Multiple sequence alignment - TraesCS6A01G351400

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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 TraesCS6A01G351400 chr6A 100.000 2471 0 0 1 2471 583326538 583329008 0 4564
1 TraesCS6A01G351400 chr4D 95.202 2480 99 8 3 2471 393458513 393460983 0 3903
2 TraesCS6A01G351400 chr3B 95.087 2483 99 10 3 2471 361795833 361798306 0 3888
3 TraesCS6A01G351400 chr3B 94.762 1699 68 14 3 1690 389719865 389721553 0 2625
4 TraesCS6A01G351400 chr3D 95.079 2479 101 8 3 2471 359527461 359524994 0 3882
5 TraesCS6A01G351400 chr2B 94.919 2480 106 8 3 2471 728070265 728067795 0 3864
6 TraesCS6A01G351400 chr1D 94.879 2480 106 9 3 2471 251020569 251023038 0 3856
7 TraesCS6A01G351400 chr6B 94.675 2479 111 7 3 2471 587366774 587364307 0 3827
8 TraesCS6A01G351400 chr5D 95.554 1732 67 2 749 2471 565809433 565811163 0 2763
9 TraesCS6A01G351400 chr5D 94.282 1714 79 9 3 1705 557793958 557795663 0 2604
10 TraesCS6A01G351400 chr5D 95.223 963 44 2 1509 2471 557795523 557796483 0 1522
11 TraesCS6A01G351400 chr2D 93.991 1714 84 9 3 1705 621997773 621999478 0 2577
12 TraesCS6A01G351400 chr2D 95.742 963 40 1 1509 2471 621999338 622000299 0 1550


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 TraesCS6A01G351400 chr6A 583326538 583329008 2470 False 4564.0 4564 100.0000 1 2471 1 chr6A.!!$F1 2470
1 TraesCS6A01G351400 chr4D 393458513 393460983 2470 False 3903.0 3903 95.2020 3 2471 1 chr4D.!!$F1 2468
2 TraesCS6A01G351400 chr3B 361795833 361798306 2473 False 3888.0 3888 95.0870 3 2471 1 chr3B.!!$F1 2468
3 TraesCS6A01G351400 chr3B 389719865 389721553 1688 False 2625.0 2625 94.7620 3 1690 1 chr3B.!!$F2 1687
4 TraesCS6A01G351400 chr3D 359524994 359527461 2467 True 3882.0 3882 95.0790 3 2471 1 chr3D.!!$R1 2468
5 TraesCS6A01G351400 chr2B 728067795 728070265 2470 True 3864.0 3864 94.9190 3 2471 1 chr2B.!!$R1 2468
6 TraesCS6A01G351400 chr1D 251020569 251023038 2469 False 3856.0 3856 94.8790 3 2471 1 chr1D.!!$F1 2468
7 TraesCS6A01G351400 chr6B 587364307 587366774 2467 True 3827.0 3827 94.6750 3 2471 1 chr6B.!!$R1 2468
8 TraesCS6A01G351400 chr5D 565809433 565811163 1730 False 2763.0 2763 95.5540 749 2471 1 chr5D.!!$F1 1722
9 TraesCS6A01G351400 chr5D 557793958 557796483 2525 False 2063.0 2604 94.7525 3 2471 2 chr5D.!!$F2 2468
10 TraesCS6A01G351400 chr2D 621997773 622000299 2526 False 2063.5 2577 94.8665 3 2471 2 chr2D.!!$F1 2468

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
163 165 0.469331 ACCTCTTCTGGGTCGACACA 60.469 55.000 21.32 21.32 30.15 3.72 F
