Multiple sequence alignment - TraesCS1A01G084700

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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 TraesCS1A01G084700 chr1A 100.000 7202 0 0 1 7202 70945770 70938569 0 13300
1 TraesCS1A01G084700 chr2A 97.841 6347 127 7 864 7202 685103462 685097118 0 10953
2 TraesCS1A01G084700 chr2A 97.448 6348 153 8 861 7202 284800769 284807113 0 10816
3 TraesCS1A01G084700 chr2A 97.322 6349 152 11 864 7202 572969065 572962725 0 10767
4 TraesCS1A01G084700 chr2A 96.785 6346 176 17 866 7202 716653299 716646973 0 10563
5 TraesCS1A01G084700 chr2A 97.229 866 24 0 1 866 685108990 685108125 0 1467
6 TraesCS1A01G084700 chr2A 97.229 866 21 2 1 866 284795233 284796095 0 1463
7 TraesCS1A01G084700 chr2A 97.113 866 24 1 1 866 270203541 270202677 0 1459
8 TraesCS1A01G084700 chr2A 91.322 991 79 6 866 1855 377553898 377554882 0 1347
9 TraesCS1A01G084700 chr5A 97.622 6350 136 11 861 7202 465654974 465661316 0 10876
10 TraesCS1A01G084700 chr5A 97.388 6356 149 11 861 7202 34942516 34936164 0 10802
11 TraesCS1A01G084700 chr5A 97.164 6348 162 8 861 7202 541977760 541984095 0 10709
12 TraesCS1A01G084700 chr5A 97.575 866 17 2 1 866 528066650 528067511 0 1480
13 TraesCS1A01G084700 chr5A 97.460 866 20 2 1 866 141897429 141898292 0 1476
14 TraesCS1A01G084700 chr5A 97.344 866 21 2 1 866 34948047 34947184 0 1471
15 TraesCS1A01G084700 chr5A 97.344 866 21 2 1 866 465649457 465650320 0 1471
16 TraesCS1A01G084700 chr3A 97.133 6348 141 14 866 7202 662009544 662003227 0 10676
17 TraesCS1A01G084700 chr3A 96.883 6352 177 13 861 7202 554828298 554834638 0 10613
18 TraesCS1A01G084700 chr7A 97.575 866 20 1 1 866 245454460 245453596 0 1482
19 TraesCS1A01G084700 chr6A 97.229 866 24 0 1 866 158996948 158996083 0 1467


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 TraesCS1A01G084700 chr1A 70938569 70945770 7201 True 13300 13300 100.000 1 7202 1 chr1A.!!$R1 7201
1 TraesCS1A01G084700 chr2A 685097118 685103462 6344 True 10953 10953 97.841 864 7202 1 chr2A.!!$R3 6338
2 TraesCS1A01G084700 chr2A 284800769 284807113 6344 False 10816 10816 97.448 861 7202 1 chr2A.!!$F2 6341
3 TraesCS1A01G084700 chr2A 572962725 572969065 6340 True 10767 10767 97.322 864 7202 1 chr2A.!!$R2 6338
4 TraesCS1A01G084700 chr2A 716646973 716653299 6326 True 10563 10563 96.785 866 7202 1 chr2A.!!$R5 6336
