Multiple sequence alignment - TraesCS1D01G056700

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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 TraesCS1D01G056700 chr1D 100.000 3824 0 0 1 3824 37445599 37449422 0.000000e+00 7062
1 TraesCS1D01G056700 chr1D 86.513 1861 247 4 966 2824 37424411 37426269 0.000000e+00 2043
2 TraesCS1D01G056700 chr1D 84.773 2003 283 14 964 2946 36617623 36615623 0.000000e+00 1989
3 TraesCS1D01G056700 chr1D 97.071 956 25 2 1 954 51932026 51932980 0.000000e+00 1607
4 TraesCS1D01G056700 chr1D 94.974 955 26 3 1 954 116477305 116478238 0.000000e+00 1478
5 TraesCS1D01G056700 chr1D 83.770 573 76 11 2966 3523 38558217 38557647 9.410000e-146 527
6 TraesCS1D01G056700 chr1D 81.469 572 76 9 2966 3526 38581930 38581378 3.510000e-120 442
7 TraesCS1D01G056700 chr1D 87.283 346 44 0 2966 3311 38365943 38365598 2.770000e-106 396
8 TraesCS1D01G056700 chr1B 94.721 1951 92 5 1027 2967 57137684 57139633 0.000000e+00 3022
9 TraesCS1D01G056700 chr1B 89.800 2000 192 10 965 2962 57220853 57222842 0.000000e+00 2553
10 TraesCS1D01G056700 chr1B 86.146 1855 255 2 964 2817 57130804 57132657 0.000000e+00 2001
11 TraesCS1D01G056700 chr1B 85.561 1863 258 9 966 2824 56619951 56618096 0.000000e+00 1940
12 TraesCS1D01G056700 chr1B 98.598 856 12 0 2966 3821 57375632 57376487 0.000000e+00 1515
13 TraesCS1D01G056700 chr1B 84.667 450 61 8 2966 3409 58326593 58326146 3.510000e-120 442
14 TraesCS1D01G056700 chr1A 92.829 2008 137 2 955 2962 36636114 36638114 0.000000e+00 2904
15 TraesCS1D01G056700 chr1A 87.929 1864 217 8 964 2824 36613759 36615617 0.000000e+00 2189
16 TraesCS1D01G056700 chr1A 84.174 2022 301 11 964 2967 36174246 36172226 0.000000e+00 1943
17 TraesCS1D01G056700 chr1A 98.254 859 15 0 2966 3824 36757681 36758539 0.000000e+00 1504
18 TraesCS1D01G056700 chr1A 83.798 574 74 13 2966 3523 37503250 37502680 9.410000e-146 527
19 TraesCS1D01G056700 chr1A 79.301 744 105 30 2968 3700 36637631 36638336 3.460000e-130 475
20 TraesCS1D01G056700 chr1A 86.590 261 31 4 616 874 384909504 384909762 6.250000e-73 285
21 TraesCS1D01G056700 chr1A 88.587 184 18 2 304 484 384909201 384909384 1.790000e-53 220
22 TraesCS1D01G056700 chr6D 93.898 295 18 0 1 295 464435864 464435570 2.710000e-121 446
23 TraesCS1D01G056700 chr7D 93.220 295 20 0 1 295 179492472 179492178 5.870000e-118 435
24 TraesCS1D01G056700 chr7D 92.881 295 21 0 1 295 43982739 43983033 2.730000e-116 429
25 TraesCS1D01G056700 chr7D 92.857 294 21 0 1 294 634965884 634966177 9.820000e-116 427
26 TraesCS1D01G056700 chr3D 91.429 315 25 2 6 319 462239664 462239351 7.590000e-117 431
27 TraesCS1D01G056700 chr5D 92.881 295 21 0 1 295 256741969 256742263 2.730000e-116 429
28 TraesCS1D01G056700 chr5D 90.086 232 16 5 726 954 397835002 397835229 1.040000e-75 294
29 TraesCS1D01G056700 chr5D 90.625 224 12 6 734 954 17468016 17467799 4.830000e-74 289
30 TraesCS1D01G056700 chrUn 92.881 295 20 1 1 295 402809041 402808748 9.820000e-116 427
31 TraesCS1D01G056700 chr6B 84.153 366 52 6 2966 3330 601867948 601868308 2.190000e-92 350
32 TraesCS1D01G056700 chr4D 78.037 642 82 35 346 954 179851574 179850959 2.190000e-92 350
33 TraesCS1D01G056700 chr7B 91.589 214 17 1 741 954 418761595 418761383 1.040000e-75 294
