Multiple sequence alignment - TraesCS2A01G185400

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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 TraesCS2A01G185400 chr2A 100.000 3030 0 0 1 3030 146726506 146723477 0.000000e+00 5596.0
1 TraesCS2A01G185400 chr2D 93.137 2375 120 19 693 3027 154291594 154293965 0.000000e+00 3443.0
2 TraesCS2A01G185400 chr2D 87.344 719 64 17 2 697 154289500 154290214 0.000000e+00 798.0
3 TraesCS2A01G185400 chr2D 86.370 719 64 21 2 697 154288536 154289243 0.000000e+00 754.0
4 TraesCS2A01G185400 chr2B 93.077 1170 67 5 839 1999 211699023 211700187 0.000000e+00 1700.0
5 TraesCS2A01G185400 chr2B 87.778 720 61 15 2 697 211698154 211698870 0.000000e+00 817.0
6 TraesCS2A01G185400 chr2B 100.000 96 0 0 687 782 211698896 211698991 8.630000e-41 178.0
7 TraesCS2A01G185400 chr2B 72.596 208 49 8 85 291 238273963 238274163 9.070000e-06 62.1
8 TraesCS2A01G185400 chr4D 81.181 728 90 27 2 697 47562169 47562881 2.660000e-150 542.0
9 TraesCS2A01G185400 chr7B 79.412 612 102 15 6 603 591465289 591464688 7.820000e-111 411.0
10 TraesCS2A01G185400 chr5D 78.457 622 104 21 2 608 4246620 4246014 2.200000e-101 379.0
11 TraesCS2A01G185400 chr7D 78.339 614 103 23 6 608 548234785 548234191 1.330000e-98 370.0
12 TraesCS2A01G185400 chr6B 81.792 346 51 8 3 343 704679549 704679211 2.300000e-71 279.0
13 TraesCS2A01G185400 chr1D 84.466 103 14 1 189 289 492981288 492981390 1.920000e-17 100.0
14 TraesCS2A01G185400 chr6D 78.151 119 22 4 188 305 61572320 61572435 4.190000e-09 73.1


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 TraesCS2A01G185400 chr2A 146723477 146726506 3029 True 5596.000000 5596 100.000000 1 3030 1 chr2A.!!$R1 3029
1 TraesCS2A01G185400 chr2D 154288536 154293965 5429 False 1665.000000 3443 88.950333 2 3027 3 chr2D.!!$F1 3025
2 TraesCS2A01G185400 chr2B 211698154 211700187 2033 False 898.333333 1700 93.618333 2 1999 3 chr2B.!!$F2 1997
3 TraesCS2A01G185400 chr4D 47562169 47562881 712 False 542.000000 542 81.181000 2 697 1 chr4D.!!$F1 695
4 TraesCS2A01G185400 chr7B 591464688 591465289 601 True 411.000000 411 79.412000 6 603 1 chr7B.!!$R1 597
5 TraesCS2A01G185400 chr5D 4246014 4246620 606 True 379.000000 379 78.457000 2 608 1 chr5D.!!$R1 606
6 TraesCS2A01G185400 chr7D 548234191 548234785 594 True 370.000000 370 78.339000 6 608 1 chr7D.!!$R1 602

