Multiple sequence alignment - TraesCS5B01G319600

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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 TraesCS5B01G319600 chr5B 100.000 3095 0 0 1 3095 504308399 504305305 0.000000e+00 5716
1 TraesCS5B01G319600 chr5D 94.896 3135 77 28 8 3095 417042148 417039050 0.000000e+00 4826
2 TraesCS5B01G319600 chr5A 95.723 2268 64 14 858 3095 530302848 530300584 0.000000e+00 3620
3 TraesCS5B01G319600 chr5A 90.590 797 17 11 1 760 530304049 530303274 0.000000e+00 1003
4 TraesCS5B01G319600 chr7A 86.047 172 24 0 1668 1839 282368854 282368683 5.270000e-43 185
5 TraesCS5B01G319600 chr7A 86.577 149 20 0 1300 1448 282369255 282369107 6.870000e-37 165
6 TraesCS5B01G319600 chr7B 85.465 172 25 0 1668 1839 239363366 239363537 2.450000e-41 180
7 TraesCS5B01G319600 chr7B 86.577 149 20 0 1300 1448 239362965 239363113 6.870000e-37 165
8 TraesCS5B01G319600 chr3B 88.514 148 15 2 1297 1443 786970547 786970401 8.820000e-41 178
9 TraesCS5B01G319600 chr3D 87.838 148 16 2 1297 1443 588489275 588489129 4.100000e-39 172
10 TraesCS5B01G319600 chr7D 87.248 149 19 0 1300 1448 259840844 259840696 1.480000e-38 171
11 TraesCS5B01G319600 chr3A 87.162 148 17 2 1297 1443 718836820 718836674 1.910000e-37 167


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 TraesCS5B01G319600 chr5B 504305305 504308399 3094 True 5716.0 5716 100.0000 1 3095 1 chr5B.!!$R1 3094
1 TraesCS5B01G319600 chr5D 417039050 417042148 3098 True 4826.0 4826 94.8960 8 3095 1 chr5D.!!$R1 3087
2 TraesCS5B01G319600 chr5A 530300584 530304049 3465 True 2311.5 3620 93.1565 1 3095 2 chr5A.!!$R1 3094

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
820 876 0.263172 TCCTCATCTCCACCTCCTCC 59.737 60.0 0.0 0.0 0.0 4.30 F
821 877 0.264359 CCTCATCTCCACCTCCTCCT 59.736 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 2057 1.770658 CCATCTGCTGATCCCCTACAA 59.229 52.381 2.65 0.0 0.0 2.41 R
2792 3210 2.203070 GGGATCGTCGCATGGCTT 60.203 61.111 0.00 0.0 0.0 4.35 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
324 331 5.756195 TGAATATTGCATTGACTAGTGCC 57.244 39.130 0.00 0.00 40.56 5.01
329 336 1.072173 TGCATTGACTAGTGCCTGTGT 59.928 47.619 0.00 0.00 40.56 3.72
506 527 3.585990 GCGCCACTGTTGTGCTGT 61.586 61.111 9.85 0.00 42.54 4.40
507 528 2.328989 CGCCACTGTTGTGCTGTG 59.671 61.111 0.00 0.00 42.54 3.66
508 529 2.026590 GCCACTGTTGTGCTGTGC 59.973 61.111 0.00 0.00 43.13 4.57
509 530 2.723746 CCACTGTTGTGCTGTGCC 59.276 61.111 0.00 0.00 43.13 5.01
510 531 2.723746 CACTGTTGTGCTGTGCCC 59.276 61.111 0.00 0.00 39.54 5.36
511 532 2.519302 ACTGTTGTGCTGTGCCCC 60.519 61.111 0.00 0.00 0.00 5.80
512 533 3.297620 CTGTTGTGCTGTGCCCCC 61.298 66.667 0.00 0.00 0.00 5.40
627 657 1.731433 CTGTGCCTGTGCTTGTGCTT 61.731 55.000 0.00 0.00 40.48 3.91
628 658 1.299620 GTGCCTGTGCTTGTGCTTG 60.300 57.895 0.00 0.00 40.48 4.01
