Multiple sequence alignment - TraesCS7A01G257900

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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 TraesCS7A01G257900 chr7A 100.000 2648 0 0 1 2648 247703404 247700757 0.000000e+00 4891
1 TraesCS7A01G257900 chr1D 94.743 2682 105 20 1 2648 83055933 83053254 0.000000e+00 4139
2 TraesCS7A01G257900 chr5A 95.170 2112 88 11 1 2100 190546091 190548200 0.000000e+00 3323
3 TraesCS7A01G257900 chr5A 88.475 564 37 11 2110 2648 190548711 190549271 0.000000e+00 656
4 TraesCS7A01G257900 chr6B 92.216 2184 129 22 1 2158 120534334 120532166 0.000000e+00 3053
5 TraesCS7A01G257900 chr6B 88.422 1451 151 10 663 2106 296847929 296849369 0.000000e+00 1733
6 TraesCS7A01G257900 chr6B 92.650 449 32 1 2 449 296846593 296847041 0.000000e+00 645
7 TraesCS7A01G257900 chr6B 88.362 464 46 7 2189 2648 513263977 513264436 3.850000e-153 551
8 TraesCS7A01G257900 chr6B 87.815 238 23 4 435 668 296847136 296847371 9.340000e-70 274
9 TraesCS7A01G257900 chr4B 94.039 1644 87 5 1 1634 32575608 32573966 0.000000e+00 2483
10 TraesCS7A01G257900 chr5B 94.692 1413 69 4 1 1408 697757450 697758861 0.000000e+00 2189
11 TraesCS7A01G257900 chr5B 85.537 484 55 12 2176 2648 129136829 129136350 2.370000e-135 492
12 TraesCS7A01G257900 chr1B 92.208 1463 99 13 816 2269 82550344 82548888 0.000000e+00 2056
13 TraesCS7A01G257900 chr1B 94.837 736 33 3 1 732 82551481 82550747 0.000000e+00 1144
14 TraesCS7A01G257900 chr2A 86.266 1165 153 6 956 2116 297541943 297540782 0.000000e+00 1258
15 TraesCS7A01G257900 chr4A 86.082 1164 156 6 956 2116 618794690 618793530 0.000000e+00 1247
16 TraesCS7A01G257900 chr4A 85.412 473 51 12 2188 2648 327030406 327029940 2.390000e-130 475
17 TraesCS7A01G257900 chr1A 86.237 1148 153 5 956 2100 84819353 84820498 0.000000e+00 1240
18 TraesCS7A01G257900 chr3B 87.393 468 46 12 2188 2648 734461657 734462118 2.330000e-145 525
19 TraesCS7A01G257900 chrUn 84.404 545 60 13 2110 2648 55650540 55650015 1.820000e-141 512
20 TraesCS7A01G257900 chr6D 86.928 459 48 9 2198 2648 192174872 192174418 3.040000e-139 505
21 TraesCS7A01G257900 chr3A 85.169 472 55 11 2188 2648 144039914 144039447 1.110000e-128 470


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 TraesCS7A01G257900 chr7A 247700757 247703404 2647 True 4891.0 4891 100.0000 1 2648 1 chr7A.!!$R1 2647
1 TraesCS7A01G257900 chr1D 83053254 83055933 2679 True 4139.0 4139 94.7430 1 2648 1 chr1D.!!$R1 2647