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
605 1586 1.481871 GTGGTGGCTAGCTACCTGTA 58.518 55.0 39.66 24.16 46.13 2.74 F
1303 3714 0.393673 TCTGACTCTGAGAGCGAGGG 60.394 60.0 12.44 0.00 32.04 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 3825 0.736325 GTGGTCGTGATCACCTTCCG 60.736 60.0 20.03 8.26 36.46 4.30 R
2897 5330 0.608130 CTCCTCCATGACCGTGAACA 59.392 55.0 0.00 0.00 0.00 3.18 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
332 1305 6.679843 TGTCCGTGTTTATAAAAATTGGTCC 58.320 36.000 0.00 0.00 0.00 4.46
338 1311 9.557338 CGTGTTTATAAAAATTGGTCCGAATTA 57.443 29.630 0.00 0.00 0.00 1.40
386 1366 6.061231 CAAGTTCTAAAGTTGTTCCCTGTC 57.939 41.667 0.14 0.00 37.12 3.51
401 1381 7.947282 TGTTCCCTGTCTTAAAATTTGGTTAG 58.053 34.615 0.00 0.00 0.00 2.34
448 1428 8.497554 AGTTTTCGAAACTTATGCGTGTTTATA 58.502 29.630 10.79 0.00 36.64 0.98
605 1586 1.481871 GTGGTGGCTAGCTACCTGTA 58.518 55.000 39.66 24.16 46.13 2.74
608 1589 1.619332 GGTGGCTAGCTACCTGTATCC 59.381 57.143 35.70 13.65 43.19 2.59
610 1591 3.499926 GGTGGCTAGCTACCTGTATCCTA 60.500 52.174 35.70 0.00 43.19 2.94
611 1592 3.506844 GTGGCTAGCTACCTGTATCCTAC 59.493 52.174 19.79 0.00 0.00 3.18
690 1692 2.653702 GACTGCTCTGTGCGAGGT 59.346 61.111 0.00 0.00 46.63 3.85
1178 3589 4.093952 CACAAGGCGCGCTTCCTG 62.094 66.667 32.29 21.74 33.43 3.86
1205 3616 0.725686 ACGACGACAAGACGATCGAT 59.274 50.000 24.34 6.97 40.86 3.59
1303 3714 0.393673 TCTGACTCTGAGAGCGAGGG 60.394 60.000 12.44 0.00 32.04 4.30
1312 3723 0.603569 GAGAGCGAGGGTTCAGTTGA 59.396 55.000 0.00 0.00 0.00 3.18
1313 3724 1.205893 GAGAGCGAGGGTTCAGTTGAT 59.794 52.381 0.00 0.00 0.00 2.57
1319 3730 2.338500 GAGGGTTCAGTTGATGACGAC 58.662 52.381 0.00 0.00 37.77 4.34
1321 3732 1.604693 GGGTTCAGTTGATGACGACGT 60.605 52.381 0.00 0.00 37.77 4.34
1326 3737 2.029380 TCAGTTGATGACGACGTGGAAT 60.029 45.455 4.58 0.00 35.70 3.01
1333 3744 2.578713 CGACGTGGAATCGGTCGG 60.579 66.667 0.00 0.00 35.92 4.79
1411 3825 0.670854 GAACCGGAGTGCAAGGAGTC 60.671 60.000 9.46 0.00 0.00 3.36
1418 3832 1.122019 AGTGCAAGGAGTCGGAAGGT 61.122 55.000 0.00 0.00 0.00 3.50
1426 3840 0.809385 GAGTCGGAAGGTGATCACGA 59.191 55.000 19.33 10.33 0.00 4.35
1539 3953 3.923864 AGACGCCGCACAAGGTCA 61.924 61.111 0.00 0.00 31.93 4.02
1612 4026 2.728690 TGCAGTTAACGTGACGGTAT 57.271 45.000 10.66 0.00 0.00 2.73
