Multiple sequence alignment - TraesCS6B01G018000

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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 TraesCS6B01G018000 chr6B 100.000 4007 0 0 1 4007 11410227 11406221 0.000000e+00 7400.0
1 TraesCS6B01G018000 chr6B 88.777 1595 138 12 175 1730 11515353 11513761 0.000000e+00 1916.0
2 TraesCS6B01G018000 chr6B 87.713 1172 95 20 2397 3550 11512743 11511603 0.000000e+00 1321.0
3 TraesCS6B01G018000 chr6B 98.292 527 8 1 2463 2989 31996567 31997092 0.000000e+00 922.0
4 TraesCS6B01G018000 chr6B 89.823 226 16 5 3785 4007 11341041 11340820 2.360000e-72 283.0
5 TraesCS6B01G018000 chr6B 89.823 226 16 5 3785 4007 11357170 11356949 2.360000e-72 283.0
6 TraesCS6B01G018000 chr6B 88.546 227 17 7 3785 4007 11380343 11380122 2.370000e-67 267.0
7 TraesCS6B01G018000 chr6B 88.957 163 18 0 2235 2397 11512955 11512793 6.790000e-48 202.0
8 TraesCS6B01G018000 chr6D 93.626 2275 86 15 1 2239 6110790 6108539 0.000000e+00 3343.0
9 TraesCS6B01G018000 chr6D 94.295 1788 68 7 2235 4007 6108502 6106734 0.000000e+00 2706.0
10 TraesCS6B01G018000 chr6D 86.552 2268 223 36 26 2241 6250224 6247987 0.000000e+00 2423.0
11 TraesCS6B01G018000 chr6D 89.140 1197 100 20 2397 3580 6247704 6246525 0.000000e+00 1463.0
12 TraesCS6B01G018000 chr6D 88.957 163 18 0 2235 2397 6247916 6247754 6.790000e-48 202.0
13 TraesCS6B01G018000 chr6D 78.689 244 47 3 1441 1684 12643005 12642767 1.490000e-34 158.0
14 TraesCS6B01G018000 chr6D 89.109 101 9 2 3688 3786 6246535 6246435 1.510000e-24 124.0
15 TraesCS6B01G018000 chr6A 92.619 2276 122 12 1 2239 5468332 5466066 0.000000e+00 3230.0
16 TraesCS6B01G018000 chr6A 90.211 2278 106 32 1 2239 5494640 5492441 0.000000e+00 2863.0
17 TraesCS6B01G018000 chr6A 94.482 1486 67 4 2235 3707 5466029 5464546 0.000000e+00 2276.0
18 TraesCS6B01G018000 chr6A 88.115 1767 126 32 4 1726 5544342 5542616 0.000000e+00 2023.0
19 TraesCS6B01G018000 chr6A 93.460 948 46 3 2567 3502 5492129 5491186 0.000000e+00 1393.0
20 TraesCS6B01G018000 chr6A 89.194 1055 86 13 2447 3482 5542148 5541103 0.000000e+00 1291.0
21 TraesCS6B01G018000 chr6A 90.643 513 43 3 3499 4007 5489425 5488914 0.000000e+00 676.0
22 TraesCS6B01G018000 chr6A 90.287 453 39 4 1775 2224 5542602 5542152 4.460000e-164 588.0
23 TraesCS6B01G018000 chr6A 95.730 281 12 0 2235 2515 5492404 5492124 1.700000e-123 453.0
24 TraesCS6B01G018000 chr6A 90.879 307 25 2 3704 4007 5445293 5444987 3.730000e-110 409.0
25 TraesCS6B01G018000 chr6A 77.007 274 55 6 1441 1711 13983797 13983529 2.490000e-32 150.0
26 TraesCS6B01G018000 chr6A 89.899 99 8 2 3687 3784 5541054 5540957 4.200000e-25 126.0
27 TraesCS6B01G018000 chr3B 88.202 178 11 7 3835 4004 508219893 508219718 1.890000e-48 204.0
