Multiple sequence alignment - TraesCS3B01G438500

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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 TraesCS3B01G438500 chr3B 100.000 3194 0 0 1 3194 677739856 677743049 0.000000e+00 5899
1 TraesCS3B01G438500 chr3A 94.976 2866 104 15 363 3194 649712522 649715381 0.000000e+00 4458
2 TraesCS3B01G438500 chr3A 96.389 360 8 4 1 355 649711739 649712098 3.550000e-164 588
3 TraesCS3B01G438500 chr3A 92.643 367 20 3 1179 1545 430665455 430665096 3.650000e-144 521
4 TraesCS3B01G438500 chr3D 95.919 2426 82 10 388 2805 515012359 515014775 0.000000e+00 3916
5 TraesCS3B01G438500 chr3D 93.267 401 14 8 2803 3194 515014844 515015240 2.140000e-161 579
6 TraesCS3B01G438500 chr3D 95.077 325 3 7 1 320 515011666 515011982 1.710000e-137 499
7 TraesCS3B01G438500 chr3D 94.332 247 12 2 1179 1425 303789156 303789400 8.360000e-101 377
8 TraesCS3B01G438500 chr3D 95.556 135 6 0 1411 1545 303789495 303789629 1.930000e-52 217


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 TraesCS3B01G438500 chr3B 677739856 677743049 3193 False 5899.000000 5899 100.000000 1 3194 1 chr3B.!!$F1 3193
1 TraesCS3B01G438500 chr3A 649711739 649715381 3642 False 2523.000000 4458 95.682500 1 3194 2 chr3A.!!$F1 3193
2 TraesCS3B01G438500 chr3D 515011666 515015240 3574 False 1664.666667 3916 94.754333 1 3194 3 chr3D.!!$F2 3193