1633 4050 7.740346 CGGTATAGAATAAATTTGTGATGTCGC 59.260 37.037 0.00 0.00 0.00 5.19
1641 4058 8.761575 ATAAATTTGTGATGTCGCTCAATTTT 57.238 26.923 15.61 11.91 34.67 1.82
1782 4199 1.901833 GGCACCTGTTTTGATGGGATT 59.098 47.619 0.00 0.00 0.00 3.01
1803 4220 0.384309 TGTGCCTATCGATCGTGTCC 59.616 55.000 15.94 2.09 0.00 4.02
1870 4293 1.439679 AGGAAGCAAATTCGTCGACC 58.560 50.000 10.58 0.00 38.95 4.79
2017 4440 3.909662 CCAAGGGCATCTCCAACG 58.090 61.111 0.00 0.00 36.21 4.10
2019 4442 2.044946 AAGGGCATCTCCAACGCC 60.045 61.111 0.00 0.00 45.47 5.68
2024 4447 1.521457 GCATCTCCAACGCCGATCA 60.521 57.895 0.00 0.00 0.00 2.92
2031 4454 2.936498 CTCCAACGCCGATCAATAAAGT 59.064 45.455 0.00 0.00 0.00 2.66
2060 4485 7.224753 ACACTGTATTTATCTGCGGACAAATAG 59.775 37.037 17.36 12.02 33.27 1.73
2067 4492 2.497675 TCTGCGGACAAATAGAGAAGCT 59.502 45.455 0.00 0.00 0.00 3.74
2081 4506 2.371510 GAGAAGCTGGCTATCCAATCCT 59.628 50.000 0.00 0.00 42.91 3.24
2085 4510 2.158696 AGCTGGCTATCCAATCCTGTTC 60.159 50.000 0.00 0.00 42.91 3.18
2087 4512 1.230324 GGCTATCCAATCCTGTTCGC 58.770 55.000 0.00 0.00 0.00 4.70
2091 4516 4.256920 GCTATCCAATCCTGTTCGCATAT 58.743 43.478 0.00 0.00 0.00 1.78
2116 4541 4.685169 TCGAATGAGATTTGAGCAAACC 57.315 40.909 0.00 0.00 32.51 3.27
2117 4542 3.125146 TCGAATGAGATTTGAGCAAACCG 59.875 43.478 0.00 0.00 32.51 4.44
2204 4637 8.376889 TCATTAAAAAGCTTTTGAATCCAACC 57.623 30.769 25.64 0.00 30.54 3.77
2219 4652 9.542462 TTGAATCCAACCTAGTATAAATCTTCG 57.458 33.333 0.00 0.00 0.00 3.79
2225 4658 4.581824 ACCTAGTATAAATCTTCGTCGGCA 59.418 41.667 0.00 0.00 0.00 5.69
2236 4669 2.264794 GTCGGCACCGTCCTTCAT 59.735 61.111 9.23 0.00 40.74 2.57
2269 4702 1.320344 CCTTCCGTGTCCATCTCCGA 61.320 60.000 0.00 0.00 0.00 4.55
2308 4741 2.359107 AGGCACACATGAGGCACG 60.359 61.111 0.00 0.00 33.87 5.34
2340 4773 1.634459 TCTCCCACGTCCTACTCTTCT 59.366 52.381 0.00 0.00 0.00 2.85
2375 4808 0.952497 TCGTCGTCGCTTGTAGAGGT 60.952 55.000 0.00 0.00 36.96 3.85
2378 4811 0.803117 TCGTCGCTTGTAGAGGTCAG 59.197 55.000 0.00 0.00 0.00 3.51
2423 4856 1.523758 GTGTTTCCGTCCTTGAGCAT 58.476 50.000 0.00 0.00 0.00 3.79
2427 4860 2.852495 TTCCGTCCTTGAGCATCGCC 62.852 60.000 0.00 0.00 38.61 5.54
2432 4865 2.110967 CCTTGAGCATCGCCTGTGG 61.111 63.158 0.00 0.00 38.61 4.17
