Multiple sequence alignment - TraesCS7B01G098800

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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 TraesCS7B01G098800 chr7B 100.000 8566 0 0 1 8566 113210315 113201750 0.000000e+00 15819.0
1 TraesCS7B01G098800 chr7B 97.826 920 14 1 2696 3615 379409786 379408873 0.000000e+00 1583.0
2 TraesCS7B01G098800 chr7B 97.136 873 23 2 2745 3615 164083270 164084142 0.000000e+00 1472.0
3 TraesCS7B01G098800 chr7B 96.296 864 31 1 2754 3616 742229014 742229877 0.000000e+00 1417.0
4 TraesCS7B01G098800 chr7B 85.714 182 26 0 5631 5812 113204613 113204432 8.780000e-45 193.0
5 TraesCS7B01G098800 chr7B 85.714 182 26 0 5703 5884 113204685 113204504 8.780000e-45 193.0
6 TraesCS7B01G098800 chr7B 92.233 103 6 2 5156 5257 113205115 113205014 2.490000e-30 145.0
7 TraesCS7B01G098800 chr7B 92.233 103 6 2 5201 5302 113205160 113205059 2.490000e-30 145.0
8 TraesCS7B01G098800 chr7B 84.956 113 15 2 5629 5740 113204543 113204432 7.030000e-21 113.0
9 TraesCS7B01G098800 chr7B 84.956 113 15 2 5773 5884 113204687 113204576 7.030000e-21 113.0
10 TraesCS7B01G098800 chr7B 93.023 43 3 0 5631 5673 113204469 113204427 7.180000e-06 63.9
11 TraesCS7B01G098800 chr7D 91.950 2385 119 44 349 2694 151329057 151326707 0.000000e+00 3273.0
12 TraesCS7B01G098800 chr7D 90.375 1974 139 22 6612 8566 151323577 151321636 0.000000e+00 2545.0
13 TraesCS7B01G098800 chr7D 94.973 1492 64 7 3808 5293 151326445 151324959 0.000000e+00 2329.0
14 TraesCS7B01G098800 chr7D 97.802 728 16 0 5156 5883 151325051 151324324 0.000000e+00 1256.0
15 TraesCS7B01G098800 chr7D 86.396 419 42 5 5631 6049 151324504 151324101 2.190000e-120 444.0
16 TraesCS7B01G098800 chr7D 94.094 254 15 0 6346 6599 151323897 151323644 3.750000e-103 387.0
17 TraesCS7B01G098800 chr7D 92.857 196 10 2 3617 3809 151326722 151326528 1.820000e-71 281.0
18 TraesCS7B01G098800 chr7D 90.187 214 21 0 6091 6304 151324104 151323891 6.550000e-71 279.0
19 TraesCS7B01G098800 chr7D 85.714 182 26 0 5703 5884 151324576 151324395 8.780000e-45 193.0
20 TraesCS7B01G098800 chr7D 93.204 103 5 2 5156 5257 151325006 151324905 5.360000e-32 150.0
21 TraesCS7B01G098800 chr7D 80.435 184 21 5 5629 5812 151324434 151324266 9.030000e-25 126.0
22 TraesCS7B01G098800 chr7D 84.956 113 15 2 5773 5884 151324578 151324467 7.030000e-21 113.0
23 TraesCS7B01G098800 chr7D 97.500 40 1 0 5634 5673 151324300 151324261 1.540000e-07 69.4
24 TraesCS7B01G098800 chr7A 95.980 2015 75 3 3873 5883 150997976 150995964 0.000000e+00 3267.0
25 TraesCS7B01G098800 chr7A 90.068 2205 129 50 541 2695 151000418 150998254 0.000000e+00 2776.0
26 TraesCS7B01G098800 chr7A 90.949 1602 116 14 5633 7221 150996142 150994557 0.000000e+00 2128.0
27 TraesCS7B01G098800 chr7A 89.019 1366 88 25 7240 8566 150994568 150993226 0.000000e+00 1635.0
28 TraesCS7B01G098800 chr7A 95.652 253 10 1 3618 3870 150998269 150998018 1.040000e-108 405.0
29 TraesCS7B01G098800 chr7A 84.615 182 28 0 5703 5884 150996216 150996035 1.900000e-41 182.0
30 TraesCS7B01G098800 chr7A 93.204 103 5 2 5156 5257 150996646 150996545 5.360000e-32 150.0
31 TraesCS7B01G098800 chr7A 93.548 93 6 0 5201 5293 150996691 150996599 1.160000e-28 139.0
32 TraesCS7B01G098800 chr7A 80.435 184 21 5 5629 5812 150996074 150995906 9.030000e-25 126.0
33 TraesCS7B01G098800 chr7A 97.500 40 1 0 5634 5673 150995940 150995901 1.540000e-07 69.4
34 TraesCS7B01G098800 chr2B 97.961 932 17 2 2696 3626 736387820 736388750 0.000000e+00 1615.0
35 TraesCS7B01G098800 chr2B 97.624 884 16 2 2733 3615 210266825 210267704 0.000000e+00 1511.0
36 TraesCS7B01G098800 chr2B 95.449 879 40 0 2736 3614 719298333 719299211 0.000000e+00 1402.0
37 TraesCS7B01G098800 chr2B 90.863 197 4 2 858 1054 187500635 187500817 1.430000e-62 252.0
38 TraesCS7B01G098800 chr2B 76.709 395 81 7 4 390 789636606 789636215 8.710000e-50 209.0
39 TraesCS7B01G098800 chr2B 76.772 254 43 12 4 249 254656121 254655876 2.510000e-25 128.0
40 TraesCS7B01G098800 chr3B 96.868 894 22 4 2733 3620 640077690 640076797 0.000000e+00 1491.0
41 TraesCS7B01G098800 chr6B 97.159 880 24 1 2737 3615 120822981 120822102 0.000000e+00 1485.0
42 TraesCS7B01G098800 chr6B 78.426 394 70 15 32 415 46890150 46890538 8.590000e-60 243.0
43 TraesCS7B01G098800 chr5B 95.721 888 38 0 2736 3623 685091303 685092190 0.000000e+00 1430.0
44 TraesCS7B01G098800 chr5B 79.475 419 69 16 22 428 44460170 44459757 1.820000e-71 281.0
45 TraesCS7B01G098800 chr1B 81.818 264 41 6 22 278 500596624 500596361 1.870000e-51 215.0
46 TraesCS7B01G098800 chr1B 76.156 411 87 8 4 405 423212585 423212993 1.130000e-48 206.0
47 TraesCS7B01G098800 chr3D 78.488 344 55 13 4 339 505067596 505067928 3.130000e-49 207.0


