Multiple sequence alignment - TraesCS2B01G442300

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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 TraesCS2B01G442300 chr2B 100.000 3122 0 0 1 3122 635021753 635024874 0.000000e+00 5766.0
1 TraesCS2B01G442300 chr2D 95.672 1756 47 14 641 2388 534309100 534310834 0.000000e+00 2795.0
2 TraesCS2B01G442300 chr2D 95.327 642 27 3 1 641 534308430 534309069 0.000000e+00 1016.0
3 TraesCS2B01G442300 chr2D 91.016 512 28 7 2403 2907 534310895 534311395 0.000000e+00 675.0
4 TraesCS2B01G442300 chr2D 95.918 98 4 0 3025 3122 534311404 534311501 3.220000e-35 159.0
5 TraesCS2B01G442300 chr6B 93.250 637 41 2 8 643 124473363 124472728 0.000000e+00 937.0
6 TraesCS2B01G442300 chr6B 79.808 104 15 6 2523 2626 134215635 134215732 1.550000e-08 71.3
7 TraesCS2B01G442300 chr1A 82.031 640 108 5 3 638 50779351 50779987 3.540000e-149 538.0
8 TraesCS2B01G442300 chr6A 82.090 201 33 3 3 201 107835677 107835478 5.350000e-38 169.0
9 TraesCS2B01G442300 chr6A 98.837 86 1 0 2901 2986 287115364 287115449 1.500000e-33 154.0
10 TraesCS2B01G442300 chr6A 98.837 86 1 0 2902 2987 591741946 591742031 1.500000e-33 154.0
11 TraesCS2B01G442300 chr7D 98.851 87 1 0 2900 2986 483929696 483929610 4.170000e-34 156.0
12 TraesCS2B01G442300 chr7D 97.701 87 2 0 2902 2988 69811216 69811302 1.940000e-32 150.0
13 TraesCS2B01G442300 chrUn 91.964 112 5 4 2883 2992 409883434 409883543 1.500000e-33 154.0
14 TraesCS2B01G442300 chrUn 80.488 82 16 0 2575 2656 89304299 89304218 2.600000e-06 63.9
15 TraesCS2B01G442300 chr6D 98.837 86 1 0 2902 2987 401777687 401777772 1.500000e-33 154.0
16 TraesCS2B01G442300 chr5A 97.778 90 1 1 2902 2991 705822060 705821972 1.500000e-33 154.0
17 TraesCS2B01G442300 chr4B 98.837 86 1 0 2901 2986 538950566 538950481 1.500000e-33 154.0
18 TraesCS2B01G442300 chr2A 98.837 86 1 0 2901 2986 750532477 750532392 1.500000e-33 154.0
19 TraesCS2B01G442300 chr4A 84.146 82 13 0 2575 2656 724692836 724692917 2.580000e-11 80.5
20 TraesCS2B01G442300 chr4A 85.915 71 10 0 2575 2645 724742134 724742204 3.340000e-10 76.8
21 TraesCS2B01G442300 chr4A 82.927 82 14 0 2575 2656 724618153 724618234 1.200000e-09 75.0
22 TraesCS2B01G442300 chr3D 82.667 75 11 2 2581 2654 23149014 23148941 7.230000e-07 65.8
23 TraesCS2B01G442300 chr3B 100.000 28 0 0 2637 2664 434987342 434987369 6.000000e-03 52.8


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 TraesCS2B01G442300 chr2B 635021753 635024874 3121 False 5766.00 5766 100.00000 1 3122 1 chr2B.!!$F1 3121
1 TraesCS2B01G442300 chr2D 534308430 534311501 3071 False 1161.25 2795 94.48325 1 3122 4 chr2D.!!$F1 3121
2 TraesCS2B01G442300 chr6B 124472728 124473363 635 True 937.00 937 93.25000 8 643 1 chr6B.!!$R1 635
3 TraesCS2B01G442300 chr1A 50779351 50779987 636 False 538.00 538 82.03100 3 638 1 chr1A.!!$F1 635

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
50 51 0.036010 CATCTTCCACCAGGCGAACT 60.036 55.0 0.0 0.0 33.74 3.01 F
894 929 0.379316 AACTTTGTGGCGAAACGGAC 59.621 50.0 0.0 0.0 0.00 4.79 F
1724 1766 0.106149 GGAGACAAGGAACCACACGT 59.894 55.0 0.0 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1746 0.393077 CGTGTGGTTCCTTGTCTCCT 59.607 55.0 0.0 0.0 0.0 3.69 R
2109 2151 0.324738 TCACCTCCTAGAGCCACAGG 60.325 60.0 0.0 0.0 0.0 4.00 R
