Multiple sequence alignment - TraesCS5A01G140500

Loading Multiple Alignment...

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 TraesCS5A01G140500 chr5A 100.000 4049 0 0 1 4049 312750552 312754600 0.000000e+00 7478.0
1 TraesCS5A01G140500 chr5D 92.280 2785 132 24 513 3271 241114472 241111745 0.000000e+00 3875.0
2 TraesCS5A01G140500 chr5D 91.393 732 42 14 3327 4049 241110356 241109637 0.000000e+00 983.0
3 TraesCS5A01G140500 chr5D 87.302 504 23 21 5 490 241114943 241114463 4.600000e-149 538.0
4 TraesCS5A01G140500 chr5D 100.000 29 0 0 3274 3302 241110384 241110356 2.000000e-03 54.7
5 TraesCS5A01G140500 chr5B 91.647 2514 120 37 1145 3617 262563664 262566128 0.000000e+00 3397.0
6 TraesCS5A01G140500 chr5B 85.694 720 52 19 505 1192 262562945 262563645 0.000000e+00 712.0
7 TraesCS5A01G140500 chr5B 91.959 485 20 10 9 490 262562494 262562962 0.000000e+00 662.0
8 TraesCS5A01G140500 chr5B 89.899 297 22 7 3755 4049 262569682 262569972 3.820000e-100 375.0
9 TraesCS5A01G140500 chr5B 98.876 89 0 1 3827 3915 692703291 692703204 1.510000e-34 158.0
10 TraesCS5A01G140500 chr5B 95.000 100 2 3 3816 3913 692556174 692556272 1.950000e-33 154.0
11 TraesCS5A01G140500 chr5B 92.857 42 2 1 442 482 61353745 61353786 4.370000e-05 60.2
12 TraesCS5A01G140500 chr4A 98.876 89 0 1 3827 3915 619380579 619380492 1.510000e-34 158.0
13 TraesCS5A01G140500 chr4A 92.453 106 7 1 3816 3920 620188164 620188059 2.520000e-32 150.0
14 TraesCS5A01G140500 chr1B 94.949 99 4 1 3816 3913 638938454 638938552 1.950000e-33 154.0
15 TraesCS5A01G140500 chr4D 93.204 103 2 5 3813 3913 109245267 109245168 3.260000e-31 147.0
16 TraesCS5A01G140500 chr6B 90.090 111 7 4 3811 3919 692737624 692737732 1.520000e-29 141.0


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 TraesCS5A01G140500 chr5A 312750552 312754600 4048 False 7478.000 7478 100.00000 1 4049 1 chr5A.!!$F1 4048
1 TraesCS5A01G140500 chr5D 241109637 241114943 5306 True 1362.675 3875 92.74375 5 4049 4 chr5D.!!$R1 4044
2 TraesCS5A01G140500 chr5B 262562494 262569972 7478 False 1286.500 3397 89.79975 9 4049 4 chr5B.!!$F3 4040

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
88 89 0.444260 GGAAGAGCTTTCGCCTTTCG 59.556 55.0 0.00 0.0 36.60 3.46 F
1016 1065 0.032813 ACCATGGGGAGCTTGATTGG 60.033 55.0 18.09 0.0 38.05 3.16 F
2442 2578 0.169672 CGAGGCATGTTCCTTTGCTG 59.830 55.0 0.00 0.0 38.88 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2032 2168 0.395862 TCCATCCAGGAGTCCTCGAC 60.396 60.0 9.36 0.0 43.07 4.20 R
2694 2830 0.393537 CTGCACCCAGGTTCCATCTC 60.394 60.0 0.00 0.0 35.38 2.75 R
3835 8835 0.472734 AACCTGGGCTCAGACAGTCT 60.473 55.0 17.43 0.0 43.49 3.24 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
41 42 4.202050 CCTCCAAAGAAGTGAAACCACAAG 60.202 45.833 0.00 0.00 37.80 3.16
82 83 1.470805 GGAGAGAGGAAGAGCTTTCGC 60.471 57.143 0.00 0.00 0.00 4.70
83 84 0.534873 AGAGAGGAAGAGCTTTCGCC 59.465 55.000 0.00 0.00 36.60 5.54
84 85 0.534873 GAGAGGAAGAGCTTTCGCCT 59.465 55.000 0.00 0.00 36.60 5.52
85 86 0.980423 AGAGGAAGAGCTTTCGCCTT 59.020 50.000 0.00 0.00 36.60 4.35
86 87 1.349357 AGAGGAAGAGCTTTCGCCTTT 59.651 47.619 0.00 0.00 36.60 3.11
87 88 1.735018 GAGGAAGAGCTTTCGCCTTTC 59.265 52.381 0.00 0.00 36.60 2.62
88 89 0.444260 GGAAGAGCTTTCGCCTTTCG 59.556 55.000 0.00 0.00 36.60 3.46
91 92 1.016653 AGAGCTTTCGCCTTTCGCTC 61.017 55.000 0.00 0.00 45.49 5.03
122 123 1.915266 CCAGGTCAGTCAGCTCCCA 60.915 63.158 0.00 0.00 0.00 4.37