629 659 1.753848 TGCCTGTGCTTGTGCTTGT 60.754 52.632 0.00 0.00 40.48 3.16
630 660 1.299620 GCCTGTGCTTGTGCTTGTG 60.300 57.895 0.00 0.00 40.48 3.33
631 661 1.299620 CCTGTGCTTGTGCTTGTGC 60.300 57.895 0.00 0.00 40.48 4.57
632 662 1.731433 CCTGTGCTTGTGCTTGTGCT 61.731 55.000 0.00 0.00 40.48 4.40
820 876 0.263172 TCCTCATCTCCACCTCCTCC 59.737 60.000 0.00 0.00 0.00 4.30
821 877 0.264359 CCTCATCTCCACCTCCTCCT 59.736 60.000 0.00 0.00 0.00 3.69
824 880 0.762461 CATCTCCACCTCCTCCTCCC 60.762 65.000 0.00 0.00 0.00 4.30
830 886 3.039526 CCTCCTCCTCCCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
831 887 2.612251 CTCCTCCTCCCCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
832 888 3.430497 TCCTCCTCCCCCTCCTCG 61.430 72.222 0.00 0.00 0.00 4.63
833 889 3.430497 CCTCCTCCCCCTCCTCGA 61.430 72.222 0.00 0.00 0.00 4.04
836 892 2.203714 CCTCCCCCTCCTCGATCC 60.204 72.222 0.00 0.00 0.00 3.36
837 893 2.203714 CTCCCCCTCCTCGATCCC 60.204 72.222 0.00 0.00 0.00 3.85
838 894 2.704198 TCCCCCTCCTCGATCCCT 60.704 66.667 0.00 0.00 0.00 4.20
840 896 2.203714 CCCCTCCTCGATCCCTCC 60.204 72.222 0.00 0.00 0.00 4.30
841 897 2.784654 CCCCTCCTCGATCCCTCCT 61.785 68.421 0.00 0.00 0.00 3.69
842 898 1.228737 CCCTCCTCGATCCCTCCTC 60.229 68.421 0.00 0.00 0.00 3.71
846 902 0.699577 TCCTCGATCCCTCCTCTCCT 60.700 60.000 0.00 0.00 0.00 3.69
851 907 1.144913 CGATCCCTCCTCTCCTCTTCT 59.855 57.143 0.00 0.00 0.00 2.85
856 1240 2.244769 CCCTCCTCTCCTCTTCTCTTCT 59.755 54.545 0.00 0.00 0.00 2.85
886 1270 1.603842 CCAGCTGCCTGACATACCA 59.396 57.895 8.66 0.00 41.77 3.25
888 1272 0.745845 CAGCTGCCTGACATACCACC 60.746 60.000 0.00 0.00 41.77 4.61
889 1273 1.452108 GCTGCCTGACATACCACCC 60.452 63.158 0.00 0.00 0.00 4.61
890 1274 1.224592 CTGCCTGACATACCACCCC 59.775 63.158 0.00 0.00 0.00 4.95
896 1282 1.072331 CTGACATACCACCCCATAGGC 59.928 57.143 0.00 0.00 40.58 3.93
907 1293 2.182312 ACCCCATAGGCAGGAAGATAGA 59.818 50.000 0.00 0.00 40.58 1.98
938 1324 3.589881 CAAGCTAGCGCATGGCCC 61.590 66.667 11.47 0.00 45.17 5.80
953 1339 4.487412 CCCGGTCGGCGACTGTAC 62.487 72.222 37.82 22.38 37.24 2.90
978 1368 1.343069 AATAGAGGGAGATCGGCACC 58.657 55.000 0.00 0.00 0.00 5.01
980 1370 2.280404 TAGAGGGAGATCGGCACCGT 62.280 60.000 9.23 0.00 40.74 4.83
1020 1410 2.444140 GCGGGCTTCCCTCTAGGA 60.444 66.667 0.00 0.00 45.68 2.94
1201 1591 2.434185 GCTTCGCCACCGATGACA 60.434 61.111 3.61 0.00 43.97 3.58
1251 1641 4.292178 GCGGCATCCTCCTCCTCG 62.292 72.222 0.00 0.00 0.00 4.63
1254 1644 1.456705 GGCATCCTCCTCCTCGTCT 60.457 63.158 0.00 0.00 0.00 4.18
1649 2041 2.685897 TGACGCTAAAACCTGTGCTTTT 59.314 40.909 0.00 0.00 0.00 2.27
2427 2826 9.520204 CAATTGACAGTGTTCTTAACAATCTTT 57.480 29.630 0.00 0.00 44.16 2.52
2700 3102 6.653740 GGTTCTGTTAGTTTTGTGGCTAGTAT 59.346 38.462 0.00 0.00 0.00 2.12