34 TraesCS1D01G056700 chr7A 90.583 223 15 5 736 954 350429348 350429128 1.340000e-74 291
35 TraesCS1D01G056700 chr5A 89.565 230 18 5 730 955 505620404 505620631 1.740000e-73 287


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 TraesCS1D01G056700 chr1D 37445599 37449422 3823 False 7062.0 7062 100.0000 1 3824 1 chr1D.!!$F2 3823
1 TraesCS1D01G056700 chr1D 37424411 37426269 1858 False 2043.0 2043 86.5130 966 2824 1 chr1D.!!$F1 1858
2 TraesCS1D01G056700 chr1D 36615623 36617623 2000 True 1989.0 1989 84.7730 964 2946 1 chr1D.!!$R1 1982
3 TraesCS1D01G056700 chr1D 51932026 51932980 954 False 1607.0 1607 97.0710 1 954 1 chr1D.!!$F3 953
4 TraesCS1D01G056700 chr1D 116477305 116478238 933 False 1478.0 1478 94.9740 1 954 1 chr1D.!!$F4 953
5 TraesCS1D01G056700 chr1D 38557647 38558217 570 True 527.0 527 83.7700 2966 3523 1 chr1D.!!$R3 557
6 TraesCS1D01G056700 chr1D 38581378 38581930 552 True 442.0 442 81.4690 2966 3526 1 chr1D.!!$R4 560
7 TraesCS1D01G056700 chr1B 57137684 57139633 1949 False 3022.0 3022 94.7210 1027 2967 1 chr1B.!!$F2 1940
8 TraesCS1D01G056700 chr1B 57220853 57222842 1989 False 2553.0 2553 89.8000 965 2962 1 chr1B.!!$F3 1997
9 TraesCS1D01G056700 chr1B 57130804 57132657 1853 False 2001.0 2001 86.1460 964 2817 1 chr1B.!!$F1 1853
10 TraesCS1D01G056700 chr1B 56618096 56619951 1855 True 1940.0 1940 85.5610 966 2824 1 chr1B.!!$R1 1858
11 TraesCS1D01G056700 chr1B 57375632 57376487 855 False 1515.0 1515 98.5980 2966 3821 1 chr1B.!!$F4 855
12 TraesCS1D01G056700 chr1A 36613759 36615617 1858 False 2189.0 2189 87.9290 964 2824 1 chr1A.!!$F1 1860
13 TraesCS1D01G056700 chr1A 36172226 36174246 2020 True 1943.0 1943 84.1740 964 2967 1 chr1A.!!$R1 2003
14 TraesCS1D01G056700 chr1A 36636114 36638336 2222 False 1689.5 2904 86.0650 955 3700 2 chr1A.!!$F3 2745
15 TraesCS1D01G056700 chr1A 36757681 36758539 858 False 1504.0 1504 98.2540 2966 3824 1 chr1A.!!$F2 858
16 TraesCS1D01G056700 chr1A 37502680 37503250 570 True 527.0 527 83.7980 2966 3523 1 chr1A.!!$R2 557
17 TraesCS1D01G056700 chr1A 384909201 384909762 561 False 252.5 285 87.5885 304 874 2 chr1A.!!$F4 570
18 TraesCS1D01G056700 chr4D 179850959 179851574 615 True 350.0 350 78.0370 346 954 1 chr4D.!!$R1 608

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
337 338 0.693049 AGCCGAATCAGTGGAAACCT 59.307 50.000 0.0 0.0 0.00 3.50 F
778 853 1.248101 TGGATCGGTGAGAGCACGAA 61.248 55.000 0.0 0.0 46.09 3.85 F
1559 1642 1.745087 CAATGGTATTGCAGCCGACTT 59.255 47.619 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1274 1.099689 GACGAAGGACTAGCTCTGCT 58.900 55.000 0.00 0.0 43.41 4.24 R
2332 2421 4.098416 GCTTCGTCTGCACAATTATTTCC 58.902 43.478 0.00 0.0 0.00 3.13 R
2865 2954 0.034089 ACTGGCAGGAGGGTTTATGC 60.034 55.000 20.34 0.0 37.95 3.14 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
60 61 6.128715 GGTCAATAGAGTCATATGCATCAACG 60.129 42.308 0.19 0.00 0.00 4.10
73 74 2.680974 ATCAACGCATCCGATGGGGG 62.681 60.000 24.62 17.50 46.33 5.40
154 155 0.885879 AGAGCGACAATCACCACGTA 59.114 50.000 0.00 0.00 0.00 3.57
180 181 2.423898 CGCCACAGGGGACGATAGT 61.424 63.158 0.00 0.00 44.88 2.12
278 279 2.699954 GTCAAAAATCTCCGGAGAGCA 58.300 47.619 35.72 16.84 41.33 4.26
