Multiple sequence alignment - TraesCS4B01G087300

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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 TraesCS4B01G087300 chr4B 100.000 3245 0 0 1 3245 87681643 87684887 0.000000e+00 5993
1 TraesCS4B01G087300 chr4A 90.586 2985 191 51 4 2921 537545833 537542872 0.000000e+00 3873
2 TraesCS4B01G087300 chr4A 90.470 808 43 13 4 789 537546797 537546002 0.000000e+00 1035
3 TraesCS4B01G087300 chr4A 88.768 276 26 3 2973 3245 537541863 537541590 1.870000e-87 333
4 TraesCS4B01G087300 chr4A 98.571 70 1 0 2899 2968 537542547 537542478 1.220000e-24 124
5 TraesCS4B01G087300 chr4D 93.043 2343 99 28 2 2310 58268254 58270566 0.000000e+00 3365
6 TraesCS4B01G087300 chr4D 92.495 986 57 9 2273 3242 58270595 58271579 0.000000e+00 1395


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 TraesCS4B01G087300 chr4B 87681643 87684887 3244 False 5993.00 5993 100.00000 1 3245 1 chr4B.!!$F1 3244
1 TraesCS4B01G087300 chr4A 537541590 537546797 5207 True 1341.25 3873 92.09875 4 3245 4 chr4A.!!$R1 3241
2 TraesCS4B01G087300 chr4D 58268254 58271579 3325 False 2380.00 3365 92.76900 2 3242 2 chr4D.!!$F1 3240

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
119 127 0.963355 TCAACATAGGGTTTGCGGCC 60.963 55.0 0.0 0.0 37.72 6.13 F
1159 2159 0.324830 CCGGTCTCCTCCTTTCTCCT 60.325 60.0 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 2772 0.597118 GAGTGCAGATCAGCGGCTAG 60.597 60.0 0.26 0.0 38.6 3.42 R
3092 5144 0.607489 GCCAGGACACATTCAGCTGT 60.607 55.0 14.67 0.0 0.0 4.40 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
119 127 0.963355 TCAACATAGGGTTTGCGGCC 60.963 55.000 0.00 0.00 37.72 6.13
126 134 3.680786 GGTTTGCGGCCCTTCACC 61.681 66.667 0.00 0.00 0.00 4.02
171 179 5.421277 TGGGTCGGTACAAATACATACAAG 58.579 41.667 0.00 0.00 32.40 3.16
276 284 5.892568 AGAATACACTCTTAGTAACCAGCG 58.107 41.667 0.00 0.00 0.00 5.18
360 368 8.497554 CAAAATTGTCAAAATACCCTTGTCATG 58.502 33.333 0.00 0.00 0.00 3.07
364 372 6.980593 TGTCAAAATACCCTTGTCATGAAAG 58.019 36.000 0.00 3.93 0.00 2.62
405 413 5.160607 TGTGGAACATAAAGGGAGTACAG 57.839 43.478 0.00 0.00 45.67 2.74
421 429 5.479306 GAGTACAGATGCAACTCTGGTTAA 58.521 41.667 18.99 2.20 45.67 2.01
422 430 6.054860 AGTACAGATGCAACTCTGGTTAAT 57.945 37.500 18.99 3.05 45.67 1.40
423 431 6.476378 AGTACAGATGCAACTCTGGTTAATT 58.524 36.000 18.99 2.58 45.67 1.40
424 432 7.620880 AGTACAGATGCAACTCTGGTTAATTA 58.379 34.615 18.99 1.74 45.67 1.40
434 442 9.556030 GCAACTCTGGTTAATTAGTAACAAATC 57.444 33.333 4.97 0.00 43.48 2.17
