Multiple sequence alignment - TraesCS5B01G065200

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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 TraesCS5B01G065200 chr5B 100.000 2605 0 0 1 2605 73346843 73349447 0 4811
1 TraesCS5B01G065200 chr5D 93.675 2656 73 22 1 2601 67323352 67325967 0 3886
2 TraesCS5B01G065200 chr5A 93.358 2650 85 37 1 2605 56839929 56837326 0 3834


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 TraesCS5B01G065200 chr5B 73346843 73349447 2604 False 4811 4811 100.000 1 2605 1 chr5B.!!$F1 2604
1 TraesCS5B01G065200 chr5D 67323352 67325967 2615 False 3886 3886 93.675 1 2601 1 chr5D.!!$F1 2600
2 TraesCS5B01G065200 chr5A 56837326 56839929 2603 True 3834 3834 93.358 1 2605 1 chr5A.!!$R1 2604

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
863 919 1.096416 TTGGTTTTTGGCGTCTCGTT 58.904 45.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2191 0.395311 CACATCTCCATGGCCTTGCT 60.395 55.0 13.15 0.0 33.82 3.91 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
104 105 4.399303 CCAGCCTCCCTACACAAATAAAAG 59.601 45.833 0.00 0.00 0.00 2.27
108 109 6.208797 AGCCTCCCTACACAAATAAAAGAAAC 59.791 38.462 0.00 0.00 0.00 2.78
109 110 6.208797 GCCTCCCTACACAAATAAAAGAAACT 59.791 38.462 0.00 0.00 0.00 2.66
279 283 7.645058 ATGCAATTATTAAATATCTCCCCCG 57.355 36.000 0.00 0.00 0.00 5.73
389 398 1.677633 CCCGTGTGGTTCCCCATTC 60.678 63.158 0.00 0.00 44.35 2.67
424 433 1.319799 CTCCCATCCCCTCCTTCCT 59.680 63.158 0.00 0.00 0.00 3.36
569 578 5.039645 TCCCTGTATCCAAGGAGAGAAATT 58.960 41.667 0.00 0.00 27.72 1.82
772 799 5.641636 TGTTCTTGCAAAAAGAGGGAAAAAC 59.358 36.000 0.00 0.00 0.00 2.43
775 802 3.516615 TGCAAAAAGAGGGAAAAACACG 58.483 40.909 0.00 0.00 0.00 4.49
776 803 3.193691 TGCAAAAAGAGGGAAAAACACGA 59.806 39.130 0.00 0.00 0.00 4.35
777 804 3.796717 GCAAAAAGAGGGAAAAACACGAG 59.203 43.478 0.00 0.00 0.00 4.18
821 877 1.217916 TTCTTTCTGTGTGGGTGGGA 58.782 50.000 0.00 0.00 0.00 4.37
855 911 6.873605 AGATTAGTTAGCAATTGGTTTTTGGC 59.126 34.615 16.43 1.19 0.00 4.52
862 918 1.314730 ATTGGTTTTTGGCGTCTCGT 58.685 45.000 0.00 0.00 0.00 4.18
863 919 1.096416 TTGGTTTTTGGCGTCTCGTT 58.904 45.000 0.00 0.00 0.00 3.85
867 923 2.106418 GTTTTTGGCGTCTCGTTTCAC 58.894 47.619 0.00 0.00 0.00 3.18
890 946 3.679502 GCAAAATTTCGTGGGAAGATTGG 59.320 43.478 0.00 0.00 32.80 3.16
1125 1187 3.314331 CTCCGGTGCCACCAGAGT 61.314 66.667 17.43 0.00 37.87 3.24
1226 1288 1.218230 GATCCATGAGTTCCTCGCGC 61.218 60.000 0.00 0.00 32.35 6.86
1228 1290 2.202610 CATGAGTTCCTCGCGCGA 60.203 61.111 32.60 32.60 32.35 5.87
1262 1324 1.674221 GGTCGCTGATGTTTCTGCTCT 60.674 52.381 3.86 0.00 42.75 4.09
1270 1332 3.817084 TGATGTTTCTGCTCTGGTTCTTG 59.183 43.478 0.00 0.00 0.00 3.02