5 TraesCS1A01G084700 chr2A 685108125 685108990 865 True 1467 1467 97.229 1 866 1 chr2A.!!$R4 865
6 TraesCS1A01G084700 chr2A 284795233 284796095 862 False 1463 1463 97.229 1 866 1 chr2A.!!$F1 865
7 TraesCS1A01G084700 chr2A 270202677 270203541 864 True 1459 1459 97.113 1 866 1 chr2A.!!$R1 865
8 TraesCS1A01G084700 chr2A 377553898 377554882 984 False 1347 1347 91.322 866 1855 1 chr2A.!!$F3 989
9 TraesCS1A01G084700 chr5A 465654974 465661316 6342 False 10876 10876 97.622 861 7202 1 chr5A.!!$F3 6341
10 TraesCS1A01G084700 chr5A 34936164 34942516 6352 True 10802 10802 97.388 861 7202 1 chr5A.!!$R1 6341
11 TraesCS1A01G084700 chr5A 541977760 541984095 6335 False 10709 10709 97.164 861 7202 1 chr5A.!!$F5 6341
12 TraesCS1A01G084700 chr5A 528066650 528067511 861 False 1480 1480 97.575 1 866 1 chr5A.!!$F4 865
13 TraesCS1A01G084700 chr5A 141897429 141898292 863 False 1476 1476 97.460 1 866 1 chr5A.!!$F1 865
14 TraesCS1A01G084700 chr5A 34947184 34948047 863 True 1471 1471 97.344 1 866 1 chr5A.!!$R2 865
15 TraesCS1A01G084700 chr5A 465649457 465650320 863 False 1471 1471 97.344 1 866 1 chr5A.!!$F2 865
16 TraesCS1A01G084700 chr3A 662003227 662009544 6317 True 10676 10676 97.133 866 7202 1 chr3A.!!$R1 6336
17 TraesCS1A01G084700 chr3A 554828298 554834638 6340 False 10613 10613 96.883 861 7202 1 chr3A.!!$F1 6341
18 TraesCS1A01G084700 chr7A 245453596 245454460 864 True 1482 1482 97.575 1 866 1 chr7A.!!$R1 865
19 TraesCS1A01G084700 chr6A 158996083 158996948 865 True 1467 1467 97.229 1 866 1 chr6A.!!$R1 865

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
671 675 0.402121 AGGACAAGAAGGCTTCCACC 59.598 55.000 23.09 19.07 30.14 4.61 F
673 677 1.239347 GACAAGAAGGCTTCCACCAC 58.761 55.000 23.09 8.21 30.14 4.16 F
1229 1233 1.591863 GCGCCAGGATTCGTAGGAC 60.592 63.158 0.00 0.00 0.00 3.85 F
2320 2334 1.941294 CGAGTACGCAGGAGTAGATGT 59.059 52.381 0.00 0.00 0.00 3.06 F
3070 3088 1.419381 AAAATTGACCGCCCAAGGTT 58.581 45.000 0.00 0.00 46.09 3.50 F
4659 4711 1.068055 GCTTCCATTTCCACTGCACAG 60.068 52.381 0.00 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 2334 0.731994 TGACTTATACGCGGCGTACA 59.268 50.000 34.25 23.33 45.07 2.90 R
2473 2487 5.275067 ACAAGATAAAAGGCAAGCACAAA 57.725 34.783 0.00 0.00 0.00 2.83 R
3070 3088 0.621571 ATTGTCAGGGCCTGCTCCTA 60.622 55.000 29.02 15.14 32.49 2.94 R
3334 3358 0.687757 TCTGGCCCAGATAGCTCGTT 60.688 55.000 10.05 0.00 35.39 3.85 R
