Multiple sequence alignment - TraesCS4B01G361100

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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 TraesCS4B01G361100 chr4B 100.000 2565 0 0 1 2565 650703395 650700831 0.000000e+00 4737.0
1 TraesCS4B01G361100 chr4B 100.000 316 0 0 2901 3216 650700495 650700180 4.620000e-163 584.0
2 TraesCS4B01G361100 chr4B 83.045 578 59 19 942 1481 650707066 650706490 3.730000e-134 488.0
3 TraesCS4B01G361100 chr4B 84.840 376 34 10 1721 2084 650706304 650705940 1.100000e-94 357.0
4 TraesCS4B01G361100 chr4B 99.465 187 1 0 2379 2565 650700495 650700309 1.100000e-89 340.0
5 TraesCS4B01G361100 chr4B 99.465 187 1 0 2901 3087 650701017 650700831 1.100000e-89 340.0
6 TraesCS4B01G361100 chr4D 90.040 1486 68 22 881 2307 504116095 504114631 0.000000e+00 1851.0
7 TraesCS4B01G361100 chr4D 90.909 616 47 6 1 615 504116979 504116372 0.000000e+00 819.0
8 TraesCS4B01G361100 chr4D 84.965 572 46 18 942 1479 504178399 504177834 7.850000e-151 544.0
9 TraesCS4B01G361100 chr4D 82.447 188 18 4 2329 2516 504114644 504114472 2.000000e-32 150.0
10 TraesCS4B01G361100 chr4D 93.151 73 5 0 586 658 241139365 241139293 1.220000e-19 108.0
11 TraesCS4B01G361100 chr5A 88.219 1477 101 36 790 2226 688832339 688830896 0.000000e+00 1696.0
12 TraesCS4B01G361100 chr5A 90.092 757 56 10 1 751 688833082 688832339 0.000000e+00 965.0
13 TraesCS4B01G361100 chr5A 83.750 560 55 16 936 1480 688841249 688840711 6.200000e-137 497.0
14 TraesCS4B01G361100 chr5A 87.079 178 18 3 3042 3216 688830640 688830465 2.530000e-46 196.0
15 TraesCS4B01G361100 chr5A 85.638 188 24 3 2329 2516 688830860 688830676 9.100000e-46 195.0
16 TraesCS4B01G361100 chr5A 80.978 184 22 9 2096 2274 688840150 688839975 2.010000e-27 134.0
17 TraesCS4B01G361100 chr5A 83.333 138 22 1 2901 3038 688830812 688830676 3.370000e-25 126.0
18 TraesCS4B01G361100 chr5A 82.524 103 12 1 469 565 688841376 688841274 5.720000e-13 86.1
19 TraesCS4B01G361100 chr3B 77.636 939 128 50 1093 1990 72478137 72477240 2.230000e-136 496.0
20 TraesCS4B01G361100 chr3D 77.254 954 141 51 1093 2003 46471864 46470944 1.040000e-134 490.0
21 TraesCS4B01G361100 chr3A 77.361 932 128 58 1093 1990 57886849 57885967 2.900000e-130 475.0
22 TraesCS4B01G361100 chr5B 83.636 330 45 8 1093 1415 212786359 212786032 5.210000e-78 302.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G361100 chr4B 650700180 650703395 3215 True 1500.250000 4737 99.732500 1 3216 4 chr4B.!!$R1 3215
1 TraesCS4B01G361100 chr4B 650705940 650707066 1126 True 422.500000 488 83.942500 942 2084 2 chr4B.!!$R2 1142
2 TraesCS4B01G361100 chr4D 504114472 504116979 2507 True 940.000000 1851 87.798667 1 2516 3 chr4D.!!$R3 2515
3 TraesCS4B01G361100 chr4D 504177834 504178399 565 True 544.000000 544 84.965000 942 1479 1 chr4D.!!$R2 537
4 TraesCS4B01G361100 chr5A 688830465 688833082 2617 True 635.600000 1696 86.872200 1 3216 5 chr5A.!!$R1 3215
5 TraesCS4B01G361100 chr5A 688839975 688841376 1401 True 239.033333 497 82.417333 469 2274 3 chr5A.!!$R2 1805
6 TraesCS4B01G361100 chr3B 72477240 72478137 897 True 496.000000 496 77.636000 1093 1990 1 chr3B.!!$R1 897
7 TraesCS4B01G361100 chr3D 46470944 46471864 920 True 490.000000 490 77.254000 1093 2003 1 chr3D.!!$R1 910
8 TraesCS4B01G361100 chr3A 57885967 57886849 882 True 475.000000 475 77.361000 1093 1990 1 chr3A.!!$R1 897

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
