Multiple sequence alignment - TraesCS5D01G509900

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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 TraesCS5D01G509900 chr5D 100.000 3038 0 0 346 3383 534869755 534872792 0.000000e+00 5611.0
1 TraesCS5D01G509900 chr5D 100.000 137 0 0 1 137 534869410 534869546 1.560000e-63 254.0
2 TraesCS5D01G509900 chr5D 84.211 190 25 4 2790 2977 291087915 291088101 2.680000e-41 180.0
3 TraesCS5D01G509900 chr5D 83.590 195 19 8 404 594 546482970 546482785 1.610000e-38 171.0
4 TraesCS5D01G509900 chr5D 100.000 36 0 0 2675 2710 534872043 534872078 2.180000e-07 67.6
5 TraesCS5D01G509900 chr5D 100.000 36 0 0 2634 2669 534872084 534872119 2.180000e-07 67.6
6 TraesCS5D01G509900 chr5D 100.000 28 0 0 3115 3142 414106034 414106061 6.000000e-03 52.8
7 TraesCS5D01G509900 chr5B 94.241 1858 75 14 836 2673 675869721 675871566 0.000000e+00 2809.0
8 TraesCS5D01G509900 chr5B 81.117 376 39 16 3020 3379 675871682 675872041 4.300000e-69 272.0
9 TraesCS5D01G509900 chr5B 83.681 288 26 15 347 628 675869115 675869387 5.600000e-63 252.0
10 TraesCS5D01G509900 chr4A 92.692 1984 81 16 836 2798 636669635 636667695 0.000000e+00 2802.0
11 TraesCS5D01G509900 chr4A 91.020 490 26 6 352 837 636670259 636669784 0.000000e+00 645.0
12 TraesCS5D01G509900 chr4A 87.435 382 28 7 3017 3383 636667655 636667279 4.040000e-114 422.0
13 TraesCS5D01G509900 chr4A 97.810 137 2 1 1 137 636670556 636670421 5.640000e-58 235.0
14 TraesCS5D01G509900 chr4A 84.483 174 19 6 2799 2967 35877948 35878118 7.510000e-37 165.0
15 TraesCS5D01G509900 chr4A 100.000 30 0 0 2679 2708 636667873 636667844 4.720000e-04 56.5
16 TraesCS5D01G509900 chrUn 94.483 145 4 3 2796 2938 70301796 70301654 1.580000e-53 220.0
17 TraesCS5D01G509900 chr7D 87.895 190 7 8 2797 2972 161459059 161459246 3.420000e-50 209.0
18 TraesCS5D01G509900 chr7D 87.845 181 13 8 2795 2967 26002471 26002292 1.590000e-48 204.0
19 TraesCS5D01G509900 chr7D 80.876 251 44 4 346 594 499961572 499961324 9.580000e-46 195.0
20 TraesCS5D01G509900 chr7D 84.127 189 18 8 2797 2976 417353454 417353269 4.490000e-39 172.0
21 TraesCS5D01G509900 chr2D 81.746 252 40 6 346 594 578336321 578336073 4.420000e-49 206.0
22 TraesCS5D01G509900 chr2D 87.356 174 16 3 2797 2967 623514861 623515031 9.580000e-46 195.0
23 TraesCS5D01G509900 chr2D 83.784 148 23 1 346 492 518264015 518263868 4.550000e-29 139.0
24 TraesCS5D01G509900 chr2D 89.216 102 10 1 493 594 518263560 518263460 3.540000e-25 126.0
25 TraesCS5D01G509900 chr2D 77.778 162 25 9 652 809 601047190 601047036 4.650000e-14 89.8
26 TraesCS5D01G509900 chr1D 88.571 175 10 6 2796 2968 473449041 473449207 1.590000e-48 204.0
27 TraesCS5D01G509900 chr6D 91.781 146 9 2 2797 2940 435078533 435078677 2.060000e-47 200.0
28 TraesCS5D01G509900 chr4D 91.447 152 4 3 2796 2940 102535228 102535377 2.060000e-47 200.0
29 TraesCS5D01G509900 chr5A 79.923 259 45 5 346 602 669621103 669620850 2.070000e-42 183.0
30 TraesCS5D01G509900 chr3B 84.103 195 19 8 2790 2978 729731561 729731373 9.650000e-41 178.0
31 TraesCS5D01G509900 chr3B 79.623 265 39 6 346 598 228740604 228740343 3.470000e-40 176.0
