Multiple sequence alignment - TraesCS4A01G123400

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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 TraesCS4A01G123400 chr4A 100.000 2852 0 0 1 2852 154924941 154927792 0.000000e+00 5267.0
1 TraesCS4A01G123400 chr4B 91.392 2544 127 37 343 2852 396450866 396448381 0.000000e+00 3400.0
2 TraesCS4A01G123400 chr4B 91.707 205 7 2 1 196 396451346 396451143 2.800000e-70 276.0
3 TraesCS4A01G123400 chr4B 83.721 86 4 2 246 321 396451026 396450941 3.940000e-09 73.1
4 TraesCS4A01G123400 chr4B 76.923 104 22 2 465 567 623057417 623057519 1.100000e-04 58.4
5 TraesCS4A01G123400 chr4D 93.772 1702 73 17 337 2023 318927143 318925460 0.000000e+00 2525.0
6 TraesCS4A01G123400 chr4D 91.595 583 26 8 2037 2613 318925062 318924497 0.000000e+00 784.0
7 TraesCS4A01G123400 chr4D 92.857 364 11 3 1 350 319084524 319084162 5.450000e-142 514.0
8 TraesCS4A01G123400 chr4D 92.857 364 11 3 1 350 319086031 319085669 5.450000e-142 514.0
9 TraesCS4A01G123400 chr4D 92.308 364 13 3 1 350 319083025 319082663 1.180000e-138 503.0
10 TraesCS4A01G123400 chr4D 94.422 251 2 6 2612 2852 318924040 318923792 2.680000e-100 375.0


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 TraesCS4A01G123400 chr4A 154924941 154927792 2851 False 5267.000000 5267 100.000 1 2852 1 chr4A.!!$F1 2851
1 TraesCS4A01G123400 chr4B 396448381 396451346 2965 True 1249.700000 3400 88.940 1 2852 3 chr4B.!!$R1 2851
2 TraesCS4A01G123400 chr4D 318923792 318927143 3351 True 1228.000000 2525 93.263 337 2852 3 chr4D.!!$R1 2515
3 TraesCS4A01G123400 chr4D 319082663 319086031 3368 True 510.333333 514 92.674 1 350 3 chr4D.!!$R2 349

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
662 2284 0.249489 ACGCGCCTCTTATGTCCATC 60.249 55.0 5.73 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 4633 0.031178 ACAACACACGGTACTCGACC 59.969 55.0 10.17 0.0 45.91 4.79 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
92 93 2.231964 TCAAAAAGCACCATGCCATCTC 59.768 45.455 0.00 0.00 46.52 2.75
184 194 2.949177 TACTCAGGTGGCACAAATGT 57.051 45.000 20.82 14.19 44.16 2.71
189 1706 3.088532 TCAGGTGGCACAAATGTATTCC 58.911 45.455 20.82 0.00 44.16 3.01
244 1761 1.071385 CCAGCAGAGGTTGAAGTGACT 59.929 52.381 0.00 0.00 0.00 3.41
417 2036 2.902705 TGGGTCATACTATGCCGAAC 57.097 50.000 0.00 0.00 0.00 3.95
430 2049 3.465122 TGCCGAACTTCTTAAATTCGC 57.535 42.857 0.23 0.00 42.96 4.70
