Multiple sequence alignment - TraesCS6B01G063400

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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 TraesCS6B01G063400 chr6B 100.000 3179 0 0 1 3179 42006735 42003557 0.000000e+00 5871.0
1 TraesCS6B01G063400 chr6B 80.590 1798 272 56 421 2188 42392470 42394220 0.000000e+00 1315.0
2 TraesCS6B01G063400 chr6B 80.238 1513 203 57 722 2188 42212263 42210801 0.000000e+00 1050.0
3 TraesCS6B01G063400 chr6B 84.710 896 107 21 1309 2181 42318474 42317586 0.000000e+00 869.0
4 TraesCS6B01G063400 chr6D 91.797 2426 119 29 1 2394 25806064 25803687 0.000000e+00 3304.0
5 TraesCS6B01G063400 chr6D 80.926 1447 208 35 777 2188 25827831 25826418 0.000000e+00 1081.0
6 TraesCS6B01G063400 chr6D 80.836 1148 139 49 444 1545 25914426 25915538 0.000000e+00 826.0
7 TraesCS6B01G063400 chr6D 92.213 488 22 9 2477 2961 25794606 25794132 0.000000e+00 676.0
8 TraesCS6B01G063400 chr6D 86.371 587 75 3 1603 2188 25915637 25916219 1.240000e-178 636.0
9 TraesCS6B01G063400 chr6D 81.729 509 65 16 770 1271 25880325 25879838 1.780000e-107 399.0
10 TraesCS6B01G063400 chr6D 97.037 135 4 0 3045 3179 25794128 25793994 8.870000e-56 228.0
11 TraesCS6B01G063400 chr6D 100.000 77 0 0 2969 3045 153190844 153190768 3.310000e-30 143.0
12 TraesCS6B01G063400 chr6D 87.778 90 3 5 2391 2479 25794713 25794631 7.260000e-17 99.0
13 TraesCS6B01G063400 chr6A 93.825 1004 46 8 1268 2257 23896453 23895452 0.000000e+00 1496.0
14 TraesCS6B01G063400 chr6A 80.738 1843 226 70 421 2188 24048069 24049857 0.000000e+00 1317.0
15 TraesCS6B01G063400 chr6A 92.580 876 54 8 384 1252 23897404 23896533 0.000000e+00 1247.0
16 TraesCS6B01G063400 chr6A 82.100 1486 197 46 722 2179 24031703 24030259 0.000000e+00 1206.0
17 TraesCS6B01G063400 chr6A 80.679 1444 201 41 788 2188 23952596 23951188 0.000000e+00 1050.0
18 TraesCS6B01G063400 chr6A 94.083 338 15 1 68 405 23897790 23897458 2.830000e-140 508.0
19 TraesCS6B01G063400 chr7A 83.502 891 109 23 1318 2181 670946942 670946063 0.000000e+00 797.0
20 TraesCS6B01G063400 chr7A 83.333 120 15 2 2471 2590 509525061 509525175 4.340000e-19 106.0
21 TraesCS6B01G063400 chr7A 75.974 154 35 2 1391 1543 516514700 516514548 9.450000e-11 78.7
22 TraesCS6B01G063400 chr7B 83.582 871 104 23 1338 2181 643462568 643463426 0.000000e+00 780.0
23 TraesCS6B01G063400 chr7B 87.040 571 71 3 1616 2185 643292159 643291591 2.670000e-180 641.0
24 TraesCS6B01G063400 chr7B 75.974 154 35 2 1391 1543 504456389 504456541 9.450000e-11 78.7
25 TraesCS6B01G063400 chr3B 98.750 80 1 0 2969 3048 70969117 70969196 3.310000e-30 143.0
26 TraesCS6B01G063400 chr3B 95.506 89 1 2 2969 3054 244019299 244019211 4.280000e-29 139.0
27 TraesCS6B01G063400 chr2B 98.765 81 0 1 2969 3049 87186110 87186031 3.310000e-30 143.0
28 TraesCS6B01G063400 chr2B 78.986 138 21 8 2462 2593 530725017 530725152 1.570000e-13 87.9
29 TraesCS6B01G063400 chr2A 98.765 81 0 1 2969 3048 527466000 527466080 3.310000e-30 143.0
