Multiple sequence alignment - TraesCS6D01G380500

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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 TraesCS6D01G380500 chr6D 100.000 2708 0 0 1 2708 461462349 461459642 0.000000e+00 5001.0
1 TraesCS6D01G380500 chr6A 92.647 1768 93 13 929 2670 608125880 608124124 0.000000e+00 2510.0
2 TraesCS6D01G380500 chr6A 87.936 746 57 16 133 856 608126625 608125891 0.000000e+00 848.0
3 TraesCS6D01G380500 chr6B 93.121 1381 56 12 929 2280 703348489 703347119 0.000000e+00 1988.0
4 TraesCS6D01G380500 chr6B 92.405 1106 66 3 930 2018 703306948 703305844 0.000000e+00 1561.0
5 TraesCS6D01G380500 chr6B 88.977 880 59 17 6 858 703349366 703348498 0.000000e+00 1053.0
6 TraesCS6D01G380500 chr6B 85.424 885 65 28 1 856 703307809 703306960 0.000000e+00 861.0
7 TraesCS6D01G380500 chr6B 94.949 396 14 5 2277 2670 703343695 703343304 1.380000e-172 616.0
8 TraesCS6D01G380500 chr7D 84.366 339 48 2 364 702 37116170 37115837 7.230000e-86 327.0
9 TraesCS6D01G380500 chr7D 93.750 48 3 0 866 913 505637045 505636998 3.740000e-09 73.1
10 TraesCS6D01G380500 chr2D 82.386 352 49 7 351 702 577685709 577685371 7.330000e-76 294.0
11 TraesCS6D01G380500 chr2B 81.657 338 51 5 365 702 694543621 694543947 1.240000e-68 270.0
12 TraesCS6D01G380500 chr2A 84.615 195 27 2 351 544 715634541 715634733 9.900000e-45 191.0
13 TraesCS6D01G380500 chr3D 71.940 335 84 7 371 702 594972863 594972536 3.710000e-14 89.8
14 TraesCS6D01G380500 chr3A 72.378 286 72 6 364 646 697282355 697282636 1.730000e-12 84.2
15 TraesCS6D01G380500 chr7B 95.918 49 2 0 866 914 135224889 135224841 2.240000e-11 80.5
16 TraesCS6D01G380500 chr3B 97.727 44 1 0 871 914 552728525 552728482 2.890000e-10 76.8
17 TraesCS6D01G380500 chr5B 88.710 62 5 2 853 913 576219530 576219590 1.040000e-09 75.0
18 TraesCS6D01G380500 chr1B 90.909 55 5 0 860 914 504960633 504960579 1.040000e-09 75.0


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 TraesCS6D01G380500 chr6D 461459642 461462349 2707 True 5001 5001 100.0000 1 2708 1 chr6D.!!$R1 2707
1 TraesCS6D01G380500 chr6A 608124124 608126625 2501 True 1679 2510 90.2915 133 2670 2 chr6A.!!$R1 2537
2 TraesCS6D01G380500 chr6B 703343304 703349366 6062 True 1219 1988 92.3490 6 2670 3 chr6B.!!$R2 2664
3 TraesCS6D01G380500 chr6B 703305844 703307809 1965 True 1211 1561 88.9145 1 2018 2 chr6B.!!$R1 2017

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
355 361 1.047002 TAACGGAAAGGTGTCCCGAA 58.953 50.0 7.06 0.0 45.58 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2138 0.11358 AGCCCGTTTAACCCACCATT 59.886 50.0 0.0 0.0 0.0 3.16 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
34 35 1.345410 ATTTATTTTGGCGCGTGTGC 58.655 45.000 8.43 0.00 37.91 4.57
65 69 8.019669 GCTCATTATGTGCTTGTTAGAATATGG 58.980 37.037 11.43 0.00 34.37 2.74
69 73 4.199310 TGTGCTTGTTAGAATATGGGAGC 58.801 43.478 0.00 0.00 0.00 4.70