32 TraesCS5D01G509900 chr3B 84.444 180 21 7 2797 2973 534983827 534984002 1.610000e-38 171.0
33 TraesCS5D01G509900 chr3B 80.263 228 34 7 376 594 379217659 379217434 9.710000e-36 161.0
34 TraesCS5D01G509900 chr3B 92.857 70 5 0 496 565 497324518 497324449 5.970000e-18 102.0
35 TraesCS5D01G509900 chr2A 85.030 167 16 6 2799 2964 594659206 594659364 9.710000e-36 161.0
36 TraesCS5D01G509900 chr2B 83.333 180 21 5 2796 2971 188018528 188018702 1.260000e-34 158.0
37 TraesCS5D01G509900 chr2B 88.462 104 12 0 496 599 418952328 418952431 3.540000e-25 126.0
38 TraesCS5D01G509900 chr3D 84.211 76 7 4 3114 3186 535397113 535397040 6.060000e-08 69.4
39 TraesCS5D01G509900 chr4B 100.000 29 0 0 3114 3142 33617811 33617839 2.000000e-03 54.7


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 TraesCS5D01G509900 chr5D 534869410 534872792 3382 False 1500.05 5611 100.000000 1 3383 4 chr5D.!!$F3 3382
1 TraesCS5D01G509900 chr5B 675869115 675872041 2926 False 1111.00 2809 86.346333 347 3379 3 chr5B.!!$F1 3032
2 TraesCS5D01G509900 chr4A 636667279 636670556 3277 True 832.10 2802 93.791400 1 3383 5 chr4A.!!$R1 3382

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
663 668 0.381801 CGTGCTTTTGTGAGCTTGGT 59.618 50.000 0.00 0.0 43.11 3.67 F
758 766 2.089980 AGCTTGCAGAATTTCATCGCT 58.910 42.857 0.00 0.0 0.00 4.93 F
2191 2506 1.446272 CTCTTCACGGCGAGGAACC 60.446 63.158 16.62 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 2034 1.812922 GTCGTCCGAGGAGTAGCGA 60.813 63.158 0.00 0.00 0.00 4.93 R
2281 2608 2.125673 CACGTCCATGTCCCCGTC 60.126 66.667 0.00 0.00 0.00 4.79 R
3228 3607 0.474273 ACGGGTGAAAGGGTCCCTTA 60.474 55.000 24.08 6.29 43.92 2.69 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
401 402 6.878317 AGACATTAGAAGATGACGGAAATGA 58.122 36.000 0.00 0.00 0.00 2.57
568 569 7.840931 TGACATGACAACATCAGATAACTAGT 58.159 34.615 0.00 0.00 41.91 2.57
607 612 4.851639 ACCATGCTATAATCAGGGGATC 57.148 45.455 9.32 0.00 39.50 3.36
617 622 2.767644 TCAGGGGATCGTATTCCTCA 57.232 50.000 4.86 0.00 38.88 3.86
627 632 6.334202 GGATCGTATTCCTCATTCTCCATAC 58.666 44.000 0.00 0.00 32.68 2.39
630 635 2.509052 TTCCTCATTCTCCATACGCG 57.491 50.000 3.53 3.53 0.00 6.01
651 656 2.017049 GCTGTTATGATCCCGTGCTTT 58.983 47.619 0.00 0.00 0.00 3.51
652 657 2.423538 GCTGTTATGATCCCGTGCTTTT 59.576 45.455 0.00 0.00 0.00 2.27
663 668 0.381801 CGTGCTTTTGTGAGCTTGGT 59.618 50.000 0.00 0.00 43.11 3.67
678 683 6.756542 GTGAGCTTGGTTGAACAGTAAAATTT 59.243 34.615 0.00 0.00 0.00 1.82
681 688 9.308318 GAGCTTGGTTGAACAGTAAAATTTAAA 57.692 29.630 0.00 0.00 0.00 1.52
746 754 8.692110 TTGACAAATATTTTGATAGCTTGCAG 57.308 30.769 6.96 0.00 0.00 4.41
758 766 2.089980 AGCTTGCAGAATTTCATCGCT 58.910 42.857 0.00 0.00 0.00 4.93
845 1142 2.743664 GCATTTTGGCAATTCCTTGTCC 59.256 45.455 0.00 0.00 36.09 4.02
847 1144 4.322650 GCATTTTGGCAATTCCTTGTCCTA 60.323 41.667 0.00 0.00 36.09 2.94
928 1225 4.683832 CGATCTTCTTTTACGGATCTGGT 58.316 43.478 6.47 0.78 34.26 4.00
930 1227 5.661458 GATCTTCTTTTACGGATCTGGTCA 58.339 41.667 6.47 0.00 33.80 4.02
1407 1710 2.677228 CCCTTCACCAAGCCCGAT 59.323 61.111 0.00 0.00 0.00 4.18