28 TraesCS6B01G018000 chr2A 87.845 181 12 7 3835 4007 27534162 27533984 1.890000e-48 204.0
29 TraesCS6B01G018000 chr1D 86.224 196 17 7 3817 4004 30289121 30289314 1.890000e-48 204.0
30 TraesCS6B01G018000 chrUn 81.818 132 24 0 1441 1572 410434832 410434963 1.180000e-20 111.0
31 TraesCS6B01G018000 chrUn 81.818 132 24 0 1441 1572 451882298 451882429 1.180000e-20 111.0
32 TraesCS6B01G018000 chr7D 94.737 38 2 0 482 519 42685800 42685837 4.320000e-05 60.2
33 TraesCS6B01G018000 chr7B 94.444 36 2 0 482 517 725520332 725520367 5.590000e-04 56.5
34 TraesCS6B01G018000 chr4B 96.970 33 1 0 482 514 3866742 3866774 5.590000e-04 56.5


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 TraesCS6B01G018000 chr6B 11406221 11410227 4006 True 7400.000000 7400 100.000000 1 4007 1 chr6B.!!$R4 4006
1 TraesCS6B01G018000 chr6B 11511603 11515353 3750 True 1146.333333 1916 88.482333 175 3550 3 chr6B.!!$R5 3375
2 TraesCS6B01G018000 chr6B 31996567 31997092 525 False 922.000000 922 98.292000 2463 2989 1 chr6B.!!$F1 526
3 TraesCS6B01G018000 chr6D 6106734 6110790 4056 True 3024.500000 3343 93.960500 1 4007 2 chr6D.!!$R2 4006
4 TraesCS6B01G018000 chr6D 6246435 6250224 3789 True 1053.000000 2423 88.439500 26 3786 4 chr6D.!!$R3 3760
5 TraesCS6B01G018000 chr6A 5464546 5468332 3786 True 2753.000000 3230 93.550500 1 3707 2 chr6A.!!$R3 3706
6 TraesCS6B01G018000 chr6A 5488914 5494640 5726 True 1346.250000 2863 92.511000 1 4007 4 chr6A.!!$R4 4006
7 TraesCS6B01G018000 chr6A 5540957 5544342 3385 True 1007.000000 2023 89.373750 4 3784 4 chr6A.!!$R5 3780


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
425 437 2.129823 TTGAGGTATAGCGCGCTAAC 57.870 50.0 40.9 33.87 31.73 2.34 F
1887 2215 0.741915 TTTCACCCGAAACTGTTGGC 59.258 50.0 0.0 0.00 36.19 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 2269 0.343372 ATTAGGGTGGCAGAGGGAGA 59.657 55.000 0.0 0.0 0.0 3.71 R
3753 6064 1.525077 GCACAACCTTCGACCACCA 60.525 57.895 0.0 0.0 0.0 4.17 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
75 76 6.085416 ACATTTTGACCCTTTAATTACCCCA 58.915 36.000 0.00 0.00 0.00 4.96
294 300 7.935520 ACATGCATATGTACCTCTCTATATCG 58.064 38.462 0.00 0.00 45.45 2.92
336 342 9.608617 GATATTGTGATTCTATGAATGCTTGTG 57.391 33.333 0.00 0.00 0.00 3.33
342 348 6.207221 TGATTCTATGAATGCTTGTGTGTTGT 59.793 34.615 0.00 0.00 0.00 3.32
425 437 2.129823 TTGAGGTATAGCGCGCTAAC 57.870 50.000 40.90 33.87 31.73 2.34
625 637 4.963318 TTAGCATGGATAGTCAAGGGAG 57.037 45.455 0.00 0.00 0.00 4.30
649 662 8.843885 AGTTTTTAGGGTGAACTTAGTATGAC 57.156 34.615 0.00 0.00 29.81 3.06
656 669 5.655532 GGGTGAACTTAGTATGACAGACCTA 59.344 44.000 0.00 0.00 0.00 3.08
675 688 9.301153 CAGACCTAAAATAAATAAAGCGCATTT 57.699 29.630 11.47 9.88 34.72 2.32
692 714 7.412853 AGCGCATTTTTGTGATATCTTTCTAG 58.587 34.615 11.47 0.00 0.00 2.43