30 TraesCS6B01G063400 chr5A 89.381 113 10 2 2969 3080 78538471 78538582 1.190000e-29 141.0
31 TraesCS6B01G063400 chr5A 100.000 75 0 0 2969 3043 442273575 442273649 4.280000e-29 139.0
32 TraesCS6B01G063400 chr1B 96.512 86 0 3 2969 3052 655769577 655769493 4.280000e-29 139.0
33 TraesCS6B01G063400 chr3A 95.349 86 2 2 2969 3054 596108794 596108711 5.530000e-28 135.0
34 TraesCS6B01G063400 chr7D 77.124 153 33 2 1392 1543 478576073 478576224 1.570000e-13 87.9


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 TraesCS6B01G063400 chr6B 42003557 42006735 3178 True 5871.000000 5871 100.000000 1 3179 1 chr6B.!!$R1 3178
1 TraesCS6B01G063400 chr6B 42392470 42394220 1750 False 1315.000000 1315 80.590000 421 2188 1 chr6B.!!$F1 1767
2 TraesCS6B01G063400 chr6B 42210801 42212263 1462 True 1050.000000 1050 80.238000 722 2188 1 chr6B.!!$R2 1466
3 TraesCS6B01G063400 chr6B 42317586 42318474 888 True 869.000000 869 84.710000 1309 2181 1 chr6B.!!$R3 872
4 TraesCS6B01G063400 chr6D 25803687 25806064 2377 True 3304.000000 3304 91.797000 1 2394 1 chr6D.!!$R1 2393
5 TraesCS6B01G063400 chr6D 25826418 25827831 1413 True 1081.000000 1081 80.926000 777 2188 1 chr6D.!!$R2 1411
6 TraesCS6B01G063400 chr6D 25914426 25916219 1793 False 731.000000 826 83.603500 444 2188 2 chr6D.!!$F1 1744
7 TraesCS6B01G063400 chr6D 25793994 25794713 719 True 334.333333 676 92.342667 2391 3179 3 chr6D.!!$R5 788
8 TraesCS6B01G063400 chr6A 24048069 24049857 1788 False 1317.000000 1317 80.738000 421 2188 1 chr6A.!!$F1 1767
9 TraesCS6B01G063400 chr6A 24030259 24031703 1444 True 1206.000000 1206 82.100000 722 2179 1 chr6A.!!$R2 1457
10 TraesCS6B01G063400 chr6A 23895452 23897790 2338 True 1083.666667 1496 93.496000 68 2257 3 chr6A.!!$R3 2189
11 TraesCS6B01G063400 chr6A 23951188 23952596 1408 True 1050.000000 1050 80.679000 788 2188 1 chr6A.!!$R1 1400
12 TraesCS6B01G063400 chr7A 670946063 670946942 879 True 797.000000 797 83.502000 1318 2181 1 chr7A.!!$R2 863
13 TraesCS6B01G063400 chr7B 643462568 643463426 858 False 780.000000 780 83.582000 1338 2181 1 chr7B.!!$F2 843
14 TraesCS6B01G063400 chr7B 643291591 643292159 568 True 641.000000 641 87.040000 1616 2185 1 chr7B.!!$R1 569

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
922 1033 0.039256 CGTGCCCACCACAATTGAAG 60.039 55.0 13.59 5.18 44.91 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2869 3219 0.31716 AAGATCACACGGCGAGAACA 59.683 50.0 16.62 0.0 0.0 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 8.821147 TCATGGTTCAAATTTGATTTCAGAAG 57.179 30.769 21.10 12.69 37.00 2.85
122 123 4.582656 TGGTGGTGTTCTATGAAGGTTTTG 59.417 41.667 0.00 0.00 0.00 2.44
270 271 2.715046 TGGAACCATGTGAGAGATTGC 58.285 47.619 0.00 0.00 0.00 3.56
504 577 7.669722 TCCTTTCTATTTTATCTTTGTGTGCCT 59.330 33.333 0.00 0.00 0.00 4.75
515 588 4.646945 TCTTTGTGTGCCTTGGAATTGTTA 59.353 37.500 0.00 0.00 0.00 2.41
516 589 4.582701 TTGTGTGCCTTGGAATTGTTAG 57.417 40.909 0.00 0.00 0.00 2.34
570 647 2.164332 TACACCCTTCTCCGCTCCCT 62.164 60.000 0.00 0.00 0.00 4.20