1635 1938 4.131088 GACGACGGGCTCCACCTC 62.131 72.222 0.00 0.00 39.10 3.85
2191 2506 1.446272 CTCTTCACGGCGAGGAACC 60.446 63.158 16.62 0.00 0.00 3.62
2364 2703 2.364186 TCCGCTGAGCTCCATCCA 60.364 61.111 12.15 0.00 0.00 3.41
2563 2904 3.603770 GTCATTGTTCTCGCGAAAATTGG 59.396 43.478 11.33 0.00 0.00 3.16
2570 2911 1.331756 CTCGCGAAAATTGGATCTGGG 59.668 52.381 11.33 0.00 0.00 4.45
2573 2914 2.091541 GCGAAAATTGGATCTGGGTCA 58.908 47.619 0.00 0.00 0.00 4.02
2596 2937 5.125900 CACCAAATGAACCAAGCATCTCATA 59.874 40.000 0.00 0.00 0.00 2.15
2597 2938 5.126061 ACCAAATGAACCAAGCATCTCATAC 59.874 40.000 0.00 0.00 0.00 2.39
2601 2942 3.264193 TGAACCAAGCATCTCATACAGGT 59.736 43.478 0.00 0.00 0.00 4.00
2636 2978 8.147058 TGTTTGCATATAAACACCAATGAACTT 58.853 29.630 0.00 0.00 43.46 2.66
2678 3022 6.096423 ACTTTTAAGGGAACAGAAACCACTTC 59.904 38.462 0.00 0.00 0.00 3.01
2679 3023 3.953542 AAGGGAACAGAAACCACTTCT 57.046 42.857 0.00 0.00 45.80 2.85
2694 3038 9.581099 GAAACCACTTCTGACTAAAATTTTCAA 57.419 29.630 6.72 0.00 0.00 2.69
2695 3039 8.926715 AACCACTTCTGACTAAAATTTTCAAC 57.073 30.769 6.72 0.93 0.00 3.18
2697 3041 8.749354 ACCACTTCTGACTAAAATTTTCAACTT 58.251 29.630 6.72 0.00 0.00 2.66
2698 3042 9.586435 CCACTTCTGACTAAAATTTTCAACTTT 57.414 29.630 6.72 0.00 0.00 2.66
2727 3085 9.969001 AGGGAACAGTTAAATTTATAGCAGTAA 57.031 29.630 0.00 0.00 0.00 2.24
2728 3086 9.999009 GGGAACAGTTAAATTTATAGCAGTAAC 57.001 33.333 0.00 0.00 0.00 2.50
2789 3154 6.196918 TCGGTGAATATTCTACTCCCTCTA 57.803 41.667 16.24 0.00 0.00 2.43
2801 3166 8.896722 TTCTACTCCCTCTATAAAGAAACAGT 57.103 34.615 0.00 0.00 0.00 3.55
2802 3167 8.896722 TCTACTCCCTCTATAAAGAAACAGTT 57.103 34.615 0.00 0.00 0.00 3.16
2803 3168 9.322769 TCTACTCCCTCTATAAAGAAACAGTTT 57.677 33.333 0.00 0.00 0.00 2.66
2804 3169 9.372369 CTACTCCCTCTATAAAGAAACAGTTTG 57.628 37.037 2.34 0.00 0.00 2.93
2805 3170 7.746703 ACTCCCTCTATAAAGAAACAGTTTGT 58.253 34.615 2.34 0.00 0.00 2.83
2806 3171 7.878644 ACTCCCTCTATAAAGAAACAGTTTGTC 59.121 37.037 2.34 0.00 0.00 3.18
2807 3172 7.974504 TCCCTCTATAAAGAAACAGTTTGTCT 58.025 34.615 2.34 0.00 0.00 3.41
2808 3173 9.096823 TCCCTCTATAAAGAAACAGTTTGTCTA 57.903 33.333 2.34 0.00 0.00 2.59
2809 3174 9.720769 CCCTCTATAAAGAAACAGTTTGTCTAA 57.279 33.333 2.34 0.00 0.00 2.10
2821 3186 9.778741 AAACAGTTTGTCTAATTCACATCTAGA 57.221 29.630 0.00 0.00 0.00 2.43
2822 3187 9.950496 AACAGTTTGTCTAATTCACATCTAGAT 57.050 29.630 0.00 0.00 0.00 1.98
2823 3188 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
2850 3215 8.561738 TTTTTAAGGATGTCACATCTAACCTC 57.438 34.615 17.46 0.00 0.00 3.85
2851 3216 4.762289 AAGGATGTCACATCTAACCTCC 57.238 45.455 17.46 0.18 32.24 4.30
2852 3217 3.041946 AGGATGTCACATCTAACCTCCC 58.958 50.000 17.46 0.00 32.42 4.30
2853 3218 2.771943 GGATGTCACATCTAACCTCCCA 59.228 50.000 17.46 0.00 0.00 4.37
2854 3219 3.432326 GGATGTCACATCTAACCTCCCAC 60.432 52.174 17.46 0.00 0.00 4.61
2855 3220 2.615391 TGTCACATCTAACCTCCCACA 58.385 47.619 0.00 0.00 0.00 4.17
2856 3221 2.976185 TGTCACATCTAACCTCCCACAA 59.024 45.455 0.00 0.00 0.00 3.33
2857 3222 3.007940 TGTCACATCTAACCTCCCACAAG 59.992 47.826 0.00 0.00 0.00 3.16
2858 3223 3.008049 GTCACATCTAACCTCCCACAAGT 59.992 47.826 0.00 0.00 0.00 3.16