165 178 2.743636 TTCTGGCGTTCTTGAGTAGG 57.256 50.000 0.00 0.00 0.00 3.18
170 183 3.159472 TGGCGTTCTTGAGTAGGAGTAA 58.841 45.455 0.00 0.00 0.00 2.24
193 209 7.611213 AACTTTAGGTTTTGGATGATCGTAG 57.389 36.000 0.00 0.00 33.90 3.51
219 236 5.010282 GTGGAGAAATGGCCTTCTTTTCTA 58.990 41.667 17.59 4.74 44.65 2.10
248 268 4.369182 TCAACGTTCCTCTTCTTGAACTC 58.631 43.478 0.00 0.00 38.93 3.01
252 272 4.141914 ACGTTCCTCTTCTTGAACTCTGTT 60.142 41.667 0.00 0.00 38.93 3.16
253 273 4.811557 CGTTCCTCTTCTTGAACTCTGTTT 59.188 41.667 0.00 0.00 38.93 2.83
254 274 5.050702 CGTTCCTCTTCTTGAACTCTGTTTC 60.051 44.000 0.00 0.00 38.93 2.78
289 309 2.789779 CGATACCGGCATTTTTGGTTCG 60.790 50.000 0.00 0.00 37.20 3.95
290 310 1.606903 TACCGGCATTTTTGGTTCGT 58.393 45.000 0.00 0.00 37.20 3.85
291 311 1.606903 ACCGGCATTTTTGGTTCGTA 58.393 45.000 0.00 0.00 29.87 3.43
310 330 5.205821 TCGTAATATGTGAGGAGGAAAGGA 58.794 41.667 0.00 0.00 0.00 3.36
316 336 2.040278 TGTGAGGAGGAAAGGAACATGG 59.960 50.000 0.00 0.00 0.00 3.66
317 337 2.305927 GTGAGGAGGAAAGGAACATGGA 59.694 50.000 0.00 0.00 0.00 3.41
318 338 2.986019 TGAGGAGGAAAGGAACATGGAA 59.014 45.455 0.00 0.00 0.00 3.53
420 441 6.128902 GGATACTTCGACACAAAGTAACACAG 60.129 42.308 0.00 0.00 41.26 3.66
472 493 6.426937 TCCTCTGTTTCTTTTGTTTCGATAGG 59.573 38.462 0.00 0.00 0.00 2.57
482 503 8.936864 TCTTTTGTTTCGATAGGAAGAAGATTC 58.063 33.333 0.00 0.00 38.19 2.52
483 504 7.611213 TTTGTTTCGATAGGAAGAAGATTCC 57.389 36.000 0.00 0.00 38.19 3.01
485 506 6.574350 TGTTTCGATAGGAAGAAGATTCCTC 58.426 40.000 12.28 0.00 45.32 3.71
486 507 6.381420 TGTTTCGATAGGAAGAAGATTCCTCT 59.619 38.462 12.28 3.46 45.32 3.69
487 508 6.398234 TTCGATAGGAAGAAGATTCCTCTG 57.602 41.667 12.28 4.78 45.32 3.35
488 509 5.450453 TCGATAGGAAGAAGATTCCTCTGT 58.550 41.667 12.28 1.36 45.32 3.41
489 510 5.894393 TCGATAGGAAGAAGATTCCTCTGTT 59.106 40.000 12.28 0.00 45.32 3.16
490 511 7.061054 TCGATAGGAAGAAGATTCCTCTGTTA 58.939 38.462 12.28 0.00 45.32 2.41
491 512 7.560262 TCGATAGGAAGAAGATTCCTCTGTTAA 59.440 37.037 12.28 0.00 45.32 2.01
492 513 8.364142 CGATAGGAAGAAGATTCCTCTGTTAAT 58.636 37.037 12.28 0.33 45.32 1.40
495 516 7.044798 AGGAAGAAGATTCCTCTGTTAATTCG 58.955 38.462 3.28 0.00 45.32 3.34
496 517 6.238239 GGAAGAAGATTCCTCTGTTAATTCGC 60.238 42.308 0.00 0.00 35.73 4.70
497 518 5.734720 AGAAGATTCCTCTGTTAATTCGCA 58.265 37.500 0.00 0.00 0.00 5.10
498 519 6.173339 AGAAGATTCCTCTGTTAATTCGCAA 58.827 36.000 0.00 0.00 0.00 4.85
499 520 6.655003 AGAAGATTCCTCTGTTAATTCGCAAA 59.345 34.615 0.00 0.00 0.00 3.68
500 521 6.817765 AGATTCCTCTGTTAATTCGCAAAA 57.182 33.333 0.00 0.00 0.00 2.44
501 522 7.214467 AGATTCCTCTGTTAATTCGCAAAAA 57.786 32.000 0.00 0.00 0.00 1.94
567 588 5.835113 TCCTGTTCTTTCAGTTCAAAAGG 57.165 39.130 0.00 0.00 35.03 3.11
640 668 7.668469 TGACCTCCCTTTCTTAAAAAGATTACC 59.332 37.037 10.05 0.00 37.38 2.85
712 740 4.421948 ACGAATCCTACTCGTCAATCAAC 58.578 43.478 0.00 0.00 46.10 3.18
745 773 1.677576 CACTGCCACCATCGCATAAAT 59.322 47.619 0.00 0.00 35.25 1.40
746 774 2.099592 CACTGCCACCATCGCATAAATT 59.900 45.455 0.00 0.00 35.25 1.82
748 776 3.117794 CTGCCACCATCGCATAAATTTG 58.882 45.455 0.00 0.00 35.25 2.32
752 780 3.491639 CCACCATCGCATAAATTTGCATG 59.508 43.478 0.00 0.00 42.91 4.06
774 802 1.799933 AATTCCACCCAGCCAACAAA 58.200 45.000 0.00 0.00 0.00 2.83
776 804 1.045911 TTCCACCCAGCCAACAAACC 61.046 55.000 0.00 0.00 0.00 3.27
781 809 0.754957 CCCAGCCAACAAACCAGTGA 60.755 55.000 0.00 0.00 0.00 3.41
782 810 1.331214 CCAGCCAACAAACCAGTGAT 58.669 50.000 0.00 0.00 0.00 3.06