574 651 1.445095 CCTTCTCCGCTCCCTCATG 59.555 63.158 0.00 0.00 0.00 3.07
576 653 0.103937 CTTCTCCGCTCCCTCATGTC 59.896 60.000 0.00 0.00 0.00 3.06
579 656 2.202797 CCGCTCCCTCATGTCACG 60.203 66.667 0.00 0.00 0.00 4.35
590 667 2.670905 CTCATGTCACGTCGCCAATTTA 59.329 45.455 0.00 0.00 0.00 1.40
602 679 9.015577 CACGTCGCCAATTTAATTTTTACATAT 57.984 29.630 0.00 0.00 0.00 1.78
717 808 5.414360 AGTGACATATAGGCGAGCAATATG 58.586 41.667 19.30 19.30 38.81 1.78
921 1032 0.466372 TCGTGCCCACCACAATTGAA 60.466 50.000 13.59 0.00 44.91 2.69
922 1033 0.039256 CGTGCCCACCACAATTGAAG 60.039 55.000 13.59 5.18 44.91 3.02
923 1034 0.318120 GTGCCCACCACAATTGAAGG 59.682 55.000 13.59 15.43 44.06 3.46
935 1060 5.182001 CCACAATTGAAGGAAACTACTGAGG 59.818 44.000 13.59 0.00 42.68 3.86
971 1100 3.879998 TGGAAAACACACTGAGCTTACA 58.120 40.909 0.00 0.00 0.00 2.41
972 1101 3.625764 TGGAAAACACACTGAGCTTACAC 59.374 43.478 0.00 0.00 0.00 2.90
990 1119 6.312180 GCTTACACACGTAGCTAGGTAAATTT 59.688 38.462 18.12 0.00 0.00 1.82
991 1120 7.585286 TTACACACGTAGCTAGGTAAATTTG 57.415 36.000 18.12 12.31 0.00 2.32
994 1123 5.636121 CACACGTAGCTAGGTAAATTTGTGA 59.364 40.000 18.12 0.00 0.00 3.58
1067 1198 1.801302 TTCCTCCTCTCCTCCACCGT 61.801 60.000 0.00 0.00 0.00 4.83
1468 1697 2.232452 CAGATCAAGAAGGACGTGGAGT 59.768 50.000 0.00 0.00 0.00 3.85
1833 2150 0.981183 AGAACTTCCGTGGCCACATA 59.019 50.000 34.16 19.29 0.00 2.29
1846 2163 1.591158 GCCACATATACAACGACACCG 59.409 52.381 0.00 0.00 42.50 4.94
2209 2527 1.417288 TCATCCATCGGCTCACATCT 58.583 50.000 0.00 0.00 0.00 2.90
2216 2534 2.941453 TCGGCTCACATCTTGTACTC 57.059 50.000 0.00 0.00 0.00 2.59
2259 2577 0.464036 TACCAACCAGCTAGCATCCG 59.536 55.000 18.83 3.12 0.00 4.18
2286 2604 1.171308 GCTGATATGCATGGCGGAAT 58.829 50.000 10.16 0.00 0.00 3.01
2317 2635 3.864789 AATCTGGTTCGGATAATGCCT 57.135 42.857 0.00 0.00 0.00 4.75
2318 2636 2.620251 TCTGGTTCGGATAATGCCTG 57.380 50.000 0.00 0.00 0.00 4.85
2319 2637 0.947244 CTGGTTCGGATAATGCCTGC 59.053 55.000 0.00 0.00 0.00 4.85
2350 2669 3.330267 GTTGGCTAGTTCAGAAGTGAGG 58.670 50.000 0.18 0.00 32.98 3.86
2358 2677 4.381411 AGTTCAGAAGTGAGGTTAGCAAC 58.619 43.478 0.00 0.00 32.98 4.17
2381 2700 2.515523 CTGCTCGGCTGGGGATTG 60.516 66.667 0.00 0.00 0.00 2.67
2405 2724 0.744874 ATGCCTGCTTCATCATGCAC 59.255 50.000 0.00 0.00 39.67 4.57
2410 2729 2.615447 CCTGCTTCATCATGCACGTAAT 59.385 45.455 0.00 0.00 35.20 1.89
2411 2730 3.809279 CCTGCTTCATCATGCACGTAATA 59.191 43.478 0.00 0.00 35.20 0.98
2412 2731 4.273235 CCTGCTTCATCATGCACGTAATAA 59.727 41.667 0.00 0.00 35.20 1.40
2413 2732 5.220835 CCTGCTTCATCATGCACGTAATAAA 60.221 40.000 0.00 0.00 35.20 1.40
2479 2799 2.359230 GGTGTGGCAGGTCTGAGC 60.359 66.667 1.65 0.00 0.00 4.26
2499 2819 2.939640 GCCGGCTGAGATTTAACCAAGA 60.940 50.000 22.15 0.00 0.00 3.02
2500 2820 2.678336 CCGGCTGAGATTTAACCAAGAC 59.322 50.000 0.00 0.00 0.00 3.01
2593 2942 8.314021 TGTAAGATTTCATGGATATAGCATCGT 58.686 33.333 0.00 0.00 0.00 3.73