337 338 0.693049 AGCCGAATCAGTGGAAACCT 59.307 50.000 0.00 0.00 0.00 3.50
778 853 1.248101 TGGATCGGTGAGAGCACGAA 61.248 55.000 0.00 0.00 46.09 3.85
838 918 7.015195 ACCATGTTAGGAAAGCAACTTGTATTT 59.985 33.333 0.00 0.00 31.39 1.40
898 978 4.598022 TGTGGAACATATGCAGGAAATCA 58.402 39.130 1.58 0.00 45.67 2.57
908 988 9.578576 ACATATGCAGGAAATCACTTATACAAT 57.421 29.630 1.58 0.00 0.00 2.71
994 1074 2.283532 AGGCACTCGACCTGCTCT 60.284 61.111 9.60 3.80 35.72 4.09
1194 1274 3.790223 GCCAGGGCAATGGACAAA 58.210 55.556 11.80 0.00 43.57 2.83
1266 1346 7.279750 TGCAGTGACATATAATTGCATGATT 57.720 32.000 0.00 0.00 36.71 2.57
1559 1642 1.745087 CAATGGTATTGCAGCCGACTT 59.255 47.619 0.00 0.00 0.00 3.01
1894 1983 8.008279 GTCCTAACATTTCGTTCTTTAGTTCAC 58.992 37.037 0.00 0.00 39.14 3.18
2138 2227 5.409826 GCTATTGTAGAAATGGAAGGATCGG 59.590 44.000 0.00 0.00 0.00 4.18
2195 2284 7.330208 GCGTAAGAGAATTAAACCTGACACTAA 59.670 37.037 0.00 0.00 43.02 2.24
2249 2338 3.492102 TTCTGGGAGAACTGTTTCTGG 57.508 47.619 0.00 0.00 42.53 3.86
2332 2421 6.205101 ACGTAATACTAGGAGGTCTTTGTG 57.795 41.667 0.00 0.00 0.00 3.33
2840 2929 4.923893 TGTTGATTTTGCACAAGACTCTG 58.076 39.130 0.00 0.00 0.00 3.35
2841 2930 3.631145 TGATTTTGCACAAGACTCTGC 57.369 42.857 0.00 0.00 0.00 4.26
2842 2931 3.216800 TGATTTTGCACAAGACTCTGCT 58.783 40.909 6.63 0.00 34.29 4.24
2843 2932 3.251729 TGATTTTGCACAAGACTCTGCTC 59.748 43.478 6.63 0.00 34.29 4.26
2844 2933 2.330440 TTTGCACAAGACTCTGCTCA 57.670 45.000 6.63 0.00 34.29 4.26
2845 2934 1.875009 TTGCACAAGACTCTGCTCAG 58.125 50.000 6.63 0.00 34.29 3.35
2846 2935 0.034476 TGCACAAGACTCTGCTCAGG 59.966 55.000 6.63 0.00 34.29 3.86
2847 2936 0.319728 GCACAAGACTCTGCTCAGGA 59.680 55.000 0.00 0.00 0.00 3.86
2848 2937 1.270518 GCACAAGACTCTGCTCAGGAA 60.271 52.381 0.00 0.00 0.00 3.36
2849 2938 2.686235 CACAAGACTCTGCTCAGGAAG 58.314 52.381 0.00 0.00 0.00 3.46
2862 2951 3.636381 CTCAGGAAGCTTGAGTTTTTGC 58.364 45.455 2.10 0.00 37.79 3.68
2863 2952 3.290710 TCAGGAAGCTTGAGTTTTTGCT 58.709 40.909 2.10 0.00 37.37 3.91
2864 2953 3.701040 TCAGGAAGCTTGAGTTTTTGCTT 59.299 39.130 2.10 0.00 46.69 3.91
2865 2954 3.800506 CAGGAAGCTTGAGTTTTTGCTTG 59.199 43.478 2.10 0.00 44.47 4.01
2866 2955 2.541346 GGAAGCTTGAGTTTTTGCTTGC 59.459 45.455 2.10 3.19 44.47 4.01
2867 2956 2.965572 AGCTTGAGTTTTTGCTTGCA 57.034 40.000 0.00 0.00 30.96 4.08
2868 2957 3.464111 AGCTTGAGTTTTTGCTTGCAT 57.536 38.095 0.00 0.00 30.96 3.96
2869 2958 4.589216 AGCTTGAGTTTTTGCTTGCATA 57.411 36.364 0.00 0.00 30.96 3.14
2870 2959 4.947645 AGCTTGAGTTTTTGCTTGCATAA 58.052 34.783 0.00 0.00 30.96 1.90
2871 2960 5.358922 AGCTTGAGTTTTTGCTTGCATAAA 58.641 33.333 7.03 7.03 30.96 1.40
2872 2961 5.234972 AGCTTGAGTTTTTGCTTGCATAAAC 59.765 36.000 23.88 23.88 30.96 2.01
2873 2962 5.558844 GCTTGAGTTTTTGCTTGCATAAACC 60.559 40.000 25.98 20.33 32.35 3.27
2874 2963 4.376146 TGAGTTTTTGCTTGCATAAACCC 58.624 39.130 25.98 19.83 32.35 4.11
2875 2964 4.100808 TGAGTTTTTGCTTGCATAAACCCT 59.899 37.500 25.98 15.68 32.35 4.34
2876 2965 4.631131 AGTTTTTGCTTGCATAAACCCTC 58.369 39.130 25.98 11.10 32.35 4.30
2877 2966 3.676291 TTTTGCTTGCATAAACCCTCC 57.324 42.857 0.00 0.00 0.00 4.30
2878 2967 2.603075 TTGCTTGCATAAACCCTCCT 57.397 45.000 0.00 0.00 0.00 3.69