2990 3085 0.034337 TACAACGCCTGGGACTTGAC 59.966 55.0 0.0 0.0 0.0 3.18 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
50 51 0.036010 CATCTTCCACCAGGCGAACT 60.036 55.000 0.00 0.00 33.74 3.01
53 54 0.741221 CTTCCACCAGGCGAACTAGC 60.741 60.000 0.00 0.00 33.74 3.42
73 74 1.409064 CGCACCCTCTTATGAGTAGCA 59.591 52.381 5.03 0.00 38.61 3.49
76 77 3.070159 GCACCCTCTTATGAGTAGCATCA 59.930 47.826 5.03 0.00 38.61 3.07
176 180 1.602311 GATGGTATTGCCTGAGCCAG 58.398 55.000 0.00 0.00 38.69 4.85
385 389 2.669364 CTTTTTGCTCCACTGATGTGC 58.331 47.619 0.00 0.00 42.54 4.57
406 410 1.032014 TGGGCTGAAAAAGACACTGC 58.968 50.000 0.00 0.00 34.40 4.40
432 436 0.886490 CAACGCTCACTTTCTGCCCT 60.886 55.000 0.00 0.00 0.00 5.19
542 546 7.414436 GCAAATAATAAATTAGTCACGGCAGA 58.586 34.615 0.00 0.00 0.00 4.26
577 581 2.907042 ACCCTTACTCCTTCCAAGTCAG 59.093 50.000 0.00 0.00 0.00 3.51
584 588 3.269178 CTCCTTCCAAGTCAGCTGATTC 58.731 50.000 21.47 8.07 0.00 2.52
684 719 3.771577 AGGTGAATCAAACTCCGTTCT 57.228 42.857 0.00 0.00 0.00 3.01
690 725 5.458779 GTGAATCAAACTCCGTTCTTTTTGG 59.541 40.000 0.00 0.00 31.20 3.28
737 772 1.726791 CTTTGTGTGTTCCGATCTCCG 59.273 52.381 0.00 0.00 38.18 4.63
781 816 5.071923 AGGGAAGTTAAGAACTACTGCTTGT 59.928 40.000 0.00 0.00 41.91 3.16
791 826 2.159142 ACTACTGCTTGTACATACCGGC 60.159 50.000 0.00 0.00 0.00 6.13
795 830 1.065053 TGCTTGTACATACCGGCCATT 60.065 47.619 0.00 0.00 0.00 3.16
825 860 1.942677 TTTCGTGGAGAAACGCAAGA 58.057 45.000 0.00 0.00 43.35 3.02
827 862 1.214367 TCGTGGAGAAACGCAAGAAC 58.786 50.000 0.00 0.00 43.26 3.01
828 863 1.202486 TCGTGGAGAAACGCAAGAACT 60.202 47.619 0.00 0.00 43.26 3.01
829 864 2.034939 TCGTGGAGAAACGCAAGAACTA 59.965 45.455 0.00 0.00 43.26 2.24
830 865 2.155155 CGTGGAGAAACGCAAGAACTAC 59.845 50.000 0.00 0.00 43.62 2.73
831 866 3.391049 GTGGAGAAACGCAAGAACTACT 58.609 45.455 0.00 0.00 43.62 2.57
832 867 3.184581 GTGGAGAAACGCAAGAACTACTG 59.815 47.826 0.00 0.00 43.62 2.74
871 906 2.833794 TGGTCCGAGAAAAGTGTGAAG 58.166 47.619 0.00 0.00 0.00 3.02
886 921 2.159448 TGTGAAGACAAACTTTGTGGCG 60.159 45.455 11.97 0.00 45.52 5.69
887 922 2.096819 GTGAAGACAAACTTTGTGGCGA 59.903 45.455 11.97 0.00 45.52 5.54
890 925 3.145212 AGACAAACTTTGTGGCGAAAC 57.855 42.857 11.97 0.00 45.52 2.78
894 929 0.379316 AACTTTGTGGCGAAACGGAC 59.621 50.000 0.00 0.00 0.00 4.79
941 976 5.878116 TGCGTAACAGTGCTATAAAAGGATT 59.122 36.000 0.00 0.00 0.00 3.01
949 984 6.971184 CAGTGCTATAAAAGGATTTGAGCAAG 59.029 38.462 11.73 6.74 43.99 4.01
983 1018 5.644644 GCATCAATCACTCTTAACCCAAAG 58.355 41.667 0.00 0.00 0.00 2.77
987 1022 1.202710 TCACTCTTAACCCAAAGCGCA 60.203 47.619 11.47 0.00 0.00 6.09
995 1030 1.181098 ACCCAAAGCGCAGAAAGCAT 61.181 50.000 11.47 0.00 46.13 3.79
1270 1307 3.641436 AGCATCCCTTCACATCGTGTATA 59.359 43.478 0.00 0.00 34.79 1.47
1271 1308 4.284490 AGCATCCCTTCACATCGTGTATAT 59.716 41.667 0.00 0.00 34.79 0.86
1272 1309 4.627467 GCATCCCTTCACATCGTGTATATC 59.373 45.833 0.00 0.00 34.79 1.63
1273 1310 5.783111 CATCCCTTCACATCGTGTATATCA 58.217 41.667 0.00 0.00 34.79 2.15
1274 1311 6.401394 CATCCCTTCACATCGTGTATATCAT 58.599 40.000 0.00 0.00 34.79 2.45
1276 1313 6.455647 TCCCTTCACATCGTGTATATCATTC 58.544 40.000 0.00 0.00 34.79 2.67
