Multiple sequence alignment - TraesCS7D01G299700

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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 TraesCS7D01G299700 chr7D 100.000 4349 0 0 1 4349 379771204 379766856 0.000000e+00 8032.0
1 TraesCS7D01G299700 chr7D 85.683 454 59 4 311 762 465162021 465162470 1.420000e-129 473.0
2 TraesCS7D01G299700 chr7D 87.980 391 38 4 1 382 585195337 585194947 1.840000e-123 453.0
3 TraesCS7D01G299700 chr7D 96.875 96 2 1 1610 1705 426558893 426558987 4.500000e-35 159.0
4 TraesCS7D01G299700 chr7D 96.809 94 2 1 1614 1707 22964254 22964346 5.820000e-34 156.0
5 TraesCS7D01G299700 chr7A 94.234 1318 42 5 2394 3682 428339510 428338198 0.000000e+00 1982.0
6 TraesCS7D01G299700 chr7A 95.405 740 29 2 883 1618 428340820 428340082 0.000000e+00 1173.0
7 TraesCS7D01G299700 chr7A 93.678 348 13 4 1894 2235 428339853 428339509 3.000000e-141 512.0
8 TraesCS7D01G299700 chr7A 84.806 283 27 8 3684 3963 428338160 428337891 1.990000e-68 270.0
9 TraesCS7D01G299700 chr7A 88.835 206 12 4 4079 4275 428333735 428333532 4.350000e-60 243.0
10 TraesCS7D01G299700 chr7A 95.652 92 3 1 1527 1618 428340058 428339968 3.500000e-31 147.0
11 TraesCS7D01G299700 chr7A 93.000 100 6 1 1731 1830 428339946 428339848 1.260000e-30 145.0
12 TraesCS7D01G299700 chr7A 95.062 81 3 1 4270 4349 428331212 428331132 4.570000e-25 126.0
13 TraesCS7D01G299700 chr7B 93.455 825 43 6 2864 3682 374775092 374774273 0.000000e+00 1214.0
14 TraesCS7D01G299700 chr7B 97.154 492 14 0 898 1389 374802767 374802276 0.000000e+00 832.0
15 TraesCS7D01G299700 chr7B 92.647 544 12 5 1699 2235 374776112 374775590 0.000000e+00 758.0
16 TraesCS7D01G299700 chr7B 94.292 473 26 1 2394 2865 374775591 374775119 0.000000e+00 723.0
17 TraesCS7D01G299700 chr7B 84.095 591 68 14 1 579 582657576 582658152 8.220000e-152 547.0
18 TraesCS7D01G299700 chr7B 94.068 236 13 1 1384 1618 374776345 374776110 1.490000e-94 357.0
19 TraesCS7D01G299700 chr7B 82.878 403 33 12 3933 4316 374773698 374773313 3.240000e-86 329.0
20 TraesCS7D01G299700 chr7B 92.553 94 6 1 3680 3772 374774236 374774143 2.730000e-27 134.0
21 TraesCS7D01G299700 chr3D 86.667 765 79 13 1 761 402498309 402497564 0.000000e+00 826.0
22 TraesCS7D01G299700 chr3D 85.825 776 88 7 1 758 517293658 517294429 0.000000e+00 804.0
23 TraesCS7D01G299700 chr3D 85.268 448 46 10 1 432 549352587 549353030 1.110000e-120 444.0
24 TraesCS7D01G299700 chr3D 94.083 169 10 0 2231 2399 595025140 595024972 1.550000e-64 257.0
25 TraesCS7D01G299700 chr3D 91.713 181 14 1 2216 2395 612268629 612268449 2.600000e-62 250.0
26 TraesCS7D01G299700 chr3D 83.645 214 27 4 3840 4046 169450401 169450189 1.230000e-45 195.0
27 TraesCS7D01G299700 chr3D 92.453 106 6 2 1608 1711 459472532 459472427 2.710000e-32 150.0
28 TraesCS7D01G299700 chr3B 86.180 767 85 9 1 750 489718380 489719142 0.000000e+00 809.0