1017 1024 1.272648 CCCATGAGTGACAACCCCATT 60.273 52.381 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1407 0.526211 GGGTCTTGAACATTTCCCGC 59.474 55.0 0.0 0.0 0.0 6.13 R
1877 1950 1.813513 AAGTCTCTTGCAACCATCCG 58.186 50.0 0.0 0.0 0.0 4.18 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
156 158 2.900106 GCAGCCACCTCTTCTGGGT 61.900 63.158 0.00 0.00 40.24 4.51
161 163 1.185618 CCACCTCTTCTGGGTCGACA 61.186 60.000 18.91 0.00 34.44 4.35
163 165 0.469331 ACCTCTTCTGGGTCGACACA 60.469 55.000 21.32 21.32 30.15 3.72
170 172 2.099652 CTGGGTCGACACAGGCAAGA 62.100 60.000 35.35 5.72 43.48 3.02
201 204 4.154347 CTGCCGCACCCTCTCCTC 62.154 72.222 0.00 0.00 0.00 3.71
209 212 2.123077 CCCTCTCCTCCGAGCCAT 60.123 66.667 0.00 0.00 35.94 4.40
213 216 2.086251 CTCTCCTCCGAGCCATGAGC 62.086 65.000 0.00 0.00 44.25 4.26
221 224 3.382803 GAGCCATGAGCCAGCGTCT 62.383 63.158 0.00 0.00 45.47 4.18
245 248 1.668151 GGACGCTGAAGCTTCGGTT 60.668 57.895 30.91 20.73 39.84 4.44
402 407 4.576873 TGTTTTCACAATACACGACCATGT 59.423 37.500 0.00 0.00 36.56 3.21
407 412 4.688879 TCACAATACACGACCATGTTCTTC 59.311 41.667 0.00 0.00 33.85 2.87
519 524 2.582172 TGGTCAGGGTGATTCAATGGAT 59.418 45.455 0.00 0.00 0.00 3.41
576 581 2.746279 TGGTTGAACAAGTGGGACAT 57.254 45.000 0.00 0.00 44.52 3.06
668 673 8.801882 ATGACCGGAATTAGTTTATCAAAGAA 57.198 30.769 9.46 0.00 0.00 2.52
688 693 3.782889 AACAACTGAAGAACAAGTGGC 57.217 42.857 0.00 0.00 0.00 5.01
783 788 4.408921 TCGAAGGGAGTTATTGTCATGGAT 59.591 41.667 0.00 0.00 0.00 3.41
824 829 3.059800 GCGAGAAAGGTTAGTGTTGTCAC 60.060 47.826 0.00 0.00 44.15 3.67
828 833 6.128902 CGAGAAAGGTTAGTGTTGTCACATAC 60.129 42.308 1.36 0.00 46.01 2.39
899 904 9.129209 GATTTTTCTTTTCTTTAGGACATTCCG 57.871 33.333 0.00 0.00 42.75 4.30
920 926 3.254657 CGGGATGTGGCAAGTTTAGAAAA 59.745 43.478 0.00 0.00 0.00 2.29
1017 1024 1.272648 CCCATGAGTGACAACCCCATT 60.273 52.381 0.00 0.00 0.00 3.16
1042 1049 5.333566 ACCCCCAAGTCAAGAGAATTTTA 57.666 39.130 0.00 0.00 27.92 1.52
1112 1119 5.948162 ACATCCCTGATGATATTGGTAATGC 59.052 40.000 10.84 0.00 42.09 3.56
1140 1156 2.192263 GGTGAGGAGGATGAGGTTTCT 58.808 52.381 0.00 0.00 0.00 2.52
1389 1407 5.765182 ACAGTTATTTGTGAAGAAGGACCAG 59.235 40.000 0.00 0.00 0.00 4.00
1601 1674 6.757897 TTTGCTTTATCTATGTTGGAGTGG 57.242 37.500 0.00 0.00 0.00 4.00
1615 1688 6.469410 TGTTGGAGTGGACTATTTTATCGTT 58.531 36.000 0.00 0.00 0.00 3.85
1620 1693 8.916062 TGGAGTGGACTATTTTATCGTTGTATA 58.084 33.333 0.00 0.00 0.00 1.47
1760 1833 5.460419 GTCTGATAGTGACAACGATGATTCC 59.540 44.000 0.00 0.00 34.80 3.01
1877 1950 6.642950 CGAGGACATCAATTCTAAGTGGTATC 59.357 42.308 0.00 0.00 0.00 2.24
1907 1980 2.928731 GCAAGAGACTTTGAGGACTCCG 60.929 54.545 0.00 0.00 0.00 4.63
