Multiple sequence alignment - TraesCS6A01G286300

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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 TraesCS6A01G286300 chr6A 100.000 5220 0 0 1 5220 518600977 518595758 0.000000e+00 9640.0
1 TraesCS6A01G286300 chr6A 96.558 4823 104 14 1 4793 518552885 518548095 0.000000e+00 7930.0
2 TraesCS6A01G286300 chr6A 90.068 2638 141 42 2100 4704 33294314 33291765 0.000000e+00 3308.0
3 TraesCS6A01G286300 chr6A 87.074 704 50 17 1305 1993 33294983 33294306 0.000000e+00 758.0
4 TraesCS6A01G286300 chr6A 83.271 807 87 21 2724 3514 14522588 14521814 0.000000e+00 699.0
5 TraesCS6A01G286300 chr6A 83.240 716 86 18 1285 1993 14553966 14553278 1.230000e-175 627.0
6 TraesCS6A01G286300 chr6A 91.323 461 25 7 69 516 33296248 33295790 2.670000e-172 616.0
7 TraesCS6A01G286300 chr6A 93.458 321 18 3 517 834 33295680 33295360 1.700000e-129 473.0
8 TraesCS6A01G286300 chr6A 88.191 398 36 7 857 1249 33295385 33294994 1.020000e-126 464.0
9 TraesCS6A01G286300 chr6A 86.818 440 26 11 4795 5220 518548066 518547645 3.680000e-126 462.0
10 TraesCS6A01G286300 chr6A 90.977 133 12 0 670 802 270600356 270600488 4.150000e-41 180.0
11 TraesCS6A01G286300 chr6D 94.778 5285 162 36 1 5220 376948608 376943373 0.000000e+00 8126.0
12 TraesCS6A01G286300 chr6D 94.379 5230 168 46 77 5220 376977464 376972275 0.000000e+00 7914.0
13 TraesCS6A01G286300 chr6D 90.650 2631 153 42 2100 4697 29114109 29116679 0.000000e+00 3410.0
14 TraesCS6A01G286300 chr6D 88.068 704 55 15 1305 1993 29113428 29114117 0.000000e+00 808.0
15 TraesCS6A01G286300 chr6D 85.815 712 66 7 1297 1993 13947742 13947051 0.000000e+00 723.0
16 TraesCS6A01G286300 chr6D 84.691 712 74 9 1297 1993 13959025 13958334 0.000000e+00 678.0
17 TraesCS6A01G286300 chr6D 90.830 458 29 4 69 516 29112177 29112631 7.480000e-168 601.0
18 TraesCS6A01G286300 chr6D 90.102 394 32 5 857 1249 29113030 29113417 6.030000e-139 505.0
19 TraesCS6A01G286300 chr6D 92.879 323 16 4 514 834 29112738 29113055 3.680000e-126 462.0
20 TraesCS6A01G286300 chr6D 83.412 211 13 2 1 190 376977666 376977457 5.370000e-40 176.0
21 TraesCS6A01G286300 chr6D 85.256 156 23 0 4704 4859 29116730 29116885 1.500000e-35 161.0
22 TraesCS6A01G286300 chr6B 93.873 5304 207 51 1 5220 563136835 563131566 0.000000e+00 7886.0
23 TraesCS6A01G286300 chr6B 95.907 2761 88 13 2477 5220 563146206 563143454 0.000000e+00 4449.0
24 TraesCS6A01G286300 chr6B 92.887 2432 89 21 1 2380 563148630 563146231 0.000000e+00 3456.0
25 TraesCS6A01G286300 chr6B 90.502 1295 53 18 2100 3367 60605325 60604074 0.000000e+00 1646.0
26 TraesCS6A01G286300 chr6B 88.701 1301 90 24 3415 4704 60604074 60602820 0.000000e+00 1535.0