2701 3103 7.360946 GGTTCTGTTAGTTTTGTGGCTAGTATG 60.361 40.741 0.00 0.00 0.00 2.39
2777 3195 4.880120 TGAGACCAAATGATCAGCTGATTC 59.120 41.667 29.26 19.97 34.37 2.52
2834 3252 4.109050 TGCTTGATTTCGGTGTTTGTTTC 58.891 39.130 0.00 0.00 0.00 2.78
2862 3280 1.604185 CGAGCTTAGCAGGTATGAGGC 60.604 57.143 7.07 0.00 0.00 4.70
2868 3286 0.394565 AGCAGGTATGAGGCGGAATC 59.605 55.000 0.00 0.00 0.00 2.52
2881 3299 1.750778 GCGGAATCATTGATTGGTGGT 59.249 47.619 16.41 0.00 31.89 4.16
2889 3307 3.577415 TCATTGATTGGTGGTGCATTCAA 59.423 39.130 0.00 0.00 0.00 2.69
2898 3316 2.788786 GTGGTGCATTCAACTCGTTTTG 59.211 45.455 0.00 0.00 0.00 2.44
2916 3334 5.334569 CGTTTTGGTTTTCGTCATCTATGGT 60.335 40.000 0.00 0.00 0.00 3.55
2936 3355 6.959671 TGGTTGAACTTGTTGATTTGTTTC 57.040 33.333 0.00 0.00 0.00 2.78
2941 3360 6.563422 TGAACTTGTTGATTTGTTTCTCCAG 58.437 36.000 0.00 0.00 0.00 3.86
3029 3448 7.961827 GTCATCTCACAAGAAATGATGAAGTTC 59.038 37.037 0.00 0.00 43.07 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.142867 GATCGCGGTCGTCGTCGTA 62.143 63.158 2.34 0.00 41.72 3.43
5 6 4.511443 GATCGCGGTCGTCGTCGT 62.511 66.667 2.34 0.00 41.72 4.34
128 129 2.626780 GGAAAACACGGGAGCCAGC 61.627 63.158 0.00 0.00 0.00 4.85
221 228 0.820871 TGTTGCTTGGTTGGTTCCAC 59.179 50.000 0.00 0.00 37.20 4.02
324 331 1.633561 CATGTCCGCTACTCACACAG 58.366 55.000 0.00 0.00 0.00 3.66
329 336 0.179076 CCATGCATGTCCGCTACTCA 60.179 55.000 24.58 0.00 0.00 3.41
512 533 4.366684 AGGGAAAAGGGCAGGGCG 62.367 66.667 0.00 0.00 0.00 6.13
513 534 2.363018 GAGGGAAAAGGGCAGGGC 60.363 66.667 0.00 0.00 0.00 5.19
514 535 2.044946 CGAGGGAAAAGGGCAGGG 60.045 66.667 0.00 0.00 0.00 4.45
515 536 2.751837 GCGAGGGAAAAGGGCAGG 60.752 66.667 0.00 0.00 0.00 4.85
516 537 1.603455 TTGCGAGGGAAAAGGGCAG 60.603 57.895 0.00 0.00 34.76 4.85
627 657 1.473258 AGTTTGGAGTTTGCAGCACA 58.527 45.000 0.00 0.00 0.00 4.57
628 658 2.195922 CAAGTTTGGAGTTTGCAGCAC 58.804 47.619 0.00 0.00 0.00 4.40
629 659 1.824230 ACAAGTTTGGAGTTTGCAGCA 59.176 42.857 0.00 0.00 0.00 4.41
630 660 2.584492 ACAAGTTTGGAGTTTGCAGC 57.416 45.000 0.00 0.00 0.00 5.25
631 661 5.890334 TCTAAACAAGTTTGGAGTTTGCAG 58.110 37.500 7.53 0.00 35.57 4.41
632 662 5.890334 CTCTAAACAAGTTTGGAGTTTGCA 58.110 37.500 23.03 0.00 46.46 4.08
779 835 0.533308 AGTAAAAGTCCGCGTGGCAA 60.533 50.000 11.05 0.00 34.14 4.52
820 876 2.203714 GGGATCGAGGAGGGGGAG 60.204 72.222 0.00 0.00 0.00 4.30
821 877 2.704198 AGGGATCGAGGAGGGGGA 60.704 66.667 0.00 0.00 0.00 4.81
824 880 1.228737 GAGGAGGGATCGAGGAGGG 60.229 68.421 0.00 0.00 0.00 4.30
830 886 1.144093 GAAGAGGAGAGGAGGGATCGA 59.856 57.143 0.00 0.00 0.00 3.59
831 887 1.144913 AGAAGAGGAGAGGAGGGATCG 59.855 57.143 0.00 0.00 0.00 3.69
832 888 2.447047 AGAGAAGAGGAGAGGAGGGATC 59.553 54.545 0.00 0.00 0.00 3.36
833 889 2.513602 AGAGAAGAGGAGAGGAGGGAT 58.486 52.381 0.00 0.00 0.00 3.85
836 892 3.053693 TGAGAAGAGAAGAGGAGAGGAGG 60.054 52.174 0.00 0.00 0.00 4.30
