Multiple sequence alignment - TraesCS5D01G322600

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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 TraesCS5D01G322600 chr5D 100.000 3335 0 0 1 3335 414096588 414099922 0.000000e+00 6159
1 TraesCS5D01G322600 chr5D 97.917 144 3 0 1 144 387110218 387110361 1.990000e-62 250
2 TraesCS5D01G322600 chr5B 96.796 2653 63 12 142 2783 499126296 499128937 0.000000e+00 4409
3 TraesCS5D01G322600 chr5B 86.678 593 32 12 2780 3335 499128987 499129569 6.120000e-172 614
4 TraesCS5D01G322600 chr5A 93.308 2077 114 15 635 2703 526587795 526589854 0.000000e+00 3042
5 TraesCS5D01G322600 chr5A 81.915 564 52 25 2781 3335 526590122 526590644 6.610000e-117 431
6 TraesCS5D01G322600 chr5A 80.098 407 39 19 237 638 526587141 526587510 7.090000e-67 265
7 TraesCS5D01G322600 chr7D 97.987 149 2 1 3 150 496155759 496155611 1.190000e-64 257
8 TraesCS5D01G322600 chrUn 97.959 147 3 0 1 147 26911121 26911267 4.270000e-64 255
9 TraesCS5D01G322600 chrUn 97.917 144 3 0 1 144 26909078 26909221 1.990000e-62 250
10 TraesCS5D01G322600 chr6D 98.611 144 2 0 1 144 20184093 20184236 4.270000e-64 255
11 TraesCS5D01G322600 chr6D 97.917 144 3 0 1 144 322583205 322583348 1.990000e-62 250
12 TraesCS5D01G322600 chr4D 98.611 144 2 0 1 144 57483444 57483301 4.270000e-64 255
13 TraesCS5D01G322600 chr2D 98.611 144 2 0 1 144 421782725 421782582 4.270000e-64 255
14 TraesCS5D01G322600 chr3D 97.945 146 3 0 1 146 424341824 424341969 1.540000e-63 254
15 TraesCS5D01G322600 chr2A 82.877 146 19 5 1083 1224 32769782 32769925 3.490000e-25 126


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 TraesCS5D01G322600 chr5D 414096588 414099922 3334 False 6159.0 6159 100.000 1 3335 1 chr5D.!!$F2 3334
1 TraesCS5D01G322600 chr5B 499126296 499129569 3273 False 2511.5 4409 91.737 142 3335 2 chr5B.!!$F1 3193
2 TraesCS5D01G322600 chr5A 526587141 526590644 3503 False 1246.0 3042 85.107 237 3335 3 chr5A.!!$F1 3098
3 TraesCS5D01G322600 chrUn 26909078 26911267 2189 False 252.5 255 97.938 1 147 2 chrUn.!!$F1 146