27 TraesCS6A01G286300 chr6B 87.872 907 66 20 2107 3001 25454414 25453540 0.000000e+00 1026.0
28 TraesCS6A01G286300 chr6B 87.775 908 67 20 2107 3002 25429122 25428247 0.000000e+00 1022.0
29 TraesCS6A01G286300 chr6B 87.047 911 69 25 2110 3002 25407912 25407033 0.000000e+00 983.0
30 TraesCS6A01G286300 chr6B 86.222 704 56 17 1305 1993 60605994 60605317 0.000000e+00 725.0
31 TraesCS6A01G286300 chr6B 83.613 714 78 15 1297 1993 25376364 25375673 7.370000e-178 634.0
32 TraesCS6A01G286300 chr6B 91.048 458 22 3 69 516 60607242 60606794 7.480000e-168 601.0
33 TraesCS6A01G286300 chr6B 87.449 486 33 13 2107 2583 25392168 25391702 7.690000e-148 534.0
34 TraesCS6A01G286300 chr6B 94.062 320 15 3 517 834 60606684 60606367 2.830000e-132 483.0
35 TraesCS6A01G286300 chr6B 89.059 393 36 5 857 1248 60606392 60606006 1.020000e-131 481.0
36 TraesCS6A01G286300 chr6B 86.866 335 19 7 2107 2432 25398055 25397737 8.320000e-93 351.0
37 TraesCS6A01G286300 chr6B 84.277 159 22 1 4704 4859 60602781 60602623 9.050000e-33 152.0
38 TraesCS6A01G286300 chrUn 88.702 832 64 19 2184 3002 355299260 355298446 0.000000e+00 989.0
39 TraesCS6A01G286300 chrUn 86.035 623 67 5 1371 1993 469507769 469507167 0.000000e+00 651.0
40 TraesCS6A01G286300 chr3D 86.854 213 25 3 66 276 196949522 196949733 8.740000e-58 235.0
41 TraesCS6A01G286300 chr2A 86.567 67 4 3 4819 4881 737493610 737493675 9.380000e-08 69.4
42 TraesCS6A01G286300 chr1A 87.302 63 4 2 4823 4881 162067298 162067360 9.380000e-08 69.4


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 TraesCS6A01G286300 chr6A 518595758 518600977 5219 True 9640.000000 9640 100.000000 1 5220 1 chr6A.!!$R3 5219
1 TraesCS6A01G286300 chr6A 518547645 518552885 5240 True 4196.000000 7930 91.688000 1 5220 2 chr6A.!!$R5 5219
2 TraesCS6A01G286300 chr6A 33291765 33296248 4483 True 1123.800000 3308 90.022800 69 4704 5 chr6A.!!$R4 4635
3 TraesCS6A01G286300 chr6A 14521814 14522588 774 True 699.000000 699 83.271000 2724 3514 1 chr6A.!!$R1 790
4 TraesCS6A01G286300 chr6A 14553278 14553966 688 True 627.000000 627 83.240000 1285 1993 1 chr6A.!!$R2 708
5 TraesCS6A01G286300 chr6D 376943373 376948608 5235 True 8126.000000 8126 94.778000 1 5220 1 chr6D.!!$R3 5219
6 TraesCS6A01G286300 chr6D 376972275 376977666 5391 True 4045.000000 7914 88.895500 1 5220 2 chr6D.!!$R4 5219
7 TraesCS6A01G286300 chr6D 29112177 29116885 4708 False 991.166667 3410 89.630833 69 4859 6 chr6D.!!$F1 4790
8 TraesCS6A01G286300 chr6D 13947051 13947742 691 True 723.000000 723 85.815000 1297 1993 1 chr6D.!!$R1 696
9 TraesCS6A01G286300 chr6D 13958334 13959025 691 True 678.000000 678 84.691000 1297 1993 1 chr6D.!!$R2 696
10 TraesCS6A01G286300 chr6B 563131566 563136835 5269 True 7886.000000 7886 93.873000 1 5220 1 chr6B.!!$R7 5219