461 469 8.948631 ACAATATCAATCCTAACACACTACAG 57.051 34.615 0.00 0.00 0.00 2.74
485 493 9.565090 CAGATATTACAGAATTTTCCTCATCCA 57.435 33.333 0.00 0.00 0.00 3.41
642 652 2.156310 GCTAACCTTTACACCGACAACG 59.844 50.000 0.00 0.00 39.43 4.10
744 754 7.809806 AGTAAAATGTTTCATGCTTTAGTGCTC 59.190 33.333 0.00 0.00 0.00 4.26
788 1770 5.370679 GGAAGTAAACCCAACTAAGTCACA 58.629 41.667 0.00 0.00 0.00 3.58
925 1910 2.978010 GCAATGTATCCGCCCCCG 60.978 66.667 0.00 0.00 0.00 5.73
1049 2034 1.504275 CCCCATCCCCATCTCCATCC 61.504 65.000 0.00 0.00 0.00 3.51
1050 2035 0.773305 CCCATCCCCATCTCCATCCA 60.773 60.000 0.00 0.00 0.00 3.41
1051 2036 1.379776 CCATCCCCATCTCCATCCAT 58.620 55.000 0.00 0.00 0.00 3.41
1052 2037 2.565631 CCATCCCCATCTCCATCCATA 58.434 52.381 0.00 0.00 0.00 2.74
1159 2159 0.324830 CCGGTCTCCTCCTTTCTCCT 60.325 60.000 0.00 0.00 0.00 3.69
1181 2182 1.405797 CGCCACCGTAAACTAATCCCA 60.406 52.381 0.00 0.00 0.00 4.37
1218 2219 2.833121 GGGCGGCGGAATCCAATT 60.833 61.111 9.78 0.00 0.00 2.32
1313 2314 3.053991 TCTTTCTTGGTTGGGAGTGTTGA 60.054 43.478 0.00 0.00 0.00 3.18
1328 2329 2.040412 GTGTTGATTTGGAGGAGAGGGT 59.960 50.000 0.00 0.00 0.00 4.34
1330 2331 2.040412 GTTGATTTGGAGGAGAGGGTGT 59.960 50.000 0.00 0.00 0.00 4.16
1354 2356 2.731571 GGGCAGAGGTGGATGCGTA 61.732 63.158 0.00 0.00 43.49 4.42
1461 2464 6.096695 CCATATTTTAGTTTTGGTTGGTCCG 58.903 40.000 0.00 0.00 39.52 4.79
1667 2678 1.678101 GTGCAGTTCTTCCAAAGCAGT 59.322 47.619 0.00 0.00 32.03 4.40
1693 2704 1.269257 TGCAGTTCAGTCACAGACTCG 60.269 52.381 0.00 0.00 41.37 4.18
1760 2772 3.118482 TCTCATTCATCTCAGTTCCTGGC 60.118 47.826 0.00 0.00 31.51 4.85
1843 2855 2.439104 GGTAGCAGGCAGAGGAGGG 61.439 68.421 0.00 0.00 0.00 4.30
1956 2968 1.076533 TCGGCATCGAAGCGTTCTTC 61.077 55.000 6.54 0.00 43.03 2.87
2016 3028 3.818787 GTGCTGCCTCCATTGCCG 61.819 66.667 0.00 0.00 0.00 5.69
2040 3052 1.153168 ACCGTCACTGCTGCTGTTT 60.153 52.632 9.60 0.00 0.00 2.83
2185 3200 6.321945 TGTTGGCATAAGATGAGTGCAATATT 59.678 34.615 0.00 0.00 40.53 1.28
2186 3201 7.501892 TGTTGGCATAAGATGAGTGCAATATTA 59.498 33.333 0.00 0.00 40.53 0.98
2187 3202 8.517878 GTTGGCATAAGATGAGTGCAATATTAT 58.482 33.333 0.00 0.00 40.53 1.28
2244 3259 7.934665 TGAATGGTTTAGTTCAGTAGCTTTACA 59.065 33.333 0.00 0.00 31.24 2.41
2245 3260 7.668525 ATGGTTTAGTTCAGTAGCTTTACAC 57.331 36.000 0.00 0.00 0.00 2.90
2246 3261 6.823497 TGGTTTAGTTCAGTAGCTTTACACT 58.177 36.000 0.00 0.00 0.00 3.55
2247 3262 7.954835 TGGTTTAGTTCAGTAGCTTTACACTA 58.045 34.615 0.00 0.00 0.00 2.74
2248 3263 7.869429 TGGTTTAGTTCAGTAGCTTTACACTAC 59.131 37.037 0.00 0.00 40.28 2.73