81 85 5.885912 AGAATATGGGAGCGTGTGTTTATTT 59.114 36.000 0.00 0.00 0.00 1.40
83 87 2.852449 TGGGAGCGTGTGTTTATTTCA 58.148 42.857 0.00 0.00 0.00 2.69
84 88 3.417101 TGGGAGCGTGTGTTTATTTCAT 58.583 40.909 0.00 0.00 0.00 2.57
87 91 3.438781 GGAGCGTGTGTTTATTTCATGGA 59.561 43.478 0.00 0.00 0.00 3.41
272 278 7.169591 TCTTTTACGTTTAGAAATGGATCCCA 58.830 34.615 9.90 0.00 38.19 4.37
293 299 3.049344 AGGAGTCAAAAGACCCAACTCT 58.951 45.455 0.00 0.00 37.20 3.24
324 330 7.652727 AGGTTCTTTTTGCAGAGAAATAGTTC 58.347 34.615 9.83 0.00 34.00 3.01
350 356 6.145696 GCATAGTGATATAACGGAAAGGTGTC 59.854 42.308 0.00 0.00 0.00 3.67
351 357 5.019785 AGTGATATAACGGAAAGGTGTCC 57.980 43.478 0.00 0.00 0.00 4.02
355 361 1.047002 TAACGGAAAGGTGTCCCGAA 58.953 50.000 7.06 0.00 45.58 4.30
360 389 3.075884 CGGAAAGGTGTCCCGAATTTTA 58.924 45.455 0.00 0.00 45.58 1.52
362 391 4.023021 CGGAAAGGTGTCCCGAATTTTAAA 60.023 41.667 0.00 0.00 45.58 1.52
396 425 6.964908 ACAAAACATGTATCAAACGTGATCA 58.035 32.000 0.00 0.00 46.40 2.92
398 427 7.378461 ACAAAACATGTATCAAACGTGATCAAC 59.622 33.333 0.00 0.00 46.40 3.18
399 428 5.545658 ACATGTATCAAACGTGATCAACC 57.454 39.130 0.00 0.00 46.40 3.77
411 440 5.702865 ACGTGATCAACCAATTCTGATTTG 58.297 37.500 0.00 5.52 32.40 2.32
422 451 8.352137 ACCAATTCTGATTTGTTGTGATATCA 57.648 30.769 0.00 0.00 0.00 2.15
454 483 7.698836 ACAAATGTTTTAGAGACATGCAAAC 57.301 32.000 0.00 0.00 37.76 2.93
467 496 4.624015 ACATGCAAACTTTCATCCACAAG 58.376 39.130 0.00 0.00 0.00 3.16
472 501 4.675114 GCAAACTTTCATCCACAAGTAACG 59.325 41.667 0.00 0.00 32.74 3.18
502 532 7.346751 AGAGCTCTCACCAAAAATAACAAAA 57.653 32.000 11.45 0.00 0.00 2.44
585 615 6.035327 GCTTCTTGAATGTTATTTGTGGATGC 59.965 38.462 0.00 0.00 0.00 3.91
756 790 8.498358 CACAATCATTTAGCTCTTATTGCGATA 58.502 33.333 0.00 0.00 35.28 2.92
771 805 4.617253 TGCGATATGCCTTTACTATGGT 57.383 40.909 0.00 0.00 45.60 3.55
772 806 5.731957 TGCGATATGCCTTTACTATGGTA 57.268 39.130 0.00 0.00 45.60 3.25
773 807 5.720202 TGCGATATGCCTTTACTATGGTAG 58.280 41.667 0.00 0.00 45.60 3.18
774 808 4.567159 GCGATATGCCTTTACTATGGTAGC 59.433 45.833 0.00 0.00 37.76 3.58
775 809 5.624738 GCGATATGCCTTTACTATGGTAGCT 60.625 44.000 0.00 0.00 37.76 3.32
776 810 6.398918 CGATATGCCTTTACTATGGTAGCTT 58.601 40.000 0.00 0.00 0.00 3.74
779 813 6.944234 ATGCCTTTACTATGGTAGCTTTTC 57.056 37.500 0.00 0.00 0.00 2.29
781 815 7.190335 TGCCTTTACTATGGTAGCTTTTCTA 57.810 36.000 0.00 0.00 0.00 2.10
784 818 9.205719 GCCTTTACTATGGTAGCTTTTCTATAC 57.794 37.037 0.00 0.00 0.00 1.47
807 843 7.531857 ACACCAATATAAAACACACCAATCA 57.468 32.000 0.00 0.00 0.00 2.57
809 845 8.250332 ACACCAATATAAAACACACCAATCATC 58.750 33.333 0.00 0.00 0.00 2.92
867 903 9.606631 AGAATTGATCCAATGTACTACTTTCTC 57.393 33.333 0.00 0.00 34.04 2.87
868 904 8.738645 AATTGATCCAATGTACTACTTTCTCC 57.261 34.615 0.00 0.00 34.04 3.71
869 905 6.867519 TGATCCAATGTACTACTTTCTCCA 57.132 37.500 0.00 0.00 0.00 3.86
