Multiple sequence alignment - TraesCS1D01G284300

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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 TraesCS1D01G284300 chr1D 100.000 2438 0 0 1 2438 382718802 382721239 0.000000e+00 4503
1 TraesCS1D01G284300 chr1A 91.842 2231 111 33 247 2438 482767251 482769449 0.000000e+00 3046
2 TraesCS1D01G284300 chr1A 90.310 258 22 2 1 255 482766968 482767225 3.880000e-88 335
3 TraesCS1D01G284300 chr1B 94.106 1544 68 12 795 2324 512630451 512631985 0.000000e+00 2326
4 TraesCS1D01G284300 chr1B 85.330 818 67 28 5 793 512623350 512624143 0.000000e+00 797
5 TraesCS1D01G284300 chr1B 87.905 463 28 18 1001 1440 641523608 641523151 9.990000e-144 520
6 TraesCS1D01G284300 chr3B 91.091 449 27 8 1001 1445 70580774 70580335 1.610000e-166 595
7 TraesCS1D01G284300 chr3D 89.888 445 35 6 1012 1449 45064589 45064148 4.550000e-157 564
8 TraesCS1D01G284300 chr3D 90.385 416 23 7 1022 1436 36822436 36822835 4.620000e-147 531
9 TraesCS1D01G284300 chr3D 89.435 407 26 11 1031 1436 50658428 50658038 4.680000e-137 497
10 TraesCS1D01G284300 chr4D 89.498 438 30 9 1012 1438 30195053 30195485 7.670000e-150 540
11 TraesCS1D01G284300 chr4D 88.196 449 27 13 1000 1429 352755520 352755079 1.670000e-141 512
12 TraesCS1D01G284300 chr4A 86.929 482 28 19 973 1429 112767144 112767615 2.160000e-140 508
13 TraesCS1D01G284300 chr4B 87.973 449 28 13 1000 1429 436312304 436311863 7.780000e-140 507
14 TraesCS1D01G284300 chr3A 89.104 413 31 10 1031 1439 605180171 605179769 3.620000e-138 501


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 TraesCS1D01G284300 chr1D 382718802 382721239 2437 False 4503.0 4503 100.000 1 2438 1 chr1D.!!$F1 2437
1 TraesCS1D01G284300 chr1A 482766968 482769449 2481 False 1690.5 3046 91.076 1 2438 2 chr1A.!!$F1 2437
2 TraesCS1D01G284300 chr1B 512630451 512631985 1534 False 2326.0 2326 94.106 795 2324 1 chr1B.!!$F2 1529
3 TraesCS1D01G284300 chr1B 512623350 512624143 793 False 797.0 797 85.330 5 793 1 chr1B.!!$F1 788

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
245 249 0.037605 AAACGAAGGGCACTACGGAG 60.038 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1579 1.108132 AACTACGAGCCTCGATCCCC 61.108 60.0 22.8 0.0 43.74 4.81 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
70 72 1.487142 TGGAAGGTCTGGTTCGACAAA 59.513 47.619 0.00 0.00 35.63 2.83
71 73 1.871676 GGAAGGTCTGGTTCGACAAAC 59.128 52.381 0.00 0.00 35.63 2.93
77 79 0.315869 CTGGTTCGACAAACGTGCAC 60.316 55.000 6.82 6.82 43.13 4.57
78 80 1.019805 TGGTTCGACAAACGTGCACA 61.020 50.000 18.64 0.00 43.13 4.57
120 122 1.938577 CCAGAAGAGTGATCATTGCCG 59.061 52.381 0.00 0.00 0.00 5.69
175 179 2.099405 TGACATGATCGTAGAGTGCCA 58.901 47.619 0.00 0.00 43.63 4.92
193 197 4.081752 GTGCCACCAATGAAATTATCACCA 60.082 41.667 0.00 0.00 41.93 4.17