783 811 1.270550 CCAGCCAACAAACCAGTGATC 59.729 52.381 0.00 0.00 0.00 2.92
784 812 1.955778 CAGCCAACAAACCAGTGATCA 59.044 47.619 0.00 0.00 0.00 2.92
785 813 2.361757 CAGCCAACAAACCAGTGATCAA 59.638 45.455 0.00 0.00 0.00 2.57
786 814 3.030291 AGCCAACAAACCAGTGATCAAA 58.970 40.909 0.00 0.00 0.00 2.69
787 815 3.642848 AGCCAACAAACCAGTGATCAAAT 59.357 39.130 0.00 0.00 0.00 2.32
788 816 4.101430 AGCCAACAAACCAGTGATCAAATT 59.899 37.500 0.00 0.00 0.00 1.82
800 828 9.754382 ACCAGTGATCAAATTATCAAAATATGC 57.246 29.630 0.00 0.00 37.61 3.14
817 845 2.325583 TGCAACTTTTCTGTCTCCGT 57.674 45.000 0.00 0.00 0.00 4.69
864 892 8.779354 AGATAATACAGTTCTGTCCTGTTTTC 57.221 34.615 8.80 5.95 42.83 2.29
865 893 7.824779 AGATAATACAGTTCTGTCCTGTTTTCC 59.175 37.037 8.80 3.74 42.83 3.13
866 894 2.932261 ACAGTTCTGTCCTGTTTTCCC 58.068 47.619 0.00 0.00 40.14 3.97
867 895 2.241176 ACAGTTCTGTCCTGTTTTCCCA 59.759 45.455 0.00 0.00 40.14 4.37
868 896 2.880890 CAGTTCTGTCCTGTTTTCCCAG 59.119 50.000 0.00 0.00 0.00 4.45
869 897 2.509964 AGTTCTGTCCTGTTTTCCCAGT 59.490 45.455 0.00 0.00 0.00 4.00
870 898 3.053619 AGTTCTGTCCTGTTTTCCCAGTT 60.054 43.478 0.00 0.00 0.00 3.16
871 899 3.208747 TCTGTCCTGTTTTCCCAGTTC 57.791 47.619 0.00 0.00 0.00 3.01
872 900 2.507886 TCTGTCCTGTTTTCCCAGTTCA 59.492 45.455 0.00 0.00 0.00 3.18
886 914 3.686726 CCCAGTTCAGAAGCTGATACAAC 59.313 47.826 12.00 0.00 40.39 3.32
887 915 4.564406 CCCAGTTCAGAAGCTGATACAACT 60.564 45.833 12.00 0.00 40.39 3.16
895 923 7.164122 TCAGAAGCTGATACAACTTTCTGAAT 58.836 34.615 11.13 0.00 35.39 2.57
1016 1065 0.032813 ACCATGGGGAGCTTGATTGG 60.033 55.000 18.09 0.00 38.05 3.16
1057 1106 4.410400 CCCTGGACCCGAAGCCAC 62.410 72.222 0.00 0.00 0.00 5.01
1092 1141 0.623324 CCATGTTCCCTACCCCTCCA 60.623 60.000 0.00 0.00 0.00 3.86
1269 1396 1.294780 CGCAGTTCCTCTCAAGGCT 59.705 57.895 0.00 0.00 43.02 4.58
1284 1411 1.883084 GGCTACACCAATCTCGGCG 60.883 63.158 0.00 0.00 38.86 6.46
1315 1442 0.949105 GCGGCGACTCAAAGAGGAAA 60.949 55.000 12.98 0.00 33.35 3.13
1316 1443 0.790814 CGGCGACTCAAAGAGGAAAC 59.209 55.000 0.00 0.00 33.35 2.78
1317 1444 1.157585 GGCGACTCAAAGAGGAAACC 58.842 55.000 0.00 0.00 33.35 3.27
1498 1625 1.373435 TCCACATCGGACAACCCAC 59.627 57.895 0.00 0.00 39.64 4.61
1640 1767 5.473504 ACCATAACAACCTGAAGATCAACAC 59.526 40.000 0.00 0.00 0.00 3.32
1701 1828 5.278266 CGGAGACATCTTCTTCTACAGGATC 60.278 48.000 0.00 0.00 33.22 3.36
1720 1847 2.124570 AGATGTGCATCGTGGGGC 60.125 61.111 6.54 0.00 42.48 5.80
1758 1885 1.065928 CGGCATCGACTACCTGTCC 59.934 63.158 0.00 0.00 42.49 4.02
1952 2088 2.982744 GCGCCAGCAAGAAGAACCC 61.983 63.158 0.00 0.00 44.35 4.11
2126 2262 1.600916 AGCCTGACGGGTTTTCAGC 60.601 57.895 1.33 0.00 37.94 4.26
2144 2280 1.554160 AGCCTGGAAGATGACAGACAG 59.446 52.381 0.00 0.00 36.86 3.51
2181 2317 2.733227 CGCCACAAGAGAAAATGCCATC 60.733 50.000 0.00 0.00 0.00 3.51
2190 2326 0.527565 AAAATGCCATCGTGCTGGAC 59.472 50.000 5.76 0.00 38.69 4.02
2193 2329 2.821366 GCCATCGTGCTGGACCTG 60.821 66.667 5.76 0.00 38.69 4.00
2404 2540 2.354773 GCGGCGATCTTCCCTACG 60.355 66.667 12.98 0.00 0.00 3.51
2436 2572 2.185350 CTCGCGAGGCATGTTCCT 59.815 61.111 28.40 0.00 39.67 3.36
2437 2573 1.448540 CTCGCGAGGCATGTTCCTT 60.449 57.895 28.40 0.00 36.38 3.36
2442 2578 0.169672 CGAGGCATGTTCCTTTGCTG 59.830 55.000 0.00 0.00 38.88 4.41
2445 2581 3.019564 GAGGCATGTTCCTTTGCTGTAT 58.980 45.455 0.00 0.00 38.88 2.29
2476 2612 2.778299 GTGACTGCCATTGTACCAAGA 58.222 47.619 0.00 0.00 0.00 3.02