870 906 7.437713 TGATCCAATGTACTACTTTCTCCAT 57.562 36.000 0.00 0.00 0.00 3.41
871 907 7.500992 TGATCCAATGTACTACTTTCTCCATC 58.499 38.462 0.00 0.00 0.00 3.51
872 908 6.235231 TCCAATGTACTACTTTCTCCATCC 57.765 41.667 0.00 0.00 0.00 3.51
873 909 5.130477 TCCAATGTACTACTTTCTCCATCCC 59.870 44.000 0.00 0.00 0.00 3.85
874 910 5.104527 CCAATGTACTACTTTCTCCATCCCA 60.105 44.000 0.00 0.00 0.00 4.37
875 911 6.414732 CAATGTACTACTTTCTCCATCCCAA 58.585 40.000 0.00 0.00 0.00 4.12
876 912 6.636454 ATGTACTACTTTCTCCATCCCAAA 57.364 37.500 0.00 0.00 0.00 3.28
877 913 6.442541 TGTACTACTTTCTCCATCCCAAAA 57.557 37.500 0.00 0.00 0.00 2.44
878 914 7.027874 TGTACTACTTTCTCCATCCCAAAAT 57.972 36.000 0.00 0.00 0.00 1.82
879 915 7.466804 TGTACTACTTTCTCCATCCCAAAATT 58.533 34.615 0.00 0.00 0.00 1.82
880 916 7.610305 TGTACTACTTTCTCCATCCCAAAATTC 59.390 37.037 0.00 0.00 0.00 2.17
881 917 6.794534 ACTACTTTCTCCATCCCAAAATTCT 58.205 36.000 0.00 0.00 0.00 2.40
882 918 6.887002 ACTACTTTCTCCATCCCAAAATTCTC 59.113 38.462 0.00 0.00 0.00 2.87
883 919 4.702131 ACTTTCTCCATCCCAAAATTCTCG 59.298 41.667 0.00 0.00 0.00 4.04
884 920 4.301072 TTCTCCATCCCAAAATTCTCGT 57.699 40.909 0.00 0.00 0.00 4.18
885 921 3.873910 TCTCCATCCCAAAATTCTCGTC 58.126 45.455 0.00 0.00 0.00 4.20
886 922 3.519510 TCTCCATCCCAAAATTCTCGTCT 59.480 43.478 0.00 0.00 0.00 4.18
887 923 4.019321 TCTCCATCCCAAAATTCTCGTCTT 60.019 41.667 0.00 0.00 0.00 3.01
888 924 5.188948 TCTCCATCCCAAAATTCTCGTCTTA 59.811 40.000 0.00 0.00 0.00 2.10
889 925 6.001449 TCCATCCCAAAATTCTCGTCTTAT 57.999 37.500 0.00 0.00 0.00 1.73
890 926 7.070696 TCTCCATCCCAAAATTCTCGTCTTATA 59.929 37.037 0.00 0.00 0.00 0.98
891 927 7.745717 TCCATCCCAAAATTCTCGTCTTATAT 58.254 34.615 0.00 0.00 0.00 0.86
892 928 8.217799 TCCATCCCAAAATTCTCGTCTTATATT 58.782 33.333 0.00 0.00 0.00 1.28
893 929 8.850156 CCATCCCAAAATTCTCGTCTTATATTT 58.150 33.333 0.00 0.00 0.00 1.40
894 930 9.669353 CATCCCAAAATTCTCGTCTTATATTTG 57.331 33.333 0.00 0.00 0.00 2.32
895 931 8.801882 TCCCAAAATTCTCGTCTTATATTTGT 57.198 30.769 0.00 0.00 0.00 2.83
896 932 8.889717 TCCCAAAATTCTCGTCTTATATTTGTC 58.110 33.333 0.00 0.00 0.00 3.18
897 933 8.893727 CCCAAAATTCTCGTCTTATATTTGTCT 58.106 33.333 0.00 0.00 0.00 3.41
904 940 9.874215 TTCTCGTCTTATATTTGTCTACATACG 57.126 33.333 0.00 0.00 0.00 3.06
905 941 8.501580 TCTCGTCTTATATTTGTCTACATACGG 58.498 37.037 0.00 0.00 0.00 4.02
906 942 8.382030 TCGTCTTATATTTGTCTACATACGGA 57.618 34.615 0.00 0.00 0.00 4.69
907 943 9.006839 TCGTCTTATATTTGTCTACATACGGAT 57.993 33.333 0.00 0.00 0.00 4.18
908 944 9.062674 CGTCTTATATTTGTCTACATACGGATG 57.937 37.037 5.94 5.94 39.16 3.51
915 951 6.954487 TTGTCTACATACGGATGTATCAGT 57.046 37.500 20.64 0.00 45.42 3.41
916 952 8.454570 TTTGTCTACATACGGATGTATCAGTA 57.545 34.615 20.64 11.53 45.42 2.74
917 953 7.668525 TGTCTACATACGGATGTATCAGTAG 57.331 40.000 20.64 10.08 45.42 2.57