437 2056 7.061326 GCCGAACTTCTTAAATTCGCATAAAAA 59.939 33.333 0.23 0.00 42.96 1.94
501 2121 9.712305 ATCAGGTCTATTATAAAAGTTCATCGG 57.288 33.333 0.00 0.00 0.00 4.18
516 2136 8.842358 AAGTTCATCGGAAGTAAAAAGTATCA 57.158 30.769 0.00 0.00 35.63 2.15
521 2141 8.717821 TCATCGGAAGTAAAAAGTATCACAAAG 58.282 33.333 0.00 0.00 0.00 2.77
554 2175 2.520069 ACATCAAGACTCGAGACCACT 58.480 47.619 21.68 9.65 0.00 4.00
574 2195 0.523072 GAACGACCACTACAGCCGTA 59.477 55.000 0.00 0.00 32.81 4.02
612 2233 1.571919 CCTATCGAAGCCGGTTTGAG 58.428 55.000 8.82 2.22 31.63 3.02
637 2258 1.441682 GACGACAACCGAGACGTCC 60.442 63.158 13.01 2.76 45.76 4.79
640 2261 1.575576 CGACAACCGAGACGTCCTCT 61.576 60.000 13.01 0.00 41.76 3.69
650 2272 4.421479 CGTCCTCTTCACGCGCCT 62.421 66.667 5.73 0.00 0.00 5.52
662 2284 0.249489 ACGCGCCTCTTATGTCCATC 60.249 55.000 5.73 0.00 0.00 3.51
733 2360 4.400251 TGAAATTTTAGCATGGCCTGAGAG 59.600 41.667 3.32 0.00 0.00 3.20
761 2388 1.372128 CTTGCCTTTTCGCTGCCAC 60.372 57.895 0.00 0.00 0.00 5.01
841 2468 1.106944 AGCCACAAAGTCCAAACCCG 61.107 55.000 0.00 0.00 0.00 5.28
888 2515 0.464036 ACACCGAGTGTCACACATGT 59.536 50.000 11.40 6.04 43.92 3.21
1063 2690 5.775195 CCCTTTATATTCAATCCCCCAACTC 59.225 44.000 0.00 0.00 0.00 3.01
1070 2697 0.479589 AATCCCCCAACTCCTCCCAA 60.480 55.000 0.00 0.00 0.00 4.12
1071 2698 0.921256 ATCCCCCAACTCCTCCCAAG 60.921 60.000 0.00 0.00 0.00 3.61
1076 2703 1.133809 CCAACTCCTCCCAAGTCCCA 61.134 60.000 0.00 0.00 0.00 4.37
1077 2704 0.036875 CAACTCCTCCCAAGTCCCAC 59.963 60.000 0.00 0.00 0.00 4.61
1078 2705 1.134438 AACTCCTCCCAAGTCCCACC 61.134 60.000 0.00 0.00 0.00 4.61
1079 2706 1.229658 CTCCTCCCAAGTCCCACCT 60.230 63.158 0.00 0.00 0.00 4.00
1080 2707 1.229529 TCCTCCCAAGTCCCACCTC 60.230 63.158 0.00 0.00 0.00 3.85
1081 2708 2.301738 CCTCCCAAGTCCCACCTCC 61.302 68.421 0.00 0.00 0.00 4.30
1082 2709 2.204090 TCCCAAGTCCCACCTCCC 60.204 66.667 0.00 0.00 0.00 4.30
1083 2710 3.339093 CCCAAGTCCCACCTCCCC 61.339 72.222 0.00 0.00 0.00 4.81
1084 2711 3.339093 CCAAGTCCCACCTCCCCC 61.339 72.222 0.00 0.00 0.00 5.40
1085 2712 2.531685 CAAGTCCCACCTCCCCCA 60.532 66.667 0.00 0.00 0.00 4.96
1086 2713 1.930656 CAAGTCCCACCTCCCCCAT 60.931 63.158 0.00 0.00 0.00 4.00
1127 2761 1.455383 CCCAACTCAAAGGCAAGCGT 61.455 55.000 0.00 0.00 0.00 5.07
1751 3794 0.671251 GAGGCCTCCGACTACATCAG 59.329 60.000 23.19 0.00 0.00 2.90
1974 4018 1.156736 CAGGTTGGTTGAGCGGTTAG 58.843 55.000 0.00 0.00 0.00 2.34
