Multiple sequence alignment - TraesCS1A01G076300

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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 TraesCS1A01G076300 chr1A 100.000 2792 0 0 1 2792 59113978 59111187 0.000000e+00 5156.0
1 TraesCS1A01G076300 chr1D 94.750 2819 115 18 1 2792 60394841 60392029 0.000000e+00 4355.0
2 TraesCS1A01G076300 chr1B 93.680 2753 145 20 1 2739 97510072 97512809 0.000000e+00 4093.0
3 TraesCS1A01G076300 chr1B 97.297 37 1 0 2754 2790 97513347 97513383 2.320000e-06 63.9
4 TraesCS1A01G076300 chr3B 92.727 55 3 1 409 462 782658591 782658645 8.290000e-11 78.7
5 TraesCS1A01G076300 chr3B 77.206 136 22 4 419 545 744632341 744632476 1.390000e-08 71.3
6 TraesCS1A01G076300 chr3B 77.206 136 22 4 419 545 744641487 744641622 1.390000e-08 71.3
7 TraesCS1A01G076300 chr4D 91.071 56 5 0 585 640 468707611 468707666 2.980000e-10 76.8
8 TraesCS1A01G076300 chr2B 95.745 47 1 1 415 460 73357661 73357615 1.070000e-09 75.0
9 TraesCS1A01G076300 chr4B 89.286 56 6 0 585 640 588442947 588443002 1.390000e-08 71.3
10 TraesCS1A01G076300 chr5D 90.196 51 5 0 585 635 216150659 216150609 1.790000e-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 TraesCS1A01G076300 chr1A 59111187 59113978 2791 True 5156.00 5156 100.0000 1 2792 1 chr1A.!!$R1 2791
1 TraesCS1A01G076300 chr1D 60392029 60394841 2812 True 4355.00 4355 94.7500 1 2792 1 chr1D.!!$R1 2791
2 TraesCS1A01G076300 chr1B 97510072 97513383 3311 False 2078.45 4093 95.4885 1 2790 2 chr1B.!!$F1 2789

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
129 131 0.465460 GGTTGGGCAATCTATCGGCA 60.465 55.000 0.0 0.0 0.00 5.69 F
855 861 1.001641 GGCCTCAGGTGAGCAACAT 60.002 57.895 0.0 0.0 40.75 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1800 0.957362 ACCGGCTTATAGGCTACGAC 59.043 55.0 0.0 0.0 38.85 4.34 R
2681 2713 0.179073 AGCCGTCCATTCCTCATTCG 60.179 55.0 0.0 0.0 0.00 3.34 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
23 24 6.688637 TTGAAGCTATTCCTTGATCATGTG 57.311 37.500 0.00 0.00 34.28 3.21
129 131 0.465460 GGTTGGGCAATCTATCGGCA 60.465 55.000 0.00 0.00 0.00 5.69
156 158 4.091800 CGAATGCAATTTTGGATGGACAAC 59.908 41.667 0.00 0.00 39.28 3.32
214 216 2.567169 TCCAAACGGAGTCACTGATGAT 59.433 45.455 0.00 0.00 45.00 2.45
269 271 5.013287 ACCGATCTAGTAGCTCTGAGGAATA 59.987 44.000 6.83 0.00 0.00 1.75
417 419 5.243283 GCTGATCCAATCATGCTAATTCCTT 59.757 40.000 0.00 0.00 38.85 3.36
744 748 2.710902 GCCAAGCTAAAAGGGGCCG 61.711 63.158 0.00 0.00 38.70 6.13
855 861 1.001641 GGCCTCAGGTGAGCAACAT 60.002 57.895 0.00 0.00 40.75 2.71
871 877 2.943690 CAACATGGAGATGAGCCTTCTG 59.056 50.000 0.00 0.00 33.36 3.02
885 891 4.017808 AGCCTTCTGTACCACTAGTAGTG 58.982 47.826 21.39 21.39 45.53 2.74