11 TraesCS6A01G286300 chr6B 563143454 563148630 5176 True 3952.500000 4449 94.397000 1 5220 2 chr6B.!!$R9 5219
12 TraesCS6A01G286300 chr6B 25453540 25454414 874 True 1026.000000 1026 87.872000 2107 3001 1 chr6B.!!$R6 894
13 TraesCS6A01G286300 chr6B 25428247 25429122 875 True 1022.000000 1022 87.775000 2107 3002 1 chr6B.!!$R5 895
14 TraesCS6A01G286300 chr6B 25407033 25407912 879 True 983.000000 983 87.047000 2110 3002 1 chr6B.!!$R4 892
15 TraesCS6A01G286300 chr6B 60602623 60607242 4619 True 803.285714 1646 89.124429 69 4859 7 chr6B.!!$R8 4790
16 TraesCS6A01G286300 chr6B 25375673 25376364 691 True 634.000000 634 83.613000 1297 1993 1 chr6B.!!$R1 696
17 TraesCS6A01G286300 chrUn 355298446 355299260 814 True 989.000000 989 88.702000 2184 3002 1 chrUn.!!$R1 818
18 TraesCS6A01G286300 chrUn 469507167 469507769 602 True 651.000000 651 86.035000 1371 1993 1 chrUn.!!$R2 622

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
280 471 0.038310 AACCAAGCAGCCCCTTAGTC 59.962 55.000 0.00 0.00 0.00 2.59 F
1295 1846 0.108138 ATGCACCGCTACTTCTCCAC 60.108 55.000 0.00 0.00 0.00 4.02 F
2081 2667 2.048603 GTCTGGGCATGCCAAGTCC 61.049 63.158 35.27 24.53 38.31 3.85 F
3212 3865 0.035458 AGCTTGGTCAGTTCCTTCCG 59.965 55.000 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 2304 2.618241 GCAGGATCACACAACTGAACAA 59.382 45.455 0.00 0.0 32.86 2.83 R
2281 2882 0.178885 AGGGTAGCAGGGTACAACCA 60.179 55.000 10.43 0.0 41.02 3.67 R
3669 4333 2.029964 GTCAAACGACCTGCCGGA 59.970 61.111 5.05 0.0 0.00 5.14 R
4666 5346 0.252479 AGCTGCACCCAGAAGAGATG 59.748 55.000 1.02 0.0 41.77 2.90 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
31 32 2.964310 GCTCTGCAGAGGAAGGCCA 61.964 63.158 37.86 5.84 42.29 5.36
37 38 1.078567 CAGAGGAAGGCCAGCTGTC 60.079 63.158 13.81 0.00 35.41 3.51
67 68 4.552355 GGCATGTTTGGTTGGTAACTAAC 58.448 43.478 0.00 0.00 31.22 2.34
280 471 0.038310 AACCAAGCAGCCCCTTAGTC 59.962 55.000 0.00 0.00 0.00 2.59
627 927 7.555965 TGTATCAAGTCTGCATATTGTACTGT 58.444 34.615 0.00 0.00 0.00 3.55
646 947 9.877178 TGTACTGTGTGTTTTGGAATTAATTTT 57.123 25.926 1.43 0.00 0.00 1.82
974 1347 1.725182 TCCTCCTCTTCCCCTCTTCTT 59.275 52.381 0.00 0.00 0.00 2.52
1061 1434 0.618981 AACAACCCCGATCTTCCCTC 59.381 55.000 0.00 0.00 0.00 4.30
1295 1846 0.108138 ATGCACCGCTACTTCTCCAC 60.108 55.000 0.00 0.00 0.00 4.02
1385 1966 2.615986 TACCTCAACTCCTACAGGCA 57.384 50.000 0.00 0.00 34.44 4.75
1597 2178 2.640826 CCCCGCCCAGTAATATCCTTTA 59.359 50.000 0.00 0.00 0.00 1.85
1833 2418 5.049405 CGAAGGCAAGTTTAGAGTTTGACAT 60.049 40.000 0.00 0.00 32.21 3.06
1915 2500 7.630242 TGATGTTATTCACCTTTCTGATTCC 57.370 36.000 0.00 0.00 0.00 3.01