837 893 4.235079 TGAGAAGAGAAGAGGAGAGGAG 57.765 50.000 0.00 0.00 0.00 3.69
838 894 4.685848 CGATGAGAAGAGAAGAGGAGAGGA 60.686 50.000 0.00 0.00 0.00 3.71
840 896 4.273480 GTCGATGAGAAGAGAAGAGGAGAG 59.727 50.000 0.00 0.00 0.00 3.20
841 897 4.196193 GTCGATGAGAAGAGAAGAGGAGA 58.804 47.826 0.00 0.00 0.00 3.71
842 898 3.002246 CGTCGATGAGAAGAGAAGAGGAG 59.998 52.174 0.00 0.00 0.00 3.69
851 907 0.679960 TGGCCTCGTCGATGAGAAGA 60.680 55.000 31.67 14.16 38.28 2.87
856 1240 2.755876 AGCTGGCCTCGTCGATGA 60.756 61.111 7.21 7.21 0.00 2.92
877 1261 1.136828 GCCTATGGGGTGGTATGTCA 58.863 55.000 0.00 0.00 37.43 3.58
886 1270 2.182312 TCTATCTTCCTGCCTATGGGGT 59.818 50.000 0.00 0.00 37.43 4.95
888 1272 2.235898 GCTCTATCTTCCTGCCTATGGG 59.764 54.545 0.00 0.00 0.00 4.00
889 1273 2.094286 CGCTCTATCTTCCTGCCTATGG 60.094 54.545 0.00 0.00 0.00 2.74
890 1274 2.560542 ACGCTCTATCTTCCTGCCTATG 59.439 50.000 0.00 0.00 0.00 2.23
896 1282 3.482436 AGGAGTACGCTCTATCTTCCTG 58.518 50.000 0.00 0.00 41.38 3.86
907 1293 1.546961 AGCTTGTGTAGGAGTACGCT 58.453 50.000 0.00 0.00 39.92 5.07
938 1324 2.202440 CTGTACAGTCGCCGACCG 60.202 66.667 14.60 6.22 32.18 4.79
941 1327 0.669619 TTTCACTGTACAGTCGCCGA 59.330 50.000 25.63 16.57 40.20 5.54
943 1329 4.106029 TCTATTTCACTGTACAGTCGCC 57.894 45.455 25.63 0.00 40.20 5.54
953 1339 3.553922 GCCGATCTCCCTCTATTTCACTG 60.554 52.174 0.00 0.00 0.00 3.66
978 1368 1.455383 GCCCAAATCCATAGGCCACG 61.455 60.000 5.01 0.00 39.60 4.94
980 1370 1.152777 CGCCCAAATCCATAGGCCA 60.153 57.895 5.01 0.00 42.66 5.36
1649 2041 4.141287 CTGATCCCCTACAAACACACAAA 58.859 43.478 0.00 0.00 0.00 2.83
1655 2054 2.265367 TCTGCTGATCCCCTACAAACA 58.735 47.619 0.00 0.00 0.00 2.83
1658 2057 1.770658 CCATCTGCTGATCCCCTACAA 59.229 52.381 2.65 0.00 0.00 2.41
2427 2826 7.230747 TGATGAAAGAAGTACCAGGAAAATCA 58.769 34.615 0.00 0.00 0.00 2.57
2700 3102 6.931281 GCATACAATAGCTCACTCCTAAATCA 59.069 38.462 0.00 0.00 0.00 2.57
2701 3103 7.158021 AGCATACAATAGCTCACTCCTAAATC 58.842 38.462 0.00 0.00 36.00 2.17
2792 3210 2.203070 GGGATCGTCGCATGGCTT 60.203 61.111 0.00 0.00 0.00 4.35
2834 3252 1.667724 CCTGCTAAGCTCGGAAACATG 59.332 52.381 0.00 0.00 0.00 3.21
2862 3280 2.480073 GCACCACCAATCAATGATTCCG 60.480 50.000 5.36 2.02 28.87 4.30
2868 3286 3.596310 TGAATGCACCACCAATCAATG 57.404 42.857 0.00 0.00 0.00 2.82
2881 3299 3.791973 AACCAAAACGAGTTGAATGCA 57.208 38.095 0.00 0.00 0.00 3.96
2889 3307 3.875134 AGATGACGAAAACCAAAACGAGT 59.125 39.130 0.00 0.00 0.00 4.18
2898 3316 5.411669 AGTTCAACCATAGATGACGAAAACC 59.588 40.000 0.00 0.00 0.00 3.27
2916 3334 6.929625 TGGAGAAACAAATCAACAAGTTCAA 58.070 32.000 0.00 0.00 0.00 2.69
2936 3355 2.408271 TGCAATCTAAGGTGCTGGAG 57.592 50.000 0.00 0.00 41.48 3.86


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

AutoCloner maintained by Alex Coulton.