958 964 1.009829 CAGGCAAGATCTAACGCACC 58.990 55.000 12.27 1.93 0.00 5.01
987 993 2.044492 TCCTTTCCTCCTCTCAAGGCTA 59.956 50.000 0.00 0.00 43.02 3.93
1003 1009 5.591472 TCAAGGCTATTGTTCTTCATGATGG 59.409 40.000 8.60 0.00 0.00 3.51
1213 1221 6.371809 TTTCACAACAACAGAAGTATGTCC 57.628 37.500 0.00 0.00 31.50 4.02
1230 1238 8.644374 AGTATGTCCCAGAGATTAAGATAGTC 57.356 38.462 0.00 0.00 0.00 2.59
1376 1385 3.536956 TGCTAGTTCTGTATTTCCCCG 57.463 47.619 0.00 0.00 0.00 5.73
1432 1441 8.102676 TGGATCTTAACTGATGAGTTCATGAAA 58.897 33.333 10.35 0.00 41.75 2.69
1610 1619 3.611766 AAGAGTGTACCATGCACCTAC 57.388 47.619 0.00 0.00 37.56 3.18
1628 1637 6.456449 GCACCTACCGTTTTGATGTTACTATG 60.456 42.308 0.00 0.00 0.00 2.23
1706 1721 2.378208 TCCAGGATCATCACCCACAAAA 59.622 45.455 0.00 0.00 0.00 2.44
1734 1749 7.064016 GCAGTAGTGAACTTCTTAAAGGATGAG 59.936 40.741 0.42 0.00 35.76 2.90
1853 1868 4.140543 TCCCTAAACTCTCCCATATGCCTA 60.141 45.833 0.00 0.00 0.00 3.93
2204 2219 5.076182 TCATTTGAATATGGGTGTGTGTGT 58.924 37.500 0.00 0.00 0.00 3.72
2205 2220 4.844998 TTTGAATATGGGTGTGTGTGTG 57.155 40.909 0.00 0.00 0.00 3.82
2282 2297 4.860802 ATTCTTGGGGTGATCATGTGTA 57.139 40.909 0.00 0.00 0.00 2.90
2289 2304 3.347216 GGGTGATCATGTGTAAGCTTGT 58.653 45.455 9.86 0.00 0.00 3.16
2290 2305 4.513442 GGGTGATCATGTGTAAGCTTGTA 58.487 43.478 9.86 0.00 0.00 2.41
2291 2306 4.332819 GGGTGATCATGTGTAAGCTTGTAC 59.667 45.833 9.86 8.54 0.00 2.90
2331 2348 1.454479 GGATGTGTGCATGGGGAGG 60.454 63.158 0.00 0.00 35.07 4.30
2377 2394 4.371624 TGTTTATCAGGGCATATCAGGG 57.628 45.455 0.00 0.00 0.00 4.45
2427 2444 4.526438 ATCTTCTCCGGGGAAATCATTT 57.474 40.909 19.46 0.00 0.00 2.32
2428 2445 4.316025 TCTTCTCCGGGGAAATCATTTT 57.684 40.909 19.46 0.00 0.00 1.82
2429 2446 4.016444 TCTTCTCCGGGGAAATCATTTTG 58.984 43.478 19.46 3.62 0.00 2.44
2462 2484 3.016736 GCTTATACCTGCAGGCTTTTCA 58.983 45.455 33.06 11.18 39.32 2.69
2614 2637 7.392393 TCATGCAATCTGATATGGTATCCAAAG 59.608 37.037 0.00 0.00 36.95 2.77
2638 2662 1.737793 CAGGGACCGCTATTTTGTCAC 59.262 52.381 0.00 0.00 32.53 3.67
2650 2681 6.343924 CGCTATTTTGTCACGTTCTCAAAAAC 60.344 38.462 18.98 13.33 41.87 2.43
2661 2692 6.090088 CACGTTCTCAAAAACAAATTCCACAA 59.910 34.615 0.00 0.00 0.00 3.33
2681 2713 7.279313 TCCACAATAGTTAAAATCTAAGCCGTC 59.721 37.037 0.00 0.00 0.00 4.79
2725 2757 3.231818 TGGTCTTCTTCTTCCTCGAACT 58.768 45.455 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.836365 TCGCCACATGATCAAGGAATA 57.164 42.857 14.37 0.00 0.00 1.75
43 44 4.758165 GGACCACCTTTTCTTCGAATGTTA 59.242 41.667 0.00 0.00 0.00 2.41
114 115 0.603975 GGACTGCCGATAGATTGCCC 60.604 60.000 0.00 0.00 39.76 5.36
129 131 3.119029 CCATCCAAAATTGCATTCGGACT 60.119 43.478 0.00 0.00 29.66 3.85