196 200 5.395546 GCCACCAATGAAATTATCACCACAT 60.396 40.000 0.00 0.00 41.93 3.21
240 244 2.895404 AGAGTGTAAACGAAGGGCACTA 59.105 45.455 0.00 0.00 40.06 2.74
241 245 2.991866 GAGTGTAAACGAAGGGCACTAC 59.008 50.000 0.00 0.00 40.06 2.73
242 246 1.723003 GTGTAAACGAAGGGCACTACG 59.277 52.381 0.00 0.00 0.00 3.51
245 249 0.037605 AAACGAAGGGCACTACGGAG 60.038 55.000 0.00 0.00 0.00 4.63
260 298 0.371645 CGGAGCAATGAGAGAAACGC 59.628 55.000 0.00 0.00 0.00 4.84
293 331 1.969923 CCCAATTGTGGTTGTGTGGAT 59.030 47.619 4.43 0.00 44.30 3.41
308 347 5.754782 TGTGTGGATATTTTACAGGCTCAT 58.245 37.500 0.00 0.00 0.00 2.90
343 382 3.663464 AATTCATCGTGCGACATGAAG 57.337 42.857 13.54 2.84 36.61 3.02
391 430 0.673333 GACATGGATGTGACACCGCA 60.673 55.000 2.45 0.00 41.95 5.69
392 431 0.250684 ACATGGATGTGACACCGCAA 60.251 50.000 2.45 0.00 40.03 4.85
393 432 0.168788 CATGGATGTGACACCGCAAC 59.831 55.000 2.45 0.00 36.26 4.17
404 443 2.671619 CCGCAACCATTGTCGGGT 60.672 61.111 13.26 0.00 42.51 5.28
410 449 0.110486 AACCATTGTCGGGTGAAGCT 59.890 50.000 0.00 0.00 39.01 3.74
418 457 0.681887 TCGGGTGAAGCTATCGGTGA 60.682 55.000 0.00 0.00 0.00 4.02
509 551 1.117150 CCAAGGGAGGCATGGAATTG 58.883 55.000 0.00 0.00 36.27 2.32
540 582 1.661341 AGAGCATGCACGAATCCTTC 58.339 50.000 21.98 5.01 0.00 3.46
558 600 3.188873 CCTTCGTATTTACCCGCAACAAA 59.811 43.478 0.00 0.00 0.00 2.83
793 862 1.180456 TAACTCTTCCCCACGCGTCA 61.180 55.000 9.86 0.00 0.00 4.35
818 887 0.038618 CTCACCGTCAACCACATCGA 60.039 55.000 0.00 0.00 0.00 3.59
852 921 4.129737 CACCTCACCGATCCGCGT 62.130 66.667 4.92 0.00 38.67 6.01
876 945 0.850883 ACCCCCTCCACCAATCACAT 60.851 55.000 0.00 0.00 0.00 3.21
953 1022 2.861101 GCGCCCTCTCCGATCATCA 61.861 63.158 0.00 0.00 0.00 3.07
956 1025 0.972134 GCCCTCTCCGATCATCATCA 59.028 55.000 0.00 0.00 0.00 3.07
1444 1527 1.104577 CACCTCCTCCTAGACGCTCC 61.105 65.000 0.00 0.00 0.00 4.70
1487 1572 1.253034 GTCGCGTTTGATGATCGTCTC 59.747 52.381 15.81 6.01 0.00 3.36
1494 1579 3.559657 GATGATCGTCTCGGCCCCG 62.560 68.421 7.73 0.00 41.35 5.73
1906 1998 3.499737 CGCACGCCAATGTCCCTC 61.500 66.667 0.00 0.00 0.00 4.30
1918 2010 5.198965 CCAATGTCCCTCAGAATCTGAAAT 58.801 41.667 14.44 1.12 40.18 2.17
1919 2011 6.359804 CCAATGTCCCTCAGAATCTGAAATA 58.640 40.000 14.44 2.17 40.18 1.40
1931 2024 8.699130 TCAGAATCTGAAATAGACAGCAAGATA 58.301 33.333 10.99 0.00 37.57 1.98
1989 2085 6.275335 CAAGAATGTTAAATCCGCCATGAAT 58.725 36.000 0.00 0.00 0.00 2.57
1990 2086 6.469782 AGAATGTTAAATCCGCCATGAATT 57.530 33.333 0.00 0.00 0.00 2.17
1991 2087 7.581213 AGAATGTTAAATCCGCCATGAATTA 57.419 32.000 0.00 0.00 0.00 1.40
1992 2088 7.651808 AGAATGTTAAATCCGCCATGAATTAG 58.348 34.615 0.00 0.00 0.00 1.73
1993 2089 6.959639 ATGTTAAATCCGCCATGAATTAGT 57.040 33.333 0.00 0.00 0.00 2.24