29 TraesCS7D01G299700 chr3B 87.195 164 20 1 3883 4046 759028105 759028267 7.430000e-43 185.0
30 TraesCS7D01G299700 chr3B 82.589 224 23 4 3838 4045 511628731 511628954 2.670000e-42 183.0
31 TraesCS7D01G299700 chr3B 92.453 106 4 3 1616 1718 302899604 302899500 9.740000e-32 148.0
32 TraesCS7D01G299700 chr2D 85.733 764 91 8 1 750 555477151 555476392 0.000000e+00 791.0
33 TraesCS7D01G299700 chr2D 83.007 765 116 12 1 761 44529502 44530256 0.000000e+00 680.0
34 TraesCS7D01G299700 chr2D 85.202 446 60 4 314 757 517258905 517258464 1.840000e-123 453.0
35 TraesCS7D01G299700 chr2D 95.092 163 8 0 2233 2395 362930970 362930808 1.550000e-64 257.0
36 TraesCS7D01G299700 chr2D 84.541 207 30 2 3838 4043 119558282 119558077 2.050000e-48 204.0
37 TraesCS7D01G299700 chr2D 82.692 208 30 4 3842 4043 349584562 349584769 3.460000e-41 180.0
38 TraesCS7D01G299700 chr2D 96.842 95 3 0 1611 1705 601266051 601266145 4.500000e-35 159.0
39 TraesCS7D01G299700 chr2A 85.477 723 93 4 1 720 26767327 26768040 0.000000e+00 743.0
40 TraesCS7D01G299700 chr4B 83.592 774 106 12 2 759 614126849 614127617 0.000000e+00 706.0
41 TraesCS7D01G299700 chr4B 95.062 162 8 0 2234 2395 135218210 135218049 5.580000e-64 255.0
42 TraesCS7D01G299700 chr4B 86.127 173 20 4 3879 4050 411490572 411490741 2.670000e-42 183.0
43 TraesCS7D01G299700 chr2B 83.745 769 102 14 1 758 747604530 747603774 0.000000e+00 706.0
44 TraesCS7D01G299700 chr2B 82.938 211 31 3 3838 4043 682945443 682945653 7.430000e-43 185.0
45 TraesCS7D01G299700 chrUn 82.745 765 118 12 1 761 399659863 399660617 0.000000e+00 669.0
46 TraesCS7D01G299700 chrUn 91.160 181 14 2 2216 2395 34210735 34210914 1.210000e-60 244.0
47 TraesCS7D01G299700 chr4D 86.010 629 72 7 143 759 483674676 483675300 0.000000e+00 660.0
48 TraesCS7D01G299700 chr1B 86.567 402 45 1 1 393 410309221 410308820 6.680000e-118 435.0
49 TraesCS7D01G299700 chr1B 93.529 170 11 0 2226 2395 652464936 652464767 2.010000e-63 254.0
50 TraesCS7D01G299700 chr1B 84.722 72 8 1 4069 4137 156962742 156962813 7.800000e-08 69.4
51 TraesCS7D01G299700 chr4A 94.578 166 9 0 2233 2398 517406633 517406468 1.550000e-64 257.0
52 TraesCS7D01G299700 chr4A 93.269 104 5 2 1605 1708 69329844 69329945 7.530000e-33 152.0
53 TraesCS7D01G299700 chr4A 94.286 35 2 0 4186 4220 484836554 484836588 2.000000e-03 54.7
54 TraesCS7D01G299700 chr5D 95.597 159 7 0 2234 2392 542693295 542693453 5.580000e-64 255.0
55 TraesCS7D01G299700 chr1D 94.048 168 10 0 2228 2395 338937206 338937373 5.580000e-64 255.0
56 TraesCS7D01G299700 chr1D 82.870 216 28 5 3838 4045 26259152 26258938 7.430000e-43 185.0
57 TraesCS7D01G299700 chr5B 83.732 209 32 2 3838 4046 663242368 663242162 3.430000e-46 196.0
58 TraesCS7D01G299700 chr5B 81.046 153 24 4 4072 4220 390703512 390703361 2.750000e-22 117.0