2611 2960 2.885266 TCGTGTGAGACTTAGCAAGACT 59.115 45.455 3.37 2.60 36.25 3.24
2724 3074 4.788100 CCACAAATCTAGCATTTTTCGTCG 59.212 41.667 0.00 0.00 0.00 5.12
2736 3086 6.142320 AGCATTTTTCGTCGAATGTTCTTTTC 59.858 34.615 8.78 0.00 36.03 2.29
2737 3087 6.142320 GCATTTTTCGTCGAATGTTCTTTTCT 59.858 34.615 8.78 0.00 36.03 2.52
2738 3088 7.305993 GCATTTTTCGTCGAATGTTCTTTTCTT 60.306 33.333 8.78 0.00 36.03 2.52
2739 3089 8.531530 CATTTTTCGTCGAATGTTCTTTTCTTT 58.468 29.630 8.78 0.00 0.00 2.52
2740 3090 8.455598 TTTTTCGTCGAATGTTCTTTTCTTTT 57.544 26.923 8.78 0.00 0.00 2.27
2741 3091 7.659290 TTTCGTCGAATGTTCTTTTCTTTTC 57.341 32.000 8.78 0.00 0.00 2.29
2791 3141 1.402984 GCGACGAAACTGAGAGACCAT 60.403 52.381 0.00 0.00 0.00 3.55
2810 3160 8.319057 AGACCATAAATATGAAGTGTGTCCTA 57.681 34.615 1.98 0.00 35.75 2.94
2835 3185 6.620253 TTTTAATTCGGAATTGCTAAACGC 57.380 33.333 22.81 0.00 39.77 4.84
2836 3186 5.554822 TTAATTCGGAATTGCTAAACGCT 57.445 34.783 22.81 0.00 40.11 5.07
2847 3197 3.751621 TGCTAAACGCTAGTCGACTAAC 58.248 45.455 24.66 19.59 41.67 2.34
2861 3211 5.068198 AGTCGACTAACACTTAACCAAGTCA 59.932 40.000 18.46 0.00 43.30 3.41
2863 3213 5.045215 CGACTAACACTTAACCAAGTCACA 58.955 41.667 0.00 0.00 43.30 3.58
2864 3214 5.175126 CGACTAACACTTAACCAAGTCACAG 59.825 44.000 0.00 0.00 43.30 3.66
2865 3215 5.985911 ACTAACACTTAACCAAGTCACAGT 58.014 37.500 0.00 0.00 43.30 3.55
2866 3216 6.047231 ACTAACACTTAACCAAGTCACAGTC 58.953 40.000 0.00 0.00 43.30 3.51
2867 3217 3.454375 ACACTTAACCAAGTCACAGTCG 58.546 45.455 0.00 0.00 43.30 4.18
2868 3218 3.131577 ACACTTAACCAAGTCACAGTCGA 59.868 43.478 0.00 0.00 43.30 4.20
2869 3219 4.202223 ACACTTAACCAAGTCACAGTCGAT 60.202 41.667 0.00 0.00 43.30 3.59
2964 3314 9.563748 TTTATATGTTATGTTACTTGGCTACCC 57.436 33.333 0.00 0.00 0.00 3.69
2965 3315 4.224991 TGTTATGTTACTTGGCTACCCC 57.775 45.455 0.00 0.00 0.00 4.95
2966 3316 3.587951 TGTTATGTTACTTGGCTACCCCA 59.412 43.478 0.00 0.00 43.51 4.96
2985 3335 4.034285 CCAACTTATGGGTTTCACCTCT 57.966 45.455 0.00 0.00 46.27 3.69
2986 3336 5.174037 CCAACTTATGGGTTTCACCTCTA 57.826 43.478 0.00 0.00 46.27 2.43
2987 3337 5.186198 CCAACTTATGGGTTTCACCTCTAG 58.814 45.833 0.00 0.00 46.27 2.43
2988 3338 4.489306 ACTTATGGGTTTCACCTCTAGC 57.511 45.455 0.00 0.00 38.64 3.42
2989 3339 3.200165 ACTTATGGGTTTCACCTCTAGCC 59.800 47.826 0.00 0.00 38.64 3.93
2990 3340 1.972588 ATGGGTTTCACCTCTAGCCT 58.027 50.000 0.00 0.00 38.64 4.58
2991 3341 2.634639 TGGGTTTCACCTCTAGCCTA 57.365 50.000 0.00 0.00 38.64 3.93
2992 3342 2.185387 TGGGTTTCACCTCTAGCCTAC 58.815 52.381 0.00 0.00 38.64 3.18
2993 3343 1.485480 GGGTTTCACCTCTAGCCTACC 59.515 57.143 0.00 0.00 38.64 3.18
2994 3344 1.485480 GGTTTCACCTCTAGCCTACCC 59.515 57.143 0.00 0.00 34.73 3.69
2995 3345 1.485480 GTTTCACCTCTAGCCTACCCC 59.515 57.143 0.00 0.00 0.00 4.95
2996 3346 0.714180 TTCACCTCTAGCCTACCCCA 59.286 55.000 0.00 0.00 0.00 4.96
2997 3347 0.714180 TCACCTCTAGCCTACCCCAA 59.286 55.000 0.00 0.00 0.00 4.12