1295 1332 1.425066 TCTTTTGCAGTGGGATCAGGT 59.575 47.619 0.00 0.00 0.00 4.00
1704 1746 2.659016 CAGTTCTGCGAGGAGGCA 59.341 61.111 0.00 0.00 41.45 4.75
1724 1766 0.106149 GGAGACAAGGAACCACACGT 59.894 55.000 0.00 0.00 0.00 4.49
1805 1847 4.719616 GCGCGCGGTCACTTCAAC 62.720 66.667 33.06 6.44 0.00 3.18
2026 2068 2.483876 CAGTATGCCACAAGGATACCG 58.516 52.381 1.33 0.00 36.89 4.02
2029 2071 2.895372 GCCACAAGGATACCGGCG 60.895 66.667 0.00 0.00 36.89 6.46
2050 2092 0.249073 CTGGGATGAGGCGTACTTCG 60.249 60.000 0.00 0.00 43.12 3.79
2058 2100 0.458543 AGGCGTACTTCGTGATGCTG 60.459 55.000 0.00 0.00 42.13 4.41
2109 2151 0.465460 TCATGCCGGCCAATTACCTC 60.465 55.000 26.77 0.00 0.00 3.85
2129 2171 1.561643 CTGTGGCTCTAGGAGGTGAA 58.438 55.000 0.00 0.00 0.00 3.18
2297 2339 6.877611 ATGTACCCCGAAAAATGATATGAC 57.122 37.500 0.00 0.00 0.00 3.06
2298 2340 5.746284 TGTACCCCGAAAAATGATATGACA 58.254 37.500 0.00 0.00 0.00 3.58
2299 2341 5.587043 TGTACCCCGAAAAATGATATGACAC 59.413 40.000 0.00 0.00 0.00 3.67
2301 2343 4.640201 ACCCCGAAAAATGATATGACACAG 59.360 41.667 0.00 0.00 0.00 3.66
2302 2344 4.640201 CCCCGAAAAATGATATGACACAGT 59.360 41.667 0.00 0.00 0.00 3.55
2375 2417 5.681337 TTTTACAGAAATGATGCGTGTCA 57.319 34.783 0.00 0.00 0.00 3.58
2378 2420 3.925379 ACAGAAATGATGCGTGTCAGTA 58.075 40.909 0.00 0.00 0.00 2.74
2388 2430 6.090783 TGATGCGTGTCAGTACTAGTTTTAG 58.909 40.000 0.00 0.00 0.00 1.85
2390 2432 4.022589 TGCGTGTCAGTACTAGTTTTAGCT 60.023 41.667 0.00 0.00 0.00 3.32
2391 2433 5.181811 TGCGTGTCAGTACTAGTTTTAGCTA 59.818 40.000 0.00 0.00 0.00 3.32
2393 2435 5.738225 CGTGTCAGTACTAGTTTTAGCTAGC 59.262 44.000 6.62 6.62 41.49 3.42
2394 2436 6.403418 CGTGTCAGTACTAGTTTTAGCTAGCT 60.403 42.308 23.12 23.12 41.49 3.32
2395 2437 6.968335 GTGTCAGTACTAGTTTTAGCTAGCTC 59.032 42.308 23.26 6.80 41.49 4.09
2396 2438 6.657966 TGTCAGTACTAGTTTTAGCTAGCTCA 59.342 38.462 23.26 7.73 41.49 4.26
2397 2439 7.339721 TGTCAGTACTAGTTTTAGCTAGCTCAT 59.660 37.037 23.26 6.42 41.49 2.90
2399 2441 9.058174 TCAGTACTAGTTTTAGCTAGCTCATAG 57.942 37.037 23.26 17.73 41.49 2.23
2400 2442 9.058174 CAGTACTAGTTTTAGCTAGCTCATAGA 57.942 37.037 23.26 0.00 41.49 1.98
2402 2444 9.059260 GTACTAGTTTTAGCTAGCTCATAGACT 57.941 37.037 23.26 18.83 41.49 3.24
2403 2445 8.528044 ACTAGTTTTAGCTAGCTCATAGACTT 57.472 34.615 23.26 3.46 41.49 3.01
2404 2446 8.973182 ACTAGTTTTAGCTAGCTCATAGACTTT 58.027 33.333 23.26 6.76 41.49 2.66
2419 2508 8.498054 TCATAGACTTTTCCATGAAATCAGAC 57.502 34.615 0.00 0.00 31.34 3.51
2423 2512 5.634118 ACTTTTCCATGAAATCAGACTCCA 58.366 37.500 0.00 0.00 31.34 3.86
2447 2536 1.226773 GCCAGCACCGAAATCATGC 60.227 57.895 0.00 0.00 39.74 4.06
2465 2554 4.641541 TCATGCCTGACAAACCAATCATAG 59.358 41.667 0.00 0.00 0.00 2.23
2471 2560 6.400568 CCTGACAAACCAATCATAGCAAATT 58.599 36.000 0.00 0.00 0.00 1.82
2473 2562 7.703621 CCTGACAAACCAATCATAGCAAATTAG 59.296 37.037 0.00 0.00 0.00 1.73
2476 2565 7.895759 ACAAACCAATCATAGCAAATTAGTGT 58.104 30.769 0.00 0.00 0.00 3.55
2506 2595 3.144657 TGCAGCTATGTATTCCCCATG 57.855 47.619 0.00 0.00 0.00 3.66
2517 2606 9.383519 CTATGTATTCCCCATGTTCACATATAC 57.616 37.037 0.00 0.00 34.26 1.47
2518 2607 7.387265 TGTATTCCCCATGTTCACATATACT 57.613 36.000 9.58 0.00 34.26 2.12
2519 2608 7.450074 TGTATTCCCCATGTTCACATATACTC 58.550 38.462 9.58 0.00 34.26 2.59