2879 2968 1.838112 TGCTTGCATAAACCCTCCTG 58.162 50.000 0.00 0.00 0.00 3.86
2880 2969 0.457443 GCTTGCATAAACCCTCCTGC 59.543 55.000 0.00 0.00 35.21 4.85
2881 2970 1.106285 CTTGCATAAACCCTCCTGCC 58.894 55.000 0.00 0.00 33.70 4.85
2882 2971 0.407528 TTGCATAAACCCTCCTGCCA 59.592 50.000 0.00 0.00 33.70 4.92
2883 2972 0.034186 TGCATAAACCCTCCTGCCAG 60.034 55.000 0.00 0.00 33.70 4.85
2884 2973 0.034089 GCATAAACCCTCCTGCCAGT 60.034 55.000 0.00 0.00 0.00 4.00
2885 2974 1.211949 GCATAAACCCTCCTGCCAGTA 59.788 52.381 0.00 0.00 0.00 2.74
2886 2975 2.158608 GCATAAACCCTCCTGCCAGTAT 60.159 50.000 0.00 0.00 0.00 2.12
2887 2976 3.480470 CATAAACCCTCCTGCCAGTATG 58.520 50.000 0.00 0.00 0.00 2.39
2888 2977 1.668826 AAACCCTCCTGCCAGTATGA 58.331 50.000 0.00 0.00 39.69 2.15
2889 2978 0.912486 AACCCTCCTGCCAGTATGAC 59.088 55.000 0.00 0.00 39.69 3.06
2890 2979 0.983378 ACCCTCCTGCCAGTATGACC 60.983 60.000 0.00 0.00 39.69 4.02
2891 2980 1.443407 CCTCCTGCCAGTATGACCG 59.557 63.158 0.00 0.00 39.69 4.79
2892 2981 1.330655 CCTCCTGCCAGTATGACCGT 61.331 60.000 0.00 0.00 39.69 4.83
2893 2982 1.399714 CTCCTGCCAGTATGACCGTA 58.600 55.000 0.00 0.00 39.69 4.02
2894 2983 1.964223 CTCCTGCCAGTATGACCGTAT 59.036 52.381 0.00 0.00 39.69 3.06
2895 2984 3.154710 CTCCTGCCAGTATGACCGTATA 58.845 50.000 0.00 0.00 39.69 1.47
2896 2985 3.568443 TCCTGCCAGTATGACCGTATAA 58.432 45.455 0.00 0.00 39.69 0.98
2897 2986 3.572682 TCCTGCCAGTATGACCGTATAAG 59.427 47.826 0.00 0.00 39.69 1.73
2898 2987 3.572682 CCTGCCAGTATGACCGTATAAGA 59.427 47.826 0.00 0.00 39.69 2.10
2899 2988 4.038763 CCTGCCAGTATGACCGTATAAGAA 59.961 45.833 0.00 0.00 39.69 2.52
2900 2989 5.452776 CCTGCCAGTATGACCGTATAAGAAA 60.453 44.000 0.00 0.00 39.69 2.52
2901 2990 6.169557 TGCCAGTATGACCGTATAAGAAAT 57.830 37.500 0.00 0.00 39.69 2.17
2902 2991 6.220930 TGCCAGTATGACCGTATAAGAAATC 58.779 40.000 0.00 0.00 39.69 2.17
2903 2992 5.638234 GCCAGTATGACCGTATAAGAAATCC 59.362 44.000 0.00 0.00 39.69 3.01
2904 2993 6.740401 GCCAGTATGACCGTATAAGAAATCCA 60.740 42.308 0.00 0.00 39.69 3.41
2905 2994 7.214381 CCAGTATGACCGTATAAGAAATCCAA 58.786 38.462 0.00 0.00 39.69 3.53
2906 2995 7.713507 CCAGTATGACCGTATAAGAAATCCAAA 59.286 37.037 0.00 0.00 39.69 3.28
2907 2996 8.548721 CAGTATGACCGTATAAGAAATCCAAAC 58.451 37.037 0.00 0.00 39.69 2.93
2908 2997 8.483758 AGTATGACCGTATAAGAAATCCAAACT 58.516 33.333 0.00 0.00 0.00 2.66
2909 2998 6.978343 TGACCGTATAAGAAATCCAAACTG 57.022 37.500 0.00 0.00 0.00 3.16
2910 2999 5.353123 TGACCGTATAAGAAATCCAAACTGC 59.647 40.000 0.00 0.00 0.00 4.40
2911 3000 5.250200 ACCGTATAAGAAATCCAAACTGCA 58.750 37.500 0.00 0.00 0.00 4.41
2912 3001 5.885912 ACCGTATAAGAAATCCAAACTGCAT 59.114 36.000 0.00 0.00 0.00 3.96
2913 3002 6.183360 ACCGTATAAGAAATCCAAACTGCATG 60.183 38.462 0.00 0.00 0.00 4.06
2914 3003 5.682862 CGTATAAGAAATCCAAACTGCATGC 59.317 40.000 11.82 11.82 0.00 4.06
2915 3004 5.927281 ATAAGAAATCCAAACTGCATGCT 57.073 34.783 20.33 0.00 0.00 3.79
2916 3005 4.612264 AAGAAATCCAAACTGCATGCTT 57.388 36.364 20.33 2.28 0.00 3.91
2917 3006 3.921677 AGAAATCCAAACTGCATGCTTG 58.078 40.909 20.33 14.69 0.00 4.01
2918 3007 3.322828 AGAAATCCAAACTGCATGCTTGT 59.677 39.130 20.33 14.68 0.00 3.16