2859 3224 4.222145 GTCACATCTAACCTCCCACAAGTA 59.778 45.833 0.00 0.00 0.00 2.24
2860 3225 4.841813 TCACATCTAACCTCCCACAAGTAA 59.158 41.667 0.00 0.00 0.00 2.24
2861 3226 5.046591 TCACATCTAACCTCCCACAAGTAAG 60.047 44.000 0.00 0.00 0.00 2.34
2862 3227 4.225267 ACATCTAACCTCCCACAAGTAAGG 59.775 45.833 0.00 0.00 34.94 2.69
2863 3228 2.570302 TCTAACCTCCCACAAGTAAGGC 59.430 50.000 0.00 0.00 31.79 4.35
2864 3229 1.145571 AACCTCCCACAAGTAAGGCA 58.854 50.000 0.00 0.00 31.79 4.75
2865 3230 1.145571 ACCTCCCACAAGTAAGGCAA 58.854 50.000 0.00 0.00 31.79 4.52
2866 3231 1.202891 ACCTCCCACAAGTAAGGCAAC 60.203 52.381 0.00 0.00 31.79 4.17
2867 3232 1.202879 CCTCCCACAAGTAAGGCAACA 60.203 52.381 0.00 0.00 41.41 3.33
2868 3233 2.582052 CTCCCACAAGTAAGGCAACAA 58.418 47.619 0.00 0.00 41.41 2.83
2869 3234 2.293399 CTCCCACAAGTAAGGCAACAAC 59.707 50.000 0.00 0.00 41.41 3.32
2870 3235 2.028130 CCCACAAGTAAGGCAACAACA 58.972 47.619 0.00 0.00 41.41 3.33
2871 3236 2.428890 CCCACAAGTAAGGCAACAACAA 59.571 45.455 0.00 0.00 41.41 2.83
2872 3237 3.118956 CCCACAAGTAAGGCAACAACAAA 60.119 43.478 0.00 0.00 41.41 2.83
2873 3238 4.111916 CCACAAGTAAGGCAACAACAAAG 58.888 43.478 0.00 0.00 41.41 2.77
2874 3239 4.142271 CCACAAGTAAGGCAACAACAAAGA 60.142 41.667 0.00 0.00 41.41 2.52
2875 3240 5.406649 CACAAGTAAGGCAACAACAAAGAA 58.593 37.500 0.00 0.00 41.41 2.52
2876 3241 5.288472 CACAAGTAAGGCAACAACAAAGAAC 59.712 40.000 0.00 0.00 41.41 3.01
2877 3242 5.047660 ACAAGTAAGGCAACAACAAAGAACA 60.048 36.000 0.00 0.00 41.41 3.18
2878 3243 5.652994 AGTAAGGCAACAACAAAGAACAA 57.347 34.783 0.00 0.00 41.41 2.83
2879 3244 6.031751 AGTAAGGCAACAACAAAGAACAAA 57.968 33.333 0.00 0.00 41.41 2.83
2880 3245 6.459923 AGTAAGGCAACAACAAAGAACAAAA 58.540 32.000 0.00 0.00 41.41 2.44
2881 3246 6.931840 AGTAAGGCAACAACAAAGAACAAAAA 59.068 30.769 0.00 0.00 41.41 1.94
2926 3291 2.949451 ACAAGCGTAGTGGAGATCAG 57.051 50.000 0.00 0.00 0.00 2.90
2927 3292 1.478510 ACAAGCGTAGTGGAGATCAGG 59.521 52.381 0.00 0.00 0.00 3.86
2928 3293 1.478510 CAAGCGTAGTGGAGATCAGGT 59.521 52.381 0.00 0.00 0.00 4.00
2929 3294 1.853963 AGCGTAGTGGAGATCAGGTT 58.146 50.000 0.00 0.00 0.00 3.50
2930 3295 3.014304 AGCGTAGTGGAGATCAGGTTA 57.986 47.619 0.00 0.00 0.00 2.85
2931 3296 2.952978 AGCGTAGTGGAGATCAGGTTAG 59.047 50.000 0.00 0.00 0.00 2.34
2932 3297 2.950309 GCGTAGTGGAGATCAGGTTAGA 59.050 50.000 0.00 0.00 0.00 2.10
2933 3298 3.570550 GCGTAGTGGAGATCAGGTTAGAT 59.429 47.826 0.00 0.00 0.00 1.98
2934 3299 4.557695 GCGTAGTGGAGATCAGGTTAGATG 60.558 50.000 0.00 0.00 0.00 2.90
2935 3300 4.580995 CGTAGTGGAGATCAGGTTAGATGT 59.419 45.833 0.00 0.00 0.00 3.06
2936 3301 5.506483 CGTAGTGGAGATCAGGTTAGATGTG 60.506 48.000 0.00 0.00 0.00 3.21
2937 3302 4.614475 AGTGGAGATCAGGTTAGATGTGA 58.386 43.478 0.00 0.00 0.00 3.58
2938 3303 4.404073 AGTGGAGATCAGGTTAGATGTGAC 59.596 45.833 0.00 0.00 0.00 3.67
2939 3304 4.160439 GTGGAGATCAGGTTAGATGTGACA 59.840 45.833 0.00 0.00 0.00 3.58
2940 3305 4.777366 TGGAGATCAGGTTAGATGTGACAA 59.223 41.667 0.00 0.00 0.00 3.18
2941 3306 5.112686 GGAGATCAGGTTAGATGTGACAAC 58.887 45.833 0.00 0.00 0.00 3.32
2942 3307 5.337571 GGAGATCAGGTTAGATGTGACAACA 60.338 44.000 0.00 0.00 41.58 3.33