1940 2013 0.451628 CACAACTTCGCATGAGCACG 60.452 55.000 0.00 0.00 42.27 5.34
1941 2014 0.599991 ACAACTTCGCATGAGCACGA 60.600 50.000 0.00 0.00 42.27 4.35
1944 2017 1.225855 ACTTCGCATGAGCACGAAAA 58.774 45.000 0.00 0.00 46.52 2.29
2030 2103 6.376299 TGAGCATCTATGAAAGTCTTGCAATT 59.624 34.615 0.00 0.00 34.92 2.32
2036 2109 8.862325 TCTATGAAAGTCTTGCAATTTTCCTA 57.138 30.769 19.77 15.58 0.00 2.94
2071 2144 2.746362 GCAATGAGTCCAACAGAAGAGG 59.254 50.000 0.00 0.00 0.00 3.69
2087 2160 6.263168 ACAGAAGAGGTCAAAATCGTTTCAAT 59.737 34.615 0.00 0.00 0.00 2.57
2094 2167 5.333798 GGTCAAAATCGTTTCAATCACTCGA 60.334 40.000 0.00 0.00 35.14 4.04
2186 2259 3.311091 ACCTAAAAACCCCAACTTTCCC 58.689 45.455 0.00 0.00 0.00 3.97
2188 2261 3.712218 CCTAAAAACCCCAACTTTCCCAA 59.288 43.478 0.00 0.00 0.00 4.12
2234 2307 0.390735 GACGGGCGTATCCACACTTT 60.391 55.000 0.00 0.00 36.21 2.66
2357 2430 6.833342 AATGTTCTTGCAATTTGTGACTTC 57.167 33.333 0.00 0.00 0.00 3.01
2388 2461 0.611200 CACTTATGTGTCCGTGGGGA 59.389 55.000 0.62 0.00 39.24 4.81
2453 2526 9.677567 GCAATAAGTGTTGATGAAAGTTTCTTA 57.322 29.630 16.33 4.96 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.782341 AGAAATTGAGGGGAGGAGGATG 59.218 50.000 0.00 0.00 0.00 3.51
1 2 3.052329 GAGAAATTGAGGGGAGGAGGAT 58.948 50.000 0.00 0.00 0.00 3.24
12 14 3.212685 GGAGATGGGCAGAGAAATTGAG 58.787 50.000 0.00 0.00 0.00 3.02
13 15 2.577563 TGGAGATGGGCAGAGAAATTGA 59.422 45.455 0.00 0.00 0.00 2.57
75 77 0.181350 GAAAGGCCGACCCTCATCAT 59.819 55.000 0.00 0.00 45.62 2.45
141 143 2.266055 CGACCCAGAAGAGGTGGC 59.734 66.667 0.00 0.00 37.88 5.01
144 146 0.469331 TGTGTCGACCCAGAAGAGGT 60.469 55.000 14.12 0.00 41.50 3.85
156 158 0.320683 CCATGTCTTGCCTGTGTCGA 60.321 55.000 0.00 0.00 0.00 4.20
161 163 2.765969 CCCCCATGTCTTGCCTGT 59.234 61.111 0.00 0.00 0.00 4.00
196 199 2.420890 GCTCATGGCTCGGAGGAG 59.579 66.667 7.20 5.95 43.46 3.69
213 216 2.821366 GTCCATGGCAGACGCTGG 60.821 66.667 6.96 0.00 38.60 4.85
221 224 2.747460 GCTTCAGCGTCCATGGCA 60.747 61.111 6.96 0.00 0.00 4.92
293 296 0.319555 GTGCTGCACGTCTCTTGGTA 60.320 55.000 17.93 0.00 0.00 3.25
314 317 1.977854 TGCTCTTCCTTAGTGGCTGAA 59.022 47.619 0.00 0.00 35.26 3.02
358 363 6.713762 ACAAATCATCTTCAACAGAACCAA 57.286 33.333 0.00 0.00 34.16 3.67
359 364 6.713762 AACAAATCATCTTCAACAGAACCA 57.286 33.333 0.00 0.00 34.16 3.67
360 365 7.706179 TGAAAACAAATCATCTTCAACAGAACC 59.294 33.333 0.00 0.00 34.16 3.62
361 366 8.534778 GTGAAAACAAATCATCTTCAACAGAAC 58.465 33.333 0.00 0.00 34.16 3.01
436 441 7.627298 ACAGACGTACTACTTCAATCTACAT 57.373 36.000 0.00 0.00 0.00 2.29
437 442 7.201591 GCTACAGACGTACTACTTCAATCTACA 60.202 40.741 0.00 0.00 0.00 2.74
