Multiple sequence alignment - TraesCS5D01G383500

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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 TraesCS5D01G383500 chr5D 100.000 3788 0 0 1 3788 453237775 453241562 0.000000e+00 6996.0
1 TraesCS5D01G383500 chr5D 87.711 1538 167 19 1232 2755 38724108 38725637 0.000000e+00 1773.0
2 TraesCS5D01G383500 chr5A 90.837 3656 177 58 1 3561 572020492 572024084 0.000000e+00 4750.0
3 TraesCS5D01G383500 chr5A 87.833 1537 166 18 1232 2755 27516306 27517834 0.000000e+00 1783.0
4 TraesCS5D01G383500 chr5A 81.967 122 16 4 3671 3787 572024308 572024428 8.660000e-17 99.0
5 TraesCS5D01G383500 chr5B 93.436 3047 93 29 263 3267 553724372 553727353 0.000000e+00 4420.0
6 TraesCS5D01G383500 chr5B 87.638 1537 170 17 1232 2755 29337728 29339257 0.000000e+00 1768.0
7 TraesCS5D01G383500 chr5B 93.519 216 7 4 3573 3786 553727802 553728012 7.900000e-82 315.0
8 TraesCS5D01G383500 chr5B 93.846 130 8 0 3433 3562 553727443 553727572 2.990000e-46 196.0
9 TraesCS5D01G383500 chr5B 91.509 106 6 3 3311 3415 553727352 553727455 3.940000e-30 143.0
10 TraesCS5D01G383500 chr1D 95.556 45 2 0 1318 1362 445097742 445097698 5.250000e-09 73.1
11 TraesCS5D01G383500 chr1B 93.333 45 3 0 1318 1362 606254096 606254052 2.440000e-07 67.6


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 TraesCS5D01G383500 chr5D 453237775 453241562 3787 False 6996.0 6996 100.0000 1 3788 1 chr5D.!!$F2 3787
1 TraesCS5D01G383500 chr5D 38724108 38725637 1529 False 1773.0 1773 87.7110 1232 2755 1 chr5D.!!$F1 1523
2 TraesCS5D01G383500 chr5A 572020492 572024428 3936 False 2424.5 4750 86.4020 1 3787 2 chr5A.!!$F2 3786
3 TraesCS5D01G383500 chr5A 27516306 27517834 1528 False 1783.0 1783 87.8330 1232 2755 1 chr5A.!!$F1 1523
4 TraesCS5D01G383500 chr5B 29337728 29339257 1529 False 1768.0 1768 87.6380 1232 2755 1 chr5B.!!$F1 1523
5 TraesCS5D01G383500 chr5B 553724372 553728012 3640 False 1268.5 4420 93.0775 263 3786 4 chr5B.!!$F2 3523

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
564 603 0.391661 TCGTTAGTCGGTACTCGCCT 60.392 55.000 0.00 0.0 40.32 5.52 F
1017 1100 0.389556 AGATGCAGACACTCACAGCG 60.390 55.000 0.00 0.0 0.00 5.18 F
1761 1883 1.672356 CTTCAACGGCCACCTCCTG 60.672 63.158 2.24 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 1604 2.357034 CCGTCGAACAGGTGGTGG 60.357 66.667 0.00 0.0 0.00 4.61 R