2501 2637 1.021202 CGAAACAGGGTTGCACAGAA 58.979 50.000 0.00 0.00 0.00 3.02
2625 2761 2.767505 GGTCAAGTCATGGACGAAACT 58.232 47.619 0.00 0.00 37.67 2.66
2694 2830 1.517242 GTCCAAGTGACAAGGCTCTG 58.483 55.000 0.00 0.00 43.85 3.35
2841 2977 0.683973 ATAGCTGCTCCCCGAATCTG 59.316 55.000 4.91 0.00 0.00 2.90
2931 3067 3.668821 ACATATCCCTCCCATGACTGAA 58.331 45.455 0.00 0.00 0.00 3.02
3015 3151 1.807886 CAAGCTCAGGCCATGCTTC 59.192 57.895 21.57 0.12 44.04 3.86
3057 3193 5.588648 TCGAGGTTCTTTCTGACACAAAATT 59.411 36.000 0.00 0.00 0.00 1.82
3076 3212 1.265236 TTGCTGGGCATAAACAAGGG 58.735 50.000 0.00 0.00 38.76 3.95
3115 3251 5.923204 ACAGATGTCATTATCTCTGTTCCC 58.077 41.667 1.00 0.00 44.39 3.97
3116 3252 5.664908 ACAGATGTCATTATCTCTGTTCCCT 59.335 40.000 1.00 0.00 44.39 4.20
3117 3253 6.157645 ACAGATGTCATTATCTCTGTTCCCTT 59.842 38.462 1.00 0.00 44.39 3.95
3118 3254 7.052873 CAGATGTCATTATCTCTGTTCCCTTT 58.947 38.462 0.00 0.00 35.28 3.11
3119 3255 7.012138 CAGATGTCATTATCTCTGTTCCCTTTG 59.988 40.741 0.00 0.00 35.28 2.77
3120 3256 6.126863 TGTCATTATCTCTGTTCCCTTTGT 57.873 37.500 0.00 0.00 0.00 2.83
3121 3257 6.542821 TGTCATTATCTCTGTTCCCTTTGTT 58.457 36.000 0.00 0.00 0.00 2.83
3122 3258 6.655003 TGTCATTATCTCTGTTCCCTTTGTTC 59.345 38.462 0.00 0.00 0.00 3.18
3123 3259 6.094186 GTCATTATCTCTGTTCCCTTTGTTCC 59.906 42.308 0.00 0.00 0.00 3.62
3136 3272 5.133830 TCCCTTTGTTCCTTCTAGGTTTTCT 59.866 40.000 0.00 0.00 36.53 2.52
3155 3291 7.646526 GGTTTTCTGGTCATGTTTAACAAGTAC 59.353 37.037 0.66 0.88 0.00 2.73
3156 3292 6.870971 TTCTGGTCATGTTTAACAAGTACC 57.129 37.500 15.43 15.43 32.28 3.34
3158 3294 6.358178 TCTGGTCATGTTTAACAAGTACCAA 58.642 36.000 21.39 13.91 37.58 3.67
3159 3295 6.485313 TCTGGTCATGTTTAACAAGTACCAAG 59.515 38.462 21.39 17.03 37.58 3.61
3160 3296 6.123651 TGGTCATGTTTAACAAGTACCAAGT 58.876 36.000 19.90 0.00 36.17 3.16
3161 3297 7.281098 TGGTCATGTTTAACAAGTACCAAGTA 58.719 34.615 19.90 4.68 36.17 2.24
3163 3299 7.285788 GTCATGTTTAACAAGTACCAAGTACG 58.714 38.462 0.66 0.00 43.05 3.67
3164 3300 6.985645 TCATGTTTAACAAGTACCAAGTACGT 59.014 34.615 0.66 0.00 43.05 3.57
3165 3301 8.140628 TCATGTTTAACAAGTACCAAGTACGTA 58.859 33.333 0.66 0.00 43.05 3.57
3166 3302 8.928733 CATGTTTAACAAGTACCAAGTACGTAT 58.071 33.333 0.66 0.00 43.05 3.06
3167 3303 8.296799 TGTTTAACAAGTACCAAGTACGTATG 57.703 34.615 0.00 0.00 43.05 2.39
3168 3304 7.925483 TGTTTAACAAGTACCAAGTACGTATGT 59.075 33.333 0.00 0.00 43.05 2.29
3169 3305 7.872163 TTAACAAGTACCAAGTACGTATGTG 57.128 36.000 0.00 0.00 43.05 3.21
3171 3307 5.846203 ACAAGTACCAAGTACGTATGTGTT 58.154 37.500 0.00 0.00 43.05 3.32
3173 3309 5.972107 AGTACCAAGTACGTATGTGTTCT 57.028 39.130 0.00 0.00 43.05 3.01
3174 3310 5.947443 AGTACCAAGTACGTATGTGTTCTC 58.053 41.667 0.00 0.00 43.05 2.87
3175 3311 5.709164 AGTACCAAGTACGTATGTGTTCTCT 59.291 40.000 0.00 0.00 43.05 3.10
3244 3411 6.092122 TGGATTTATTAGTCGTGTCTTTGCTG 59.908 38.462 0.00 0.00 0.00 4.41
3272 3439 7.826252 AGAAGAACGTATCCTACACACTACTAA 59.174 37.037 0.00 0.00 0.00 2.24
3302 4827 7.684937 AGTAGACAACGTAACTATCTGTCTT 57.315 36.000 18.78 3.15 43.14 3.01
3303 4828 7.750769 AGTAGACAACGTAACTATCTGTCTTC 58.249 38.462 18.78 14.65 43.14 2.87
3304 4829 6.570672 AGACAACGTAACTATCTGTCTTCA 57.429 37.500 10.28 0.00 43.14 3.02
3305 4830 6.613233 AGACAACGTAACTATCTGTCTTCAG 58.387 40.000 10.28 0.00 43.14 3.02
3315 4840 3.475566 TCTGTCTTCAGACCCAAACTG 57.524 47.619 4.48 0.00 44.58 3.16
3316 4841 1.876156 CTGTCTTCAGACCCAAACTGC 59.124 52.381 4.48 0.00 44.15 4.40
