCATGA 58.757 45.455 0.00 0.00 0.00 3.07
2383 2739 2.222596 GCGAACGAGTACAAGCTTCATG 60.223 50.000 0.00 0.00 0.00 3.07
2428 2784 2.279120 CGGTGCGAGCTCCTGATC 60.279 66.667 8.47 0.00 0.00 2.92
2429 2785 3.842923 CCGGTGCGAGCTCCTGAT 61.843 66.667 8.47 0.00 0.00 2.90
2434 2790 3.858868 TTCACACCGGTGCGAGCTC 62.859 63.158 34.26 2.73 44.87 4.09
2439 2795 0.662970 CCAAATTTCACACCGGTGCG 60.663 55.000 34.26 25.66 44.87 5.34
2442 2798 3.818773 CTCTAACCAAATTTCACACCGGT 59.181 43.478 0.00 0.00 0.00 5.28
2447 2803 3.146066 AGCGCTCTAACCAAATTTCACA 58.854 40.909 2.64 0.00 0.00 3.58
2448 2804 3.831715 AGCGCTCTAACCAAATTTCAC 57.168 42.857 2.64 0.00 0.00 3.18
2454 2810 3.472652 TGAAAGAAGCGCTCTAACCAAA 58.527 40.909 12.06 0.00 32.46 3.28
2461 2817 3.614616 CGATAAACTGAAAGAAGCGCTCT 59.385 43.478 12.06 7.00 37.43 4.09
2464 2820 3.724295 ACGATAAACTGAAAGAAGCGC 57.276 42.857 0.00 0.00 37.43 5.92
2467 2838 7.352719 ACTAGCAACGATAAACTGAAAGAAG 57.647 36.000 0.00 0.00 37.43 2.85
2472 2843 6.237728 CGCATAACTAGCAACGATAAACTGAA 60.238 38.462 0.00 0.00 0.00 3.02
2474 2845 5.005394 ACGCATAACTAGCAACGATAAACTG 59.995 40.000 0.00 0.00 0.00 3.16
2475 2846 5.005394 CACGCATAACTAGCAACGATAAACT 59.995 40.000 0.00 0.00 0.00 2.66
2476 2847 5.188194 CACGCATAACTAGCAACGATAAAC 58.812 41.667 0.00 0.00 0.00 2.01
2478 2849 4.266739 CACACGCATAACTAGCAACGATAA 59.733 41.667 0.00 0.00 0.00 1.75
2480 2851 2.603110 CACACGCATAACTAGCAACGAT 59.397 45.455 0.00 0.00 0.00 3.73
2481 2852 1.989864 CACACGCATAACTAGCAACGA 59.010 47.619 0.00 0.00 0.00 3.85
2482 2853 1.989864 TCACACGCATAACTAGCAACG 59.010 47.619 0.00 0.00 0.00 4.10
2483 2854 3.250744 TCTCACACGCATAACTAGCAAC 58.749 45.455 0.00 0.00 0.00 4.17
2484 2855 3.586100 TCTCACACGCATAACTAGCAA 57.414 42.857 0.00 0.00 0.00 3.91
2486 2857 2.282820 GCTTCTCACACGCATAACTAGC 59.717 50.000 0.00 0.00 0.00 3.42
2490 2861 3.722082 CGAAAGCTTCTCACACGCATAAC 60.722 47.826 0.00 0.00 0.00 1.89
2492 2863 1.992667 CGAAAGCTTCTCACACGCATA 59.007 47.619 0.00 0.00 0.00 3.14
2507 2878 3.589982 CGACGGATCTCGCGAAAG 58.410 61.111 11.33 0.00 43.89 2.62
2513 2884 2.589492 GCAATGGCGACGGATCTCG 61.589 63.158 0.00 0.22 45.88 4.04
2541 2912 4.689549 TTCTCACGGGGAGGCGGA 62.690 66.667 7.54 0.00 44.19 5.54
2608 2990 2.108157 GCACATGGCATGGCATGG 59.892 61.111 45.64 37.32 43.97 3.66
2686 3072 3.627395 TCAATATTTGTGGCGGAGACT 57.373 42.857 0.00 0.00 34.59 3.24
2868 3267 6.878317 TGACGAATCAAATTGATACTCTCCT 58.122 36.000 9.09 0.00 35.76 3.69
2972 3375 0.327576 CCAACTCACCCCCTCCCTAT 60.328 60.000 0.00 0.00 0.00 2.57
3015 3418 0.317770 TTTCTTTTGGCTTGCTCGCG 60.318 50.000 0.00 0.00 0.00 5.87
3066 3473 0.171455 GACGACAGCGAGAAGGACAT 59.829 55.000 0.00 0.00 41.64 3.06
3111 3522 2.171237 AGGCTTTGCTTTCCTTTTGCTT 59.829 40.909 0.00 0.00 0.00 3.91
3114 3525 2.397549 CGAGGCTTTGCTTTCCTTTTG 58.602 47.619 0.00 0.00 0.00 2.44
3120 3531 2.176792 CGCCGAGGCTTTGCTTTC 59.823 61.111 12.70 0.00 39.32 2.62
3174 3587 4.408821 GCCCACCGCCACTGATGA 62.409 66.667 0.00 0.00 0.00 2.92
3230 3643 4.383861 TGAGGCTCACTGCTGCGG 62.384 66.667 14.43 6.98 42.39 5.69
3231 3644 3.117171 GTGAGGCTCACTGCTGCG 61.117 66.667 34.49 0.00 43.73 5.18
3301 3725 2.202401 GCACGTACGTCCGGAGAC 60.202 66.667 19.94 2.17 39.83 3.36
3339 3763 3.005539 GCCACTGGAGCTCTGGGA 61.006 66.667 19.13 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.