Multiple sequence alignment - TraesCS3A01G257700

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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 TraesCS3A01G257700 chr3A 100.000 3635 0 0 1 3635 479473776 479477410 0.000000e+00 6713
1 TraesCS3A01G257700 chr3A 99.286 140 1 0 2706 2845 479471374 479471235 1.680000e-63 254
2 TraesCS3A01G257700 chr3D 97.219 2697 49 8 8 2684 360039516 360042206 0.000000e+00 4542
3 TraesCS3A01G257700 chr3D 96.744 952 31 0 2684 3635 360042235 360043186 0.000000e+00 1587
4 TraesCS3A01G257700 chr3B 94.684 2709 105 19 8 2684 466099547 466102248 0.000000e+00 4169
5 TraesCS3A01G257700 chr3B 95.925 957 38 1 2679 3635 466102272 466103227 0.000000e+00 1550


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 TraesCS3A01G257700 chr3A 479473776 479477410 3634 False 6713.0 6713 100.0000 1 3635 1 chr3A.!!$F1 3634
1 TraesCS3A01G257700 chr3D 360039516 360043186 3670 False 3064.5 4542 96.9815 8 3635 2 chr3D.!!$F1 3627
2 TraesCS3A01G257700 chr3B 466099547 466103227 3680 False 2859.5 4169 95.3045 8 3635 2 chr3B.!!$F1 3627