2998 3348 0.831307 CACCTCTAGCCTACCCCAAC 59.169 60.000 0.00 0.00 0.00 3.77
2999 3349 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.00 0.00 3.16
3000 3350 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.00 0.00 2.66
3001 3351 1.486726 CCTCTAGCCTACCCCAACTTG 59.513 57.143 0.00 0.00 0.00 3.16
3002 3352 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
3003 3353 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
3004 3354 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
3005 3355 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
3016 3366 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
3017 3367 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
3018 3368 3.910989 ACTTGTTTGGGACTAAAGGCTT 58.089 40.909 0.00 0.00 0.00 4.35
3019 3369 4.286707 ACTTGTTTGGGACTAAAGGCTTT 58.713 39.130 17.76 17.76 0.00 3.51
3020 3370 4.099419 ACTTGTTTGGGACTAAAGGCTTTG 59.901 41.667 22.32 13.97 0.00 2.77
3021 3371 3.637769 TGTTTGGGACTAAAGGCTTTGT 58.362 40.909 22.32 16.86 0.00 2.83
3022 3372 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
3023 3373 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
3024 3374 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
3025 3375 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
3026 3376 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
3027 3377 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
3028 3378 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
3029 3379 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
3030 3380 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
3031 3381 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
3032 3382 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
3033 3383 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
3034 3384 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
3035 3385 3.745458 AGGCTTTGTTGTTGTTGTTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
3036 3386 3.496507 GGCTTTGTTGTTGTTGTTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
3037 3387 4.024472 GGCTTTGTTGTTGTTGTTGTTGTT 60.024 37.500 0.00 0.00 0.00 2.83
3038 3388 4.903016 GCTTTGTTGTTGTTGTTGTTGTTG 59.097 37.500 0.00 0.00 0.00 3.33
3039 3389 5.503194 GCTTTGTTGTTGTTGTTGTTGTTGT 60.503 36.000 0.00 0.00 0.00 3.32
3040 3390 6.422776 TTTGTTGTTGTTGTTGTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
3041 3391 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
3042 3392 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
3043 3393 5.005779 TGTTGTTGTTGTTGTTGTTGTTGTC 59.994 36.000 0.00 0.00 0.00 3.18
3054 3404 4.102649 GTTGTTGTTGTCACTTGGCTAAC 58.897 43.478 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.656948 TCTGAAATCAAATTTGAACCATGAACC 59.343 33.333 23.91 7.37 41.13 3.62
80 81 6.016276 ACCACCATGAAAGTTAATTGAGACAC 60.016 38.462 0.00 0.00 0.00 3.67
122 123 9.781834 TTGAACCATCGATATATTGTGAAAAAC 57.218 29.630 0.00 0.00 0.00 2.43
450 521 6.599638 AGACAATTAAGGAACCATAAGAGCAC 59.400 38.462 0.00 0.00 0.00 4.40