2520 2609 4.974645 TCCCCATGTTCACATATACTCC 57.025 45.455 0.00 0.00 34.26 3.85
2521 2610 3.323691 TCCCCATGTTCACATATACTCCG 59.676 47.826 0.00 0.00 34.26 4.63
2522 2611 3.071023 CCCCATGTTCACATATACTCCGT 59.929 47.826 0.00 0.00 34.26 4.69
2523 2612 4.282449 CCCCATGTTCACATATACTCCGTA 59.718 45.833 0.00 0.00 34.26 4.02
2593 2688 6.382821 TTTGTGTGTTTGTTCGTTCATTTC 57.617 33.333 0.00 0.00 0.00 2.17
2608 2703 8.373048 TCGTTCATTTCAGTTTGTATGTAGTT 57.627 30.769 0.00 0.00 0.00 2.24
2690 2785 1.561643 TTAGAGCACCCCACTCTCTG 58.438 55.000 0.00 0.00 43.42 3.35
2701 2796 1.193323 CACTCTCTGGGCTGACTCAT 58.807 55.000 0.00 0.00 0.00 2.90
2708 2803 3.295093 TCTGGGCTGACTCATTCTCTAG 58.705 50.000 0.00 0.00 0.00 2.43
2742 2837 7.852550 ATATCACTCTCTGAAATCTCCATCA 57.147 36.000 0.00 0.00 30.60 3.07
2743 2838 6.750660 ATCACTCTCTGAAATCTCCATCAT 57.249 37.500 0.00 0.00 30.60 2.45
2766 2861 1.110442 CTCACCTGAAGCCTCTCGAT 58.890 55.000 0.00 0.00 0.00 3.59
2803 2898 3.069443 GTCTCTCTCCATCTCAATCCCAC 59.931 52.174 0.00 0.00 0.00 4.61
2827 2922 3.644966 ACAGTGTTTCTCTCCCAACAA 57.355 42.857 0.00 0.00 34.70 2.83
2878 2973 0.955428 TCAACTCCAGAACGCCATGC 60.955 55.000 0.00 0.00 0.00 4.06
2880 2975 3.197790 CTCCAGAACGCCATGCCG 61.198 66.667 0.00 0.00 0.00 5.69
2906 3001 3.465403 CCGCCTGGCTGCTACTCT 61.465 66.667 17.92 0.00 0.00 3.24
2907 3002 2.105930 CGCCTGGCTGCTACTCTC 59.894 66.667 17.92 0.00 0.00 3.20
2908 3003 2.422231 CGCCTGGCTGCTACTCTCT 61.422 63.158 17.92 0.00 0.00 3.10
2909 3004 1.441311 GCCTGGCTGCTACTCTCTC 59.559 63.158 12.43 0.00 0.00 3.20
2910 3005 2.026945 GCCTGGCTGCTACTCTCTCC 62.027 65.000 12.43 0.00 0.00 3.71
2913 3008 0.255033 TGGCTGCTACTCTCTCCGTA 59.745 55.000 0.00 0.00 0.00 4.02
2914 3009 1.340697 TGGCTGCTACTCTCTCCGTAA 60.341 52.381 0.00 0.00 0.00 3.18
2915 3010 1.749634 GGCTGCTACTCTCTCCGTAAA 59.250 52.381 0.00 0.00 0.00 2.01
2916 3011 2.479901 GGCTGCTACTCTCTCCGTAAAC 60.480 54.545 0.00 0.00 0.00 2.01
2917 3012 2.424246 GCTGCTACTCTCTCCGTAAACT 59.576 50.000 0.00 0.00 0.00 2.66
2918 3013 3.626670 GCTGCTACTCTCTCCGTAAACTA 59.373 47.826 0.00 0.00 0.00 2.24
2919 3014 4.096081 GCTGCTACTCTCTCCGTAAACTAA 59.904 45.833 0.00 0.00 0.00 2.24
2920 3015 5.221087 GCTGCTACTCTCTCCGTAAACTAAT 60.221 44.000 0.00 0.00 0.00 1.73
2921 3016 6.017275 GCTGCTACTCTCTCCGTAAACTAATA 60.017 42.308 0.00 0.00 0.00 0.98
2922 3017 7.308710 GCTGCTACTCTCTCCGTAAACTAATAT 60.309 40.741 0.00 0.00 0.00 1.28
2923 3018 9.217278 CTGCTACTCTCTCCGTAAACTAATATA 57.783 37.037 0.00 0.00 0.00 0.86
2924 3019 9.565090 TGCTACTCTCTCCGTAAACTAATATAA 57.435 33.333 0.00 0.00 0.00 0.98
2928 3023 8.785946 ACTCTCTCCGTAAACTAATATAAGAGC 58.214 37.037 0.00 0.00 30.91 4.09
2929 3024 7.804712 TCTCTCCGTAAACTAATATAAGAGCG 58.195 38.462 0.00 0.00 0.00 5.03
2930 3025 7.443575 TCTCTCCGTAAACTAATATAAGAGCGT 59.556 37.037 0.00 0.00 0.00 5.07
2931 3026 7.934457 TCTCCGTAAACTAATATAAGAGCGTT 58.066 34.615 0.00 0.00 0.00 4.84
2932 3027 8.408601 TCTCCGTAAACTAATATAAGAGCGTTT 58.591 33.333 0.00 0.00 0.00 3.60
2933 3028 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2934 3029 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2935 3030 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2982 3077 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
