Multiple sequence alignment - TraesCS7A01G503400

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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 TraesCS7A01G503400 chr7A 100.000 2627 0 0 1 2627 692229361 692231987 0.000000e+00 4852
1 TraesCS7A01G503400 chr7A 93.036 560 26 1 1547 2093 375178317 375178876 0.000000e+00 806
2 TraesCS7A01G503400 chr5D 96.997 2098 58 3 1 2093 375001987 375004084 0.000000e+00 3520
3 TraesCS7A01G503400 chr5D 96.379 2099 68 6 1 2093 184453020 184455116 0.000000e+00 3448
4 TraesCS7A01G503400 chr5D 95.422 2097 89 4 1 2093 397473185 397471092 0.000000e+00 3334
5 TraesCS7A01G503400 chr5D 94.850 2097 99 5 1 2093 397466568 397468659 0.000000e+00 3265
6 TraesCS7A01G503400 chr3A 96.142 1970 71 3 128 2093 720600566 720598598 0.000000e+00 3212
7 TraesCS7A01G503400 chr3A 95.893 1948 74 4 149 2091 117786785 117784839 0.000000e+00 3149
8 TraesCS7A01G503400 chr3A 95.140 535 25 1 2093 2627 720598640 720598107 0.000000e+00 843
9 TraesCS7A01G503400 chr3A 94.776 536 23 3 2095 2627 117784877 117784344 0.000000e+00 830
10 TraesCS7A01G503400 chr3A 94.195 534 23 5 2094 2627 315886315 315885790 0.000000e+00 808
11 TraesCS7A01G503400 chr6B 93.711 2099 126 4 1 2093 666360973 666358875 0.000000e+00 3140
12 TraesCS7A01G503400 chr4A 95.076 1970 89 5 128 2093 444377901 444379866 0.000000e+00 3094
13 TraesCS7A01G503400 chr2A 95.161 1798 83 2 1 1794 33472834 33471037 0.000000e+00 2835
14 TraesCS7A01G503400 chr2A 94.259 540 22 5 2093 2627 33470817 33470282 0.000000e+00 817
15 TraesCS7A01G503400 chr1D 94.963 536 24 3 2094 2627 422495765 422496299 0.000000e+00 837
16 TraesCS7A01G503400 chr1D 94.052 538 24 7 2094 2627 393950131 393949598 0.000000e+00 809
17 TraesCS7A01G503400 chr7D 94.786 537 23 4 2094 2627 27352439 27351905 0.000000e+00 832
18 TraesCS7A01G503400 chr1A 93.911 542 25 2 2093 2627 205579493 205580033 0.000000e+00 811
19 TraesCS7A01G503400 chr3B 94.052 538 25 5 2094 2627 697442115 697441581 0.000000e+00 809
20 TraesCS7A01G503400 chr6A 95.413 109 5 0 1 109 138421421 138421529 9.660000e-40 174


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 TraesCS7A01G503400 chr7A 692229361 692231987 2626 False 4852.0 4852 100.0000 1 2627 1 chr7A.!!$F2 2626
1 TraesCS7A01G503400 chr7A 375178317 375178876 559 False 806.0 806 93.0360 1547 2093 1 chr7A.!!$F1 546
2 TraesCS7A01G503400 chr5D 375001987 375004084 2097 False 3520.0 3520 96.9970 1 2093 1 chr5D.!!$F2 2092
3 TraesCS7A01G503400 chr5D 184453020 184455116 2096 False 3448.0 3448 96.3790 1 2093 1 chr5D.!!$F1 2092
4 TraesCS7A01G503400 chr5D 397471092 397473185 2093 True 3334.0 3334 95.4220 1 2093 1 chr5D.!!$R1 2092