533 610 8.150827 AGGGTGTATGCTGTGATGTATATATT 57.849 34.615 0.00 0.00 0.00 1.28
547 624 0.978146 AGCGGAGAAGGGTGTATGCT 60.978 55.000 0.00 0.00 0.00 3.79
570 647 1.518325 AAATTGGCGACGTGACATGA 58.482 45.000 0.00 0.00 33.63 3.07
574 651 5.815964 AAAAATTAAATTGGCGACGTGAC 57.184 34.783 0.00 0.00 0.00 3.67
576 653 6.677027 TGTAAAAATTAAATTGGCGACGTG 57.323 33.333 0.00 0.00 0.00 4.49
717 808 5.863935 GCCAAAAACTGATCCATCTTTACAC 59.136 40.000 0.00 0.00 0.00 2.90
916 1027 5.248477 TGCTACCTCAGTAGTTTCCTTCAAT 59.752 40.000 2.48 0.00 46.60 2.57
921 1032 5.026790 AGATTGCTACCTCAGTAGTTTCCT 58.973 41.667 2.48 0.00 46.60 3.36
922 1033 5.346181 AGATTGCTACCTCAGTAGTTTCC 57.654 43.478 2.48 0.00 46.60 3.13
923 1034 7.321153 TGTAAGATTGCTACCTCAGTAGTTTC 58.679 38.462 2.48 0.00 46.60 2.78
935 1060 6.017440 TGTGTTTTCCACTGTAAGATTGCTAC 60.017 38.462 0.00 0.00 44.81 3.58
971 1100 5.786311 TCACAAATTTACCTAGCTACGTGT 58.214 37.500 0.00 0.00 0.00 4.49
972 1101 6.097356 TCTCACAAATTTACCTAGCTACGTG 58.903 40.000 0.00 0.00 0.00 4.49
1131 1262 2.904866 GCCTTTGTCACCGTGGCA 60.905 61.111 0.47 0.47 42.79 4.92
1252 1384 8.152309 TGCATACAAATCAATCGACATGAATA 57.848 30.769 0.00 0.00 0.00 1.75
1330 1547 3.585862 CGTCGCAACCCTATATAGCAAT 58.414 45.455 4.04 0.00 0.00 3.56
1662 1979 1.344837 CATCATGTTCGCCGTCGTG 59.655 57.895 0.00 0.00 36.96 4.35
1833 2150 1.469703 TCGATGTCGGTGTCGTTGTAT 59.530 47.619 2.25 0.00 38.85 2.29
1846 2163 2.884207 GAACGCCGGGTCGATGTC 60.884 66.667 15.84 7.63 0.00 3.06
2267 2585 1.171308 ATTCCGCCATGCATATCAGC 58.829 50.000 0.00 0.00 0.00 4.26
2268 2586 4.256110 TCTTATTCCGCCATGCATATCAG 58.744 43.478 0.00 0.00 0.00 2.90
2269 2587 4.256110 CTCTTATTCCGCCATGCATATCA 58.744 43.478 0.00 0.00 0.00 2.15
2270 2588 3.064545 GCTCTTATTCCGCCATGCATATC 59.935 47.826 0.00 0.00 0.00 1.63
2271 2589 3.012518 GCTCTTATTCCGCCATGCATAT 58.987 45.455 0.00 0.00 0.00 1.78
2272 2590 2.426522 GCTCTTATTCCGCCATGCATA 58.573 47.619 0.00 0.00 0.00 3.14
2282 2600 4.704965 ACCAGATTAACGGCTCTTATTCC 58.295 43.478 0.00 0.00 0.00 3.01
2286 2604 3.429822 CCGAACCAGATTAACGGCTCTTA 60.430 47.826 0.00 0.00 37.32 2.10
2326 2645 1.002087 ACTTCTGAACTAGCCAACCCG 59.998 52.381 0.00 0.00 0.00 5.28
2330 2649 2.972713 ACCTCACTTCTGAACTAGCCAA 59.027 45.455 0.00 0.00 0.00 4.52
2350 2669 0.393132 GAGCAGGAGGGGTTGCTAAC 60.393 60.000 0.00 0.00 37.79 2.34
2381 2700 0.812811 TGATGAAGCAGGCATCTCGC 60.813 55.000 12.59 0.00 42.00 5.03
2418 2737 6.997655 AGTACTGCATGCATAGTATACATGT 58.002 36.000 22.97 13.58 42.50 3.21
2479 2799 2.678336 GTCTTGGTTAAATCTCAGCCGG 59.322 50.000 0.00 0.00 0.00 6.13
2482 2802 6.372659 TGATTGAGTCTTGGTTAAATCTCAGC 59.627 38.462 0.00 0.00 33.36 4.26
2499 2819 5.297547 ACATGTTACGTCACTTGATTGAGT 58.702 37.500 19.16 0.00 0.00 3.41
2500 2820 5.845985 ACATGTTACGTCACTTGATTGAG 57.154 39.130 19.16 0.00 0.00 3.02
2581 2930 5.797934 GCTAAGTCTCACACGATGCTATATC 59.202 44.000 0.00 0.00 0.00 1.63
2587 2936 1.996292 TGCTAAGTCTCACACGATGC 58.004 50.000 0.00 0.00 0.00 3.91