3317 4842 1.490490 TGTCTTCAGACCCAAACTGCT 59.510 47.619 4.48 0.00 44.15 4.24
3318 4843 2.092429 TGTCTTCAGACCCAAACTGCTT 60.092 45.455 4.48 0.00 44.15 3.91
3319 4844 2.550180 GTCTTCAGACCCAAACTGCTTC 59.450 50.000 0.00 0.00 39.07 3.86
3320 4845 2.439507 TCTTCAGACCCAAACTGCTTCT 59.560 45.455 0.00 0.00 35.61 2.85
3321 4846 2.260844 TCAGACCCAAACTGCTTCTG 57.739 50.000 0.00 0.00 35.93 3.02
3322 4847 1.202806 TCAGACCCAAACTGCTTCTGG 60.203 52.381 0.00 0.00 35.42 3.86
3323 4848 1.140312 AGACCCAAACTGCTTCTGGA 58.860 50.000 0.00 0.00 31.38 3.86
3324 4849 1.707427 AGACCCAAACTGCTTCTGGAT 59.293 47.619 0.00 0.00 31.38 3.41
3325 4850 2.912956 AGACCCAAACTGCTTCTGGATA 59.087 45.455 0.00 0.00 31.38 2.59
3326 4851 3.525199 AGACCCAAACTGCTTCTGGATAT 59.475 43.478 0.00 0.00 31.38 1.63
3351 4876 4.662961 GTGCCTTGGCCGCCAAAC 62.663 66.667 24.83 19.44 43.44 2.93
3391 4916 5.046878 TCTCCTTTTCAGGTTATTACGCTGA 60.047 40.000 0.00 0.00 41.69 4.26
3407 4938 3.821600 ACGCTGATGTATGGTAGGAGTAG 59.178 47.826 0.00 0.00 0.00 2.57
3492 5023 1.754621 TAGGCAGCCGTCCTCTCTG 60.755 63.158 5.55 0.00 35.21 3.35
3493 5024 2.500815 TAGGCAGCCGTCCTCTCTGT 62.501 60.000 5.55 0.00 35.21 3.41
3494 5025 2.125753 GCAGCCGTCCTCTCTGTG 60.126 66.667 0.00 0.00 0.00 3.66
3539 5076 0.394565 AGAGTGTGTCTGGTGGCTTC 59.605 55.000 0.00 0.00 32.57 3.86
3554 5091 2.892215 TGGCTTCTGTGATGCAAAATCA 59.108 40.909 0.00 0.00 34.94 2.57
3564 5101 7.064966 TCTGTGATGCAAAATCATGTGTAGTAG 59.935 37.037 0.00 0.00 0.00 2.57
3623 8623 4.305769 CAGCAGCTGTCATCTATAAGACC 58.694 47.826 16.64 0.00 33.89 3.85
3634 8634 7.151308 GTCATCTATAAGACCTGAACCATCTG 58.849 42.308 0.00 0.00 0.00 2.90
3636 8636 3.567478 ATAAGACCTGAACCATCTGGC 57.433 47.619 0.00 0.00 45.86 4.85
3661 8661 6.539649 TCATGTGTTCTTACTTACTGTTGC 57.460 37.500 0.00 0.00 0.00 4.17
3667 8667 3.735591 TCTTACTTACTGTTGCACCACC 58.264 45.455 0.00 0.00 0.00 4.61
3680 8680 2.049802 CCACCGCTGCTGCTTTTG 60.050 61.111 14.03 7.37 36.97 2.44
3705 8705 3.405831 TCTGAACTGCTTCTGTGAATGG 58.594 45.455 0.00 0.00 0.00 3.16
3738 8738 4.149598 AGGACCTTGTTTGGTTTGGTATC 58.850 43.478 0.00 0.00 41.00 2.24
3762 8762 5.186797 CCTTGATGTCCTCTGTAGAAGAAGT 59.813 44.000 0.00 0.00 33.37 3.01
3921 8921 0.474184 ACCACCCAGACCTTTGTGAG 59.526 55.000 0.00 0.00 0.00 3.51
3923 8923 1.142870 CCACCCAGACCTTTGTGAGAA 59.857 52.381 0.00 0.00 0.00 2.87
3925 8925 1.202818 ACCCAGACCTTTGTGAGAAGC 60.203 52.381 0.00 0.00 0.00 3.86
3972 8972 7.155328 ACAGACTAGTTTGTTGATGGAGTAAG 58.845 38.462 13.05 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 1.595882 CTGGGAGCTGACTGACCTG 59.404 63.158 0.00 0.00 0.00 4.00
165 178 7.333672 ACGATCATCCAAAACCTAAAGTTACTC 59.666 37.037 0.00 0.00 37.88 2.59
170 183 5.585047 GCTACGATCATCCAAAACCTAAAGT 59.415 40.000 0.00 0.00 0.00 2.66
193 209 0.813821 GAAGGCCATTTCTCCACAGC 59.186 55.000 5.01 0.00 0.00 4.40
219 236 1.718280 AGAGGAACGTTGAGGAACCT 58.282 50.000 5.00 4.26 0.00 3.50
248 268 6.777526 ATCGACAGAAAGAAGAAGAAACAG 57.222 37.500 0.00 0.00 0.00 3.16
252 272 5.399858 CGGTATCGACAGAAAGAAGAAGAA 58.600 41.667 0.00 0.00 39.00 2.52
253 273 4.142447 CCGGTATCGACAGAAAGAAGAAGA 60.142 45.833 0.00 0.00 39.00 2.87
254 274 4.106197 CCGGTATCGACAGAAAGAAGAAG 58.894 47.826 0.00 0.00 39.00 2.85
289 309 6.650120 TGTTCCTTTCCTCCTCACATATTAC 58.350 40.000 0.00 0.00 0.00 1.89
290 310 6.884472 TGTTCCTTTCCTCCTCACATATTA 57.116 37.500 0.00 0.00 0.00 0.98
291 311 5.779241 TGTTCCTTTCCTCCTCACATATT 57.221 39.130 0.00 0.00 0.00 1.28