5 TraesCS7A01G503400 chr5D 397466568 397468659 2091 False 3265.0 3265 94.8500 1 2093 1 chr5D.!!$F3 2092
6 TraesCS7A01G503400 chr3A 720598107 720600566 2459 True 2027.5 3212 95.6410 128 2627 2 chr3A.!!$R3 2499
7 TraesCS7A01G503400 chr3A 117784344 117786785 2441 True 1989.5 3149 95.3345 149 2627 2 chr3A.!!$R2 2478
8 TraesCS7A01G503400 chr3A 315885790 315886315 525 True 808.0 808 94.1950 2094 2627 1 chr3A.!!$R1 533
9 TraesCS7A01G503400 chr6B 666358875 666360973 2098 True 3140.0 3140 93.7110 1 2093 1 chr6B.!!$R1 2092
10 TraesCS7A01G503400 chr4A 444377901 444379866 1965 False 3094.0 3094 95.0760 128 2093 1 chr4A.!!$F1 1965
11 TraesCS7A01G503400 chr2A 33470282 33472834 2552 True 1826.0 2835 94.7100 1 2627 2 chr2A.!!$R1 2626
12 TraesCS7A01G503400 chr1D 422495765 422496299 534 False 837.0 837 94.9630 2094 2627 1 chr1D.!!$F1 533
13 TraesCS7A01G503400 chr1D 393949598 393950131 533 True 809.0 809 94.0520 2094 2627 1 chr1D.!!$R1 533
14 TraesCS7A01G503400 chr7D 27351905 27352439 534 True 832.0 832 94.7860 2094 2627 1 chr7D.!!$R1 533
15 TraesCS7A01G503400 chr1A 205579493 205580033 540 False 811.0 811 93.9110 2093 2627 1 chr1A.!!$F1 534
16 TraesCS7A01G503400 chr3B 697441581 697442115 534 True 809.0 809 94.0520 2094 2627 1 chr3B.!!$R1 533

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
966 978 0.671781 GCTTCACTCGTGTCTGCCAT 60.672 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2596 2679 2.677542 AGTGTCTATATGGGCCGAGA 57.322 50.0 0.0 0.0 0.0 4.04 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
153 154 8.417176 GTGATGAATGAACGAACAAACAATAAC 58.583 33.333 0.00 0.00 0.00 1.89
383 387 1.215924 ACCAGACTAGAGGTAGAGGCC 59.784 57.143 0.00 0.00 36.07 5.19
386 390 2.059490 AGACTAGAGGTAGAGGCCGAT 58.941 52.381 0.00 0.00 0.00 4.18
475 480 2.476241 GTGCTTTTTCATTTCCTTGCCG 59.524 45.455 0.00 0.00 0.00 5.69
501 506 5.106317 GCCAAATAAAGGATGTTGTTCTCGA 60.106 40.000 0.00 0.00 0.00 4.04
642 651 7.315142 ACCTGATTGTAAACATAACTGCAATG 58.685 34.615 0.00 0.00 0.00 2.82
643 652 7.039784 ACCTGATTGTAAACATAACTGCAATGT 60.040 33.333 0.00 0.00 39.22 2.71
671 680 9.178427 GTATATATGTCGACAGTCTGGTAAAAC 57.822 37.037 24.41 7.65 0.00 2.43
831 843 9.077885 AGCCACTTCTTATGACAAGAAAAATAA 57.922 29.630 1.52 0.00 36.01 1.40
966 978 0.671781 GCTTCACTCGTGTCTGCCAT 60.672 55.000 0.00 0.00 0.00 4.40
1107 1120 5.600908 TTTAGCTTTTCCACACGTGTATC 57.399 39.130 22.90 0.51 0.00 2.24
1142 1155 5.516339 ACTTTCAGTTTTCTTTTCATGTGCG 59.484 36.000 0.00 0.00 0.00 5.34
1201 1214 2.666272 TTATGGCAGTGACAAACCCA 57.334 45.000 0.77 0.00 0.00 4.51
1505 1518 3.581101 AGATGCTACCCTCATCTTGCTA 58.419 45.455 0.09 0.00 45.99 3.49
1597 1610 4.717991 TGTTCTATTTTGAAATGGACGCG 58.282 39.130 3.53 3.53 35.92 6.01