2965 3330 5.916661 TCTAGATGTGTCCTAAACAGACC 57.083 43.478 0.00 0.00 38.97 3.85
2966 3331 3.983044 AGATGTGTCCTAAACAGACCC 57.017 47.619 0.00 0.00 38.97 4.46
2967 3332 3.248024 AGATGTGTCCTAAACAGACCCA 58.752 45.455 0.00 0.00 38.97 4.51
2968 3333 2.922740 TGTGTCCTAAACAGACCCAC 57.077 50.000 0.00 0.00 38.97 4.61
2969 3334 2.120312 TGTGTCCTAAACAGACCCACA 58.880 47.619 0.00 0.00 38.97 4.17
2970 3335 2.506231 TGTGTCCTAAACAGACCCACAA 59.494 45.455 0.00 0.00 38.97 3.33
2971 3336 3.054287 TGTGTCCTAAACAGACCCACAAA 60.054 43.478 0.00 0.00 38.97 2.83
2972 3337 3.949113 GTGTCCTAAACAGACCCACAAAA 59.051 43.478 0.00 0.00 38.97 2.44
2973 3338 4.399934 GTGTCCTAAACAGACCCACAAAAA 59.600 41.667 0.00 0.00 38.97 1.94
2997 3362 9.475620 AAAAATATATTTCTTTTCGGAGGGAGT 57.524 29.630 11.08 0.00 0.00 3.85
2999 3364 9.557061 AAATATATTTCTTTTCGGAGGGAGTAC 57.443 33.333 4.81 0.00 0.00 2.73
3000 3365 4.903045 ATTTCTTTTCGGAGGGAGTACA 57.097 40.909 0.00 0.00 0.00 2.90
3001 3366 4.903045 TTTCTTTTCGGAGGGAGTACAT 57.097 40.909 0.00 0.00 0.00 2.29
3002 3367 6.555463 ATTTCTTTTCGGAGGGAGTACATA 57.445 37.500 0.00 0.00 0.00 2.29
3003 3368 4.996788 TCTTTTCGGAGGGAGTACATAC 57.003 45.455 0.00 0.00 0.00 2.39
3004 3369 4.607239 TCTTTTCGGAGGGAGTACATACT 58.393 43.478 0.00 0.00 39.71 2.12
3005 3370 5.021458 TCTTTTCGGAGGGAGTACATACTT 58.979 41.667 0.00 0.00 36.50 2.24
3006 3371 4.730949 TTTCGGAGGGAGTACATACTTG 57.269 45.455 0.00 0.00 36.50 3.16
3007 3372 2.662866 TCGGAGGGAGTACATACTTGG 58.337 52.381 0.00 0.00 36.50 3.61
3008 3373 2.242965 TCGGAGGGAGTACATACTTGGA 59.757 50.000 0.00 0.00 36.50 3.53
3009 3374 3.028850 CGGAGGGAGTACATACTTGGAA 58.971 50.000 0.00 0.00 36.50 3.53
3010 3375 3.449737 CGGAGGGAGTACATACTTGGAAA 59.550 47.826 0.00 0.00 36.50 3.13
3011 3376 4.679905 CGGAGGGAGTACATACTTGGAAAC 60.680 50.000 0.00 0.00 36.50 2.78
3012 3377 4.470304 GGAGGGAGTACATACTTGGAAACT 59.530 45.833 0.00 0.00 36.50 2.66
3013 3378 5.045797 GGAGGGAGTACATACTTGGAAACTT 60.046 44.000 0.00 0.00 36.50 2.66
3014 3379 6.051179 AGGGAGTACATACTTGGAAACTTC 57.949 41.667 0.00 0.00 36.50 3.01
3015 3380 5.785940 AGGGAGTACATACTTGGAAACTTCT 59.214 40.000 0.00 0.00 36.50 2.85
3173 3547 7.083858 TGCACATAGAAAACTAAGCAATGTTC 58.916 34.615 0.00 0.00 0.00 3.18
3179 3553 7.254227 AGAAAACTAAGCAATGTTCGTTGTA 57.746 32.000 6.62 0.00 0.00 2.41
3236 3615 3.827302 TGAGCTCGAGATTATAAGGGACC 59.173 47.826 18.75 0.00 0.00 4.46
3242 3621 5.213519 TCGAGATTATAAGGGACCCTTTCA 58.786 41.667 30.80 14.75 41.69 2.69
3246 3625 0.916809 ATAAGGGACCCTTTCACCCG 59.083 55.000 30.80 0.00 41.69 5.28
3289 3669 4.913335 ACACAATCATCATTCATCAGCC 57.087 40.909 0.00 0.00 0.00 4.85
3296 3676 3.129813 TCATCATTCATCAGCCAAGCAAC 59.870 43.478 0.00 0.00 0.00 4.17
3301 3681 3.138884 TCATCAGCCAAGCAACAACTA 57.861 42.857 0.00 0.00 0.00 2.24
3344 3725 1.258676 GTGTTCTCGAGGGTCCTCTT 58.741 55.000 13.56 0.00 40.69 2.85
3367 3748 2.349886 GCAATCTTCTTGTCCTACTGCG 59.650 50.000 0.00 0.00 0.00 5.18
3379 3760 3.002348 GTCCTACTGCGCATTCAAATACC 59.998 47.826 12.24 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.158449 CCAGAACATGTTTCGAGAGTGC 59.842 50.000 13.36 0.00 0.00 4.40