918 954 7.447594 TGTCTACATACGGATGTATCAGTAGA 58.552 38.462 20.64 12.29 45.42 2.59
919 955 8.101419 TGTCTACATACGGATGTATCAGTAGAT 58.899 37.037 20.64 0.00 45.42 1.98
920 956 9.597170 GTCTACATACGGATGTATCAGTAGATA 57.403 37.037 20.64 0.00 45.42 1.98
1057 1093 0.171455 GTCAGGAGATTCGTCGCAGT 59.829 55.000 0.00 0.00 0.00 4.40
1074 1110 2.619147 CAGTCTCAGCCACAAGAGATG 58.381 52.381 0.00 0.00 42.34 2.90
1081 1117 1.911357 AGCCACAAGAGATGATCACCA 59.089 47.619 0.00 0.00 0.00 4.17
1569 1605 2.281484 TGCTTCGTGACCTTGGGC 60.281 61.111 0.00 0.00 0.00 5.36
1683 1719 2.496070 CTGGGTTCTGGACTTCATCGTA 59.504 50.000 0.00 0.00 0.00 3.43
1794 1830 6.877611 AATTTTGTAATCAGAAGACACCGT 57.122 33.333 0.00 0.00 0.00 4.83
1887 1939 1.340399 TGCATCCGATCCTTCAGCCT 61.340 55.000 0.00 0.00 0.00 4.58
1945 1997 3.708403 TGGCTCACAAATCAGACATCT 57.292 42.857 0.00 0.00 0.00 2.90
1967 2019 9.844790 CATCTGCAACAAGAGTTAATTTAATCA 57.155 29.630 0.00 0.00 35.85 2.57
2051 2123 2.265367 TCTCCTATTGGCACTTGGACA 58.735 47.619 4.01 0.00 0.00 4.02
2066 2138 6.356556 CACTTGGACAACTCCATGGATAATA 58.643 40.000 16.63 0.00 46.64 0.98
2067 2139 6.828273 CACTTGGACAACTCCATGGATAATAA 59.172 38.462 16.63 4.08 46.64 1.40
2068 2140 7.503566 CACTTGGACAACTCCATGGATAATAAT 59.496 37.037 16.63 0.00 46.64 1.28
2074 2146 5.261040 ACTCCATGGATAATAATGGTGGG 57.739 43.478 16.63 0.70 43.31 4.61
2093 2165 0.601057 GTTAAACGGGCTGGCACAAT 59.399 50.000 2.88 0.00 38.70 2.71
2094 2166 1.813786 GTTAAACGGGCTGGCACAATA 59.186 47.619 2.88 0.00 38.70 1.90
2095 2167 2.201921 TAAACGGGCTGGCACAATAA 57.798 45.000 2.88 0.00 38.70 1.40
2144 2226 3.953612 TGCTTGTCACTTGGAGAATTTGT 59.046 39.130 0.00 0.00 0.00 2.83
2146 2228 5.239306 TGCTTGTCACTTGGAGAATTTGTAG 59.761 40.000 0.00 0.00 0.00 2.74
2152 2234 6.367422 GTCACTTGGAGAATTTGTAGTGAGAG 59.633 42.308 0.00 0.00 41.65 3.20
2162 2244 7.768120 AGAATTTGTAGTGAGAGAAATGCTAGG 59.232 37.037 0.00 0.00 28.49 3.02
2217 2299 5.499313 TCATGCTAAACATCATCAAGGTGA 58.501 37.500 0.00 0.00 36.64 4.02
2269 2351 7.711339 TGCCGAAAAACTATTGGTTGTTTTATT 59.289 29.630 0.00 0.00 43.04 1.40
2270 2352 8.007152 GCCGAAAAACTATTGGTTGTTTTATTG 58.993 33.333 0.00 0.00 43.04 1.90
2292 5802 6.620877 TGGGAGAGTAATCTTGTATGTTGT 57.379 37.500 0.00 0.00 0.00 3.32
2293 5803 7.727578 TGGGAGAGTAATCTTGTATGTTGTA 57.272 36.000 0.00 0.00 0.00 2.41
2428 5938 4.220382 TGCACGGGAATTGAATCAAATTCT 59.780 37.500 0.00 0.00 43.25 2.40
2451 5961 5.968254 TGAATGTTTATGCAGCATGTTCAT 58.032 33.333 18.81 14.78 39.31 2.57
2469 5979 9.153721 CATGTTCATGGCAAGTTATTAACAAAT 57.846 29.630 9.15 0.00 0.00 2.32
2490 6001 6.872585 AATAAAATCAGCCATCCCTTTCAA 57.127 33.333 0.00 0.00 0.00 2.69
2506 6017 6.016610 TCCCTTTCAACAAAAATACGAAGAGG 60.017 38.462 0.00 0.00 0.00 3.69
2510 6021 7.562454 TTCAACAAAAATACGAAGAGGAAGT 57.438 32.000 0.00 0.00 0.00 3.01
2511 6022 6.954944 TCAACAAAAATACGAAGAGGAAGTG 58.045 36.000 0.00 0.00 0.00 3.16
2528 6039 0.747283 GTGCAAGGAGGAGCTGATGG 60.747 60.000 0.00 0.00 0.00 3.51