773 827 0.443869 GCGTGATGCGTGATGTCTTT 59.556 50.0 0.0 0.0 43.66 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2430 2733 0.394565 ATCTAGTTGGATCCTGCGGC 59.605 55.0 14.23 0.0 0.0 6.53 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
47 48 2.047061 AGGGTACTGCAGTGACTTGAA 58.953 47.619 29.57 4.12 0.00 2.69
48 49 2.037772 AGGGTACTGCAGTGACTTGAAG 59.962 50.000 29.57 0.00 0.00 3.02
57 58 4.156556 TGCAGTGACTTGAAGGAATATTGC 59.843 41.667 0.00 0.00 0.00 3.56
83 84 7.040617 CGTAGCCTTGACTTGGATAGTATAGAA 60.041 40.741 0.00 0.00 37.17 2.10
89 90 9.553064 CTTGACTTGGATAGTATAGAAAGCATT 57.447 33.333 0.00 0.00 37.17 3.56
90 91 9.905713 TTGACTTGGATAGTATAGAAAGCATTT 57.094 29.630 0.00 0.00 38.08 2.32
128 129 9.635520 GGTCCTTTATTTAGTTTTAGAAAAGGC 57.364 33.333 6.15 2.73 40.70 4.35
179 180 6.756542 ACATGTTTTCTAAAAGGTGAAACTGC 59.243 34.615 0.00 0.00 36.74 4.40
188 189 8.257306 TCTAAAAGGTGAAACTGCTTTTGAATT 58.743 29.630 0.00 0.00 38.29 2.17
325 332 5.456921 AAGGATACCACCTTGACATGATT 57.543 39.130 0.00 0.00 46.85 2.57
340 347 3.275143 CATGATTGGGTAAGTGGCGTAA 58.725 45.455 0.00 0.00 0.00 3.18
346 353 2.814919 TGGGTAAGTGGCGTAAATTGTG 59.185 45.455 0.00 0.00 0.00 3.33
368 375 3.143728 GCCGAAAAGGTAGAGGTTGAAA 58.856 45.455 0.00 0.00 43.70 2.69
372 379 5.511888 CCGAAAAGGTAGAGGTTGAAACCTA 60.512 44.000 14.66 0.00 46.99 3.08
388 395 3.920231 ACCTAATGCATGAGCTCTTCA 57.080 42.857 16.19 10.17 42.74 3.02
418 425 0.532862 ACAACCTGCCTGTCTTCACG 60.533 55.000 0.00 0.00 0.00 4.35
436 443 1.781676 GATATCCCTCCCTCCCGGA 59.218 63.158 0.73 0.00 38.83 5.14
567 582 8.408043 TTCTCAGCTAAAATCCATTTCTTTCA 57.592 30.769 0.00 0.00 32.27 2.69
612 627 6.569179 ACTGAATGCGGTAACTATGTTTTT 57.431 33.333 0.00 0.00 0.00 1.94
621 663 7.175293 TGCGGTAACTATGTTTTTCAAATACCT 59.825 33.333 0.00 0.00 0.00 3.08
751 805 4.597404 TTTTGTGGTGCAATATGCTCAA 57.403 36.364 3.78 2.33 45.31 3.02
752 806 4.597404 TTTGTGGTGCAATATGCTCAAA 57.403 36.364 3.78 7.41 45.31 2.69
753 807 4.804868 TTGTGGTGCAATATGCTCAAAT 57.195 36.364 3.78 0.00 45.31 2.32
754 808 4.112716 TGTGGTGCAATATGCTCAAATG 57.887 40.909 3.78 0.00 45.31 2.32
755 809 2.861935 GTGGTGCAATATGCTCAAATGC 59.138 45.455 3.78 0.00 45.31 3.56
756 810 2.121786 GGTGCAATATGCTCAAATGCG 58.878 47.619 3.78 0.00 45.31 4.73
758 812 2.532723 GTGCAATATGCTCAAATGCGTG 59.467 45.455 3.78 0.00 45.31 5.34
759 813 2.422832 TGCAATATGCTCAAATGCGTGA 59.577 40.909 3.78 0.00 45.31 4.35
760 814 3.067040 TGCAATATGCTCAAATGCGTGAT 59.933 39.130 3.78 0.00 45.31 3.06
761 815 3.424198 GCAATATGCTCAAATGCGTGATG 59.576 43.478 0.00 0.00 40.96 3.07
762 816 2.761392 TATGCTCAAATGCGTGATGC 57.239 45.000 0.00 0.00 46.70 3.91
771 825 3.786101 GCGTGATGCGTGATGTCT 58.214 55.556 0.00 0.00 43.66 3.41
772 826 2.081526 GCGTGATGCGTGATGTCTT 58.918 52.632 0.00 0.00 43.66 3.01
773 827 0.443869 GCGTGATGCGTGATGTCTTT 59.556 50.000 0.00 0.00 43.66 2.52
774 828 1.135972 GCGTGATGCGTGATGTCTTTT 60.136 47.619 0.00 0.00 43.66 2.27
775 829 2.665519 GCGTGATGCGTGATGTCTTTTT 60.666 45.455 0.00 0.00 43.66 1.94
948 1035 1.478105 CGGCATGATCGATCTCCCATA 59.522 52.381 25.02 5.16 0.00 2.74
1014 1101 4.014406 CAACACACCTATAAAACCCTCCC 58.986 47.826 0.00 0.00 0.00 4.30
1016 1103 2.237893 CACACCTATAAAACCCTCCCGT 59.762 50.000 0.00 0.00 0.00 5.28
1050 1164 1.147376 CACCACCAGTTCACCGGAA 59.853 57.895 9.46 0.00 0.00 4.30
1051 1165 0.884704 CACCACCAGTTCACCGGAAG 60.885 60.000 9.46 0.00 32.62 3.46