1741 1767 2.172293 AGCTCCCTATTTTCTGCTCCTG 59.828 50.000 0.00 0.00 0.00 3.86
1794 1820 2.620115 GCAGTAGCCTACCGTGTATACA 59.380 50.000 0.08 0.08 33.58 2.29
1879 1942 2.869101 TGCTTGTGGTAGCCATTACA 57.131 45.000 0.00 0.00 40.49 2.41
2218 2281 5.806818 TGTGTAAGGAAATGTATTCCCGAA 58.193 37.500 3.67 0.00 39.39 4.30
2279 2342 7.608761 TGTTATGTGATGTGATATGATGGATGG 59.391 37.037 0.00 0.00 0.00 3.51
2366 2429 3.330701 TGGATTAAAGAGGTCTTGTGCCT 59.669 43.478 0.00 0.00 39.42 4.75
2562 2644 1.302383 TGGCCCGTGCAGAAATTACG 61.302 55.000 0.00 0.00 40.13 3.18
2596 2679 7.784550 ACATACTAAATGGGCTGAATTAATGGT 59.215 33.333 0.00 0.00 0.00 3.55
2615 2698 2.240279 GTCTCGGCCCATATAGACACT 58.760 52.381 0.00 0.00 38.56 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 1.679977 CCTGGTGCCCATGTTCCTG 60.680 63.158 0.00 0.00 30.82 3.86
383 387 6.429624 TGACTGAAACAACAAGAAATCATCG 58.570 36.000 0.00 0.00 0.00 3.84
386 390 7.028962 CACTTGACTGAAACAACAAGAAATCA 58.971 34.615 17.58 0.00 41.16 2.57
475 480 4.222810 AGAACAACATCCTTTATTTGGCCC 59.777 41.667 0.00 0.00 0.00 5.80
501 506 0.254178 ATCCTCAAGCGCAACTCCAT 59.746 50.000 11.47 0.00 0.00 3.41
642 651 6.736123 ACCAGACTGTCGACATATATACAAC 58.264 40.000 20.40 3.29 0.00 3.32
643 652 6.954487 ACCAGACTGTCGACATATATACAA 57.046 37.500 20.40 0.00 0.00 2.41
655 664 3.463944 ACAAGGTTTTACCAGACTGTCG 58.536 45.455 1.52 0.00 41.95 4.35
671 680 0.104671 CAAACCCAGGCACAACAAGG 59.895 55.000 0.00 0.00 0.00 3.61
714 724 6.433093 GGGCTTTTTGTATGAGTAAGGAAAGA 59.567 38.462 0.00 0.00 0.00 2.52
831 843 4.875561 TGTTTAAATTTAGGGGCGCTTT 57.124 36.364 10.13 0.00 0.00 3.51
886 898 7.325821 CACTGCTCGATTTTTGCAATAGTTTAA 59.674 33.333 0.00 0.00 36.22 1.52
1142 1155 7.150640 AGCATCAAAGATTTCTTTCAGTTTCC 58.849 34.615 2.59 0.00 43.72 3.13
1201 1214 4.074970 AGCAGATCGAAGTCATGGTTTTT 58.925 39.130 0.00 0.00 0.00 1.94
1500 1513 3.934457 TCGATTGACAGACAGTAGCAA 57.066 42.857 0.00 0.00 0.00 3.91
1505 1518 5.178252 CAGTTTGATTCGATTGACAGACAGT 59.822 40.000 0.00 0.00 0.00 3.55
1640 1653 1.071471 CCTCAAGAAGCACCACCGT 59.929 57.895 0.00 0.00 0.00 4.83
1687 1713 0.530288 GGAGCTGACTCACTGGAGAC 59.470 60.000 0.00 0.00 45.42 3.36
1741 1767 4.253685 TCTAAACCAACAGAGCATGCTAC 58.746 43.478 22.74 14.27 0.00 3.58
1879 1942 3.386078 AGACACGGACATGATTCAGCTAT 59.614 43.478 0.00 0.00 0.00 2.97
2161 2224 6.071334 GGCACATCTGCTACTATCCTAACATA 60.071 42.308 0.00 0.00 43.66 2.29
2279 2342 6.918022 AGGAAAACTCAATGTCGAATTCAAAC 59.082 34.615 6.22 3.74 0.00 2.93
2530 2612 3.558321 GCACGGGCCATACTTCCATATTA 60.558 47.826 4.39 0.00 0.00 0.98
2562 2644 6.823689 TCAGCCCATTTAGTATGTTTTCTCTC 59.176 38.462 0.00 0.00 0.00 3.20
2596 2679 2.677542 AGTGTCTATATGGGCCGAGA 57.322 50.000 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.