2 TraesCS7A01G257900 chr5A 190546091 190549271 3180 False 1989.5 3323 91.8225 1 2648 2 chr5A.!!$F1 2647
3 TraesCS7A01G257900 chr6B 120532166 120534334 2168 True 3053.0 3053 92.2160 1 2158 1 chr6B.!!$R1 2157
4 TraesCS7A01G257900 chr6B 296846593 296849369 2776 False 884.0 1733 89.6290 2 2106 3 chr6B.!!$F2 2104
5 TraesCS7A01G257900 chr4B 32573966 32575608 1642 True 2483.0 2483 94.0390 1 1634 1 chr4B.!!$R1 1633
6 TraesCS7A01G257900 chr5B 697757450 697758861 1411 False 2189.0 2189 94.6920 1 1408 1 chr5B.!!$F1 1407
7 TraesCS7A01G257900 chr1B 82548888 82551481 2593 True 1600.0 2056 93.5225 1 2269 2 chr1B.!!$R1 2268
8 TraesCS7A01G257900 chr2A 297540782 297541943 1161 True 1258.0 1258 86.2660 956 2116 1 chr2A.!!$R1 1160
9 TraesCS7A01G257900 chr4A 618793530 618794690 1160 True 1247.0 1247 86.0820 956 2116 1 chr4A.!!$R2 1160
10 TraesCS7A01G257900 chr1A 84819353 84820498 1145 False 1240.0 1240 86.2370 956 2100 1 chr1A.!!$F1 1144
11 TraesCS7A01G257900 chrUn 55650015 55650540 525 True 512.0 512 84.4040 2110 2648 1 chrUn.!!$R1 538

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
33 34 1.20283 TCACATTTACTGCACCCGGTT 60.203 47.619 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 2816 0.597637 CCGGGCTGTACGAATAGCAG 60.598 60.0 0.0 0.0 41.36 4.24 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
33 34 1.202830 TCACATTTACTGCACCCGGTT 60.203 47.619 0.00 0.00 0.00 4.44
255 258 5.278266 CGTACTCTTTCAGAGGATGATCTCC 60.278 48.000 5.77 0.00 43.47 3.71
737 1415 4.723789 AGGTTGATCATGGTCTAGGTGATT 59.276 41.667 7.64 0.00 33.03 2.57
919 1916 9.755064 CTCTTTGACATTATTATTCGTCGTTTT 57.245 29.630 0.00 0.00 0.00 2.43
954 1951 9.912634 TTAATTTTACTTCTTTCTCCATTGCAG 57.087 29.630 0.00 0.00 0.00 4.41
1117 2114 6.011893 AGCCTTAGAAACCCCTACATTAACTT 60.012 38.462 0.00 0.00 0.00 2.66
1127 2124 7.924541 ACCCCTACATTAACTTATTCTCAACA 58.075 34.615 0.00 0.00 0.00 3.33
1130 2127 9.838339 CCCTACATTAACTTATTCTCAACATCT 57.162 33.333 0.00 0.00 0.00 2.90
1172 2169 2.203280 TGTGCTTCCGGTTGGTGG 60.203 61.111 0.00 0.00 36.30 4.61
1215 2213 0.178975 TCCGCACAGGTTGGGAAAAT 60.179 50.000 0.00 0.00 40.70 1.82
1235 2233 7.809806 GGAAAATTTTGTTTCGATCTCAGATGT 59.190 33.333 8.47 0.00 38.21 3.06
1331 2329 2.163010 AGGCTGAATCAATTGAAGCGTG 59.837 45.455 19.67 8.90 34.66 5.34
1345 2343 3.191581 TGAAGCGTGTTTGAAAACCTCAA 59.808 39.130 3.59 0.00 42.48 3.02