2919 3008 4.523943 AGAAATCCAAACTGCATGCTTGTA 59.476 37.500 20.33 2.38 0.00 2.41
2920 3009 4.445452 AATCCAAACTGCATGCTTGTAG 57.555 40.909 20.33 14.79 40.98 2.74
2921 3010 1.541147 TCCAAACTGCATGCTTGTAGC 59.459 47.619 20.33 0.00 38.99 3.58
2931 3020 3.264574 GCTTGTAGCATTGGGGTCA 57.735 52.632 0.00 0.00 41.89 4.02
2932 3021 1.767759 GCTTGTAGCATTGGGGTCAT 58.232 50.000 0.00 0.00 41.89 3.06
2933 3022 2.102578 GCTTGTAGCATTGGGGTCATT 58.897 47.619 0.00 0.00 41.89 2.57
2934 3023 2.497273 GCTTGTAGCATTGGGGTCATTT 59.503 45.455 0.00 0.00 41.89 2.32
2935 3024 3.699038 GCTTGTAGCATTGGGGTCATTTA 59.301 43.478 0.00 0.00 41.89 1.40
2936 3025 4.202050 GCTTGTAGCATTGGGGTCATTTAG 60.202 45.833 0.00 0.00 41.89 1.85
2937 3026 3.287222 TGTAGCATTGGGGTCATTTAGC 58.713 45.455 0.00 0.00 0.00 3.09
2938 3027 1.392589 AGCATTGGGGTCATTTAGCG 58.607 50.000 0.00 0.00 0.00 4.26
2939 3028 0.385390 GCATTGGGGTCATTTAGCGG 59.615 55.000 0.00 0.00 0.00 5.52
2940 3029 1.762708 CATTGGGGTCATTTAGCGGT 58.237 50.000 0.00 0.00 0.00 5.68
2941 3030 1.405105 CATTGGGGTCATTTAGCGGTG 59.595 52.381 0.00 0.00 0.00 4.94
2942 3031 0.402504 TTGGGGTCATTTAGCGGTGT 59.597 50.000 0.00 0.00 0.00 4.16
2943 3032 0.322098 TGGGGTCATTTAGCGGTGTG 60.322 55.000 0.00 0.00 0.00 3.82
2944 3033 0.322187 GGGGTCATTTAGCGGTGTGT 60.322 55.000 0.00 0.00 0.00 3.72
2945 3034 1.084289 GGGTCATTTAGCGGTGTGTC 58.916 55.000 0.00 0.00 0.00 3.67
2946 3035 1.609580 GGGTCATTTAGCGGTGTGTCA 60.610 52.381 0.00 0.00 0.00 3.58
2947 3036 2.147958 GGTCATTTAGCGGTGTGTCAA 58.852 47.619 0.00 0.00 0.00 3.18
2948 3037 2.550606 GGTCATTTAGCGGTGTGTCAAA 59.449 45.455 0.00 0.00 0.00 2.69
2949 3038 3.003897 GGTCATTTAGCGGTGTGTCAAAA 59.996 43.478 0.00 0.00 0.00 2.44
2950 3039 4.498345 GGTCATTTAGCGGTGTGTCAAAAA 60.498 41.667 0.00 0.00 0.00 1.94
2951 3040 5.219633 GTCATTTAGCGGTGTGTCAAAAAT 58.780 37.500 0.00 0.00 0.00 1.82
2952 3041 5.342259 GTCATTTAGCGGTGTGTCAAAAATC 59.658 40.000 0.00 0.00 0.00 2.17
2953 3042 4.902443 TTTAGCGGTGTGTCAAAAATCA 57.098 36.364 0.00 0.00 0.00 2.57
2954 3043 2.774439 AGCGGTGTGTCAAAAATCAC 57.226 45.000 0.00 0.00 35.43 3.06
2955 3044 2.020720 AGCGGTGTGTCAAAAATCACA 58.979 42.857 0.00 0.00 41.37 3.58
2956 3045 2.425312 AGCGGTGTGTCAAAAATCACAA 59.575 40.909 0.00 0.00 44.37 3.33
2957 3046 2.788786 GCGGTGTGTCAAAAATCACAAG 59.211 45.455 0.00 0.00 44.37 3.16
2958 3047 3.488384 GCGGTGTGTCAAAAATCACAAGA 60.488 43.478 0.00 0.00 44.37 3.02
2959 3048 4.282068 CGGTGTGTCAAAAATCACAAGAG 58.718 43.478 0.00 0.00 44.37 2.85
2960 3049 4.201910 CGGTGTGTCAAAAATCACAAGAGT 60.202 41.667 0.00 0.00 44.37 3.24
2961 3050 5.036737 GGTGTGTCAAAAATCACAAGAGTG 58.963 41.667 0.00 0.00 44.37 3.51
3628 3747 3.578716 TCTTTTCTACCAGACACCTGAGG 59.421 47.826 0.00 0.00 43.02 3.86
3775 3897 1.607148 GGACAAACGGGTTCTTGAAGG 59.393 52.381 0.00 0.00 0.00 3.46
3788 3910 5.582665 GGTTCTTGAAGGATGTATGTCTGAC 59.417 44.000 0.00 0.00 0.00 3.51
3789 3911 6.166279 GTTCTTGAAGGATGTATGTCTGACA 58.834 40.000 13.60 13.60 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 155 3.374402 CCCTGTGGCGACTCTCGT 61.374 66.667 0.00 0.00 42.81 4.18
180 181 1.174078 TTGGTGCTCGTCCGTCTGTA 61.174 55.000 0.00 0.00 0.00 2.74
204 205 0.518636 CACACATGTGCCTTTCCTCG 59.481 55.000 25.68 0.00 39.39 4.63