4998 5051 0.874607 GTTCCTCGACGCACAACTGT 60.875 55.000 0.00 0.00 0.00 3.55 R
6458 6518 1.560505 TCTCCATGACTAGTGCTGCA 58.439 50.000 0.00 0.00 0.00 4.41 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
255 257 4.586884 AGTCATGCATGAGTTCAATGTCT 58.413 39.130 29.38 16.07 37.15 3.41
491 495 5.565509 TGGATATTTCAACAGTACAGGCAA 58.434 37.500 0.00 0.00 0.00 4.52
550 554 6.231211 ACAGGTCCTTCTATACAACAAACAG 58.769 40.000 0.00 0.00 0.00 3.16
559 563 7.132694 TCTATACAACAAACAGCAATGTCTG 57.867 36.000 3.74 3.74 39.86 3.51
560 564 6.934083 TCTATACAACAAACAGCAATGTCTGA 59.066 34.615 10.68 0.00 37.51 3.27
648 652 1.738830 CCCCAGCGCATGCAAAAAG 60.739 57.895 19.57 1.33 46.23 2.27
671 675 0.402121 AGGACAAGAAGGCTTCCACC 59.598 55.000 23.09 19.07 30.14 4.61
673 677 1.239347 GACAAGAAGGCTTCCACCAC 58.761 55.000 23.09 8.21 30.14 4.16
696 700 2.352651 CGCTCCGTCAACATCAATCATT 59.647 45.455 0.00 0.00 0.00 2.57
703 707 4.093514 GTCAACATCAATCATTCGTGCTG 58.906 43.478 0.00 0.00 0.00 4.41
721 725 2.437850 GCAAAAGCAGTTGCGATGG 58.562 52.632 8.40 0.00 44.05 3.51
761 765 5.574188 AGACAGAAATTTTGGCCACTCTAT 58.426 37.500 3.88 0.00 0.00 1.98
1214 1218 3.130160 CTGGAGGAAGCTTGGCGC 61.130 66.667 2.10 0.00 39.57 6.53
1229 1233 1.591863 GCGCCAGGATTCGTAGGAC 60.592 63.158 0.00 0.00 0.00 3.85
1387 1391 7.564660 TCATTTTCCCTGCATATGGTTTATCTT 59.435 33.333 4.56 0.00 0.00 2.40
2058 2071 5.521010 CAGCATGACAAGTTGTTCACATTTT 59.479 36.000 10.45 0.00 39.69 1.82
2320 2334 1.941294 CGAGTACGCAGGAGTAGATGT 59.059 52.381 0.00 0.00 0.00 3.06
2473 2487 2.140717 CTGCCTTCGTTTTACTTCCGT 58.859 47.619 0.00 0.00 0.00 4.69
2563 2578 6.370166 TGATTATGTCGTGCTTGTCATGTTTA 59.630 34.615 0.00 0.00 33.44 2.01
2708 2724 4.959631 CGTTGTCGTTGCTCTAAAGTAA 57.040 40.909 0.00 0.00 0.00 2.24
2865 2881 6.940867 ACTATCAGTACAACTCAGTCTACACA 59.059 38.462 0.00 0.00 0.00 3.72
2900 2916 6.302269 AGTTCTGAAAATGACACCAGAAGAT 58.698 36.000 0.00 0.00 43.62 2.40
3070 3088 1.419381 AAAATTGACCGCCCAAGGTT 58.581 45.000 0.00 0.00 46.09 3.50
3142 3160 2.181125 TCCCTAGTAATCCGCACAACA 58.819 47.619 0.00 0.00 0.00 3.33
3151 3169 2.203139 CGCACAACACAGGACCCA 60.203 61.111 0.00 0.00 0.00 4.51
3171 3189 3.580319 GACCAGGGCCCACAGGTT 61.580 66.667 28.01 15.71 33.77 3.50
3227 3251 4.039245 CAGGTAAGTGTTCAGAGGAGTTCA 59.961 45.833 0.00 0.00 0.00 3.18
4225 4256 3.763897 ACAAGTTTTGAGCAACAACTCCT 59.236 39.130 9.53 0.00 38.29 3.69