2250 2372 2.584608 CCGATCACCACCACCTCC 59.415 66.667 0.00 0.0 0.00 4.30 R
3677 4077 0.658897 AAACCAAATCGCGTGTTCGT 59.341 45.000 5.77 0.0 39.49 3.85 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
52 58 5.652744 AAGCCACGATTTGTTATACGATC 57.347 39.130 0.00 0.00 0.00 3.69
53 59 4.945246 AGCCACGATTTGTTATACGATCT 58.055 39.130 0.00 0.00 0.00 2.75
54 60 6.080648 AGCCACGATTTGTTATACGATCTA 57.919 37.500 0.00 0.00 0.00 1.98
110 116 4.962836 GGCGATCCCCCTGGCATG 62.963 72.222 0.00 0.00 0.00 4.06
125 131 1.607148 GGCATGGCCTTCGTTTATACC 59.393 52.381 8.35 0.00 46.69 2.73
126 132 1.263217 GCATGGCCTTCGTTTATACCG 59.737 52.381 3.32 0.00 0.00 4.02
218 224 1.755783 CAGCAAATCAGGGCCTCCC 60.756 63.158 0.95 0.00 45.90 4.30
232 238 1.379044 CTCCCCGGCTTGATTTGCT 60.379 57.895 0.00 0.00 0.00 3.91
255 261 4.203076 GTCCCCGGACGGACGATG 62.203 72.222 13.13 0.00 42.88 3.84
367 405 5.654650 TCAACGGGGATGCTGTTTAATTATT 59.345 36.000 0.00 0.00 0.00 1.40
399 437 3.430042 ACCTACTGTACCAGAGTCGAA 57.570 47.619 0.00 0.00 35.18 3.71
454 493 2.027385 CCAAGCAAAAGGATAGGAGGC 58.973 52.381 0.00 0.00 0.00 4.70
500 539 0.825840 GGTGCAAGTACCAAGGGCAA 60.826 55.000 2.26 0.00 40.54 4.52
513 552 3.493176 CCAAGGGCAAAGAAAACAAGAGG 60.493 47.826 0.00 0.00 0.00 3.69
534 573 1.809619 CCGAATTGGCGCGAGAGAA 60.810 57.895 12.10 0.00 0.00 2.87
564 603 0.391661 TCGTTAGTCGGTACTCGCCT 60.392 55.000 0.00 0.00 40.32 5.52
762 815 1.209127 CGCCATTCAAACCGTCCAC 59.791 57.895 0.00 0.00 0.00 4.02
763 816 1.209127 GCCATTCAAACCGTCCACG 59.791 57.895 0.00 0.00 39.44 4.94
764 817 1.209127 CCATTCAAACCGTCCACGC 59.791 57.895 0.00 0.00 38.18 5.34
765 818 1.209127 CATTCAAACCGTCCACGCC 59.791 57.895 0.00 0.00 38.18 5.68
766 819 1.969589 ATTCAAACCGTCCACGCCC 60.970 57.895 0.00 0.00 38.18 6.13
767 820 4.629523 TCAAACCGTCCACGCCCC 62.630 66.667 0.00 0.00 38.18 5.80
774 827 4.796495 GTCCACGCCCCCACCATC 62.796 72.222 0.00 0.00 0.00 3.51
828 887 3.069318 GACGCGTCTCCCTTCCCT 61.069 66.667 31.12 0.00 0.00 4.20
935 1018 2.507992 CGCTCTCTCCCGCAACAG 60.508 66.667 0.00 0.00 0.00 3.16
984 1067 4.965858 GACTCTCGCCGCGATCCG 62.966 72.222 17.22 9.95 34.61 4.18
1017 1100 0.389556 AGATGCAGACACTCACAGCG 60.390 55.000 0.00 0.00 0.00 5.18
1082 1174 4.135153 CCGGTCCAGCTCGGTCAG 62.135 72.222 3.49 0.00 41.23 3.51
1761 1883 1.672356 CTTCAACGGCCACCTCCTG 60.672 63.158 2.24 0.00 0.00 3.86