278 279 1.001641 GCCATGGTGTCTCTTGCCT 60.002 57.895 14.67 0.00 0.00 4.75
337 338 2.499693 TGCCTAATCTGATCCGTGTTCA 59.500 45.455 0.00 0.00 0.00 3.18
908 988 8.434392 GTCATGTACCCCTTTGTATTTATCCTA 58.566 37.037 0.00 0.00 0.00 2.94
909 989 7.128883 AGTCATGTACCCCTTTGTATTTATCCT 59.871 37.037 0.00 0.00 0.00 3.24
958 1038 1.153269 GCTGGCTCCTGCTACCTTC 60.153 63.158 10.08 0.00 39.59 3.46
981 1061 2.336478 CGTCCAGAGCAGGTCGAGT 61.336 63.158 4.11 0.00 41.67 4.18
994 1074 3.432186 CCTCTATCTTTTGCCATCGTCCA 60.432 47.826 0.00 0.00 0.00 4.02
1104 1184 4.079038 ACCCCTTGATGGATCATTTCATGA 60.079 41.667 0.00 0.00 44.55 3.07
1194 1274 1.099689 GACGAAGGACTAGCTCTGCT 58.900 55.000 0.00 0.00 43.41 4.24
1894 1983 6.760770 CCTTCTTGGCAGAGACTCTTTATTAG 59.239 42.308 0.98 0.00 0.00 1.73
2138 2227 4.380531 TCTGAACAGAGTCAAACCATCAC 58.619 43.478 0.00 0.00 32.82 3.06
2195 2284 6.095860 CCCATCCATTATGACGCAATATGAAT 59.904 38.462 0.00 0.00 37.86 2.57
2332 2421 4.098416 GCTTCGTCTGCACAATTATTTCC 58.902 43.478 0.00 0.00 0.00 3.13
2709 2798 6.566197 AATGAAGTTGTTGAAGCTTCTAGG 57.434 37.500 26.09 0.00 39.30 3.02
2712 2801 7.945134 ACATTAATGAAGTTGTTGAAGCTTCT 58.055 30.769 26.09 4.88 39.30 2.85
2799 2888 7.418840 TCAACAAAATCCATCGAAAAATTGG 57.581 32.000 0.00 0.00 0.00 3.16
2841 2930 3.317430 AGCAAAAACTCAAGCTTCCTGAG 59.683 43.478 11.56 11.56 32.52 3.35
2842 2931 3.290710 AGCAAAAACTCAAGCTTCCTGA 58.709 40.909 0.00 0.00 32.52 3.86
2843 2932 3.722728 AGCAAAAACTCAAGCTTCCTG 57.277 42.857 0.00 0.00 32.52 3.86
2844 2933 3.739209 GCAAGCAAAAACTCAAGCTTCCT 60.739 43.478 0.00 0.00 44.77 3.36
2845 2934 2.541346 GCAAGCAAAAACTCAAGCTTCC 59.459 45.455 0.00 0.00 44.77 3.46
2846 2935 3.189285 TGCAAGCAAAAACTCAAGCTTC 58.811 40.909 0.00 0.00 44.77 3.86
2848 2937 2.965572 TGCAAGCAAAAACTCAAGCT 57.034 40.000 0.00 0.00 39.37 3.74
2849 2938 5.434706 GTTTATGCAAGCAAAAACTCAAGC 58.565 37.500 0.00 0.00 0.00 4.01
2850 2939 5.050159 GGGTTTATGCAAGCAAAAACTCAAG 60.050 40.000 0.00 0.00 33.46 3.02
2851 2940 4.813697 GGGTTTATGCAAGCAAAAACTCAA 59.186 37.500 0.00 0.00 33.46 3.02
2852 2941 4.100808 AGGGTTTATGCAAGCAAAAACTCA 59.899 37.500 0.00 0.00 35.27 3.41
2853 2942 4.631131 AGGGTTTATGCAAGCAAAAACTC 58.369 39.130 0.00 0.00 34.23 3.01
2854 2943 4.503123 GGAGGGTTTATGCAAGCAAAAACT 60.503 41.667 0.00 4.05 34.23 2.66
2855 2944 3.745975 GGAGGGTTTATGCAAGCAAAAAC 59.254 43.478 0.00 4.31 34.23 2.43
2856 2945 3.645687 AGGAGGGTTTATGCAAGCAAAAA 59.354 39.130 0.00 0.00 34.23 1.94
2857 2946 3.006752 CAGGAGGGTTTATGCAAGCAAAA 59.993 43.478 0.00 0.00 34.23 2.44
2858 2947 2.562298 CAGGAGGGTTTATGCAAGCAAA 59.438 45.455 0.00 0.00 34.23 3.68
2859 2948 2.170166 CAGGAGGGTTTATGCAAGCAA 58.830 47.619 0.00 0.00 34.23 3.91
2860 2949 1.838112 CAGGAGGGTTTATGCAAGCA 58.162 50.000 0.00 0.00 34.23 3.91
2861 2950 0.457443 GCAGGAGGGTTTATGCAAGC 59.543 55.000 0.00 0.00 38.54 4.01
2862 2951 1.106285 GGCAGGAGGGTTTATGCAAG 58.894 55.000 0.00 0.00 40.46 4.01
2863 2952 0.407528 TGGCAGGAGGGTTTATGCAA 59.592 50.000 0.00 0.00 40.46 4.08
2864 2953 0.034186 CTGGCAGGAGGGTTTATGCA 60.034 55.000 6.61 0.00 40.46 3.96
2865 2954 0.034089 ACTGGCAGGAGGGTTTATGC 60.034 55.000 20.34 0.00 37.95 3.14
2866 2955 3.136443 TCATACTGGCAGGAGGGTTTATG 59.864 47.826 20.34 14.72 0.00 1.90