348 349 5.240183 CCTCCATATAGGCAAAACTGACATG 59.760 44.000 0.00 0.00 37.29 3.21
350 351 4.385199 CCCTCCATATAGGCAAAACTGACA 60.385 45.833 0.00 0.00 37.29 3.58
607 612 3.921021 GCGTATGGAGAATGAGGAATACG 59.079 47.826 8.27 8.27 43.37 3.06
617 622 0.178068 AACAGCCGCGTATGGAGAAT 59.822 50.000 4.92 0.00 0.00 2.40
627 632 2.310233 CGGGATCATAACAGCCGCG 61.310 63.158 0.00 0.00 0.00 6.46
630 635 0.179045 AGCACGGGATCATAACAGCC 60.179 55.000 0.00 0.00 0.00 4.85
651 656 2.722094 ACTGTTCAACCAAGCTCACAA 58.278 42.857 0.00 0.00 0.00 3.33
652 657 2.418368 ACTGTTCAACCAAGCTCACA 57.582 45.000 0.00 0.00 0.00 3.58
730 738 7.434307 CGATGAAATTCTGCAAGCTATCAAAAT 59.566 33.333 0.00 0.00 0.00 1.82
758 766 8.363390 TGCCACATTTTACACAAATTTCATCTA 58.637 29.630 0.00 0.00 0.00 1.98
928 1225 3.618019 GCCGTGGTTACAGAGGTAATTGA 60.618 47.826 0.00 0.00 41.28 2.57
930 1227 2.355412 GGCCGTGGTTACAGAGGTAATT 60.355 50.000 0.00 0.00 41.28 1.40
1722 2034 1.812922 GTCGTCCGAGGAGTAGCGA 60.813 63.158 0.00 0.00 0.00 4.93
2278 2605 4.832608 GTCCATGTCCCCGTCGCC 62.833 72.222 0.00 0.00 0.00 5.54
2280 2607 3.755628 ACGTCCATGTCCCCGTCG 61.756 66.667 0.00 0.00 0.00 5.12
2281 2608 2.125673 CACGTCCATGTCCCCGTC 60.126 66.667 0.00 0.00 0.00 4.79
2345 2684 2.430610 GGATGGAGCTCAGCGGAGT 61.431 63.158 17.19 2.37 43.37 3.85
2563 2904 2.755103 GGTTCATTTGGTGACCCAGATC 59.245 50.000 0.00 0.00 43.15 2.75
2570 2911 3.256631 AGATGCTTGGTTCATTTGGTGAC 59.743 43.478 0.00 0.00 36.32 3.67
2573 2914 3.499338 TGAGATGCTTGGTTCATTTGGT 58.501 40.909 0.00 0.00 0.00 3.67
2596 2937 3.495331 TGCAAACAATCCATGTACCTGT 58.505 40.909 0.00 0.00 42.99 4.00
2597 2938 4.724074 ATGCAAACAATCCATGTACCTG 57.276 40.909 0.00 0.00 42.99 4.00
2601 2942 8.194104 GGTGTTTATATGCAAACAATCCATGTA 58.806 33.333 3.34 0.00 46.81 2.29
2685 3029 9.733556 AACTGTTCCCTTAAAAGTTGAAAATTT 57.266 25.926 0.00 0.00 30.17 1.82
2699 3043 9.969001 ACTGCTATAAATTTAACTGTTCCCTTA 57.031 29.630 1.21 0.00 0.00 2.69
2700 3044 8.879427 ACTGCTATAAATTTAACTGTTCCCTT 57.121 30.769 1.21 0.00 0.00 3.95
2701 3045 9.969001 TTACTGCTATAAATTTAACTGTTCCCT 57.031 29.630 1.21 0.00 0.00 4.20
2702 3046 9.999009 GTTACTGCTATAAATTTAACTGTTCCC 57.001 33.333 1.21 0.00 0.00 3.97
2738 3100 4.512198 TGCTGCCAAAGAAATCATGTTTTG 59.488 37.500 6.48 4.93 0.00 2.44
2825 3190 7.610305 GGAGGTTAGATGTGACATCCTTAAAAA 59.390 37.037 21.05 4.81 42.00 1.94
2827 3192 6.352737 GGGAGGTTAGATGTGACATCCTTAAA 60.353 42.308 21.05 8.69 44.05 1.52
2828 3193 5.130477 GGGAGGTTAGATGTGACATCCTTAA 59.870 44.000 21.05 11.73 44.05 1.85
2830 3195 3.456277 GGGAGGTTAGATGTGACATCCTT 59.544 47.826 21.05 7.22 44.05 3.36
2832 3197 2.771943 TGGGAGGTTAGATGTGACATCC 59.228 50.000 21.05 9.65 43.91 3.51
2833 3198 3.197766 TGTGGGAGGTTAGATGTGACATC 59.802 47.826 17.46 17.46 0.00 3.06
2834 3199 3.181329 TGTGGGAGGTTAGATGTGACAT 58.819 45.455 0.00 0.00 0.00 3.06
2837 3202 3.248024 ACTTGTGGGAGGTTAGATGTGA 58.752 45.455 0.00 0.00 0.00 3.58
2838 3203 3.703001 ACTTGTGGGAGGTTAGATGTG 57.297 47.619 0.00 0.00 0.00 3.21
2839 3204 4.225267 CCTTACTTGTGGGAGGTTAGATGT 59.775 45.833 0.00 0.00 0.00 3.06
2840 3205 4.770795 CCTTACTTGTGGGAGGTTAGATG 58.229 47.826 0.00 0.00 0.00 2.90