1067 1183 5.017490 ACCGGAAGAAGAAGAAGATAGACA 58.983 41.667 9.46 0.00 0.00 3.41
1086 1225 0.898789 ACTGAACCACCTCGACCGAT 60.899 55.000 0.00 0.00 0.00 4.18
1869 2101 3.530910 CTGACGCTCGGGTTTGGGT 62.531 63.158 0.00 0.00 0.00 4.51
2175 2464 1.536766 TGTGTATGCTGAGTGCTTTGC 59.463 47.619 0.00 0.00 43.37 3.68
2178 2467 2.289882 TGTATGCTGAGTGCTTTGCTCT 60.290 45.455 0.00 0.00 43.37 4.09
2194 2483 6.148480 GCTTTGCTCTAGGGTATACATCAATG 59.852 42.308 5.01 0.00 0.00 2.82
2314 2603 7.804614 TTAAATACAACAAATGGTTCGATGC 57.195 32.000 0.00 0.00 37.72 3.91
2315 2604 5.384063 AATACAACAAATGGTTCGATGCA 57.616 34.783 0.00 0.00 37.72 3.96
2316 2605 3.724508 ACAACAAATGGTTCGATGCAA 57.275 38.095 0.00 0.00 37.72 4.08
2317 2606 4.052159 ACAACAAATGGTTCGATGCAAA 57.948 36.364 0.00 0.00 37.72 3.68
2318 2607 4.437239 ACAACAAATGGTTCGATGCAAAA 58.563 34.783 0.00 0.00 37.72 2.44
2319 2608 4.872691 ACAACAAATGGTTCGATGCAAAAA 59.127 33.333 0.00 0.00 37.72 1.94
2383 2672 9.395707 GATACATGTACTTTTGTAGGTAGATCG 57.604 37.037 7.96 0.00 35.28 3.69
2403 2706 0.748450 AAACTTCACGGACCTCGACA 59.252 50.000 0.00 0.00 42.43 4.35
2404 2707 0.031721 AACTTCACGGACCTCGACAC 59.968 55.000 0.00 0.00 42.43 3.67
2405 2708 1.105167 ACTTCACGGACCTCGACACA 61.105 55.000 0.00 0.00 42.43 3.72
2406 2709 0.663568 CTTCACGGACCTCGACACAC 60.664 60.000 0.00 0.00 42.43 3.82
2407 2710 2.049433 CACGGACCTCGACACACC 60.049 66.667 0.00 0.00 42.43 4.16
2409 2712 4.415332 CGGACCTCGACACACCGG 62.415 72.222 0.00 0.00 42.43 5.28
2410 2713 4.736896 GGACCTCGACACACCGGC 62.737 72.222 0.00 0.00 0.00 6.13
2411 2714 3.986006 GACCTCGACACACCGGCA 61.986 66.667 0.00 0.00 0.00 5.69
2412 2715 4.295119 ACCTCGACACACCGGCAC 62.295 66.667 0.00 0.00 0.00 5.01
2456 2759 2.708386 GATCCAACTAGATCCGACGG 57.292 55.000 7.84 7.84 37.31 4.79
2472 2775 2.669113 CGACGGAACATAACCTTCACGA 60.669 50.000 0.00 0.00 0.00 4.35
2480 2783 1.344065 TAACCTTCACGAGCCCTTCA 58.656 50.000 0.00 0.00 0.00 3.02
2481 2784 0.472471 AACCTTCACGAGCCCTTCAA 59.528 50.000 0.00 0.00 0.00 2.69
2482 2785 0.693049 ACCTTCACGAGCCCTTCAAT 59.307 50.000 0.00 0.00 0.00 2.57
2517 2820 3.972227 CCGAGCAGGGACAAAGTG 58.028 61.111 0.00 0.00 35.97 3.16
2919 3254 2.365408 AGATCGAAACTTCACGGACC 57.635 50.000 0.00 0.00 0.00 4.46
2920 3255 1.893801 AGATCGAAACTTCACGGACCT 59.106 47.619 0.00 0.00 0.00 3.85
2921 3256 2.094649 AGATCGAAACTTCACGGACCTC 60.095 50.000 0.00 0.00 0.00 3.85
2922 3257 0.039798 TCGAAACTTCACGGACCTCG 60.040 55.000 0.00 0.00 45.88 4.63
2923 3258 0.039798 CGAAACTTCACGGACCTCGA 60.040 55.000 0.00 0.00 42.43 4.04
2924 3259 1.416373 GAAACTTCACGGACCTCGAC 58.584 55.000 0.00 0.00 42.43 4.20
2925 3260 0.748450 AAACTTCACGGACCTCGACA 59.252 50.000 0.00 0.00 42.43 4.35
2926 3261 0.031721 AACTTCACGGACCTCGACAC 59.968 55.000 0.00 0.00 42.43 3.67
2927 3262 1.105167 ACTTCACGGACCTCGACACA 61.105 55.000 0.00 0.00 42.43 3.72
2928 3263 0.663568 CTTCACGGACCTCGACACAC 60.664 60.000 0.00 0.00 42.43 3.82
2929 3264 2.049433 CACGGACCTCGACACACC 60.049 66.667 0.00 0.00 42.43 4.16
2931 3266 4.415332 CGGACCTCGACACACCGG 62.415 72.222 0.00 0.00 42.43 5.28
2932 3267 4.736896 GGACCTCGACACACCGGC 62.737 72.222 0.00 0.00 0.00 6.13
2933 3268 3.986006 GACCTCGACACACCGGCA 61.986 66.667 0.00 0.00 0.00 5.69
2934 3269 4.295119 ACCTCGACACACCGGCAC 62.295 66.667 0.00 0.00 0.00 5.01
2978 3313 2.708386 GATCCAACTAGATCCGACGG 57.292 55.000 7.84 7.84 37.31 4.79
2979 3314 2.228059 GATCCAACTAGATCCGACGGA 58.772 52.381 20.85 20.85 37.31 4.69