2867 2956 3.136626 GTCATACTGGCAGGAGGGTTTAT 59.863 47.826 20.34 2.56 0.00 1.40
2868 2957 2.504175 GTCATACTGGCAGGAGGGTTTA 59.496 50.000 20.34 0.00 0.00 2.01
2869 2958 1.282157 GTCATACTGGCAGGAGGGTTT 59.718 52.381 20.34 0.00 0.00 3.27
2870 2959 0.912486 GTCATACTGGCAGGAGGGTT 59.088 55.000 20.34 0.00 0.00 4.11
2871 2960 0.983378 GGTCATACTGGCAGGAGGGT 60.983 60.000 20.34 0.00 0.00 4.34
2872 2961 1.832912 GGTCATACTGGCAGGAGGG 59.167 63.158 20.34 7.17 0.00 4.30
2873 2962 1.330655 ACGGTCATACTGGCAGGAGG 61.331 60.000 20.34 13.09 0.00 4.30
2874 2963 1.399714 TACGGTCATACTGGCAGGAG 58.600 55.000 20.34 8.08 0.00 3.69
2875 2964 2.082140 ATACGGTCATACTGGCAGGA 57.918 50.000 20.34 11.65 0.00 3.86
2876 2965 3.572682 TCTTATACGGTCATACTGGCAGG 59.427 47.826 20.34 0.62 0.00 4.85
2877 2966 4.848562 TCTTATACGGTCATACTGGCAG 57.151 45.455 14.16 14.16 0.00 4.85
2878 2967 5.601583 TTTCTTATACGGTCATACTGGCA 57.398 39.130 0.00 0.00 0.00 4.92
2879 2968 5.638234 GGATTTCTTATACGGTCATACTGGC 59.362 44.000 0.00 0.00 0.00 4.85
2880 2969 6.755206 TGGATTTCTTATACGGTCATACTGG 58.245 40.000 0.00 0.00 0.00 4.00
2881 2970 8.548721 GTTTGGATTTCTTATACGGTCATACTG 58.451 37.037 0.00 0.00 0.00 2.74
2882 2971 8.483758 AGTTTGGATTTCTTATACGGTCATACT 58.516 33.333 0.00 0.00 0.00 2.12
2883 2972 8.548721 CAGTTTGGATTTCTTATACGGTCATAC 58.451 37.037 0.00 0.00 0.00 2.39
2884 2973 7.225931 GCAGTTTGGATTTCTTATACGGTCATA 59.774 37.037 0.00 0.00 0.00 2.15
2885 2974 6.038271 GCAGTTTGGATTTCTTATACGGTCAT 59.962 38.462 0.00 0.00 0.00 3.06
2886 2975 5.353123 GCAGTTTGGATTTCTTATACGGTCA 59.647 40.000 0.00 0.00 0.00 4.02
2887 2976 5.353123 TGCAGTTTGGATTTCTTATACGGTC 59.647 40.000 0.00 0.00 0.00 4.79
2888 2977 5.250200 TGCAGTTTGGATTTCTTATACGGT 58.750 37.500 0.00 0.00 0.00 4.83
2889 2978 5.811399 TGCAGTTTGGATTTCTTATACGG 57.189 39.130 0.00 0.00 0.00 4.02
2890 2979 5.682862 GCATGCAGTTTGGATTTCTTATACG 59.317 40.000 14.21 0.00 0.00 3.06
2891 2980 6.799512 AGCATGCAGTTTGGATTTCTTATAC 58.200 36.000 21.98 0.00 0.00 1.47
2892 2981 7.093814 ACAAGCATGCAGTTTGGATTTCTTATA 60.094 33.333 21.98 0.00 42.11 0.98
2893 2982 5.927281 AGCATGCAGTTTGGATTTCTTAT 57.073 34.783 21.98 0.00 0.00 1.73
2894 2983 5.010922 ACAAGCATGCAGTTTGGATTTCTTA 59.989 36.000 21.98 0.00 42.11 2.10
2895 2984 4.202284 ACAAGCATGCAGTTTGGATTTCTT 60.202 37.500 21.98 0.00 42.11 2.52
2896 2985 3.322828 ACAAGCATGCAGTTTGGATTTCT 59.677 39.130 21.98 0.00 42.11 2.52
2897 2986 3.656559 ACAAGCATGCAGTTTGGATTTC 58.343 40.909 21.98 0.00 42.11 2.17
2898 2987 3.756933 ACAAGCATGCAGTTTGGATTT 57.243 38.095 21.98 0.00 42.11 2.17
2899 2988 3.367703 GCTACAAGCATGCAGTTTGGATT 60.368 43.478 21.98 0.00 42.11 3.01
2900 2989 2.165030 GCTACAAGCATGCAGTTTGGAT 59.835 45.455 21.98 3.69 42.11 3.41
2901 2990 1.541147 GCTACAAGCATGCAGTTTGGA 59.459 47.619 21.98 11.62 42.11 3.53
2902 2991 1.986698 GCTACAAGCATGCAGTTTGG 58.013 50.000 21.98 11.94 42.11 3.28
2913 3002 1.767759 ATGACCCCAATGCTACAAGC 58.232 50.000 0.00 0.00 42.82 4.01
2914 3003 4.202050 GCTAAATGACCCCAATGCTACAAG 60.202 45.833 0.00 0.00 0.00 3.16
2915 3004 3.699038 GCTAAATGACCCCAATGCTACAA 59.301 43.478 0.00 0.00 0.00 2.41
2916 3005 3.287222 GCTAAATGACCCCAATGCTACA 58.713 45.455 0.00 0.00 0.00 2.74