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
242 243 0.250901 GGAGCCAAGTTCCTTCAGCA 60.251 55.000 0.00 0.0 30.11 4.41 F
1268 1291 1.666553 CGACTTTACAGCGGGTGCA 60.667 57.895 7.17 0.0 46.23 4.57 F
2056 2079 2.857186 TGCTGCAGACCTTGATAACA 57.143 45.000 20.43 0.0 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1931 0.251634 TGCTCACCAACAGACACACA 59.748 50.000 0.0 0.0 0.00 3.72 R
2131 2155 3.004839 TGGATACGAGATAAGCAGCAGAC 59.995 47.826 0.0 0.0 42.51 3.51 R
3525 3594 2.496070 TCCAGGGACGACTAATGTTGAG 59.504 50.000 0.0 0.0 0.00 3.02 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
91 92 4.275524 AGCTCGACTGCTTGCTTC 57.724 55.556 0.00 0.00 40.93 3.86
116 117 4.175962 AGTTGGGACCTCTAAATCTTCCA 58.824 43.478 0.00 0.00 0.00 3.53
142 143 2.991190 TCGGTAAAATCTGCACGAAGTC 59.009 45.455 0.00 0.00 41.61 3.01
167 168 2.227388 CAGTTTTGCCTACAGCCTTCTG 59.773 50.000 0.00 0.00 45.71 3.02
177 178 0.534412 CAGCCTTCTGTCCAGATCGT 59.466 55.000 0.00 0.00 37.29 3.73
226 227 2.870175 AGAGACATAGATGACCCGGAG 58.130 52.381 0.73 0.00 0.00 4.63
242 243 0.250901 GGAGCCAAGTTCCTTCAGCA 60.251 55.000 0.00 0.00 30.11 4.41
254 255 1.876156 CCTTCAGCACGAGAAGCTTTT 59.124 47.619 0.00 0.00 41.14 2.27
257 258 2.688507 TCAGCACGAGAAGCTTTTAGG 58.311 47.619 0.00 0.00 41.14 2.69
262 263 1.716172 GAGAAGCTTTTAGGCGGCG 59.284 57.895 0.51 0.51 37.29 6.46
321 322 4.037803 CACCACAAGAAATTGACATGTCCA 59.962 41.667 22.85 12.96 0.00 4.02
382 386 3.476552 TGCCTTAATTCCGATGGATCAC 58.523 45.455 0.00 0.00 0.00 3.06
601 622 5.711506 ACAGAATGATGCACTACAAATCCAA 59.288 36.000 0.00 0.00 39.69 3.53
638 660 8.564574 CATAAAGTTTGCAGTGTTACTAAAGGA 58.435 33.333 0.00 0.00 0.00 3.36
1101 1124 7.309499 CCTCTATTCCAGCGTAATCAGAAGTAT 60.309 40.741 0.00 0.00 0.00 2.12
1242 1265 8.466798 GCCACTAATGAAAACACCAATATAGTT 58.533 33.333 0.00 0.00 0.00 2.24
1268 1291 1.666553 CGACTTTACAGCGGGTGCA 60.667 57.895 7.17 0.00 46.23 4.57
1371 1394 3.894427 ACACACCATCAATTACAAGGCAA 59.106 39.130 0.00 0.00 0.00 4.52
1689 1712 3.146066 GCTGAACAGGGTATTTGACACA 58.854 45.455 3.99 0.00 31.73 3.72
1908 1931 3.453679 GGAAGGCTCTCCGCGACT 61.454 66.667 8.23 0.00 40.44 4.18
2034 2057 3.441572 AGAAGAAAATGGACAATGAGCCG 59.558 43.478 0.00 0.00 0.00 5.52
2056 2079 2.857186 TGCTGCAGACCTTGATAACA 57.143 45.000 20.43 0.00 0.00 2.41
2131 2155 6.403333 TTTGTACTTAACATGCGCTTCTAG 57.597 37.500 9.73 1.01 38.10 2.43
2246 2275 7.413000 GCACGACAAAGAGCTAATAATTTCTCA 60.413 37.037 0.00 0.00 0.00 3.27
2499 2531 4.891168 TCCATATGCAACAGCAAATCAGAT 59.109 37.500 0.00 0.00 42.37 2.90
2538 2570 3.133003 TGAAAGAGATGGGGAAGATCGAC 59.867 47.826 0.00 0.00 0.00 4.20
2794 2863 5.350365 TGTCGTATACAATTGAACTTGGAGC 59.650 40.000 13.59 0.00 34.29 4.70
2796 2865 4.260212 CGTATACAATTGAACTTGGAGCCG 60.260 45.833 13.59 0.00 0.00 5.52
2810 2879 6.646267 ACTTGGAGCCGTATTTCTTGTAATA 58.354 36.000 0.00 0.00 0.00 0.98
2825 2894 6.894682 TCTTGTAATATGGTTGGTCATAGCA 58.105 36.000 0.00 0.00 33.69 3.49
2974 3043 4.888326 AGAAAGAGACAGAGCTTGACAT 57.112 40.909 0.00 0.00 0.00 3.06
3076 3145 4.825085 TCGCAATCCTGGAAAAGTTAGTTT 59.175 37.500 0.00 0.00 0.00 2.66
3117 3186 0.897863 TTCGGTTTGGGGATGCCAAG 60.898 55.000 5.30 0.00 0.00 3.61
3164 3233 6.606234 TTAGTGCATTTGTGACTTTTCGTA 57.394 33.333 0.00 0.00 0.00 3.43
3166 3235 4.334203 AGTGCATTTGTGACTTTTCGTACA 59.666 37.500 0.00 0.00 0.00 2.90
3287 3356 4.479158 TCTTTTGCTAATTGGGAACTGGT 58.521 39.130 0.00 0.00 0.00 4.00
3387 3456 2.158559 TCCATGATGTTTGTTGGGTCG 58.841 47.619 0.00 0.00 0.00 4.79
3504 3573 4.698304 TCATCAATTTTACCGGAGAACACC 59.302 41.667 9.46 0.00 0.00 4.16
3525 3594 4.351111 ACCCTTATATGGTCATTGGAGTCC 59.649 45.833 0.73 0.73 0.00 3.85
3532 3601 2.644299 TGGTCATTGGAGTCCTCAACAT 59.356 45.455 11.33 0.00 0.00 2.71