310 330 2.420022 GCATGCTACGTTCTTCCATGTT 59.580 45.455 11.37 0.00 36.54 2.71
316 336 4.606457 ATTTCAGCATGCTACGTTCTTC 57.394 40.909 22.19 0.00 34.76 2.87
317 337 5.419542 TCTATTTCAGCATGCTACGTTCTT 58.580 37.500 22.19 4.48 34.76 2.52
318 338 5.011090 TCTATTTCAGCATGCTACGTTCT 57.989 39.130 22.19 5.93 34.76 3.01
420 441 2.879002 TATGCTGCTCTGCTCACTAC 57.121 50.000 0.00 0.00 0.00 2.73
472 493 6.313905 TGCGAATTAACAGAGGAATCTTCTTC 59.686 38.462 0.00 0.00 33.89 2.87
505 526 6.510536 CAAGCAGAAACAGAGGAATCTTTTT 58.489 36.000 0.00 0.00 0.00 1.94
506 527 5.508657 GCAAGCAGAAACAGAGGAATCTTTT 60.509 40.000 0.00 0.00 0.00 2.27
507 528 4.022503 GCAAGCAGAAACAGAGGAATCTTT 60.023 41.667 0.00 0.00 0.00 2.52
508 529 3.505293 GCAAGCAGAAACAGAGGAATCTT 59.495 43.478 0.00 0.00 0.00 2.40
509 530 3.080319 GCAAGCAGAAACAGAGGAATCT 58.920 45.455 0.00 0.00 0.00 2.40
510 531 3.080319 AGCAAGCAGAAACAGAGGAATC 58.920 45.455 0.00 0.00 0.00 2.52
511 532 2.818432 CAGCAAGCAGAAACAGAGGAAT 59.182 45.455 0.00 0.00 0.00 3.01
612 633 5.631119 TCTTTTTAAGAAAGGGAGGTCAGG 58.369 41.667 9.02 0.00 33.83 3.86
679 707 7.061752 CGAGTAGGATTCGTTTGAAATCTTT 57.938 36.000 0.00 0.00 37.71 2.52
692 720 5.277058 GCATGTTGATTGACGAGTAGGATTC 60.277 44.000 0.00 0.00 0.00 2.52
707 735 4.931002 GCAGTGTAAAAATGGCATGTTGAT 59.069 37.500 3.09 0.00 0.00 2.57
712 740 3.316071 TGGCAGTGTAAAAATGGCATG 57.684 42.857 0.00 0.00 43.62 4.06
745 773 3.306641 GCTGGGTGGAATTAACATGCAAA 60.307 43.478 0.00 0.00 0.00 3.68
746 774 2.233431 GCTGGGTGGAATTAACATGCAA 59.767 45.455 0.00 0.00 0.00 4.08
748 776 1.136891 GGCTGGGTGGAATTAACATGC 59.863 52.381 0.00 0.00 0.00 4.06
752 780 2.243810 TGTTGGCTGGGTGGAATTAAC 58.756 47.619 0.00 0.00 0.00 2.01
774 802 9.754382 GCATATTTTGATAATTTGATCACTGGT 57.246 29.630 0.00 0.00 35.56 4.00
800 828 3.788797 GCAACACGGAGACAGAAAAGTTG 60.789 47.826 0.00 0.00 38.41 3.16
812 840 0.592637 TGAAATGCAGCAACACGGAG 59.407 50.000 0.00 0.00 0.00 4.63
817 845 2.426381 TGTGAAGTGAAATGCAGCAACA 59.574 40.909 0.00 0.00 0.00 3.33
852 880 2.880890 CTGAACTGGGAAAACAGGACAG 59.119 50.000 0.00 0.00 42.75 3.51
864 892 3.616956 TGTATCAGCTTCTGAACTGGG 57.383 47.619 15.20 0.00 44.04 4.45
865 893 4.573900 AGTTGTATCAGCTTCTGAACTGG 58.426 43.478 15.20 0.00 44.04 4.00
866 894 6.426328 AGAAAGTTGTATCAGCTTCTGAACTG 59.574 38.462 11.37 11.37 44.04 3.16
867 895 6.426328 CAGAAAGTTGTATCAGCTTCTGAACT 59.574 38.462 4.04 0.00 44.04 3.01
868 896 6.425114 TCAGAAAGTTGTATCAGCTTCTGAAC 59.575 38.462 9.28 2.43 44.04 3.18
869 897 6.524734 TCAGAAAGTTGTATCAGCTTCTGAA 58.475 36.000 9.28 0.00 44.04 3.02
870 898 6.101650 TCAGAAAGTTGTATCAGCTTCTGA 57.898 37.500 7.95 7.95 44.99 3.27
871 899 6.791887 TTCAGAAAGTTGTATCAGCTTCTG 57.208 37.500 3.74 3.74 34.01 3.02
872 900 7.992754 AATTCAGAAAGTTGTATCAGCTTCT 57.007 32.000 0.00 0.00 34.01 2.85
912 940 9.722184 GGAAGATCAGATATGATCAAATGAAGA 57.278 33.333 27.40 0.00 45.20 2.87
913 941 9.503399 TGGAAGATCAGATATGATCAAATGAAG 57.497 33.333 27.40 0.00 45.20 3.02
921 949 9.695526 GCTGTATATGGAAGATCAGATATGATC 57.304 37.037 20.37 20.37 43.63 2.92
922 950 9.210228 TGCTGTATATGGAAGATCAGATATGAT 57.790 33.333 1.59 1.59 0.00 2.45
923 951 8.599624 TGCTGTATATGGAAGATCAGATATGA 57.400 34.615 0.00 0.00 0.00 2.15
924 952 7.438757 GCTGCTGTATATGGAAGATCAGATATG 59.561 40.741 0.00 0.00 0.00 1.78
929 975 5.149973 AGCTGCTGTATATGGAAGATCAG 57.850 43.478 0.00 0.00 0.00 2.90
946 992 6.978080 GGATAGACTTAATAGATGCTAGCTGC 59.022 42.308 17.23 7.78 43.25 5.25