2440 4873 3.006756 ATCGCCTGTGGGTCTGACG 62.007 63.158 1.07 0.00 34.45 4.35
2484 4917 4.724602 GCACGCTGCTCCTCGACA 62.725 66.667 0.00 0.00 40.96 4.35
2529 4962 1.372087 CCTTCATGGCTTCCGTGCTC 61.372 60.000 0.00 0.00 40.13 4.26
2549 4982 4.682787 CTCGTGCACTCACCATAGATTTA 58.317 43.478 16.19 0.00 40.04 1.40
2554 4987 3.393800 CACTCACCATAGATTTAGCCGG 58.606 50.000 0.00 0.00 0.00 6.13
2575 5008 2.125952 CCAGCGAGTGATGCACGA 60.126 61.111 0.00 0.00 39.64 4.35
2661 5094 2.584418 CGCTCCTCTGCCATGACG 60.584 66.667 0.00 0.00 0.00 4.35
2733 5166 2.283809 GGGAGGGGCTCTAGCTCA 59.716 66.667 3.89 0.00 45.20 4.26
2739 5172 0.825840 GGGGCTCTAGCTCATCGTCT 60.826 60.000 3.89 0.00 45.20 4.18
2769 5202 2.150218 CATCGTCGGGTTGTCGTCG 61.150 63.158 0.00 0.00 41.41 5.12
2818 5251 4.392940 GCTTACCTCTATTCACCATGCAT 58.607 43.478 0.00 0.00 0.00 3.96
2832 5265 0.464373 ATGCATAACGACCCTGGCAG 60.464 55.000 7.75 7.75 34.43 4.85
2890 5323 1.110442 CGAGAGGCTCTTCCACATCT 58.890 55.000 19.80 0.00 37.29 2.90
2897 5330 2.393646 GCTCTTCCACATCTCCCTAGT 58.606 52.381 0.00 0.00 0.00 2.57
2941 5374 2.092699 GTGGAAGGAGGAGGATTGGAAG 60.093 54.545 0.00 0.00 0.00 3.46
2943 5376 0.543749 AAGGAGGAGGATTGGAAGCG 59.456 55.000 0.00 0.00 0.00 4.68
2969 5402 1.135689 GTTTGTGATGCGGATGGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
2976 5409 4.221422 CGGATGGTGTCGGGCGAT 62.221 66.667 0.00 0.00 0.00 4.58
2995 5428 2.264794 CCGCGTTTAGAGGGTGCT 59.735 61.111 4.92 0.00 36.04 4.40
3019 5452 2.047274 GCCAAGCAGCGAGGTGTA 60.047 61.111 7.84 0.00 0.00 2.90
3021 5454 1.709147 GCCAAGCAGCGAGGTGTATG 61.709 60.000 7.84 3.86 0.00 2.39
3027 5460 2.496070 AGCAGCGAGGTGTATGAAACTA 59.504 45.455 4.17 0.00 0.00 2.24
3028 5461 3.133003 AGCAGCGAGGTGTATGAAACTAT 59.867 43.478 4.17 0.00 0.00 2.12
3029 5462 3.491267 GCAGCGAGGTGTATGAAACTATC 59.509 47.826 4.17 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
374 1354 6.578944 ACCAAATTTTAAGACAGGGAACAAC 58.421 36.000 0.00 0.00 0.00 3.32
401 1381 9.767684 AAAACTTGTGGAAAATTTTCGAATTTC 57.232 25.926 21.53 12.30 38.06 2.17
415 1395 5.974751 GCATAAGTTTCGAAAACTTGTGGAA 59.025 36.000 28.69 16.04 44.37 3.53
457 1437 9.748708 TCTGAATACTGTTTTTCAAAATTCTGG 57.251 29.630 7.12 0.00 32.97 3.86
820 3208 7.124147 GGGTCCAAATTATTCCAAATGAGAAGA 59.876 37.037 0.00 0.00 0.00 2.87
821 3209 7.093377 TGGGTCCAAATTATTCCAAATGAGAAG 60.093 37.037 0.00 0.00 0.00 2.85
