Multiple sequence alignment - TraesCS3B01G143400

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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 TraesCS3B01G143400 chr3B 100.000 3179 0 0 1 3179 132169978 132173156 0 5871
1 TraesCS3B01G143400 chr3B 97.579 3180 66 8 1 3179 796294987 796298156 0 5435
2 TraesCS3B01G143400 chr4B 92.197 3204 191 33 1 3179 251709930 251713099 0 4477
3 TraesCS3B01G143400 chr4B 93.590 1794 111 3 966 2756 251687993 251689785 0 2673
4 TraesCS3B01G143400 chr4B 92.707 905 50 9 1 901 251297044 251297936 0 1291
5 TraesCS3B01G143400 chr4B 91.501 906 58 12 1 901 251687096 251687987 0 1229
6 TraesCS3B01G143400 chr2B 90.047 2351 185 30 857 3177 219377521 219379852 0 3000
7 TraesCS3B01G143400 chr2B 91.561 2121 149 22 856 2954 310925196 310923084 0 2898
8 TraesCS3B01G143400 chr2B 93.400 803 44 6 1 797 310925989 310925190 0 1181
9 TraesCS3B01G143400 chr2D 89.940 2346 194 34 855 3176 143545356 143547683 0 2987
10 TraesCS3B01G143400 chr2D 94.389 802 38 4 1 798 143544565 143545363 0 1225
11 TraesCS3B01G143400 chr7D 89.067 2369 187 34 855 3172 368316615 368318962 0 2874
12 TraesCS3B01G143400 chr7D 94.389 802 37 5 1 798 383922971 383923768 0 1225
13 TraesCS3B01G143400 chr7D 94.382 801 38 4 1 797 368315824 368316621 0 1223
14 TraesCS3B01G143400 chr3A 88.258 2359 203 40 857 3179 647250522 647252842 0 2754
15 TraesCS3B01G143400 chr6A 87.394 2356 225 40 856 3179 140428562 140430877 0 2639
16 TraesCS3B01G143400 chr2A 87.378 2361 221 42 856 3179 184077860 184080180 0 2638
17 TraesCS3B01G143400 chr6D 94.279 804 38 5 1 799 85381417 85380617 0 1223


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 TraesCS3B01G143400 chr3B 132169978 132173156 3178 False 5871.0 5871 100.0000 1 3179 1 chr3B.!!$F1 3178
1 TraesCS3B01G143400 chr3B 796294987 796298156 3169 False 5435.0 5435 97.5790 1 3179 1 chr3B.!!$F2 3178
2 TraesCS3B01G143400 chr4B 251709930 251713099 3169 False 4477.0 4477 92.1970 1 3179 1 chr4B.!!$F2 3178
3 TraesCS3B01G143400 chr4B 251687096 251689785 2689 False 1951.0 2673 92.5455 1 2756 2 chr4B.!!$F3 2755
4 TraesCS3B01G143400 chr4B 251297044 251297936 892 False 1291.0 1291 92.7070 1 901 1 chr4B.!!$F1 900
5 TraesCS3B01G143400 chr2B 219377521 219379852 2331 False 3000.0 3000 90.0470 857 3177 1 chr2B.!!$F1 2320
6 TraesCS3B01G143400 chr2B 310923084 310925989 2905 True 2039.5 2898 92.4805 1 2954 2 chr2B.!!$R1 2953
7 TraesCS3B01G143400 chr2D 143544565 143547683 3118 False 2106.0 2987 92.1645 1 3176 2 chr2D.!!$F1 3175
8 TraesCS3B01G143400 chr7D 368315824 368318962 3138 False 2048.5 2874 91.7245 1 3172 2 chr7D.!!$F2 3171
9 TraesCS3B01G143400 chr7D 383922971 383923768 797 False 1225.0 1225 94.3890 1 798 1 chr7D.!!$F1 797
10 TraesCS3B01G143400 chr3A 647250522 647252842 2320 False 2754.0 2754 88.2580 857 3179 1 chr3A.!!$F1 2322
11 TraesCS3B01G143400 chr6A 140428562 140430877 2315 False 2639.0 2639 87.3940 856 3179 1 chr6A.!!$F1 2323
12 TraesCS3B01G143400 chr2A 184077860 184080180 2320 False 2638.0 2638 87.3780 856 3179 1 chr2A.!!$F1 2323
13 TraesCS3B01G143400 chr6D 85380617 85381417 800 True 1223.0 1223 94.2790 1 799 1 chr6D.!!$R1 798