1372 2370 1.485480 AGATGTCATCTGTGCTGGAGG 59.515 52.381 14.73 0.00 38.44 4.30
1532 2530 2.283298 GCATGAAGATTTGCTCGAGGA 58.717 47.619 15.58 9.02 35.95 3.71
1556 2554 2.851195 TGTGAAAGCTTCAGAGGAACC 58.149 47.619 0.00 0.00 41.01 3.62
1648 2646 0.674895 GCGCTCCAAGTCCAACTGAT 60.675 55.000 0.00 0.00 0.00 2.90
1725 2726 0.690762 ATAAGGCGGCCAATCGGTAT 59.309 50.000 23.09 5.76 33.28 2.73
1729 2730 1.370064 GCGGCCAATCGGTATACCT 59.630 57.895 19.68 0.00 33.28 3.08
1815 2816 4.188247 TGTGTACTGAAGGACTATGCAC 57.812 45.455 0.00 0.00 0.00 4.57
1846 2847 2.281484 GCCCGGCTTTCTGTGTGA 60.281 61.111 0.71 0.00 0.00 3.58
1861 2862 6.465439 TCTGTGTGATATGGATACTTCGTT 57.535 37.500 0.00 0.00 37.61 3.85
1888 2889 2.173356 TGCATGAGCTAGCTTGGGTAAT 59.827 45.455 20.42 3.64 42.74 1.89
1992 3019 6.995511 TGTATTTTTATGTACACTGCCCTC 57.004 37.500 0.00 0.00 0.00 4.30
2088 3119 6.909550 TTGGAGTAACATTTTATGTGCCTT 57.090 33.333 0.00 0.00 44.07 4.35
2163 3695 6.297694 CTCGTAAGGGTGTAGAGTGTATAC 57.702 45.833 0.00 0.00 38.47 1.47
2256 3790 3.585289 TGTGCCCCAGTTATACTCTTGAA 59.415 43.478 0.00 0.00 0.00 2.69
2260 3794 4.683671 GCCCCAGTTATACTCTTGAAGGTC 60.684 50.000 0.00 0.00 0.00 3.85
2269 3803 8.697292 GTTATACTCTTGAAGGTCTGGAGTATT 58.303 37.037 15.75 4.79 43.38 1.89
2271 3805 6.441088 ACTCTTGAAGGTCTGGAGTATTTT 57.559 37.500 0.00 0.00 35.79 1.82
2272 3806 6.234177 ACTCTTGAAGGTCTGGAGTATTTTG 58.766 40.000 0.00 0.00 35.79 2.44
2274 3808 7.016268 ACTCTTGAAGGTCTGGAGTATTTTGTA 59.984 37.037 0.00 0.00 35.79 2.41
2275 3809 7.918076 TCTTGAAGGTCTGGAGTATTTTGTAT 58.082 34.615 0.00 0.00 0.00 2.29
2276 3810 7.824289 TCTTGAAGGTCTGGAGTATTTTGTATG 59.176 37.037 0.00 0.00 0.00 2.39
2277 3811 6.414732 TGAAGGTCTGGAGTATTTTGTATGG 58.585 40.000 0.00 0.00 0.00 2.74
2278 3812 6.012858 TGAAGGTCTGGAGTATTTTGTATGGT 60.013 38.462 0.00 0.00 0.00 3.55
2358 3909 5.992217 CCAGTTTATACTCTTGAGGGTATGC 59.008 44.000 12.68 4.55 30.26 3.14
2368 4030 6.151312 ACTCTTGAGGGTATGCAGTATATACG 59.849 42.308 7.23 4.16 32.96 3.06
2440 4107 0.163788 GCGGACAATATTCGCCATCG 59.836 55.000 8.41 0.00 43.17 3.84
2518 4185 2.159382 TCCCATTTTGGCTCGAACTTC 58.841 47.619 0.00 0.00 35.79 3.01
2642 4309 0.889638 TCTAGCCTGATACGCCTCCG 60.890 60.000 0.00 0.00 41.14 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.039480 GGCATGCTGGATATCCTCTTGA 59.961 50.000 22.35 0.84 36.82 3.02
480 592 7.174946 TCCATTTTCTTTCGCTTCTGTAGAAAT 59.825 33.333 0.00 0.00 35.48 2.17
