Multiple sequence alignment - TraesCS7A01G513800

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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 TraesCS7A01G513800 chr7A 100.000 3914 0 0 1 3914 700337024 700340937 0.000000e+00 7228.0
1 TraesCS7A01G513800 chr7A 99.208 3914 26 2 1 3914 700299211 700303119 0.000000e+00 7051.0
2 TraesCS7A01G513800 chr7A 86.842 152 20 0 1310 1461 700387290 700387441 1.870000e-38 171.0
3 TraesCS7A01G513800 chr7A 89.189 111 11 1 1580 1689 700377539 700377649 1.900000e-28 137.0
4 TraesCS7A01G513800 chr7D 93.932 2373 103 15 741 3099 610421864 610419519 0.000000e+00 3546.0
5 TraesCS7A01G513800 chr7D 92.653 2382 119 18 740 3099 608272528 608274875 0.000000e+00 3378.0
6 TraesCS7A01G513800 chr7D 90.361 2158 126 26 740 2889 608222218 608224301 0.000000e+00 2758.0
7 TraesCS7A01G513800 chr7D 92.264 1396 98 6 1706 3099 514918648 514920035 0.000000e+00 1971.0
8 TraesCS7A01G513800 chr7D 92.308 689 38 7 1 676 514907545 514908231 0.000000e+00 965.0
9 TraesCS7A01G513800 chr7D 90.177 621 33 14 3297 3914 608274970 608275565 0.000000e+00 784.0
10 TraesCS7A01G513800 chr7D 89.837 492 31 12 3427 3914 514930675 514931151 7.190000e-172 614.0
11 TraesCS7A01G513800 chr7D 87.129 404 18 13 3075 3465 610419591 610419209 1.010000e-115 427.0
12 TraesCS7A01G513800 chr7D 89.272 261 20 5 420 676 608221448 608221704 1.750000e-83 320.0
13 TraesCS7A01G513800 chr7D 96.203 158 6 0 3075 3232 608274803 608274960 3.880000e-65 259.0
14 TraesCS7A01G513800 chr7D 92.135 178 13 1 6 182 610425234 610425057 2.330000e-62 250.0
15 TraesCS7A01G513800 chr7D 100.000 28 0 0 715 742 610421928 610421901 7.000000e-03 52.8
16 TraesCS7A01G513800 chr7B 91.811 2369 151 14 761 3099 696238503 696240858 0.000000e+00 3260.0
17 TraesCS7A01G513800 chr7B 94.051 2118 115 6 983 3099 698682699 698684806 0.000000e+00 3203.0
18 TraesCS7A01G513800 chr7B 94.389 1711 93 3 1391 3099 693664476 693666185 0.000000e+00 2625.0
19 TraesCS7A01G513800 chr7B 90.344 1626 116 11 741 2346 693681605 693683209 0.000000e+00 2095.0
20 TraesCS7A01G513800 chr7B 94.751 762 30 3 2338 3099 693684866 693685617 0.000000e+00 1177.0
21 TraesCS7A01G513800 chr7B 94.488 762 32 3 2338 3099 693698819 693699570 0.000000e+00 1166.0
22 TraesCS7A01G513800 chr7B 90.432 857 33 16 3075 3914 696240786 696241610 0.000000e+00 1083.0
23 TraesCS7A01G513800 chr7B 89.988 859 38 17 3075 3914 698684734 698685563 0.000000e+00 1066.0
24 TraesCS7A01G513800 chr7B 87.620 832 47 18 3075 3880 693699498 693700299 0.000000e+00 915.0
25 TraesCS7A01G513800 chr7B 91.875 640 42 5 1 630 693662276 693662915 0.000000e+00 885.0
26 TraesCS7A01G513800 chr7B 87.371 776 45 23 3075 3838 694749363 694750097 0.000000e+00 841.0
27 TraesCS7A01G513800 chr7B 93.059 461 21 4 3457 3914 693716743 693717195 0.000000e+00 664.0
28 TraesCS7A01G513800 chr7B 89.775 489 39 6 1 480 696229556 696230042 2.000000e-172 616.0
29 TraesCS7A01G513800 chr7B 88.296 487 28 12 5 481 694745887 694746354 1.230000e-154 556.0
30 TraesCS7A01G513800 chr7B 77.505 938 131 39 743 1666 696297608 696298479 1.260000e-134 490.0
31 TraesCS7A01G513800 chr7B 87.376 404 17 9 3075 3465 693685545 693685927 2.160000e-117 433.0
32 TraesCS7A01G513800 chr7B 90.728 302 7 7 3076 3377 693716444 693716724 2.210000e-102 383.0