2255 3270 5.416952 TCAGTAGCTTTACACTACAGGGTAC 59.583 44.000 0.00 0.00 42.04 3.34
2289 3366 4.965814 TGGAAATTTTGGTGCATTGCTTA 58.034 34.783 10.49 0.00 0.00 3.09
2302 3379 5.463061 GTGCATTGCTTAAACAAGATTGTGT 59.537 36.000 10.49 0.00 41.31 3.72
2328 3405 5.710513 TTTTCTGTCATGGAACCAATCTG 57.289 39.130 0.00 0.00 0.00 2.90
2330 3407 1.747355 CTGTCATGGAACCAATCTGCC 59.253 52.381 0.00 0.00 0.00 4.85
2555 3634 3.530265 TGTCCACTTTCAGTAACGTGT 57.470 42.857 0.00 0.00 0.00 4.49
2640 3719 9.856488 GATTATTATTAGGTCGATCTGCAAGTA 57.144 33.333 8.91 0.00 33.76 2.24
2706 3791 2.560105 AGCAAGCTCCCAAAGAATTGTC 59.440 45.455 0.00 0.00 34.60 3.18
3041 5093 4.580580 ACTCTACAAGGCAACCTTTGAAAG 59.419 41.667 0.00 0.00 41.69 2.62
3067 5119 9.688592 GTTTGTTGAGATGAAGAAATTTCAGAT 57.311 29.630 19.99 8.38 0.00 2.90
3072 5124 6.127814 TGAGATGAAGAAATTTCAGATGGTGC 60.128 38.462 19.99 4.20 0.00 5.01
3073 5125 4.789012 TGAAGAAATTTCAGATGGTGCC 57.211 40.909 19.99 0.00 0.00 5.01
3078 5130 4.702131 AGAAATTTCAGATGGTGCCACTAC 59.298 41.667 19.99 0.00 0.00 2.73
3087 5139 1.283321 TGGTGCCACTACCATTGCATA 59.717 47.619 0.00 0.00 45.46 3.14
3092 5144 3.278574 GCCACTACCATTGCATAGTCAA 58.721 45.455 0.00 0.00 28.91 3.18
3183 5235 7.804843 TTTTTCAACAATGATTTTGCATCCT 57.195 28.000 0.00 0.00 34.96 3.24
3184 5236 7.424227 TTTTCAACAATGATTTTGCATCCTC 57.576 32.000 0.00 0.00 34.96 3.71
3190 5242 7.414222 ACAATGATTTTGCATCCTCAGTAAT 57.586 32.000 0.00 0.00 0.00 1.89
3228 5280 6.406692 TCGGTAGAATAATTCCCAGAAGAG 57.593 41.667 0.00 0.00 0.00 2.85
3242 5294 6.782986 TCCCAGAAGAGAAATCAATTGAAGA 58.217 36.000 13.09 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.696374 TGTAGTAGTTGAGAAATAAGGATGGAG 58.304 37.037 0.00 0.00 0.00 3.86
59 67 4.512944 CGAGACAAATGATGGTGGAATAGG 59.487 45.833 0.00 0.00 0.00 2.57
62 70 3.941483 GTCGAGACAAATGATGGTGGAAT 59.059 43.478 0.00 0.00 0.00 3.01
119 127 3.560068 GGTGTAAATGATAGCGGTGAAGG 59.440 47.826 0.00 0.00 0.00 3.46
126 134 6.658831 CCAATTAGTGGTGTAAATGATAGCG 58.341 40.000 0.00 0.00 43.20 4.26
171 179 9.327529 CCTAAGTCGACGACATATTTTAGTATC 57.672 37.037 28.31 0.00 34.60 2.24
274 282 5.030874 AGACAAGCTTTACATTGTTACGC 57.969 39.130 0.00 0.00 39.66 4.42
276 284 9.724839 TTTACAAGACAAGCTTTACATTGTTAC 57.275 29.630 16.67 0.00 39.66 2.50
386 394 4.816925 GCATCTGTACTCCCTTTATGTTCC 59.183 45.833 0.00 0.00 0.00 3.62
405 413 8.263940 TGTTACTAATTAACCAGAGTTGCATC 57.736 34.615 0.00 0.00 39.64 3.91
434 442 9.161629 TGTAGTGTGTTAGGATTGATATTGTTG 57.838 33.333 0.00 0.00 0.00 3.33
491 499 3.254166 GCCTTTGAATGCAGTTGAGAAGA 59.746 43.478 0.00 0.00 0.00 2.87