2980 3315 2.133281 TCCAACTAGATCCGACGGAA 57.867 50.000 22.55 3.25 34.34 4.30
2981 3316 1.747355 TCCAACTAGATCCGACGGAAC 59.253 52.381 22.55 18.92 34.34 3.62
2982 3317 1.475280 CCAACTAGATCCGACGGAACA 59.525 52.381 22.55 7.94 34.34 3.18
2983 3318 2.100916 CCAACTAGATCCGACGGAACAT 59.899 50.000 22.55 12.11 34.34 2.71
2984 3319 3.317149 CCAACTAGATCCGACGGAACATA 59.683 47.826 22.55 12.61 34.34 2.29
2985 3320 4.202080 CCAACTAGATCCGACGGAACATAA 60.202 45.833 22.55 7.15 34.34 1.90
2986 3321 4.564940 ACTAGATCCGACGGAACATAAC 57.435 45.455 22.55 8.34 34.34 1.89
2987 3322 2.884894 AGATCCGACGGAACATAACC 57.115 50.000 22.55 4.48 34.34 2.85
2988 3323 2.385803 AGATCCGACGGAACATAACCT 58.614 47.619 22.55 0.45 34.34 3.50
2989 3324 2.764572 AGATCCGACGGAACATAACCTT 59.235 45.455 22.55 0.00 34.34 3.50
2990 3325 2.660189 TCCGACGGAACATAACCTTC 57.340 50.000 15.79 0.00 0.00 3.46
2991 3326 1.894466 TCCGACGGAACATAACCTTCA 59.106 47.619 15.79 0.00 0.00 3.02
2992 3327 1.997606 CCGACGGAACATAACCTTCAC 59.002 52.381 8.64 0.00 0.00 3.18
2993 3328 1.652124 CGACGGAACATAACCTTCACG 59.348 52.381 0.00 0.00 0.00 4.35
2994 3329 2.669113 CGACGGAACATAACCTTCACGA 60.669 50.000 0.00 0.00 0.00 4.35
2995 3330 2.921754 GACGGAACATAACCTTCACGAG 59.078 50.000 0.00 0.00 0.00 4.18
2996 3331 1.659098 CGGAACATAACCTTCACGAGC 59.341 52.381 0.00 0.00 0.00 5.03
2997 3332 2.007608 GGAACATAACCTTCACGAGCC 58.992 52.381 0.00 0.00 0.00 4.70
2998 3333 2.007608 GAACATAACCTTCACGAGCCC 58.992 52.381 0.00 0.00 0.00 5.19
2999 3334 1.276622 ACATAACCTTCACGAGCCCT 58.723 50.000 0.00 0.00 0.00 5.19
3000 3335 1.628846 ACATAACCTTCACGAGCCCTT 59.371 47.619 0.00 0.00 0.00 3.95
3001 3336 2.280628 CATAACCTTCACGAGCCCTTC 58.719 52.381 0.00 0.00 0.00 3.46
3002 3337 1.344065 TAACCTTCACGAGCCCTTCA 58.656 50.000 0.00 0.00 0.00 3.02
3003 3338 0.472471 AACCTTCACGAGCCCTTCAA 59.528 50.000 0.00 0.00 0.00 2.69
3004 3339 0.693049 ACCTTCACGAGCCCTTCAAT 59.307 50.000 0.00 0.00 0.00 2.57
3005 3340 1.089920 CCTTCACGAGCCCTTCAATG 58.910 55.000 0.00 0.00 0.00 2.82
3006 3341 1.089920 CTTCACGAGCCCTTCAATGG 58.910 55.000 0.00 0.00 0.00 3.16
3015 3350 1.755179 CCCTTCAATGGCACTAGTGG 58.245 55.000 23.95 7.34 0.00 4.00
3039 3374 3.972227 CCGAGCAGGGACAAAGTG 58.028 61.111 0.00 0.00 35.97 3.16
3040 3375 1.672356 CCGAGCAGGGACAAAGTGG 60.672 63.158 0.00 0.00 35.97 4.00
3041 3376 2.328099 CGAGCAGGGACAAAGTGGC 61.328 63.158 0.00 0.00 0.00 5.01
3042 3377 2.281761 AGCAGGGACAAAGTGGCG 60.282 61.111 0.00 0.00 0.00 5.69
3043 3378 2.594592 GCAGGGACAAAGTGGCGT 60.595 61.111 0.00 0.00 0.00 5.68
3044 3379 2.617274 GCAGGGACAAAGTGGCGTC 61.617 63.158 0.00 0.00 0.00 5.19
3045 3380 1.071471 CAGGGACAAAGTGGCGTCT 59.929 57.895 0.00 0.00 32.57 4.18
3046 3381 0.951040 CAGGGACAAAGTGGCGTCTC 60.951 60.000 0.00 0.00 32.48 3.36
3047 3382 1.122019 AGGGACAAAGTGGCGTCTCT 61.122 55.000 0.00 0.00 38.16 3.10
3048 3383 0.670854 GGGACAAAGTGGCGTCTCTC 60.671 60.000 0.00 0.00 32.57 3.20
3049 3384 1.009389 GGACAAAGTGGCGTCTCTCG 61.009 60.000 0.00 0.00 43.12 4.04
3068 3403 2.338620 CGCTCCGGAACAGACACA 59.661 61.111 5.23 0.00 0.00 3.72
3069 3404 1.300620 CGCTCCGGAACAGACACAA 60.301 57.895 5.23 0.00 0.00 3.33
3070 3405 0.878523 CGCTCCGGAACAGACACAAA 60.879 55.000 5.23 0.00 0.00 2.83
3071 3406 1.305201 GCTCCGGAACAGACACAAAA 58.695 50.000 5.23 0.00 0.00 2.44
3072 3407 1.002792 GCTCCGGAACAGACACAAAAC 60.003 52.381 5.23 0.00 0.00 2.43
3073 3408 1.260561 CTCCGGAACAGACACAAAACG 59.739 52.381 5.23 0.00 0.00 3.60