1960 2082 5.066246 CCCTACCTCAAGTACTTCTACTTCG 59.934 48.000 4.77 0.00 40.64 3.79
1961 2083 4.437772 ACCTCAAGTACTTCTACTTCGC 57.562 45.455 4.77 0.00 40.64 4.70
2052 2174 2.357327 TCACCGAGAATTACGTGGTG 57.643 50.000 11.63 11.63 44.24 4.17
2250 2372 1.152839 GGAGGAGGAGGAGACCGAG 60.153 68.421 0.00 0.00 34.73 4.63
3016 3147 1.064758 ACTTGCTTCAGTCCACACCAA 60.065 47.619 0.00 0.00 0.00 3.67
3017 3148 1.605710 CTTGCTTCAGTCCACACCAAG 59.394 52.381 0.00 0.00 0.00 3.61
3052 3183 4.243270 CGCTTGTAGTAAAACCTAGCTGT 58.757 43.478 0.00 0.00 0.00 4.40
3229 3377 5.305902 TCATCACACGGGTTGGTATATGTAT 59.694 40.000 0.00 0.00 0.00 2.29
3230 3378 4.951254 TCACACGGGTTGGTATATGTATG 58.049 43.478 0.00 0.00 0.00 2.39
3231 3379 4.406326 TCACACGGGTTGGTATATGTATGT 59.594 41.667 0.00 0.00 0.00 2.29
3232 3380 5.597594 TCACACGGGTTGGTATATGTATGTA 59.402 40.000 0.00 0.00 0.00 2.29
3233 3381 5.693104 CACACGGGTTGGTATATGTATGTAC 59.307 44.000 0.00 0.00 0.00 2.90
3234 3382 5.363292 ACACGGGTTGGTATATGTATGTACA 59.637 40.000 0.00 0.00 40.98 2.90
3386 3546 0.735978 TGGCGATTGTGCTGACTACG 60.736 55.000 0.00 0.00 34.52 3.51
3397 3557 2.792674 TGCTGACTACGTTTTCTTGTCG 59.207 45.455 0.00 0.00 0.00 4.35
3403 3563 2.798834 ACGTTTTCTTGTCGTGTGTG 57.201 45.000 0.00 0.00 36.46 3.82
3413 3573 0.776451 GTCGTGTGTGTCGCTTAGTG 59.224 55.000 0.00 0.00 0.00 2.74
3416 3576 1.071502 CGTGTGTGTCGCTTAGTGTTG 60.072 52.381 0.00 0.00 0.00 3.33
3417 3577 2.198406 GTGTGTGTCGCTTAGTGTTGA 58.802 47.619 0.00 0.00 0.00 3.18
3418 3578 2.218759 GTGTGTGTCGCTTAGTGTTGAG 59.781 50.000 0.00 0.00 0.00 3.02
3422 3582 2.985139 GTGTCGCTTAGTGTTGAGTACC 59.015 50.000 0.00 0.00 0.00 3.34
3430 3593 5.520649 GCTTAGTGTTGAGTACCTTCTATGC 59.479 44.000 0.00 0.00 0.00 3.14
3432 3595 5.078411 AGTGTTGAGTACCTTCTATGCAG 57.922 43.478 0.00 0.00 0.00 4.41
3503 3684 2.351418 CGTCTCTCTGCTCTGTCAGTAG 59.649 54.545 0.00 0.00 36.19 2.57
3523 3704 9.737427 TCAGTAGAAGATAAAAATCAGATCGAC 57.263 33.333 0.00 0.00 0.00 4.20
3633 4033 2.802787 ACAGTCTGGTGAGTTCGAAG 57.197 50.000 0.00 0.00 0.00 3.79
3634 4034 1.269831 ACAGTCTGGTGAGTTCGAAGC 60.270 52.381 0.00 0.00 0.00 3.86
3635 4035 0.039074 AGTCTGGTGAGTTCGAAGCG 60.039 55.000 0.00 0.00 0.00 4.68
3636 4036 1.372997 TCTGGTGAGTTCGAAGCGC 60.373 57.895 0.00 0.00 0.00 5.92
3677 4077 0.392998 GGGAGGCTCGAGCAAAATGA 60.393 55.000 36.27 0.00 44.36 2.57