33 TraesCS7A01G513800 chr7B 88.851 296 29 3 2807 3099 693716221 693716515 1.030000e-95 361.0
34 TraesCS7A01G513800 chr7B 89.964 279 12 7 740 1004 693663757 693664033 2.890000e-91 346.0
35 TraesCS7A01G513800 chr7B 94.475 181 7 2 740 919 698682486 698682664 3.850000e-70 276.0
36 TraesCS7A01G513800 chr7B 95.070 142 6 1 1038 1178 693664325 693664466 5.090000e-54 222.0
37 TraesCS7A01G513800 chr7B 95.745 94 3 1 494 587 694746337 694746429 2.440000e-32 150.0
38 TraesCS7A01G513800 chr7B 94.286 35 1 1 708 742 693714095 693714128 7.000000e-03 52.8
39 TraesCS7A01G513800 chr7B 100.000 28 0 0 715 742 696238411 696238438 7.000000e-03 52.8
40 TraesCS7A01G513800 chrUn 93.193 2189 119 8 917 3099 77521232 77523396 0.000000e+00 3190.0
41 TraesCS7A01G513800 chrUn 90.301 1629 117 11 741 2349 364810900 364809293 0.000000e+00 2095.0
42 TraesCS7A01G513800 chrUn 94.488 762 32 3 2338 3099 349917742 349916991 0.000000e+00 1166.0
43 TraesCS7A01G513800 chrUn 89.836 856 42 14 3075 3914 77523324 77524150 0.000000e+00 1057.0
44 TraesCS7A01G513800 chrUn 87.240 674 54 10 741 1394 344773387 344772726 0.000000e+00 739.0
45 TraesCS7A01G513800 chrUn 89.109 303 12 7 3075 3377 349917063 349916782 1.340000e-94 357.0
46 TraesCS7A01G513800 chrUn 89.450 218 10 1 3261 3465 254016968 254017185 3.000000e-66 263.0
47 TraesCS7A01G513800 chrUn 89.450 218 10 1 3261 3465 254027857 254028074 3.000000e-66 263.0
48 TraesCS7A01G513800 chrUn 91.803 183 15 0 1 183 77514478 77514660 5.020000e-64 255.0
49 TraesCS7A01G513800 chr4A 92.076 631 40 5 5 625 662054552 662053922 0.000000e+00 880.0
50 TraesCS7A01G513800 chr4A 91.434 537 35 6 3377 3910 735216070 735215542 0.000000e+00 726.0
51 TraesCS7A01G513800 chr4A 85.225 467 61 5 2640 3099 662021098 662020633 1.270000e-129 473.0
52 TraesCS7A01G513800 chr4A 85.491 448 57 5 2659 3099 662051488 662051042 9.910000e-126 460.0
53 TraesCS7A01G513800 chr4A 86.701 391 28 6 740 1116 662053132 662052752 2.810000e-111 412.0
54 TraesCS7A01G513800 chr4A 89.844 256 16 7 423 675 735185010 735184762 1.750000e-83 320.0
55 TraesCS7A01G513800 chr4A 91.257 183 16 0 1 183 735185204 735185022 2.330000e-62 250.0


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 TraesCS7A01G513800 chr7A 700337024 700340937 3913 False 7228.000000 7228 100.000000 1 3914 1 chr7A.!!$F2 3913
1 TraesCS7A01G513800 chr7A 700299211 700303119 3908 False 7051.000000 7051 99.208000 1 3914 1 chr7A.!!$F1 3913
2 TraesCS7A01G513800 chr7D 514918648 514920035 1387 False 1971.000000 1971 92.264000 1706 3099 1 chr7D.!!$F2 1393
3 TraesCS7A01G513800 chr7D 608221448 608224301 2853 False 1539.000000 2758 89.816500 420 2889 2 chr7D.!!$F4 2469
4 TraesCS7A01G513800 chr7D 608272528 608275565 3037 False 1473.666667 3378 93.011000 740 3914 3 chr7D.!!$F5 3174
5 TraesCS7A01G513800 chr7D 610419209 610425234 6025 True 1068.950000 3546 93.299000 6 3465 4 chr7D.!!$R1 3459
6 TraesCS7A01G513800 chr7D 514907545 514908231 686 False 965.000000 965 92.308000 1 676 1 chr7D.!!$F1 675
7 TraesCS7A01G513800 chr7B 698682486 698685563 3077 False 1515.000000 3203 92.838000 740 3914 3 chr7B.!!$F9 3174
8 TraesCS7A01G513800 chr7B 696238411 696241610 3199 False 1465.266667 3260 94.081000 715 3914 3 chr7B.!!$F8 3199
9 TraesCS7A01G513800 chr7B 693681605 693685927 4322 False 1235.000000 2095 90.823667 741 3465 3 chr7B.!!$F4 2724