3074 3409 1.134759 TCCGGAACAGACACAAAACGA 60.135 47.619 0.00 0.00 0.00 3.85
3075 3410 1.666700 CCGGAACAGACACAAAACGAA 59.333 47.619 0.00 0.00 0.00 3.85
3076 3411 2.096174 CCGGAACAGACACAAAACGAAA 59.904 45.455 0.00 0.00 0.00 3.46
3077 3412 3.426426 CCGGAACAGACACAAAACGAAAA 60.426 43.478 0.00 0.00 0.00 2.29
3078 3413 4.159857 CGGAACAGACACAAAACGAAAAA 58.840 39.130 0.00 0.00 0.00 1.94
3118 3453 1.043116 TACTGATGGCGTGAGAGGGG 61.043 60.000 0.00 0.00 0.00 4.79
3119 3454 3.083349 TGATGGCGTGAGAGGGGG 61.083 66.667 0.00 0.00 0.00 5.40
3167 3502 9.906660 ATTAAAATCAAAACATGACGTGTACAT 57.093 25.926 0.00 0.00 41.93 2.29
3177 3512 7.803279 ACATGACGTGTACATCTTAGAGATA 57.197 36.000 0.00 0.00 39.91 1.98
3178 3513 8.221965 ACATGACGTGTACATCTTAGAGATAA 57.778 34.615 0.00 0.00 39.91 1.75
3204 3539 7.893124 TGTACTTTTAGAGGTAGATCGGAAT 57.107 36.000 0.00 0.00 0.00 3.01
3207 3542 9.247126 GTACTTTTAGAGGTAGATCGGAATTTC 57.753 37.037 0.00 0.00 0.00 2.17
3209 3544 7.764901 ACTTTTAGAGGTAGATCGGAATTTCAC 59.235 37.037 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.134804 AGTCAAGGCTACGCAATATTCCT 59.865 43.478 0.00 0.00 0.00 3.36
48 49 3.467803 AGTCAAGGCTACGCAATATTCC 58.532 45.455 0.00 0.00 0.00 3.01
57 58 3.802948 ACTATCCAAGTCAAGGCTACG 57.197 47.619 0.00 0.00 30.33 3.51
105 106 9.902196 TTCGCCTTTTCTAAAACTAAATAAAGG 57.098 29.630 0.00 0.00 41.77 3.11
304 311 4.385643 CCAATCATGTCAAGGTGGTATCCT 60.386 45.833 0.00 0.00 39.84 3.24
323 330 4.082463 CACAATTTACGCCACTTACCCAAT 60.082 41.667 0.00 0.00 0.00 3.16
325 332 2.814919 CACAATTTACGCCACTTACCCA 59.185 45.455 0.00 0.00 0.00 4.51
340 347 3.081804 CTCTACCTTTTCGGCCACAATT 58.918 45.455 2.24 0.00 35.61 2.32
346 353 1.002773 TCAACCTCTACCTTTTCGGCC 59.997 52.381 0.00 0.00 35.61 6.13
368 375 3.920231 TGAAGAGCTCATGCATTAGGT 57.080 42.857 17.77 12.22 42.74 3.08
377 384 3.768215 TCTGTCTGACATGAAGAGCTCAT 59.232 43.478 17.77 2.97 46.25 2.90
380 387 3.591196 GTCTGTCTGACATGAAGAGCT 57.409 47.619 11.45 0.00 44.73 4.09
621 663 4.220821 GCCGGTCTTCTATGATAGGAATGA 59.779 45.833 1.90 0.00 0.00 2.57
712 766 9.331282 ACCACAAAATAATCGGAATTTTCAAAA 57.669 25.926 0.00 0.00 35.00 2.44
713 767 8.768955 CACCACAAAATAATCGGAATTTTCAAA 58.231 29.630 0.00 0.00 35.00 2.69
772 826 4.158579 TGTGTGTTATGTCAGTGGCAAAAA 59.841 37.500 0.00 0.00 0.00 1.94
773 827 3.696548 TGTGTGTTATGTCAGTGGCAAAA 59.303 39.130 0.00 0.00 0.00 2.44
774 828 3.282885 TGTGTGTTATGTCAGTGGCAAA 58.717 40.909 0.00 0.00 0.00 3.68
775 829 2.924421 TGTGTGTTATGTCAGTGGCAA 58.076 42.857 0.00 0.00 0.00 4.52
776 830 2.629336 TGTGTGTTATGTCAGTGGCA 57.371 45.000 0.00 0.00 0.00 4.92
777 831 3.073678 TCATGTGTGTTATGTCAGTGGC 58.926 45.455 0.00 0.00 0.00 5.01
778 832 3.125829 GCTCATGTGTGTTATGTCAGTGG 59.874 47.826 0.00 0.00 0.00 4.00
779 833 3.747529 TGCTCATGTGTGTTATGTCAGTG 59.252 43.478 0.00 0.00 0.00 3.66
780 834 4.006780 TGCTCATGTGTGTTATGTCAGT 57.993 40.909 0.00 0.00 0.00 3.41
781 835 5.556355 AATGCTCATGTGTGTTATGTCAG 57.444 39.130 0.00 0.00 0.00 3.51
782 836 5.963176 AAATGCTCATGTGTGTTATGTCA 57.037 34.783 0.00 0.00 0.00 3.58
788 842 4.141981 TGGTTCAAAATGCTCATGTGTGTT 60.142 37.500 0.00 0.00 0.00 3.32
854 908 8.481314 TCTCTCATATGAGCAACAGTAAAATCT 58.519 33.333 25.27 0.00 41.80 2.40
1016 1103 4.671590 TGTGGGACGGCGGAGAGA 62.672 66.667 13.24 0.00 0.00 3.10
1050 1164 6.495181 TGGTTCAGTGTCTATCTTCTTCTTCT 59.505 38.462 0.00 0.00 0.00 2.85