2917 3006 2.290641 CGCTAAATGACCCCAATGCTAC 59.709 50.000 0.00 0.00 0.00 3.58
2918 3007 2.571212 CGCTAAATGACCCCAATGCTA 58.429 47.619 0.00 0.00 0.00 3.49
2919 3008 1.392589 CGCTAAATGACCCCAATGCT 58.607 50.000 0.00 0.00 0.00 3.79
2920 3009 0.385390 CCGCTAAATGACCCCAATGC 59.615 55.000 0.00 0.00 0.00 3.56
2921 3010 1.405105 CACCGCTAAATGACCCCAATG 59.595 52.381 0.00 0.00 0.00 2.82
2922 3011 1.005450 ACACCGCTAAATGACCCCAAT 59.995 47.619 0.00 0.00 0.00 3.16
2923 3012 0.402504 ACACCGCTAAATGACCCCAA 59.597 50.000 0.00 0.00 0.00 4.12
2924 3013 0.322098 CACACCGCTAAATGACCCCA 60.322 55.000 0.00 0.00 0.00 4.96
2925 3014 0.322187 ACACACCGCTAAATGACCCC 60.322 55.000 0.00 0.00 0.00 4.95
2926 3015 1.084289 GACACACCGCTAAATGACCC 58.916 55.000 0.00 0.00 0.00 4.46
2927 3016 1.803334 TGACACACCGCTAAATGACC 58.197 50.000 0.00 0.00 0.00 4.02
2928 3017 3.889196 TTTGACACACCGCTAAATGAC 57.111 42.857 0.00 0.00 0.00 3.06
2929 3018 4.902443 TTTTTGACACACCGCTAAATGA 57.098 36.364 0.00 0.00 0.00 2.57
2930 3019 5.116983 GTGATTTTTGACACACCGCTAAATG 59.883 40.000 0.00 0.00 37.05 2.32
2931 3020 5.219633 GTGATTTTTGACACACCGCTAAAT 58.780 37.500 0.00 0.00 37.05 1.40
2932 3021 4.096532 TGTGATTTTTGACACACCGCTAAA 59.903 37.500 0.00 0.00 41.19 1.85
2933 3022 3.628032 TGTGATTTTTGACACACCGCTAA 59.372 39.130 0.00 0.00 41.19 3.09
2934 3023 3.206964 TGTGATTTTTGACACACCGCTA 58.793 40.909 0.00 0.00 41.19 4.26
2935 3024 2.020720 TGTGATTTTTGACACACCGCT 58.979 42.857 0.00 0.00 41.19 5.52
2936 3025 2.483583 TGTGATTTTTGACACACCGC 57.516 45.000 0.00 0.00 41.19 5.68
2937 3026 4.201910 ACTCTTGTGATTTTTGACACACCG 60.202 41.667 0.00 0.00 44.81 4.94
2938 3027 5.036737 CACTCTTGTGATTTTTGACACACC 58.963 41.667 0.00 0.00 46.55 4.16
2952 3041 5.742453 GCTGATATTGCATTTCACTCTTGTG 59.258 40.000 0.00 0.00 45.07 3.33
2953 3042 5.163581 GGCTGATATTGCATTTCACTCTTGT 60.164 40.000 0.00 0.00 0.00 3.16
2954 3043 5.163591 TGGCTGATATTGCATTTCACTCTTG 60.164 40.000 0.00 0.00 0.00 3.02
2955 3044 4.951715 TGGCTGATATTGCATTTCACTCTT 59.048 37.500 0.00 0.00 0.00 2.85
2956 3045 4.529897 TGGCTGATATTGCATTTCACTCT 58.470 39.130 0.00 0.00 0.00 3.24
2957 3046 4.337555 ACTGGCTGATATTGCATTTCACTC 59.662 41.667 0.00 0.00 0.00 3.51
2958 3047 4.097437 CACTGGCTGATATTGCATTTCACT 59.903 41.667 0.00 0.00 0.00 3.41
2959 3048 4.357142 CACTGGCTGATATTGCATTTCAC 58.643 43.478 0.00 0.00 0.00 3.18
2960 3049 3.382227 CCACTGGCTGATATTGCATTTCA 59.618 43.478 0.00 0.00 0.00 2.69
2961 3050 3.243636 CCCACTGGCTGATATTGCATTTC 60.244 47.826 0.00 0.00 0.00 2.17
2962 3051 2.696707 CCCACTGGCTGATATTGCATTT 59.303 45.455 0.00 0.00 0.00 2.32
2963 3052 2.313317 CCCACTGGCTGATATTGCATT 58.687 47.619 0.00 0.00 0.00 3.56
2964 3053 1.216175 ACCCACTGGCTGATATTGCAT 59.784 47.619 0.00 0.00 33.59 3.96
3628 3747 7.039313 AGTGACTGTTTCAAAGGGATAAAAC 57.961 36.000 0.00 0.00 35.39 2.43
3678 3800 4.223700 AGCAGACCACTGAGAATGACATTA 59.776 41.667 0.00 0.00 46.03 1.90
3775 3897 5.560375 GCATCAGCAATGTCAGACATACATC 60.560 44.000 16.71 6.36 37.97 3.06
3788 3910 4.895224 ACTCAACATAGCATCAGCAATG 57.105 40.909 0.00 0.00 45.49 2.82
3789 3911 5.008415 GCTAACTCAACATAGCATCAGCAAT 59.992 40.000 0.20 0.00 45.49 3.56


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

AutoCloner maintained by Alex Coulton.