Multiple sequence alignment - TraesCS2D01G320300

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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 TraesCS2D01G320300 chr2D 100.000 3486 0 0 1 3486 411420214 411416729 0.000000e+00 6438
1 TraesCS2D01G320300 chr2D 96.617 3518 70 19 1 3486 411706316 411702816 0.000000e+00 5792
2 TraesCS2D01G320300 chr2A 94.489 2522 118 5 650 3162 579212704 579210195 0.000000e+00 3868
3 TraesCS2D01G320300 chr2A 86.647 674 56 14 8 654 579213411 579212745 0.000000e+00 715
4 TraesCS2D01G320300 chr2A 94.955 337 14 3 3152 3486 579143474 579143139 3.080000e-145 525
5 TraesCS2D01G320300 chr4B 87.049 471 61 0 996 1466 423777152 423776682 1.840000e-147 532
6 TraesCS2D01G320300 chr4B 85.772 492 69 1 993 1484 424060246 424060736 1.430000e-143 520
7 TraesCS2D01G320300 chr5B 86.837 471 62 0 996 1466 593945331 593944861 8.570000e-146 527
8 TraesCS2D01G320300 chr5B 86.624 471 63 0 996 1466 593660341 593659871 3.990000e-144 521
9 TraesCS2D01G320300 chr4A 86.837 471 62 0 996 1466 125027942 125028412 8.570000e-146 527
10 TraesCS2D01G320300 chr4A 86.624 471 63 0 996 1466 124405884 124405414 3.990000e-144 521
11 TraesCS2D01G320300 chr4D 86.624 471 63 0 996 1466 341697082 341696612 3.990000e-144 521


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 TraesCS2D01G320300 chr2D 411416729 411420214 3485 True 6438.0 6438 100.000 1 3486 1 chr2D.!!$R1 3485
1 TraesCS2D01G320300 chr2D 411702816 411706316 3500 True 5792.0 5792 96.617 1 3486 1 chr2D.!!$R2 3485
2 TraesCS2D01G320300 chr2A 579210195 579213411 3216 True 2291.5 3868 90.568 8 3162 2 chr2A.!!$R2 3154