1051 1165 6.588373 GTGGTTCAGTGTCTATCTTCTTCTTC 59.412 42.308 0.00 0.00 0.00 2.87
1067 1183 0.898789 ATCGGTCGAGGTGGTTCAGT 60.899 55.000 0.00 0.00 0.00 3.41
1546 1706 4.733371 TGAACATGGCGCGCGAGA 62.733 61.111 37.18 19.69 0.00 4.04
2293 2582 5.384063 TGCATCGAACCATTTGTTGTATT 57.616 34.783 0.00 0.00 37.29 1.89
2294 2583 5.384063 TTGCATCGAACCATTTGTTGTAT 57.616 34.783 0.00 0.00 37.29 2.29
2295 2584 4.837896 TTGCATCGAACCATTTGTTGTA 57.162 36.364 0.00 0.00 37.29 2.41
2296 2585 3.724508 TTGCATCGAACCATTTGTTGT 57.275 38.095 0.00 0.00 37.29 3.32
2297 2586 5.401033 TTTTTGCATCGAACCATTTGTTG 57.599 34.783 0.00 0.00 37.29 3.33
2322 2611 5.582665 ACACGCCATTTGTTGTATTGTTTTT 59.417 32.000 0.00 0.00 0.00 1.94
2323 2612 5.112686 ACACGCCATTTGTTGTATTGTTTT 58.887 33.333 0.00 0.00 0.00 2.43
2324 2613 4.688021 ACACGCCATTTGTTGTATTGTTT 58.312 34.783 0.00 0.00 0.00 2.83
2325 2614 4.314740 ACACGCCATTTGTTGTATTGTT 57.685 36.364 0.00 0.00 0.00 2.83
2326 2615 4.276183 TGTACACGCCATTTGTTGTATTGT 59.724 37.500 0.00 0.00 0.00 2.71
2327 2616 4.615121 GTGTACACGCCATTTGTTGTATTG 59.385 41.667 10.84 0.00 0.00 1.90
2383 2672 1.269413 TGTCGAGGTCCGTGAAGTTTC 60.269 52.381 0.00 0.00 39.75 2.78
2430 2733 0.394565 ATCTAGTTGGATCCTGCGGC 59.605 55.000 14.23 0.00 0.00 6.53
2441 2744 2.933495 TGTTCCGTCGGATCTAGTTG 57.067 50.000 16.23 0.00 0.00 3.16
2445 2748 3.559069 AGGTTATGTTCCGTCGGATCTA 58.441 45.455 16.23 4.93 0.00 1.98
2450 2753 1.997606 GTGAAGGTTATGTTCCGTCGG 59.002 52.381 4.39 4.39 36.52 4.79
2452 2755 2.921754 CTCGTGAAGGTTATGTTCCGTC 59.078 50.000 0.00 0.00 34.84 4.79
2456 2759 2.007608 GGGCTCGTGAAGGTTATGTTC 58.992 52.381 0.00 0.00 0.00 3.18
2480 2783 0.609131 GTGGTGCCACTAGTGCCATT 60.609 55.000 19.66 0.00 43.12 3.16
2481 2784 1.002134 GTGGTGCCACTAGTGCCAT 60.002 57.895 19.66 0.00 43.12 4.40
2482 2785 2.429930 GTGGTGCCACTAGTGCCA 59.570 61.111 17.86 16.01 43.12 4.92
2485 2788 2.047274 CGGGTGGTGCCACTAGTG 60.047 66.667 16.34 16.34 45.52 2.74
2502 2805 2.328099 CGCCACTTTGTCCCTGCTC 61.328 63.158 0.00 0.00 0.00 4.26
2506 2809 1.122019 AGAGACGCCACTTTGTCCCT 61.122 55.000 0.00 0.00 35.71 4.20
2530 2865 1.002792 GTTTTGTGTCTGTTCCGGAGC 60.003 52.381 11.99 11.99 0.00 4.70
2532 2867 1.292061 CGTTTTGTGTCTGTTCCGGA 58.708 50.000 0.00 0.00 0.00 5.14
2534 2869 3.929417 TTACGTTTTGTGTCTGTTCCG 57.071 42.857 0.00 0.00 0.00 4.30
2900 3235 1.893801 AGGTCCGTGAAGTTTCGATCT 59.106 47.619 0.00 0.00 0.00 2.75
2901 3236 2.260481 GAGGTCCGTGAAGTTTCGATC 58.740 52.381 0.00 0.00 0.00 3.69
2902 3237 1.402456 CGAGGTCCGTGAAGTTTCGAT 60.402 52.381 0.00 0.00 0.00 3.59
2903 3238 0.039798 CGAGGTCCGTGAAGTTTCGA 60.040 55.000 3.57 0.00 0.00 3.71
2904 3239 0.039798 TCGAGGTCCGTGAAGTTTCG 60.040 55.000 0.00 0.00 39.75 3.46
2905 3240 1.269413 TGTCGAGGTCCGTGAAGTTTC 60.269 52.381 0.00 0.00 39.75 2.78
2906 3241 0.748450 TGTCGAGGTCCGTGAAGTTT 59.252 50.000 0.00 0.00 39.75 2.66
2907 3242 0.031721 GTGTCGAGGTCCGTGAAGTT 59.968 55.000 0.00 0.00 39.75 2.66
2908 3243 1.105167 TGTGTCGAGGTCCGTGAAGT 61.105 55.000 0.00 0.00 39.75 3.01
2909 3244 0.663568 GTGTGTCGAGGTCCGTGAAG 60.664 60.000 0.00 0.00 39.75 3.02
2910 3245 1.361271 GTGTGTCGAGGTCCGTGAA 59.639 57.895 0.00 0.00 39.75 3.18
2911 3246 2.558286 GGTGTGTCGAGGTCCGTGA 61.558 63.158 0.00 0.00 39.75 4.35
2912 3247 2.049433 GGTGTGTCGAGGTCCGTG 60.049 66.667 0.00 0.00 39.75 4.94
2913 3248 3.667282 CGGTGTGTCGAGGTCCGT 61.667 66.667 9.20 0.00 39.75 4.69
2914 3249 4.415332 CCGGTGTGTCGAGGTCCG 62.415 72.222 10.09 10.09 40.72 4.79