923 951 4.602340 ATGGTACCCTAGTAATCAAGCG 57.398 45.455 10.07 0.00 0.00 4.68
944 973 5.127031 AGCGCCCATTTATTGATGTTTTACT 59.873 36.000 2.29 0.00 0.00 2.24
1124 1153 6.183360 GGAGCAAGAGATATTAACCAAACCAC 60.183 42.308 0.00 0.00 0.00 4.16
1258 1290 5.940192 TGGCATCGACATAAATGGTTATC 57.060 39.130 0.00 0.00 0.00 1.75
1356 1388 7.384387 GGTTATCCTCACGGTAATTCTAATGAC 59.616 40.741 0.00 0.00 0.00 3.06
1387 1419 2.634600 GTAATGGTAATGGTGGTCGCA 58.365 47.619 0.00 0.00 0.00 5.10
1388 1420 2.208132 AATGGTAATGGTGGTCGCAA 57.792 45.000 0.00 0.00 0.00 4.85
1574 1678 2.488545 GAGATGGTGTAGTGACAGACGT 59.511 50.000 0.00 0.00 35.82 4.34
1577 1681 2.235891 TGGTGTAGTGACAGACGTGAT 58.764 47.619 0.00 0.00 35.82 3.06
1580 1684 3.119459 GGTGTAGTGACAGACGTGATGAT 60.119 47.826 0.00 0.00 35.82 2.45
1617 1721 8.832735 ACTATGGAGGAATTAGAAAACCTTACA 58.167 33.333 0.00 0.00 32.53 2.41
1635 1739 3.207474 ACAAAGCACTAGGTACGTACG 57.793 47.619 18.98 15.01 0.00 3.67
1677 1781 5.177327 GCATGGATGTTTTCGTTTCATTGTT 59.823 36.000 0.00 0.00 0.00 2.83
1683 1787 7.011016 GGATGTTTTCGTTTCATTGTTCCTTTT 59.989 33.333 0.00 0.00 0.00 2.27
1726 1830 1.332144 CCCTTGCACCCCATTCCATG 61.332 60.000 0.00 0.00 0.00 3.66
1812 2140 4.840271 CCCCATCTTACCGTTTAGTTTCT 58.160 43.478 0.00 0.00 0.00 2.52
1834 2162 4.838904 AGGGGAGTAACATAAAGACCAC 57.161 45.455 0.00 0.00 0.00 4.16
1849 2177 2.909006 AGACCACTCACATCCATGTTCT 59.091 45.455 0.00 0.00 39.39 3.01
1887 2215 0.741915 TTTCACCCGAAACTGTTGGC 59.258 50.000 0.00 0.00 36.19 4.52
1941 2269 3.434167 GCCACCCTCATGATCACTGTTAT 60.434 47.826 0.00 0.00 0.00 1.89
1981 2309 3.303049 TCTGAGCTCATCATCCTTGCTA 58.697 45.455 18.63 0.00 37.28 3.49
1987 2316 2.171237 CTCATCATCCTTGCTACCACCA 59.829 50.000 0.00 0.00 0.00 4.17
2052 2383 1.334869 GTGTGTGTCTTTCCTTGGCAG 59.665 52.381 0.00 0.00 0.00 4.85
2160 2492 5.804639 ACAACTATGCAGGTAGTCAAATGA 58.195 37.500 0.54 0.00 33.92 2.57
2301 2712 1.790387 GTCCGTGTGCAGCAGATTC 59.210 57.895 0.00 0.00 0.00 2.52
2303 2714 1.376424 CCGTGTGCAGCAGATTCCT 60.376 57.895 0.00 0.00 0.00 3.36
2452 2913 3.257375 GCTCCAAATAACGGAAAAAGGGT 59.743 43.478 0.00 0.00 30.33 4.34
2526 2988 6.114187 TCTGCTCCTTAATCTGAAACTTGA 57.886 37.500 0.00 0.00 0.00 3.02
2574 3093 3.386768 TTCAGTGTGTAGCCTGAACTC 57.613 47.619 0.00 0.00 41.47 3.01
2852 3378 4.330250 AGTCCAAACATGAAGATGGTGAG 58.670 43.478 0.00 0.00 33.39 3.51
3171 3712 4.993584 ACAACACTCTCTTATCTTGCACAG 59.006 41.667 0.00 0.00 0.00 3.66
3331 3872 0.317160 TGCAACACCCGTGAGAGTAG 59.683 55.000 0.96 0.00 0.00 2.57
3609 5918 0.970937 TACCGGAAGCTGAGGAGTGG 60.971 60.000 9.46 0.00 0.00 4.00
3621 5930 1.342174 GAGGAGTGGTGTACCGACAAA 59.658 52.381 0.00 0.00 37.31 2.83
3674 5983 6.768381 GGGAGAATTCTAAAAGTCATACAGGG 59.232 42.308 8.25 0.00 31.94 4.45