492 500 3.255149 AGCCTTTGAATGCAGTTGAGAAG 59.745 43.478 0.00 0.00 0.00 2.85
493 501 3.225104 AGCCTTTGAATGCAGTTGAGAA 58.775 40.909 0.00 0.00 0.00 2.87
494 502 2.867624 AGCCTTTGAATGCAGTTGAGA 58.132 42.857 0.00 0.00 0.00 3.27
495 503 3.755378 ACTAGCCTTTGAATGCAGTTGAG 59.245 43.478 0.00 0.00 0.00 3.02
497 505 4.510038 AACTAGCCTTTGAATGCAGTTG 57.490 40.909 0.00 0.00 31.98 3.16
539 549 4.428294 ACGATGGTGGAAGATGATCAAT 57.572 40.909 0.00 0.00 0.00 2.57
642 652 1.486310 TGTGGCATCTACATGGGTCTC 59.514 52.381 0.00 0.00 0.00 3.36
780 1762 7.225931 GGATGTTACTGTTGTCTTTGTGACTTA 59.774 37.037 0.00 0.00 45.54 2.24
788 1770 4.275936 GCAGTGGATGTTACTGTTGTCTTT 59.724 41.667 6.95 0.00 45.60 2.52
925 1910 2.269241 CTTGGAGGGGAGGCGAAC 59.731 66.667 0.00 0.00 0.00 3.95
950 1935 6.588719 TTTATGAGTGGGGTTTGAAATCTG 57.411 37.500 0.00 0.00 0.00 2.90
1049 2034 1.712081 GACGCTGCTGCTGTGTATG 59.288 57.895 22.72 4.93 36.97 2.39
1050 2035 1.807165 CGACGCTGCTGCTGTGTAT 60.807 57.895 22.72 4.49 36.97 2.29
1051 2036 2.430751 CGACGCTGCTGCTGTGTA 60.431 61.111 22.72 0.00 36.97 2.90
1159 2159 1.361793 GATTAGTTTACGGTGGCGCA 58.638 50.000 10.83 0.00 0.00 6.09
1181 2182 2.338015 CCAGCAGCAGCCACGAAAT 61.338 57.895 0.00 0.00 43.56 2.17
1313 2314 2.637165 AGAACACCCTCTCCTCCAAAT 58.363 47.619 0.00 0.00 0.00 2.32
1328 2329 1.455849 CACCTCTGCCCCAAGAACA 59.544 57.895 0.00 0.00 0.00 3.18
1330 2331 0.846427 ATCCACCTCTGCCCCAAGAA 60.846 55.000 0.00 0.00 0.00 2.52
1354 2356 2.747446 GCATTTTGGTGATGTCCGTACT 59.253 45.455 0.00 0.00 0.00 2.73
1411 2413 2.679837 AGCGTGGACAATCAAGCATAAG 59.320 45.455 5.68 0.00 42.93 1.73
1413 2415 2.009051 CAGCGTGGACAATCAAGCATA 58.991 47.619 5.68 0.00 42.93 3.14
1414 2416 0.806868 CAGCGTGGACAATCAAGCAT 59.193 50.000 5.68 0.00 42.93 3.79
1461 2464 0.949105 ACATGAGCCAACGAACCGAC 60.949 55.000 0.00 0.00 0.00 4.79
1606 2617 5.529430 TGTGGAGCGAAGAAAATTGTTAGAA 59.471 36.000 0.00 0.00 0.00 2.10
1625 2636 1.886222 GCAAGTGGCAATACCTGTGGA 60.886 52.381 0.00 0.00 43.97 4.02
1667 2678 2.874086 CTGTGACTGAACTGCACATCAA 59.126 45.455 0.00 0.00 41.21 2.57
1693 2704 7.294473 GTTTTTAACAGATCTGAAGTCTCTGC 58.706 38.462 29.27 7.52 40.01 4.26
1760 2772 0.597118 GAGTGCAGATCAGCGGCTAG 60.597 60.000 0.26 0.00 38.60 3.42
1843 2855 4.096003 TCTGGCTAACGCAGGGCC 62.096 66.667 0.00 0.00 45.45 5.80
1850 2862 2.351726 GCAGTATTTGGTCTGGCTAACG 59.648 50.000 0.00 0.00 32.94 3.18
2019 3031 4.996434 AGCAGCAGTGACGGTGGC 62.996 66.667 0.00 1.73 34.93 5.01
2040 3052 4.254709 AGCAAGCAGACCGGCACA 62.255 61.111 0.00 0.00 35.83 4.57