2915 3250 4.736896 GCCGGTGTGTCGAGGTCC 62.737 72.222 1.90 0.00 0.00 4.46
2916 3251 3.986006 TGCCGGTGTGTCGAGGTC 61.986 66.667 1.90 0.00 0.00 3.85
2917 3252 4.295119 GTGCCGGTGTGTCGAGGT 62.295 66.667 1.90 0.00 0.00 3.85
2947 3282 4.758251 TGGATCCTGCGGCGTGTG 62.758 66.667 14.23 0.00 0.00 3.82
2948 3283 4.015406 TTGGATCCTGCGGCGTGT 62.015 61.111 14.23 0.00 0.00 4.49
2949 3284 2.572095 TAGTTGGATCCTGCGGCGTG 62.572 60.000 14.23 1.44 0.00 5.34
2950 3285 2.298158 CTAGTTGGATCCTGCGGCGT 62.298 60.000 14.23 0.00 0.00 5.68
2951 3286 1.592669 CTAGTTGGATCCTGCGGCG 60.593 63.158 14.23 0.51 0.00 6.46
2952 3287 0.394565 ATCTAGTTGGATCCTGCGGC 59.605 55.000 14.23 0.00 0.00 6.53
2953 3288 2.447244 GATCTAGTTGGATCCTGCGG 57.553 55.000 14.23 4.89 36.91 5.69
2959 3294 2.228059 TCCGTCGGATCTAGTTGGATC 58.772 52.381 10.71 0.00 40.78 3.36
2960 3295 2.359981 TCCGTCGGATCTAGTTGGAT 57.640 50.000 10.71 0.00 0.00 3.41
2961 3296 1.747355 GTTCCGTCGGATCTAGTTGGA 59.253 52.381 16.23 0.00 0.00 3.53
2962 3297 1.475280 TGTTCCGTCGGATCTAGTTGG 59.525 52.381 16.23 0.00 0.00 3.77
2963 3298 2.933495 TGTTCCGTCGGATCTAGTTG 57.067 50.000 16.23 0.00 0.00 3.16
2964 3299 4.202090 GGTTATGTTCCGTCGGATCTAGTT 60.202 45.833 16.23 4.24 0.00 2.24
2965 3300 3.317430 GGTTATGTTCCGTCGGATCTAGT 59.683 47.826 16.23 7.59 0.00 2.57
2966 3301 3.568853 AGGTTATGTTCCGTCGGATCTAG 59.431 47.826 16.23 0.00 0.00 2.43
2967 3302 3.559069 AGGTTATGTTCCGTCGGATCTA 58.441 45.455 16.23 4.93 0.00 1.98
2968 3303 2.385803 AGGTTATGTTCCGTCGGATCT 58.614 47.619 16.23 5.43 0.00 2.75
2969 3304 2.884894 AGGTTATGTTCCGTCGGATC 57.115 50.000 16.23 15.13 0.00 3.36
2970 3305 2.498481 TGAAGGTTATGTTCCGTCGGAT 59.502 45.455 16.23 2.53 36.52 4.18
2971 3306 1.894466 TGAAGGTTATGTTCCGTCGGA 59.106 47.619 10.71 10.71 36.52 4.55
2972 3307 1.997606 GTGAAGGTTATGTTCCGTCGG 59.002 52.381 4.39 4.39 36.52 4.79
2973 3308 1.652124 CGTGAAGGTTATGTTCCGTCG 59.348 52.381 0.00 0.00 36.52 5.12
2974 3309 2.921754 CTCGTGAAGGTTATGTTCCGTC 59.078 50.000 0.00 0.00 34.84 4.79
2975 3310 2.929592 GCTCGTGAAGGTTATGTTCCGT 60.930 50.000 0.00 0.00 0.00 4.69
2976 3311 1.659098 GCTCGTGAAGGTTATGTTCCG 59.341 52.381 0.00 0.00 0.00 4.30
2977 3312 2.007608 GGCTCGTGAAGGTTATGTTCC 58.992 52.381 0.00 0.00 0.00 3.62
2978 3313 2.007608 GGGCTCGTGAAGGTTATGTTC 58.992 52.381 0.00 0.00 0.00 3.18
2979 3314 1.628846 AGGGCTCGTGAAGGTTATGTT 59.371 47.619 0.00 0.00 0.00 2.71
2980 3315 1.276622 AGGGCTCGTGAAGGTTATGT 58.723 50.000 0.00 0.00 0.00 2.29
2981 3316 2.280628 GAAGGGCTCGTGAAGGTTATG 58.719 52.381 0.00 0.00 0.00 1.90
2982 3317 1.906574 TGAAGGGCTCGTGAAGGTTAT 59.093 47.619 0.00 0.00 0.00 1.89
2983 3318 1.344065 TGAAGGGCTCGTGAAGGTTA 58.656 50.000 0.00 0.00 0.00 2.85
2984 3319 0.472471 TTGAAGGGCTCGTGAAGGTT 59.528 50.000 0.00 0.00 0.00 3.50
2985 3320 0.693049 ATTGAAGGGCTCGTGAAGGT 59.307 50.000 0.00 0.00 0.00 3.50
2986 3321 1.089920 CATTGAAGGGCTCGTGAAGG 58.910 55.000 0.00 0.00 0.00 3.46
2987 3322 1.089920 CCATTGAAGGGCTCGTGAAG 58.910 55.000 0.00 0.00 0.00 3.02
2988 3323 3.248043 CCATTGAAGGGCTCGTGAA 57.752 52.632 0.00 0.00 0.00 3.18
2996 3331 1.755179 CCACTAGTGCCATTGAAGGG 58.245 55.000 17.86 0.00 0.00 3.95
2997 3332 1.098050 GCCACTAGTGCCATTGAAGG 58.902 55.000 17.86 1.43 0.00 3.46
2998 3333 1.470098 GTGCCACTAGTGCCATTGAAG 59.530 52.381 17.86 2.32 0.00 3.02
2999 3334 1.533625 GTGCCACTAGTGCCATTGAA 58.466 50.000 17.86 0.00 0.00 2.69