1975 4019 0.763035 AGGTTGGTTGAGCGGTTAGT 59.237 50.000 0.00 0.00 0.00 2.24
1976 4020 0.872388 GGTTGGTTGAGCGGTTAGTG 59.128 55.000 0.00 0.00 0.00 2.74
2176 4605 5.528690 TCTCTGATAAATGTAACAGGCATGC 59.471 40.000 9.90 9.90 32.41 4.06
2179 4608 5.834169 TGATAAATGTAACAGGCATGCATG 58.166 37.500 29.33 29.33 0.00 4.06
2180 4609 3.530265 AAATGTAACAGGCATGCATGG 57.470 42.857 33.08 17.64 31.33 3.66
2181 4610 2.440517 ATGTAACAGGCATGCATGGA 57.559 45.000 33.08 19.54 31.33 3.41
2182 4611 1.753930 TGTAACAGGCATGCATGGAG 58.246 50.000 33.08 11.81 31.33 3.86
2204 4633 0.392193 ATGTTCAGAGCGCTCCCTTG 60.392 55.000 32.94 24.19 0.00 3.61
2222 4655 2.805277 GGTCGAGTACCGTGTGTTG 58.195 57.895 0.00 0.00 38.88 3.33
2230 4663 2.093341 AGTACCGTGTGTTGTTTCCTGT 60.093 45.455 0.00 0.00 0.00 4.00
2262 4705 1.817447 GCATGCCTCTCTTGCTTTCTT 59.183 47.619 6.36 0.00 41.21 2.52
2263 4706 2.230750 GCATGCCTCTCTTGCTTTCTTT 59.769 45.455 6.36 0.00 41.21 2.52
2264 4707 3.672781 GCATGCCTCTCTTGCTTTCTTTC 60.673 47.826 6.36 0.00 41.21 2.62
2265 4708 2.146342 TGCCTCTCTTGCTTTCTTTCG 58.854 47.619 0.00 0.00 0.00 3.46
2297 4740 2.158959 CGCGCTTAACCTCCGAGTG 61.159 63.158 5.56 0.00 0.00 3.51
2298 4741 1.080025 GCGCTTAACCTCCGAGTGT 60.080 57.895 0.00 0.00 0.00 3.55
2299 4742 0.171903 GCGCTTAACCTCCGAGTGTA 59.828 55.000 0.00 0.00 0.00 2.90
2300 4743 1.798079 GCGCTTAACCTCCGAGTGTAG 60.798 57.143 0.00 0.00 0.00 2.74
2301 4744 1.471684 CGCTTAACCTCCGAGTGTAGT 59.528 52.381 0.00 0.00 0.00 2.73
2302 4745 2.679837 CGCTTAACCTCCGAGTGTAGTA 59.320 50.000 0.00 0.00 0.00 1.82
2303 4746 3.486542 CGCTTAACCTCCGAGTGTAGTAC 60.487 52.174 0.00 0.00 0.00 2.73
2304 4747 3.441572 GCTTAACCTCCGAGTGTAGTACA 59.558 47.826 0.00 0.00 0.00 2.90
2334 4777 8.717717 TGTAACCTTCATCATCTCCTAATCATT 58.282 33.333 0.00 0.00 0.00 2.57
2343 4786 4.602340 TCTCCTAATCATTCTTACCGCC 57.398 45.455 0.00 0.00 0.00 6.13
2405 4848 2.417515 GGTTCTCTGTTCCATCTCGGTC 60.418 54.545 0.00 0.00 35.57 4.79
2493 4937 3.112709 GCGACCGACTTGGCACTC 61.113 66.667 0.00 0.00 43.94 3.51
2501 4945 2.120232 CGACTTGGCACTCATCGATAC 58.880 52.381 0.00 0.00 31.56 2.24
2577 5029 3.058160 CTGGGCTTGGCGTTCCTG 61.058 66.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.649674 GTGGTCCTCCTCACATTGTAGATA 59.350 45.833 0.00 0.00 34.32 1.98
184 194 1.672441 GCGTACGGTTGGTGTGGAATA 60.672 52.381 18.39 0.00 0.00 1.75
189 1706 2.314647 CCTGCGTACGGTTGGTGTG 61.315 63.158 18.39 0.00 0.00 3.82