2984 3079 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
3001 3096 3.810310 GAGTATCCTGTCAAGTCCCAG 57.190 52.381 0.00 0.00 0.00 4.45
3003 3098 1.134371 GTATCCTGTCAAGTCCCAGGC 60.134 57.143 0.77 0.00 46.43 4.85
3004 3099 1.903877 ATCCTGTCAAGTCCCAGGCG 61.904 60.000 0.77 0.00 46.43 5.52
3005 3100 2.743718 CTGTCAAGTCCCAGGCGT 59.256 61.111 0.00 0.00 0.00 5.68
3006 3101 1.071471 CTGTCAAGTCCCAGGCGTT 59.929 57.895 0.00 0.00 0.00 4.84
3007 3102 1.227823 TGTCAAGTCCCAGGCGTTG 60.228 57.895 0.00 0.00 0.00 4.10
3008 3103 1.227853 GTCAAGTCCCAGGCGTTGT 60.228 57.895 0.00 0.00 0.00 3.32
3009 3104 0.034337 GTCAAGTCCCAGGCGTTGTA 59.966 55.000 0.00 0.00 0.00 2.41
3010 3105 0.981183 TCAAGTCCCAGGCGTTGTAT 59.019 50.000 0.00 0.00 0.00 2.29
3011 3106 2.093869 GTCAAGTCCCAGGCGTTGTATA 60.094 50.000 0.00 0.00 0.00 1.47
3012 3107 2.093869 TCAAGTCCCAGGCGTTGTATAC 60.094 50.000 0.00 0.00 0.00 1.47
3013 3108 1.563924 AGTCCCAGGCGTTGTATACA 58.436 50.000 0.08 0.08 0.00 2.29
3014 3109 1.903860 AGTCCCAGGCGTTGTATACAA 59.096 47.619 14.35 14.35 0.00 2.41
3015 3110 2.093658 AGTCCCAGGCGTTGTATACAAG 60.094 50.000 18.56 13.15 36.39 3.16
3016 3111 1.014352 CCCAGGCGTTGTATACAAGC 58.986 55.000 18.56 20.58 36.39 4.01
3017 3112 1.406887 CCCAGGCGTTGTATACAAGCT 60.407 52.381 25.53 15.91 36.39 3.74
3018 3113 2.356135 CCAGGCGTTGTATACAAGCTT 58.644 47.619 25.53 20.37 36.39 3.74
3019 3114 2.095853 CCAGGCGTTGTATACAAGCTTG 59.904 50.000 26.74 26.74 37.12 4.01
3020 3115 3.000041 CAGGCGTTGTATACAAGCTTGA 59.000 45.455 32.50 16.27 38.27 3.02
3021 3116 3.000727 AGGCGTTGTATACAAGCTTGAC 58.999 45.455 32.50 20.03 36.39 3.18
3022 3117 2.222729 GGCGTTGTATACAAGCTTGACG 60.223 50.000 32.50 27.50 36.39 4.35
3023 3118 2.664568 GCGTTGTATACAAGCTTGACGA 59.335 45.455 32.50 16.93 36.39 4.20
3038 3133 1.208535 TGACGAGTTTCAGTTGGGTGT 59.791 47.619 0.00 0.00 0.00 4.16
3050 3145 2.642807 AGTTGGGTGTAGCAGTTATGGT 59.357 45.455 0.00 0.00 40.99 3.55
3079 3174 1.071542 TCAACTTGATCCAACGGCTCA 59.928 47.619 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.776662 ACTCATAAGAGGGTGCGCTA 58.223 50.000 9.73 0.00 46.44 4.26
53 54 1.409064 TGCTACTCATAAGAGGGTGCG 59.591 52.381 0.00 0.00 46.44 5.34
57 58 5.477510 GTGATGATGCTACTCATAAGAGGG 58.522 45.833 0.00 0.00 46.44 4.30
73 74 2.423373 GCAATACTGGTGGGGTGATGAT 60.423 50.000 0.00 0.00 0.00 2.45
76 77 0.107214 CGCAATACTGGTGGGGTGAT 60.107 55.000 0.00 0.00 0.00 3.06
176 180 5.646793 GGGAAGGAGGTGTTACTTAAATCAC 59.353 44.000 0.00 0.00 0.00 3.06
385 389 2.544486 GCAGTGTCTTTTTCAGCCCAAG 60.544 50.000 0.00 0.00 0.00 3.61
406 410 4.461405 CAGAAAGTGAGCGTTGAGAAATG 58.539 43.478 0.00 0.00 0.00 2.32
432 436 5.455183 CCTTGATATGTATTGTCTGGCCTCA 60.455 44.000 3.32 0.00 0.00 3.86
491 495 5.990120 TGACTCACTCATTCTGATGAAGA 57.010 39.130 0.00 0.00 41.55 2.87
542 546 5.280062 GGAGTAAGGGTTTGTAGAGAAGCTT 60.280 44.000 0.00 0.00 0.00 3.74
584 588 3.545624 GCGCTATTGTCTCATGCTGAAAG 60.546 47.826 0.00 0.00 0.00 2.62
765 800 6.405065 CCGGTATGTACAAGCAGTAGTTCTTA 60.405 42.308 0.00 0.00 32.19 2.10
769 804 3.677976 GCCGGTATGTACAAGCAGTAGTT 60.678 47.826 1.90 0.00 32.19 2.24
781 816 3.018149 GGAAACAAATGGCCGGTATGTA 58.982 45.455 1.90 0.00 0.00 2.29
823 858 3.829601 AGTCTGTGCTTAGCAGTAGTTCT 59.170 43.478 7.34 9.39 40.08 3.01