2841 3206 3.200165 GCCTTACTTGTGGGAGGTTAGAT 59.800 47.826 0.00 0.00 0.00 1.98
2842 3207 2.570302 GCCTTACTTGTGGGAGGTTAGA 59.430 50.000 0.00 0.00 0.00 2.10
2843 3208 2.304761 TGCCTTACTTGTGGGAGGTTAG 59.695 50.000 0.00 0.00 0.00 2.34
2844 3209 2.340731 TGCCTTACTTGTGGGAGGTTA 58.659 47.619 0.00 0.00 0.00 2.85
2845 3210 1.145571 TGCCTTACTTGTGGGAGGTT 58.854 50.000 0.00 0.00 0.00 3.50
2846 3211 1.145571 TTGCCTTACTTGTGGGAGGT 58.854 50.000 0.00 0.00 0.00 3.85
2847 3212 1.202879 TGTTGCCTTACTTGTGGGAGG 60.203 52.381 0.00 0.00 0.00 4.30
2848 3213 2.270352 TGTTGCCTTACTTGTGGGAG 57.730 50.000 0.00 0.00 0.00 4.30
2849 3214 2.303175 GTTGTTGCCTTACTTGTGGGA 58.697 47.619 0.00 0.00 0.00 4.37
2850 3215 2.028130 TGTTGTTGCCTTACTTGTGGG 58.972 47.619 0.00 0.00 0.00 4.61
2851 3216 3.791973 TTGTTGTTGCCTTACTTGTGG 57.208 42.857 0.00 0.00 0.00 4.17
2852 3217 4.992688 TCTTTGTTGTTGCCTTACTTGTG 58.007 39.130 0.00 0.00 0.00 3.33
2853 3218 5.047660 TGTTCTTTGTTGTTGCCTTACTTGT 60.048 36.000 0.00 0.00 0.00 3.16
2854 3219 5.406649 TGTTCTTTGTTGTTGCCTTACTTG 58.593 37.500 0.00 0.00 0.00 3.16
2855 3220 5.652994 TGTTCTTTGTTGTTGCCTTACTT 57.347 34.783 0.00 0.00 0.00 2.24
2856 3221 5.652994 TTGTTCTTTGTTGTTGCCTTACT 57.347 34.783 0.00 0.00 0.00 2.24
2857 3222 6.713792 TTTTGTTCTTTGTTGTTGCCTTAC 57.286 33.333 0.00 0.00 0.00 2.34
2906 3271 2.688446 CCTGATCTCCACTACGCTTGTA 59.312 50.000 0.00 0.00 0.00 2.41
2907 3272 1.478510 CCTGATCTCCACTACGCTTGT 59.521 52.381 0.00 0.00 0.00 3.16
2908 3273 1.478510 ACCTGATCTCCACTACGCTTG 59.521 52.381 0.00 0.00 0.00 4.01
2909 3274 1.853963 ACCTGATCTCCACTACGCTT 58.146 50.000 0.00 0.00 0.00 4.68
2910 3275 1.853963 AACCTGATCTCCACTACGCT 58.146 50.000 0.00 0.00 0.00 5.07
2911 3276 2.950309 TCTAACCTGATCTCCACTACGC 59.050 50.000 0.00 0.00 0.00 4.42
2912 3277 4.580995 ACATCTAACCTGATCTCCACTACG 59.419 45.833 0.00 0.00 0.00 3.51
2913 3278 5.594725 TCACATCTAACCTGATCTCCACTAC 59.405 44.000 0.00 0.00 0.00 2.73
2914 3279 5.594725 GTCACATCTAACCTGATCTCCACTA 59.405 44.000 0.00 0.00 0.00 2.74
2915 3280 4.404073 GTCACATCTAACCTGATCTCCACT 59.596 45.833 0.00 0.00 0.00 4.00
2916 3281 4.160439 TGTCACATCTAACCTGATCTCCAC 59.840 45.833 0.00 0.00 0.00 4.02
2917 3282 4.352893 TGTCACATCTAACCTGATCTCCA 58.647 43.478 0.00 0.00 0.00 3.86
2918 3283 5.112686 GTTGTCACATCTAACCTGATCTCC 58.887 45.833 0.00 0.00 0.00 3.71
2919 3284 5.724328 TGTTGTCACATCTAACCTGATCTC 58.276 41.667 0.00 0.00 0.00 2.75
2920 3285 5.745312 TGTTGTCACATCTAACCTGATCT 57.255 39.130 0.00 0.00 0.00 2.75
2941 3306 6.276847 GGTCTGTTTAGGACACATCTAGATG 58.723 44.000 27.63 27.63 44.15 2.90
2942 3307 5.364157 GGGTCTGTTTAGGACACATCTAGAT 59.636 44.000 0.00 0.00 37.11 1.98
2943 3308 4.710375 GGGTCTGTTTAGGACACATCTAGA 59.290 45.833 0.00 0.00 37.11 2.43
2944 3309 4.466370 TGGGTCTGTTTAGGACACATCTAG 59.534 45.833 0.00 0.00 41.46 2.43
2945 3310 4.222145 GTGGGTCTGTTTAGGACACATCTA 59.778 45.833 2.15 0.00 46.69 1.98
2946 3311 3.008049 GTGGGTCTGTTTAGGACACATCT 59.992 47.826 2.15 0.00 46.69 2.90
2947 3312 3.244422 TGTGGGTCTGTTTAGGACACATC 60.244 47.826 2.15 0.00 46.69 3.06
2948 3313 2.708861 TGTGGGTCTGTTTAGGACACAT 59.291 45.455 2.15 0.00 46.69 3.21