3759 4174 3.378427 CCATGTTTTCCTTGTAGCTAGCC 59.622 47.826 12.13 0.00 0.00 3.93
3760 4175 4.265073 CATGTTTTCCTTGTAGCTAGCCT 58.735 43.478 12.13 1.20 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.584185 AACAAATCGTGGCTTAATTAACCT 57.416 33.333 14.14 0.00 0.00 3.50
52 58 7.059260 CGAACAGAGACACGTTTTACTTAGTAG 59.941 40.741 0.00 0.00 0.00 2.57
53 59 6.852853 CGAACAGAGACACGTTTTACTTAGTA 59.147 38.462 0.00 0.00 0.00 1.82
54 60 5.684626 CGAACAGAGACACGTTTTACTTAGT 59.315 40.000 0.00 0.00 0.00 2.24
94 100 4.962836 CCATGCCAGGGGGATCGC 62.963 72.222 0.06 0.06 29.13 4.58
95 101 4.962836 GCCATGCCAGGGGGATCG 62.963 72.222 0.00 0.00 29.13 3.69
110 116 0.533531 CCCCGGTATAAACGAAGGCC 60.534 60.000 0.00 0.00 0.00 5.19
115 121 2.770802 TCATTTCCCCCGGTATAAACGA 59.229 45.455 0.00 0.00 0.00 3.85
120 126 2.304761 GAGCATCATTTCCCCCGGTATA 59.695 50.000 0.00 0.00 33.17 1.47
121 127 1.073923 GAGCATCATTTCCCCCGGTAT 59.926 52.381 0.00 0.00 33.17 2.73
122 128 0.472471 GAGCATCATTTCCCCCGGTA 59.528 55.000 0.00 0.00 33.17 4.02
123 129 1.227383 GAGCATCATTTCCCCCGGT 59.773 57.895 0.00 0.00 33.17 5.28
125 131 1.893808 CGGAGCATCATTTCCCCCG 60.894 63.158 0.00 0.00 36.25 5.73
126 132 1.529244 CCGGAGCATCATTTCCCCC 60.529 63.158 0.00 0.00 36.25 5.40
223 229 2.238521 GGGGACAGTTGAGCAAATCAA 58.761 47.619 0.00 0.00 45.79 2.57
232 238 3.307906 CCGTCCGGGGACAGTTGA 61.308 66.667 17.43 0.00 44.77 3.18
255 261 2.047274 TACAGCGAGGCCTTGTGC 60.047 61.111 21.55 18.27 40.16 4.57
320 358 3.257561 CATCCCTTGACGAGCGCG 61.258 66.667 8.75 8.75 44.79 6.86
321 359 2.629050 TAGCATCCCTTGACGAGCGC 62.629 60.000 0.00 0.00 0.00 5.92
322 360 0.872021 GTAGCATCCCTTGACGAGCG 60.872 60.000 0.00 0.00 0.00 5.03
323 361 0.175760 TGTAGCATCCCTTGACGAGC 59.824 55.000 0.00 0.00 0.00 5.03
324 362 2.101415 TGATGTAGCATCCCTTGACGAG 59.899 50.000 6.65 0.00 0.00 4.18
325 363 2.107366 TGATGTAGCATCCCTTGACGA 58.893 47.619 6.65 0.00 0.00 4.20
326 364 2.602257 TGATGTAGCATCCCTTGACG 57.398 50.000 6.65 0.00 0.00 4.35
327 365 2.609459 CGTTGATGTAGCATCCCTTGAC 59.391 50.000 6.65 0.00 0.00 3.18
328 366 2.419990 CCGTTGATGTAGCATCCCTTGA 60.420 50.000 6.65 0.00 0.00 3.02
329 367 1.942657 CCGTTGATGTAGCATCCCTTG 59.057 52.381 6.65 0.00 0.00 3.61
330 368 1.134098 CCCGTTGATGTAGCATCCCTT 60.134 52.381 6.65 0.00 0.00 3.95
331 369 0.469917 CCCGTTGATGTAGCATCCCT 59.530 55.000 6.65 0.00 0.00 4.20