10 TraesCS7A01G513800 chr7B 693698819 693700299 1480 False 1040.500000 1166 91.054000 2338 3880 2 chr7B.!!$F5 1542
11 TraesCS7A01G513800 chr7B 693662276 693666185 3909 False 1019.500000 2625 92.824500 1 3099 4 chr7B.!!$F3 3098
12 TraesCS7A01G513800 chr7B 694745887 694750097 4210 False 515.666667 841 90.470667 5 3838 3 chr7B.!!$F7 3833
13 TraesCS7A01G513800 chr7B 696297608 696298479 871 False 490.000000 490 77.505000 743 1666 1 chr7B.!!$F2 923
14 TraesCS7A01G513800 chr7B 693714095 693717195 3100 False 365.200000 664 91.731000 708 3914 4 chr7B.!!$F6 3206
15 TraesCS7A01G513800 chrUn 77521232 77524150 2918 False 2123.500000 3190 91.514500 917 3914 2 chrUn.!!$F4 2997
16 TraesCS7A01G513800 chrUn 364809293 364810900 1607 True 2095.000000 2095 90.301000 741 2349 1 chrUn.!!$R2 1608
17 TraesCS7A01G513800 chrUn 349916782 349917742 960 True 761.500000 1166 91.798500 2338 3377 2 chrUn.!!$R3 1039
18 TraesCS7A01G513800 chrUn 344772726 344773387 661 True 739.000000 739 87.240000 741 1394 1 chrUn.!!$R1 653
19 TraesCS7A01G513800 chr4A 735215542 735216070 528 True 726.000000 726 91.434000 3377 3910 1 chr4A.!!$R2 533
20 TraesCS7A01G513800 chr4A 662051042 662054552 3510 True 584.000000 880 88.089333 5 3099 3 chr4A.!!$R3 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
621 2754 2.288152 GGCCCAAATAAGTGTGTGTGTG 60.288 50.000 0.0 0.0 0.00 3.82 F
622 2755 2.360801 GCCCAAATAAGTGTGTGTGTGT 59.639 45.455 0.0 0.0 0.00 3.72 F
1779 5388 1.067821 GAGAAGGAAGCCGTCATCGAT 59.932 52.381 0.0 0.0 39.71 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 5046 0.461961 GGTGATCCCAGAGAAGTCGG 59.538 60.0 0.0 0.0 0.00 4.79 R
2364 7638 0.946221 CGAGCAGGCGTTGAACTTCT 60.946 55.0 0.0 0.0 0.00 2.85 R
2926 8550 1.766494 TGGTAATGAAGCCTGCATGG 58.234 50.0 0.0 0.0 39.35 3.66 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
54 56 6.252441 CACGCTACTCTCATGTTCTTCTAAAG 59.748 42.308 0.0 0.0 0.00 1.85
277 282 4.410099 AGCCCAATGAGAAGAAATTGTCA 58.590 39.130 0.0 0.0 32.90 3.58
621 2754 2.288152 GGCCCAAATAAGTGTGTGTGTG 60.288 50.000 0.0 0.0 0.00 3.82
622 2755 2.360801 GCCCAAATAAGTGTGTGTGTGT 59.639 45.455 0.0 0.0 0.00 3.72
623 2756 3.795150 GCCCAAATAAGTGTGTGTGTGTG 60.795 47.826 0.0 0.0 0.00 3.82
624 2757 3.380004 CCCAAATAAGTGTGTGTGTGTGT 59.620 43.478 0.0 0.0 0.00 3.72
1439 5046 3.944476 ACCATGAAGAGGTCACTGC 57.056 52.632 0.0 0.0 39.72 4.40
1779 5388 1.067821 GAGAAGGAAGCCGTCATCGAT 59.932 52.381 0.0 0.0 39.71 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 2.514803 AGCCCAACAACCAATACTGTC 58.485 47.619 0.00 0.00 0.00 3.51
111 116 0.320771 AGCACTGACGGCTAGTTTGG 60.321 55.000 0.00 0.00 40.47 3.28
277 282 2.036890 ACCTAGGGTTCGACGCCT 59.963 61.111 14.81 0.00 27.29 5.52
933 4237 1.070843 CATGTGTTGTCGTGGTCGTTC 60.071 52.381 0.00 0.00 38.33 3.95
1439 5046 0.461961 GGTGATCCCAGAGAAGTCGG 59.538 60.000 0.00 0.00 0.00 4.79
1779 5388 1.296392 CTGGAACGCCATGAGGTCA 59.704 57.895 8.16 0.00 44.91 4.02
2364 7638 0.946221 CGAGCAGGCGTTGAACTTCT 60.946 55.000 0.00 0.00 0.00 2.85
2926 8550 1.766494 TGGTAATGAAGCCTGCATGG 58.234 50.000 0.00 0.00 39.35 3.66
3010 8634 5.986741 GCTTAATTAACTCTAGGAGCAGGAC 59.013 44.000 0.00 0.00 32.04 3.85
3750 9422 9.807649 GATACTAATTTGGCATTCAATTTCTGT 57.192 29.630 1.34 2.67 34.98 3.41


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

AutoCloner maintained by Alex Coulton.