2549 6060 6.258230 TGGATCAACTGAACATTGTCATTC 57.742 37.500 0.00 0.00 0.00 2.67
2671 6182 9.996554 AATACAAGGTTGGAAAGAAAAATTAGG 57.003 29.630 0.00 0.00 0.00 2.69
2672 6183 7.432148 ACAAGGTTGGAAAGAAAAATTAGGT 57.568 32.000 0.00 0.00 0.00 3.08
2673 6184 7.857456 ACAAGGTTGGAAAGAAAAATTAGGTT 58.143 30.769 0.00 0.00 0.00 3.50
2674 6185 7.768582 ACAAGGTTGGAAAGAAAAATTAGGTTG 59.231 33.333 0.00 0.00 0.00 3.77
2675 6186 7.432148 AGGTTGGAAAGAAAAATTAGGTTGT 57.568 32.000 0.00 0.00 0.00 3.32
2676 6187 8.541899 AGGTTGGAAAGAAAAATTAGGTTGTA 57.458 30.769 0.00 0.00 0.00 2.41
2677 6188 8.638873 AGGTTGGAAAGAAAAATTAGGTTGTAG 58.361 33.333 0.00 0.00 0.00 2.74
2678 6189 7.384115 GGTTGGAAAGAAAAATTAGGTTGTAGC 59.616 37.037 0.00 0.00 0.00 3.58
2679 6190 6.674066 TGGAAAGAAAAATTAGGTTGTAGCG 58.326 36.000 0.00 0.00 0.00 4.26
2680 6191 5.571741 GGAAAGAAAAATTAGGTTGTAGCGC 59.428 40.000 0.00 0.00 0.00 5.92
2681 6192 5.699097 AAGAAAAATTAGGTTGTAGCGCA 57.301 34.783 11.47 0.00 0.00 6.09
2682 6193 5.699097 AGAAAAATTAGGTTGTAGCGCAA 57.301 34.783 11.47 0.00 34.16 4.85
2683 6194 5.699839 AGAAAAATTAGGTTGTAGCGCAAG 58.300 37.500 11.47 0.00 37.83 4.01
2684 6195 5.240844 AGAAAAATTAGGTTGTAGCGCAAGT 59.759 36.000 11.47 0.00 37.83 3.16
2685 6196 4.419522 AAATTAGGTTGTAGCGCAAGTG 57.580 40.909 11.47 0.00 37.83 3.16
2686 6197 2.823924 TTAGGTTGTAGCGCAAGTGA 57.176 45.000 11.47 0.00 37.83 3.41
2687 6198 3.328382 TTAGGTTGTAGCGCAAGTGAT 57.672 42.857 11.47 0.00 37.83 3.06
2688 6199 1.726853 AGGTTGTAGCGCAAGTGATC 58.273 50.000 11.47 0.00 37.83 2.92
2689 6200 0.727398 GGTTGTAGCGCAAGTGATCC 59.273 55.000 11.47 0.00 37.83 3.36
2690 6201 0.727398 GTTGTAGCGCAAGTGATCCC 59.273 55.000 11.47 0.00 37.83 3.85
2691 6202 0.392461 TTGTAGCGCAAGTGATCCCC 60.392 55.000 11.47 0.00 41.68 4.81
2692 6203 1.883084 GTAGCGCAAGTGATCCCCG 60.883 63.158 11.47 0.00 41.68 5.73
2693 6204 2.355986 TAGCGCAAGTGATCCCCGT 61.356 57.895 11.47 0.00 41.68 5.28
2694 6205 1.895020 TAGCGCAAGTGATCCCCGTT 61.895 55.000 11.47 0.00 41.68 4.44
2695 6206 2.332654 GCGCAAGTGATCCCCGTTT 61.333 57.895 0.30 0.00 41.68 3.60
2696 6207 1.022451 GCGCAAGTGATCCCCGTTTA 61.022 55.000 0.30 0.00 41.68 2.01
2697 6208 1.663695 CGCAAGTGATCCCCGTTTAT 58.336 50.000 0.00 0.00 0.00 1.40
2698 6209 1.330521 CGCAAGTGATCCCCGTTTATG 59.669 52.381 0.00 0.00 0.00 1.90
2699 6210 1.065551 GCAAGTGATCCCCGTTTATGC 59.934 52.381 0.00 0.00 0.00 3.14
2700 6211 2.364632 CAAGTGATCCCCGTTTATGCA 58.635 47.619 0.00 0.00 0.00 3.96
2701 6212 2.752354 CAAGTGATCCCCGTTTATGCAA 59.248 45.455 0.00 0.00 0.00 4.08
2702 6213 3.297134 AGTGATCCCCGTTTATGCAAT 57.703 42.857 0.00 0.00 0.00 3.56
2703 6214 2.951642 AGTGATCCCCGTTTATGCAATG 59.048 45.455 0.00 0.00 0.00 2.82
2704 6215 2.034558 GTGATCCCCGTTTATGCAATGG 59.965 50.000 0.00 0.00 40.95 3.16