3698 6007 8.358895 GGGAACTACACCTAGAATATTGTCTAC 58.641 40.741 0.00 0.00 0.00 2.59
3780 6091 2.811431 TCGAAGGTTGTGCATTTAGTGG 59.189 45.455 0.00 0.00 0.00 4.00
3808 6119 2.697431 TGGTTATTTCAGTTGCGCAC 57.303 45.000 11.12 5.61 0.00 5.34
3915 6229 2.953821 CGCACAAAGGGCACGATT 59.046 55.556 0.00 0.00 0.00 3.34
3925 6239 0.383949 GGGCACGATTGTTGTGTGTT 59.616 50.000 0.00 0.00 39.53 3.32
3928 6242 1.064803 GCACGATTGTTGTGTGTTCCA 59.935 47.619 0.00 0.00 39.53 3.53
3963 6278 3.037833 CAGCTGCACGACTTCGCA 61.038 61.111 0.00 0.00 44.43 5.10
3964 6279 2.047844 AGCTGCACGACTTCGCAT 60.048 55.556 1.02 0.00 44.43 4.73
4004 6319 2.700773 GGGGTTGTTGCGAGCATCC 61.701 63.158 0.00 0.16 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 7.817478 GGGTAATTAAAGGGTCAAAATGTTCTG 59.183 37.037 0.00 0.00 0.00 3.02
75 76 8.833231 AGATAATTTAGCTTGCGTATACACAT 57.167 30.769 3.32 0.00 0.00 3.21
329 335 4.717233 ATCTTTCAACAACACACAAGCA 57.283 36.364 0.00 0.00 0.00 3.91
336 342 9.959749 TGGATAACTAAAATCTTTCAACAACAC 57.040 29.630 0.00 0.00 0.00 3.32
342 348 8.801299 TGCACATGGATAACTAAAATCTTTCAA 58.199 29.630 0.00 0.00 0.00 2.69
400 412 2.599848 GCGCGCTATACCTCAATTTGTG 60.600 50.000 26.67 0.00 0.00 3.33
425 437 5.762218 AGCCATTTAGCACTATTTAGCTCAG 59.238 40.000 0.00 0.00 42.05 3.35
606 618 2.769209 ACTCCCTTGACTATCCATGCT 58.231 47.619 0.00 0.00 0.00 3.79
625 637 8.611654 TGTCATACTAAGTTCACCCTAAAAAC 57.388 34.615 0.00 0.00 0.00 2.43
649 662 8.856490 AATGCGCTTTATTTATTTTAGGTCTG 57.144 30.769 9.73 0.00 0.00 3.51
731 757 7.994425 TTCTCTTATATTGTTTGGCTTGTCA 57.006 32.000 0.00 0.00 0.00 3.58
736 762 9.657419 CCAAAAATTCTCTTATATTGTTTGGCT 57.343 29.630 0.00 0.00 36.95 4.75
787 813 3.636679 AGATGGCTACTGACTTGAGCTA 58.363 45.455 0.00 0.00 36.43 3.32
1124 1153 2.436646 CACCACCGCTTAGCCAGG 60.437 66.667 0.00 0.41 0.00 4.45
1258 1290 6.368243 GCACTGAGAGTACCATAATGATGATG 59.632 42.308 0.00 0.00 34.73 3.07
1387 1419 6.245408 TGCTTCCACTTGTTATAACTCCATT 58.755 36.000 16.33 0.00 0.00 3.16
1388 1420 5.815581 TGCTTCCACTTGTTATAACTCCAT 58.184 37.500 16.33 0.00 0.00 3.41
1435 1509 1.417517 AGCATCTCCACGCATTCCATA 59.582 47.619 0.00 0.00 0.00 2.74
1471 1548 1.737355 TTTTGAGGCTGCACTGCACC 61.737 55.000 0.00 7.04 33.79 5.01
1556 1633 2.235891 TCACGTCTGTCACTACACCAT 58.764 47.619 0.00 0.00 0.00 3.55
1574 1678 4.503123 CCATAGTTAGCCCACGAATCATCA 60.503 45.833 0.00 0.00 0.00 3.07
1577 1681 3.035363 TCCATAGTTAGCCCACGAATCA 58.965 45.455 0.00 0.00 0.00 2.57
1580 1684 1.760613 CCTCCATAGTTAGCCCACGAA 59.239 52.381 0.00 0.00 0.00 3.85
1617 1721 2.162681 ACCGTACGTACCTAGTGCTTT 58.837 47.619 19.67 0.00 0.00 3.51
1635 1739 5.474532 TCCATGCATGCAAATATAGAGAACC 59.525 40.000 26.68 0.00 0.00 3.62
1677 1781 9.913310 AGGAAAAATGGTGAAATTTTAAAAGGA 57.087 25.926 6.79 0.00 38.49 3.36