2214 3229 7.649057 AGCTACTGAACTAAACCATTCAAAAC 58.351 34.615 0.00 0.00 34.52 2.43
2222 3237 6.823497 AGTGTAAAGCTACTGAACTAAACCA 58.177 36.000 0.00 0.00 0.00 3.67
2226 3241 7.309621 CCCTGTAGTGTAAAGCTACTGAACTAA 60.310 40.741 9.77 0.00 39.30 2.24
2227 3242 6.152323 CCCTGTAGTGTAAAGCTACTGAACTA 59.848 42.308 9.77 0.00 39.30 2.24
2232 3247 4.803098 ACCCTGTAGTGTAAAGCTACTG 57.197 45.455 0.00 0.00 39.47 2.74
2237 3252 3.260128 ACCAGTACCCTGTAGTGTAAAGC 59.740 47.826 7.96 0.00 36.95 3.51
2244 3259 1.975680 CACCAACCAGTACCCTGTAGT 59.024 52.381 0.00 0.00 36.95 2.73
2245 3260 1.975680 ACACCAACCAGTACCCTGTAG 59.024 52.381 0.00 0.00 36.95 2.74
2246 3261 2.106187 ACACCAACCAGTACCCTGTA 57.894 50.000 0.00 0.00 36.95 2.74
2247 3262 1.218844 AACACCAACCAGTACCCTGT 58.781 50.000 0.00 0.00 36.95 4.00
2248 3263 1.953686 CAAACACCAACCAGTACCCTG 59.046 52.381 0.00 0.00 38.50 4.45
2255 3270 4.335037 CCAAAATTTCCAAACACCAACCAG 59.665 41.667 0.00 0.00 0.00 4.00
2263 3278 4.201990 GCAATGCACCAAAATTTCCAAACA 60.202 37.500 0.00 0.00 0.00 2.83
2264 3279 4.036616 AGCAATGCACCAAAATTTCCAAAC 59.963 37.500 8.35 0.00 0.00 2.93
2265 3280 4.205587 AGCAATGCACCAAAATTTCCAAA 58.794 34.783 8.35 0.00 0.00 3.28
2289 3366 8.902806 TGACAGAAAATCTACACAATCTTGTTT 58.097 29.630 0.00 0.00 39.91 2.83
2302 3379 7.337689 CAGATTGGTTCCATGACAGAAAATCTA 59.662 37.037 0.00 0.00 32.73 1.98
2328 3405 3.309954 CAGAGGCTGTTAATTTACTCGGC 59.690 47.826 0.00 0.48 0.00 5.54
2330 3407 4.522297 GCAGAGGCTGTTAATTTACTCG 57.478 45.455 0.00 0.00 36.96 4.18
2399 3477 7.704472 GGTCAACATGAGAGAATAGTCACTTAG 59.296 40.741 0.00 0.00 0.00 2.18
2416 3495 1.067364 TGCACTTTGCTGGTCAACATG 59.933 47.619 0.00 0.00 45.31 3.21
3021 5073 4.918810 ACTTTCAAAGGTTGCCTTGTAG 57.081 40.909 1.31 0.57 43.92 2.74
3030 5082 7.169158 TCATCTCAACAAACTTTCAAAGGTT 57.831 32.000 1.31 0.00 39.51 3.50
3041 5093 9.688592 ATCTGAAATTTCTTCATCTCAACAAAC 57.311 29.630 18.64 0.00 0.00 2.93
3072 5124 4.260985 TGTTGACTATGCAATGGTAGTGG 58.739 43.478 2.48 0.00 38.55 4.00
3073 5125 4.201851 GCTGTTGACTATGCAATGGTAGTG 60.202 45.833 2.48 0.00 38.55 2.74
3078 5130 3.011818 TCAGCTGTTGACTATGCAATGG 58.988 45.455 14.67 0.00 0.00 3.16
3087 5139 2.105477 AGGACACATTCAGCTGTTGACT 59.895 45.455 21.00 12.39 34.94 3.41
3092 5144 0.607489 GCCAGGACACATTCAGCTGT 60.607 55.000 14.67 0.00 0.00 4.40
3158 5210 8.398878 AGGATGCAAAATCATTGTTGAAAAAT 57.601 26.923 0.00 0.00 34.96 1.82
3163 5215 5.244402 ACTGAGGATGCAAAATCATTGTTGA 59.756 36.000 0.00 0.00 36.00 3.18
3199 5251 8.123639 TCTGGGAATTATTCTACCGATCTAAG 57.876 38.462 4.87 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.