59 TraesCS7D01G299700 chr3A 83.019 212 23 7 3840 4043 197850721 197850927 3.460000e-41 180.0
60 TraesCS7D01G299700 chr6D 95.876 97 4 0 1611 1707 62245407 62245311 1.620000e-34 158.0
61 TraesCS7D01G299700 chr6B 94.000 100 4 2 1609 1708 14523413 14523316 2.710000e-32 150.0
62 TraesCS7D01G299700 chr6A 94.737 95 4 1 1609 1703 557970041 557970134 3.500000e-31 147.0


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 TraesCS7D01G299700 chr7D 379766856 379771204 4348 True 8032.000000 8032 100.000000 1 4349 1 chr7D.!!$R1 4348
1 TraesCS7D01G299700 chr7A 428337891 428340820 2929 True 704.833333 1982 92.795833 883 3963 6 chr7A.!!$R2 3080
2 TraesCS7D01G299700 chr7B 374773313 374776345 3032 True 585.833333 1214 91.648833 1384 4316 6 chr7B.!!$R2 2932
3 TraesCS7D01G299700 chr7B 582657576 582658152 576 False 547.000000 547 84.095000 1 579 1 chr7B.!!$F1 578
4 TraesCS7D01G299700 chr3D 402497564 402498309 745 True 826.000000 826 86.667000 1 761 1 chr3D.!!$R2 760
5 TraesCS7D01G299700 chr3D 517293658 517294429 771 False 804.000000 804 85.825000 1 758 1 chr3D.!!$F1 757
6 TraesCS7D01G299700 chr3B 489718380 489719142 762 False 809.000000 809 86.180000 1 750 1 chr3B.!!$F1 749
7 TraesCS7D01G299700 chr2D 555476392 555477151 759 True 791.000000 791 85.733000 1 750 1 chr2D.!!$R4 749
8 TraesCS7D01G299700 chr2D 44529502 44530256 754 False 680.000000 680 83.007000 1 761 1 chr2D.!!$F1 760
9 TraesCS7D01G299700 chr2A 26767327 26768040 713 False 743.000000 743 85.477000 1 720 1 chr2A.!!$F1 719
10 TraesCS7D01G299700 chr4B 614126849 614127617 768 False 706.000000 706 83.592000 2 759 1 chr4B.!!$F2 757
11 TraesCS7D01G299700 chr2B 747603774 747604530 756 True 706.000000 706 83.745000 1 758 1 chr2B.!!$R1 757
12 TraesCS7D01G299700 chrUn 399659863 399660617 754 False 669.000000 669 82.745000 1 761 1 chrUn.!!$F2 760
13 TraesCS7D01G299700 chr4D 483674676 483675300 624 False 660.000000 660 86.010000 143 759 1 chr4D.!!$F1 616


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
580 637 0.027324 TACGCCGCGTTTTCGTTTTT 59.973 45.0 25.47 0.00 46.03 1.94 F
721 779 0.040351 TCCATTTTCATCCCGCCCAA 59.960 50.0 0.00 0.00 0.00 4.12 F
1631 1695 0.042131 AATGTACTCCCTCCGTCCCA 59.958 55.0 0.00 0.00 0.00 4.37 F
1963 2135 0.249657 TTGTGGTTGCGAATTTGCCC 60.250 50.0 15.20 10.25 0.00 5.36 F
1998 2170 0.593128 ATTTGTCGCCAACTGTGCTC 59.407 50.0 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2211 0.613777 AGAAAGTTACAGGGAGGGCG 59.386 55.0 0.00 0.0 0.00 6.13 R
2683 2888 0.319813 GTGGCCACCTTTGTTGCATC 60.320 55.0 26.31 0.0 34.91 3.91 R
2844 3050 0.394192 CCTCACAGTGACAGGCTCAA 59.606 55.0 0.00 0.0 0.00 3.02 R
3151 3386 0.541764 GCCCTGGTTCCCATGTTCAA 60.542 55.0 0.00 0.0 30.82 2.69 R
3762 4042 1.338107 CCCTTTTCACCAAGTTCCCC 58.662 55.0 0.00 0.0 0.00 4.81 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.