2081 2667 2.048603 GTCTGGGCATGCCAAGTCC 61.049 63.158 35.27 24.53 38.31 3.85
2423 3029 5.091552 AGAATAGTCCCACAACCTTCTACA 58.908 41.667 0.00 0.00 0.00 2.74
2427 3033 2.633481 GTCCCACAACCTTCTACACTCT 59.367 50.000 0.00 0.00 0.00 3.24
2438 3044 6.702329 ACCTTCTACACTCTCCAAATACTTG 58.298 40.000 0.00 0.00 0.00 3.16
2788 3399 4.127171 CCGGATAGTTGAATGAAACCGAT 58.873 43.478 0.00 0.00 41.30 4.18
3212 3865 0.035458 AGCTTGGTCAGTTCCTTCCG 59.965 55.000 0.00 0.00 0.00 4.30
3404 4068 1.053424 ACGCCCCTTCTGTCTAAACA 58.947 50.000 0.00 0.00 0.00 2.83
3669 4333 8.181904 TCCATGTTTAATCTTTTCTTCTTGCT 57.818 30.769 0.00 0.00 0.00 3.91
3811 4478 0.871722 TGCATTGTGGTTACGCAGTC 59.128 50.000 0.00 0.00 43.93 3.51
4137 4811 5.636543 CAGTCCTGCAAAATCCAAATTTCTC 59.363 40.000 0.00 0.00 33.93 2.87
4296 4970 3.531538 TCGCTCGCCTTTCTTTATGATT 58.468 40.909 0.00 0.00 0.00 2.57
4617 5297 2.223249 CGAGGAATATTGTTGTTGCGGG 60.223 50.000 0.00 0.00 0.00 6.13
4666 5346 3.639538 TGTTTACTTCTCTGTGAGTCGC 58.360 45.455 0.00 0.00 0.00 5.19
4887 5643 7.323052 GGATTTAGATCCCTAGGAATGTTCT 57.677 40.000 11.48 6.36 45.21 3.01
4889 5645 8.315482 GGATTTAGATCCCTAGGAATGTTCTAC 58.685 40.741 11.48 0.00 45.21 2.59
4892 5648 4.585162 AGATCCCTAGGAATGTTCTACACG 59.415 45.833 11.48 0.00 34.34 4.49
4914 5670 5.529800 ACGTTGTTATTCCTGTAGCTTTGTT 59.470 36.000 0.00 0.00 0.00 2.83
5187 5960 5.922544 CCTGTTTTCCTAGTTTTGCATTGAG 59.077 40.000 0.00 0.00 0.00 3.02
5193 5966 6.899393 TCCTAGTTTTGCATTGAGTTTGAT 57.101 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.283029 ACATGCCCTACATTGACAGCT 59.717 47.619 0.00 0.00 36.64 4.24
37 38 3.587923 CAACCAAACATGCCCTACATTG 58.412 45.455 0.00 0.00 36.64 2.82
67 68 1.208052 TGAGCACCTAAGCTAAGGCAG 59.792 52.381 0.00 0.00 46.75 4.85
116 159 4.198530 CAAAAAGTGTGGCAAAATTCCCT 58.801 39.130 0.00 0.00 0.00 4.20
280 471 6.015519 TCACCAAAATAGTGAAGGTTGGATTG 60.016 38.462 7.69 0.00 41.17 2.67
344 535 5.667539 TCAGAATAGGCATATACCTCAGC 57.332 43.478 0.00 0.00 41.50 4.26
479 670 6.489361 GCAAGGGATAAATCATCATGTTCTCT 59.511 38.462 0.00 0.00 35.11 3.10
974 1347 2.194212 GGCGGCGGAGTAGATCTGA 61.194 63.158 9.78 0.00 36.25 3.27
1061 1434 2.545952 CCGAAGAGAATACCCATGTCGG 60.546 54.545 0.00 0.00 40.61 4.79
1295 1846 4.530875 AGGGTTTGCATTTAGATCTGGAG 58.469 43.478 5.18 0.00 0.00 3.86
1385 1966 4.444449 GGTTAACACTCAGGTTCAGGTCTT 60.444 45.833 8.10 0.00 32.29 3.01
1597 2178 2.676471 GCTCCGGTTTGGCATGGT 60.676 61.111 0.00 0.00 37.80 3.55
1718 2303 3.548818 GCAGGATCACACAACTGAACAAC 60.549 47.826 0.00 0.00 32.86 3.32
1719 2304 2.618241 GCAGGATCACACAACTGAACAA 59.382 45.455 0.00 0.00 32.86 2.83
1915 2500 5.990386 ACCATCAGAATCAGAATCAGAATCG 59.010 40.000 0.00 0.00 0.00 3.34
2273 2874 5.444744 AGCAGGGTACAACCATACAAATA 57.555 39.130 0.00 0.00 41.02 1.40