1280 1342 2.044946 GGTTCTTGGCAGGGCGAT 60.045 61.111 0.00 0.00 0.00 4.58
1388 1450 2.047274 CGGTTCGGCATGGACTGT 60.047 61.111 0.00 0.00 0.00 3.55
1889 1956 4.287326 GGGATGGGGTAGAAGAAATCTAGG 59.713 50.000 0.00 0.00 41.31 3.02
1893 1960 3.635531 GGGGTAGAAGAAATCTAGGGGGT 60.636 52.174 0.00 0.00 41.31 4.95
1989 2057 4.324563 CCTTTGCCTTCCTTCTGGATTAGA 60.325 45.833 0.00 0.00 42.81 2.10
1990 2058 5.444176 CTTTGCCTTCCTTCTGGATTAGAT 58.556 41.667 0.00 0.00 42.81 1.98
2011 2079 7.084268 AGATATTCAATTAGGTTGGAGGGAG 57.916 40.000 0.00 0.00 38.39 4.30
2123 2191 0.486879 ACCAAGAAATCCAGGGCCAA 59.513 50.000 6.18 0.00 0.00 4.52
2252 2320 7.381408 TGATGTATTCGTGATATCGTTTTCTCC 59.619 37.037 0.00 0.00 0.00 3.71
2340 2408 7.309744 CCAGCCCTTGTGACATCTTTTATTTTA 60.310 37.037 0.00 0.00 0.00 1.52
2383 2451 4.653341 TCATTTTCTTGGTGGTTGGTTGAT 59.347 37.500 0.00 0.00 0.00 2.57
2385 2453 4.399004 TTTCTTGGTGGTTGGTTGATTG 57.601 40.909 0.00 0.00 0.00 2.67
2386 2454 3.304911 TCTTGGTGGTTGGTTGATTGA 57.695 42.857 0.00 0.00 0.00 2.57
2387 2455 3.636679 TCTTGGTGGTTGGTTGATTGAA 58.363 40.909 0.00 0.00 0.00 2.69
2388 2456 4.222336 TCTTGGTGGTTGGTTGATTGAAT 58.778 39.130 0.00 0.00 0.00 2.57
2389 2457 4.280677 TCTTGGTGGTTGGTTGATTGAATC 59.719 41.667 0.00 0.00 0.00 2.52
2390 2458 2.556189 TGGTGGTTGGTTGATTGAATCG 59.444 45.455 0.18 0.00 0.00 3.34
2391 2459 2.556622 GGTGGTTGGTTGATTGAATCGT 59.443 45.455 0.18 0.00 0.00 3.73
2392 2460 3.754323 GGTGGTTGGTTGATTGAATCGTA 59.246 43.478 0.18 0.00 0.00 3.43
2395 2463 4.397730 TGGTTGGTTGATTGAATCGTATGG 59.602 41.667 0.18 0.00 0.00 2.74
2473 2541 4.202245 TGGTGACTAGCCAATGACTAAC 57.798 45.455 0.00 0.00 32.29 2.34
2525 2593 0.396695 CAAGCTGGCTCATGGGGATT 60.397 55.000 0.00 0.00 0.00 3.01
2554 2622 5.338300 GGGCCAAAGATGAAATACCATGTTT 60.338 40.000 4.39 0.00 39.59 2.83
2555 2623 6.172630 GGCCAAAGATGAAATACCATGTTTT 58.827 36.000 0.00 0.00 37.75 2.43
2556 2624 6.654582 GGCCAAAGATGAAATACCATGTTTTT 59.345 34.615 0.00 0.00 37.75 1.94
2601 2671 7.415989 CCCATATGTCCTTTTCTTTGAGATGTG 60.416 40.741 1.24 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 3.384789 AGGCCACCTTTTCTTTCAGTTTC 59.615 43.478 5.01 0.00 0.00 2.78
108 109 1.889170 GGAGGCCACCTTTTCTTTCAG 59.111 52.381 12.67 0.00 31.76 3.02
109 110 1.216678 TGGAGGCCACCTTTTCTTTCA 59.783 47.619 20.77 0.00 31.76 2.69
424 433 0.034477 GCCGATGGGAGGAAGGAAAA 60.034 55.000 0.00 0.00 34.06 2.29
569 578 1.188219 ACCTGAAGCTTCGCCTCTGA 61.188 55.000 21.11 1.14 0.00 3.27
643 670 2.240667 ACAGATCCCCAACAGAAGATGG 59.759 50.000 0.00 0.00 37.43 3.51
772 799 0.905357 ACTGGAGATTTCCCCTCGTG 59.095 55.000 0.00 0.00 43.33 4.35