156 158 3.548818 CGAAGGTGAAGTTCTTTGCTTGG 60.549 47.826 4.17 0.00 0.00 3.61
214 216 1.969208 TCCTCGGAGCTACTAGATCGA 59.031 52.381 0.00 0.00 29.85 3.59
318 320 8.154856 ACGGTATTACTAATGTTATCAATGGCT 58.845 33.333 0.00 0.00 0.00 4.75
417 419 9.209048 ACGTATTAGGCCTATATATTTGGATGA 57.791 33.333 14.74 0.00 0.00 2.92
504 506 9.743057 TTTGTATGTGAAAGGAGTTTGTAAATG 57.257 29.630 0.00 0.00 0.00 2.32
534 536 4.382291 TGCATGTTACAGAAGTTACCGTT 58.618 39.130 0.00 0.00 0.00 4.44
623 627 1.276622 AGTGTACACCCTCCATCCAC 58.723 55.000 22.28 0.00 0.00 4.02
744 748 2.273449 CTGGAGGTGGGGACATGC 59.727 66.667 0.00 0.00 46.14 4.06
855 861 2.111384 GGTACAGAAGGCTCATCTCCA 58.889 52.381 0.00 0.00 0.00 3.86
885 891 6.711645 AGATTCTTCGGAGATGTAGTAGTACC 59.288 42.308 0.00 0.00 35.04 3.34
958 964 4.080129 TGAGAGGAGGAAAGGAAATGGATG 60.080 45.833 0.00 0.00 0.00 3.51
987 993 4.205587 GAGGCTCCATCATGAAGAACAAT 58.794 43.478 2.15 0.00 0.00 2.71
1131 1139 8.391106 GTTGACAAAGTTATACATAGGCAAGAG 58.609 37.037 0.00 0.00 0.00 2.85
1213 1221 6.647334 TCAGCTGACTATCTTAATCTCTGG 57.353 41.667 13.74 0.00 0.00 3.86
1230 1238 7.130917 GCTGATACAACATTTATCTTCAGCTG 58.869 38.462 7.63 7.63 46.94 4.24
1376 1385 7.689446 AGAAAGATAAGGGTTAAACAGAAGC 57.311 36.000 0.00 0.00 0.00 3.86
1432 1441 4.271661 TGCACATGTTACATCATGGTCAT 58.728 39.130 0.00 0.00 46.39 3.06
1734 1749 4.638421 TCATGGATCGTTTTGGTGGTATTC 59.362 41.667 0.00 0.00 0.00 1.75
1785 1800 0.957362 ACCGGCTTATAGGCTACGAC 59.043 55.000 0.00 0.00 38.85 4.34
1853 1868 7.068716 GGAGTGGCCAGAAAATGATTTAACTAT 59.931 37.037 5.11 0.00 36.34 2.12
2089 2104 8.353423 AGTAGCACTCACATGGAAATAAAAAT 57.647 30.769 0.00 0.00 0.00 1.82
2168 2183 4.888038 TTCAAATGAGAGGCGATTGATG 57.112 40.909 0.00 0.00 30.81 3.07
2282 2297 6.115446 ACACACATGCATATAGTACAAGCTT 58.885 36.000 0.00 0.00 0.00 3.74
2289 2304 5.622346 TGGGAACACACATGCATATAGTA 57.378 39.130 0.00 0.00 33.40 1.82
2290 2305 4.502105 TGGGAACACACATGCATATAGT 57.498 40.909 0.00 0.00 33.40 2.12
2331 2348 3.503748 ACAAAAGATAACCTGCACTCTGC 59.496 43.478 0.00 0.00 45.29 4.26
2377 2394 4.442706 AGCCTACATATATATGTTGCGCC 58.557 43.478 28.62 17.77 43.99 6.53
2443 2465 5.951747 AGATTTGAAAAGCCTGCAGGTATAA 59.048 36.000 32.81 17.22 37.57 0.98
2614 2637 2.817844 ACAAAATAGCGGTCCCTGAAAC 59.182 45.455 0.00 0.00 0.00 2.78
2638 2662 6.639671 TTGTGGAATTTGTTTTTGAGAACG 57.360 33.333 0.00 0.00 32.18 3.95
2661 2692 7.924412 TCATTCGACGGCTTAGATTTTAACTAT 59.076 33.333 0.00 0.00 0.00 2.12
2676 2708 0.179084 TCCATTCCTCATTCGACGGC 60.179 55.000 0.00 0.00 0.00 5.68
2681 2713 0.179073 AGCCGTCCATTCCTCATTCG 60.179 55.000 0.00 0.00 0.00 3.34
2725 2757 2.874664 CGGACGTGGGGAGGAAACA 61.875 63.158 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.