2014 2110 1.636148 TTCAAGTACGTACCTGGGCT 58.364 50.000 21.80 0.00 0.00 5.19
2101 2197 1.523758 CTTGGTCCTGCAGGTTGTAC 58.476 55.000 31.58 21.67 36.34 2.90
2197 2293 2.646445 CTCGATCAGCTGCATCGCG 61.646 63.158 28.53 23.26 42.42 5.87
2293 2389 0.247460 CCAGCACGTCTTCTCCATCA 59.753 55.000 0.00 0.00 0.00 3.07
2336 2432 2.096013 GCCTCAAACTGTAAAGATCGCC 59.904 50.000 0.00 0.00 0.00 5.54
2339 2435 2.028839 TCAAACTGTAAAGATCGCCGGA 60.029 45.455 5.05 0.00 0.00 5.14
2355 2451 1.328680 CCGGAGATTGAATCGCACAAG 59.671 52.381 10.93 0.00 0.00 3.16
2359 2455 3.423571 GAGATTGAATCGCACAAGCAAG 58.576 45.455 3.99 0.00 42.27 4.01
2384 2480 0.957888 GGCTCACTGGTTTCTGCTCC 60.958 60.000 0.00 0.00 0.00 4.70
2417 2513 6.785191 TGTCAGAGAAACACAACAAGAATTC 58.215 36.000 0.00 0.00 0.00 2.17
2420 2516 6.547141 TCAGAGAAACACAACAAGAATTCCAT 59.453 34.615 0.65 0.00 0.00 3.41
2428 2524 7.209475 ACACAACAAGAATTCCATTTACCTTG 58.791 34.615 0.65 0.00 37.57 3.61
2434 2530 3.866883 ATTCCATTTACCTTGGCAACG 57.133 42.857 0.00 0.00 42.51 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 0.927537 CTCTGTGCACGTTTGTCGAA 59.072 50.000 13.13 0.00 42.86 3.71
77 79 6.204688 TGGTGTAAAATTGTACTTCTGCTCTG 59.795 38.462 7.31 0.00 0.00 3.35
78 80 6.296026 TGGTGTAAAATTGTACTTCTGCTCT 58.704 36.000 7.31 0.00 0.00 4.09
83 85 8.211629 ACTCTTCTGGTGTAAAATTGTACTTCT 58.788 33.333 7.31 0.00 0.00 2.85
120 122 4.054671 CACTATTTCTCGCCTCTTCCATC 58.945 47.826 0.00 0.00 0.00 3.51
175 179 6.550854 CCCTATGTGGTGATAATTTCATTGGT 59.449 38.462 0.00 0.00 36.54 3.67
193 197 1.844497 GGGCAAAGACTACCCCTATGT 59.156 52.381 0.00 0.00 37.70 2.29
196 200 1.913419 CTTGGGCAAAGACTACCCCTA 59.087 52.381 0.00 0.00 43.54 3.53
219 223 1.692519 AGTGCCCTTCGTTTACACTCT 59.307 47.619 0.00 0.00 36.95 3.24
240 244 1.714794 CGTTTCTCTCATTGCTCCGT 58.285 50.000 0.00 0.00 0.00 4.69
241 245 0.371645 GCGTTTCTCTCATTGCTCCG 59.628 55.000 0.00 0.00 0.00 4.63
242 246 0.729690 GGCGTTTCTCTCATTGCTCC 59.270 55.000 0.00 0.00 0.00 4.70
245 249 2.927553 ATTGGCGTTTCTCTCATTGC 57.072 45.000 0.00 0.00 0.00 3.56
260 298 3.384467 CACAATTGGGTAGGCCTTATTGG 59.616 47.826 12.58 4.86 38.55 3.16
279 317 5.475220 CCTGTAAAATATCCACACAACCACA 59.525 40.000 0.00 0.00 0.00 4.17
308 347 9.462174 GCACGATGAATTTATCCATATTTTTCA 57.538 29.630 4.75 0.00 0.00 2.69
331 370 2.299993 TCATCTCCTTCATGTCGCAC 57.700 50.000 0.00 0.00 0.00 5.34
343 382 0.734889 CATTGGTGGCGTTCATCTCC 59.265 55.000 0.00 0.00 0.00 3.71
391 430 0.110486 AGCTTCACCCGACAATGGTT 59.890 50.000 0.00 0.00 32.46 3.67
392 431 0.981183 TAGCTTCACCCGACAATGGT 59.019 50.000 0.00 0.00 36.21 3.55
393 432 2.213499 GATAGCTTCACCCGACAATGG 58.787 52.381 0.00 0.00 0.00 3.16
404 443 5.344743 AGAGAAATTCACCGATAGCTTCA 57.655 39.130 0.00 0.00 0.00 3.02
406 445 4.162320 TGGAGAGAAATTCACCGATAGCTT 59.838 41.667 0.00 0.00 39.22 3.74