825 860 4.608948 AAGTCTGTGCTTAGCAGTAGTT 57.391 40.909 7.34 2.45 40.08 2.24
827 862 3.124297 GCAAAGTCTGTGCTTAGCAGTAG 59.876 47.826 7.34 9.59 40.08 2.57
828 863 3.067106 GCAAAGTCTGTGCTTAGCAGTA 58.933 45.455 7.34 0.00 40.08 2.74
829 864 1.876156 GCAAAGTCTGTGCTTAGCAGT 59.124 47.619 7.34 0.00 40.08 4.40
830 865 1.875514 TGCAAAGTCTGTGCTTAGCAG 59.124 47.619 16.07 0.00 40.08 4.24
831 866 1.965935 TGCAAAGTCTGTGCTTAGCA 58.034 45.000 16.07 1.39 42.69 3.49
832 867 2.415090 CCATGCAAAGTCTGTGCTTAGC 60.415 50.000 16.07 0.00 42.69 3.09
871 906 1.843753 CGTTTCGCCACAAAGTTTGTC 59.156 47.619 18.34 7.73 43.23 3.18
886 921 5.033507 GGAGATAAGAGTTACGTCCGTTTC 58.966 45.833 0.00 0.00 0.00 2.78
887 922 4.460382 TGGAGATAAGAGTTACGTCCGTTT 59.540 41.667 0.00 0.00 0.00 3.60
890 925 4.599047 CTTGGAGATAAGAGTTACGTCCG 58.401 47.826 0.00 0.00 0.00 4.79
894 929 4.030134 ACGCTTGGAGATAAGAGTTACG 57.970 45.455 0.00 0.00 37.40 3.18
923 958 5.945784 TGCTCAAATCCTTTTATAGCACTGT 59.054 36.000 0.00 0.00 37.75 3.55
983 1018 3.602491 CGTCATACTAATGCTTTCTGCGC 60.602 47.826 0.00 0.00 46.63 6.09
987 1022 6.146837 GCATGATCGTCATACTAATGCTTTCT 59.853 38.462 0.00 0.00 34.28 2.52
995 1030 4.022329 ACATCCGCATGATCGTCATACTAA 60.022 41.667 0.00 0.00 34.28 2.24
1270 1307 4.346730 TGATCCCACTGCAAAAGAATGAT 58.653 39.130 0.00 0.00 0.00 2.45
1271 1308 3.760151 CTGATCCCACTGCAAAAGAATGA 59.240 43.478 0.00 0.00 0.00 2.57
1272 1309 3.119245 CCTGATCCCACTGCAAAAGAATG 60.119 47.826 0.00 0.00 0.00 2.67
1273 1310 3.094572 CCTGATCCCACTGCAAAAGAAT 58.905 45.455 0.00 0.00 0.00 2.40
1274 1311 2.158475 ACCTGATCCCACTGCAAAAGAA 60.158 45.455 0.00 0.00 0.00 2.52
1276 1313 1.542915 CACCTGATCCCACTGCAAAAG 59.457 52.381 0.00 0.00 0.00 2.27
1437 1479 3.390521 TGATGCTTCGGAGGCGGT 61.391 61.111 7.63 0.00 0.00 5.68
1647 1689 3.741476 GCTTGCTTGGAGCCGTGG 61.741 66.667 0.00 0.00 41.51 4.94
1704 1746 0.393077 CGTGTGGTTCCTTGTCTCCT 59.607 55.000 0.00 0.00 0.00 3.69
1724 1766 3.268603 CCACAGACGTTGCGCACA 61.269 61.111 11.12 0.00 0.00 4.57
1755 1797 3.956317 AAAACGGTGGCGGCGAAC 61.956 61.111 12.98 7.99 0.00 3.95
1822 1864 2.183555 CACGTAGCGGAGGGGTTC 59.816 66.667 0.00 0.00 0.00 3.62
1950 1992 1.663695 CAACAAGTTGGACACGGAGT 58.336 50.000 7.96 0.00 37.98 3.85
2026 2068 4.899239 CGCCTCATCCCAGTCGCC 62.899 72.222 0.00 0.00 0.00 5.54
2029 2071 0.824759 AAGTACGCCTCATCCCAGTC 59.175 55.000 0.00 0.00 0.00 3.51
2043 2085 1.654105 CCGTTCAGCATCACGAAGTAC 59.346 52.381 3.41 0.00 41.61 2.73
2050 2092 1.154205 CGGGATCCGTTCAGCATCAC 61.154 60.000 5.45 0.00 42.73 3.06
2109 2151 0.324738 TCACCTCCTAGAGCCACAGG 60.325 60.000 0.00 0.00 0.00 4.00
2129 2171 0.387367 CGTACTTGCTGCTCGTGTCT 60.387 55.000 0.00 0.00 0.00 3.41
2307 2349 9.741647 ACGCATCATCACAATATACTATATCTG 57.258 33.333 0.00 0.00 0.00 2.90
2309 2351 9.521503 ACACGCATCATCACAATATACTATATC 57.478 33.333 0.00 0.00 0.00 1.63
2310 2352 9.521503 GACACGCATCATCACAATATACTATAT 57.478 33.333 0.00 0.00 0.00 0.86
2311 2353 8.519526 TGACACGCATCATCACAATATACTATA 58.480 33.333 0.00 0.00 0.00 1.31
2312 2354 7.378181 TGACACGCATCATCACAATATACTAT 58.622 34.615 0.00 0.00 0.00 2.12
2313 2355 6.744112 TGACACGCATCATCACAATATACTA 58.256 36.000 0.00 0.00 0.00 1.82
2314 2356 5.600696 TGACACGCATCATCACAATATACT 58.399 37.500 0.00 0.00 0.00 2.12