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 TraesCS7B01G098800 chr7B 113201750 113210315 8565 True 15819.000000 15819 100.000000 1 8566 1 chr7B.!!$R1 8565
1 TraesCS7B01G098800 chr7B 379408873 379409786 913 True 1583.000000 1583 97.826000 2696 3615 1 chr7B.!!$R2 919
2 TraesCS7B01G098800 chr7B 164083270 164084142 872 False 1472.000000 1472 97.136000 2745 3615 1 chr7B.!!$F1 870
3 TraesCS7B01G098800 chr7B 742229014 742229877 863 False 1417.000000 1417 96.296000 2754 3616 1 chr7B.!!$F2 862
4 TraesCS7B01G098800 chr7D 151321636 151329057 7421 True 880.415385 3273 90.803308 349 8566 13 chr7D.!!$R1 8217
5 TraesCS7B01G098800 chr7A 150993226 151000418 7192 True 1087.740000 3267 91.097000 541 8566 10 chr7A.!!$R1 8025
6 TraesCS7B01G098800 chr2B 736387820 736388750 930 False 1615.000000 1615 97.961000 2696 3626 1 chr2B.!!$F4 930
7 TraesCS7B01G098800 chr2B 210266825 210267704 879 False 1511.000000 1511 97.624000 2733 3615 1 chr2B.!!$F2 882
8 TraesCS7B01G098800 chr2B 719298333 719299211 878 False 1402.000000 1402 95.449000 2736 3614 1 chr2B.!!$F3 878
9 TraesCS7B01G098800 chr3B 640076797 640077690 893 True 1491.000000 1491 96.868000 2733 3620 1 chr3B.!!$R1 887
10 TraesCS7B01G098800 chr6B 120822102 120822981 879 True 1485.000000 1485 97.159000 2737 3615 1 chr6B.!!$R1 878
11 TraesCS7B01G098800 chr5B 685091303 685092190 887 False 1430.000000 1430 95.721000 2736 3623 1 chr5B.!!$F1 887


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
299 300 0.032540 TCTGCCATCGATCCATGACG 59.967 55.000 1.38 0.00 0.00 4.35 F
1574 1626 0.101759 TAATGAGTACCACGCGGCTC 59.898 55.000 12.47 10.21 34.57 4.70 F
1722 1797 1.884075 AACGGGCACGACAGCATAGA 61.884 55.000 19.19 0.00 44.60 1.98 F
2693 2770 3.253230 GCACATTAAACCATCAACTGCC 58.747 45.455 0.00 0.00 0.00 4.85 F
4412 4628 0.179018 ACAAGCCAGGTCAAGGTGAC 60.179 55.000 0.00 0.00 46.23 3.67 F
6056 6374 0.990374 ATGCCTCTTCTGACAAGCCT 59.010 50.000 0.00 0.00 0.00 4.58 F
6605 6971 0.179176 CAGAGCCTGAGAAGTCGTCG 60.179 60.000 0.00 0.00 32.44 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2150 0.102300 AGCCGCAAACAGGAAAACAC 59.898 50.000 0.00 0.0 0.00 3.32 R
2435 2512 0.644843 CAAACACACAAAAGGCGTGC 59.355 50.000 0.00 0.0 37.93 5.34 R
2939 3019 1.006571 GAAGCCAAGACGTCGGACA 60.007 57.895 13.06 0.0 0.00 4.02 R
4520 4736 0.039437 TCTCGACTGTGCTTTCCGAC 60.039 55.000 0.00 0.0 0.00 4.79 R
6302 6668 0.384669 GCTGAGATTCCAATGCCTGC 59.615 55.000 0.00 0.0 0.00 4.85 R
7534 7969 0.250467 GTTCTTCTCTGTGGCAGGCA 60.250 55.000 0.00 0.0 31.51 4.75 R
8359 8834 0.321671 TCTGCTTCCACACCTACAGC 59.678 55.000 0.00 0.0 0.00 4.40 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)



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AutoCloner maintained by Alex Coulton.