Multiple sequence alignment - TraesCS1B01G191300

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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 TraesCS1B01G191300 chr1B 100.000 2273 0 0 1 2273 342121447 342123719 0.000000e+00 4198.0
1 TraesCS1B01G191300 chr1B 99.346 153 1 0 363 515 342121756 342121908 6.180000e-71 278.0
2 TraesCS1B01G191300 chr1B 99.346 153 1 0 310 462 342121809 342121961 6.180000e-71 278.0
3 TraesCS1B01G191300 chr1B 85.897 234 32 1 1 233 613948816 613948583 4.850000e-62 248.0
4 TraesCS1B01G191300 chr1B 92.029 138 11 0 1376 1513 176763749 176763612 6.410000e-46 195.0
5 TraesCS1B01G191300 chr1B 99.010 101 1 0 416 516 342121756 342121856 4.990000e-42 182.0
6 TraesCS1B01G191300 chr1B 99.010 101 1 0 310 410 342121862 342121962 4.990000e-42 182.0
7 TraesCS1B01G191300 chr1B 100.000 48 0 0 310 357 342121915 342121962 3.110000e-14 89.8
8 TraesCS1B01G191300 chr1D 92.462 597 26 9 803 1381 236808653 236809248 0.000000e+00 835.0
9 TraesCS1B01G191300 chr1D 92.157 408 15 4 1507 1913 236809242 236809633 5.480000e-156 560.0
10 TraesCS1B01G191300 chr5B 98.704 463 5 1 1 462 692366887 692367349 0.000000e+00 821.0
11 TraesCS1B01G191300 chr5B 98.387 434 5 1 363 794 692367197 692367630 0.000000e+00 761.0
12 TraesCS1B01G191300 chr5B 100.000 101 0 0 310 410 692367250 692367350 1.070000e-43 187.0
13 TraesCS1B01G191300 chr5B 100.000 48 0 0 310 357 692367303 692367350 3.110000e-14 89.8
14 TraesCS1B01G191300 chr1A 90.070 574 31 11 804 1369 308811608 308811053 0.000000e+00 721.0
15 TraesCS1B01G191300 chr1A 94.225 329 18 1 468 795 323962646 323962318 3.370000e-138 501.0
16 TraesCS1B01G191300 chr1A 91.643 347 21 2 1575 1913 308810991 308810645 7.350000e-130 473.0
17 TraesCS1B01G191300 chr1A 93.671 316 17 3 1 313 323962984 323962669 9.510000e-129 470.0
18 TraesCS1B01G191300 chr5A 95.266 338 15 1 464 800 612160345 612160008 3.320000e-148 534.0
19 TraesCS1B01G191300 chr5A 93.994 333 19 1 464 795 612160742 612160410 9.370000e-139 503.0
20 TraesCS1B01G191300 chr5A 93.949 314 18 1 1 313 612161074 612160761 7.350000e-130 473.0
21 TraesCS1B01G191300 chr5A 91.111 225 17 3 573 796 612160009 612159787 3.670000e-78 302.0
22 TraesCS1B01G191300 chr5A 83.183 333 49 4 472 800 481101252 481101581 4.750000e-77 298.0
23 TraesCS1B01G191300 chr5A 84.681 235 34 2 4 237 513969564 513969331 1.360000e-57 233.0
24 TraesCS1B01G191300 chr5A 92.647 136 10 0 1375 1510 32937938 32938073 1.780000e-46 196.0
25 TraesCS1B01G191300 chr5A 100.000 55 0 0 356 410 612160347 612160293 3.990000e-18 102.0
26 TraesCS1B01G191300 chr5A 100.000 54 0 0 409 462 612160347 612160294 1.440000e-17 100.0
27 TraesCS1B01G191300 chr5A 98.182 55 1 0 356 410 612160744 612160690 1.860000e-16 97.1
28 TraesCS1B01G191300 chr5A 98.148 54 1 0 409 462 612160744 612160691 6.680000e-16 95.3
29 TraesCS1B01G191300 chr5A 100.000 48 0 0 310 357 612160340 612160293 3.110000e-14 89.8
30 TraesCS1B01G191300 chr5A 97.917 48 1 0 310 357 612160737 612160690 1.450000e-12 84.2
31 TraesCS1B01G191300 chr5A 95.556 45 2 0 267 311 612160410 612160366 3.130000e-09 73.1
32 TraesCS1B01G191300 chr4A 94.721 341 14 2 464 800 6020190 6019850 5.560000e-146 527.0
33 TraesCS1B01G191300 chr4A 93.750 320 13 4 1 313 6020528 6020209 7.350000e-130 473.0
34 TraesCS1B01G191300 chr6D 90.769 260 15 4 2022 2273 439414648 439414390 2.800000e-89 339.0
35 TraesCS1B01G191300 chr7B 85.163 337 34 11 464 794 583929901 583930227 4.680000e-87 331.0
36 TraesCS1B01G191300 chr7B 84.615 338 36 11 464 795 583929228 583929555 2.820000e-84 322.0
37 TraesCS1B01G191300 chr7B 78.723 423 57 10 1 408 583928874 583929278 3.750000e-63 252.0
38 TraesCS1B01G191300 chr7B 78.302 424 58 11 1 408 583928236 583928641 2.260000e-60 243.0
39 TraesCS1B01G191300 chr7B 85.455 165 13 6 464 625 583928591 583928747 6.500000e-36 161.0
40 TraesCS1B01G191300 chr7B 93.478 46 3 0 310 355 583928596 583928641 4.050000e-08 69.4
41 TraesCS1B01G191300 chr5D 88.341 223 16 3 2059 2272 230420787 230420566 2.240000e-65 259.0
42 TraesCS1B01G191300 chr5D 91.549 142 10 2 1375 1514 485934442 485934583 6.410000e-46 195.0
43 TraesCS1B01G191300 chr5D 85.027 187 27 1 2021 2206 230419113 230419299 2.980000e-44 189.0
44 TraesCS1B01G191300 chr5D 83.838 198 26 4 2022 2215 518916752 518916557 1.390000e-42 183.0
45 TraesCS1B01G191300 chr5D 92.683 41 3 0 1942 1982 456566111 456566151 2.440000e-05 60.2
46 TraesCS1B01G191300 chr4B 78.538 424 57 10 1 408 47656119 47656524 4.850000e-62 248.0
47 TraesCS1B01G191300 chr4B 92.086 139 11 0 1375 1513 403331547 403331409 1.780000e-46 196.0
48 TraesCS1B01G191300 chr4B 92.086 139 10 1 1375 1512 214045489 214045351 6.410000e-46 195.0
49 TraesCS1B01G191300 chr2A 87.027 185 23 1 2022 2205 742303860 742303676 8.230000e-50 207.0
50 TraesCS1B01G191300 chr3A 93.893 131 8 0 1378 1508 732394967 732394837 4.950000e-47 198.0
51 TraesCS1B01G191300 chr2D 85.128 195 28 1 2022 2215 17160582 17160388 4.950000e-47 198.0
52 TraesCS1B01G191300 chr2D 85.263 190 22 4 2021 2206 13618916 13619103 8.290000e-45 191.0
53 TraesCS1B01G191300 chr7D 92.029 138 11 0 1375 1512 564074973 564074836 6.410000e-46 195.0
54 TraesCS1B01G191300 chr7A 90.541 148 13 1 1376 1522 681028441 681028294 6.410000e-46 195.0
55 TraesCS1B01G191300 chr7A 83.871 186 29 1 2022 2206 200598134 200598319 2.320000e-40 176.0
56 TraesCS1B01G191300 chr7A 82.383 193 30 4 2017 2206 149419980 149420171 5.020000e-37 165.0
57 TraesCS1B01G191300 chr3D 90.845 142 11 2 1375 1514 405859327 405859186 2.980000e-44 189.0
58 TraesCS1B01G191300 chr3B 91.429 105 9 0 1915 2019 467893167 467893271 6.540000e-31 145.0