454 459 3.788434 AACAAATCGTTGCTACAGACG 57.212 42.857 0.00 0.00 38.39 4.18
484 489 5.760253 CACCCTGACCATGATAGTTCAATAC 59.240 44.000 0.00 0.00 34.96 1.89
487 492 3.843619 TCACCCTGACCATGATAGTTCAA 59.156 43.478 0.00 0.00 34.96 2.69
519 524 0.813184 GGACGTACTCATCGGTCCAA 59.187 55.000 9.66 0.00 32.86 3.53
668 673 3.088532 TGCCACTTGTTCTTCAGTTGTT 58.911 40.909 0.00 0.00 0.00 2.83
688 693 5.805728 AGACCAGTCACCCTTTAACTTATG 58.194 41.667 0.00 0.00 0.00 1.90
740 745 2.344093 ACTGTCCTAACCTGTCCCAT 57.656 50.000 0.00 0.00 0.00 4.00
752 757 1.718280 AACTCCCTTCGAACTGTCCT 58.282 50.000 0.00 0.00 0.00 3.85
783 788 2.354704 CGCCTTCTTCCACCACTCATTA 60.355 50.000 0.00 0.00 0.00 1.90
899 904 4.864704 TTTTCTAAACTTGCCACATCCC 57.135 40.909 0.00 0.00 0.00 3.85
920 926 5.011329 TGCTCCAGATTTTGAAGATGCTTTT 59.989 36.000 0.00 0.00 0.00 2.27
926 932 6.096564 GGAAAGATGCTCCAGATTTTGAAGAT 59.903 38.462 0.00 0.00 32.77 2.40
1017 1024 6.652205 AAATTCTCTTGACTTGGGGGTATA 57.348 37.500 0.00 0.00 0.00 1.47
1042 1049 6.379133 ACTCCAACAACATTATCAGCATCAAT 59.621 34.615 0.00 0.00 0.00 2.57
1112 1119 0.978146 ATCCTCCTCACCTCCAACCG 60.978 60.000 0.00 0.00 0.00 4.44
1254 1272 3.818210 TCATTGAAGTAAAAGAAGCGGCA 59.182 39.130 1.45 0.00 0.00 5.69
1389 1407 0.526211 GGGTCTTGAACATTTCCCGC 59.474 55.000 0.00 0.00 0.00 6.13
1444 1462 6.583912 ATTTCCATACTTGTCGTTGTATCG 57.416 37.500 0.00 0.00 0.00 2.92
1663 1736 9.817809 AATAGTTCAAGTCACATACAACGATAT 57.182 29.630 0.00 0.00 0.00 1.63
1733 1806 5.343249 TCATCGTTGTCACTATCAGACATG 58.657 41.667 0.00 0.00 44.66 3.21
1760 1833 6.036408 TGCAAAACTTCATACTCTCATCATCG 59.964 38.462 0.00 0.00 0.00 3.84
1877 1950 1.813513 AAGTCTCTTGCAACCATCCG 58.186 50.000 0.00 0.00 0.00 4.18
1940 2013 6.316390 AGTCGTGAAGGTCCATGAATATTTTC 59.684 38.462 0.00 0.00 34.25 2.29
1941 2014 6.180472 AGTCGTGAAGGTCCATGAATATTTT 58.820 36.000 0.00 0.00 34.25 1.82
1944 2017 5.118990 CAAGTCGTGAAGGTCCATGAATAT 58.881 41.667 0.00 0.00 34.25 1.28
2011 2084 7.765695 AGGAAAATTGCAAGACTTTCATAGA 57.234 32.000 22.66 0.00 30.89 1.98
2030 2103 3.010027 TGCCACCACAGATGAATAGGAAA 59.990 43.478 0.00 0.00 0.00 3.13
2036 2109 3.021695 CTCATTGCCACCACAGATGAAT 58.978 45.455 0.00 0.00 0.00 2.57
2071 2144 5.675970 TCGAGTGATTGAAACGATTTTGAC 58.324 37.500 0.00 0.00 0.00 3.18
2087 2160 2.230508 ACTAATGGTTTCGCTCGAGTGA 59.769 45.455 24.28 24.28 0.00 3.41
2094 2167 6.657541 TCAAATTTCCTACTAATGGTTTCGCT 59.342 34.615 0.00 0.00 0.00 4.93
2186 2259 9.993454 TCATCTCTTATCCTCTTATGAACATTG 57.007 33.333 0.00 0.00 0.00 2.82
2388 2461 2.025981 TGTCATGCATAGCTCCTGGTTT 60.026 45.455 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.