2593 2942 4.937201 TTCAGTCTTGCTAAGTCTCACA 57.063 40.909 0.00 0.00 0.00 3.58
2724 3074 8.168626 ACGCAAAAAGAAAAGAAAAGAACATTC 58.831 29.630 0.00 0.00 0.00 2.67
2736 3086 3.769536 AGGACACACGCAAAAAGAAAAG 58.230 40.909 0.00 0.00 0.00 2.27
2737 3087 3.191581 TGAGGACACACGCAAAAAGAAAA 59.808 39.130 0.00 0.00 0.00 2.29
2738 3088 2.750166 TGAGGACACACGCAAAAAGAAA 59.250 40.909 0.00 0.00 0.00 2.52
2739 3089 2.360844 TGAGGACACACGCAAAAAGAA 58.639 42.857 0.00 0.00 0.00 2.52
2740 3090 2.031258 TGAGGACACACGCAAAAAGA 57.969 45.000 0.00 0.00 0.00 2.52
2741 3091 2.842208 TTGAGGACACACGCAAAAAG 57.158 45.000 0.00 0.00 0.00 2.27
2833 3183 4.094212 GGTTAAGTGTTAGTCGACTAGCG 58.906 47.826 27.42 0.00 42.69 4.26
2835 3185 6.675987 ACTTGGTTAAGTGTTAGTCGACTAG 58.324 40.000 23.51 12.54 45.17 2.57
2836 3186 6.262944 TGACTTGGTTAAGTGTTAGTCGACTA 59.737 38.462 21.25 21.25 46.79 2.59
2847 3197 3.713288 TCGACTGTGACTTGGTTAAGTG 58.287 45.455 0.00 0.00 46.79 3.16
2867 3217 0.924090 GATCACACGGCGAGAACATC 59.076 55.000 16.62 6.53 0.00 3.06
2868 3218 0.532573 AGATCACACGGCGAGAACAT 59.467 50.000 16.62 0.06 0.00 2.71
2869 3219 0.317160 AAGATCACACGGCGAGAACA 59.683 50.000 16.62 0.00 0.00 3.18
2877 3227 1.471287 TCTCCACGTAAGATCACACGG 59.529 52.381 19.29 10.56 42.35 4.94
2952 3302 3.201266 CCATAAGTTGGGGTAGCCAAGTA 59.799 47.826 14.06 0.00 42.33 2.24
2975 3325 1.485480 GGGGTAGGCTAGAGGTGAAAC 59.515 57.143 0.00 0.00 0.00 2.78
2976 3326 1.079825 TGGGGTAGGCTAGAGGTGAAA 59.920 52.381 0.00 0.00 0.00 2.69
2977 3327 0.714180 TGGGGTAGGCTAGAGGTGAA 59.286 55.000 0.00 0.00 0.00 3.18
2978 3328 0.714180 TTGGGGTAGGCTAGAGGTGA 59.286 55.000 0.00 0.00 0.00 4.02
2979 3329 0.831307 GTTGGGGTAGGCTAGAGGTG 59.169 60.000 0.00 0.00 0.00 4.00
2980 3330 0.717196 AGTTGGGGTAGGCTAGAGGT 59.283 55.000 0.00 0.00 0.00 3.85
2981 3331 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.00 0.00 3.69
2982 3332 2.188817 ACAAGTTGGGGTAGGCTAGAG 58.811 52.381 7.96 0.00 0.00 2.43
2983 3333 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
2984 3334 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
2985 3335 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
2986 3336 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
2995 3345 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
2996 3346 3.910989 AGCCTTTAGTCCCAAACAAGTT 58.089 40.909 0.00 0.00 0.00 2.66
2997 3347 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16
2998 3348 4.099419 ACAAAGCCTTTAGTCCCAAACAAG 59.901 41.667 0.00 0.00 0.00 3.16
2999 3349 4.027437 ACAAAGCCTTTAGTCCCAAACAA 58.973 39.130 0.00 0.00 0.00 2.83
3000 3350 3.637769 ACAAAGCCTTTAGTCCCAAACA 58.362 40.909 0.00 0.00 0.00 2.83
3001 3351 4.142026 ACAACAAAGCCTTTAGTCCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
3002 3352 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
3003 3353 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
3004 3354 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
3005 3355 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