598 713 6.653740 CGTTTAGAGTATCCACCTTCCTTTTT 59.346 38.462 0.00 0.00 33.66 1.94
759 1437 6.163135 AGACCTAGCTTGATACACCATAAC 57.837 41.667 0.00 0.00 0.00 1.89
862 1859 7.439108 AGAGCTGTATAAATCTACCCTGTTT 57.561 36.000 0.00 0.00 0.00 2.83
954 1951 0.984995 AAGCTCCTTCTGTACCACCC 59.015 55.000 0.00 0.00 0.00 4.61
1101 2098 8.387813 TGTTGAGAATAAGTTAATGTAGGGGTT 58.612 33.333 0.00 0.00 0.00 4.11
1117 2114 8.634335 TGGAAAATGTCAAGATGTTGAGAATA 57.366 30.769 5.37 0.00 43.55 1.75
1127 2124 3.771216 ACTGCCTGGAAAATGTCAAGAT 58.229 40.909 0.00 0.00 26.66 2.40
1130 2127 2.293122 CGAACTGCCTGGAAAATGTCAA 59.707 45.455 0.00 0.00 0.00 3.18
1172 2169 1.804372 CGGCAATCTGAGGAGCAGTAC 60.804 57.143 0.00 0.00 45.14 2.73
1215 2213 6.128553 GCACTACATCTGAGATCGAAACAAAA 60.129 38.462 0.00 0.00 0.00 2.44
1331 2329 4.096382 TCTCTGCTGTTGAGGTTTTCAAAC 59.904 41.667 0.00 0.00 46.85 2.93
1345 2343 2.677325 GCACAGATGACATCTCTGCTGT 60.677 50.000 28.44 16.62 44.63 4.40
1372 2370 2.677337 GCTCCTTCTTCTCAGCATGTTC 59.323 50.000 0.00 0.00 37.40 3.18
1532 2530 5.649831 GGTTCCTCTGAAGCTTTCACATTAT 59.350 40.000 0.00 0.00 43.90 1.28
1556 2554 1.831736 TCTTCCCTTTAAGAGCCTCCG 59.168 52.381 0.00 0.00 31.85 4.63
1725 2726 5.702209 GTGGGAAAACACGAGAAAATAGGTA 59.298 40.000 0.00 0.00 0.00 3.08
1729 2730 5.427036 GTGTGGGAAAACACGAGAAAATA 57.573 39.130 0.00 0.00 44.21 1.40
1815 2816 0.597637 CCGGGCTGTACGAATAGCAG 60.598 60.000 0.00 0.00 41.36 4.24
1846 2847 8.939929 CATGCAATTAGAACGAAGTATCCATAT 58.060 33.333 0.00 0.00 45.00 1.78
1861 2862 4.132336 CCAAGCTAGCTCATGCAATTAGA 58.868 43.478 19.65 0.00 42.74 2.10
1911 2916 9.019656 TGAAATAAAGTAATAAGCCTTCAAGCA 57.980 29.630 0.00 0.00 34.23 3.91
1970 2996 7.120726 ACAAGAGGGCAGTGTACATAAAAATAC 59.879 37.037 0.00 0.00 0.00 1.89
1992 3019 5.700832 TCATGAGCTTAAACTGGTGTACAAG 59.299 40.000 0.00 0.00 0.00 3.16
2131 3663 8.267894 ACTCTACACCCTTACGAGTATAAACTA 58.732 37.037 0.00 0.00 35.56 2.24
2256 3790 6.388619 AACCATACAAAATACTCCAGACCT 57.611 37.500 0.00 0.00 0.00 3.85
2292 3843 9.570468 ACTCCAACGATCTATGAGTATAAACTA 57.430 33.333 0.00 0.00 35.56 2.24
2440 4107 4.762251 GGTGCATACAGGATAATTTCTCCC 59.238 45.833 0.00 0.00 32.89 4.30
2562 4229 3.176924 TCAAGCAAGGAGACCTAGAGT 57.823 47.619 0.00 0.00 31.13 3.24
2564 4231 4.096681 TCATTCAAGCAAGGAGACCTAGA 58.903 43.478 0.00 0.00 31.13 2.43


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

AutoCloner maintained by Alex Coulton.