3536 3605 5.491982 GTCATTGGAGTCCTCAACATTAGT 58.508 41.667 11.33 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.608055 CAGAGTTTGTGGCCACATCA 58.392 50.000 37.97 24.93 41.52 3.07
1 2 0.883833 CCAGAGTTTGTGGCCACATC 59.116 55.000 37.97 30.49 41.52 3.06
2 3 0.478072 TCCAGAGTTTGTGGCCACAT 59.522 50.000 37.97 24.58 41.52 3.21
3 4 0.478072 ATCCAGAGTTTGTGGCCACA 59.522 50.000 34.74 34.74 39.98 4.17
4 5 2.084546 GTATCCAGAGTTTGTGGCCAC 58.915 52.381 29.67 29.67 34.77 5.01
5 6 1.702401 TGTATCCAGAGTTTGTGGCCA 59.298 47.619 0.00 0.00 34.77 5.36
6 7 2.359900 CTGTATCCAGAGTTTGTGGCC 58.640 52.381 0.00 0.00 41.50 5.36
7 8 2.027192 TCCTGTATCCAGAGTTTGTGGC 60.027 50.000 0.00 0.00 41.50 5.01
8 9 3.981071 TCCTGTATCCAGAGTTTGTGG 57.019 47.619 0.00 0.00 41.50 4.17
9 10 7.331026 TCTTTATCCTGTATCCAGAGTTTGTG 58.669 38.462 0.00 0.00 41.50 3.33
91 92 2.766828 AGATTTAGAGGTCCCAACTCCG 59.233 50.000 0.00 0.00 35.58 4.63
116 117 2.993899 CGTGCAGATTTTACCGAAGACT 59.006 45.455 0.00 0.00 0.00 3.24
142 143 1.463444 GGCTGTAGGCAAAACTGTACG 59.537 52.381 0.01 0.00 44.01 3.67
167 168 5.416013 TCTGTATGGATCATACGATCTGGAC 59.584 44.000 11.81 0.00 46.69 4.02
168 169 5.416013 GTCTGTATGGATCATACGATCTGGA 59.584 44.000 11.81 3.26 46.69 3.86
177 178 3.572682 GGTCGGTGTCTGTATGGATCATA 59.427 47.826 0.00 0.00 0.00 2.15
242 243 1.019805 GCCGCCTAAAAGCTTCTCGT 61.020 55.000 0.00 0.00 0.00 4.18
254 255 2.278989 GTACGATTGCGCCGCCTA 60.279 61.111 6.63 0.00 42.48 3.93
257 258 3.627218 GAGGTACGATTGCGCCGC 61.627 66.667 4.18 0.00 42.48 6.53
262 263 0.179081 GGTGAGGGAGGTACGATTGC 60.179 60.000 0.00 0.00 0.00 3.56
321 322 0.532862 CCGTTCTGCAACTGGAGTGT 60.533 55.000 0.00 0.00 34.87 3.55
601 622 4.168760 GCAAACTTTATGCTGAGCGATTT 58.831 39.130 0.00 0.00 40.64 2.17
638 660 1.694696 GCGGGGGATTCTCACTTCTAT 59.305 52.381 0.00 0.00 0.00 1.98
1242 1265 0.947180 GCTGTAAAGTCGGCGTGGAA 60.947 55.000 6.85 0.00 0.00 3.53
1371 1394 8.478775 TGTATAGGATGACACTAACAATAGCT 57.521 34.615 0.00 0.00 31.96 3.32
1689 1712 7.558161 TTTCTTTTCAGCATCGATCATGTAT 57.442 32.000 0.00 0.00 34.56 2.29
1908 1931 0.251634 TGCTCACCAACAGACACACA 59.748 50.000 0.00 0.00 0.00 3.72
2034 2057 1.742761 TATCAAGGTCTGCAGCAAGC 58.257 50.000 9.47 2.17 45.96 4.01
2056 2079 7.645058 ATTTACAATACCTTACAGCTGCATT 57.355 32.000 15.27 0.00 0.00 3.56
2131 2155 3.004839 TGGATACGAGATAAGCAGCAGAC 59.995 47.826 0.00 0.00 42.51 3.51
2246 2275 8.132995 CGTGTTTGGTAAAAGACTAAAAGGAAT 58.867 33.333 0.00 0.00 39.88 3.01
2499 2531 9.896645 ATCTCTTTCAGCTTGTAGATCATAAAA 57.103 29.630 0.00 0.00 0.00 1.52
2538 2570 4.605968 AGATCATCGTGACATCTTTCTCG 58.394 43.478 0.00 0.00 34.55 4.04
2794 2863 7.281324 TGACCAACCATATTACAAGAAATACGG 59.719 37.037 0.00 0.00 32.25 4.02
2810 2879 3.766545 AGTTGTTGCTATGACCAACCAT 58.233 40.909 0.00 0.00 41.33 3.55
2825 2894 8.706322 ATATGTAAAGAAACCCTGAAGTTGTT 57.294 30.769 0.00 0.00 0.00 2.83
2829 2898 9.588096 AGAAAATATGTAAAGAAACCCTGAAGT 57.412 29.630 0.00 0.00 0.00 3.01
2974 3043 8.763356 GCAAACTACAAAACATTGAATTCATCA 58.237 29.630 9.40 0.00 35.85 3.07
3076 3145 6.201615 CGAATATGCTTGAGCTTCATTACAGA 59.798 38.462 4.44 0.00 42.66 3.41
3164 3233 3.588569 AGGTTAGTCTTGAAGGAGGTGT 58.411 45.455 0.00 0.00 0.00 4.16
3166 3235 4.908481 AGAAAGGTTAGTCTTGAAGGAGGT 59.092 41.667 0.00 0.00 0.00 3.85
3387 3456 3.376546 GCTTCACATTCTCCAAGGATCAC 59.623 47.826 0.00 0.00 0.00 3.06
3452 3521 6.402222 GTGGATGAGACTAGTGATTCAAACT 58.598 40.000 0.00 0.00 0.00 2.66
3504 3573 5.307976 TGAGGACTCCAATGACCATATAAGG 59.692 44.000 0.00 0.00 0.00 2.69
3525 3594 2.496070 TCCAGGGACGACTAATGTTGAG 59.504 50.000 0.00 0.00 0.00 3.02



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

AutoCloner maintained by Alex Coulton.