332 370 0.535102 CCCCGTTGATGTAGCATCCC 60.535 60.000 6.65 0.00 0.00 3.85
333 371 0.468226 TCCCCGTTGATGTAGCATCC 59.532 55.000 6.65 0.00 0.00 3.51
334 372 2.146342 CATCCCCGTTGATGTAGCATC 58.854 52.381 2.44 2.44 37.85 3.91
335 373 1.815408 GCATCCCCGTTGATGTAGCAT 60.815 52.381 11.61 0.00 43.28 3.79
354 392 9.665264 GTACCATTAGCAGAATAATTAAACAGC 57.335 33.333 0.00 0.00 0.00 4.40
386 424 2.342910 TTTCGCTTCGACTCTGGTAC 57.657 50.000 0.00 0.00 34.89 3.34
396 434 4.452447 CATCAGCAGATATTTTCGCTTCG 58.548 43.478 0.00 0.00 33.77 3.79
399 437 2.551459 GCCATCAGCAGATATTTTCGCT 59.449 45.455 0.00 0.00 42.97 4.93
500 539 2.930826 TCGGAGCCTCTTGTTTTCTT 57.069 45.000 0.00 0.00 0.00 2.52
534 573 3.190118 ACCGACTAACGATCGAGTTTCTT 59.810 43.478 24.34 6.88 45.77 2.52
564 603 4.038282 ACATGTGTCGACAGGTAACAGTAA 59.962 41.667 20.73 0.00 45.09 2.24
745 798 1.209127 CGTGGACGGTTTGAATGGC 59.791 57.895 0.00 0.00 35.37 4.40
748 801 1.969589 GGGCGTGGACGGTTTGAAT 60.970 57.895 0.71 0.00 40.23 2.57
765 818 3.976701 GAGTGTGGCGATGGTGGGG 62.977 68.421 0.00 0.00 0.00 4.96
766 819 2.436646 GAGTGTGGCGATGGTGGG 60.437 66.667 0.00 0.00 0.00 4.61
767 820 2.436646 GGAGTGTGGCGATGGTGG 60.437 66.667 0.00 0.00 0.00 4.61
768 821 2.436646 GGGAGTGTGGCGATGGTG 60.437 66.667 0.00 0.00 0.00 4.17
769 822 2.257409 GATGGGAGTGTGGCGATGGT 62.257 60.000 0.00 0.00 0.00 3.55
770 823 1.524621 GATGGGAGTGTGGCGATGG 60.525 63.158 0.00 0.00 0.00 3.51
771 824 1.884464 CGATGGGAGTGTGGCGATG 60.884 63.158 0.00 0.00 0.00 3.84
772 825 1.402896 ATCGATGGGAGTGTGGCGAT 61.403 55.000 0.00 0.00 34.12 4.58
773 826 2.016393 GATCGATGGGAGTGTGGCGA 62.016 60.000 0.54 0.00 0.00 5.54
774 827 1.592669 GATCGATGGGAGTGTGGCG 60.593 63.158 0.54 0.00 0.00 5.69
775 828 1.227674 GGATCGATGGGAGTGTGGC 60.228 63.158 0.54 0.00 0.00 5.01
823 876 4.344865 GTTGGAGCGGGCAGGGAA 62.345 66.667 0.00 0.00 0.00 3.97
828 887 1.717032 ATATAGAGTTGGAGCGGGCA 58.283 50.000 0.00 0.00 0.00 5.36
935 1018 2.874751 CGGAATTGGCGTGGGTTC 59.125 61.111 0.00 0.00 0.00 3.62
1209 1331 0.616111 TCTTCTCCTGCCTCTCCACC 60.616 60.000 0.00 0.00 0.00 4.61
1482 1604 2.357034 CCGTCGAACAGGTGGTGG 60.357 66.667 0.00 0.00 0.00 4.61
1761 1883 3.458163 TCGTCCTCGGACATGGCC 61.458 66.667 7.86 7.86 44.77 5.36
1878 2000 2.741211 GTGGCGGGGTCGAGTTTC 60.741 66.667 0.00 0.00 39.00 2.78
2250 2372 2.584608 CCGATCACCACCACCTCC 59.415 66.667 0.00 0.00 0.00 4.30