969 1018 1.202710 TGGCAGTAGCGAAAAACAGGA 60.203 47.619 0.00 0.00 43.41 3.86
979 1028 0.737715 GTGAACTCCTGGCAGTAGCG 60.738 60.000 14.43 0.00 43.41 4.26
1074 1123 0.839946 CTGGAGGGGTAGGGAACATG 59.160 60.000 0.00 0.00 0.00 3.21
1092 1141 3.307691 CGGATATTGCCACATCATACCCT 60.308 47.826 0.00 0.00 0.00 4.34
1269 1396 1.966901 ATGCCGCCGAGATTGGTGTA 61.967 55.000 0.00 0.00 37.84 2.90
1317 1444 3.651803 GGAGTGTAATCCTCATCCGAG 57.348 52.381 0.00 0.00 39.16 4.63
1326 1453 1.480954 TCGGAAGCAGGAGTGTAATCC 59.519 52.381 0.00 0.00 39.89 3.01
1329 1456 1.919240 TCTCGGAAGCAGGAGTGTAA 58.081 50.000 0.00 0.00 0.00 2.41
1512 1639 2.774799 GAACATGGCCATGGTCGCC 61.775 63.158 40.44 24.10 44.50 5.54
1640 1767 1.749033 GGGCCTATCGTCTTGAGGG 59.251 63.158 0.84 0.00 0.00 4.30
1701 1828 1.884464 CCCCACGATGCACATCTCG 60.884 63.158 5.91 5.91 40.62 4.04
1720 1847 2.335011 CATGGATGGCGCATGCAG 59.665 61.111 19.57 11.69 44.63 4.41
1758 1885 2.892425 CTCCCGGCAAGCTTAGCG 60.892 66.667 0.00 2.75 0.00 4.26
1952 2088 4.758251 TGCGCACCACCCTGATCG 62.758 66.667 5.66 0.00 0.00 3.69
2032 2168 0.395862 TCCATCCAGGAGTCCTCGAC 60.396 60.000 9.36 0.00 43.07 4.20
2106 2242 1.228124 TGAAAACCCGTCAGGCTGG 60.228 57.895 15.73 0.00 40.58 4.85
2118 2254 3.149196 TGTCATCTTCCAGGCTGAAAAC 58.851 45.455 17.94 0.00 0.00 2.43
2126 2262 1.905215 ACCTGTCTGTCATCTTCCAGG 59.095 52.381 0.00 0.00 43.98 4.45
2160 2296 0.597568 TGGCATTTTCTCTTGTGGCG 59.402 50.000 0.00 0.00 39.70 5.69
2181 2317 0.738762 CTGATGACAGGTCCAGCACG 60.739 60.000 0.00 0.00 40.14 5.34
2193 2329 0.396060 GGATCTCAGCCCCTGATGAC 59.604 60.000 0.00 0.00 39.92 3.06
2404 2540 1.139095 CGAGCACCCCGTCTAAGTC 59.861 63.158 0.00 0.00 0.00 3.01
2436 2572 2.029020 ACGAGAGCACTCATACAGCAAA 60.029 45.455 11.83 0.00 42.72 3.68
2437 2573 1.546029 ACGAGAGCACTCATACAGCAA 59.454 47.619 11.83 0.00 42.72 3.91
2442 2578 2.791567 CAGTCACGAGAGCACTCATAC 58.208 52.381 11.83 5.82 42.72 2.39
2445 2581 1.287191 GCAGTCACGAGAGCACTCA 59.713 57.895 11.83 0.00 42.72 3.41
2476 2612 1.021968 GCAACCCTGTTTCGACAGTT 58.978 50.000 5.89 0.00 36.06 3.16
2501 2637 3.620488 TCAAAGTTGAGCTGAACACCTT 58.380 40.909 18.52 5.63 32.50 3.50
2541 2677 4.530857 CGGAGACCCCATCCACGC 62.531 72.222 0.00 0.00 36.57 5.34
2625 2761 3.434024 CCTGGACATCCATGCTCATGTTA 60.434 47.826 0.00 0.00 46.46 2.41
2694 2830 0.393537 CTGCACCCAGGTTCCATCTC 60.394 60.000 0.00 0.00 35.38 2.75
2931 3067 8.045507 CCTCTTATGCCATAATCATATGTCAGT 58.954 37.037 1.90 0.00 37.75 3.41
3015 3151 1.462283 CGACAGTTTGCAGATCCACAG 59.538 52.381 0.00 0.00 0.00 3.66
3057 3193 1.203112 TCCCTTGTTTATGCCCAGCAA 60.203 47.619 0.00 0.00 43.62 3.91
3076 3212 8.149973 TGACATCTGTTTAGTTACCTTGTTTC 57.850 34.615 0.00 0.00 0.00 2.78
3115 3251 5.828328 ACCAGAAAACCTAGAAGGAACAAAG 59.172 40.000 0.00 0.00 37.67 2.77
3116 3252 5.762279 ACCAGAAAACCTAGAAGGAACAAA 58.238 37.500 0.00 0.00 37.67 2.83
3117 3253 5.104277 TGACCAGAAAACCTAGAAGGAACAA 60.104 40.000 0.00 0.00 37.67 2.83
3118 3254 4.410883 TGACCAGAAAACCTAGAAGGAACA 59.589 41.667 0.00 0.00 37.67 3.18
3119 3255 4.969484 TGACCAGAAAACCTAGAAGGAAC 58.031 43.478 0.00 0.00 37.67 3.62
3120 3256 5.073144 ACATGACCAGAAAACCTAGAAGGAA 59.927 40.000 0.00 0.00 37.67 3.36
3121 3257 4.597507 ACATGACCAGAAAACCTAGAAGGA 59.402 41.667 0.00 0.00 37.67 3.36
3122 3258 4.911390 ACATGACCAGAAAACCTAGAAGG 58.089 43.478 0.00 0.00 42.49 3.46
3123 3259 6.884280 AAACATGACCAGAAAACCTAGAAG 57.116 37.500 0.00 0.00 0.00 2.85
3136 3272 6.123651 ACTTGGTACTTGTTAAACATGACCA 58.876 36.000 0.00 0.00 34.74 4.02