2705 6216 1.000274 GATCCCCGTTTATGCAATGGC 60.000 52.381 0.00 0.00 40.01 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.014702 CGCGCCAAAATAAATTCAGAATTTTT 58.985 30.769 23.24 14.47 41.16 1.94
34 35 4.895224 ACAAGCACATAATGAGCATCTG 57.105 40.909 0.00 0.00 36.40 2.90
65 69 3.438781 TCCATGAAATAAACACACGCTCC 59.561 43.478 0.00 0.00 0.00 4.70
69 73 9.995957 TTTATGTATCCATGAAATAAACACACG 57.004 29.630 0.00 0.00 32.29 4.49
293 299 5.680619 TCTCTGCAAAAAGAACCTCTACAA 58.319 37.500 0.00 0.00 0.00 2.41
324 330 5.118664 CACCTTTCCGTTATATCACTATGCG 59.881 44.000 0.00 0.00 0.00 4.73
396 425 8.805175 TGATATCACAACAAATCAGAATTGGTT 58.195 29.630 0.00 0.00 39.21 3.67
398 427 9.642327 TTTGATATCACAACAAATCAGAATTGG 57.358 29.630 4.48 0.00 30.53 3.16
411 440 9.195411 ACATTTGTTCATGTTTGATATCACAAC 57.805 29.630 4.48 12.95 33.29 3.32
454 483 4.446385 TCGAACGTTACTTGTGGATGAAAG 59.554 41.667 0.00 0.00 0.00 2.62
467 496 2.909863 GTGAGAGCTCTTCGAACGTTAC 59.090 50.000 19.36 0.94 0.00 2.50
472 501 2.440539 TTGGTGAGAGCTCTTCGAAC 57.559 50.000 19.36 13.53 0.00 3.95
502 532 3.890756 TGCAGAAAACATTGACCTGTGAT 59.109 39.130 0.00 0.00 0.00 3.06
563 593 6.587206 TGCATCCACAAATAACATTCAAGA 57.413 33.333 0.00 0.00 0.00 3.02
585 615 4.730657 TGTTTTTGGTTGCTGCAAAATTG 58.269 34.783 17.80 0.00 0.00 2.32
680 714 4.277174 TCGTACTACACCCGAGTTTACAAA 59.723 41.667 0.00 0.00 0.00 2.83
681 715 3.818210 TCGTACTACACCCGAGTTTACAA 59.182 43.478 0.00 0.00 0.00 2.41
725 759 8.680903 CAATAAGAGCTAAATGATTGTGGTCTT 58.319 33.333 20.41 20.41 40.61 3.01
756 790 6.663734 AGAAAAGCTACCATAGTAAAGGCAT 58.336 36.000 0.00 0.00 0.00 4.40
781 815 9.249053 TGATTGGTGTGTTTTATATTGGTGTAT 57.751 29.630 0.00 0.00 0.00 2.29
784 818 8.469200 AGATGATTGGTGTGTTTTATATTGGTG 58.531 33.333 0.00 0.00 0.00 4.17
858 894 6.037610 CGAGAATTTTGGGATGGAGAAAGTAG 59.962 42.308 0.00 0.00 0.00 2.57
859 895 5.880332 CGAGAATTTTGGGATGGAGAAAGTA 59.120 40.000 0.00 0.00 0.00 2.24
861 897 4.702131 ACGAGAATTTTGGGATGGAGAAAG 59.298 41.667 0.00 0.00 0.00 2.62
864 900 3.519510 AGACGAGAATTTTGGGATGGAGA 59.480 43.478 0.00 0.00 0.00 3.71
865 901 3.878778 AGACGAGAATTTTGGGATGGAG 58.121 45.455 0.00 0.00 0.00 3.86
866 902 4.301072 AAGACGAGAATTTTGGGATGGA 57.699 40.909 0.00 0.00 0.00 3.41
867 903 7.986085 ATATAAGACGAGAATTTTGGGATGG 57.014 36.000 0.00 0.00 0.00 3.51
868 904 9.669353 CAAATATAAGACGAGAATTTTGGGATG 57.331 33.333 0.00 0.00 0.00 3.51
869 905 9.408648 ACAAATATAAGACGAGAATTTTGGGAT 57.591 29.630 0.00 0.00 0.00 3.85
870 906 8.801882 ACAAATATAAGACGAGAATTTTGGGA 57.198 30.769 0.00 0.00 0.00 4.37
871 907 8.893727 AGACAAATATAAGACGAGAATTTTGGG 58.106 33.333 0.00 0.00 0.00 4.12
878 914 9.874215 CGTATGTAGACAAATATAAGACGAGAA 57.126 33.333 0.00 0.00 0.00 2.87
879 915 8.501580 CCGTATGTAGACAAATATAAGACGAGA 58.498 37.037 0.00 0.00 0.00 4.04
880 916 8.501580 TCCGTATGTAGACAAATATAAGACGAG 58.498 37.037 0.00 0.00 0.00 4.18
881 917 8.382030 TCCGTATGTAGACAAATATAAGACGA 57.618 34.615 0.00 0.00 0.00 4.20