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
566 601 0.404426 ACCCCAAAACCCTAGTGCTC 59.596 55.0 0.0 0.0 0.00 4.26 F
2260 2341 0.625316 TATGGCCCTGCAAGATGTGT 59.375 50.0 0.0 0.0 34.07 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2438 2527 2.235898 CTGAGACTGGAAGAAAGGGGAG 59.764 54.545 0.0 0.0 37.43 4.30 R
3234 3323 1.065126 AGTGATGTCCCTAGCCTTTGC 60.065 52.381 0.0 0.0 37.95 3.68 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
162 163 2.758737 GACCCGACCCGACCTGAT 60.759 66.667 0.00 0.00 0.00 2.90
164 165 2.442272 CCCGACCCGACCTGATCT 60.442 66.667 0.00 0.00 0.00 2.75
165 166 2.786495 CCCGACCCGACCTGATCTG 61.786 68.421 0.00 0.00 0.00 2.90
166 167 1.753078 CCGACCCGACCTGATCTGA 60.753 63.158 0.38 0.00 0.00 3.27
168 169 1.817209 GACCCGACCTGATCTGACC 59.183 63.158 0.38 0.00 0.00 4.02
169 170 2.005960 GACCCGACCTGATCTGACCG 62.006 65.000 0.38 4.24 0.00 4.79
170 171 2.786495 CCCGACCTGATCTGACCGG 61.786 68.421 18.60 18.60 36.98 5.28
171 172 1.753078 CCGACCTGATCTGACCGGA 60.753 63.158 9.46 0.00 39.31 5.14
210 229 1.627297 GCCCAATCCTCCCGACTCTT 61.627 60.000 0.00 0.00 0.00 2.85
299 324 5.337554 GCGTATTCCATTTTGGGACTAAAC 58.662 41.667 0.00 0.00 38.32 2.01
317 342 3.876198 GCCCAACACGCCGCTATG 61.876 66.667 0.00 0.00 0.00 2.23
566 601 0.404426 ACCCCAAAACCCTAGTGCTC 59.596 55.000 0.00 0.00 0.00 4.26
578 613 2.154798 TAGTGCTCTGCTTTCGCGGT 62.155 55.000 6.13 0.00 43.19 5.68
587 622 1.133407 TGCTTTCGCGGTTTGTTCTTT 59.867 42.857 6.13 0.00 39.65 2.52
738 818 1.033574 ATCTGTCGCCTAGGCTACAC 58.966 55.000 31.39 23.61 40.95 2.90
761 841 2.363975 GGTACGGTGCTGGGATCCA 61.364 63.158 15.23 0.00 0.00 3.41
863 943 4.226427 TCTGTCTTCATCTTCCCCATTG 57.774 45.455 0.00 0.00 0.00 2.82
1071 1152 1.458777 TGGGAAGTCGACCACCACT 60.459 57.895 23.56 0.00 0.00 4.00
1155 1236 3.731089 AGCTGCTGAGATGAATAAGAGC 58.269 45.455 0.00 0.00 0.00 4.09
1797 1878 9.244292 TGTGGGTGTGCTTATGTTTAAATTATA 57.756 29.630 0.00 0.00 0.00 0.98
1940 2021 5.774498 AGTTAGGTTTCTGGAAAAGCAAG 57.226 39.130 0.00 0.00 31.33 4.01
2260 2341 0.625316 TATGGCCCTGCAAGATGTGT 59.375 50.000 0.00 0.00 34.07 3.72
2367 2448 3.266772 AGATGGATTGCACTACTCCCAAA 59.733 43.478 0.00 0.00 0.00 3.28
2481 2570 2.746279 TTTGAGGGTGACAACATGGT 57.254 45.000 0.00 0.00 0.00 3.55
2631 2720 0.774276 TGGTATTGGAACTGTGCCCA 59.226 50.000 1.39 0.00 0.00 5.36
2972 3061 2.418368 AGTTTGCTCAGTTGGTGACA 57.582 45.000 0.00 0.00 39.83 3.58
3067 3156 4.210331 GTGAATATGATTCCCACCAAGCT 58.790 43.478 0.00 0.00 0.00 3.74
3115 3204 0.613777 CCTCCTCTAGGCCGTTTTGT 59.386 55.000 0.00 0.00 38.97 2.83
3234 3323 1.664321 GCCTCTGCTGCCTCAATTGG 61.664 60.000 5.42 0.00 33.53 3.16
3307 3396 0.326927 ACCGAACCTAATGTGGTGGG 59.673 55.000 0.00 0.00 40.73 4.61
3383 3472 6.415573 AGTCTTCAAGTTGACCTACTTTGTT 58.584 36.000 4.68 0.00 36.24 2.83
3471 3561 0.974383 AAGGGAACAGACACCTACGG 59.026 55.000 0.00 0.00 33.37 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.604378 CCAGAACTGCGGGGATCTT 59.396 57.895 0.00 0.00 0.00 2.40
114 115 1.730451 GCTAGCTCCACTCCGGTCTC 61.730 65.000 7.70 0.00 35.57 3.36
115 116 1.755008 GCTAGCTCCACTCCGGTCT 60.755 63.158 7.70 0.00 35.57 3.85
116 117 2.809010 GCTAGCTCCACTCCGGTC 59.191 66.667 7.70 0.00 35.57 4.79
117 118 3.141488 CGCTAGCTCCACTCCGGT 61.141 66.667 13.93 0.00 35.57 5.28
118 119 3.905678 CCGCTAGCTCCACTCCGG 61.906 72.222 13.93 0.00 37.16 5.14
119 120 2.136196 GATCCGCTAGCTCCACTCCG 62.136 65.000 13.93 0.00 0.00 4.63
120 121 0.825840 AGATCCGCTAGCTCCACTCC 60.826 60.000 13.93 0.00 0.00 3.85
210 229 1.681780 CGGGCTAAAATCTCCAGGCAA 60.682 52.381 0.00 0.00 36.63 4.52
281 303 2.559231 GGCGTTTAGTCCCAAAATGGAA 59.441 45.455 0.00 0.00 40.96 3.53
317 342 4.364409 GTGCGAACCAACGGTCGC 62.364 66.667 15.20 15.20 45.23 5.19
578 613 6.292923 TCGGAACTAGGAATCAAAGAACAAA 58.707 36.000 0.00 0.00 0.00 2.83
587 622 1.340248 GCGGATCGGAACTAGGAATCA 59.660 52.381 4.16 0.00 0.00 2.57
761 841 4.850680 TGGGCAATTCGGTAAGACTAAAT 58.149 39.130 0.00 0.00 0.00 1.40
839 919 4.226427 TGGGGAAGATGAAGACAGATTG 57.774 45.455 0.00 0.00 0.00 2.67
1071 1152 2.390696 AGCAAGCATATCAAATGGCCA 58.609 42.857 8.56 8.56 0.00 5.36
1155 1236 0.999406 CCCACGCGTACTTGAATGAG 59.001 55.000 13.44 0.00 0.00 2.90
1726 1807 6.071784 TGCTAGCAGTTGAATGACAATGAAAT 60.072 34.615 14.93 0.00 40.76 2.17
1797 1878 4.817318 ACAAAATTAATGGCCAACGGAT 57.183 36.364 10.96 0.00 0.00 4.18
1963 2044 2.742774 ACTTGCGAATTTCAAGGCAAC 58.257 42.857 19.15 0.00 43.77 4.17
2367 2448 7.815068 GCTTCACTATTTCATCATACCGAGTAT 59.185 37.037 0.00 0.00 0.00 2.12
2438 2527 2.235898 CTGAGACTGGAAGAAAGGGGAG 59.764 54.545 0.00 0.00 37.43 4.30
2481 2570 3.725754 GGTTGGCAGACCTCTCAAA 57.274 52.632 10.41 0.00 36.73 2.69
2631 2720 0.036010 CCAGTCTGAAGCCGACCAAT 60.036 55.000 0.00 0.00 31.83 3.16
2972 3061 2.636830 CCAGATCGCCTGTCAATCTTT 58.363 47.619 4.40 0.00 41.33 2.52
3067 3156 3.773119 GGTGAAGGTCTCCACTACCATAA 59.227 47.826 0.00 0.00 39.64 1.90
3115 3204 4.377943 CCGTTTGCTTCATATCACGAACAA 60.378 41.667 0.00 0.00 0.00 2.83
3234 3323 1.065126 AGTGATGTCCCTAGCCTTTGC 60.065 52.381 0.00 0.00 37.95 3.68
3307 3396 1.202557 TGGCCACGACCGAAATATACC 60.203 52.381 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.