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
249 255 3.009916 AGACTCATGCATCCACTTTTCCT 59.990 43.478 0.0 0.0 0.0 3.36 F
1930 2019 0.036765 CCCCGAGTTTTCCGTGATCA 60.037 55.000 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2136 0.461548 CGCTGATGGTGCTAAGAGGA 59.538 55.000 0.0 0.0 0.00 3.71 R
2873 2985 3.679725 CACATGTACACACACACACAAC 58.320 45.455 0.0 0.0 37.54 3.32 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
194 200 3.379650 GCTAATGGCTCGCTGGTTA 57.620 52.632 0.00 0.0 38.06 2.85
249 255 3.009916 AGACTCATGCATCCACTTTTCCT 59.990 43.478 0.00 0.0 0.00 3.36
273 280 3.060473 GCGACTTGCGGAGTACATATTTC 60.060 47.826 0.00 0.0 39.19 2.17
307 314 7.093354 TCAACTGCACTTATGTTGTTTTTCAA 58.907 30.769 13.52 0.0 41.05 2.69
449 456 4.090090 GGCTATGAAGAGTAGATGCCCTA 58.910 47.826 0.00 0.0 33.66 3.53
691 698 5.163612 CGTCACAGAAGAGATGGTATCAGAA 60.164 44.000 0.00 0.0 0.00 3.02
822 829 9.517868 AAAAATCATCATCTCTTCTCAAGTTCT 57.482 29.630 0.00 0.0 0.00 3.01
824 831 9.598517 AAATCATCATCTCTTCTCAAGTTCTAC 57.401 33.333 0.00 0.0 0.00 2.59
825 832 7.106439 TCATCATCTCTTCTCAAGTTCTACC 57.894 40.000 0.00 0.0 0.00 3.18
826 833 6.894654 TCATCATCTCTTCTCAAGTTCTACCT 59.105 38.462 0.00 0.0 0.00 3.08
827 834 6.767524 TCATCTCTTCTCAAGTTCTACCTC 57.232 41.667 0.00 0.0 0.00 3.85
828 835 6.489603 TCATCTCTTCTCAAGTTCTACCTCT 58.510 40.000 0.00 0.0 0.00 3.69
829 836 6.601613 TCATCTCTTCTCAAGTTCTACCTCTC 59.398 42.308 0.00 0.0 0.00 3.20
830 837 5.258051 TCTCTTCTCAAGTTCTACCTCTCC 58.742 45.833 0.00 0.0 0.00 3.71
834 841 6.831353 TCTTCTCAAGTTCTACCTCTCCTATG 59.169 42.308 0.00 0.0 0.00 2.23
836 843 7.209340 TCTCAAGTTCTACCTCTCCTATGTA 57.791 40.000 0.00 0.0 0.00 2.29
838 845 8.946248 TCTCAAGTTCTACCTCTCCTATGTATA 58.054 37.037 0.00 0.0 0.00 1.47
1095 1168 0.950836 TTCTGGGTGTGTTGATTGCG 59.049 50.000 0.00 0.0 0.00 4.85
1121 1208 2.429610 ACTACACAGTGTTTCACGACCT 59.570 45.455 12.53 0.0 39.64 3.85
1132 1219 3.605013 CACGACCTGTGTTCCATGA 57.395 52.632 0.00 0.0 43.88 3.07
1192 1280 4.485875 TGTCCCTTCTAGGTTCAGTGTTA 58.514 43.478 0.00 0.0 31.93 2.41
1441 1530 3.823873 CACATTTTTACCACCACCAGCTA 59.176 43.478 0.00 0.0 0.00 3.32
1510 1599 2.038975 ACCGCCCAGCTCCTAGAA 59.961 61.111 0.00 0.0 0.00 2.10
1666 1755 0.532573 GAACAGCGAGATGTCCTCCA 59.467 55.000 0.00 0.0 38.71 3.86
1708 1797 2.007576 GGTATGGCCCTCAACCCTT 58.992 57.895 0.00 0.0 0.00 3.95
1743 1832 1.159664 ACCTTCTGCCTCTCCAGGT 59.840 57.895 0.00 0.0 42.74 4.00
1930 2019 0.036765 CCCCGAGTTTTCCGTGATCA 60.037 55.000 0.00 0.0 0.00 2.92
2009 2099 1.336609 GGAGTACCTTCGTGTCGCTTT 60.337 52.381 0.00 0.0 0.00 3.51
2216 2309 4.010349 AGTAGTTTGTATTCTGGCAAGGC 58.990 43.478 0.00 0.0 0.00 4.35
2366 2460 1.242076 CCTTCCAGAGTTTGCACAGG 58.758 55.000 0.00 0.0 0.00 4.00
2639 2739 4.096984 GCATTCCTTACTCTGTTGATTGGG 59.903 45.833 0.00 0.0 0.00 4.12
2646 2746 6.488006 CCTTACTCTGTTGATTGGGATATTGG 59.512 42.308 0.00 0.0 0.00 3.16
2873 2985 4.778534 TTTAGTCCTGTACGTGAAGAGG 57.221 45.455 0.00 0.0 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 255 1.884075 ATGTACTCCGCAAGTCGCCA 61.884 55.000 0.00 0.00 39.55 5.69