882 918 9.062674 CATCCGTATGTAGACAAATATAAGACG 57.937 37.037 0.00 0.00 0.00 4.18
883 919 9.909644 ACATCCGTATGTAGACAAATATAAGAC 57.090 33.333 0.00 0.00 44.66 3.01
909 945 5.452255 AGGTTTCGGGTGTATCTACTGATA 58.548 41.667 0.00 0.00 34.32 2.15
910 946 4.287552 AGGTTTCGGGTGTATCTACTGAT 58.712 43.478 0.00 0.00 36.74 2.90
911 947 3.705051 AGGTTTCGGGTGTATCTACTGA 58.295 45.455 0.00 0.00 0.00 3.41
912 948 4.181578 CAAGGTTTCGGGTGTATCTACTG 58.818 47.826 0.00 0.00 0.00 2.74
913 949 3.836562 ACAAGGTTTCGGGTGTATCTACT 59.163 43.478 0.00 0.00 0.00 2.57
914 950 4.198028 ACAAGGTTTCGGGTGTATCTAC 57.802 45.455 0.00 0.00 0.00 2.59
915 951 5.126061 GTCTACAAGGTTTCGGGTGTATCTA 59.874 44.000 0.00 0.00 0.00 1.98
916 952 4.081807 GTCTACAAGGTTTCGGGTGTATCT 60.082 45.833 0.00 0.00 0.00 1.98
917 953 4.081807 AGTCTACAAGGTTTCGGGTGTATC 60.082 45.833 0.00 0.00 0.00 2.24
918 954 3.836562 AGTCTACAAGGTTTCGGGTGTAT 59.163 43.478 0.00 0.00 0.00 2.29
919 955 3.233507 AGTCTACAAGGTTTCGGGTGTA 58.766 45.455 0.00 0.00 0.00 2.90
920 956 2.044758 AGTCTACAAGGTTTCGGGTGT 58.955 47.619 0.00 0.00 0.00 4.16
921 957 2.833631 AGTCTACAAGGTTTCGGGTG 57.166 50.000 0.00 0.00 0.00 4.61
922 958 4.961438 TTAAGTCTACAAGGTTTCGGGT 57.039 40.909 0.00 0.00 0.00 5.28
923 959 5.704053 ACAATTAAGTCTACAAGGTTTCGGG 59.296 40.000 0.00 0.00 0.00 5.14
924 960 6.796705 ACAATTAAGTCTACAAGGTTTCGG 57.203 37.500 0.00 0.00 0.00 4.30
975 1011 2.032426 CCCTGTAACGACAAACAACACC 59.968 50.000 0.00 0.00 34.35 4.16
1057 1093 3.102204 TGATCATCTCTTGTGGCTGAGA 58.898 45.455 0.00 0.00 42.56 3.27
1074 1110 3.429085 GCGTTGATTGTCAATGGTGATC 58.571 45.455 1.88 0.00 42.17 2.92
1081 1117 1.269448 GTGTGGGCGTTGATTGTCAAT 59.731 47.619 0.00 0.00 38.79 2.57
1156 1192 1.153289 CGCTGGAGGGGATGAACAG 60.153 63.158 0.00 0.00 0.00 3.16
1569 1605 0.459899 TGCCGGTGATGTAGCTAGTG 59.540 55.000 1.90 0.00 0.00 2.74
1683 1719 2.867793 TAGCACGGCGTTGCATCCAT 62.868 55.000 27.16 14.32 45.62 3.41
1794 1830 4.141482 GGGCAGGGATTTACAGATACAAGA 60.141 45.833 0.00 0.00 0.00 3.02
1945 1997 7.598493 GCCTTGATTAAATTAACTCTTGTTGCA 59.402 33.333 0.00 0.00 37.59 4.08
1967 2019 3.146104 ACAAGAAGCTACACATGCCTT 57.854 42.857 0.00 0.00 0.00 4.35
2051 2123 5.136048 ACCCACCATTATTATCCATGGAGTT 59.864 40.000 21.33 6.86 42.49 3.01
2066 2138 0.113580 AGCCCGTTTAACCCACCATT 59.886 50.000 0.00 0.00 0.00 3.16
2067 2139 0.610785 CAGCCCGTTTAACCCACCAT 60.611 55.000 0.00 0.00 0.00 3.55
2068 2140 1.228306 CAGCCCGTTTAACCCACCA 60.228 57.895 0.00 0.00 0.00 4.17
2074 2146 0.601057 ATTGTGCCAGCCCGTTTAAC 59.399 50.000 0.00 0.00 0.00 2.01
2093 2165 2.172717 GGAGGCCTATTTGTGGAGCTTA 59.827 50.000 4.42 0.00 0.00 3.09
2094 2166 1.064389 GGAGGCCTATTTGTGGAGCTT 60.064 52.381 4.42 0.00 0.00 3.74
2095 2167 0.548510 GGAGGCCTATTTGTGGAGCT 59.451 55.000 4.42 0.00 0.00 4.09
2144 2226 6.374417 AAAACCCTAGCATTTCTCTCACTA 57.626 37.500 0.00 0.00 0.00 2.74
2146 2228 5.390991 CGAAAAACCCTAGCATTTCTCTCAC 60.391 44.000 0.00 0.00 31.29 3.51