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
435 861 0.459489 ACTCTGGCGATCTCTGCTTC 59.541 55.0 0.0 0.0 0.0 3.86 F
1081 1511 0.676151 CTTTGCTGCTCTGGGTCTCC 60.676 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1924 0.108585 TTCCCTGTGCACTGTTCTCC 59.891 55.0 19.41 0.0 0.0 3.71 R
2681 3112 1.057275 TTTTTGGGGTTTCTGGGGCC 61.057 55.0 0.00 0.0 0.0 5.80 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
135 145 2.022035 TCCTCCTCTCTCTCTCTCCTCT 60.022 54.545 0.00 0.00 0.00 3.69
435 861 0.459489 ACTCTGGCGATCTCTGCTTC 59.541 55.000 0.00 0.00 0.00 3.86
501 927 3.651803 ACGAGTAGAATATGCTGCTCC 57.348 47.619 19.91 5.90 42.44 4.70
521 947 2.415090 CCAGTGCTATGCTTGCTGTTTC 60.415 50.000 0.00 0.00 0.00 2.78
522 948 2.227149 CAGTGCTATGCTTGCTGTTTCA 59.773 45.455 0.00 0.00 0.00 2.69
556 982 5.627780 GCTGGTTAAATGTTACCGTCTTTTG 59.372 40.000 0.00 0.00 37.23 2.44
611 1037 3.865684 GCAAGCAATGTTTTACATGCCCT 60.866 43.478 0.00 0.00 37.97 5.19
647 1073 4.515191 TGATTAGCTGGTTAAATCGGATGC 59.485 41.667 0.00 0.00 33.28 3.91
703 1133 4.910195 ACTCCATGTCTTTATGAACTGCA 58.090 39.130 0.00 0.00 0.00 4.41
729 1159 7.221450 TGTGTGCTAGTAACTAATGGAACTTT 58.779 34.615 0.00 0.00 0.00 2.66
742 1172 8.520351 ACTAATGGAACTTTTTATTACTGTGGC 58.480 33.333 0.00 0.00 0.00 5.01
816 1246 3.118811 AGCTGGCTTTGTTTGTTTTAGCA 60.119 39.130 0.00 0.00 33.60 3.49
841 1271 6.005198 TGTACCTGTACTTACCAAATTTGGG 58.995 40.000 34.69 22.18 43.16 4.12
852 1282 2.134346 CAAATTTGGGTTGTTGCCTCG 58.866 47.619 10.49 0.00 0.00 4.63
872 1302 8.251026 TGCCTCGATCGATCTAATGTAATTATT 58.749 33.333 19.78 0.00 38.29 1.40
873 1303 8.747666 GCCTCGATCGATCTAATGTAATTATTC 58.252 37.037 19.78 0.00 38.29 1.75
1026 1456 2.604686 ACCAGAGGAGCTGCCGAA 60.605 61.111 0.00 0.00 43.50 4.30
1058 1488 2.604614 GGTTGACGATTGGACTGTTTGC 60.605 50.000 0.00 0.00 0.00 3.68
1077 1507 2.282745 GCCTTTGCTGCTCTGGGT 60.283 61.111 0.00 0.00 33.53 4.51
1081 1511 0.676151 CTTTGCTGCTCTGGGTCTCC 60.676 60.000 0.00 0.00 0.00 3.71
1099 1529 3.817084 TCTCCACTGCATTTTTCAGTCAG 59.183 43.478 0.00 0.00 42.38 3.51
1125 1555 2.380084 TCTGGTTTCGGATTCGGAAG 57.620 50.000 6.74 0.00 34.09 3.46
1146 1576 1.446966 GACCTTGCTCTCACTCGGC 60.447 63.158 0.00 0.00 0.00 5.54
1188 1618 2.539274 GACTCGCATTGCTCTGATTCTC 59.461 50.000 7.12 0.00 0.00 2.87
1278 1708 2.706555 TAGTATGGCAGAAGATCGCG 57.293 50.000 0.00 0.00 0.00 5.87
1284 1714 0.807667 GGCAGAAGATCGCGTGTGAT 60.808 55.000 5.77 0.00 0.00 3.06
1494 1924 3.963129 TGGGCCTACATTTGTTAAGGAG 58.037 45.455 4.53 0.00 0.00 3.69
1800 2230 6.320672 CAGGAGATAAAGCATTTGAGGTCATT 59.679 38.462 0.00 0.00 39.63 2.57
2142 2572 2.048222 TCGCCTGCAGGTTCTTCG 60.048 61.111 32.81 25.80 37.57 3.79
2235 2665 1.144057 CCCGTCTACCATGTGCTCC 59.856 63.158 0.00 0.00 0.00 4.70
2476 2906 2.044053 GCTGCCCCCACAATGCTA 60.044 61.111 0.00 0.00 0.00 3.49
2536 2966 1.367659 GGCTCATCTTGTCTGTCTGC 58.632 55.000 0.00 0.00 0.00 4.26
2693 3124 2.223464 TATGCAGGGCCCCAGAAACC 62.223 60.000 21.43 0.00 0.00 3.27
2740 3179 9.316730 GCAAAAATATCTGGCAGAATTGATTTA 57.683 29.630 22.84 7.76 0.00 1.40
2786 3225 2.123589 TCACTTTCACCTGGACTGGAA 58.876 47.619 0.00 0.00 0.00 3.53
2787 3226 2.711009 TCACTTTCACCTGGACTGGAAT 59.289 45.455 0.00 0.00 0.00 3.01
2826 3339 3.306641 CCATAGATGTCTAGGCAGGCTTC 60.307 52.174 2.27 0.00 32.17 3.86
2956 3475 2.865119 TTGACATGGTCTGCAGATGT 57.135 45.000 21.47 20.01 33.15 3.06
3092 3620 1.609208 GCAGTCAACTGGGACAATGT 58.391 50.000 11.87 0.00 43.94 2.71
3169 3703 2.034221 GCCCCCTGTTGTCCAGTC 59.966 66.667 0.00 0.00 39.74 3.51
3172 3706 1.127567 CCCCCTGTTGTCCAGTCTCA 61.128 60.000 0.00 0.00 39.74 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 145 0.252742 GGAGAAGGTGGAAGGGGAGA 60.253 60.000 0.00 0.00 0.00 3.71
355 365 4.741239 ATCACCTCGGCAGGGGGT 62.741 66.667 7.96 0.00 44.68 4.95
356 366 3.406595 GAATCACCTCGGCAGGGGG 62.407 68.421 7.96 0.00 44.68 5.40