2315 2357 5.905480 TGACACGCATCATCACAATATAC 57.095 39.130 0.00 0.00 0.00 1.47
2357 2399 2.771089 ACTGACACGCATCATTTCTGT 58.229 42.857 0.00 0.00 0.00 3.41
2358 2400 3.928992 AGTACTGACACGCATCATTTCTG 59.071 43.478 0.00 0.00 0.00 3.02
2375 2417 9.059260 GTCTATGAGCTAGCTAAAACTAGTACT 57.941 37.037 19.38 0.00 41.49 2.73
2378 2420 8.528044 AAGTCTATGAGCTAGCTAAAACTAGT 57.472 34.615 19.38 2.17 41.49 2.57
2388 2430 5.605534 TCATGGAAAAGTCTATGAGCTAGC 58.394 41.667 6.62 6.62 44.30 3.42
2394 2436 8.324306 AGTCTGATTTCATGGAAAAGTCTATGA 58.676 33.333 0.00 0.00 46.62 2.15
2395 2437 8.503458 AGTCTGATTTCATGGAAAAGTCTATG 57.497 34.615 0.00 0.00 42.56 2.23
2396 2438 7.772757 GGAGTCTGATTTCATGGAAAAGTCTAT 59.227 37.037 0.00 0.00 35.11 1.98
2397 2439 7.106239 GGAGTCTGATTTCATGGAAAAGTCTA 58.894 38.462 0.00 0.00 35.11 2.59
2399 2441 5.707298 TGGAGTCTGATTTCATGGAAAAGTC 59.293 40.000 0.00 0.00 35.11 3.01
2400 2442 5.634118 TGGAGTCTGATTTCATGGAAAAGT 58.366 37.500 0.00 0.00 35.11 2.66
2402 2444 5.105635 GCATGGAGTCTGATTTCATGGAAAA 60.106 40.000 19.39 0.00 35.11 2.29
2403 2445 4.400251 GCATGGAGTCTGATTTCATGGAAA 59.600 41.667 19.39 0.00 36.62 3.13
2404 2446 3.949754 GCATGGAGTCTGATTTCATGGAA 59.050 43.478 19.39 0.00 36.62 3.53
2447 2536 5.389859 TTTGCTATGATTGGTTTGTCAGG 57.610 39.130 0.00 0.00 0.00 3.86
2493 2582 7.988937 AGTATATGTGAACATGGGGAATACAT 58.011 34.615 6.19 2.05 37.15 2.29
2494 2583 7.387265 AGTATATGTGAACATGGGGAATACA 57.613 36.000 6.19 0.00 37.15 2.29
2495 2584 6.879458 GGAGTATATGTGAACATGGGGAATAC 59.121 42.308 6.19 5.86 37.15 1.89
2496 2585 6.295632 CGGAGTATATGTGAACATGGGGAATA 60.296 42.308 6.19 0.00 37.15 1.75
2497 2586 5.513094 CGGAGTATATGTGAACATGGGGAAT 60.513 44.000 6.19 0.00 37.15 3.01
2498 2587 4.202315 CGGAGTATATGTGAACATGGGGAA 60.202 45.833 6.19 0.00 37.15 3.97
2499 2588 3.323691 CGGAGTATATGTGAACATGGGGA 59.676 47.826 6.19 0.00 37.15 4.81
2544 2633 9.601217 AAAAGTGTCTATATACATCCAACTCAC 57.399 33.333 0.00 0.00 0.00 3.51
2571 2666 5.461526 TGAAATGAACGAACAAACACACAA 58.538 33.333 0.00 0.00 0.00 3.33
2626 2721 6.442952 CCTCCGTTCACAAATGTTAAATTGA 58.557 36.000 4.46 0.00 0.00 2.57
2628 2723 5.536916 TCCCTCCGTTCACAAATGTTAAATT 59.463 36.000 0.00 0.00 0.00 1.82
2633 2728 2.158667 ACTCCCTCCGTTCACAAATGTT 60.159 45.455 0.00 0.00 0.00 2.71
2690 2785 1.759445 TGCTAGAGAATGAGTCAGCCC 59.241 52.381 0.00 0.00 0.00 5.19
2738 2833 3.118334 AGGCTTCAGGTGAGAGAATGATG 60.118 47.826 0.00 0.00 0.00 3.07
2742 2837 2.765699 GAGAGGCTTCAGGTGAGAGAAT 59.234 50.000 0.00 0.00 0.00 2.40
2743 2838 2.175202 GAGAGGCTTCAGGTGAGAGAA 58.825 52.381 0.00 0.00 0.00 2.87
2766 2861 0.678366 GAGACACCGAGAGCTCAGGA 60.678 60.000 28.05 0.00 0.00 3.86
2803 2898 3.475566 TGGGAGAGAAACACTGTTGAG 57.524 47.619 0.00 0.00 0.00 3.02
2827 2922 2.448582 TTGACGTGGGCAGGAAGGT 61.449 57.895 0.00 0.00 0.00 3.50
2903 2998 7.958567 CGCTCTTATATTAGTTTACGGAGAGAG 59.041 40.741 0.00 0.00 32.02 3.20
2904 2999 7.443575 ACGCTCTTATATTAGTTTACGGAGAGA 59.556 37.037 0.00 0.00 32.02 3.10
2905 3000 7.583230 ACGCTCTTATATTAGTTTACGGAGAG 58.417 38.462 0.00 0.00 33.16 3.20
2906 3001 7.502120 ACGCTCTTATATTAGTTTACGGAGA 57.498 36.000 0.00 0.00 0.00 3.71
2907 3002 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2908 3003 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2909 3004 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2956 3051 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