2949 3314 2.120312 TGTGGGTCTGTTTAGGACACA 58.880 47.619 0.00 0.00 43.69 3.72
2950 3315 2.922740 TGTGGGTCTGTTTAGGACAC 57.077 50.000 0.00 0.00 37.60 3.67
2951 3316 3.935818 TTTGTGGGTCTGTTTAGGACA 57.064 42.857 0.00 0.00 35.61 4.02
2971 3336 9.475620 ACTCCCTCCGAAAAGAAATATATTTTT 57.524 29.630 11.92 3.85 30.48 1.94
2973 3338 9.557061 GTACTCCCTCCGAAAAGAAATATATTT 57.443 33.333 10.51 10.51 0.00 1.40
2974 3339 8.711170 TGTACTCCCTCCGAAAAGAAATATATT 58.289 33.333 0.00 0.00 0.00 1.28
2975 3340 8.258850 TGTACTCCCTCCGAAAAGAAATATAT 57.741 34.615 0.00 0.00 0.00 0.86
2976 3341 7.664552 TGTACTCCCTCCGAAAAGAAATATA 57.335 36.000 0.00 0.00 0.00 0.86
2977 3342 6.555463 TGTACTCCCTCCGAAAAGAAATAT 57.445 37.500 0.00 0.00 0.00 1.28
2978 3343 6.555463 ATGTACTCCCTCCGAAAAGAAATA 57.445 37.500 0.00 0.00 0.00 1.40
2979 3344 4.903045 TGTACTCCCTCCGAAAAGAAAT 57.097 40.909 0.00 0.00 0.00 2.17
2980 3345 4.903045 ATGTACTCCCTCCGAAAAGAAA 57.097 40.909 0.00 0.00 0.00 2.52
2981 3346 5.021458 AGTATGTACTCCCTCCGAAAAGAA 58.979 41.667 0.00 0.00 0.00 2.52
2982 3347 4.607239 AGTATGTACTCCCTCCGAAAAGA 58.393 43.478 0.00 0.00 0.00 2.52
2983 3348 5.109903 CAAGTATGTACTCCCTCCGAAAAG 58.890 45.833 0.00 0.00 34.99 2.27
2984 3349 4.081309 CCAAGTATGTACTCCCTCCGAAAA 60.081 45.833 0.00 0.00 34.99 2.29
2985 3350 3.449737 CCAAGTATGTACTCCCTCCGAAA 59.550 47.826 0.00 0.00 34.99 3.46
2986 3351 3.028850 CCAAGTATGTACTCCCTCCGAA 58.971 50.000 0.00 0.00 34.99 4.30
2987 3352 2.242965 TCCAAGTATGTACTCCCTCCGA 59.757 50.000 0.00 0.00 34.99 4.55
2988 3353 2.662866 TCCAAGTATGTACTCCCTCCG 58.337 52.381 0.00 0.00 34.99 4.63
2989 3354 4.470304 AGTTTCCAAGTATGTACTCCCTCC 59.530 45.833 0.00 0.00 34.99 4.30
2990 3355 5.678955 AGTTTCCAAGTATGTACTCCCTC 57.321 43.478 0.00 0.00 34.99 4.30
2991 3356 5.785940 AGAAGTTTCCAAGTATGTACTCCCT 59.214 40.000 0.00 0.00 34.99 4.20
2992 3357 6.051179 AGAAGTTTCCAAGTATGTACTCCC 57.949 41.667 0.00 0.00 34.99 4.30
2993 3358 7.159372 TCAAGAAGTTTCCAAGTATGTACTCC 58.841 38.462 0.00 0.00 34.99 3.85
2994 3359 8.603242 TTCAAGAAGTTTCCAAGTATGTACTC 57.397 34.615 0.00 0.00 34.99 2.59
2995 3360 8.974060 TTTCAAGAAGTTTCCAAGTATGTACT 57.026 30.769 0.00 0.00 38.39 2.73
3103 3477 3.887621 TTCGTGGAGGTCTAGGATTTG 57.112 47.619 0.00 0.00 0.00 2.32
3104 3478 3.775316 ACATTCGTGGAGGTCTAGGATTT 59.225 43.478 0.00 0.00 0.00 2.17
3112 3486 3.334691 TGAAATCACATTCGTGGAGGTC 58.665 45.455 0.00 0.00 43.79 3.85
3187 3561 7.663081 AGAGCTCATGAACAATAAAAGTCTGAA 59.337 33.333 17.77 0.00 0.00 3.02
3228 3607 0.474273 ACGGGTGAAAGGGTCCCTTA 60.474 55.000 24.08 6.29 43.92 2.69
3236 3615 1.068434 ACAATGCAAACGGGTGAAAGG 59.932 47.619 0.00 0.00 0.00 3.11
3242 3621 2.427453 TGTGTAAACAATGCAAACGGGT 59.573 40.909 0.00 0.00 0.00 5.28
3246 3625 3.696898 TCGGTGTGTAAACAATGCAAAC 58.303 40.909 0.00 0.00 31.52 2.93
3289 3669 2.791004 GCTGCAGTTTAGTTGTTGCTTG 59.209 45.455 16.64 0.00 37.45 4.01
3296 3676 4.227512 TGATGTTGCTGCAGTTTAGTTG 57.772 40.909 16.64 0.00 0.00 3.16
3301 3681 1.401931 GCGATGATGTTGCTGCAGTTT 60.402 47.619 16.64 0.00 34.16 2.66
3344 3725 3.753272 GCAGTAGGACAAGAAGATTGCAA 59.247 43.478 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.