273 280 5.805486 ACATAAGTGCAGTTGAGTACGTATG 59.195 40.000 17.21 11.59 44.97 2.39
285 292 7.738345 GTTTTGAAAAACAACATAAGTGCAGT 58.262 30.769 12.61 0.00 45.72 4.40
307 314 8.964476 TCAAAGTTCTCATAACTCTCTTGTTT 57.036 30.769 0.00 0.00 0.00 2.83
449 456 2.237392 GAGCCTTCTAGACCAACCATGT 59.763 50.000 0.00 0.00 0.00 3.21
567 574 2.535012 TCATGTACAAGACGGTGCAA 57.465 45.000 0.00 0.00 36.96 4.08
691 698 1.770061 TGACTGTTTCCTTAACGGGGT 59.230 47.619 0.00 0.00 45.66 4.95
796 803 9.517868 AGAACTTGAGAAGAGATGATGATTTTT 57.482 29.630 0.00 0.00 0.00 1.94
799 806 8.203485 GGTAGAACTTGAGAAGAGATGATGATT 58.797 37.037 0.00 0.00 0.00 2.57
800 807 7.564660 AGGTAGAACTTGAGAAGAGATGATGAT 59.435 37.037 0.00 0.00 0.00 2.45
801 808 6.894654 AGGTAGAACTTGAGAAGAGATGATGA 59.105 38.462 0.00 0.00 0.00 2.92
803 810 7.125391 AGAGGTAGAACTTGAGAAGAGATGAT 58.875 38.462 0.00 0.00 0.00 2.45
806 813 5.891551 GGAGAGGTAGAACTTGAGAAGAGAT 59.108 44.000 0.00 0.00 0.00 2.75
807 814 5.014755 AGGAGAGGTAGAACTTGAGAAGAGA 59.985 44.000 0.00 0.00 0.00 3.10
808 815 5.261216 AGGAGAGGTAGAACTTGAGAAGAG 58.739 45.833 0.00 0.00 0.00 2.85
809 816 5.263872 AGGAGAGGTAGAACTTGAGAAGA 57.736 43.478 0.00 0.00 0.00 2.87
810 817 6.605594 ACATAGGAGAGGTAGAACTTGAGAAG 59.394 42.308 0.00 0.00 0.00 2.85
856 863 8.450578 TTCACTTGTCATGAGTCACTATTTTT 57.549 30.769 0.00 0.00 0.00 1.94
857 864 7.933577 TCTTCACTTGTCATGAGTCACTATTTT 59.066 33.333 0.00 0.00 0.00 1.82
859 866 6.997655 TCTTCACTTGTCATGAGTCACTATT 58.002 36.000 0.00 0.00 0.00 1.73
860 867 6.596309 TCTTCACTTGTCATGAGTCACTAT 57.404 37.500 0.00 0.00 0.00 2.12
861 868 6.596309 ATCTTCACTTGTCATGAGTCACTA 57.404 37.500 0.00 0.00 0.00 2.74
862 869 4.944619 TCTTCACTTGTCATGAGTCACT 57.055 40.909 0.00 0.00 0.00 3.41
1095 1168 3.122948 CGTGAAACACTGTGTAGTATGGC 59.877 47.826 14.69 0.99 35.74 4.40
1132 1219 1.271656 GTGCACCGTGACTAAGTACCT 59.728 52.381 5.22 0.00 0.00 3.08
1192 1280 3.242188 GCTGAAACAAAGTCGTAACGTGT 60.242 43.478 0.00 0.00 32.08 4.49
1510 1599 1.367848 AGAGGAGGAACCCCTGAAGAT 59.632 52.381 5.79 0.00 35.83 2.40
1666 1755 1.530013 CGGGTGTAGTCCCTCAACGT 61.530 60.000 0.25 0.00 44.95 3.99
1708 1797 4.646945 AGAAGGTGAGCTATCGATCTGAAA 59.353 41.667 0.00 0.00 0.00 2.69
1930 2019 1.540267 AGCTCTGAGTAAGTGACGCT 58.460 50.000 6.53 0.00 0.00 5.07
2009 2099 1.248486 CTCAGAGGGAGTGACGTCAA 58.752 55.000 21.95 1.15 38.90 3.18
2046 2136 0.461548 CGCTGATGGTGCTAAGAGGA 59.538 55.000 0.00 0.00 0.00 3.71
2201 2294 2.680805 GCTACAGCCTTGCCAGAATACA 60.681 50.000 0.00 0.00 34.31 2.29
2320 2413 1.418637 ACGGCTACAAGACCTTTCCAA 59.581 47.619 0.00 0.00 0.00 3.53
2366 2460 4.968788 CGGAACTAGTCTGAATAACTACGC 59.031 45.833 0.00 0.00 34.07 4.42
2639 2739 4.700692 AGCAGCATCATCACATCCAATATC 59.299 41.667 0.00 0.00 0.00 1.63
2646 2746 2.477825 ACGTAGCAGCATCATCACATC 58.522 47.619 0.00 0.00 0.00 3.06
2873 2985 3.679725 CACATGTACACACACACACAAC 58.320 45.455 0.00 0.00 37.54 3.32


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

AutoCloner maintained by Alex Coulton.