2958 3053 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2988 3083 1.071471 AACGCCTGGGACTTGACAG 59.929 57.895 0.00 0.00 34.54 3.51
2989 3084 1.227823 CAACGCCTGGGACTTGACA 60.228 57.895 0.00 0.00 0.00 3.58
2990 3085 0.034337 TACAACGCCTGGGACTTGAC 59.966 55.000 0.00 0.00 0.00 3.18
2991 3086 0.981183 ATACAACGCCTGGGACTTGA 59.019 50.000 0.00 0.00 0.00 3.02
2992 3087 2.277084 GTATACAACGCCTGGGACTTG 58.723 52.381 0.00 0.00 0.00 3.16
2993 3088 1.903860 TGTATACAACGCCTGGGACTT 59.096 47.619 2.20 0.00 0.00 3.01
2994 3089 1.563924 TGTATACAACGCCTGGGACT 58.436 50.000 2.20 0.00 0.00 3.85
2995 3090 2.277084 CTTGTATACAACGCCTGGGAC 58.723 52.381 14.35 0.00 0.00 4.46
2996 3091 1.406341 GCTTGTATACAACGCCTGGGA 60.406 52.381 14.35 0.00 0.00 4.37
2997 3092 1.014352 GCTTGTATACAACGCCTGGG 58.986 55.000 14.35 4.50 0.00 4.45
2998 3093 2.024176 AGCTTGTATACAACGCCTGG 57.976 50.000 24.22 13.22 33.53 4.45
2999 3094 3.000041 TCAAGCTTGTATACAACGCCTG 59.000 45.455 25.19 22.47 33.53 4.85
3000 3095 3.000727 GTCAAGCTTGTATACAACGCCT 58.999 45.455 25.19 15.67 33.53 5.52
3001 3096 2.222729 CGTCAAGCTTGTATACAACGCC 60.223 50.000 25.19 13.62 33.53 5.68
3002 3097 2.664568 TCGTCAAGCTTGTATACAACGC 59.335 45.455 25.19 22.15 33.37 4.84
3003 3098 3.918591 ACTCGTCAAGCTTGTATACAACG 59.081 43.478 25.19 23.85 0.00 4.10
3004 3099 5.840940 AACTCGTCAAGCTTGTATACAAC 57.159 39.130 25.19 14.03 0.00 3.32
3005 3100 5.986741 TGAAACTCGTCAAGCTTGTATACAA 59.013 36.000 25.19 17.16 0.00 2.41
3006 3101 5.534407 TGAAACTCGTCAAGCTTGTATACA 58.466 37.500 25.19 0.08 0.00 2.29
3007 3102 5.634020 ACTGAAACTCGTCAAGCTTGTATAC 59.366 40.000 25.19 15.42 0.00 1.47
3008 3103 5.779922 ACTGAAACTCGTCAAGCTTGTATA 58.220 37.500 25.19 11.04 0.00 1.47
3009 3104 4.632153 ACTGAAACTCGTCAAGCTTGTAT 58.368 39.130 25.19 5.71 0.00 2.29
3010 3105 4.054780 ACTGAAACTCGTCAAGCTTGTA 57.945 40.909 25.19 10.13 0.00 2.41
3011 3106 2.906354 ACTGAAACTCGTCAAGCTTGT 58.094 42.857 25.19 4.69 0.00 3.16
3012 3107 3.546815 CCAACTGAAACTCGTCAAGCTTG 60.547 47.826 20.81 20.81 0.00 4.01
3013 3108 2.614057 CCAACTGAAACTCGTCAAGCTT 59.386 45.455 0.00 0.00 0.00 3.74
3014 3109 2.213499 CCAACTGAAACTCGTCAAGCT 58.787 47.619 0.00 0.00 0.00 3.74
3015 3110 1.264288 CCCAACTGAAACTCGTCAAGC 59.736 52.381 0.00 0.00 0.00 4.01
3016 3111 2.287915 CACCCAACTGAAACTCGTCAAG 59.712 50.000 0.00 0.00 0.00 3.02
3017 3112 2.285083 CACCCAACTGAAACTCGTCAA 58.715 47.619 0.00 0.00 0.00 3.18
3018 3113 1.208535 ACACCCAACTGAAACTCGTCA 59.791 47.619 0.00 0.00 0.00 4.35
3019 3114 1.949465 ACACCCAACTGAAACTCGTC 58.051 50.000 0.00 0.00 0.00 4.20
3020 3115 2.805657 GCTACACCCAACTGAAACTCGT 60.806 50.000 0.00 0.00 0.00 4.18
3021 3116 1.798813 GCTACACCCAACTGAAACTCG 59.201 52.381 0.00 0.00 0.00 4.18
3022 3117 2.808543 CTGCTACACCCAACTGAAACTC 59.191 50.000 0.00 0.00 0.00 3.01
3023 3118 2.172717 ACTGCTACACCCAACTGAAACT 59.827 45.455 0.00 0.00 0.00 2.66
3038 3133 7.717875 AGTTGAACTGTTTTACCATAACTGCTA 59.282 33.333 0.00 0.00 0.00 3.49
3050 3145 6.459024 CCGTTGGATCAAGTTGAACTGTTTTA 60.459 38.462 10.14 0.00 0.00 1.52
3079 3174 2.796557 TGTGAGAACGAGGAGTGATCT 58.203 47.619 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.