4408 4459 3.794028 GCAGATCGTAAGTACAGCTTGAG 59.206 47.826 0.00 0.00 38.05 3.02
4577 4628 4.230002 CCACACACCACCGTCGGT 62.230 66.667 12.23 12.23 41.07 4.69
4659 4711 1.068055 GCTTCCATTTCCACTGCACAG 60.068 52.381 0.00 0.00 0.00 3.66
4998 5051 1.685765 ACAGATGGCGGCAGTCCTA 60.686 57.895 19.29 0.00 0.00 2.94
6200 6260 2.224042 ACTTCGCGGATGAAGATGCATA 60.224 45.455 6.13 0.00 46.64 3.14
6282 6342 6.039616 TGTTGTTTCAGATTTGTAGTTTGCC 58.960 36.000 0.00 0.00 0.00 4.52
6324 6384 5.451937 GCTACCTTATGCTATGTGTGTCAGA 60.452 44.000 0.00 0.00 0.00 3.27
6348 6408 4.846779 TTGAACAAGTTTGCCTATGTCC 57.153 40.909 0.00 0.00 0.00 4.02
6458 6518 4.321042 AGTTGAAACTTGATGGCTGCCAT 61.321 43.478 33.02 33.02 41.00 4.40
6570 6633 1.334243 GTAGCCTTCGACGCTCAGTAT 59.666 52.381 9.38 0.00 37.79 2.12
6654 6722 6.945072 ACACTAAAAAGACTAAGTTTCAGCG 58.055 36.000 0.00 0.00 0.00 5.18
6809 6878 3.069872 TGGTACAGTTGAACACACGGTAT 59.930 43.478 0.00 0.00 0.00 2.73
6869 6938 5.759506 TCAGTTCGCATTCCTTAAAACAA 57.240 34.783 0.00 0.00 0.00 2.83
6963 7032 6.072452 GCTAGGATTATACCAAACATTGCCTC 60.072 42.308 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
280 282 3.762288 ACACGGATGTACTGATGTACTGT 59.238 43.478 7.67 1.52 46.70 3.55
281 283 4.371855 ACACGGATGTACTGATGTACTG 57.628 45.455 7.67 1.00 46.70 2.74
327 331 7.368059 GGATTAATCTGGTTTCGTTTTCAGTT 58.632 34.615 14.95 0.00 0.00 3.16
491 495 5.895636 TGATTGCGGTGTATCTTCAAATT 57.104 34.783 0.00 0.00 0.00 1.82
543 547 4.558095 GCATTCTCAGACATTGCTGTTTGT 60.558 41.667 7.61 0.00 38.35 2.83
550 554 2.163815 AGCTTGCATTCTCAGACATTGC 59.836 45.455 0.00 0.00 0.00 3.56
648 652 0.884514 GAAGCCTTCTTGTCCTTGGC 59.115 55.000 0.00 0.00 43.52 4.52
671 675 0.388520 TGATGTTGACGGAGCGAGTG 60.389 55.000 0.00 0.00 0.00 3.51
673 677 1.590238 GATTGATGTTGACGGAGCGAG 59.410 52.381 0.00 0.00 0.00 5.03
710 714 0.321564 TGGTCTTCCCATCGCAACTG 60.322 55.000 0.00 0.00 38.72 3.16
719 723 0.263172 TTTTTGCCCTGGTCTTCCCA 59.737 50.000 0.00 0.00 42.51 4.37
721 725 1.613925 GTCTTTTTGCCCTGGTCTTCC 59.386 52.381 0.00 0.00 0.00 3.46
761 765 7.334421 GCTCATATCTTGTACTTTTGAACCTGA 59.666 37.037 0.00 0.00 0.00 3.86
782 786 3.514539 TGCTCCTGTCTATATGGCTCAT 58.485 45.455 0.00 0.00 0.00 2.90
1214 1218 1.000163 CGATGGTCCTACGAATCCTGG 60.000 57.143 0.00 0.00 0.00 4.45
1229 1233 4.101790 GCACACCAACGCCGATGG 62.102 66.667 12.24 12.24 43.84 3.51