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 TraesCS1B01G191300 chr1B 342121447 342123719 2272 False 867.966667 4198 99.452000 1 2273 6 chr1B.!!$F1 2272
1 TraesCS1B01G191300 chr1D 236808653 236809633 980 False 697.500000 835 92.309500 803 1913 2 chr1D.!!$F1 1110
2 TraesCS1B01G191300 chr5B 692366887 692367630 743 False 464.700000 821 99.272750 1 794 4 chr5B.!!$F1 793
3 TraesCS1B01G191300 chr1A 308810645 308811608 963 True 597.000000 721 90.856500 804 1913 2 chr1A.!!$R1 1109
4 TraesCS1B01G191300 chr1A 323962318 323962984 666 True 485.500000 501 93.948000 1 795 2 chr1A.!!$R2 794
5 TraesCS1B01G191300 chr5A 612159787 612161074 1287 True 223.045455 534 96.738455 1 800 11 chr5A.!!$R2 799
6 TraesCS1B01G191300 chr4A 6019850 6020528 678 True 500.000000 527 94.235500 1 800 2 chr4A.!!$R1 799
7 TraesCS1B01G191300 chr7B 583928236 583930227 1991 False 229.733333 331 84.289333 1 795 6 chr7B.!!$F1 794


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
441 1097 0.035439 TTTCCACCGATTGCTCCTCC 60.035 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 3257 0.037734 CCCCTAAGGCTTTGTTCGGT 59.962 55.0 4.45 0.0 0.0 4.69 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.