832 3220 4.380128 GGTCGTGTTGGGTCCAAATTATTC 60.380 45.833 3.74 0.00 37.70 1.75
1005 3410 0.383590 ACGAGGCGATGATCTCACAG 59.616 55.000 0.00 0.00 0.00 3.66
1193 3604 2.345641 GTGGTTCACATCGATCGTCTTG 59.654 50.000 15.94 13.45 34.08 3.02
1205 3616 1.070786 GGAGGCGAAGTGGTTCACA 59.929 57.895 0.78 0.00 36.74 3.58
1303 3714 1.455786 CCACGTCGTCATCAACTGAAC 59.544 52.381 0.00 0.00 35.07 3.18
1312 3723 0.179145 GACCGATTCCACGTCGTCAT 60.179 55.000 0.00 0.00 37.39 3.06
1313 3724 1.210931 GACCGATTCCACGTCGTCA 59.789 57.895 0.00 0.00 37.39 4.35
1333 3744 2.747855 CCTTCTCCAACAGGCCGC 60.748 66.667 0.00 0.00 0.00 6.53
1397 3811 0.390472 CTTCCGACTCCTTGCACTCC 60.390 60.000 0.00 0.00 0.00 3.85
1411 3825 0.736325 GTGGTCGTGATCACCTTCCG 60.736 60.000 20.03 8.26 36.46 4.30
1418 3832 2.654289 CACCCGTGGTCGTGATCA 59.346 61.111 0.00 0.00 31.02 2.92
1612 4026 7.841915 TGAGCGACATCACAAATTTATTCTA 57.158 32.000 0.00 0.00 0.00 2.10
1645 4062 2.375174 ACCTTAGTCACCTGCATTGGAA 59.625 45.455 0.00 0.00 0.00 3.53
1646 4063 1.985159 ACCTTAGTCACCTGCATTGGA 59.015 47.619 0.00 0.00 0.00 3.53
1647 4064 2.496899 ACCTTAGTCACCTGCATTGG 57.503 50.000 0.00 0.00 0.00 3.16
1648 4065 3.820467 TGAAACCTTAGTCACCTGCATTG 59.180 43.478 0.00 0.00 0.00 2.82
1649 4066 4.074970 CTGAAACCTTAGTCACCTGCATT 58.925 43.478 0.00 0.00 0.00 3.56
1782 4199 0.815095 ACACGATCGATAGGCACACA 59.185 50.000 24.34 0.00 0.00 3.72
1895 4318 1.076332 AAATACAGACCGAACTGCGC 58.924 50.000 0.00 0.00 41.06 6.09
2017 4440 3.063997 CAGTGTCCACTTTATTGATCGGC 59.936 47.826 0.00 0.00 40.20 5.54
2019 4442 7.539712 AATACAGTGTCCACTTTATTGATCG 57.460 36.000 14.77 0.00 40.67 3.69
2024 4447 8.893727 GCAGATAAATACAGTGTCCACTTTATT 58.106 33.333 11.29 11.29 42.70 1.40
2031 4454 3.449377 TCCGCAGATAAATACAGTGTCCA 59.551 43.478 0.00 0.00 0.00 4.02
2048 4471 2.621338 CAGCTTCTCTATTTGTCCGCA 58.379 47.619 0.00 0.00 0.00 5.69
2060 4485 2.371510 AGGATTGGATAGCCAGCTTCTC 59.628 50.000 0.00 0.00 46.91 2.87
2067 4492 1.475034 GCGAACAGGATTGGATAGCCA 60.475 52.381 0.00 0.00 44.17 4.75
2081 4506 7.889589 ATCTCATTCGAAATATATGCGAACA 57.110 32.000 19.66 11.94 45.28 3.18
2085 4510 7.424738 GCTCAAATCTCATTCGAAATATATGCG 59.575 37.037 0.00 2.70 0.00 4.73
2091 4516 7.250569 GGTTTGCTCAAATCTCATTCGAAATA 58.749 34.615 0.00 0.00 32.36 1.40