437 2056 7.566138 ACATGAACATAAGAATGAATGGGGATT 59.434 33.333 0.00 0.00 36.54 3.01
438 2057 7.071273 ACATGAACATAAGAATGAATGGGGAT 58.929 34.615 0.00 0.00 36.54 3.85
439 2058 6.434302 ACATGAACATAAGAATGAATGGGGA 58.566 36.000 0.00 0.00 36.54 4.81
440 2059 6.720112 ACATGAACATAAGAATGAATGGGG 57.280 37.500 0.00 0.00 36.54 4.96
441 2060 9.439500 AAAAACATGAACATAAGAATGAATGGG 57.561 29.630 0.00 0.00 36.54 4.00
532 2152 4.097135 CAGTGGTCTCGAGTCTTGATGTAT 59.903 45.833 13.13 0.00 0.00 2.29
543 2163 0.109689 GGTCGTTCAGTGGTCTCGAG 60.110 60.000 5.93 5.93 0.00 4.04
554 2175 1.287815 CGGCTGTAGTGGTCGTTCA 59.712 57.895 0.00 0.00 0.00 3.18
637 2258 1.203928 CATAAGAGGCGCGTGAAGAG 58.796 55.000 7.63 0.00 0.00 2.85
640 2261 0.459585 GGACATAAGAGGCGCGTGAA 60.460 55.000 7.63 0.00 0.00 3.18
761 2388 0.107993 TCTGCTTCCTTCCATGCTCG 60.108 55.000 0.00 0.00 0.00 5.03
819 2446 1.067060 GGTTTGGACTTTGTGGCTCAC 59.933 52.381 0.00 0.00 34.56 3.51
841 2468 3.142174 GCAGCTAATTATGAGGTCCACC 58.858 50.000 0.00 0.00 0.00 4.61
888 2515 8.415950 TCTTTGCTTTTGGTCTATCCATTTTA 57.584 30.769 0.00 0.00 46.60 1.52
939 2566 4.687215 TCCTCTGTGCTGCCGTGC 62.687 66.667 0.00 0.00 0.00 5.34
1063 2690 2.301738 GGAGGTGGGACTTGGGAGG 61.302 68.421 0.00 0.00 0.00 4.30
1070 2697 2.042930 GATGGGGGAGGTGGGACT 59.957 66.667 0.00 0.00 0.00 3.85
1071 2698 3.097162 GGATGGGGGAGGTGGGAC 61.097 72.222 0.00 0.00 0.00 4.46
1076 2703 2.038330 GGGATGGATGGGGGAGGT 60.038 66.667 0.00 0.00 0.00 3.85
1077 2704 2.038438 TGGGATGGATGGGGGAGG 60.038 66.667 0.00 0.00 0.00 4.30
1078 2705 2.464403 GGTGGGATGGATGGGGGAG 61.464 68.421 0.00 0.00 0.00 4.30
1079 2706 2.369568 GGTGGGATGGATGGGGGA 60.370 66.667 0.00 0.00 0.00 4.81
1080 2707 2.370123 AGGTGGGATGGATGGGGG 60.370 66.667 0.00 0.00 0.00 5.40
1081 2708 0.995675 AAGAGGTGGGATGGATGGGG 60.996 60.000 0.00 0.00 0.00 4.96
1082 2709 0.475906 GAAGAGGTGGGATGGATGGG 59.524 60.000 0.00 0.00 0.00 4.00
1083 2710 1.419387 GAGAAGAGGTGGGATGGATGG 59.581 57.143 0.00 0.00 0.00 3.51
1084 2711 1.419387 GGAGAAGAGGTGGGATGGATG 59.581 57.143 0.00 0.00 0.00 3.51
1085 2712 1.296523 AGGAGAAGAGGTGGGATGGAT 59.703 52.381 0.00 0.00 0.00 3.41
1086 2713 0.719015 AGGAGAAGAGGTGGGATGGA 59.281 55.000 0.00 0.00 0.00 3.41
1127 2761 0.685785 CCTGAGCTGAGCTGGGTCTA 60.686 60.000 13.71 0.00 39.88 2.59
1302 2940 4.057428 GCGGACGCTGTGGACTCT 62.057 66.667 9.76 0.00 38.26 3.24
1728 3771 2.829003 TAGTCGGAGGCCTCGCTG 60.829 66.667 26.36 18.05 0.00 5.18