2152 2234 2.230266 TGGCGAAAAACCCTAGCATTTC 59.770 45.455 0.00 0.00 0.00 2.17
2162 2244 3.649073 AGCACTTTTATGGCGAAAAACC 58.351 40.909 0.00 0.00 0.00 3.27
2217 2299 2.034221 GACCCAAAGCCTCGCCTT 59.966 61.111 0.00 0.00 0.00 4.35
2244 2326 5.977171 AAAACAACCAATAGTTTTTCGGC 57.023 34.783 0.00 0.00 43.26 5.54
2247 2329 9.549078 TCCCAATAAAACAACCAATAGTTTTTC 57.451 29.630 8.34 0.00 43.26 2.29
2269 2351 6.620877 ACAACATACAAGATTACTCTCCCA 57.379 37.500 0.00 0.00 0.00 4.37
2292 5802 5.595814 TTGTTACAACCACCCCCTTTATA 57.404 39.130 0.00 0.00 0.00 0.98
2293 5803 4.472690 TTGTTACAACCACCCCCTTTAT 57.527 40.909 0.00 0.00 0.00 1.40
2347 5857 2.134789 AGAAGGTGGCTTATGCTTGG 57.865 50.000 0.13 0.00 39.59 3.61
2428 5938 5.388408 TGAACATGCTGCATAAACATTCA 57.612 34.783 15.78 15.55 0.00 2.57
2469 5979 5.083122 TGTTGAAAGGGATGGCTGATTTTA 58.917 37.500 0.00 0.00 0.00 1.52
2490 6001 4.819630 TGCACTTCCTCTTCGTATTTTTGT 59.180 37.500 0.00 0.00 0.00 2.83
2506 6017 0.322975 TCAGCTCCTCCTTGCACTTC 59.677 55.000 0.00 0.00 0.00 3.01
2510 6021 0.911045 TCCATCAGCTCCTCCTTGCA 60.911 55.000 0.00 0.00 0.00 4.08
2511 6022 0.473326 ATCCATCAGCTCCTCCTTGC 59.527 55.000 0.00 0.00 0.00 4.01
2528 6039 6.805271 CCTTGAATGACAATGTTCAGTTGATC 59.195 38.462 0.00 0.00 37.88 2.92
2549 6060 7.603784 CCCAAATATTTTTCCAGAGAAACCTTG 59.396 37.037 0.00 0.00 41.69 3.61
2670 6181 0.727398 GGATCACTTGCGCTACAACC 59.273 55.000 9.73 0.00 33.68 3.77
2671 6182 0.727398 GGGATCACTTGCGCTACAAC 59.273 55.000 9.73 0.00 33.68 3.32
2672 6183 0.392461 GGGGATCACTTGCGCTACAA 60.392 55.000 9.73 0.00 36.62 2.41
2673 6184 1.220749 GGGGATCACTTGCGCTACA 59.779 57.895 9.73 0.00 0.00 2.74
2674 6185 1.883084 CGGGGATCACTTGCGCTAC 60.883 63.158 9.73 0.00 0.00 3.58
2675 6186 1.895020 AACGGGGATCACTTGCGCTA 61.895 55.000 9.73 0.00 0.00 4.26
2676 6187 2.748058 AAACGGGGATCACTTGCGCT 62.748 55.000 9.73 0.00 0.00 5.92
2677 6188 1.022451 TAAACGGGGATCACTTGCGC 61.022 55.000 0.00 0.00 0.00 6.09
2678 6189 1.330521 CATAAACGGGGATCACTTGCG 59.669 52.381 0.00 0.00 0.00 4.85
2679 6190 1.065551 GCATAAACGGGGATCACTTGC 59.934 52.381 0.00 0.00 0.00 4.01
2680 6191 2.364632 TGCATAAACGGGGATCACTTG 58.635 47.619 0.00 0.00 0.00 3.16
2681 6192 2.799126 TGCATAAACGGGGATCACTT 57.201 45.000 0.00 0.00 0.00 3.16
2682 6193 2.799126 TTGCATAAACGGGGATCACT 57.201 45.000 0.00 0.00 0.00 3.41
2683 6194 2.034558 CCATTGCATAAACGGGGATCAC 59.965 50.000 0.00 0.00 0.00 3.06
2684 6195 2.305928 CCATTGCATAAACGGGGATCA 58.694 47.619 0.00 0.00 0.00 2.92
2685 6196 1.000274 GCCATTGCATAAACGGGGATC 60.000 52.381 0.00 0.00 37.47 3.36
2686 6197 1.039856 GCCATTGCATAAACGGGGAT 58.960 50.000 0.00 0.00 37.47 3.85
2687 6198 0.323816 TGCCATTGCATAAACGGGGA 60.324 50.000 0.00 0.00 44.23 4.81
2688 6199 2.197250 TGCCATTGCATAAACGGGG 58.803 52.632 0.00 0.00 44.23 5.73


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

AutoCloner maintained by Alex Coulton.