2116 4541 5.280945 TCCGGTTTATATAAAAGTCGTCCG 58.719 41.667 18.68 18.68 31.34 4.79
2117 4542 6.925165 TCATCCGGTTTATATAAAAGTCGTCC 59.075 38.462 9.48 5.11 0.00 4.79
2194 4627 8.701895 ACGAAGATTTATACTAGGTTGGATTCA 58.298 33.333 0.00 0.00 0.00 2.57
2196 4629 7.866393 CGACGAAGATTTATACTAGGTTGGATT 59.134 37.037 0.00 0.00 0.00 3.01
2204 4637 4.916249 GGTGCCGACGAAGATTTATACTAG 59.084 45.833 0.00 0.00 0.00 2.57
2219 4652 2.100631 CATGAAGGACGGTGCCGAC 61.101 63.158 18.16 11.10 42.83 4.79
2225 4658 2.859165 ACAATGACATGAAGGACGGT 57.141 45.000 0.00 0.00 0.00 4.83
2236 4669 5.067273 ACACGGAAGGAAATAACAATGACA 58.933 37.500 0.00 0.00 0.00 3.58
2290 4723 2.683859 CGTGCCTCATGTGTGCCTG 61.684 63.158 0.00 0.00 0.00 4.85
2295 4728 2.046892 GCCTCGTGCCTCATGTGT 60.047 61.111 0.00 0.00 0.00 3.72
2308 4741 1.377202 TGGGAGACAATTGCGCCTC 60.377 57.895 4.18 14.79 0.00 4.70
2362 4795 1.174783 GACCTGACCTCTACAAGCGA 58.825 55.000 0.00 0.00 0.00 4.93
2364 4797 1.174783 TCGACCTGACCTCTACAAGC 58.825 55.000 0.00 0.00 0.00 4.01
2423 4856 3.680786 CGTCAGACCCACAGGCGA 61.681 66.667 0.00 0.00 35.20 5.54
2481 4914 3.869246 TCGTTGAGAACCTGAACTTTGTC 59.131 43.478 0.00 0.00 0.00 3.18
2484 4917 3.203716 GGTCGTTGAGAACCTGAACTTT 58.796 45.455 0.00 0.00 0.00 2.66
2529 4962 3.246226 GCTAAATCTATGGTGAGTGCACG 59.754 47.826 12.01 0.00 46.09 5.34
2533 4966 3.393800 CCGGCTAAATCTATGGTGAGTG 58.606 50.000 0.00 0.00 0.00 3.51
2575 5008 2.023501 AGCAGTACAATCTCTCCCTCCT 60.024 50.000 0.00 0.00 0.00 3.69
2661 5094 2.099062 CAAGCGCACTTCGATGCC 59.901 61.111 11.47 0.00 42.99 4.40
2718 5151 0.825840 ACGATGAGCTAGAGCCCCTC 60.826 60.000 0.00 0.00 43.38 4.30
2798 5231 5.989168 CGTTATGCATGGTGAATAGAGGTAA 59.011 40.000 10.16 0.00 0.00 2.85
2818 5251 1.911269 TCAGCTGCCAGGGTCGTTA 60.911 57.895 9.47 0.00 0.00 3.18
2832 5265 4.410743 GCAGGCTTTGCGGTCAGC 62.411 66.667 0.00 0.00 44.09 4.26
2890 5323 1.548719 CATGACCGTGAACACTAGGGA 59.451 52.381 0.00 0.00 0.00 4.20
2897 5330 0.608130 CTCCTCCATGACCGTGAACA 59.392 55.000 0.00 0.00 0.00 3.18
2941 5374 1.440353 GCATCACAAACACGTCCGC 60.440 57.895 0.00 0.00 0.00 5.54
2943 5376 1.206578 CCGCATCACAAACACGTCC 59.793 57.895 0.00 0.00 0.00 4.79
2976 5409 2.047655 CACCCTCTAAACGCGGCA 60.048 61.111 12.47 0.00 0.00 5.69
2982 5415 1.339151 CCTGACCAGCACCCTCTAAAC 60.339 57.143 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.