3006 3356 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
3007 3357 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
3008 3358 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
3009 3359 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
3010 3360 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
3011 3361 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
3012 3362 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
3013 3363 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
3014 3364 3.496507 ACAACAACAACAACAACAAAGCC 59.503 39.130 0.00 0.00 0.00 4.35
3015 3365 4.723879 ACAACAACAACAACAACAAAGC 57.276 36.364 0.00 0.00 0.00 3.51
3016 3366 6.042144 ACAACAACAACAACAACAACAAAG 57.958 33.333 0.00 0.00 0.00 2.77
3017 3367 6.128282 ACAACAACAACAACAACAACAACAAA 60.128 30.769 0.00 0.00 0.00 2.83
3018 3368 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
3019 3369 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
3020 3370 5.005779 TGACAACAACAACAACAACAACAAC 59.994 36.000 0.00 0.00 0.00 3.32
3021 3371 5.005779 GTGACAACAACAACAACAACAACAA 59.994 36.000 0.00 0.00 0.00 2.83
3022 3372 4.504461 GTGACAACAACAACAACAACAACA 59.496 37.500 0.00 0.00 0.00 3.33
3023 3373 4.742659 AGTGACAACAACAACAACAACAAC 59.257 37.500 0.00 0.00 0.00 3.32
3024 3374 4.938080 AGTGACAACAACAACAACAACAA 58.062 34.783 0.00 0.00 0.00 2.83
3025 3375 4.576216 AGTGACAACAACAACAACAACA 57.424 36.364 0.00 0.00 0.00 3.33
3026 3376 4.149747 CCAAGTGACAACAACAACAACAAC 59.850 41.667 0.00 0.00 0.00 3.32
3027 3377 4.302455 CCAAGTGACAACAACAACAACAA 58.698 39.130 0.00 0.00 0.00 2.83
3028 3378 3.858877 GCCAAGTGACAACAACAACAACA 60.859 43.478 0.00 0.00 0.00 3.33
3029 3379 2.666022 GCCAAGTGACAACAACAACAAC 59.334 45.455 0.00 0.00 0.00 3.32
3030 3380 2.560542 AGCCAAGTGACAACAACAACAA 59.439 40.909 0.00 0.00 0.00 2.83
3031 3381 2.166829 AGCCAAGTGACAACAACAACA 58.833 42.857 0.00 0.00 0.00 3.33
3032 3382 2.939460 AGCCAAGTGACAACAACAAC 57.061 45.000 0.00 0.00 0.00 3.32
3033 3383 4.013728 AGTTAGCCAAGTGACAACAACAA 58.986 39.130 0.00 0.00 0.00 2.83
3034 3384 3.616219 AGTTAGCCAAGTGACAACAACA 58.384 40.909 0.00 0.00 0.00 3.33
3035 3385 3.877508 AGAGTTAGCCAAGTGACAACAAC 59.122 43.478 0.00 0.00 0.00 3.32
3036 3386 4.127171 GAGAGTTAGCCAAGTGACAACAA 58.873 43.478 0.00 0.00 0.00 2.83
3037 3387 3.133901 TGAGAGTTAGCCAAGTGACAACA 59.866 43.478 0.00 0.00 0.00 3.33
3038 3388 3.728845 TGAGAGTTAGCCAAGTGACAAC 58.271 45.455 0.00 0.00 0.00 3.32
3039 3389 3.803715 GCTGAGAGTTAGCCAAGTGACAA 60.804 47.826 0.00 0.00 35.15 3.18
3040 3390 2.289072 GCTGAGAGTTAGCCAAGTGACA 60.289 50.000 0.00 0.00 35.15 3.58
3041 3391 2.342179 GCTGAGAGTTAGCCAAGTGAC 58.658 52.381 0.00 0.00 35.15 3.67
3042 3392 2.751166 GCTGAGAGTTAGCCAAGTGA 57.249 50.000 0.00 0.00 35.15 3.41
3063 3413 2.237392 AGGGTGTGGCTAGATTTCAGTC 59.763 50.000 0.00 0.00 0.00 3.51
3069 3419 5.717119 ATTAGAAAGGGTGTGGCTAGATT 57.283 39.130 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.