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
151 2195 1.191535 CCGGTCATAACAGGGACTCA 58.808 55.000 0.0 0.0 37.12 3.41 F
1401 3744 1.072159 GACACTGAAGCCCTGCTGT 59.928 57.895 0.0 0.0 39.62 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 4056 2.158813 TCAGAAGTGGTTGTTCCTGGAC 60.159 50.0 0.0 0.0 37.07 4.02 R
3034 5627 0.614697 GCCCATAGCCCCACTGTTTT 60.615 55.0 0.0 0.0 34.35 2.43 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
151 2195 1.191535 CCGGTCATAACAGGGACTCA 58.808 55.000 0.00 0.0 37.12 3.41
344 2388 4.633126 TGAAAGCATCTGCATCTTACTGTC 59.367 41.667 4.79 0.0 45.16 3.51
593 2639 1.671261 CCTGTCTGTGAGGAAAGCTCG 60.671 57.143 0.00 0.0 31.48 5.03
1034 3368 6.583562 AGGTATACATTTAACTCCTGCTGAC 58.416 40.000 5.01 0.0 0.00 3.51
1401 3744 1.072159 GACACTGAAGCCCTGCTGT 59.928 57.895 0.00 0.0 39.62 4.40
1427 3770 4.604976 GTGATGTGCTTCTTAATGGCATC 58.395 43.478 0.00 0.0 38.27 3.91
1706 4049 4.137543 GTGAAGTTGAAGTGGAGGATGTT 58.862 43.478 0.00 0.0 0.00 2.71
1713 4056 4.326826 TGAAGTGGAGGATGTTGCTAAAG 58.673 43.478 0.00 0.0 0.00 1.85
1881 4224 5.301551 ACTTCAAAACCTACATTGTGCATGA 59.698 36.000 0.00 0.0 36.24 3.07
1925 4268 1.679139 TAAAGCCAATGCCAGATCCG 58.321 50.000 0.00 0.0 38.69 4.18
1982 4325 6.542735 GGCTTTCTTCGTCCCTATCTTTTATT 59.457 38.462 0.00 0.0 0.00 1.40
2088 4431 6.989659 TGTTACTTACCTAGAAGTGGTTCAG 58.010 40.000 7.01 0.0 39.96 3.02
2107 4450 4.894784 TCAGATTCACCACTTTACTCCAC 58.105 43.478 0.00 0.0 0.00 4.02
2496 4842 6.595716 TGGTTTGTTTACCATTTCAAGGTTTG 59.404 34.615 0.00 0.0 43.14 2.93
2517 4863 7.418597 GGTTTGTTAAGATTTTCTTCCTTGGGT 60.419 37.037 0.00 0.0 37.89 4.51
2592 4938 2.848071 GGGTCCCCTTGGTCAAGTATAA 59.152 50.000 9.51 0.0 36.72 0.98
2673 5019 8.621532 AGAATCTGTGCATTGTTTAGACTTAA 57.378 30.769 0.00 0.0 0.00 1.85
2750 5230 7.900782 TGAAACTGATGGTAGCTTTAAGTAC 57.099 36.000 0.00 0.0 0.00 2.73
2751 5231 7.676947 TGAAACTGATGGTAGCTTTAAGTACT 58.323 34.615 0.00 0.0 0.00 2.73
2752 5232 7.817962 TGAAACTGATGGTAGCTTTAAGTACTC 59.182 37.037 0.00 0.0 0.00 2.59
2753 5233 6.223351 ACTGATGGTAGCTTTAAGTACTCC 57.777 41.667 0.00 0.0 0.00 3.85
2754 5234 5.958987 ACTGATGGTAGCTTTAAGTACTCCT 59.041 40.000 0.00 0.0 0.00 3.69
2866 5410 1.997340 ACTCCTGGGGACTACTCCTA 58.003 55.000 0.00 0.0 37.59 2.94
2941 5532 1.542492 AGCTTTCTTGAGCACATGGG 58.458 50.000 0.00 0.0 45.12 4.00
3112 5716 5.338056 GGACTTCCTGACCATACAATACACA 60.338 44.000 0.00 0.0 0.00 3.72
3129 5733 1.728971 CACAAACATCTCTGCGGTCTC 59.271 52.381 0.00 0.0 0.00 3.36
3257 5862 1.492176 CCATTGGATCCCTACAGTGCT 59.508 52.381 9.90 0.0 0.00 4.40
3281 5886 0.253327 AGGTCCGGATTCCTTTGCTC 59.747 55.000 7.81 0.0 0.00 4.26
3282 5887 0.748367 GGTCCGGATTCCTTTGCTCC 60.748 60.000 7.81 0.0 0.00 4.70
3329 5934 0.233590 CGTTCGCCGACAATGTTTCA 59.766 50.000 0.00 0.0 39.56 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 2195 6.276847 GCATTAGAGTGCATAGACAAGTAGT 58.723 40.000 0.00 0.0 44.43 2.73
266 2310 8.902540 AACTGTCACACTAATTGTTCATAGAA 57.097 30.769 0.00 0.0 35.67 2.10