3000 3335 0.322456 GGTGCCACTAGTGCCATTGA 60.322 55.000 17.86 0.00 0.00 2.57
3001 3336 0.608856 TGGTGCCACTAGTGCCATTG 60.609 55.000 17.86 4.55 0.00 2.82
3002 3337 0.609131 GTGGTGCCACTAGTGCCATT 60.609 55.000 19.66 0.00 43.12 3.16
3003 3338 1.002134 GTGGTGCCACTAGTGCCAT 60.002 57.895 19.66 0.00 43.12 4.40
3004 3339 2.429930 GTGGTGCCACTAGTGCCA 59.570 61.111 17.86 16.01 43.12 4.92
3005 3340 2.359975 GGTGGTGCCACTAGTGCC 60.360 66.667 17.86 13.57 45.52 5.01
3006 3341 2.359975 GGGTGGTGCCACTAGTGC 60.360 66.667 17.86 13.07 45.52 4.40
3007 3342 2.047274 CGGGTGGTGCCACTAGTG 60.047 66.667 16.34 16.34 45.52 2.74
3008 3343 2.203728 TCGGGTGGTGCCACTAGT 60.204 61.111 19.37 0.00 45.52 2.57
3009 3344 2.579201 CTCGGGTGGTGCCACTAG 59.421 66.667 19.37 13.75 45.52 2.57
3010 3345 3.702048 GCTCGGGTGGTGCCACTA 61.702 66.667 19.37 6.42 45.52 2.74
3022 3357 1.672356 CCACTTTGTCCCTGCTCGG 60.672 63.158 0.00 0.00 0.00 4.63
3023 3358 2.328099 GCCACTTTGTCCCTGCTCG 61.328 63.158 0.00 0.00 0.00 5.03
3024 3359 2.328099 CGCCACTTTGTCCCTGCTC 61.328 63.158 0.00 0.00 0.00 4.26
3025 3360 2.281761 CGCCACTTTGTCCCTGCT 60.282 61.111 0.00 0.00 0.00 4.24
3026 3361 2.594592 ACGCCACTTTGTCCCTGC 60.595 61.111 0.00 0.00 0.00 4.85
3027 3362 0.951040 GAGACGCCACTTTGTCCCTG 60.951 60.000 0.00 0.00 35.71 4.45
3028 3363 1.122019 AGAGACGCCACTTTGTCCCT 61.122 55.000 0.00 0.00 35.71 4.20
3029 3364 0.670854 GAGAGACGCCACTTTGTCCC 60.671 60.000 0.00 0.00 35.71 4.46
3030 3365 1.009389 CGAGAGACGCCACTTTGTCC 61.009 60.000 0.00 0.00 35.71 4.02
3031 3366 2.435741 CGAGAGACGCCACTTTGTC 58.564 57.895 0.00 0.00 35.33 3.18
3032 3367 4.655527 CGAGAGACGCCACTTTGT 57.344 55.556 0.00 0.00 34.51 2.83
3051 3386 0.878523 TTTGTGTCTGTTCCGGAGCG 60.879 55.000 14.03 8.64 0.00 5.03
3052 3387 1.002792 GTTTTGTGTCTGTTCCGGAGC 60.003 52.381 11.99 11.99 0.00 4.70
3053 3388 1.260561 CGTTTTGTGTCTGTTCCGGAG 59.739 52.381 3.34 0.00 0.00 4.63
3054 3389 1.134759 TCGTTTTGTGTCTGTTCCGGA 60.135 47.619 0.00 0.00 0.00 5.14
3055 3390 1.292061 TCGTTTTGTGTCTGTTCCGG 58.708 50.000 0.00 0.00 0.00 5.14
3056 3391 3.392769 TTTCGTTTTGTGTCTGTTCCG 57.607 42.857 0.00 0.00 0.00 4.30
3076 3411 3.259876 GGGCTTCCGTTTATTCCCTTTTT 59.740 43.478 0.00 0.00 0.00 1.94
3077 3412 2.829720 GGGCTTCCGTTTATTCCCTTTT 59.170 45.455 0.00 0.00 0.00 2.27
3078 3413 2.042569 AGGGCTTCCGTTTATTCCCTTT 59.957 45.455 0.00 0.00 41.03 3.11
3079 3414 1.639108 AGGGCTTCCGTTTATTCCCTT 59.361 47.619 0.00 0.00 41.03 3.95
3080 3415 1.296002 AGGGCTTCCGTTTATTCCCT 58.704 50.000 0.00 0.00 39.16 4.20
3081 3416 2.172082 AGTAGGGCTTCCGTTTATTCCC 59.828 50.000 0.00 0.00 35.17 3.97
3086 3421 2.169769 CCATCAGTAGGGCTTCCGTTTA 59.830 50.000 0.00 0.00 35.17 2.01
3121 3456 2.134789 AGCACAATCAATCACTCCCC 57.865 50.000 0.00 0.00 0.00 4.81
3122 3457 6.942532 TTAATAGCACAATCAATCACTCCC 57.057 37.500 0.00 0.00 0.00 4.30
3123 3458 9.455847 GATTTTAATAGCACAATCAATCACTCC 57.544 33.333 0.00 0.00 0.00 3.85
3137 3472 8.079203 ACACGTCATGTTTTGATTTTAATAGCA 58.921 29.630 0.00 0.00 38.98 3.49
3138 3473 8.447787 ACACGTCATGTTTTGATTTTAATAGC 57.552 30.769 0.00 0.00 38.98 2.97
3151 3486 6.920817 TCTCTAAGATGTACACGTCATGTTT 58.079 36.000 0.00 0.00 43.19 2.83
3158 3493 9.947669 GTACATTTATCTCTAAGATGTACACGT 57.052 33.333 15.96 0.00 46.09 4.49
3177 3512 8.302515 TCCGATCTACCTCTAAAAGTACATTT 57.697 34.615 1.26 1.26 0.00 2.32
3178 3513 7.893124 TCCGATCTACCTCTAAAAGTACATT 57.107 36.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.