2281 2882 0.178885 AGGGTAGCAGGGTACAACCA 60.179 55.000 10.43 0.00 41.02 3.67
2404 3010 3.830755 GAGTGTAGAAGGTTGTGGGACTA 59.169 47.826 0.00 0.00 0.00 2.59
2423 3029 4.202461 TGCCAAGACAAGTATTTGGAGAGT 60.202 41.667 15.96 0.00 43.15 3.24
2427 3033 2.819608 GCTGCCAAGACAAGTATTTGGA 59.180 45.455 15.96 0.00 43.15 3.53
2438 3044 1.210478 TCCTATGAAGGCTGCCAAGAC 59.790 52.381 22.65 9.24 43.31 3.01
2669 3278 4.098960 AGCAGCTCAATGATTACCATTTGG 59.901 41.667 0.00 0.00 42.55 3.28
2838 3449 9.314133 TCTAAATACAGGCAGTGATATATGAGT 57.686 33.333 0.00 0.00 0.00 3.41
3046 3668 9.996554 TGAAAGACACAGAAAGACAATCTATTA 57.003 29.630 0.00 0.00 0.00 0.98
3588 4252 9.897744 CATAAACAATCATTAGCGGAACATAAT 57.102 29.630 0.00 0.00 0.00 1.28
3589 4253 8.898761 ACATAAACAATCATTAGCGGAACATAA 58.101 29.630 0.00 0.00 0.00 1.90
3604 4268 5.473504 AGACTGGAACACCACATAAACAATC 59.526 40.000 0.00 0.00 0.00 2.67
3669 4333 2.029964 GTCAAACGACCTGCCGGA 59.970 61.111 5.05 0.00 0.00 5.14
3811 4478 2.032979 GGTTGCTTGGCGAAACAATTTG 60.033 45.455 0.53 0.00 0.00 2.32
4137 4811 0.461961 GGACCTAGTAGCCTGTGCAG 59.538 60.000 0.00 0.00 41.13 4.41
4394 5070 4.390297 CCTCGAAAGAAAGAGCTCGATTTT 59.610 41.667 8.37 3.40 39.39 1.82
4469 5147 2.024176 TCAACCAGCCAGACCTAGAA 57.976 50.000 0.00 0.00 0.00 2.10
4599 5279 1.476488 AGCCCGCAACAACAATATTCC 59.524 47.619 0.00 0.00 0.00 3.01
4617 5297 3.047796 CAGAAATGCAGAAACACACAGC 58.952 45.455 0.00 0.00 0.00 4.40
4666 5346 0.252479 AGCTGCACCCAGAAGAGATG 59.748 55.000 1.02 0.00 41.77 2.90
4739 5465 7.758495 AGCTAAAACCGATAAACCTACAAATG 58.242 34.615 0.00 0.00 0.00 2.32
4751 5477 6.860023 GCTAATCGTTCTAGCTAAAACCGATA 59.140 38.462 13.77 2.26 38.99 2.92
4803 5556 8.638873 CCCTAAAACTCCTGAAACTACAAATTT 58.361 33.333 0.00 0.00 0.00 1.82
4819 5572 5.010282 TGAATCAAAGGAGCCCTAAAACTC 58.990 41.667 0.00 0.00 31.13 3.01
4875 5631 8.475331 AATAACAACGTGTAGAACATTCCTAG 57.525 34.615 0.00 0.00 0.00 3.02
4887 5643 5.395682 AGCTACAGGAATAACAACGTGTA 57.604 39.130 0.00 0.00 36.68 2.90
4889 5645 5.049680 ACAAAGCTACAGGAATAACAACGTG 60.050 40.000 0.00 0.00 0.00 4.49
4892 5648 8.947115 AGATAACAAAGCTACAGGAATAACAAC 58.053 33.333 0.00 0.00 0.00 3.32
4914 5670 8.772250 AGGATTCTCAAAACACAGGAATAGATA 58.228 33.333 0.00 0.00 0.00 1.98
5050 5822 7.551585 CAGCAGATATATCTAAAGGTACCAGG 58.448 42.308 15.94 0.85 34.85 4.45
5052 5824 6.726299 AGCAGCAGATATATCTAAAGGTACCA 59.274 38.462 15.94 0.00 34.85 3.25
5056 5828 5.936956 GCAAGCAGCAGATATATCTAAAGGT 59.063 40.000 14.92 9.92 44.79 3.50
5187 5960 7.511959 AACAGGTTAGAGAAAGGAATCAAAC 57.488 36.000 0.00 0.00 0.00 2.93
5193 5966 6.887545 TGAAACAAACAGGTTAGAGAAAGGAA 59.112 34.615 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.