410 449 6.098266 TGAAGATGGAGAGAAATTCACCGATA 59.902 38.462 0.00 0.00 39.22 2.92
418 457 4.702131 CGGGTTTGAAGATGGAGAGAAATT 59.298 41.667 0.00 0.00 0.00 1.82
507 549 5.122239 GTGCATGCTCTACACAAGTATTCAA 59.878 40.000 20.33 0.00 34.43 2.69
509 551 4.259970 CGTGCATGCTCTACACAAGTATTC 60.260 45.833 20.33 0.00 33.89 1.75
637 685 5.127491 TCCACCGTCAAAAGTCTACAAATT 58.873 37.500 0.00 0.00 0.00 1.82
793 862 0.762418 TGGTTGACGGTGAGGATTGT 59.238 50.000 0.00 0.00 0.00 2.71
818 887 0.250513 GTGGAAGGATCTCAGGCGTT 59.749 55.000 0.00 0.00 0.00 4.84
852 921 2.431047 ATTGGTGGAGGGGGTGAGGA 62.431 60.000 0.00 0.00 0.00 3.71
883 952 2.561478 TTGGATTTATAGAGGGGCGC 57.439 50.000 0.00 0.00 0.00 6.53
953 1022 2.527875 GGCGGGGAGGAGGATGAT 60.528 66.667 0.00 0.00 0.00 2.45
1444 1527 3.157949 GAGAGAAGGGCGGGGGAG 61.158 72.222 0.00 0.00 0.00 4.30
1494 1579 1.108132 AACTACGAGCCTCGATCCCC 61.108 60.000 22.80 0.00 43.74 4.81
1640 1732 2.125147 CCACCACACGATCCGCAT 60.125 61.111 0.00 0.00 0.00 4.73
1643 1735 1.879737 TACACCCACCACACGATCCG 61.880 60.000 0.00 0.00 0.00 4.18
1906 1998 7.789273 ATCTTGCTGTCTATTTCAGATTCTG 57.211 36.000 7.38 7.38 35.17 3.02
1918 2010 4.469586 TGATGGTGGTTATCTTGCTGTCTA 59.530 41.667 0.00 0.00 0.00 2.59
1919 2011 3.264193 TGATGGTGGTTATCTTGCTGTCT 59.736 43.478 0.00 0.00 0.00 3.41
1931 2024 4.665451 TGTCTTGATGATTGATGGTGGTT 58.335 39.130 0.00 0.00 0.00 3.67
1989 2085 5.163519 GCCCAGGTACGTACTTGAATACTAA 60.164 44.000 32.31 0.00 35.55 2.24
1990 2086 4.339247 GCCCAGGTACGTACTTGAATACTA 59.661 45.833 32.31 0.00 35.55 1.82
1991 2087 3.131755 GCCCAGGTACGTACTTGAATACT 59.868 47.826 32.31 14.49 35.55 2.12
1992 2088 3.131755 AGCCCAGGTACGTACTTGAATAC 59.868 47.826 32.31 19.90 35.55 1.89
1993 2089 3.368248 AGCCCAGGTACGTACTTGAATA 58.632 45.455 32.31 0.00 35.55 1.75
2014 2110 4.246206 CGCGAGTACGGCATCGGA 62.246 66.667 0.00 0.00 41.39 4.55
2170 2266 3.082579 GCTGATCGAGAAGGCCGGT 62.083 63.158 1.90 0.00 0.00 5.28
2293 2389 1.758440 ATGTGCAGGGCGATATCGGT 61.758 55.000 25.51 0.00 40.23 4.69
2318 2414 2.028839 TCCGGCGATCTTTACAGTTTGA 60.029 45.455 9.30 0.00 0.00 2.69
2324 2420 2.429250 TCAATCTCCGGCGATCTTTACA 59.571 45.455 9.30 0.00 0.00 2.41
2325 2421 3.093717 TCAATCTCCGGCGATCTTTAC 57.906 47.619 9.30 0.00 0.00 2.01
2336 2432 1.267732 GCTTGTGCGATTCAATCTCCG 60.268 52.381 0.00 0.00 0.00 4.63
2339 2435 2.415090 GCTTGCTTGTGCGATTCAATCT 60.415 45.455 0.00 0.00 43.34 2.40
2359 2455 1.569479 GAAACCAGTGAGCCACTCGC 61.569 60.000 5.02 0.00 43.43 5.03
2384 2480 3.362237 GTGTTTCTCTGACAGAACGATCG 59.638 47.826 14.88 14.88 41.13 3.69
2417 2513 0.108851 GCCGTTGCCAAGGTAAATGG 60.109 55.000 9.34 9.34 41.08 3.16
2420 2516 3.346101 CGCCGTTGCCAAGGTAAA 58.654 55.556 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.