302 2346 4.782019 TCACTTGGGTTTTGATGTATGC 57.218 40.909 0.00 0.0 0.00 3.14
593 2639 0.969894 ATAGCATGGACCGAGTAGGC 59.030 55.000 0.00 0.0 46.52 3.93
1095 3429 9.424319 GACTTGAATCTTACATCACAGTTTAGA 57.576 33.333 0.00 0.0 0.00 2.10
1096 3430 8.660373 GGACTTGAATCTTACATCACAGTTTAG 58.340 37.037 0.00 0.0 0.00 1.85
1103 3437 4.878397 CCAGGGACTTGAATCTTACATCAC 59.122 45.833 0.00 0.0 34.60 3.06
1401 3744 3.689161 CCATTAAGAAGCACATCACGGAA 59.311 43.478 0.00 0.0 0.00 4.30
1706 4049 2.173782 TGGTTGTTCCTGGACTTTAGCA 59.826 45.455 0.00 0.0 37.07 3.49
1713 4056 2.158813 TCAGAAGTGGTTGTTCCTGGAC 60.159 50.000 0.00 0.0 37.07 4.02
1881 4224 8.962884 ATTGGCTTCTTTTTATGTGTCTTTTT 57.037 26.923 0.00 0.0 0.00 1.94
1925 4268 5.351740 ACTTAATTTTCTCGTAGCCTTCAGC 59.648 40.000 0.00 0.0 44.25 4.26
2011 4354 6.832520 TTTGCAGAAGAACTAATGGCAATA 57.167 33.333 0.00 0.0 39.23 1.90
2088 4431 3.000727 CCGTGGAGTAAAGTGGTGAATC 58.999 50.000 0.00 0.0 0.00 2.52
2107 4450 7.798516 GCAATATATAAAACACTGTCATGTCCG 59.201 37.037 0.00 0.0 30.55 4.79
2158 4503 5.815233 AGATAGGCTAAGCTGCATAAAGA 57.185 39.130 1.02 0.0 32.92 2.52
2412 4758 7.456725 CCTTGAGAAGGGTACATCATTGATAT 58.543 38.462 0.00 0.0 45.27 1.63
2413 4759 6.830912 CCTTGAGAAGGGTACATCATTGATA 58.169 40.000 0.00 0.0 45.27 2.15
2496 4842 5.185249 GGGACCCAAGGAAGAAAATCTTAAC 59.815 44.000 5.33 0.0 36.73 2.01
2592 4938 2.900546 TCGTTGGGCCCATAAACAAATT 59.099 40.909 29.23 0.0 0.00 1.82
2652 4998 5.178623 CGGTTAAGTCTAAACAATGCACAGA 59.821 40.000 0.00 0.0 0.00 3.41
2673 5019 2.199652 CCCAATGTGTTGCCACGGT 61.200 57.895 0.00 0.0 44.92 4.83
2709 5186 6.021596 CAGTTTCAAGGAATATTTTCGTCGG 58.978 40.000 0.00 0.0 32.28 4.79
2710 5187 6.827641 TCAGTTTCAAGGAATATTTTCGTCG 58.172 36.000 0.00 0.0 32.28 5.12
2750 5230 8.327941 TCAAACTTACATCATTCTTTCAGGAG 57.672 34.615 0.00 0.0 0.00 3.69
2751 5231 7.939039 ACTCAAACTTACATCATTCTTTCAGGA 59.061 33.333 0.00 0.0 0.00 3.86
2752 5232 8.019669 CACTCAAACTTACATCATTCTTTCAGG 58.980 37.037 0.00 0.0 0.00 3.86
2753 5233 8.562892 ACACTCAAACTTACATCATTCTTTCAG 58.437 33.333 0.00 0.0 0.00 3.02
2754 5234 8.450578 ACACTCAAACTTACATCATTCTTTCA 57.549 30.769 0.00 0.0 0.00 2.69
2866 5410 2.119495 CCCATGCCTTGGTACTACTCT 58.881 52.381 2.44 0.0 44.83 3.24
2972 5564 4.927782 TTGCAGGCTCGCCGTTGT 62.928 61.111 1.69 0.0 41.95 3.32
3034 5627 0.614697 GCCCATAGCCCCACTGTTTT 60.615 55.000 0.00 0.0 34.35 2.43
3092 5696 6.299922 TGTTTGTGTATTGTATGGTCAGGAA 58.700 36.000 0.00 0.0 0.00 3.36
3098 5702 6.094048 GCAGAGATGTTTGTGTATTGTATGGT 59.906 38.462 0.00 0.0 0.00 3.55
3112 5716 1.674221 GCAGAGACCGCAGAGATGTTT 60.674 52.381 0.00 0.0 0.00 2.83
3129 5733 2.744202 ACACAAGGCGATAAAAGAGCAG 59.256 45.455 0.00 0.0 0.00 4.24
3208 5813 3.259064 CATGATCCTGCAAAGCAAAAGG 58.741 45.455 0.00 0.0 38.41 3.11
3281 5886 1.271543 TGTGGTTGGATGCTTCTCTGG 60.272 52.381 0.00 0.0 0.00 3.86
3282 5887 2.189594 TGTGGTTGGATGCTTCTCTG 57.810 50.000 0.00 0.0 0.00 3.35


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

AutoCloner maintained by Alex Coulton.