775 802 3.457749 AGATGAACTGGAGATTTCCCCTC 59.542 47.826 0.00 0.00 43.33 4.30
776 803 3.468850 AGATGAACTGGAGATTTCCCCT 58.531 45.455 0.00 0.00 43.33 4.79
777 804 3.941704 AGATGAACTGGAGATTTCCCC 57.058 47.619 0.00 0.00 43.33 4.81
829 885 8.032451 GCCAAAAACCAATTGCTAACTAATCTA 58.968 33.333 0.00 0.00 0.00 1.98
844 900 1.096416 AACGAGACGCCAAAAACCAA 58.904 45.000 0.00 0.00 0.00 3.67
867 923 2.697431 TCTTCCCACGAAATTTTGCG 57.303 45.000 5.27 1.56 0.00 4.85
881 937 5.001874 ACCTCTAAAAACGTCCAATCTTCC 58.998 41.667 0.00 0.00 0.00 3.46
890 946 5.558463 GCTCAGTTTCACCTCTAAAAACGTC 60.558 44.000 0.00 0.00 37.82 4.34
995 1051 1.648467 GGCGAAGTGGCTCATGGTTC 61.648 60.000 0.00 0.00 40.72 3.62
1226 1288 0.109226 GACCCGTTGGAGAGAAGTCG 60.109 60.000 0.00 0.00 34.81 4.18
1228 1290 1.965219 CGACCCGTTGGAGAGAAGT 59.035 57.895 0.00 0.00 34.81 3.01
1262 1324 2.905996 ATCGCCCTGCCAAGAACCA 61.906 57.895 0.00 0.00 0.00 3.67
1270 1332 2.955022 ATTGCTCTCATCGCCCTGCC 62.955 60.000 0.00 0.00 0.00 4.85
1280 1342 0.740868 CCGCCGAAAGATTGCTCTCA 60.741 55.000 0.00 0.00 0.00 3.27
1317 1379 1.301716 GAGGCGAGCCACAGAACAA 60.302 57.895 17.18 0.00 38.92 2.83
1406 1468 2.746277 GACATCACCGGCCACCAC 60.746 66.667 0.00 0.00 0.00 4.16
1478 1540 4.446413 GAACGGGGCGACATCGGT 62.446 66.667 8.09 0.43 40.23 4.69
1538 1600 0.250295 CGAGGCAGTCAAAACCCTCA 60.250 55.000 6.38 0.00 43.15 3.86
1585 1647 2.369257 CTAGACCATGGCGGCGATGT 62.369 60.000 21.04 10.95 39.03 3.06
1889 1956 3.097162 GTCCCTGATCCCCACCCC 61.097 72.222 0.00 0.00 0.00 4.95
1893 1960 1.003442 CCTCTGTCCCTGATCCCCA 59.997 63.158 0.00 0.00 0.00 4.96
1989 2057 5.075067 CCCTCCCTCCAACCTAATTGAATAT 59.925 44.000 0.00 0.00 41.23 1.28
1990 2058 4.415512 CCCTCCCTCCAACCTAATTGAATA 59.584 45.833 0.00 0.00 41.23 1.75
2011 2079 0.556258 CTAATTCCCAACCCCTCCCC 59.444 60.000 0.00 0.00 0.00 4.81
2123 2191 0.395311 CACATCTCCATGGCCTTGCT 60.395 55.000 13.15 0.00 33.82 3.91
2283 2351 8.728337 ATCATGGCATGAGATATTACACATAC 57.272 34.615 31.39 0.00 43.53 2.39
2355 2423 3.160679 ACCACCAAGAAAATGAGAGGG 57.839 47.619 0.00 0.00 0.00 4.30
2363 2431 4.467795 TCAATCAACCAACCACCAAGAAAA 59.532 37.500 0.00 0.00 0.00 2.29
2383 2451 1.208706 TGGGGCTCCATACGATTCAA 58.791 50.000 0.00 0.00 38.32 2.69
2395 2463 0.813184 CATGTGTTGTGATGGGGCTC 59.187 55.000 0.00 0.00 0.00 4.70
2428 2496 3.617263 CCTTATCACCTACGTGTTGCTTC 59.383 47.826 0.00 0.00 41.09 3.86
2473 2541 1.919956 CTCAGGCAGGCTCTTTTGCG 61.920 60.000 0.00 0.00 41.17 4.85
2525 2593 4.466015 GGTATTTCATCTTTGGCCCTTCAA 59.534 41.667 0.00 0.00 0.00 2.69
2556 2624 7.937257 TATGGGGTGAAGGCCACAAGAAAAA 62.937 44.000 5.01 0.00 46.20 1.94


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

AutoCloner maintained by Alex Coulton.