357 367 2.190578 GAATCACCTCGGCAGGGG 59.809 66.667 0.00 0.00 46.24 4.79
358 368 2.190578 GGAATCACCTCGGCAGGG 59.809 66.667 7.70 0.10 45.53 4.45
359 369 2.190578 GGGAATCACCTCGGCAGG 59.809 66.667 2.01 2.01 46.87 4.85
360 370 2.202932 CGGGAATCACCTCGGCAG 60.203 66.667 0.00 0.00 38.98 4.85
361 371 4.467084 GCGGGAATCACCTCGGCA 62.467 66.667 0.00 0.00 38.98 5.69
390 816 4.276678 GCTGGCAGCAATATTAAGATGACA 59.723 41.667 33.33 0.27 41.89 3.58
394 820 6.302269 AGTAAGCTGGCAGCAATATTAAGAT 58.698 36.000 38.09 13.34 45.56 2.40
478 904 4.261825 GGAGCAGCATATTCTACTCGTTCT 60.262 45.833 0.00 0.00 29.23 3.01
479 905 3.984633 GGAGCAGCATATTCTACTCGTTC 59.015 47.826 0.00 0.00 29.23 3.95
501 927 2.227149 TGAAACAGCAAGCATAGCACTG 59.773 45.455 0.00 0.00 34.22 3.66
521 947 4.037923 ACATTTAACCAGCAAACACTCCTG 59.962 41.667 0.00 0.00 0.00 3.86
522 948 4.215109 ACATTTAACCAGCAAACACTCCT 58.785 39.130 0.00 0.00 0.00 3.69
556 982 7.210718 ACTAAAACCTTACAATTACAGCACC 57.789 36.000 0.00 0.00 0.00 5.01
591 1017 3.306919 CCAGGGCATGTAAAACATTGCTT 60.307 43.478 0.00 2.75 36.53 3.91
611 1037 3.004629 CAGCTAATCAACAAGCACAACCA 59.995 43.478 0.00 0.00 41.32 3.67
647 1073 3.131396 CCCTAAGCCGTAACAAGCATAG 58.869 50.000 0.00 0.00 31.70 2.23
703 1133 6.947464 AGTTCCATTAGTTACTAGCACACAT 58.053 36.000 0.00 0.00 0.00 3.21
742 1172 1.614317 CCTAAACCTCAGGGGCACAAG 60.614 57.143 0.00 0.00 39.10 3.16
816 1246 7.696992 CCAAATTTGGTAAGTACAGGTACAT 57.303 36.000 26.34 2.73 43.43 2.29
841 1271 1.927895 AGATCGATCGAGGCAACAAC 58.072 50.000 23.84 7.01 41.41 3.32
852 1282 9.486857 TCGACGAATAATTACATTAGATCGATC 57.513 33.333 17.91 17.91 38.88 3.69
872 1302 2.293955 TCCACAACACTGTAATCGACGA 59.706 45.455 0.00 0.00 33.22 4.20
873 1303 2.668250 TCCACAACACTGTAATCGACG 58.332 47.619 0.00 0.00 33.22 5.12
1010 1440 2.186384 CTTCGGCAGCTCCTCTGG 59.814 66.667 0.00 0.00 43.06 3.86
1026 1456 1.594293 CGTCAACCAACCGACTGCT 60.594 57.895 0.00 0.00 0.00 4.24
1058 1488 3.437795 CCAGAGCAGCAAAGGCCG 61.438 66.667 0.00 0.00 42.56 6.13
1077 1507 3.817084 CTGACTGAAAAATGCAGTGGAGA 59.183 43.478 0.00 0.00 45.94 3.71
1081 1511 4.825546 AGACTGACTGAAAAATGCAGTG 57.174 40.909 0.00 0.00 45.94 3.66
1099 1529 3.858238 CGAATCCGAAACCAGAAGTAGAC 59.142 47.826 0.00 0.00 38.22 2.59
1125 1555 1.599576 GAGTGAGAGCAAGGTCCCC 59.400 63.158 0.00 0.00 0.00 4.81
1146 1576 3.521937 TCACCCAGGGACCATTAAAGTAG 59.478 47.826 14.54 0.00 0.00 2.57
1188 1618 3.652057 ACTCCCCACCAAATAGTGATG 57.348 47.619 0.00 0.00 40.34 3.07
1278 1708 3.118629 TGGAGAGAATGTAGGCATCACAC 60.119 47.826 0.00 0.00 33.50 3.82
1284 1714 4.590647 CCTAGATTGGAGAGAATGTAGGCA 59.409 45.833 0.00 0.00 40.54 4.75
1494 1924 0.108585 TTCCCTGTGCACTGTTCTCC 59.891 55.000 19.41 0.00 0.00 3.71
1800 2230 4.881920 TCATCACGAATGACAAGAAGACA 58.118 39.130 0.00 0.00 39.52 3.41
2074 2504 1.605202 GGAGAAGCCGATCTCATCTGC 60.605 57.143 12.27 0.00 46.24 4.26
2151 2581 3.776781 GGCAGCATGGGCATTGCA 61.777 61.111 11.39 0.00 41.53 4.08
2220 2650 1.527370 GGGGGAGCACATGGTAGAC 59.473 63.158 0.00 0.00 0.00 2.59
2681 3112 1.057275 TTTTTGGGGTTTCTGGGGCC 61.057 55.000 0.00 0.00 0.00 5.80
2711 3150 6.606796 TCAATTCTGCCAGATATTTTTGCCTA 59.393 34.615 0.00 0.00 0.00 3.93
2740 3179 2.926329 TCCTAGGAGGCAAGGGAAAAAT 59.074 45.455 7.62 0.00 34.61 1.82
2786 3225 6.582636 TCTATGGTAGATTTCAAGCGACAAT 58.417 36.000 0.00 0.00 0.00 2.71
2787 3226 5.972935 TCTATGGTAGATTTCAAGCGACAA 58.027 37.500 0.00 0.00 0.00 3.18
2826 3339 4.375569 GCAGCTAGCAGCCATAGG 57.624 61.111 20.58 0.00 43.77 2.57
2956 3475 3.577848 CCACTGGTGAATTTTCAATGGGA 59.422 43.478 1.93 0.00 39.21 4.37
3092 3620 6.663523 AGAAAAGAAAAGAAAACCAGAGACCA 59.336 34.615 0.00 0.00 0.00 4.02
3169 3703 2.646175 TTCTCGGGGCGAAGGTGAG 61.646 63.158 0.00 0.00 34.74 3.51
3172 3706 4.065281 CGTTCTCGGGGCGAAGGT 62.065 66.667 0.00 0.00 34.74 3.50


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

AutoCloner maintained by Alex Coulton.