1974 4018 4.142403 CCATCATTATCACCAACACACCAC 60.142 45.833 0.00 0.00 0.00 4.16
1975 4019 4.015764 CCATCATTATCACCAACACACCA 58.984 43.478 0.00 0.00 0.00 4.17
1976 4020 3.181487 GCCATCATTATCACCAACACACC 60.181 47.826 0.00 0.00 0.00 4.16
2176 4605 2.223203 GCGCTCTGAACATTTCTCCATG 60.223 50.000 0.00 0.00 0.00 3.66
2179 4608 1.663135 GAGCGCTCTGAACATTTCTCC 59.337 52.381 29.88 0.00 0.00 3.71
2180 4609 1.663135 GGAGCGCTCTGAACATTTCTC 59.337 52.381 34.46 11.47 0.00 2.87
2181 4610 1.677217 GGGAGCGCTCTGAACATTTCT 60.677 52.381 34.46 0.00 0.00 2.52
2182 4611 0.729690 GGGAGCGCTCTGAACATTTC 59.270 55.000 34.46 15.76 0.00 2.17
2204 4633 0.031178 ACAACACACGGTACTCGACC 59.969 55.000 10.17 0.00 45.91 4.79
2222 4655 4.683334 GCACCGCGCACAGGAAAC 62.683 66.667 8.75 0.00 41.79 2.78
2247 4690 2.739379 GACCGAAAGAAAGCAAGAGAGG 59.261 50.000 0.00 0.00 0.00 3.69
2262 4705 1.376683 CGCTTTCCCATGGACCGAA 60.377 57.895 15.22 5.48 0.00 4.30
2263 4706 2.267642 CGCTTTCCCATGGACCGA 59.732 61.111 15.22 0.00 0.00 4.69
2264 4707 3.508840 GCGCTTTCCCATGGACCG 61.509 66.667 15.22 9.04 0.00 4.79
2265 4708 3.508840 CGCGCTTTCCCATGGACC 61.509 66.667 15.22 0.00 0.00 4.46
2297 4740 9.680315 GATGATGAAGGTTACATACTGTACTAC 57.320 37.037 0.00 0.00 31.69 2.73
2298 4741 9.642343 AGATGATGAAGGTTACATACTGTACTA 57.358 33.333 0.00 0.00 31.69 1.82
2299 4742 8.540507 AGATGATGAAGGTTACATACTGTACT 57.459 34.615 0.00 0.00 31.69 2.73
2300 4743 7.868415 GGAGATGATGAAGGTTACATACTGTAC 59.132 40.741 0.00 0.00 31.69 2.90
2301 4744 7.785028 AGGAGATGATGAAGGTTACATACTGTA 59.215 37.037 0.00 0.00 0.00 2.74
2302 4745 6.613271 AGGAGATGATGAAGGTTACATACTGT 59.387 38.462 0.00 0.00 0.00 3.55
2303 4746 7.060383 AGGAGATGATGAAGGTTACATACTG 57.940 40.000 0.00 0.00 0.00 2.74
2304 4747 8.783660 TTAGGAGATGATGAAGGTTACATACT 57.216 34.615 0.00 0.00 0.00 2.12
2334 4777 1.403814 CAGAGGATCAGGCGGTAAGA 58.596 55.000 0.00 0.00 37.82 2.10
2343 4786 1.467734 GCTTGTGTTGCAGAGGATCAG 59.532 52.381 0.00 0.00 37.82 2.90
2405 4848 3.260475 TCCAGGACACATGATTTACCG 57.740 47.619 0.00 0.00 0.00 4.02
2493 4937 3.798878 CCAGCACAACTGTAGTATCGATG 59.201 47.826 8.54 0.00 45.68 3.84
2501 4945 1.151668 GAGCACCAGCACAACTGTAG 58.848 55.000 0.00 0.00 45.68 2.74
2565 5017 0.598065 CTTTTCCCAGGAACGCCAAG 59.402 55.000 0.00 0.00 36.29 3.61
2577 5029 3.186702 AGCGAGCTCTTATCTTTTCCC 57.813 47.619 12.85 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.