3155 3291 6.128090 TGACTAGAGAACACATACGTACTTGG 60.128 42.308 0.00 0.00 0.00 3.61
3156 3292 6.741811 GTGACTAGAGAACACATACGTACTTG 59.258 42.308 0.00 0.00 35.06 3.16
3158 3294 5.936372 TGTGACTAGAGAACACATACGTACT 59.064 40.000 0.00 0.00 39.17 2.73
3159 3295 6.174451 TGTGACTAGAGAACACATACGTAC 57.826 41.667 0.00 0.00 39.17 3.67
3166 3302 7.468141 ACTTATCATGTGACTAGAGAACACA 57.532 36.000 14.67 14.67 46.04 3.72
3208 3373 8.612619 ACGACTAATAAATCCATCAACATCAAC 58.387 33.333 0.00 0.00 0.00 3.18
3244 3411 4.398673 AGTGTGTAGGATACGTTCTTCTCC 59.601 45.833 0.00 0.00 46.99 3.71
3272 3439 8.784994 CAGATAGTTACGTTGTCTACTATGGAT 58.215 37.037 0.00 0.00 34.78 3.41
3302 4827 1.202806 CCAGAAGCAGTTTGGGTCTGA 60.203 52.381 0.00 0.00 35.20 3.27
3303 4828 1.202806 TCCAGAAGCAGTTTGGGTCTG 60.203 52.381 0.00 0.00 36.18 3.51
3304 4829 1.140312 TCCAGAAGCAGTTTGGGTCT 58.860 50.000 0.00 0.00 32.76 3.85
3305 4830 2.206576 ATCCAGAAGCAGTTTGGGTC 57.793 50.000 0.00 0.00 32.76 4.46
3306 4831 3.372025 GGATATCCAGAAGCAGTTTGGGT 60.372 47.826 17.34 0.00 35.64 4.51
3307 4832 3.217626 GGATATCCAGAAGCAGTTTGGG 58.782 50.000 17.34 0.00 35.64 4.12
3308 4833 3.889815 TGGATATCCAGAAGCAGTTTGG 58.110 45.455 20.98 0.00 42.01 3.28
3320 4845 3.824133 CAAGGCACAGATTGGATATCCA 58.176 45.455 20.98 20.98 45.94 3.41
3351 4876 6.939132 AAAGGAGAACAATATCAGCATCAG 57.061 37.500 0.00 0.00 0.00 2.90
3391 4916 5.010933 CCACGATCTACTCCTACCATACAT 58.989 45.833 0.00 0.00 0.00 2.29
3492 5023 2.098443 CCACCGGCATACAAAATACCAC 59.902 50.000 0.00 0.00 0.00 4.16
3493 5024 2.291024 ACCACCGGCATACAAAATACCA 60.291 45.455 0.00 0.00 0.00 3.25
3494 5025 2.098443 CACCACCGGCATACAAAATACC 59.902 50.000 0.00 0.00 0.00 2.73
3539 5076 5.946298 ACTACACATGATTTTGCATCACAG 58.054 37.500 0.00 0.00 0.00 3.66
3554 5091 6.791887 GCATATGCAACATCTACTACACAT 57.208 37.500 22.84 0.00 41.59 3.21
3623 8623 2.357952 CACATGATGCCAGATGGTTCAG 59.642 50.000 0.00 2.61 34.55 3.02
3634 8634 5.643777 ACAGTAAGTAAGAACACATGATGCC 59.356 40.000 0.00 0.00 0.00 4.40
3636 8636 7.017645 GCAACAGTAAGTAAGAACACATGATG 58.982 38.462 0.00 0.00 0.00 3.07
3680 8680 2.067766 CACAGAAGCAGTTCAGAGAGC 58.932 52.381 0.00 0.00 34.82 4.09
3705 8705 5.450550 CCAAACAAGGTCCTTCACTTTCTTC 60.451 44.000 0.00 0.00 0.00 2.87
3738 8738 5.186797 ACTTCTTCTACAGAGGACATCAAGG 59.813 44.000 0.00 0.00 32.72 3.61
3762 8762 7.669427 ACAAAAATCTGATCAAACTTGGCATA 58.331 30.769 0.00 0.00 0.00 3.14
3832 8832 1.618345 CCTGGGCTCAGACAGTCTACT 60.618 57.143 17.43 0.00 43.49 2.57
3835 8835 0.472734 AACCTGGGCTCAGACAGTCT 60.473 55.000 17.43 0.00 43.49 3.24
3937 8937 9.841295 TCAACAAACTAGTCTGTTAAATAGGTT 57.159 29.630 14.08 0.00 34.04 3.50
3948 8948 6.591834 CCTTACTCCATCAACAAACTAGTCTG 59.408 42.308 0.00 0.00 0.00 3.51
3952 8952 5.805728 ACCCTTACTCCATCAACAAACTAG 58.194 41.667 0.00 0.00 0.00 2.57
3954 8954 4.724279 ACCCTTACTCCATCAACAAACT 57.276 40.909 0.00 0.00 0.00 2.66
3955 8955 6.316390 CAGATACCCTTACTCCATCAACAAAC 59.684 42.308 0.00 0.00 0.00 2.93
3957 8957 5.629133 GCAGATACCCTTACTCCATCAACAA 60.629 44.000 0.00 0.00 0.00 2.83
3958 8958 4.141711 GCAGATACCCTTACTCCATCAACA 60.142 45.833 0.00 0.00 0.00 3.33
3959 8959 4.141711 TGCAGATACCCTTACTCCATCAAC 60.142 45.833 0.00 0.00 0.00 3.18
3960 8960 4.037222 TGCAGATACCCTTACTCCATCAA 58.963 43.478 0.00 0.00 0.00 2.57
3972 8972 1.940613 GATTTGTCGGTGCAGATACCC 59.059 52.381 0.00 0.00 37.44 3.69


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

AutoCloner maintained by Alex Coulton.