1683 1787 8.151596 GGGTACAGGAAAAATGGTGAAATTTTA 58.848 33.333 0.00 0.00 38.49 1.52
1726 1830 9.914131 AAAGGCTCTATACAAAAGATTTTTGTC 57.086 29.630 19.63 7.71 42.10 3.18
1812 2140 5.596763 AGTGGTCTTTATGTTACTCCCCTA 58.403 41.667 0.00 0.00 0.00 3.53
1834 2162 7.485913 CCGAATTAAAAAGAACATGGATGTGAG 59.514 37.037 0.00 0.00 41.61 3.51
1849 2177 6.370166 GGTGAAAATGCATCCCGAATTAAAAA 59.630 34.615 0.00 0.00 0.00 1.94
1887 2215 1.478105 GGCCCTTGTGAAGCAATTAGG 59.522 52.381 0.00 0.00 36.36 2.69
1941 2269 0.343372 ATTAGGGTGGCAGAGGGAGA 59.657 55.000 0.00 0.00 0.00 3.71
1987 2316 3.785859 ATCACAGCGACGGGGCAT 61.786 61.111 0.00 0.00 34.64 4.40
2230 2564 6.211587 ACATGTATTTGTAGTGCGTACCTA 57.788 37.500 0.00 0.00 0.00 3.08
2274 2685 1.529438 CTGCACACGGACGTTGTAAAT 59.471 47.619 0.00 0.00 0.00 1.40
2380 2791 7.112122 TCATGCTTGGAGAACAGTAAATGTAT 58.888 34.615 0.00 0.00 43.00 2.29
2452 2913 1.804151 GTTGTTCAGCGGTGCTCAATA 59.196 47.619 20.36 4.29 36.40 1.90
2574 3093 0.731417 CGAGCCCTGCATTCTGAAAG 59.269 55.000 0.00 0.00 0.00 2.62
2782 3308 4.154942 ACTCTTGGTGCAATCAATTTCCT 58.845 39.130 4.50 0.00 0.00 3.36
2852 3378 3.273434 TGCATCTTTGTCCATCACTAGC 58.727 45.455 0.00 0.00 0.00 3.42
3036 3563 9.423061 GAACCAAGATACTACAATTGCAAAATT 57.577 29.630 1.71 0.00 0.00 1.82
3149 3690 5.233225 TCTGTGCAAGATAAGAGAGTGTTG 58.767 41.667 0.00 0.00 0.00 3.33
3235 3776 3.055385 TCGCCTAAACCTATGTTGCTTCT 60.055 43.478 0.00 0.00 34.13 2.85
3331 3872 2.224784 AGGACGAACGGTTGCATTTTAC 59.775 45.455 0.00 0.00 0.00 2.01
3578 5887 6.056884 TCAGCTTCCGGTAAACTAAGAAAAA 58.943 36.000 0.00 0.00 0.00 1.94
3628 5937 7.726291 TCTCCCTGTTATACCATTTGTTTTGAA 59.274 33.333 0.00 0.00 0.00 2.69
3634 5943 7.643123 AGAATTCTCCCTGTTATACCATTTGT 58.357 34.615 0.88 0.00 0.00 2.83
3635 5944 9.627123 TTAGAATTCTCCCTGTTATACCATTTG 57.373 33.333 12.24 0.00 0.00 2.32
3674 5983 8.619546 ACGTAGACAATATTCTAGGTGTAGTTC 58.380 37.037 8.35 0.00 42.72 3.01
3698 6007 4.380841 TTTACACTATGAGGGCAGTACG 57.619 45.455 0.00 0.00 0.00 3.67
3753 6064 1.525077 GCACAACCTTCGACCACCA 60.525 57.895 0.00 0.00 0.00 4.17
3780 6091 7.462724 GCGCAACTGAAATAACCAACAATAATC 60.463 37.037 0.30 0.00 0.00 1.75
3833 6144 8.311836 TCTGAAGAAAAACTAACACCTATCGAT 58.688 33.333 2.16 2.16 0.00 3.59
3891 6205 1.103987 TGCCCTTTGTGCGCTAACAA 61.104 50.000 9.73 9.33 38.26 2.83
3903 6217 1.066908 CACACAACAATCGTGCCCTTT 59.933 47.619 0.00 0.00 37.93 3.11
3925 6239 4.037222 TGGCTCCTAACTATTCACATGGA 58.963 43.478 0.00 0.00 0.00 3.41
3928 6242 3.713764 AGCTGGCTCCTAACTATTCACAT 59.286 43.478 0.00 0.00 0.00 3.21
3977 6292 2.282887 AACAACCCCATCGTGCCC 60.283 61.111 0.00 0.00 0.00 5.36



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

AutoCloner maintained by Alex Coulton.