2499 2621 2.750350 AGGTCCACCTTGGCGAAG 59.250 61.111 0.74 0.74 46.09 3.79
3016 3147 6.218108 ACTACAAGCGCTACTTAATTACCT 57.782 37.500 12.05 0.00 36.04 3.08
3017 3148 7.992180 TTACTACAAGCGCTACTTAATTACC 57.008 36.000 12.05 0.00 36.04 2.85
3206 3349 3.804036 ACATATACCAACCCGTGTGATG 58.196 45.455 0.00 0.00 0.00 3.07
3229 3377 4.328536 ACAACCGGAGCATATTTTGTACA 58.671 39.130 9.46 0.00 0.00 2.90
3230 3378 4.957759 ACAACCGGAGCATATTTTGTAC 57.042 40.909 9.46 0.00 0.00 2.90
3231 3379 4.762765 ACAACAACCGGAGCATATTTTGTA 59.237 37.500 9.46 0.00 0.00 2.41
3232 3380 3.572255 ACAACAACCGGAGCATATTTTGT 59.428 39.130 9.46 2.04 0.00 2.83
3233 3381 4.165779 GACAACAACCGGAGCATATTTTG 58.834 43.478 9.46 1.26 0.00 2.44
3234 3382 3.823873 TGACAACAACCGGAGCATATTTT 59.176 39.130 9.46 0.00 0.00 1.82
3311 3459 4.326766 CCAACAACACCGGCAGCG 62.327 66.667 0.00 0.00 0.00 5.18
3330 3490 1.299014 AACAAATGCACACACGCGG 60.299 52.632 12.47 1.27 33.35 6.46
3333 3493 6.966066 TCATAATATCAACAAATGCACACACG 59.034 34.615 0.00 0.00 0.00 4.49
3370 3530 3.428870 AGAAAACGTAGTCAGCACAATCG 59.571 43.478 0.00 0.00 45.00 3.34
3386 3546 2.689635 CGACACACACGACAAGAAAAC 58.310 47.619 0.00 0.00 0.00 2.43
3397 3557 2.198406 TCAACACTAAGCGACACACAC 58.802 47.619 0.00 0.00 0.00 3.82
3403 3563 3.572604 AGGTACTCAACACTAAGCGAC 57.427 47.619 0.00 0.00 0.00 5.19
3413 3573 4.116238 GAGCTGCATAGAAGGTACTCAAC 58.884 47.826 1.02 0.00 38.49 3.18
3416 3576 3.976169 CAGAGCTGCATAGAAGGTACTC 58.024 50.000 1.02 0.00 38.49 2.59
3430 3593 3.969117 TTAAACACACAAGCAGAGCTG 57.031 42.857 0.00 0.00 39.62 4.24
3432 3595 5.801947 CCAATATTAAACACACAAGCAGAGC 59.198 40.000 0.00 0.00 0.00 4.09
3523 3704 1.959042 ACCTCGCAGCAATGGATTAG 58.041 50.000 0.00 0.00 0.00 1.73
3525 3706 1.065491 TGTACCTCGCAGCAATGGATT 60.065 47.619 0.00 0.00 0.00 3.01
3586 3986 3.288242 CGGCGAAATCATATTTGGAACG 58.712 45.455 0.00 0.00 0.00 3.95
3618 4018 1.372997 GCGCTTCGAACTCACCAGA 60.373 57.895 0.00 0.00 0.00 3.86
3634 4034 3.312504 CATCCACGACTACGCGCG 61.313 66.667 30.96 30.96 43.96 6.86
3635 4035 3.617538 GCATCCACGACTACGCGC 61.618 66.667 5.73 0.00 43.96 6.86
3636 4036 2.202557 TGCATCCACGACTACGCG 60.203 61.111 3.53 3.53 43.96 6.01
3677 4077 0.658897 AAACCAAATCGCGTGTTCGT 59.341 45.000 5.77 0.00 39.49 3.85


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

AutoCloner maintained by Alex Coulton.