2058 2071 1.269448 GCTTTCAATGCTGAAACCGGA 59.731 47.619 9.46 0.00 44.76 5.14
2320 2334 0.731994 TGACTTATACGCGGCGTACA 59.268 50.000 34.25 23.33 45.07 2.90
2473 2487 5.275067 ACAAGATAAAAGGCAAGCACAAA 57.725 34.783 0.00 0.00 0.00 2.83
2708 2724 8.962884 TGTGTGATTAGTTGCATCATAACTAT 57.037 30.769 0.00 0.00 39.56 2.12
2865 2881 7.936847 TGTCATTTTCAGAACTATGGTACTTGT 59.063 33.333 0.00 0.00 0.00 3.16
2945 2962 7.714813 TGTGAGTGTAATCTTTTTCATGTGAGA 59.285 33.333 0.00 0.00 0.00 3.27
2950 2968 8.854979 TTTGTGTGAGTGTAATCTTTTTCATG 57.145 30.769 0.00 0.00 0.00 3.07
3070 3088 0.621571 ATTGTCAGGGCCTGCTCCTA 60.622 55.000 29.02 15.14 32.49 2.94
3142 3160 1.990060 CCTGGTCGATGGGTCCTGT 60.990 63.158 0.00 0.00 0.00 4.00
3151 3169 3.402681 CTGTGGGCCCTGGTCGAT 61.403 66.667 25.70 0.00 0.00 3.59
3171 3189 1.440938 GGCGCTCGCTCTCTCTCTTA 61.441 60.000 7.64 0.00 41.60 2.10
3227 3251 3.616721 AGCCGACGCTCACCAGTT 61.617 61.111 0.00 0.00 43.95 3.16
3334 3358 0.687757 TCTGGCCCAGATAGCTCGTT 60.688 55.000 10.05 0.00 35.39 3.85
4408 4459 3.931578 ACTGGTGCACTGATTAGTCTTC 58.068 45.455 17.98 0.00 34.07 2.87
4659 4711 0.892063 AGAGAGACGCTGGAGGTTTC 59.108 55.000 0.00 0.00 0.00 2.78
4998 5051 0.874607 GTTCCTCGACGCACAACTGT 60.875 55.000 0.00 0.00 0.00 3.55
5539 5597 7.334171 GCTTTACCAAATGCTTCACCAAATTAT 59.666 33.333 0.00 0.00 33.97 1.28
5590 5648 9.667989 AAATTAAATTCAACTACACCGTGTTAC 57.332 29.630 9.98 0.00 0.00 2.50
5625 5683 7.806487 TGAATGTAGTTCAGAAACTAGTACACG 59.194 37.037 0.00 0.00 46.14 4.49
5859 5919 3.138283 TGATTTCCAAACCAGACTCCTGT 59.862 43.478 0.00 0.00 38.74 4.00
6200 6260 7.224557 GGTTCAACATAACAAATGCAGACTTTT 59.775 33.333 0.00 0.00 0.00 2.27
6282 6342 5.473504 AGGTAGCTGGTTCAACATAACAAAG 59.526 40.000 0.00 0.00 0.00 2.77
6324 6384 5.221244 GGACATAGGCAAACTTGTTCAAACT 60.221 40.000 0.00 0.00 0.00 2.66
6348 6408 7.585210 CGACATAAGCAAATGATGTACTTGATG 59.415 37.037 5.41 0.00 33.99 3.07
6458 6518 1.560505 TCTCCATGACTAGTGCTGCA 58.439 50.000 0.00 0.00 0.00 4.41
6570 6633 6.118170 AGTACTACCGTTCATGTCTAAGCTA 58.882 40.000 0.00 0.00 0.00 3.32
6627 6695 8.395633 GCTGAAACTTAGTCTTTTTAGTGTTCA 58.604 33.333 0.00 0.00 0.00 3.18
6654 6722 7.573283 GCTTTTTAGTACTGAATGTTGTCCTCC 60.573 40.741 5.39 0.00 0.00 4.30
6869 6938 8.046708 TGCCACTGTTAATTCTTAGTATGTCAT 58.953 33.333 0.00 0.00 0.00 3.06
6963 7032 1.819288 TCTAGGCTGTGGTTCTTCTCG 59.181 52.381 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.